"""
Functions for loading FreeSurfer data on different levels.

The high-level functions are available directly in the package namespace. Using the functions in here should not be necessary.
"""

import os
import sys
import errno
import numpy as np
import collections
import gzip
import nibabel.freesurfer.io as fsio
import nibabel.freesurfer.mghformat as fsmgh
from . import nitools as nit
from . import annotations as an
import nibabel as nib
import numpy.linalg as npl  # for matrix inversion
import struct   # for reading binary data


def read_m3z_file(m3z_file):
    """
    Read a file in FreeSurfer m3z format.

    Read a file in FreeSurfer m3z format, usually mri/transforms/talairach.m3z of a subject. An m3z file is a gzipped binary file containing a dense vector field that describes a 3D registration between two volumes/images. This implementation follows the Matlab implementation from the FreeSurfer source repository at github, see https://github.com/freesurfer/freesurfer/blob/dev/matlab/mris_read_m3z.m. This function is released under the Freesurfer license: https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense

    Parameters
    ----------
    m3z_file: str
        Path to a file in m3z format

    Returns
    -------
    vol_orig: numpy 4D array
        Array of np.single, containing 3 numbers per voxel. The shape is (width, height, depth, 3), where width, height, and depth are the dimensions of the source volume.

    vol_dest: numpy 4D array
        Array of np.single, containing 3 numbers per voxel. The shape is (width, height, depth, 3), where width, height, and depth are the dimensions of the destination volume.

    vol_ind0: numpy 4D array
        Array of np.int32, containing 3 numbers per voxel. The shape is (width, height, depth, 3).

    meta_data: dictionary
        Contains meta data on the registration. The following keys are included:
            - version: float, File format version
            - width: int, Volume width
            - height: int, Volume height
            - depth: int, Volume depth
            - spacing: int, voxel spacing of the volume
            - exp_k: float, exp_k of the volume

    Examples
    --------
    Read a talairach.m3z file that has been generated by FreeSurfer's ```recon-all``` command.

    >>> import brainload.freesurferdata as fsd
    >>> import os
    >>> m3z_file = os.path.join(os.getenv('HOME'), 'my_study_data', 'subject1', 'mri', 'transforms', 'talairach.m3z')
    >>> vol_orig, vol_dest, vol_ind0, meta_data = fsd.read_m3z_file(m3z_file)
    """
    m3z = gzip.open(m3z_file, 'rb')
    fdata = m3z.read()      # read the whole file contents
    # Read the file header
    data_start_pos = 24
    (version, width, height, depth, spacing, exp_k) = struct.unpack(">fiiiif", fdata[:data_start_pos])
    meta_data = {}
    meta_data['version'] = version
    meta_data['width'] = width
    meta_data['height'] = height
    meta_data['depth'] = depth
    meta_data['spacing'] = spacing
    meta_data['exp_k'] = exp_k
    meta_data['data_start_pos'] = data_start_pos

    numbers_per_voxel = 9
    bytes_uint8 = 4
    numbers_to_read = width * height * depth * numbers_per_voxel
    bytes_to_read = numbers_to_read * bytes_uint8
    data_end_pos = data_start_pos + bytes_to_read
    vol_data = struct.unpack(">%dB" % (numbers_to_read * 4), fdata[data_start_pos:data_end_pos])    # vol_data is a tuple
    meta_data['data_end_pos'] = data_end_pos
    meta_data['bytes_to_read'] = bytes_to_read
    meta_data['numbers_to_read'] = numbers_to_read
    meta_data['remaining_data_tag'] = struct.unpack(">i", fdata[data_end_pos:data_end_pos+4])[0]    # the first 4 bytes after the data are an integer tag, that holds information on what kind of data follows. We do not read that data but check the tag here.
    meta_data['file_end_pos'] = len(fdata)

    # create indices into the vol_data where data resides
    indices = np.kron(np.ones((12,1), dtype=np.int), range(width * height * depth))
    vox_offset = 9 * 4 * indices
    to_repeat = np.array([3, 2, 1, 0, 7, 6, 5, 4, 11, 10, 9, 8])
    reshaped_offsets = np.reshape(vox_offset, -1, order='F').copy()
    repeated = np.kron(np.ones((width * height * depth, ), dtype=int), to_repeat)
    inds = repeated + reshaped_offsets;
    inds = inds.astype(int)

    # Extract the three interleaved volumes and permute the result to match the original looped read. Start with viol_orig.
    buf = np.array(vol_data, dtype=np.uint8)
    buf_at_inds = buf[inds]
    single_casted = buf_at_inds.view(dtype=np.single)
    vol_orig_step1 = np.reshape(single_casted, (3, depth, width, height), order='F').copy()
    vol_orig = np.transpose(vol_orig_step1, (3, 2, 1, 0))

    # OK, vol_orig is reconstructed. Now for vol_dest
    inds = inds + 12
    buf_at_inds = buf[inds]
    single_casted = buf_at_inds.view(dtype=np.single)
    vol_dest_step1 = np.reshape(single_casted, (3, depth, width, height), order='F').copy()
    vol_dest = np.transpose(vol_dest_step1, (3, 2, 1, 0))

    # now for vol_ind0
    inds = inds + 12
    buf_at_inds = buf[inds]
    casted = buf_at_inds.view(dtype=np.int32)
    vol_ind0_step1 = np.reshape(casted, (3, depth, width, height), order='F').copy()
    vol_ind0 = np.transpose(vol_ind0_step1, (3, 2, 1, 0))
    return vol_orig, vol_dest, vol_ind0, meta_data




def read_lookup_file(lookup_file, dtype='<U50'):
    """
    Read a FreeSurfer lookup table file in text format.

    Read a FreeSurfer lookup table file in text format, this is used for the FreeSurferColorLUT.txt file.

    Parameters
    ----------
    lookup_file: str
        Path to the FreeSurferColorLUT.txt file. It comes with FreeSurfer and can be found directly in $FREESURFER_HOME for v6.

    Returns
    -------
    numpy 2D str array
        Array with shape (n, 6) for a file with n relevant lines. A relevant line is a line describing a segmentation in 6 fields (seg_code, structure_name, color_red, color_green, color_blue, color_alpha). There are 2 types of ignored lines in the file: empty lines and those starting with the comment character '#'. All other lines are considered relevant and split into the 6 parts.
    """
    with open(lookup_file, 'r') as fh:
        lines = [line.rstrip('\n') for line in fh]
    all_line_parts = []
    for line in lines:
        if line.startswith("#") or not line:
            pass
        else:
            line_parts = line.split()
            all_line_parts.append(line_parts)
    return np.array(all_line_parts, dtype=dtype)



def get_vox2ras_and_ras2vox_from_nifti_file(nifti_file, use_sform=True):
    """
    Load the vox2ras and ras2vox matrices from a nifti file header.

    Load the vox2ras and ras2vox matrices from a nifti file header. The file can be in nifti (.nii) or gzipped nifti (.nii.gz) format. To understand qform and sform, read the nibabel docs or better https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Orientation%20Explained.

    Parameters
    ----------
    nifti_file: str
        Path to a nifti or gzipped nifti file.

    use_sform: bool, optional
        Whether to report the sform matrix or qform matrix from the nifti header. Defaults to True (=sform). If set to False, the qform will be used.

    Returns
    -------
    vox2ras: 2D numpy array
        The sform or qform matrix

    ras2vox: 2D numpy array
        The inverse of the vox2ras matrix.

    Examples
    --------
    >>> import brainload.freesurferdata as fsd
    >>> vox2ras, ras2vox = fsd.get_vox2ras_and_ras2vox_from_nifti_file("mni152_volume.nii.gz")
    """
    img = nib.load(nifti_file)
    if use_sform:
        vox2ras = img.header.get_sform()
    else:
        vox2ras = img.header.get_qform()
    ras2vox = npl.inv(vox2ras)
    return vox2ras, ras2vox


def read_mgh_header_matrices(mgh_file_name):
    """
    Read the 3 affine transformation matrices from a MGH file header.

    Read the 3 affine transformation matrices ras2vox, vox2ras, and vox2ras_tkr from a MGH file header. The input file is assumed to be gzipped (and extracted appropriately) if the file name ends with '.mgz' or '.mgh.gz'. See the FreeSurfer wiki on coordinate systems for details on what these matrices are. In short, RAS coordinates are used to specify positions of vertices in FreeSurfer surface files.

    In short, VOX is the voxel index and the RAS coordinate is used for the surface coordinate of a vertex.

    VOX: After FreeSurfer pre-processing, this is a triplet of integers in range 0 - 255 for 3D images. Note though that the original T1 images (before pre-processing) from a study can - and usually will - have different numbers of voxels (both different between the axes of a single image as well as between subjects). The VOX is sometimes called CRS for voxel column, row, slice.

    RAS: Right-Anterior-Superior (anatomical coordinates). According to http://www.grahamwideman.com/gw/brain/fs/coords/fscoords.htm, the RAS coordinate origin (0, 0, 0) is the center of the voxel (128, 128, 128). Note that this voxel could or could NOT be the center of the MRI volume.

    Parameters
    ----------
    mgh_file_name: string
        Path to a file in MGH format. The input file is assumed to be gzipped (and extracted appropriately) if the file name ends with '.mgz' or '.mgh.gz'.

    Returns
    -------
    ras2vox: numpy array
        2D numpy array with shape (4, 4). Transformation matrix from RAS coordinate to voxel index.

    vox2ras: numpy array
        2D numpy array with shape (4, 4). Transformation matrix from voxel index to RAS coordinate.

    vox2ras_tkr: numpy array
        2D numpy array with shape (4, 4). Transformation matrix from voxel index to (tkregister) surface RAS coordinate. This is a RAS coordinate of a vertex on the surface.

    Examples
    --------
    >>> import os; import brainload.freesurferdata as fsd
    >>> mgh_file = os.path.join(TEST_DATA_DIR, 'subject1', 'mri', 'orig.mgh')
    >>> ras2vox, vox2ras, vox2ras_tkr = fsd.read_mgh_header_matrices(mgh_file)
    """
    _, mgh_meta_data = read_mgh_file(mgh_file_name, collect_data=False)
    ras2vox = mgh_meta_data['ras2vox']
    vox2ras = mgh_meta_data['vox2ras']
    vox2ras_tkr = mgh_meta_data['vox2ras_tkr']
    return ras2vox, vox2ras, vox2ras_tkr


def read_mgh_file(mgh_file_name, collect_meta_data=True, collect_data=True):
    """
    Read data from a FreeSurfer output file in mgh format.

    Read all data from the MGH file and return it as a numpy array. Optionally, collect meta data from the mgh file header.

    Parameters
    ----------
    mgh_file_name: string
        A string representing a full path to a file in FreeSurfer MGH file format. If the file name end with '.mgz' or '.mgh.gz', the file is assumed to be in gzipped MGH format.

    collect_meta_data: bool, optional
        Whether or not to collect meta data from the MGH file header. Defaults to True.

    collect_data: bool, optional
        Whether or not to collect the file data (voxel values) from the MGH file. Defaults to True.

    Returns
    -------
    mgh_data: numpy array
        The data from the MGH file, usually one scalar value per voxel.

    mgh_meta_data: dictionary
        The meta data collected from the header, or an empty dictionary if the argument `collect_meta_data` was 'False'. The keys correspond to the names of the respective nibabel function used to retrieve the data. The values are the data as returned by nibabel.

    Examples
    --------
    Read a file in MGH format from the surf dir of a subject:

    >>> import os
    >>> import brainload.freesurferdata as fsd
    >>> mgh_file = os.path.join('my_subjects_dir', 'subject1', 'surf', 'rh.area.fsaverage.mgh')
    >>> mgh_data, mgh_meta_data = fsd.read_mgh_file(mgh_file)

    See also
    --------
        - https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
        - https://github.com/nipy/nibabel/blob/master/nibabel/freesurfer/mghformat.py
        - https://surfer.nmr.mgh.harvard.edu/fswiki/FileFormats
    """
    mgh_meta_data = {}
    if mgh_file_name.endswith(".mgz") or mgh_file_name.endswith(".gz"):
        mgh_file_handle = gzip.open(mgh_file_name, 'rb')
    else:
        mgh_file_handle = open(mgh_file_name, 'rb')

    header = fsmgh.MGHHeader.from_fileobj(mgh_file_handle)

    if collect_meta_data:
        mgh_meta_data['data_shape'] = header.get_data_shape()
        mgh_meta_data['affine'] = header.get_affine()
        mgh_meta_data['best_affine'] = header.get_best_affine()             # identical to get_affine for MGH format
        mgh_meta_data['data_bytespervox'] = header.get_data_bytespervox()
        mgh_meta_data['data_dtype'] = header.get_data_dtype()
        mgh_meta_data['data_offset'] =  header.get_data_offset()            # MGH format has a header, then data, then a footer
        mgh_meta_data['data_shape'] =  header.get_data_shape()
        mgh_meta_data['data_size'] = header.get_data_size()
        mgh_meta_data['footer_offset'] =  header.get_footer_offset()
        mgh_meta_data['ras2vox'] =  header.get_ras2vox()
        mgh_meta_data['slope_inter'] =  header.get_slope_inter()
        mgh_meta_data['vox2ras'] =  header.get_vox2ras()
        mgh_meta_data['vox2ras_tkr'] =  header.get_vox2ras_tkr()
        mgh_meta_data['zooms'] =  header.get_zooms()                        # the voxel dimensions (along all 3 axes in space)

    mgh_data = None
    if collect_data:
        mgh_data = header.data_from_fileobj(mgh_file_handle)
    mgh_file_handle.close()
    return mgh_data, mgh_meta_data


def get_num_fsaverage_verts_per_hemi(fsversion=6):
    """
    Return the number of vertices per fsaverage hemisphere.

    Returns
    -------
    vertcount: int
         The number of vertices per fsaverage hemisphere.
    """
    if fsversion == 6:
        return 163842
    else:
        raise ValueError("Currently the only supported FreeSurfer version is 6.")

def merge_morphometry_data(morphometry_data_arrays, dtype=float):
    """
    Merge morphometry data horizontally.

    Merge morphometry data read from several meshes of the same subject horizontally. This is used to merge data from the left and right hemispheres.

    Parameters
    ----------
    morphometry_data_arrays: 2D array
        An array of arrays, each of which represents morphometry data from different hemispheres of the same subject.

    dtype: data type, optional
        Data type for the output numpy array. Defaults to float.

    Returns
    -------
    numpy array
        Horizontally stacked array containing the data from all arrays in the input array.

    Examples
    --------
    Merge some data:

    >>> lh_morphometry_data = np.array([0.0, 0.1, 0.2, 0.3])   # some fake data
    >>> rh_morphometry_data = np.array([0.5, 0.6])
    >>> merged_data = fsd.merge_morphometry_data(np.array([lh_morphometry_data, rh_morphometry_data]))
    >>> print merged_data.shape
    (6, )

    Typically, the `lh_morphometry_data` and `rh_morphometry_data` come from calls to `read_fs_morphometry_data_file_and_record_meta_data` as shown here:

    >>> lh_morphometry_data, meta_data = read_fs_morphometry_data_file_and_record_meta_data(lh_morphometry_data_file, 'lh')
    >>> rh_morphometry_data, meta_data = read_fs_morphometry_data_file_and_record_meta_data(rh_morphometry_data_file, 'rh', meta_data=meta_data)
    >>> both_hemis_morphometry_data = merge_morphometry_data(np.array([lh_morphometry_data, rh_morphometry_data]))
    """
    merged_data = np.empty((0), dtype=dtype)
    for morphometry_data in morphometry_data_arrays:
        merged_data = np.hstack((merged_data, morphometry_data))
    return merged_data


def _get_morphometry_data_suffix_for_surface(surf):
    """
    Determine FreeSurfer surface representation string.

    Determine the substring representing the given surface in a FreeSurfer output curv file. For FreeSurfer's default surface 'white', the surface is not represented in the output file name pattern. For all others, it is represented by a dot followed by the name.

    Parameters
    ----------
    surf: string
        A string representing a FreeSurfer surface, e.g., 'white' or 'pial'.

    Returns
    -------
    string
        The empty string if `surf` is 'white'. A dot followed by the string in the input argument `surf` otherwise.

    Examples
    --------
    >>> import brainload.freesurferdata as fsd
    >>> print fsd._get_morphometry_data_suffix_for_surface('pial')
    .pial
    """
    if surf == 'white':
        return ''
    return '.' + surf


def read_fs_surface_file_and_record_meta_data(surf_file, hemisphere_label, meta_data=None):
    """
    Read a surface file and record meta data on it.

    Read a surface file and record meta data on it. A surface file is a mesh file in FreeSurfer format, e.g., 'lh.white'. It contains vertices and 3-faces made out of them.

    Parameters
    ----------
    surf_file: string
        A string representing an absolute path to a surface (or 'mesh') file (e.g., the path to 'lh.white').

    hemisphere_label: {'lh' or 'rh'}
        A string representing the hemisphere this file belongs to. This is used to write the correct meta data.

    meta_data: dictionary | None, optional
        Meta data to merge into the output `meta_data`. Defaults to the empty dictionary.

    Returns
    -------
    vert_coords: numpy array
        A 2D array containing 3 coordinates for each vertex in the `surf_file`.

    faces: numpy array
        A 2D array containing 3 vertex indices per face. Look at the respective indices in `vert_coords` to get the vertex coordinates.

    meta_data: dictionary
        Contains detailed information on the data that was loaded. The following keys are available (replace `?h` with the value of the argument `hemisphere_label`, which must be 'lh' or 'rh').
            - `?h.num_vertices` : number of vertices in the loaded mesh
            - `?h.num_faces` : number of faces in the loaded mesh
            - `?lh.surf_file` : value of the `surf_file` argument: the mesh file that was loaded

    Examples
    --------
    >>> vert_coords, faces, meta_data = fsd.read_fs_surface_file_and_record_meta_data(surf_file, 'lh')
    >>> print meta_data['lh.num_vertices']
    121567                  # arbitrary number, depends on the subject mesh
    """
    if hemisphere_label not in ('lh', 'rh'):
        raise ValueError("ERROR: hemisphere_label must be one of {'lh', 'rh'} but is '%s'." % hemisphere_label)

    if meta_data is None:
        meta_data = {}

    vert_coords, faces = fsio.read_geometry(surf_file)

    label_num_vertices = hemisphere_label + '.num_vertices'
    meta_data[label_num_vertices] = vert_coords.shape[0]

    label_num_faces = hemisphere_label + '.num_faces'
    meta_data[label_num_faces] = faces.shape[0]

    label_surf_file = hemisphere_label + '.surf_file'
    meta_data[label_surf_file] = surf_file

    return vert_coords, faces, meta_data

def _deduce_hemisphere_label_from_file_path(file_path, default="lh"):
    """
    Guess a hemisphere label from a file path.

    Guess a hemisphere label, i.e., one of ```lh``` or ```rh```, from a file path like ```/some/path/to/subjects/subject1/surf/lh.area```.

    Parameters
    ----------
    file_path: str
        The full path to a file.

    default: str
        What to return if the function cannot deduce the information from the given file_path.

    Returns
    -------
    hemi: str
        The hemisphere label

    is_default: boolean
        True if the file_path contained no information to deduce the hemisphere label, and the returned ```hemi``` value thus is the one from the ```default``` parameter.
    """
    path, file_name = os.path.split(file_path)
    accepted_third_chars = [".", "_"]
    for h in ["lh", "rh"]:
        for c in accepted_third_chars:
            if file_name.startswith(h + c):
                return h, False
    return default, True


def read_fs_morphometry_data_file_and_record_meta_data(curv_file, hemisphere_label, meta_data=None, format='curv'):
    """
    Read a morphometry file and record meta data on it.

    Read a morphometry file and record meta data on it. A morphometry file is file containing a scalar value for each vertex on the surface of a FreeSurfer mesh. An example is the file 'lh.area', which contains the area values for all vertices of the left hemisphere of the white surface. Such a file can be in two different formats: 'curv' or 'mgh'. The former is used when the data refers to the surface mesh of the original subject, the latter when it has been mapped to a standard subject like fsaverage.

    Parameters
    ----------
    curv_file: string
        A string representing a path to a morphometry file (e.g., the path to 'lh.area').

    hemisphere_label: {'lh' or 'rh'}
        A string representing the hemisphere this file belongs to. This is used to write the correct meta data.

    meta_data: dictionary | None, optional
        Meta data to merge into the output `meta_data`. Defaults to the empty dictionary.

    format: {'curv', 'mgh'}, optional
        The file format for the files that are to be loaded. Defaults to 'curv'.

    Returns
    -------
    per_vertex_data: numpy array
        A 1D array containing one scalar value per vertex.

    meta_data: dictionary
        Contains detailed information on the data that was loaded. The following keys are available (replace `?h` with the value of the argument `hemisphere_label`, which must be 'lh' or 'rh').
            - `?h.num_data_points` : the number of data points loaded.
            - `?h.morphometry_file` : the value of the `curv_file` argument (data file that was loaded)
            - `?h.morphometry_file_format` : the value for `format` that was used

    Examples
    --------
    >>> import brainload.freesurferdata as fsd; import os
    >>> lh_morphometry_file = os.path.join('my_subjects_dir', 'subject1', 'surf', 'lh.area')
    >>> lh_morphometry_data, meta_data = read_fs_morphometry_data_file_and_record_meta_data(lh_morphometry_file, 'lh')
    >>> print meta_data['lh.num_data_points']
    121567                  # arbitrary number, depends on the subject mesh
    >>> print meta_data['lh.morphometry_file']
    my_subjects_dir/subject1/surf/lh.area             # on UNIX-like systems
    """
    if format not in ('curv', 'mgh'):
        raise ValueError("ERROR: format must be one of {'curv', 'mgh'} but is '%s'." % format)

    if hemisphere_label not in ('lh', 'rh'):
        raise ValueError("ERROR: hemisphere_label must be one of {'lh', 'rh'} but is '%s'." % hemisphere_label)

    if meta_data is None:
        meta_data = {}

    if format == 'mgh' or curv_file.endswith(".mgh") or curv_file.endswith(".mgz"):
        full_mgh_data, mgh_meta_data = read_mgh_file(curv_file, collect_meta_data=False)
        relevant_data_inner_array = full_mgh_data[:,0]
        per_vertex_data = relevant_data_inner_array[:,0]
    else:
        per_vertex_data = fsio.read_morph_data(curv_file)

    per_vertex_data = per_vertex_data.astype(float)

    label_num_values = hemisphere_label + '.num_data_points'
    meta_data[label_num_values] = per_vertex_data.shape[0]

    label_file = hemisphere_label + '.morphometry_file'
    meta_data[label_file] = curv_file

    label_file_format = hemisphere_label + '.morphometry_file_format'
    meta_data[label_file_format] = format

    return per_vertex_data, meta_data


def load_subject_mesh_files(lh_surf_file, rh_surf_file, hemi='both', meta_data=None):
    """
    Load mesh files for a subject.

    Load one or two mesh files for a subject. Which of the two files `lh_surf_file` and `rh_surf_file` are actually loaded is determined by the `hemi` parameter.

    Parameters
    ----------
    lh_surf_file: string | None
        A string representing an absolute path to a mesh file for the left hemisphere (e.g., the path to 'lh.white'). If `hemi` is 'rh', this will be ignored and can thus be None.

    rh_surf_file: string | None
        A string representing an absolute path to a mesh file for the right hemisphere (e.g., the path to 'rh.white'). If `hemi` is 'lh', this will be ignored and can thus be None.

    hemi: {'both', 'lh', 'rh'}, optional
        The hemisphere for which data should actually be loaded. Defaults to 'both'.

    meta_data: dictionary | None, optional
        Meta data to merge into the output `meta_data`. Defaults to the empty dictionary.

    Returns
    -------
    vert_coords: numpy array of floats
        A 2D array containing 3 coordinates for each vertex. Dimension is (n, 3) for n vertices. If the argument `hemi` was 'both', this includes vertices from several meshes. You can check the `meta_data` return values to get the border between meshes, see `meta_data['lh.num_vertices']` and  `meta_data['rh.num_vertices']`.

    faces: numpy array of integers
        A 2D array containing 3 vertex indices per face. Dimension is (m, 3) for m faces. Look at the respective indices in `vert_coords` to get the vertex coordinates. If the argument `hemi` was 'both', this includes faces from several meshes. You can check the `meta_data` return values to get the border between meshes, see `meta_data['lh.num_faces']` and  `meta_data['rh.num_faces']`.

    meta_data: dictionary
        Contains detailed information on the data that was loaded. The following keys are available (depending on the value of the `hemi` argument, you can replace ?h with 'lh' or 'rh' or both 'lh' and 'rh'):
            - `?h.num_vertices` : number of vertices in the loaded mesh
            - `?h.num_faces` : number of faces in the loaded mesh
            - `?h.surf_file` : the mesh file that was loaded for this hemisphere

    Examples
    --------
    >>> import brainload.freesurferdata as fsd; import os
    >>> lh_surf_file = os.path.join('my_subjects_dir', 'subject1', 'surf', 'lh.white')
    >>> rh_surf_file = os.path.join('my_subjects_dir', 'subject1', 'surf', 'rh.white')
    >>> vert_coords, faces, meta_data = fsd.load_subject_mesh_files(lh_surf_file, rh_surf_file)
    """
    if hemi not in ('lh', 'rh', 'both'):
        raise ValueError("ERROR: hemi must be one of {'lh', 'rh', 'both'} but is '%s'." % hemi)

    if meta_data is None:
        meta_data = {}

    if hemi == 'lh':
        vert_coords, faces, meta_data = read_fs_surface_file_and_record_meta_data(lh_surf_file, 'lh', meta_data=meta_data)
    elif hemi == 'rh':
        vert_coords, faces, meta_data = read_fs_surface_file_and_record_meta_data(rh_surf_file, 'rh', meta_data=meta_data)
    else:
        lh_vert_coords, lh_faces, meta_data = read_fs_surface_file_and_record_meta_data(lh_surf_file, 'lh', meta_data=meta_data)
        rh_vert_coords, rh_faces, meta_data = read_fs_surface_file_and_record_meta_data(rh_surf_file, 'rh', meta_data=meta_data)
        vert_coords, faces = _merge_meshes(np.array([[lh_vert_coords, lh_faces], [rh_vert_coords, rh_faces]]))
    return vert_coords, faces, meta_data


def rhi(rh_relative_index, meta_data):
    """
    Computes the absolute data index given an index relative to the right hemisphere.

    This function makes sense only given a `morphometry_data` and associated `meta_data` that contains data on two hemispheres (even though the `morphometry_data` array itself is not passed to this function). E.g., the return value of a function like `subject()` or `subject_avg()` when called with `hemi='both'`. For such data, it computes the absolute index in the data given a request index relative to the right hemisphere. The name is short for 'right hemisphere index'.

    Parameters
    ----------
    rh_relative_index: int
        An index relative to the right hemisphere. E.g., `0` if you want to get the index of the first vertex of the right hemisphere. Its absolute value must be between 0 and the number of vertices of the right hemisphere. Negative values are allowed, and `-1` will get you the second-to-last possible index, `-2` the third-to-last, and so on.

    meta_data: dictionary
        The meta data dictionary returned for your data. It must contain the keys 'lh.num_data_points' and 'rh.num_data_points'.

    Returns
    -------
    The absolute index into the data for the given `rh_relative_index`.

    Examples
    --------
    >>> import brainload as bl
    >>> morphometry_data, meta_data = bl.subject('heinz', hemi='both')[2:4]
    >>> print "rh value at index 10, relative to start of right hemisphere: %d." % morphometry_data[bl.rhi(10, meta_data)]
    """
    lh_key = 'lh.num_data_points'
    rh_key = 'rh.num_data_points'
    if not isinstance(meta_data, collections.Mapping):
        raise ValueError("rhi: meta_data must be a meta data dictionary containing the keys '%s' and '%s'." % (lh_key, rh_key))

    if not ('lh.num_data_points' in meta_data and 'rh.num_data_points' in meta_data):
        raise ValueError("rhi: meta_data must be a meta data dictionary containing the keys '%s' and '%s'." % (lh_key, rh_key))

    num_lh = meta_data[lh_key]
    num_rh = meta_data[rh_key]
    if abs(rh_relative_index) >= num_rh:
        raise ValueError('rhi: rh_relative_index %d out of bounds: right hemisphere has %d values, valid index range is -%d .. %d.' % (rh_relative_index, num_rh, num_rh+1, num_rh-1))
    if rh_relative_index < 0:
        return num_lh + num_rh + rh_relative_index -1
    else:
        return num_lh + rh_relative_index


def hemi_range(morphometry_meta_data, hemi):
    """
    Compute start and end index in the hemisphere data for the given hemisphere.

    Parameters
    ----------
    morphometry_meta_data: dictionary as returned by the functions that read morphometry data (e.g., ```subject_data_native```).

    hemi: string, one of 'lh' or 'rh'. The hemisphere you want to get the start and end index for.

    Returns
    -------
    start_index: integer
        The start index of the lh data.

    end_index: integer
        The end index of the lh data.

    Examples
    --------
    >>> import brainload as bl
    >>> morphometry_data, meta_data = bl.subject_data_native('subject1', '/mnt/study1_data', 'thickness', 'both')
    >>> s, e = bl.hemi_range(meta_data, 'lh')
    >>> print("Mean lh thickness value is: %f" % (np.mean(morphometry_data[s:e])))
    """
    if hemi not in ('lh', 'rh'):
        raise ValueError("ERROR: hemi must be one of {'lh', 'rh'} but is '%s'." % hemi)

    if hemi == 'lh':
        return 0, morphometry_meta_data['lh.num_data_points'] -1
    else:
        return rhi(0, morphometry_meta_data), rhi(-1, morphometry_meta_data)+1


def rhv(rh_relative_index, morphometry_data, meta_data):
    """
    Returns the value in `morphometry_data` at an index relative to the right hemisphere.

    This function makes sense only given a `morphometry_data` and associated `meta_data` that contains data on two hemispheres. E.g., the return value of a function like `subject()` or `subject_avg()` when called with `hemi='both'`. For such data, it returns the value in `morphometry_data` at a request index given relative to the right hemisphere. The name is short for 'right hemisphere value'.

    Parameters
    ----------
    rh_relative_index: int
        An index relative to the start of the right hemisphere in the data. E.g., `0` if you want to get the value for the first vertex of the right hemisphere. Its absolute value must be between 0 and the number of vertices of the right hemisphere. Negative values are allowed, and `-1` will get you the last possible value, `-2` the second-to-last, and so on.

    morphometry_data: numpy array
        The morphometry data array, must represent data for both hemispheres.

    meta_data: dictionary
        The meta data dictionary returned for your data. It must contain the keys 'lh.num_data_points' and 'rh.num_data_points'.

    Returns
    -------
    The value at the given index that is relative to the start of the right hemisphere in the data.

    Examples
    --------
    >>> import brainload as bl
    >>> morphometry_data, meta_data = bl.subject('heinz', hemi='both')[2:4]
    >>> print "rh value at index 10, relative to start of right hemisphere: %d." % bl.rhv(10, morphometry_data, meta_data)
    """
    abs_index = rhi(rh_relative_index, meta_data)
    return morphometry_data[abs_index]



def load_subject_morphometry_data_files(lh_morphometry_data_file, rh_morphometry_data_file, hemi='both', format='curv', meta_data=None):
    """
    Load morphometry data files for a subject.

    Load one or two morphometry data files for a subject. Which of the two files `lh_morphometry_data_file` and `rh_morphometry_data_file` are actually loaded is determined by the `hemi` parameter.

    Parameters
    ----------
    lh_morphometry_data_file: string | None
        A string representing an absolute path to a morphometry data file for the left hemisphere. If `hemi` is 'rh', this will be ignored and can thus be None.

    rh_morphometry_data_file: string | None
        A string representing an absolute path to a morphometry data file for the right hemisphere. If `hemi` is 'lh', this will be ignored and can thus be None.

    hemi: {'both', 'lh', 'rh'}, optional
        The hemisphere for which data should actually be loaded. Defaults to 'both'.

    format: {'curv', 'mgh'}, optional
        The file format for the files that are to be loaded. Defaults to 'curv'.

    meta_data: dictionary | None, optional
        Meta data to merge into the output `meta_data`. Defaults to the empty dictionary.

    Returns
    -------
    morphometry_data: numpy array
        An array containing the scalar per-vertex data loaded from the file(s).

    meta_data: dictionary
        Contains detailed information on the data that was loaded. The following keys are available (depending on the value of the `hemi` argument, you can replace ?h with 'lh' or 'rh' or both 'lh' and 'rh'):
            - `?h.num_data_points` : the number of data points loaded.
            - `?h.morphometry_file` : the value of the `?h_morphometry_data_file` argument (data file that was loaded)
            - `?h.morphometry_file_format` : the value for `format` that was used

    Examples
    --------
    Load the lh and rh area files for subject1.

    >>> import brainload.freesurferdata as fsd; import os
    >>> lh_morphometry_file = os.path.join('path', 'to', 'subjects_dir', 'subject1', 'surf', 'lh.area')
    >>> rh_morphometry_file = os.path.join('path', 'to', 'subjects_dir', 'subject1', 'surf', 'rh.area')
    >>> morphometry_data, meta_data = fsd.load_subject_morphometry_data_files(lh_morphometry_file, rh_morphometry_file)

    Now let's look at the area value for the vertex at index 10:

    >>> print "lh value at index 10: %d." % morphometry_data[10]

    But what about the value of vertex 10 at the right hemisphere? We loaded 2 hemispheres, so the data is concatinated. But you can use the `meta_data` to get the correct index relative to the right hemisphere:

    >>> print "rh value at index 10: %d." % morphometry_data[fsd.rhi(10, meta_data)]

    You could also get the value directly using the `rhv` function:

    >>> print "rh value at index 10: %d." % fsd.rhv(10, morphometry_data, meta_data)
    """
    if hemi not in ('lh', 'rh', 'both'):
        raise ValueError("ERROR: hemi must be one of {'lh', 'rh', 'both'} but is '%s'." % hemi)

    if format not in ('curv', 'mgh'):
        raise ValueError("ERROR: format must be one of {'curv', 'mgh'} but is '%s'." % format)

    if meta_data is None:
        meta_data = {}

    if hemi == 'lh':
        morphometry_data, meta_data = read_fs_morphometry_data_file_and_record_meta_data(lh_morphometry_data_file, 'lh', meta_data=meta_data, format=format)
        meta_data['rh.num_data_points'] = 0
    elif hemi == 'rh':
        morphometry_data, meta_data = read_fs_morphometry_data_file_and_record_meta_data(rh_morphometry_data_file, 'rh', meta_data=meta_data, format=format)
        meta_data['lh.num_data_points'] = 0
    else:
        lh_morphometry_data, meta_data = read_fs_morphometry_data_file_and_record_meta_data(lh_morphometry_data_file, 'lh', meta_data=meta_data, format=format)
        rh_morphometry_data, meta_data = read_fs_morphometry_data_file_and_record_meta_data(rh_morphometry_data_file, 'rh', meta_data=meta_data, format=format)
        morphometry_data = merge_morphometry_data(np.array([lh_morphometry_data, rh_morphometry_data]))
    return morphometry_data, meta_data


def subject_mesh(subject_id, subjects_dir, surf='white', hemi='both'):
    """
    Load a surface mesh of a subject.

    Convenience function to load a FreeSurfer surface mesh of a subject.

    Parameters
    ----------
    subject_id: string
        The subject identifier of the subject.

    surf : string, optional
        The brain surface where the data has been measured, e.g., 'white' or 'pial'. This will become part of the file name that is loaded. Defaults to 'white'.

    hemi : {'both', 'lh', 'rh'}, optional
        The hemisphere that should be loaded. Defaults to 'both'.

    subjects_dir: string
        A string representing the full path to a directory. This should be the directory containing all subjects of your study.

    Returns
    -------
    vert_coords: numpy array
        A 2-dimensional array containing the vertices of the mesh(es) of the subject. Each vertex entry contains 3 coordinates. Each coordinate describes a 3D position in a FreeSurfer surface file (e.g., 'lh.white'), as returned by the `nibabel` function `nibabel.freesurfer.io.read_geometry`.

    faces: numpy array
        A 2-dimensional array containing the 3-faces of the mesh(es) of the subject. Each face entry contains 3 indices. Each index references the respective vertex in the `vert_coords` array.

    meta_data: dictionary
        A dictionary containing detailed information on all files that were loaded and used settings. The following keys are available (depending on the value of the `hemi` argument, you can replace ?h with 'lh' or 'rh' or both 'lh' and 'rh'):
            - `?h.num_vertices` : number of vertices in the loaded mesh
            - `?h.num_faces` : number of faces in the loaded mesh
            - `?lh.surf_file` : the mesh file that was loaded for this hemisphere

    Raises
    ------
    ValueError
        If one of the parameters with a fixed set of values receives a value that is not allowed.

    Examples
    --------
    Load the pial surface mesh for both hemispheres of the Freeurfer example subject bert:

    >>> import brainload as bl, import os
    >>> subjects_dir = os.path.join('Applications', 'freesurfer', 'subjects')
    >>> verts, faced, meta_data = bl.subject_mesh('bert', subjects_dir, surf='pial')
    """
    vert_coords, faces, meta_data = fsaverage_mesh(subject_id=subject_id, surf=surf, hemi=hemi, subjects_dir=subjects_dir, use_freesurfer_home_if_missing=False)
    return vert_coords, faces, meta_data



def fsaverage_mesh(subject_id='fsaverage', surf='white', hemi='both', subjects_dir=None, use_freesurfer_home_if_missing=True):
    """
    Load a surface mesh of the fsaverage subject.

    Convenience function to load a FreeSurfer surface mesh of the fsaverage subject. Use the subject_mesh function to load the mesh of any other subject.

    Parameters
    ----------
    subject_id: string, optional
        The subject identifier of the subject. Defaults to 'fsaverage'.

    surf : string, optional
        The brain surface where the data has been measured, e.g., 'white' or 'pial'. This will become part of the file name that is loaded. Defaults to 'white'.

    hemi : {'both', 'lh', 'rh'}, optional
        The hemisphere that should be loaded. Defaults to 'both'.

    subjects_dir: string, optional
        A string representing the full path to a directory. This should be the directory containing all subjects of your study. Defaults to the environment variable SUBJECTS_DIR if omitted. If that is not set, used the current working directory instead. This is the directory from which the application was executed.

    use_freesurfer_home_if_missing: boolean, optional
        If set to True, first checks whether the directory for the given subject exists in the `subjects_dir`. If it does not, it will reset the `subjects_dir` to '${FREESURFER_HOME}/subjects' before proceeding.

    Returns
    -------
    vert_coords: numpy array
        A 2-dimensional array containing the vertices of the mesh(es) of the subject. Each vertex entry contains 3 coordinates. Each coordinate describes a 3D position in a FreeSurfer surface file (e.g., 'lh.white'), as returned by the `nibabel` function `nibabel.freesurfer.io.read_geometry`.

    faces: numpy array
        A 2-dimensional array containing the 3-faces of the mesh(es) of the subject. Each face entry contains 3 indices. Each index references the respective vertex in the `vert_coords` array.

    meta_data: dictionary
        A dictionary containing detailed information on all files that were loaded and used settings. The following keys are available (depending on the value of the `hemi` argument, you can replace ?h with 'lh' or 'rh' or both 'lh' and 'rh'):
            - `?h.num_vertices` : number of vertices in the loaded mesh
            - `?h.num_faces` : number of faces in the loaded mesh
            - `?lh.surf_file` : the mesh file that was loaded for this hemisphere

    Raises
    ------
    ValueError
        If one of the parameters with a fixed set of values receives a value that is not allowed.

    Examples
    --------
    Load area data for both hemispheres and white surface of subject1 in the directory defined by the environment variable SUBJECTS_DIR:

    >>> import brainload as bl
    >>> verts, faced, meta_data = bl.fsaverage_mesh()
    """
    if subjects_dir is None:
        subjects_dir = os.getenv('SUBJECTS_DIR', os.getcwd())

    if use_freesurfer_home_if_missing and not os.path.isdir(os.path.join(subjects_dir, subject_id)):
        freesurfer_home = os.getenv('FREESURFER_HOME', os.getcwd())
        subjects_dir = os.path.join(freesurfer_home, 'subjects')

    vert_coords, faces, morphometry_data, meta_data = subject(subject_id, surf=surf, hemi=hemi, subjects_dir=subjects_dir, measure=None, load_morphometry_data=False)
    return vert_coords, faces, meta_data


def subject_data_native(subject_id, subjects_dir, measure, hemi, surf='white'):
    """
    Load native space morphometry data for a subject (e.g., lh.area).

    Parameters
    ----------
    subject_id: string
        The subject identifier of the subject. As always, it is assumed that this is the name of the directory containing the subject's data, relative to `subjects_dir`. Example: 'subject33'.

    measure : string
        The measure to load, e.g., 'area' or 'curv'. Defaults to 'area'.

    surf : string, optional
        The brain surface where the data has been measured, e.g., 'white' or 'pial'. This will become part of the file name that is loaded. For white, nothing will be added. Defaults to 'white'.

    hemi : {'both', 'lh', 'rh'}
        The hemisphere that should be loaded.

    subjects_dir: string
        A string representing the full path to a directory. This should be the directory containing all subjects of your study.

    Returns
    -------
    morphometry_data: numpy array
        A numpy array with as many entries as there are vertices in the subject. If you load two hemispheres instead of one, the length doubles. You can get the start indices for data of the hemispheres in the returned `meta_data`, see `meta_data['lh.num_vertices']` and `meta_data['rh.num_vertices']`. You can be sure that the data for the left hemisphere will always come first (if both were loaded). Indices start at 0, of course. So if the left hemisphere has `n` vertices, the data for them are at indices `0..n-1`, and the data for the right hemisphere start at index `n`. Note that the two hemispheres do in general NOT have the same number of vertices.

    meta_data: dictionary
        A dictionary containing detailed information on all files that were loaded and used settings. The following keys are available (depending on the value of the `hemi` argument, you can replace ?h with 'lh' or 'rh' or both 'lh' and 'rh'):
            - `?h.num_data_points` : the number of data points loaded.
            - `?h.morphometry_file` : the value of the `?h_morphometry_data_file` argument (data file that was loaded)
            - `?h.morphometry_file_format` : the value for `format` that was used
            - `subject_id` : the subject id
            - `subjects_dir` : the subjects dir that was used
            - `surf` : the surf that was used, e.g., 'white'
            - `measure` : the measure that was loaded as morphometry data, e.g., 'area'
            - `space` : always the string 'subject'. This means that the data loaded represent morphometry data taken from the subject's surface (as opposed to data mapped to a common or average subject).
            - `hemi` : the `hemi` value that was used

    Examples
    --------
    >>> import brainload as bl
    >>> morphometry_data, meta_data = bl.subject_data_native('subject1', '/mnt/study1_data', 'thickness', 'both')
    """
    vert_coords, faces, morphometry_data, meta_data = subject(subject_id, surf=surf, measure=measure, hemi=hemi, subjects_dir=subjects_dir, load_surface_files=False)
    return morphometry_data, meta_data


def subject_data_standard(subject_id, subjects_dir, measure, hemi, fwhm, average_subject='fsaverage', surf='white'):
    """
    Load standard space data for a subject (e.g., lh.area.fwhm10.fsaverage.mgh).

    Parameters
    ----------
    subject_id: string
        The subject identifier of the subject. As always, it is assumed that this is the name of the directory containing the subject's data, relative to `subjects_dir`. Example: 'subject33'.

    measure : string
        The measure to load, e.g., 'area' or 'curv'.

    surf : string, optional
        The brain surface where the data has been measured, e.g., 'white' or 'pial'. This will become part of the file name that is loaded. Defaults to 'white'.

    hemi : {'both', 'lh', 'rh'}
        The hemisphere that should be loaded.

    fwhm : string or None
        Which averaging version of the data should be loaded. FreeSurfer usually generates different standard space files with a number of smoothing settings. If None is passed, the `.fwhmX` part is omitted from the file name completely. Set this to '0' to get the unsmoothed version.

    subjects_dir: string
        A string representing the full path to a directory. This should be the directory containing all subjects of your study.

    average_subject: string, optional
        The name of the average subject to which the data was mapped. Defaults to 'fsaverage'.

    Returns
    -------
    morphometry_data: numpy array
        A numpy array with as many entries as there are vertices in the subject. If you load two hemispheres instead of one, the length doubles. You can get the start indices for data of the hemispheres in the returned `meta_data`, see `meta_data['lh.num_vertices']` and `meta_data['rh.num_vertices']`. You can be sure that the data for the left hemisphere will always come first (if both were loaded). Indices start at 0, of course. So if the left hemisphere has `n` vertices, the data for them are at indices `0..n-1`, and the data for the right hemisphere start at index `n`. Note that the two hemispheres do in general NOT have the same number of vertices.

    meta_data: dictionary
        A dictionary containing detailed information on all files that were loaded and used settings. The following keys are available (depending on the value of the `hemi` argument, you can replace ?h with 'lh' or 'rh' or both 'lh' and 'rh'):
            - `?h.num_data_points` : the number of data points loaded.
            - `?h.morphometry_file` : the value of the `?h_morphometry_data_file` argument (data file that was loaded)
            - `?h.morphometry_file_format` : the value for `format` that was used
            - `subject_id` : the subject id
            - `subjects_dir` : the subjects dir that was used
            - `surf` : the surf that was used, e.g., 'white'
            - `measure` : the measure that was loaded as morphometry data, e.g., 'area'
            - `space` : always the string 'common'. This means that the data loaded represent morphometry data that has been mapped to a common or average subject.
            - `hemi` : the `hemi` value that was used
    """
    vert_coords, faces, morphometry_data, meta_data = subject_avg(subject_id, measure=measure, surf=surf, hemi=hemi, fwhm=fwhm, subjects_dir=subjects_dir, average_subject=average_subject, load_surface_files=False)
    return morphometry_data, meta_data


def subject(subject_id, surf='white', measure='area', hemi='both', subjects_dir=None, meta_data=None, load_surface_files=True, load_morphometry_data=True):
    """
    Load FreeSurfer brain morphometry and/or mesh data for a single subject.

    High-level interface to load FreeSurfer brain data for a single space. This parses the data for the surfaces of this subject. If you want to load data that has been mapped to an average subject like 'fsaverage', use `subject_avg` instead.

    Parameters
    ----------
    subject_id: string
        The subject identifier of the subject. As always, it is assumed that this is the name of the directory containing the subject's data, relative to `subjects_dir`. Example: 'subject33'.

    measure : string, optional
        The measure to load, e.g., 'area' or 'curv'. Defaults to 'area'.

    surf : string, optional
        The brain surface where the data has been measured, e.g., 'white' or 'pial'. This will become part of the file name that is loaded. Defaults to 'white'.

    hemi : {'both', 'lh', 'rh'}, optional
        The hemisphere that should be loaded. Defaults to 'both'.

    subjects_dir: string, optional
        A string representing the full path to a directory. This should be the directory containing all subjects of your study. Defaults to the environment variable SUBJECTS_DIR if omitted. If that is not set, used the current working directory instead. This is the directory from which the application was executed.

    meta_data: dictionary, optional
        A dictionary that should be merged into the return value `meta_data`. Defaults to the empty dictionary if omitted.

    load_surface_files: boolean, optional
        Whether to load mesh data. If set to `False`, the first return values `vert_coords` and `faces` will be `None`. Defaults to `True`.

    load_morphometry_data: boolean, optional
        Whether to load morphometry data. If set to `False`, the first return value `morphometry_data` will be `None`. Defaults to `True`.

    Returns
    -------
    vert_coords: numpy array
        A 2-dimensional array containing the vertices of the mesh(es) of the subject. Each vertex entry contains 3 coordinates. Each coordinate describes a 3D position in a FreeSurfer surface file (e.g., 'lh.white'), as returned by the `nibabel` function `nibabel.freesurfer.io.read_geometry`.

    faces: numpy array
        A 2-dimensional array containing the 3-faces of the mesh(es) of the subject. Each face entry contains 3 indices. Each index references the respective vertex in the `vert_coords` array.

    morphometry_data: numpy array
        A numpy array with as many entries as there are vertices in the subject. If you load two hemispheres instead of one, the length doubles. You can get the start indices for data of the hemispheres in the returned `meta_data`, see `meta_data['lh.num_vertices']` and `meta_data['rh.num_vertices']`. You can be sure that the data for the left hemisphere will always come first (if both were loaded). Indices start at 0, of course. So if the left hemisphere has `n` vertices, the data for them are at indices `0..n-1`, and the data for the right hemisphere start at index `n`. Note that the two hemispheres do in general NOT have the same number of vertices.

    meta_data: dictionary
        A dictionary containing detailed information on all files that were loaded and used settings. The following keys are available (depending on the value of the `hemi` argument, you can replace ?h with 'lh' or 'rh' or both 'lh' and 'rh'):
            - `?h.num_data_points` : the number of data points loaded.
            - `?h.morphometry_file` : the value of the `?h_morphometry_data_file` argument (data file that was loaded)
            - `?h.morphometry_file_format` : the value for `format` that was used
            - `?h.num_vertices` : number of vertices in the loaded mesh
            - `?h.num_faces` : number of faces in the loaded mesh
            - `?lh.surf_file` : the mesh file that was loaded for this hemisphere
            - `subject_id` : the subject id
            - `subjects_dir` : the subjects dir that was used
            - `surf` : the surf that was used, e.g., 'white'
            - `measure` : the measure that was loaded as morphometry data, e.g., 'area'
            - `space` : always the string 'subject'. This means that the data loaded represent morphometry data taken from the subject's surface (as opposed to data mapped to a common or average subject).
            - `hemi` : the `hemi` value that was used

    Raises
    ------
    ValueError
        If one of the parameters with a fixed set of values receives a value that is not allowed.

    Examples
    --------
    Load area data for both hemispheres and white surface of subject1 in the directory defined by the environment variable SUBJECTS_DIR:

    >>> import brainload as bl
    >>> vertices, faces, data, md = bl.subject('subject1')

    Here, we are a bit more explicit about what we want to load:

    >>> import os
    >>> user_home = os.getenv('HOME')
    >>> subjects_dir = os.path.join(user_home, 'data', 'my_study_x')
    >>> vertices, faces, data, md = bl.subject('subject1', hemi='lh', measure='curv', subjects_dir=subjects_dir)

    Sometimes we do not care for the mesh, e.g., we only want the morphometry data:

    >>> data, md = bl.subject('subject1', hemi='rh', load_surface_files=False)[2:4]

    ...or the other way around (mesh only, no morphometry data):

    >>> vertices, faces = bl.subject('subject1', hemi='rh', load_morphometry_data=False)[0:2]


    """
    if hemi not in ('lh', 'rh', 'both'):
        raise ValueError("ERROR: hemi must be one of {'lh', 'rh', 'both'} but is '%s'." % hemi)

    if meta_data is None:
        meta_data = {}

    if subjects_dir is None:
        subjects_dir = os.getenv('SUBJECTS_DIR', os.getcwd())
    subject_surf_dir = os.path.join(subjects_dir, subject_id, 'surf')

    vert_coords = None
    faces = None
    if load_surface_files:
        display_subject = subject_id
        display_surf = surf
        lh_surf_file = os.path.join(subject_surf_dir, ('lh.' + surf))
        rh_surf_file = os.path.join(subject_surf_dir, ('rh.' + surf))
        vert_coords, faces, meta_data = load_subject_mesh_files(lh_surf_file, rh_surf_file, hemi=hemi, meta_data=meta_data)
    else:
        display_subject = None
        display_surf = None

    morphometry_data = None
    if load_morphometry_data:
        lh_morphometry_file = os.path.join(subject_surf_dir, ('lh.' + measure + _get_morphometry_data_suffix_for_surface(surf)))
        rh_morphometry_file = os.path.join(subject_surf_dir, ('rh.' + measure + _get_morphometry_data_suffix_for_surface(surf)))
        morphometry_data, meta_data = load_subject_morphometry_data_files(lh_morphometry_file, rh_morphometry_file, hemi=hemi, format='curv', meta_data=meta_data)
    else:
        measure = None


    meta_data['subject_id'] = subject_id
    meta_data['display_subject'] = display_subject
    meta_data['subjects_dir'] = subjects_dir
    meta_data['surf'] = surf
    meta_data['display_surf'] = display_surf
    meta_data['measure'] = measure
    meta_data['space'] = 'native_space'
    meta_data['hemi'] = hemi

    return vert_coords, faces, morphometry_data, meta_data


def get_surface_file_path(subjects_dir, subject_id, hemi, surf, subdir='surf'):
    """
    Determine the path to a surface file, e.g., `lh.white`.
    """
    return os.path.join(subjects_dir, subject_id, subdir, (hemi + '.' + surf))


def get_standard_space_morphometry_file_path(subjects_dir, subject_id, hemi, measure, fwhm="10", average_subject="fsaverage", surf='white', subdir='surf', file_ext='mgh'):
    """
    Determine the path to a standard space morphometry file, e.g., `lh.area.fwhm10.fsaverage.mgh`.
    """
    fwhm_tag = _get_fwhm_tag(fwhm)
    return os.path.join(subjects_dir, subject_id, subdir, (hemi + '.' + measure + _get_morphometry_data_suffix_for_surface(surf) + fwhm_tag + '.' + average_subject + '.' + file_ext))


def get_morphometry_file_path(subjects_dir, subject_id, surf, hemi, measure, subdir='surf'):
    """
    Determine the path to a native space morphometry file, e.g., `lh.area`.
    """
    return os.path.join(subjects_dir, subject_id, subdir, (hemi + '.' + measure + _get_morphometry_data_suffix_for_surface(surf)))


def _get_fwhm_tag(fwhm_string):
    if fwhm_string is None:
        fwhm_tag = ''
    else:
        fwhm_tag = '.fwhm' + fwhm_string
    return fwhm_tag


def _merge_meshes(meshes):
    """
    Merge several meshes into a single one.

    Merge a list of meshes into a single one. Each mesh is given by a vertex list and a face list. The merged vertex list is just a vstack of the individual lists, and the vertex coordinates are not altered in any way. As a face id defined by the indices of its 3 vertices, these indices get adjusted for all meshes but the first one.

    Parameters
    ----------
    meshes: array-like
        A array of meshes. Each mesh is represented as an array of length 2, where the entry at index 0 is the vertex list, and the one at index 2 is the face list.

    Returns
    -------
    all_vert_coords: numpy array
        An array of vertex coordinates with shape(3, n), where n is the sum of the vertex counts of all input meshes.

    all_faces: numpy_array (2d)
        An array of faces with shape(3, m), where m is the sum of the face counts of all input meshes. For each face, each of its 3 values represent the vertex at the respective index in the `all_vert_coords` array.
    """
    all_vert_coords = np.empty((0, 3), dtype=float)
    all_faces = np.empty((0, 3), dtype=int)

    for mesh in meshes:
        new_vert_coords = mesh[0]
        new_faces = mesh[1]
        # Keep track of the total number of vertices we had *before* adding the new ones. This is the shift we need for the faces.
        vertex_index_shift = all_vert_coords.shape[0]
        all_vert_coords = np.vstack((all_vert_coords, new_vert_coords))

        new_faces_shifted = new_faces + vertex_index_shift
        all_faces = np.vstack((all_faces, new_faces_shifted))
    return all_vert_coords, all_faces


def subject_avg(subject_id, measure='area', surf='white', display_surf='white', hemi='both', fwhm='10', subjects_dir=None, average_subject='fsaverage', subjects_dir_for_average_subject=None, meta_data=None, load_surface_files=True, load_morphometry_data=True, custom_morphometry_files=None):
    """
    Load morphometry data that has been mapped to an average subject for a subject, i.e., standard space data.

    Load data for a single subject that has been mapped to an average subject like the `fsaverage` subject from FreeSurfer. Can also load the mesh of an arbitrary surface for the average subject.

    Parameters
    ----------
    subject_id: string
        The subject identifier of the subject. As always, it is assumed that this is the name of the directory containing the subject's data, relative to `subjects_dir`. Example: 'subject33'.

    measure : string, optional
        The measure to load, e.g., 'area' or 'curv'. Defaults to 'area'.

    surf : string, optional
        The brain surface where the data has been measured, e.g., 'white' or 'pial'. This will become part of the file name that is loaded. Defaults to 'white'.

    hemi : {'both', 'lh', 'rh'}, optional
        The hemisphere that should be loaded. Defaults to 'both'.

    fwhm : string or None, optional
        Which averaging version of the data should be loaded. FreeSurfer usually generates different standard space files with a number of smoothing settings. Defaults to '10'. If None is passed, the `.fwhmX` part is omitted from the file name completely. Set this to '0' to get the unsmoothed version.

    subjects_dir: string, optional
        A string representing the full path to a directory. This should be the directory containing all subjects of your study. Defaults to the environment variable SUBJECTS_DIR if omitted. If that is not set, used the current working directory instead. This is the directory from which the application was executed.

    average_subject: string, optional
        The name of the average subject to which the data was mapped. Defaults to 'fsaverage'.

    display_surf: string, optional
        The surface of the average subject for which the mesh should be loaded, e.g., 'white', 'pial', 'inflated', or 'sphere'. Defaults to 'white'. Ignored if `load_surface_files` is `False`.

    subjects_dir_for_average_subject: string, optional
        A string representing the full path to a directory. This can be used if the average subject is not in the same directory as all your study subjects. Defaults to the setting of `subjects_dir`.

    meta_data: dictionary, optional
        A dictionary that should be merged into the return value `meta_data`. Defaults to the empty dictionary if omitted.

    load_surface_files: boolean, optional
        Whether to load mesh data. If set to `False`, the first return values `vert_coords` and `faces` will be `None`. Defaults to `True`.

    load_morphometry_data: boolean, optional
        Whether to load morphometry data. If set to `False`, the first return value `morphometry_data` will be `None`. Defaults to `True`.

    custom_morphometry_files: dictionary, optional
        Cutom filenames for the left and right hemispjere data files that should be loaded. A dictionary of strings with exactly the following two keys: `lh` and `rh`. The value strings must contain hardcoded file names or template strings for them. As always, the files will be loaded relative to the `surf/` directory of the respective subject. Example: `{'lh': 'lefthemi.nonstandard.mymeasure44.mgh', 'rh': 'righthemi.nonstandard.mymeasure44.mgh'}`.

    Returns
    -------
    vert_coords: numpy array
        A 2-dimensional array containing the vertices of the mesh(es) of the average subject. Each vertex entry contains 3 coordinates. Each coordinate describes a 3D position in a FreeSurfer surface file (e.g., 'lh.white'), as returned by the `nibabel` function `nibabel.freesurfer.io.read_geometry`.

    faces: numpy array
        A 2-dimensional array containing the 3-faces of the mesh(es) of the average subject. Each face entry contains 3 indices. Each index references the respective vertex in the `vert_coords` array.

    morphometry_data: numpy array
        A numpy array with as many entries as there are vertices in the average subject. If you load two hemispheres instead of one, the length doubles. You can get the start indices for data of the hemispheres in the returned `meta_data`, see `meta_data['lh.num_vertices']` and `meta_data['rh.num_vertices']`. You can be sure that the data for the left hemisphere will always come first (if both were loaded). Indices start at 0, of course. So if the left hemisphere has `n` vertices, the data for them are at indices `0..n-1`, and the data for the right hemisphere start at index `n`. In many cases, your average subject will have the same number of vertices for both hemispheres and you will know this number beforehand, so you may not have to worry about this at all.

    meta_data: dictionary
        A dictionary containing detailed information on all files that were loaded and used settings. The following keys are available (depending on the value of the `hemi` argument, you can replace ?h with 'lh' or 'rh' or both 'lh' and 'rh'):
            - `?h.num_data_points` : the number of data points loaded.
            - `?h.morphometry_file` : the value of the `?h_morphometry_data_file` argument (data file that was loaded)
            - `?h.morphometry_file_format` : the value for `format` that was used
            - `?h.num_vertices` : number of vertices in the loaded mesh
            - `?h.num_faces` : number of faces in the loaded mesh
            - `?lh.surf_file` : the mesh file that was loaded for this hemisphere
            - `subject_id` : the subject id
            - `subjects_dir` : the subjects dir that was used
            - `surf` : the surf that was used, e.g., 'white'
            - `measure` : the measure that was loaded as morphometry data, e.g., 'area'
            - `space` : always the string 'common'. This means that the data loaded represent morphometry data that has been mapped to a common or average subject.
            - `hemi` : the `hemi` value that was used
            - `display_subject` : the name of the common or average subject. This is the subject the surface meshes originate from. Ususally 'fsaverage'.
            - `display_surf` : the surface of the common subject that has been loaded. Something like 'pial', 'white', or 'inflated'.

    Raises
    ------
    ValueError
        If one of the parameters with a fixed set of values receives a value that is not allowed.

    Examples
    --------
    Load area data for both hemispheres and white surface of subject1 in the directory defined by the environment variable SUBJECTS_DIR, mapped to fsaverage:

    >>> import brainload as bl
    >>> v, f, data, md = bl.subject_avg('subject1')
    >>> print md['surf']
    white

    Here, we are a bit more picky and explicit about what we want to load:

    >>> import os
    >>> import brainload as bl
    >>> user_home = os.getenv('HOME')
    >>> subjects_dir = os.path.join(user_home, 'data', 'my_study_x')
    >>> v, f, data, md = bl.subject_avg('subject1', hemi='lh', measure='curv', fwhm='15', display_surf='inflated', subjects_dir=subjects_dir)

    Sometime we do not care for the mesh, e.g., we only want the morphometry data:

    >>> import brainload as bl
    >>> data, md = bl.subject_avg('subject1', hemi='rh', fwhm='15', load_surface_files=False)[2:4]

    """
    if hemi not in ('lh', 'rh', 'both'):
        raise ValueError("ERROR: hemi must be one of {'lh', 'rh', 'both'} but is '%s'." % hemi)

    if subjects_dir is None:
        subjects_dir = os.getenv('SUBJECTS_DIR', os.getcwd())

    if subjects_dir_for_average_subject is None:
        subjects_dir_for_average_subject = subjects_dir

    if meta_data is None:
        meta_data = {}

    # Retrieve the surface mesh on which to display the data. This is the average subject's surface.
    vert_coords = None
    faces = None
    if load_surface_files:
        display_subject = average_subject
        fsaverage_surf_dir = os.path.join(subjects_dir_for_average_subject, average_subject, 'surf')
        lh_surf_file = os.path.join(fsaverage_surf_dir, ('lh.' + display_surf))
        rh_surf_file = os.path.join(fsaverage_surf_dir, ('rh.' + display_surf))
        vert_coords, faces, meta_data = load_subject_mesh_files(lh_surf_file, rh_surf_file, hemi=hemi, meta_data=meta_data)
    else:
        display_surf = None
        display_subject = None

    # Parse the subject's morphometry data, mapped to standard space by FreeSurfer's recon-all.
    morphometry_data = None
    if load_morphometry_data:
        subject_surf_dir = os.path.join(subjects_dir, subject_id, 'surf')

        if custom_morphometry_files is None:
            meta_data['custom_morphometry_files_used'] = False
            lh_morphometry_data_mapped_to_fsaverage = get_standard_space_morphometry_file_path(subjects_dir, subject_id, 'lh', measure, fwhm=fwhm, average_subject=average_subject, surf=surf)
            rh_morphometry_data_mapped_to_fsaverage = get_standard_space_morphometry_file_path(subjects_dir, subject_id, 'rh', measure, fwhm=fwhm, average_subject=average_subject, surf=surf)
        else:
            meta_data['custom_morphometry_files_used'] = True
            lh_morphometry_data_mapped_to_fsaverage = os.path.join(subject_surf_dir, custom_morphometry_files['lh'])
            rh_morphometry_data_mapped_to_fsaverage = os.path.join(subject_surf_dir, custom_morphometry_files['rh'])

        morphometry_data, meta_data = load_subject_morphometry_data_files(lh_morphometry_data_mapped_to_fsaverage, rh_morphometry_data_mapped_to_fsaverage, hemi=hemi, format='mgh', meta_data=meta_data)
    else:
        measure = None


    meta_data['measure'] = measure
    meta_data['subject_id'] = subject_id
    meta_data['subjects_dir'] = subjects_dir
    meta_data['display_surf'] = display_surf
    meta_data['display_subject'] = display_subject
    meta_data['average_subjects_dir'] = subjects_dir_for_average_subject
    meta_data['surf'] = surf
    meta_data['space'] = 'standard_space'
    meta_data['average_subject'] = average_subject
    meta_data['fwhm'] = fwhm
    meta_data['hemi'] = hemi

    return vert_coords, faces, morphometry_data, meta_data


def group_native(measure, subjects_dir, subjects_list, surf='white', hemi='both'):
    """
    Load native space morphometry data for a number of subjects.

    Load native space group data, i.e., morphometry data for all subjects in a study.
    The information given in the parameters `measure`, `surf`, and `hemi` are used to construct the file name that will be loaded by default. This function will NOT load the meshes.

    Parameters
    ----------
    measure : string
        The measure to load, e.g., 'area' or 'curv'. Data files for this measure have to exist for all subjects.

    surf : string, optional
        The brain surface where the data has been measured, e.g., 'white' or 'pial'. Defaults to 'white'. Will be added after the measure name unless left at default.

    hemi : {'both', 'lh', 'rh'}, optional
        The hemisphere that should be loaded. Defaults to 'both'.

    subjects_dir: string, optional
        A string representing the full path to a directory. Defaults to the environment variable SUBJECTS_DIR if omitted. If that is not set, used the current working directory instead. This is the directory from which the application was executed.

    subjects_list: list of strings, optional (unless `subjects_detection_mode` is set to `list`)
        A list of subject identifiers or directory names that should be loaded from the `subjects_dir`. Example list: `['subject1', 'subject2']`. Defaults to None. Only allowed if `subjects_detection_mode` is `auto` or `list`. In `auto` mode, this takes
        precedence over all other options, i.e., if a `subjects_list` *and* the (default or custom) `subjects_file` are given, the `subjects_list` will be used.

    Returns
    -------
    morphdata_by_subject: dictionary
        A dictionary containing the morphometry data. Keys are subject identifiers, and values are the morphometry data numpy 1D arrays.

    metadata_by_subject: dictionary
        A dictionary containing detailed information on all subjects and files that were loaded. Each of its keys is a subject identifier. The data value is another dictionary that contains all meta data for this subject.
    """
    morphdata_by_subject = dict()
    metadata_by_subject = dict()
    for subject_id in subjects_list:
        morphometry_data, metadata = subject_data_native(subject_id, subjects_dir, measure, hemi, surf=surf)
        morphdata_by_subject[subject_id] = morphometry_data
        metadata_by_subject[subject_id] = metadata
    return morphdata_by_subject, metadata_by_subject


def group(measure, surf='white', hemi='both', fwhm='10', subjects_dir=None, average_subject='fsaverage', group_meta_data=None, subjects_list=None, subjects_file='subjects.txt', subjects_file_dir=None, custom_morphometry_file_templates=None, subjects_detection_mode='auto'):
    """
    Load standard space morphometry data for a number of subjects.

    Load group data, i.e., morphometry data for all subjects in a study that has already been mapped to standard space and is ready for group analysis.
    The information given in the parameters `measure`, `surf`, `hemi`, and `fwhm` are used to construct the file name that will be loaded by default. This function will NOT load the meshes.

    Parameters
    ----------
    measure : string
        The measure to load, e.g., 'area' or 'curv'. Data files for this measure have to exist for all subjects.

    surf : string, optional
        The brain surface where the data has been measured, e.g., 'white' or 'pial'. Defaults to 'white'.

    hemi : {'both', 'lh', 'rh'}, optional
        The hemisphere that should be loaded. Defaults to 'both'.

    fwhm : string or None, optional
        Which averaging version of the data should be loaded. FreeSurfer usually generates different standard space files with a number of smoothing settings. Defaults to '10'. If None is passed, the `.fwhmX` part is omitted from the file name completely. Set this to '0' to get the unsmoothed version.

    subjects_dir: string, optional
        A string representing the full path to a directory. Defaults to the environment variable SUBJECTS_DIR if omitted. If that is not set, used the current working directory instead. This is the directory from which the application was executed.

    average_subject: string, optional
        The name of the average subject to which the data was mapped. Defaults to 'fsaverage'.

    group_meta_data: dictionary, optional
        A dictionary that should be merged into the return value `group_meta_data`. Defaults to the empty dictionary if omitted.

    subjects_list: list of strings, optional (unless `subjects_detection_mode` is set to `list`)
        A list of subject identifiers or directory names that should be loaded from the `subjects_dir`. Example list: `['subject1', 'subject2']`. Defaults to None. Only allowed if `subjects_detection_mode` is `auto` or `list`. In `auto` mode, this takes
        precedence over all other options, i.e., if a `subjects_list` *and* the (default or custom) `subjects_file` are given, the `subjects_list` will be used.

    subjects_file_dir: string, optional
        A string representing the full path to a directory. This directory must contain the `subjects_file` (see below). Defaults to the `subjects_dir`.

    subjects_file: string, optional
        The name of the subjects file, relative to the `subjects_file_dir`. Defaults to 'subjects.txt'. The file must be a simple text file that contains one `subject_id` per line. It can be a CSV file that has other data following, but the `subject_id` has to be the first item on each line and the separator must be a comma. So a line is allowed to look like this: `subject1, 35, center1, 147`. No header is allowed. If you have a different format, consider reading the file yourself and pass the result as `subjects_list` instead.

    custom_morphometry_file_templates: dictionary, optional
        Cutom filenames for the left and right hemisphere data files that should be loaded. A dictionary of strings with exactly the following two keys: `lh` and `rh`. The value strings can contain hardcoded file names or template strings for them. As always, the files will be loaded relative to the `surf/` directory of the respective subject. Example for hard-coded files: `{'lh': 'lefthemi.nonstandard.mymeasure44.mgh', 'rh': 'righthemi.nonstandard.mymeasure44.mgh'}`. The strings may contain any of the following variabes, which will be replaced by what you supplied to the other arguments of this function:
            - `${MEASURE}` will be replaced with the value of `measure`.
            - `${SURF}` will be replaced with the FreeSurfer file name part for the surface `surf`. This is the empty string if `surf` is 'white', and a dot followed by the value of `surf` for all other settings of surf. Examples: when `surf` is 'pial', this will be replaced with '.pial' (Note the dot!). If `surf` is 'white', this will be replaced with the empty string.
            - `${SURF_RAW}` will be replaced with the value of `surf`.
            - `${HEMI}` will be replaced with 'lh' for the left hemisphere, and with 'rh' for the right hemisphere.
            - `${FWHM}` will be replaced with the value of `fwhm`, so something like '10'.
            - `${SUBJECT_ID}` will be replaced by the id of the subject that is being loaded, e.g., 'subject3'.
            - `${AVERAGE_SUBJECT}` will be replaced by the value of `average_subject`.

            Note that only `${SURF}` and `${HEMI}` are usually needed, everything else can be hardcoded (or is not part of typical FreeSurfer file names at all, like `${SUBJECT_ID}`).
            Example template string: `subj_${SUBJECT_ID}_hemi_${HEMI}.alsononstandard.mgh`. Complete example for template strings in dictionary: `{'lh': 'subj_${SUBJECT_ID}_hemi_${HEMI}.alsononstandard.mgh', 'rh': 'subj_${SUBJECT_ID}_hemi_${HEMI}.alsononstandard.mgh'}`.

    subjects_detection_mode: {'auto', 'list', 'file', 'search_dir'}, optional
        The method used to determine the subjects that should be loaded. Defaults to 'auto'. You can always see which mode was used by looking at the returned `run_meta_data`, see `run_meta_data['subjects_detection_mode']`.
            - 'auto': In this mode, all available methods will be tried in the following order: If a `subjects_list` is given, it is used. Then, the `subjects_file` is used if it exists. Note that this may be the default file, '$SUBJECTS_DIR/subject_surf_dir.txt', or another if one has explicitely been defined by setting `subjects_file` and/or `subjects_file_dir`. If the file does not exist, the directory is searched for directories containing FreeSurfer data as defined in the section for 'search_dir' mode below. You can always see which method was used in auto mode by looking at the returned `run_meta_data`, see `run_meta_data['subjects_detection_mode_auto_used_method']`.

            - 'list': In this mode, the given `subjects_list` is used, and you have to supply one. If not, an error is raised. You are not allowed to supply a `subjects_file` in this mode, or an error will be raised.

            - 'file': In this mode, the subjects file is used. Note that this may be the default file, '$SUBJECTS_DIR/subjects.txt', or another if one has explicitely been defined by setting `subjects_file` and/or `subjects_file_dir`. If the file does not exist, an error is raised. You can see which file was used by looking at the returned `run_meta_data`, see `run_meta_data['subjects_file']`. You are not allowed to supply a `subjects_list` in this mode, or an error will be raised.

            - 'search_dir': In this mode, the `subjects_dir` (default or explicitely given) is searched for sub directories which look as if they could contain FreeSurfer data. The latter means that they contain a sub directory named 'surf'. There is one exception though: if the name of one such directory equals the name of the `average_subject`, the directory is skipped. You are not allowed to supply a `subjects_list` in this mode, or an error will be raised.

    Returns
    -------
    group_morphometry_data: numpy array
        An array filled with the morphometry data for the subjects. The array has shape `(n, m)` where `n` is the number of subjects, and `m` is the number of vertices of the standard subject. (If you load both hemispheres instead of one, m doubles.) To get the subject id for the entries, look at the respective index in the returned `subjects_list`.

    subjects_list: list of strings
        A list containing the subject identifiers in the same order as the data in `group_morphometry_data`. (If `subjects_detection_mode` is 'list' or 'file', the order in these is guaranteed to be preserved. But in mode 'search_dir' or 'auto' which may have chosen to fall back to 'search_dir' as a last resort, this is helpful: You can use the index of a subject in this list to find its data in `group_morphometry_data`, as it will have the same index. See the examples below.)

    group_meta_data: dictionary
        A dictionary containing detailed information on all subjects and files that were loaded. Each of its keys is a subject identifier. The data value is another dictionary that contains all meta data for this subject as returned by the `subject_avg` function.

    run_meta_data: dictionary
        A dictionary containing general information on the settings used when executing the function and determining which subjects to load.

    Raises
    ------
    ValueError
        If one of the parameters with a fixed set of values receives a value that is not allowed.

    Examples
    --------
    Load area data for all subjects in the directory defined by the environment variable SUBJECTS_DIR:

    >>> import brainload as bl
    >>> data, subjects, group_md, run_md = bl.group('area')

    Here, we load curv data for the right hemisphere, computed on the pial surface with smooting of 20:

    >>> data, subjects, group_md, run_md = bl.group('curv', hemi='rh', surf='pial', fwhm='20')

    We may want to be a but more explicit on which subjects are loaded from where:

    >>> import os
    >>> import brainload as bl
    >>> subjects_dir = os.path.join(os.getenv('HOME'), 'data', 'my_study_x')
    >>> subjects_list = ['subject1', 'subject4', 'subject8']
    >>> data, subjects, group_md, run_md = bl.group('curv', fwhm='20', subjects_dir=subjects_dir, subjects_list=subjects_list)

    Continuing the last example, we may want to have a look at the curv value of the vertex at index 100000 of the subject 'subject4':

    >>> subject4_idx = subjects.index('subject4')
    >>> print data[subject4_idx][100000]

    """


    if hemi not in ('lh', 'rh', 'both'):
        raise ValueError("ERROR: hemi must be one of {'lh', 'rh', 'both'} but is '%s'." % hemi)

    run_meta_data = {}

    if subjects_detection_mode not in ('auto', 'file', 'list', 'search_dir'):
        raise ValueError("ERROR: subjects_detection_mode must be one of {'auto', 'file', 'list', 'search_dir'} but is '%s'." % subjects_detection_mode)
    else:
        run_meta_data['subjects_detection_mode'] = subjects_detection_mode

    # supplying a list is only valid in modes 'auto' and 'list'
    if subjects_detection_mode in ('file', 'search_dir') and subjects_list is not None:
        raise ValueError("ERROR: subjects_detection_mode is set to '%s' but a subjects_list was given. Not supported in subjects_detection_mode 'file' and 'search_dir'." % subjects_detection_mode)

    if subjects_dir is None:
        subjects_dir = os.getenv('SUBJECTS_DIR', os.getcwd())

    if subjects_file_dir is None:
        subjects_file_dir = subjects_dir

    if group_meta_data is None:
        group_meta_data = {}

    run_meta_data['subjects_file_used'] = False
    if subjects_detection_mode == 'auto' and subjects_list is not None:
        run_meta_data['subjects_detection_mode_auto_used_method'] = 'list'  # just use the existing list
    elif subjects_detection_mode == 'list':
        if subjects_list is None:
            raise ValueError("ERROR: subjects_detection_mode is set to 'list' but the subjects_list parameter was not given.")
    elif subjects_detection_mode == 'search_dir':
        subjects_list = nit.detect_subjects_in_directory(subjects_dir, ignore_dir_names=[average_subject])
    else:
        # we are in modes 'auto' or 'file'
        subjects_file_with_path = os.path.join(subjects_file_dir, subjects_file)
        assumed_subjects_file_exists = os.path.isfile(subjects_file_with_path)

        # in file mode, the file has to exist.
        if subjects_detection_mode == 'file' and not assumed_subjects_file_exists:
            raise ValueError("ERROR: subjects_detection_mode is set to 'file' but the subjects_file '%s' does not exist." % subjects_file_with_path)

        auto_mode_done = False
        if assumed_subjects_file_exists:    # we are still in modes 'auto' or 'file', and the file exists.
            subjects_list = nit.read_subjects_file(subjects_file_with_path)
            run_meta_data['subjects_file_used'] = True
            run_meta_data['subjects_file'] = subjects_file_with_path
            if subjects_detection_mode == 'auto':   # in auto mode, we prefer/use the subject file if it exists. If it does not exist, we try to guess the list from the directory later.
                auto_mode_done = True
                run_meta_data['subjects_detection_mode_auto_used_method'] = 'file'

        if subjects_detection_mode == 'auto' and not auto_mode_done:            # last chance in auto mode: try to detect subjects from the contents of the subjects dir.
            run_meta_data['subjects_detection_mode_auto_used_method'] = 'search_dir'
            subjects_list = nit.detect_subjects_in_directory(subjects_dir, ignore_dir_names=[average_subject])

    if custom_morphometry_file_templates is not None:
        run_meta_data['custom_morphometry_file_templates_used'] = True
        run_meta_data['lh.custom_morphometry_file_template'] = custom_morphometry_file_templates['lh']
        run_meta_data['rh.custom_morphometry_file_template'] = custom_morphometry_file_templates['rh']
    else:
        run_meta_data['custom_morphometry_file_templates_used'] = False

    group_morphometry_data = []
    for subject_id in subjects_list:

        custom_morphometry_files = None
        subject_meta_data = {}
        if custom_morphometry_file_templates is not None:
            surf_file_part = _get_morphometry_data_suffix_for_surface(surf)
            substitution_dict_lh = {'MEASURE': measure, 'SURF_RAW': surf, 'SURF': surf_file_part, 'HEMI': 'lh', 'FWHM': fwhm, 'SUBJECT_ID': subject_id, 'AVERAGE_SUBJECT': average_subject}
            substitution_dict_rh = {'MEASURE': measure, 'SURF_RAW': surf, 'SURF': surf_file_part, 'HEMI': 'rh', 'FWHM': fwhm, 'SUBJECT_ID': subject_id, 'AVERAGE_SUBJECT': average_subject}
            custom_morphometry_file_lh = nit.fill_template_filename(custom_morphometry_file_templates['lh'], substitution_dict_lh)
            custom_morphometry_file_rh = nit.fill_template_filename(custom_morphometry_file_templates['rh'], substitution_dict_rh)
            custom_morphometry_files = {'lh': custom_morphometry_file_lh, 'rh': custom_morphometry_file_rh}

        # In the next function call, we discard the first two return values (vert_coords and faces), as these are None anyways because we did not load surface files.
        subject_morphometry_data, subject_meta_data = subject_avg(subject_id, measure=measure, surf=surf, hemi=hemi, fwhm=fwhm, subjects_dir=subjects_dir, average_subject=average_subject, meta_data=subject_meta_data, load_surface_files=False, custom_morphometry_files=custom_morphometry_files)[2:4]

        group_meta_data[subject_id] = subject_meta_data
        group_morphometry_data.append(subject_morphometry_data)
    group_morphometry_data = np.array(group_morphometry_data)
    return group_morphometry_data, subjects_list, group_meta_data, run_meta_data


def parse_talairach_file(file_name):
    """
    Parse a talairach matrix from a talairach.xfm file.

    Parse a talairach matrix from the mri/transforms/talairach.xfm file of a subject. Talairach space is a RAS space with the coordinate center at the Anterior Commisure. RAS (Right-Anterior-Superior) means X points to the right (from subjects point of view), Y points up out of the nose (subject is lying in scanner), and Z points out of the top of the head (so the axis is parallel to the floor). From the Freeurfer Wiki on coordinate systems: 'Note on Talairach: FreeSurfer does not report true "Talairach" coordinates. The coordinates listed unter "Talairach" are actually based on Matthew Brett's 10/8/98 non-linear transform from MNI305 space (see http://www.mrc-cbu.cam.ac.uk/Imaging/mnispace.html). FreeSurfer also reports "Talairach MNI" coordinates. These are MNI305 space.'

    Parameters
    ----------
    file_name: str
        Path to the file, usually SUBJECT/mri/transforms/talairach.xfm

    Returns
    -------
    numpy 2D array
        The matrix, a float array with shape (3, 4).
    """
    with open(file_name, 'r') as fh:
        lines = [line.rstrip('\n') for line in fh]
    if len(lines) == 8:
        return _parse_talairach_matrix_lines(lines[5:8])
    else:
        raise ValueError("Expected talairach file with 8 lines, got %d." % (len(lines)))


def _parse_talairach_matrix_lines(matrix_lines):
    """
    Parse a 3x4 talairach matrix.

    Parse a talairach matrix from the 3 lines representing it in the mri/transforms/talairach.xfm file of a subject.

    Parameters
    ----------
    matrix_lines: list of str
        The 3 matrix lines of a file in talairach.xfm format. Each line must contain 4 floats, separated by spaces. The last line may end with an ';', which will be removed by this function.

    Returns
    -------
    2D numpy array of floats
        The parsed matrix, with dimension (3, 4).
    """
    if len(matrix_lines) != 3:
        raise ValueError("Talairach matrix has wrong line count. Expected exactly 3 lines, got %d." % len(matrix_lines))

    last_line = matrix_lines[2]
    if last_line.endswith(';'):
        matrix_lines[2] = last_line[:-1]

    tal_matrix = np.zeros((3, 4))
    for idx, line in enumerate(matrix_lines):
        tal_matrix[idx] = np.fromstring(line, dtype=np.float_, sep=' ')
    return tal_matrix

"""
Functions for loading FreeSurfer data on different levels.

The high-level functions are available directly in the package namespace. Using the functions in here should not be necessary.
"""

import os
import sys
import errno
import numpy as np
import collections
import gzip
import nibabel.freesurfer.io as fsio
import nibabel.freesurfer.mghformat as fsmgh
from . import nitools as nit
from . import annotations as an
import nibabel as nib
import numpy.linalg as npl  # for matrix inversion
import struct   # for reading binary data


def read_m3z_file(m3z_file):
    """
    Read a file in FreeSurfer m3z format.

    Read a file in FreeSurfer m3z format, usually mri/transforms/talairach.m3z of a subject. An m3z file is a gzipped binary file containing a dense vector field that describes a 3D registration between two volumes/images. This implementation follows the Matlab implementation from the FreeSurfer source repository at github, see https://github.com/freesurfer/freesurfer/blob/dev/matlab/mris_read_m3z.m. This function is released under the Freesurfer license: https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense

    Parameters
    ----------
    m3z_file: str
        Path to a file in m3z format

    Returns
    -------
    vol_orig: numpy 4D array
        Array of np.single, containing 3 numbers per voxel. The shape is (width, height, depth, 3), where width, height, and depth are the dimensions of the source volume.

    vol_dest: numpy 4D array
        Array of np.single, containing 3 numbers per voxel. The shape is (width, height, depth, 3), where width, height, and depth are the dimensions of the destination volume.

    vol_ind0: numpy 4D array
        Array of np.int32, containing 3 numbers per voxel. The shape is (width, height, depth, 3).

    meta_data: dictionary
        Contains meta data on the registration. The following keys are included:
            - version: float, File format version
            - width: int, Volume width
            - height: int, Volume height
            - depth: int, Volume depth
            - spacing: int, voxel spacing of the volume
            - exp_k: float, exp_k of the volume

    Examples
    --------
    Read a talairach.m3z file that has been generated by FreeSurfer's ```recon-all``` command.

    >>> import brainload.freesurferdata as fsd
    >>> import os
    >>> m3z_file = os.path.join(os.getenv('HOME'), 'my_study_data', 'subject1', 'mri', 'transforms', 'talairach.m3z')
    >>> vol_orig, vol_dest, vol_ind0, meta_data = fsd.read_m3z_file(m3z_file)
    """
    m3z = gzip.open(m3z_file, 'rb')
    fdata = m3z.read()      # read the whole file contents
    # Read the file header
    data_start_pos = 24
    (version, width, height, depth, spacing, exp_k) = struct.unpack(">fiiiif", fdata[:data_start_pos])
    meta_data = {}
    meta_data['version'] = version
    meta_data['width'] = width
    meta_data['height'] = height
    meta_data['depth'] = depth
    meta_data['spacing'] = spacing
    meta_data['exp_k'] = exp_k
    meta_data['data_start_pos'] = data_start_pos

    numbers_per_voxel = 9
    bytes_uint8 = 4
    numbers_to_read = width * height * depth * numbers_per_voxel
    bytes_to_read = numbers_to_read * bytes_uint8
    data_end_pos = data_start_pos + bytes_to_read
    vol_data = struct.unpack(">%dB" % (numbers_to_read * 4), fdata[data_start_pos:data_end_pos])    # vol_data is a tuple
    meta_data['data_end_pos'] = data_end_pos
    meta_data['bytes_to_read'] = bytes_to_read
    meta_data['numbers_to_read'] = numbers_to_read
    meta_data['remaining_data_tag'] = struct.unpack(">i", fdata[data_end_pos:data_end_pos+4])[0]    # the first 4 bytes after the data are an integer tag, that holds information on what kind of data follows. We do not read that data but check the tag here.
    meta_data['file_end_pos'] = len(fdata)

    # create indices into the vol_data where data resides
    indices = np.kron(np.ones((12,1), dtype=np.int), range(width * height * depth))
    vox_offset = 9 * 4 * indices
    to_repeat = np.array([3, 2, 1, 0, 7, 6, 5, 4, 11, 10, 9, 8])
    reshaped_offsets = np.reshape(vox_offset, -1, order='F').copy()
    repeated = np.kron(np.ones((width * height * depth, ), dtype=int), to_repeat)
    inds = repeated + reshaped_offsets;
    inds = inds.astype(int)

    # Extract the three interleaved volumes and permute the result to match the original looped read. Start with viol_orig.
    buf = np.array(vol_data, dtype=np.uint8)
    buf_at_inds = buf[inds]
    single_casted = buf_at_inds.view(dtype=np.single)
    vol_orig_step1 = np.reshape(single_casted, (3, depth, width, height), order='F').copy()
    vol_orig = np.transpose(vol_orig_step1, (3, 2, 1, 0))

    # OK, vol_orig is reconstructed. Now for vol_dest
    inds = inds + 12
    buf_at_inds = buf[inds]
    single_casted = buf_at_inds.view(dtype=np.single)
    vol_dest_step1 = np.reshape(single_casted, (3, depth, width, height), order='F').copy()
    vol_dest = np.transpose(vol_dest_step1, (3, 2, 1, 0))

    # now for vol_ind0
    inds = inds + 12
    buf_at_inds = buf[inds]
    casted = buf_at_inds.view(dtype=np.int32)
    vol_ind0_step1 = np.reshape(casted, (3, depth, width, height), order='F').copy()
    vol_ind0 = np.transpose(vol_ind0_step1, (3, 2, 1, 0))
    return vol_orig, vol_dest, vol_ind0, meta_data




def read_lookup_file(lookup_file, dtype='<U50'):
    """
    Read a FreeSurfer lookup table file in text format.

    Read a FreeSurfer lookup table file in text format, this is used for the FreeSurferColorLUT.txt file.

    Parameters
    ----------
    lookup_file: str
        Path to the FreeSurferColorLUT.txt file. It comes with FreeSurfer and can be found directly in $FREESURFER_HOME for v6.

    Returns
    -------
    numpy 2D str array
        Array with shape (n, 6) for a file with n relevant lines. A relevant line is a line describing a segmentation in 6 fields (seg_code, structure_name, color_red, color_green, color_blue, color_alpha). There are 2 types of ignored lines in the file: empty lines and those starting with the comment character '#'. All other lines are considered relevant and split into the 6 parts.
    """
    with open(lookup_file, 'r') as fh:
        lines = [line.rstrip('\n') for line in fh]
    all_line_parts = []
    for line in lines:
        if line.startswith("#") or not line:
            pass
        else:
            line_parts = line.split()
            all_line_parts.append(line_parts)
    return np.array(all_line_parts, dtype=dtype)



def get_vox2ras_and_ras2vox_from_nifti_file(nifti_file, use_sform=True):
    """
    Load the vox2ras and ras2vox matrices from a nifti file header.

    Load the vox2ras and ras2vox matrices from a nifti file header. The file can be in nifti (.nii) or gzipped nifti (.nii.gz) format. To understand qform and sform, read the nibabel docs or better https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Orientation%20Explained.

    Parameters
    ----------
    nifti_file: str
        Path to a nifti or gzipped nifti file.

    use_sform: bool, optional
        Whether to report the sform matrix or qform matrix from the nifti header. Defaults to True (=sform). If set to False, the qform will be used.

    Returns
    -------
    vox2ras: 2D numpy array
        The sform or qform matrix

    ras2vox: 2D numpy array
        The inverse of the vox2ras matrix.

    Examples
    --------
    >>> import brainload.freesurferdata as fsd
    >>> vox2ras, ras2vox = fsd.get_vox2ras_and_ras2vox_from_nifti_file("mni152_volume.nii.gz")
    """
    img = nib.load(nifti_file)
    if use_sform:
        vox2ras = img.header.get_sform()
    else:
        vox2ras = img.header.get_qform()
    ras2vox = npl.inv(vox2ras)
    return vox2ras, ras2vox


def read_mgh_header_matrices(mgh_file_name):
    """
    Read the 3 affine transformation matrices from a MGH file header.

    Read the 3 affine transformation matrices ras2vox, vox2ras, and vox2ras_tkr from a MGH file header. The input file is assumed to be gzipped (and extracted appropriately) if the file name ends with '.mgz' or '.mgh.gz'. See the FreeSurfer wiki on coordinate systems for details on what these matrices are. In short, RAS coordinates are used to specify positions of vertices in FreeSurfer surface files.

    In short, VOX is the voxel index and the RAS coordinate is used for the surface coordinate of a vertex.

    VOX: After FreeSurfer pre-processing, this is a triplet of integers in range 0 - 255 for 3D images. Note though that the original T1 images (before pre-processing) from a study can - and usually will - have different numbers of voxels (both different between the axes of a single image as well as between subjects). The VOX is sometimes called CRS for voxel column, row, slice.

    RAS: Right-Anterior-Superior (anatomical coordinates). According to http://www.grahamwideman.com/gw/brain/fs/coords/fscoords.htm, the RAS coordinate origin (0, 0, 0) is the center of the voxel (128, 128, 128). Note that this voxel could or could NOT be the center of the MRI volume.

    Parameters
    ----------
    mgh_file_name: string
        Path to a file in MGH format. The input file is assumed to be gzipped (and extracted appropriately) if the file name ends with '.mgz' or '.mgh.gz'.

    Returns
    -------
    ras2vox: numpy array
        2D numpy array with shape (4, 4). Transformation matrix from RAS coordinate to voxel index.

    vox2ras: numpy array
        2D numpy array with shape (4, 4). Transformation matrix from voxel index to RAS coordinate.

    vox2ras_tkr: numpy array
        2D numpy array with shape (4, 4). Transformation matrix from voxel index to (tkregister) surface RAS coordinate. This is a RAS coordinate of a vertex on the surface.

    Examples
    --------
    >>> import os; import brainload.freesurferdata as fsd
    >>> mgh_file = os.path.join(TEST_DATA_DIR, 'subject1', 'mri', 'orig.mgh')
    >>> ras2vox, vox2ras, vox2ras_tkr = fsd.read_mgh_header_matrices(mgh_file)
    """
    _, mgh_meta_data = read_mgh_file(mgh_file_name, collect_data=False)
    ras2vox = mgh_meta_data['ras2vox']
    vox2ras = mgh_meta_data['vox2ras']
    vox2ras_tkr = mgh_meta_data['vox2ras_tkr']
    return ras2vox, vox2ras, vox2ras_tkr


def read_mgh_file(mgh_file_name, collect_meta_data=True, collect_data=True):
    """
    Read data from a FreeSurfer output file in mgh format.

    Read all data from the MGH file and return it as a numpy array. Optionally, collect meta data from the mgh file header.

    Parameters
    ----------
    mgh_file_name: string
        A string representing a full path to a file in FreeSurfer MGH file format. If the file name end with '.mgz' or '.mgh.gz', the file is assumed to be in gzipped MGH format.

    collect_meta_data: bool, optional
        Whether or not to collect meta data from the MGH file header. Defaults to True.

    collect_data: bool, optional
        Whether or not to collect the file data (voxel values) from the MGH file. Defaults to True.

    Returns
    -------
    mgh_data: numpy array
        The data from the MGH file, usually one scalar value per voxel.

    mgh_meta_data: dictionary
        The meta data collected from the header, or an empty dictionary if the argument `collect_meta_data` was 'False'. The keys correspond to the names of the respective nibabel function used to retrieve the data. The values are the data as returned by nibabel.

    Examples
    --------
    Read a file in MGH format from the surf dir of a subject:

    >>> import os
    >>> import brainload.freesurferdata as fsd
    >>> mgh_file = os.path.join('my_subjects_dir', 'subject1', 'surf', 'rh.area.fsaverage.mgh')
    >>> mgh_data, mgh_meta_data = fsd.read_mgh_file(mgh_file)

    See also
    --------
        - https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
        - https://github.com/nipy/nibabel/blob/master/nibabel/freesurfer/mghformat.py
        - https://surfer.nmr.mgh.harvard.edu/fswiki/FileFormats
    """
    mgh_meta_data = {}
    if mgh_file_name.endswith(".mgz") or mgh_file_name.endswith(".gz"):
        mgh_file_handle = gzip.open(mgh_file_name, 'rb')
    else:
        mgh_file_handle = open(mgh_file_name, 'rb')

    header = fsmgh.MGHHeader.from_fileobj(mgh_file_handle)

    if collect_meta_data:
        mgh_meta_data['data_shape'] = header.get_data_shape()
        mgh_meta_data['affine'] = header.get_affine()
        mgh_meta_data['best_affine'] = header.get_best_affine()             # identical to get_affine for MGH format
        mgh_meta_data['data_bytespervox'] = header.get_data_bytespervox()
        mgh_meta_data['data_dtype'] = header.get_data_dtype()
        mgh_meta_data['data_offset'] =  header.get_data_offset()            # MGH format has a header, then data, then a footer
        mgh_meta_data['data_shape'] =  header.get_data_shape()
        mgh_meta_data['data_size'] = header.get_data_size()
        mgh_meta_data['footer_offset'] =  header.get_footer_offset()
        mgh_meta_data['ras2vox'] =  header.get_ras2vox()
        mgh_meta_data['slope_inter'] =  header.get_slope_inter()
        mgh_meta_data['vox2ras'] =  header.get_vox2ras()
        mgh_meta_data['vox2ras_tkr'] =  header.get_vox2ras_tkr()
        mgh_meta_data['zooms'] =  header.get_zooms()                        # the voxel dimensions (along all 3 axes in space)

    mgh_data = None
    if collect_data:
        mgh_data = header.data_from_fileobj(mgh_file_handle)
    mgh_file_handle.close()
    return mgh_data, mgh_meta_data


def get_num_fsaverage_verts_per_hemi(fsversion=6):
    """
    Return the number of vertices per fsaverage hemisphere.

    Returns
    -------
    vertcount: int
         The number of vertices per fsaverage hemisphere.
    """
    if fsversion == 6:
        return 163842
    else:
        raise ValueError("Currently the only supported FreeSurfer version is 6.")

def merge_morphometry_data(morphometry_data_arrays, dtype=float):
    """
    Merge morphometry data horizontally.

    Merge morphometry data read from several meshes of the same subject horizontally. This is used to merge data from the left and right hemispheres.

    Parameters
    ----------
    morphometry_data_arrays: 2D array
        An array of arrays, each of which represents morphometry data from different hemispheres of the same subject.

    dtype: data type, optional
        Data type for the output numpy array. Defaults to float.

    Returns
    -------
    numpy array
        Horizontally stacked array containing the data from all arrays in the input array.

    Examples
    --------
    Merge some data:

    >>> lh_morphometry_data = np.array([0.0, 0.1, 0.2, 0.3])   # some fake data
    >>> rh_morphometry_data = np.array([0.5, 0.6])
    >>> merged_data = fsd.merge_morphometry_data(np.array([lh_morphometry_data, rh_morphometry_data]))
    >>> print merged_data.shape
    (6, )

    Typically, the `lh_morphometry_data` and `rh_morphometry_data` come from calls to `read_fs_morphometry_data_file_and_record_meta_data` as shown here:

    >>> lh_morphometry_data, meta_data = read_fs_morphometry_data_file_and_record_meta_data(lh_morphometry_data_file, 'lh')
    >>> rh_morphometry_data, meta_data = read_fs_morphometry_data_file_and_record_meta_data(rh_morphometry_data_file, 'rh', meta_data=meta_data)
    >>> both_hemis_morphometry_data = merge_morphometry_data(np.array([lh_morphometry_data, rh_morphometry_data]))
    """
    merged_data = np.empty((0), dtype=dtype)
    for morphometry_data in morphometry_data_arrays:
        merged_data = np.hstack((merged_data, morphometry_data))
    return merged_data


def _get_morphometry_data_suffix_for_surface(surf):
    """
    Determine FreeSurfer surface representation string.

    Determine the substring representing the given surface in a FreeSurfer output curv file. For FreeSurfer's default surface 'white', the surface is not represented in the output file name pattern. For all others, it is represented by a dot followed by the name.

    Parameters
    ----------
    surf: string
        A string representing a FreeSurfer surface, e.g., 'white' or 'pial'.

    Returns
    -------
    string
        The empty string if `surf` is 'white'. A dot followed by the string in the input argument `surf` otherwise.

    Examples
    --------
    >>> import brainload.freesurferdata as fsd
    >>> print fsd._get_morphometry_data_suffix_for_surface('pial')
    .pial
    """
    if surf == 'white':
        return ''
    return '.' + surf


def read_fs_surface_file_and_record_meta_data(surf_file, hemisphere_label, meta_data=None):
    """
    Read a surface file and record meta data on it.

    Read a surface file and record meta data on it. A surface file is a mesh file in FreeSurfer format, e.g., 'lh.white'. It contains vertices and 3-faces made out of them.

    Parameters
    ----------
    surf_file: string
        A string representing an absolute path to a surface (or 'mesh') file (e.g., the path to 'lh.white').

    hemisphere_label: {'lh' or 'rh'}
        A string representing the hemisphere this file belongs to. This is used to write the correct meta data.

    meta_data: dictionary | None, optional
        Meta data to merge into the output `meta_data`. Defaults to the empty dictionary.

    Returns
    -------
    vert_coords: numpy array
        A 2D array containing 3 coordinates for each vertex in the `surf_file`.

    faces: numpy array
        A 2D array containing 3 vertex indices per face. Look at the respective indices in `vert_coords` to get the vertex coordinates.

    meta_data: dictionary
        Contains detailed information on the data that was loaded. The following keys are available (replace `?h` with the value of the argument `hemisphere_label`, which must be 'lh' or 'rh').
            - `?h.num_vertices` : number of vertices in the loaded mesh
            - `?h.num_faces` : number of faces in the loaded mesh
            - `?lh.surf_file` : value of the `surf_file` argument: the mesh file that was loaded

    Examples
    --------
    >>> vert_coords, faces, meta_data = fsd.read_fs_surface_file_and_record_meta_data(surf_file, 'lh')
    >>> print meta_data['lh.num_vertices']
    121567                  # arbitrary number, depends on the subject mesh
    """
    if hemisphere_label not in ('lh', 'rh'):
        raise ValueError("ERROR: hemisphere_label must be one of {'lh', 'rh'} but is '%s'." % hemisphere_label)

    if meta_data is None:
        meta_data = {}

    vert_coords, faces = fsio.read_geometry(surf_file)

    label_num_vertices = hemisphere_label + '.num_vertices'
    meta_data[label_num_vertices] = vert_coords.shape[0]

    label_num_faces = hemisphere_label + '.num_faces'
    meta_data[label_num_faces] = faces.shape[0]

    label_surf_file = hemisphere_label + '.surf_file'
    meta_data[label_surf_file] = surf_file

    return vert_coords, faces, meta_data

def _deduce_hemisphere_label_from_file_path(file_path, default="lh"):
    """
    Guess a hemisphere label from a file path.

    Guess a hemisphere label, i.e., one of ```lh``` or ```rh```, from a file path like ```/some/path/to/subjects/subject1/surf/lh.area```.

    Parameters
    ----------
    file_path: str
        The full path to a file.

    default: str
        What to return if the function cannot deduce the information from the given file_path.

    Returns
    -------
    hemi: str
        The hemisphere label

    is_default: boolean
        True if the file_path contained no information to deduce the hemisphere label, and the returned ```hemi``` value thus is the one from the ```default``` parameter.
    """
    path, file_name = os.path.split(file_path)
    accepted_third_chars = [".", "_"]
    for h in ["lh", "rh"]:
        for c in accepted_third_chars:
            if file_name.startswith(h + c):
                return h, False
    return default, True


def read_fs_morphometry_data_file_and_record_meta_data(curv_file, hemisphere_label, meta_data=None, format='curv'):
    """
    Read a morphometry file and record meta data on it.

    Read a morphometry file and record meta data on it. A morphometry file is file containing a scalar value for each vertex on the surface of a FreeSurfer mesh. An example is the file 'lh.area', which contains the area values for all vertices of the left hemisphere of the white surface. Such a file can be in two different formats: 'curv' or 'mgh'. The former is used when the data refers to the surface mesh of the original subject, the latter when it has been mapped to a standard subject like fsaverage.

    Parameters
    ----------
    curv_file: string
        A string representing a path to a morphometry file (e.g., the path to 'lh.area').

    hemisphere_label: {'lh' or 'rh'}
        A string representing the hemisphere this file belongs to. This is used to write the correct meta data.

    meta_data: dictionary | None, optional
        Meta data to merge into the output `meta_data`. Defaults to the empty dictionary.

    format: {'curv', 'mgh'}, optional
        The file format for the files that are to be loaded. Defaults to 'curv'.

    Returns
    -------
    per_vertex_data: numpy array
        A 1D array containing one scalar value per vertex.

    meta_data: dictionary
        Contains detailed information on the data that was loaded. The following keys are available (replace `?h` with the value of the argument `hemisphere_label`, which must be 'lh' or 'rh').
            - `?h.num_data_points` : the number of data points loaded.
            - `?h.morphometry_file` : the value of the `curv_file` argument (data file that was loaded)
            - `?h.morphometry_file_format` : the value for `format` that was used

    Examples
    --------
    >>> import brainload.freesurferdata as fsd; import os
    >>> lh_morphometry_file = os.path.join('my_subjects_dir', 'subject1', 'surf', 'lh.area')
    >>> lh_morphometry_data, meta_data = read_fs_morphometry_data_file_and_record_meta_data(lh_morphometry_file, 'lh')
    >>> print meta_data['lh.num_data_points']
    121567                  # arbitrary number, depends on the subject mesh
    >>> print meta_data['lh.morphometry_file']
    my_subjects_dir/subject1/surf/lh.area             # on UNIX-like systems
    """
    if format not in ('curv', 'mgh'):
        raise ValueError("ERROR: format must be one of {'curv', 'mgh'} but is '%s'." % format)

    if hemisphere_label not in ('lh', 'rh'):
        raise ValueError("ERROR: hemisphere_label must be one of {'lh', 'rh'} but is '%s'." % hemisphere_label)

    if meta_data is None:
        meta_data = {}

    if format == 'mgh' or curv_file.endswith(".mgh") or curv_file.endswith(".mgz"):
        full_mgh_data, mgh_meta_data = read_mgh_file(curv_file, collect_meta_data=False)
        relevant_data_inner_array = full_mgh_data[:,0]
        per_vertex_data = relevant_data_inner_array[:,0]
    else:
        per_vertex_data = fsio.read_morph_data(curv_file)

    per_vertex_data = per_vertex_data.astype(float)

    label_num_values = hemisphere_label + '.num_data_points'
    meta_data[label_num_values] = per_vertex_data.shape[0]

    label_file = hemisphere_label + '.morphometry_file'
    meta_data[label_file] = curv_file

    label_file_format = hemisphere_label + '.morphometry_file_format'
    meta_data[label_file_format] = format

    return per_vertex_data, meta_data


def load_subject_mesh_files(lh_surf_file, rh_surf_file, hemi='both', meta_data=None):
    """
    Load mesh files for a subject.

    Load one or two mesh files for a subject. Which of the two files `lh_surf_file` and `rh_surf_file` are actually loaded is determined by the `hemi` parameter.

    Parameters
    ----------
    lh_surf_file: string | None
        A string representing an absolute path to a mesh file for the left hemisphere (e.g., the path to 'lh.white'). If `hemi` is 'rh', this will be ignored and can thus be None.

    rh_surf_file: string | None
        A string representing an absolute path to a mesh file for the right hemisphere (e.g., the path to 'rh.white'). If `hemi` is 'lh', this will be ignored and can thus be None.

    hemi: {'both', 'lh', 'rh'}, optional
        The hemisphere for which data should actually be loaded. Defaults to 'both'.

    meta_data: dictionary | None, optional
        Meta data to merge into the output `meta_data`. Defaults to the empty dictionary.

    Returns
    -------
    vert_coords: numpy array of floats
        A 2D array containing 3 coordinates for each vertex. Dimension is (n, 3) for n vertices. If the argument `hemi` was 'both', this includes vertices from several meshes. You can check the `meta_data` return values to get the border between meshes, see `meta_data['lh.num_vertices']` and  `meta_data['rh.num_vertices']`.

    faces: numpy array of integers
        A 2D array containing 3 vertex indices per face. Dimension is (m, 3) for m faces. Look at the respective indices in `vert_coords` to get the vertex coordinates. If the argument `hemi` was 'both', this includes faces from several meshes. You can check the `meta_data` return values to get the border between meshes, see `meta_data['lh.num_faces']` and  `meta_data['rh.num_faces']`.

    meta_data: dictionary
        Contains detailed information on the data that was loaded. The following keys are available (depending on the value of the `hemi` argument, you can replace ?h with 'lh' or 'rh' or both 'lh' and 'rh'):
            - `?h.num_vertices` : number of vertices in the loaded mesh
            - `?h.num_faces` : number of faces in the loaded mesh
            - `?h.surf_file` : the mesh file that was loaded for this hemisphere

    Examples
    --------
    >>> import brainload.freesurferdata as fsd; import os
    >>> lh_surf_file = os.path.join('my_subjects_dir', 'subject1', 'surf', 'lh.white')
    >>> rh_surf_file = os.path.join('my_subjects_dir', 'subject1', 'surf', 'rh.white')
    >>> vert_coords, faces, meta_data = fsd.load_subject_mesh_files(lh_surf_file, rh_surf_file)
    """
    if hemi not in ('lh', 'rh', 'both'):
        raise ValueError("ERROR: hemi must be one of {'lh', 'rh', 'both'} but is '%s'." % hemi)

    if meta_data is None:
        meta_data = {}

    if hemi == 'lh':
        vert_coords, faces, meta_data = read_fs_surface_file_and_record_meta_data(lh_surf_file, 'lh', meta_data=meta_data)
    elif hemi == 'rh':
        vert_coords, faces, meta_data = read_fs_surface_file_and_record_meta_data(rh_surf_file, 'rh', meta_data=meta_data)
    else:
        lh_vert_coords, lh_faces, meta_data = read_fs_surface_file_and_record_meta_data(lh_surf_file, 'lh', meta_data=meta_data)
        rh_vert_coords, rh_faces, meta_data = read_fs_surface_file_and_record_meta_data(rh_surf_file, 'rh', meta_data=meta_data)
        vert_coords, faces = _merge_meshes(np.array([[lh_vert_coords, lh_faces], [rh_vert_coords, rh_faces]]))
    return vert_coords, faces, meta_data


def rhi(rh_relative_index, meta_data):
    """
    Computes the absolute data index given an index relative to the right hemisphere.

    This function makes sense only given a `morphometry_data` and associated `meta_data` that contains data on two hemispheres (even though the `morphometry_data` array itself is not passed to this function). E.g., the return value of a function like `subject()` or `subject_avg()` when called with `hemi='both'`. For such data, it computes the absolute index in the data given a request index relative to the right hemisphere. The name is short for 'right hemisphere index'.

    Parameters
    ----------
    rh_relative_index: int
        An index relative to the right hemisphere. E.g., `0` if you want to get the index of the first vertex of the right hemisphere. Its absolute value must be between 0 and the number of vertices of the right hemisphere. Negative values are allowed, and `-1` will get you the second-to-last possible index, `-2` the third-to-last, and so on.

    meta_data: dictionary
        The meta data dictionary returned for your data. It must contain the keys 'lh.num_data_points' and 'rh.num_data_points'.

    Returns
    -------
    The absolute index into the data for the given `rh_relative_index`.

    Examples
    --------
    >>> import brainload as bl
    >>> morphometry_data, meta_data = bl.subject('heinz', hemi='both')[2:4]
    >>> print "rh value at index 10, relative to start of right hemisphere: %d." % morphometry_data[bl.rhi(10, meta_data)]
    """
    lh_key = 'lh.num_data_points'
    rh_key = 'rh.num_data_points'
    if not isinstance(meta_data, collections.Mapping):
        raise ValueError("rhi: meta_data must be a meta data dictionary containing the keys '%s' and '%s'." % (lh_key, rh_key))

    if not ('lh.num_data_points' in meta_data and 'rh.num_data_points' in meta_data):
        raise ValueError("rhi: meta_data must be a meta data dictionary containing the keys '%s' and '%s'." % (lh_key, rh_key))

    num_lh = meta_data[lh_key]
    num_rh = meta_data[rh_key]
    if abs(rh_relative_index) >= num_rh:
        raise ValueError('rhi: rh_relative_index %d out of bounds: right hemisphere has %d values, valid index range is -%d .. %d.' % (rh_relative_index, num_rh, num_rh+1, num_rh-1))
    if rh_relative_index < 0:
        return num_lh + num_rh + rh_relative_index -1
    else:
        return num_lh + rh_relative_index


def hemi_range(morphometry_meta_data, hemi):
    """
    Compute start and end index in the hemisphere data for the given hemisphere.

    Parameters
    ----------
    morphometry_meta_data: dictionary as returned by the functions that read morphometry data (e.g., ```subject_data_native```).

    hemi: string, one of 'lh' or 'rh'. The hemisphere you want to get the start and end index for.

    Returns
    -------
    start_index: integer
        The start index of the lh data.

    end_index: integer
        The end index of the lh data.

    Examples
    --------
    >>> import brainload as bl
    >>> morphometry_data, meta_data = bl.subject_data_native('subject1', '/mnt/study1_data', 'thickness', 'both')
    >>> s, e = bl.hemi_range(meta_data, 'lh')
    >>> print("Mean lh thickness value is: %f" % (np.mean(morphometry_data[s:e])))
    """
    if hemi not in ('lh', 'rh'):
        raise ValueError("ERROR: hemi must be one of {'lh', 'rh'} but is '%s'." % hemi)

    if hemi == 'lh':
        return 0, morphometry_meta_data['lh.num_data_points'] -1
    else:
        return rhi(0, morphometry_meta_data), rhi(-1, morphometry_meta_data)+1


def rhv(rh_relative_index, morphometry_data, meta_data):
    """
    Returns the value in `morphometry_data` at an index relative to the right hemisphere.

    This function makes sense only given a `morphometry_data` and associated `meta_data` that contains data on two hemispheres. E.g., the return value of a function like `subject()` or `subject_avg()` when called with `hemi='both'`. For such data, it returns the value in `morphometry_data` at a request index given relative to the right hemisphere. The name is short for 'right hemisphere value'.

    Parameters
    ----------
    rh_relative_index: int
        An index relative to the start of the right hemisphere in the data. E.g., `0` if you want to get the value for the first vertex of the right hemisphere. Its absolute value must be between 0 and the number of vertices of the right hemisphere. Negative values are allowed, and `-1` will get you the last possible value, `-2` the second-to-last, and so on.

    morphometry_data: numpy array
        The morphometry data array, must represent data for both hemispheres.

    meta_data: dictionary
        The meta data dictionary returned for your data. It must contain the keys 'lh.num_data_points' and 'rh.num_data_points'.

    Returns
    -------
    The value at the given index that is relative to the start of the right hemisphere in the data.

    Examples
    --------
    >>> import brainload as bl
    >>> morphometry_data, meta_data = bl.subject('heinz', hemi='both')[2:4]
    >>> print "rh value at index 10, relative to start of right hemisphere: %d." % bl.rhv(10, morphometry_data, meta_data)
    """
    abs_index = rhi(rh_relative_index, meta_data)
    return morphometry_data[abs_index]



def load_subject_morphometry_data_files(lh_morphometry_data_file, rh_morphometry_data_file, hemi='both', format='curv', meta_data=None):
    """
    Load morphometry data files for a subject.

    Load one or two morphometry data files for a subject. Which of the two files `lh_morphometry_data_file` and `rh_morphometry_data_file` are actually loaded is determined by the `hemi` parameter.

    Parameters
    ----------
    lh_morphometry_data_file: string | None
        A string representing an absolute path to a morphometry data file for the left hemisphere. If `hemi` is 'rh', this will be ignored and can thus be None.

    rh_morphometry_data_file: string | None
        A string representing an absolute path to a morphometry data file for the right hemisphere. If `hemi` is 'lh', this will be ignored and can thus be None.

    hemi: {'both', 'lh', 'rh'}, optional
        The hemisphere for which data should actually be loaded. Defaults to 'both'.

    format: {'curv', 'mgh'}, optional
        The file format for the files that are to be loaded. Defaults to 'curv'.

    meta_data: dictionary | None, optional
        Meta data to merge into the output `meta_data`. Defaults to the empty dictionary.

    Returns
    -------
    morphometry_data: numpy array
        An array containing the scalar per-vertex data loaded from the file(s).

    meta_data: dictionary
        Contains detailed information on the data that was loaded. The following keys are available (depending on the value of the `hemi` argument, you can replace ?h with 'lh' or 'rh' or both 'lh' and 'rh'):
            - `?h.num_data_points` : the number of data points loaded.
            - `?h.morphometry_file` : the value of the `?h_morphometry_data_file` argument (data file that was loaded)
            - `?h.morphometry_file_format` : the value for `format` that was used

    Examples
    --------
    Load the lh and rh area files for subject1.

    >>> import brainload.freesurferdata as fsd; import os
    >>> lh_morphometry_file = os.path.join('path', 'to', 'subjects_dir', 'subject1', 'surf', 'lh.area')
    >>> rh_morphometry_file = os.path.join('path', 'to', 'subjects_dir', 'subject1', 'surf', 'rh.area')
    >>> morphometry_data, meta_data = fsd.load_subject_morphometry_data_files(lh_morphometry_file, rh_morphometry_file)

    Now let's look at the area value for the vertex at index 10:

    >>> print "lh value at index 10: %d." % morphometry_data[10]

    But what about the value of vertex 10 at the right hemisphere? We loaded 2 hemispheres, so the data is concatinated. But you can use the `meta_data` to get the correct index relative to the right hemisphere:

    >>> print "rh value at index 10: %d." % morphometry_data[fsd.rhi(10, meta_data)]

    You could also get the value directly using the `rhv` function:

    >>> print "rh value at index 10: %d." % fsd.rhv(10, morphometry_data, meta_data)
    """
    if hemi not in ('lh', 'rh', 'both'):
        raise ValueError("ERROR: hemi must be one of {'lh', 'rh', 'both'} but is '%s'." % hemi)

    if format not in ('curv', 'mgh'):
        raise ValueError("ERROR: format must be one of {'curv', 'mgh'} but is '%s'." % format)

    if meta_data is None:
        meta_data = {}

    if hemi == 'lh':
        morphometry_data, meta_data = read_fs_morphometry_data_file_and_record_meta_data(lh_morphometry_data_file, 'lh', meta_data=meta_data, format=format)
        meta_data['rh.num_data_points'] = 0
    elif hemi == 'rh':
        morphometry_data, meta_data = read_fs_morphometry_data_file_and_record_meta_data(rh_morphometry_data_file, 'rh', meta_data=meta_data, format=format)
        meta_data['lh.num_data_points'] = 0
    else:
        lh_morphometry_data, meta_data = read_fs_morphometry_data_file_and_record_meta_data(lh_morphometry_data_file, 'lh', meta_data=meta_data, format=format)
        rh_morphometry_data, meta_data = read_fs_morphometry_data_file_and_record_meta_data(rh_morphometry_data_file, 'rh', meta_data=meta_data, format=format)
        morphometry_data = merge_morphometry_data(np.array([lh_morphometry_data, rh_morphometry_data]))
    return morphometry_data, meta_data


def subject_mesh(subject_id, subjects_dir, surf='white', hemi='both'):
    """
    Load a surface mesh of a subject.

    Convenience function to load a FreeSurfer surface mesh of a subject.

    Parameters
    ----------
    subject_id: string
        The subject identifier of the subject.

    surf : string, optional
        The brain surface where the data has been measured, e.g., 'white' or 'pial'. This will become part of the file name that is loaded. Defaults to 'white'.

    hemi : {'both', 'lh', 'rh'}, optional
        The hemisphere that should be loaded. Defaults to 'both'.

    subjects_dir: string
        A string representing the full path to a directory. This should be the directory containing all subjects of your study.

    Returns
    -------
    vert_coords: numpy array
        A 2-dimensional array containing the vertices of the mesh(es) of the subject. Each vertex entry contains 3 coordinates. Each coordinate describes a 3D position in a FreeSurfer surface file (e.g., 'lh.white'), as returned by the `nibabel` function `nibabel.freesurfer.io.read_geometry`.

    faces: numpy array
        A 2-dimensional array containing the 3-faces of the mesh(es) of the subject. Each face entry contains 3 indices. Each index references the respective vertex in the `vert_coords` array.

    meta_data: dictionary
        A dictionary containing detailed information on all files that were loaded and used settings. The following keys are available (depending on the value of the `hemi` argument, you can replace ?h with 'lh' or 'rh' or both 'lh' and 'rh'):
            - `?h.num_vertices` : number of vertices in the loaded mesh
            - `?h.num_faces` : number of faces in the loaded mesh
            - `?lh.surf_file` : the mesh file that was loaded for this hemisphere

    Raises
    ------
    ValueError
        If one of the parameters with a fixed set of values receives a value that is not allowed.

    Examples
    --------
    Load the pial surface mesh for both hemispheres of the Freeurfer example subject bert:

    >>> import brainload as bl, import os
    >>> subjects_dir = os.path.join('Applications', 'freesurfer', 'subjects')
    >>> verts, faced, meta_data = bl.subject_mesh('bert', subjects_dir, surf='pial')
    """
    vert_coords, faces, meta_data = fsaverage_mesh(subject_id=subject_id, surf=surf, hemi=hemi, subjects_dir=subjects_dir, use_freesurfer_home_if_missing=False)
    return vert_coords, faces, meta_data



def fsaverage_mesh(subject_id='fsaverage', surf='white', hemi='both', subjects_dir=None, use_freesurfer_home_if_missing=True):
    """
    Load a surface mesh of the fsaverage subject.

    Convenience function to load a FreeSurfer surface mesh of the fsaverage subject. Use the subject_mesh function to load the mesh of any other subject.

    Parameters
    ----------
    subject_id: string, optional
        The subject identifier of the subject. Defaults to 'fsaverage'.

    surf : string, optional
        The brain surface where the data has been measured, e.g., 'white' or 'pial'. This will become part of the file name that is loaded. Defaults to 'white'.

    hemi : {'both', 'lh', 'rh'}, optional
        The hemisphere that should be loaded. Defaults to 'both'.

    subjects_dir: string, optional
        A string representing the full path to a directory. This should be the directory containing all subjects of your study. Defaults to the environment variable SUBJECTS_DIR if omitted. If that is not set, used the current working directory instead. This is the directory from which the application was executed.

    use_freesurfer_home_if_missing: boolean, optional
        If set to True, first checks whether the directory for the given subject exists in the `subjects_dir`. If it does not, it will reset the `subjects_dir` to '${FREESURFER_HOME}/subjects' before proceeding.

    Returns
    -------
    vert_coords: numpy array
        A 2-dimensional array containing the vertices of the mesh(es) of the subject. Each vertex entry contains 3 coordinates. Each coordinate describes a 3D position in a FreeSurfer surface file (e.g., 'lh.white'), as returned by the `nibabel` function `nibabel.freesurfer.io.read_geometry`.

    faces: numpy array
        A 2-dimensional array containing the 3-faces of the mesh(es) of the subject. Each face entry contains 3 indices. Each index references the respective vertex in the `vert_coords` array.

    meta_data: dictionary
        A dictionary containing detailed information on all files that were loaded and used settings. The following keys are available (depending on the value of the `hemi` argument, you can replace ?h with 'lh' or 'rh' or both 'lh' and 'rh'):
            - `?h.num_vertices` : number of vertices in the loaded mesh
            - `?h.num_faces` : number of faces in the loaded mesh
            - `?lh.surf_file` : the mesh file that was loaded for this hemisphere

    Raises
    ------
    ValueError
        If one of the parameters with a fixed set of values receives a value that is not allowed.

    Examples
    --------
    Load area data for both hemispheres and white surface of subject1 in the directory defined by the environment variable SUBJECTS_DIR:

    >>> import brainload as bl
    >>> verts, faced, meta_data = bl.fsaverage_mesh()
    """
    if subjects_dir is None:
        subjects_dir = os.getenv('SUBJECTS_DIR', os.getcwd())

    if use_freesurfer_home_if_missing and not os.path.isdir(os.path.join(subjects_dir, subject_id)):
        freesurfer_home = os.getenv('FREESURFER_HOME', os.getcwd())
        subjects_dir = os.path.join(freesurfer_home, 'subjects')

    vert_coords, faces, morphometry_data, meta_data = subject(subject_id, surf=surf, hemi=hemi, subjects_dir=subjects_dir, measure=None, load_morphometry_data=False)
    return vert_coords, faces, meta_data


def subject_data_native(subject_id, subjects_dir, measure, hemi, surf='white'):
    """
    Load native space morphometry data for a subject (e.g., lh.area).

    Parameters
    ----------
    subject_id: string
        The subject identifier of the subject. As always, it is assumed that this is the name of the directory containing the subject's data, relative to `subjects_dir`. Example: 'subject33'.

    measure : string
        The measure to load, e.g., 'area' or 'curv'. Defaults to 'area'.

    surf : string, optional
        The brain surface where the data has been measured, e.g., 'white' or 'pial'. This will become part of the file name that is loaded. For white, nothing will be added. Defaults to 'white'.

    hemi : {'both', 'lh', 'rh'}
        The hemisphere that should be loaded.

    subjects_dir: string
        A string representing the full path to a directory. This should be the directory containing all subjects of your study.

    Returns
    -------
    morphometry_data: numpy array
        A numpy array with as many entries as there are vertices in the subject. If you load two hemispheres instead of one, the length doubles. You can get the start indices for data of the hemispheres in the returned `meta_data`, see `meta_data['lh.num_vertices']` and `meta_data['rh.num_vertices']`. You can be sure that the data for the left hemisphere will always come first (if both were loaded). Indices start at 0, of course. So if the left hemisphere has `n` vertices, the data for them are at indices `0..n-1`, and the data for the right hemisphere start at index `n`. Note that the two hemispheres do in general NOT have the same number of vertices.

    meta_data: dictionary
        A dictionary containing detailed information on all files that were loaded and used settings. The following keys are available (depending on the value of the `hemi` argument, you can replace ?h with 'lh' or 'rh' or both 'lh' and 'rh'):
            - `?h.num_data_points` : the number of data points loaded.
            - `?h.morphometry_file` : the value of the `?h_morphometry_data_file` argument (data file that was loaded)
            - `?h.morphometry_file_format` : the value for `format` that was used
            - `subject_id` : the subject id
            - `subjects_dir` : the subjects dir that was used
            - `surf` : the surf that was used, e.g., 'white'
            - `measure` : the measure that was loaded as morphometry data, e.g., 'area'
            - `space` : always the string 'subject'. This means that the data loaded represent morphometry data taken from the subject's surface (as opposed to data mapped to a common or average subject).
            - `hemi` : the `hemi` value that was used

    Examples
    --------
    >>> import brainload as bl
    >>> morphometry_data, meta_data = bl.subject_data_native('subject1', '/mnt/study1_data', 'thickness', 'both')
    """
    vert_coords, faces, morphometry_data, meta_data = subject(subject_id, surf=surf, measure=measure, hemi=hemi, subjects_dir=subjects_dir, load_surface_files=False)
    return morphometry_data, meta_data


def subject_data_standard(subject_id, subjects_dir, measure, hemi, fwhm, average_subject='fsaverage', surf='white'):
    """
    Load standard space data for a subject (e.g., lh.area.fwhm10.fsaverage.mgh).

    Parameters
    ----------
    subject_id: string
        The subject identifier of the subject. As always, it is assumed that this is the name of the directory containing the subject's data, relative to `subjects_dir`. Example: 'subject33'.

    measure : string
        The measure to load, e.g., 'area' or 'curv'.

    surf : string, optional
        The brain surface where the data has been measured, e.g., 'white' or 'pial'. This will become part of the file name that is loaded. Defaults to 'white'.

    hemi : {'both', 'lh', 'rh'}
        The hemisphere that should be loaded.

    fwhm : string or None
        Which averaging version of the data should be loaded. FreeSurfer usually generates different standard space files with a number of smoothing settings. If None is passed, the `.fwhmX` part is omitted from the file name completely. Set this to '0' to get the unsmoothed version.

    subjects_dir: string
        A string representing the full path to a directory. This should be the directory containing all subjects of your study.

    average_subject: string, optional
        The name of the average subject to which the data was mapped. Defaults to 'fsaverage'.

    Returns
    -------
    morphometry_data: numpy array
        A numpy array with as many entries as there are vertices in the subject. If you load two hemispheres instead of one, the length doubles. You can get the start indices for data of the hemispheres in the returned `meta_data`, see `meta_data['lh.num_vertices']` and `meta_data['rh.num_vertices']`. You can be sure that the data for the left hemisphere will always come first (if both were loaded). Indices start at 0, of course. So if the left hemisphere has `n` vertices, the data for them are at indices `0..n-1`, and the data for the right hemisphere start at index `n`. Note that the two hemispheres do in general NOT have the same number of vertices.

    meta_data: dictionary
        A dictionary containing detailed information on all files that were loaded and used settings. The following keys are available (depending on the value of the `hemi` argument, you can replace ?h with 'lh' or 'rh' or both 'lh' and 'rh'):
            - `?h.num_data_points` : the number of data points loaded.
            - `?h.morphometry_file` : the value of the `?h_morphometry_data_file` argument (data file that was loaded)
            - `?h.morphometry_file_format` : the value for `format` that was used
            - `subject_id` : the subject id
            - `subjects_dir` : the subjects dir that was used
            - `surf` : the surf that was used, e.g., 'white'
            - `measure` : the measure that was loaded as morphometry data, e.g., 'area'
            - `space` : always the string 'common'. This means that the data loaded represent morphometry data that has been mapped to a common or average subject.
            - `hemi` : the `hemi` value that was used
    """
    vert_coords, faces, morphometry_data, meta_data = subject_avg(subject_id, measure=measure, surf=surf, hemi=hemi, fwhm=fwhm, subjects_dir=subjects_dir, average_subject=average_subject, load_surface_files=False)
    return morphometry_data, meta_data


def subject(subject_id, surf='white', measure='area', hemi='both', subjects_dir=None, meta_data=None, load_surface_files=True, load_morphometry_data=True):
    """
    Load FreeSurfer brain morphometry and/or mesh data for a single subject.

    High-level interface to load FreeSurfer brain data for a single space. This parses the data for the surfaces of this subject. If you want to load data that has been mapped to an average subject like 'fsaverage', use `subject_avg` instead.

    Parameters
    ----------
    subject_id: string
        The subject identifier of the subject. As always, it is assumed that this is the name of the directory containing the subject's data, relative to `subjects_dir`. Example: 'subject33'.

    measure : string, optional
        The measure to load, e.g., 'area' or 'curv'. Defaults to 'area'.

    surf : string, optional
        The brain surface where the data has been measured, e.g., 'white' or 'pial'. This will become part of the file name that is loaded. Defaults to 'white'.

    hemi : {'both', 'lh', 'rh'}, optional
        The hemisphere that should be loaded. Defaults to 'both'.

    subjects_dir: string, optional
        A string representing the full path to a directory. This should be the directory containing all subjects of your study. Defaults to the environment variable SUBJECTS_DIR if omitted. If that is not set, used the current working directory instead. This is the directory from which the application was executed.

    meta_data: dictionary, optional
        A dictionary that should be merged into the return value `meta_data`. Defaults to the empty dictionary if omitted.

    load_surface_files: boolean, optional
        Whether to load mesh data. If set to `False`, the first return values `vert_coords` and `faces` will be `None`. Defaults to `True`.

    load_morphometry_data: boolean, optional
        Whether to load morphometry data. If set to `False`, the first return value `morphometry_data` will be `None`. Defaults to `True`.

    Returns
    -------
    vert_coords: numpy array
        A 2-dimensional array containing the vertices of the mesh(es) of the subject. Each vertex entry contains 3 coordinates. Each coordinate describes a 3D position in a FreeSurfer surface file (e.g., 'lh.white'), as returned by the `nibabel` function `nibabel.freesurfer.io.read_geometry`.

    faces: numpy array
        A 2-dimensional array containing the 3-faces of the mesh(es) of the subject. Each face entry contains 3 indices. Each index references the respective vertex in the `vert_coords` array.

    morphometry_data: numpy array
        A numpy array with as many entries as there are vertices in the subject. If you load two hemispheres instead of one, the length doubles. You can get the start indices for data of the hemispheres in the returned `meta_data`, see `meta_data['lh.num_vertices']` and `meta_data['rh.num_vertices']`. You can be sure that the data for the left hemisphere will always come first (if both were loaded). Indices start at 0, of course. So if the left hemisphere has `n` vertices, the data for them are at indices `0..n-1`, and the data for the right hemisphere start at index `n`. Note that the two hemispheres do in general NOT have the same number of vertices.

    meta_data: dictionary
        A dictionary containing detailed information on all files that were loaded and used settings. The following keys are available (depending on the value of the `hemi` argument, you can replace ?h with 'lh' or 'rh' or both 'lh' and 'rh'):
            - `?h.num_data_points` : the number of data points loaded.
            - `?h.morphometry_file` : the value of the `?h_morphometry_data_file` argument (data file that was loaded)
            - `?h.morphometry_file_format` : the value for `format` that was used
            - `?h.num_vertices` : number of vertices in the loaded mesh
            - `?h.num_faces` : number of faces in the loaded mesh
            - `?lh.surf_file` : the mesh file that was loaded for this hemisphere
            - `subject_id` : the subject id
            - `subjects_dir` : the subjects dir that was used
            - `surf` : the surf that was used, e.g., 'white'
            - `measure` : the measure that was loaded as morphometry data, e.g., 'area'
            - `space` : always the string 'subject'. This means that the data loaded represent morphometry data taken from the subject's surface (as opposed to data mapped to a common or average subject).
            - `hemi` : the `hemi` value that was used

    Raises
    ------
    ValueError
        If one of the parameters with a fixed set of values receives a value that is not allowed.

    Examples
    --------
    Load area data for both hemispheres and white surface of subject1 in the directory defined by the environment variable SUBJECTS_DIR:

    >>> import brainload as bl
    >>> vertices, faces, data, md = bl.subject('subject1')

    Here, we are a bit more explicit about what we want to load:

    >>> import os
    >>> user_home = os.getenv('HOME')
    >>> subjects_dir = os.path.join(user_home, 'data', 'my_study_x')
    >>> vertices, faces, data, md = bl.subject('subject1', hemi='lh', measure='curv', subjects_dir=subjects_dir)

    Sometimes we do not care for the mesh, e.g., we only want the morphometry data:

    >>> data, md = bl.subject('subject1', hemi='rh', load_surface_files=False)[2:4]

    ...or the other way around (mesh only, no morphometry data):

    >>> vertices, faces = bl.subject('subject1', hemi='rh', load_morphometry_data=False)[0:2]


    """
    if hemi not in ('lh', 'rh', 'both'):
        raise ValueError("ERROR: hemi must be one of {'lh', 'rh', 'both'} but is '%s'." % hemi)

    if meta_data is None:
        meta_data = {}

    if subjects_dir is None:
        subjects_dir = os.getenv('SUBJECTS_DIR', os.getcwd())
    subject_surf_dir = os.path.join(subjects_dir, subject_id, 'surf')

    vert_coords = None
    faces = None
    if load_surface_files:
        display_subject = subject_id
        display_surf = surf
        lh_surf_file = os.path.join(subject_surf_dir, ('lh.' + surf))
        rh_surf_file = os.path.join(subject_surf_dir, ('rh.' + surf))
        vert_coords, faces, meta_data = load_subject_mesh_files(lh_surf_file, rh_surf_file, hemi=hemi, meta_data=meta_data)
    else:
        display_subject = None
        display_surf = None

    morphometry_data = None
    if load_morphometry_data:
        lh_morphometry_file = os.path.join(subject_surf_dir, ('lh.' + measure + _get_morphometry_data_suffix_for_surface(surf)))
        rh_morphometry_file = os.path.join(subject_surf_dir, ('rh.' + measure + _get_morphometry_data_suffix_for_surface(surf)))
        morphometry_data, meta_data = load_subject_morphometry_data_files(lh_morphometry_file, rh_morphometry_file, hemi=hemi, format='curv', meta_data=meta_data)
    else:
        measure = None


    meta_data['subject_id'] = subject_id
    meta_data['display_subject'] = display_subject
    meta_data['subjects_dir'] = subjects_dir
    meta_data['surf'] = surf
    meta_data['display_surf'] = display_surf
    meta_data['measure'] = measure
    meta_data['space'] = 'native_space'
    meta_data['hemi'] = hemi

    return vert_coords, faces, morphometry_data, meta_data


def get_surface_file_path(subjects_dir, subject_id, hemi, surf, subdir='surf'):
    """
    Determine the path to a surface file, e.g., `lh.white`.
    """
    return os.path.join(subjects_dir, subject_id, subdir, (hemi + '.' + surf))


def get_standard_space_morphometry_file_path(subjects_dir, subject_id, hemi, measure, fwhm="10", average_subject="fsaverage", surf='white', subdir='surf', file_ext='mgh'):
    """
    Determine the path to a standard space morphometry file, e.g., `lh.area.fwhm10.fsaverage.mgh`.
    """
    fwhm_tag = _get_fwhm_tag(fwhm)
    return os.path.join(subjects_dir, subject_id, subdir, (hemi + '.' + measure + _get_morphometry_data_suffix_for_surface(surf) + fwhm_tag + '.' + average_subject + '.' + file_ext))


def get_morphometry_file_path(subjects_dir, subject_id, surf, hemi, measure, subdir='surf'):
    """
    Determine the path to a native space morphometry file, e.g., `lh.area`.
    """
    return os.path.join(subjects_dir, subject_id, subdir, (hemi + '.' + measure + _get_morphometry_data_suffix_for_surface(surf)))


def _get_fwhm_tag(fwhm_string):
    if fwhm_string is None:
        fwhm_tag = ''
    else:
        fwhm_tag = '.fwhm' + fwhm_string
    return fwhm_tag


def _merge_meshes(meshes):
    """
    Merge several meshes into a single one.

    Merge a list of meshes into a single one. Each mesh is given by a vertex list and a face list. The merged vertex list is just a vstack of the individual lists, and the vertex coordinates are not altered in any way. As a face id defined by the indices of its 3 vertices, these indices get adjusted for all meshes but the first one.

    Parameters
    ----------
    meshes: array-like
        A array of meshes. Each mesh is represented as an array of length 2, where the entry at index 0 is the vertex list, and the one at index 2 is the face list.

    Returns
    -------
    all_vert_coords: numpy array
        An array of vertex coordinates with shape(3, n), where n is the sum of the vertex counts of all input meshes.

    all_faces: numpy_array (2d)
        An array of faces with shape(3, m), where m is the sum of the face counts of all input meshes. For each face, each of its 3 values represent the vertex at the respective index in the `all_vert_coords` array.
    """
    all_vert_coords = np.empty((0, 3), dtype=float)
    all_faces = np.empty((0, 3), dtype=int)

    for mesh in meshes:
        new_vert_coords = mesh[0]
        new_faces = mesh[1]
        # Keep track of the total number of vertices we had *before* adding the new ones. This is the shift we need for the faces.
        vertex_index_shift = all_vert_coords.shape[0]
        all_vert_coords = np.vstack((all_vert_coords, new_vert_coords))

        new_faces_shifted = new_faces + vertex_index_shift
        all_faces = np.vstack((all_faces, new_faces_shifted))
    return all_vert_coords, all_faces


def subject_avg(subject_id, measure='area', surf='white', display_surf='white', hemi='both', fwhm='10', subjects_dir=None, average_subject='fsaverage', subjects_dir_for_average_subject=None, meta_data=None, load_surface_files=True, load_morphometry_data=True, custom_morphometry_files=None):
    """
    Load morphometry data that has been mapped to an average subject for a subject, i.e., standard space data.

    Load data for a single subject that has been mapped to an average subject like the `fsaverage` subject from FreeSurfer. Can also load the mesh of an arbitrary surface for the average subject.

    Parameters
    ----------
    subject_id: string
        The subject identifier of the subject. As always, it is assumed that this is the name of the directory containing the subject's data, relative to `subjects_dir`. Example: 'subject33'.

    measure : string, optional
        The measure to load, e.g., 'area' or 'curv'. Defaults to 'area'.

    surf : string, optional
        The brain surface where the data has been measured, e.g., 'white' or 'pial'. This will become part of the file name that is loaded. Defaults to 'white'.

    hemi : {'both', 'lh', 'rh'}, optional
        The hemisphere that should be loaded. Defaults to 'both'.

    fwhm : string or None, optional
        Which averaging version of the data should be loaded. FreeSurfer usually generates different standard space files with a number of smoothing settings. Defaults to '10'. If None is passed, the `.fwhmX` part is omitted from the file name completely. Set this to '0' to get the unsmoothed version.

    subjects_dir: string, optional
        A string representing the full path to a directory. This should be the directory containing all subjects of your study. Defaults to the environment variable SUBJECTS_DIR if omitted. If that is not set, used the current working directory instead. This is the directory from which the application was executed.

    average_subject: string, optional
        The name of the average subject to which the data was mapped. Defaults to 'fsaverage'.

    display_surf: string, optional
        The surface of the average subject for which the mesh should be loaded, e.g., 'white', 'pial', 'inflated', or 'sphere'. Defaults to 'white'. Ignored if `load_surface_files` is `False`.

    subjects_dir_for_average_subject: string, optional
        A string representing the full path to a directory. This can be used if the average subject is not in the same directory as all your study subjects. Defaults to the setting of `subjects_dir`.

    meta_data: dictionary, optional
        A dictionary that should be merged into the return value `meta_data`. Defaults to the empty dictionary if omitted.

    load_surface_files: boolean, optional
        Whether to load mesh data. If set to `False`, the first return values `vert_coords` and `faces` will be `None`. Defaults to `True`.

    load_morphometry_data: boolean, optional
        Whether to load morphometry data. If set to `False`, the first return value `morphometry_data` will be `None`. Defaults to `True`.

    custom_morphometry_files: dictionary, optional
        Cutom filenames for the left and right hemispjere data files that should be loaded. A dictionary of strings with exactly the following two keys: `lh` and `rh`. The value strings must contain hardcoded file names or template strings for them. As always, the files will be loaded relative to the `surf/` directory of the respective subject. Example: `{'lh': 'lefthemi.nonstandard.mymeasure44.mgh', 'rh': 'righthemi.nonstandard.mymeasure44.mgh'}`.

    Returns
    -------
    vert_coords: numpy array
        A 2-dimensional array containing the vertices of the mesh(es) of the average subject. Each vertex entry contains 3 coordinates. Each coordinate describes a 3D position in a FreeSurfer surface file (e.g., 'lh.white'), as returned by the `nibabel` function `nibabel.freesurfer.io.read_geometry`.

    faces: numpy array
        A 2-dimensional array containing the 3-faces of the mesh(es) of the average subject. Each face entry contains 3 indices. Each index references the respective vertex in the `vert_coords` array.

    morphometry_data: numpy array
        A numpy array with as many entries as there are vertices in the average subject. If you load two hemispheres instead of one, the length doubles. You can get the start indices for data of the hemispheres in the returned `meta_data`, see `meta_data['lh.num_vertices']` and `meta_data['rh.num_vertices']`. You can be sure that the data for the left hemisphere will always come first (if both were loaded). Indices start at 0, of course. So if the left hemisphere has `n` vertices, the data for them are at indices `0..n-1`, and the data for the right hemisphere start at index `n`. In many cases, your average subject will have the same number of vertices for both hemispheres and you will know this number beforehand, so you may not have to worry about this at all.

    meta_data: dictionary
        A dictionary containing detailed information on all files that were loaded and used settings. The following keys are available (depending on the value of the `hemi` argument, you can replace ?h with 'lh' or 'rh' or both 'lh' and 'rh'):
            - `?h.num_data_points` : the number of data points loaded.
            - `?h.morphometry_file` : the value of the `?h_morphometry_data_file` argument (data file that was loaded)
            - `?h.morphometry_file_format` : the value for `format` that was used
            - `?h.num_vertices` : number of vertices in the loaded mesh
            - `?h.num_faces` : number of faces in the loaded mesh
            - `?lh.surf_file` : the mesh file that was loaded for this hemisphere
            - `subject_id` : the subject id
            - `subjects_dir` : the subjects dir that was used
            - `surf` : the surf that was used, e.g., 'white'
            - `measure` : the measure that was loaded as morphometry data, e.g., 'area'
            - `space` : always the string 'common'. This means that the data loaded represent morphometry data that has been mapped to a common or average subject.
            - `hemi` : the `hemi` value that was used
            - `display_subject` : the name of the common or average subject. This is the subject the surface meshes originate from. Ususally 'fsaverage'.
            - `display_surf` : the surface of the common subject that has been loaded. Something like 'pial', 'white', or 'inflated'.

    Raises
    ------
    ValueError
        If one of the parameters with a fixed set of values receives a value that is not allowed.

    Examples
    --------
    Load area data for both hemispheres and white surface of subject1 in the directory defined by the environment variable SUBJECTS_DIR, mapped to fsaverage:

    >>> import brainload as bl
    >>> v, f, data, md = bl.subject_avg('subject1')
    >>> print md['surf']
    white

    Here, we are a bit more picky and explicit about what we want to load:

    >>> import os
    >>> import brainload as bl
    >>> user_home = os.getenv('HOME')
    >>> subjects_dir = os.path.join(user_home, 'data', 'my_study_x')
    >>> v, f, data, md = bl.subject_avg('subject1', hemi='lh', measure='curv', fwhm='15', display_surf='inflated', subjects_dir=subjects_dir)

    Sometime we do not care for the mesh, e.g., we only want the morphometry data:

    >>> import brainload as bl
    >>> data, md = bl.subject_avg('subject1', hemi='rh', fwhm='15', load_surface_files=False)[2:4]

    """
    if hemi not in ('lh', 'rh', 'both'):
        raise ValueError("ERROR: hemi must be one of {'lh', 'rh', 'both'} but is '%s'." % hemi)

    if subjects_dir is None:
        subjects_dir = os.getenv('SUBJECTS_DIR', os.getcwd())

    if subjects_dir_for_average_subject is None:
        subjects_dir_for_average_subject = subjects_dir

    if meta_data is None:
        meta_data = {}

    # Retrieve the surface mesh on which to display the data. This is the average subject's surface.
    vert_coords = None
    faces = None
    if load_surface_files:
        display_subject = average_subject
        fsaverage_surf_dir = os.path.join(subjects_dir_for_average_subject, average_subject, 'surf')
        lh_surf_file = os.path.join(fsaverage_surf_dir, ('lh.' + display_surf))
        rh_surf_file = os.path.join(fsaverage_surf_dir, ('rh.' + display_surf))
        vert_coords, faces, meta_data = load_subject_mesh_files(lh_surf_file, rh_surf_file, hemi=hemi, meta_data=meta_data)
    else:
        display_surf = None
        display_subject = None

    # Parse the subject's morphometry data, mapped to standard space by FreeSurfer's recon-all.
    morphometry_data = None
    if load_morphometry_data:
        subject_surf_dir = os.path.join(subjects_dir, subject_id, 'surf')

        if custom_morphometry_files is None:
            meta_data['custom_morphometry_files_used'] = False
            lh_morphometry_data_mapped_to_fsaverage = get_standard_space_morphometry_file_path(subjects_dir, subject_id, 'lh', measure, fwhm=fwhm, average_subject=average_subject, surf=surf)
            rh_morphometry_data_mapped_to_fsaverage = get_standard_space_morphometry_file_path(subjects_dir, subject_id, 'rh', measure, fwhm=fwhm, average_subject=average_subject, surf=surf)
        else:
            meta_data['custom_morphometry_files_used'] = True
            lh_morphometry_data_mapped_to_fsaverage = os.path.join(subject_surf_dir, custom_morphometry_files['lh'])
            rh_morphometry_data_mapped_to_fsaverage = os.path.join(subject_surf_dir, custom_morphometry_files['rh'])

        morphometry_data, meta_data = load_subject_morphometry_data_files(lh_morphometry_data_mapped_to_fsaverage, rh_morphometry_data_mapped_to_fsaverage, hemi=hemi, format='mgh', meta_data=meta_data)
    else:
        measure = None


    meta_data['measure'] = measure
    meta_data['subject_id'] = subject_id
    meta_data['subjects_dir'] = subjects_dir
    meta_data['display_surf'] = display_surf
    meta_data['display_subject'] = display_subject
    meta_data['average_subjects_dir'] = subjects_dir_for_average_subject
    meta_data['surf'] = surf
    meta_data['space'] = 'standard_space'
    meta_data['average_subject'] = average_subject
    meta_data['fwhm'] = fwhm
    meta_data['hemi'] = hemi

    return vert_coords, faces, morphometry_data, meta_data


def group_native(measure, subjects_dir, subjects_list, surf='white', hemi='both'):
    """
    Load native space morphometry data for a number of subjects.

    Load native space group data, i.e., morphometry data for all subjects in a study.
    The information given in the parameters `measure`, `surf`, and `hemi` are used to construct the file name that will be loaded by default. This function will NOT load the meshes.

    Parameters
    ----------
    measure : string
        The measure to load, e.g., 'area' or 'curv'. Data files for this measure have to exist for all subjects.

    surf : string, optional
        The brain surface where the data has been measured, e.g., 'white' or 'pial'. Defaults to 'white'. Will be added after the measure name unless left at default.

    hemi : {'both', 'lh', 'rh'}, optional
        The hemisphere that should be loaded. Defaults to 'both'.

    subjects_dir: string, optional
        A string representing the full path to a directory. Defaults to the environment variable SUBJECTS_DIR if omitted. If that is not set, used the current working directory instead. This is the directory from which the application was executed.

    subjects_list: list of strings, optional (unless `subjects_detection_mode` is set to `list`)
        A list of subject identifiers or directory names that should be loaded from the `subjects_dir`. Example list: `['subject1', 'subject2']`. Defaults to None. Only allowed if `subjects_detection_mode` is `auto` or `list`. In `auto` mode, this takes
        precedence over all other options, i.e., if a `subjects_list` *and* the (default or custom) `subjects_file` are given, the `subjects_list` will be used.

    Returns
    -------
    morphdata_by_subject: dictionary
        A dictionary containing the morphometry data. Keys are subject identifiers, and values are the morphometry data numpy 1D arrays.

    metadata_by_subject: dictionary
        A dictionary containing detailed information on all subjects and files that were loaded. Each of its keys is a subject identifier. The data value is another dictionary that contains all meta data for this subject.
    """
    morphdata_by_subject = dict()
    metadata_by_subject = dict()
    for subject_id in subjects_list:
        morphometry_data, metadata = subject_data_native(subject_id, subjects_dir, measure, hemi, surf=surf)
        morphdata_by_subject[subject_id] = morphometry_data
        metadata_by_subject[subject_id] = metadata
    return morphdata_by_subject, metadata_by_subject


def group(measure, surf='white', hemi='both', fwhm='10', subjects_dir=None, average_subject='fsaverage', group_meta_data=None, subjects_list=None, subjects_file='subjects.txt', subjects_file_dir=None, custom_morphometry_file_templates=None, subjects_detection_mode='auto'):
    """
    Load standard space morphometry data for a number of subjects.

    Load group data, i.e., morphometry data for all subjects in a study that has already been mapped to standard space and is ready for group analysis.
    The information given in the parameters `measure`, `surf`, `hemi`, and `fwhm` are used to construct the file name that will be loaded by default. This function will NOT load the meshes.

    Parameters
    ----------
    measure : string
        The measure to load, e.g., 'area' or 'curv'. Data files for this measure have to exist for all subjects.

    surf : string, optional
        The brain surface where the data has been measured, e.g., 'white' or 'pial'. Defaults to 'white'.

    hemi : {'both', 'lh', 'rh'}, optional
        The hemisphere that should be loaded. Defaults to 'both'.

    fwhm : string or None, optional
        Which averaging version of the data should be loaded. FreeSurfer usually generates different standard space files with a number of smoothing settings. Defaults to '10'. If None is passed, the `.fwhmX` part is omitted from the file name completely. Set this to '0' to get the unsmoothed version.

    subjects_dir: string, optional
        A string representing the full path to a directory. Defaults to the environment variable SUBJECTS_DIR if omitted. If that is not set, used the current working directory instead. This is the directory from which the application was executed.

    average_subject: string, optional
        The name of the average subject to which the data was mapped. Defaults to 'fsaverage'.

    group_meta_data: dictionary, optional
        A dictionary that should be merged into the return value `group_meta_data`. Defaults to the empty dictionary if omitted.

    subjects_list: list of strings, optional (unless `subjects_detection_mode` is set to `list`)
        A list of subject identifiers or directory names that should be loaded from the `subjects_dir`. Example list: `['subject1', 'subject2']`. Defaults to None. Only allowed if `subjects_detection_mode` is `auto` or `list`. In `auto` mode, this takes
        precedence over all other options, i.e., if a `subjects_list` *and* the (default or custom) `subjects_file` are given, the `subjects_list` will be used.

    subjects_file_dir: string, optional
        A string representing the full path to a directory. This directory must contain the `subjects_file` (see below). Defaults to the `subjects_dir`.

    subjects_file: string, optional
        The name of the subjects file, relative to the `subjects_file_dir`. Defaults to 'subjects.txt'. The file must be a simple text file that contains one `subject_id` per line. It can be a CSV file that has other data following, but the `subject_id` has to be the first item on each line and the separator must be a comma. So a line is allowed to look like this: `subject1, 35, center1, 147`. No header is allowed. If you have a different format, consider reading the file yourself and pass the result as `subjects_list` instead.

    custom_morphometry_file_templates: dictionary, optional
        Cutom filenames for the left and right hemisphere data files that should be loaded. A dictionary of strings with exactly the following two keys: `lh` and `rh`. The value strings can contain hardcoded file names or template strings for them. As always, the files will be loaded relative to the `surf/` directory of the respective subject. Example for hard-coded files: `{'lh': 'lefthemi.nonstandard.mymeasure44.mgh', 'rh': 'righthemi.nonstandard.mymeasure44.mgh'}`. The strings may contain any of the following variabes, which will be replaced by what you supplied to the other arguments of this function:
            - `${MEASURE}` will be replaced with the value of `measure`.
            - `${SURF}` will be replaced with the FreeSurfer file name part for the surface `surf`. This is the empty string if `surf` is 'white', and a dot followed by the value of `surf` for all other settings of surf. Examples: when `surf` is 'pial', this will be replaced with '.pial' (Note the dot!). If `surf` is 'white', this will be replaced with the empty string.
            - `${SURF_RAW}` will be replaced with the value of `surf`.
            - `${HEMI}` will be replaced with 'lh' for the left hemisphere, and with 'rh' for the right hemisphere.
            - `${FWHM}` will be replaced with the value of `fwhm`, so something like '10'.
            - `${SUBJECT_ID}` will be replaced by the id of the subject that is being loaded, e.g., 'subject3'.
            - `${AVERAGE_SUBJECT}` will be replaced by the value of `average_subject`.

            Note that only `${SURF}` and `${HEMI}` are usually needed, everything else can be hardcoded (or is not part of typical FreeSurfer file names at all, like `${SUBJECT_ID}`).
            Example template string: `subj_${SUBJECT_ID}_hemi_${HEMI}.alsononstandard.mgh`. Complete example for template strings in dictionary: `{'lh': 'subj_${SUBJECT_ID}_hemi_${HEMI}.alsononstandard.mgh', 'rh': 'subj_${SUBJECT_ID}_hemi_${HEMI}.alsononstandard.mgh'}`.

    subjects_detection_mode: {'auto', 'list', 'file', 'search_dir'}, optional
        The method used to determine the subjects that should be loaded. Defaults to 'auto'. You can always see which mode was used by looking at the returned `run_meta_data`, see `run_meta_data['subjects_detection_mode']`.
            - 'auto': In this mode, all available methods will be tried in the following order: If a `subjects_list` is given, it is used. Then, the `subjects_file` is used if it exists. Note that this may be the default file, '$SUBJECTS_DIR/subject_surf_dir.txt', or another if one has explicitely been defined by setting `subjects_file` and/or `subjects_file_dir`. If the file does not exist, the directory is searched for directories containing FreeSurfer data as defined in the section for 'search_dir' mode below. You can always see which method was used in auto mode by looking at the returned `run_meta_data`, see `run_meta_data['subjects_detection_mode_auto_used_method']`.

            - 'list': In this mode, the given `subjects_list` is used, and you have to supply one. If not, an error is raised. You are not allowed to supply a `subjects_file` in this mode, or an error will be raised.

            - 'file': In this mode, the subjects file is used. Note that this may be the default file, '$SUBJECTS_DIR/subjects.txt', or another if one has explicitely been defined by setting `subjects_file` and/or `subjects_file_dir`. If the file does not exist, an error is raised. You can see which file was used by looking at the returned `run_meta_data`, see `run_meta_data['subjects_file']`. You are not allowed to supply a `subjects_list` in this mode, or an error will be raised.

            - 'search_dir': In this mode, the `subjects_dir` (default or explicitely given) is searched for sub directories which look as if they could contain FreeSurfer data. The latter means that they contain a sub directory named 'surf'. There is one exception though: if the name of one such directory equals the name of the `average_subject`, the directory is skipped. You are not allowed to supply a `subjects_list` in this mode, or an error will be raised.

    Returns
    -------
    group_morphometry_data: numpy array
        An array filled with the morphometry data for the subjects. The array has shape `(n, m)` where `n` is the number of subjects, and `m` is the number of vertices of the standard subject. (If you load both hemispheres instead of one, m doubles.) To get the subject id for the entries, look at the respective index in the returned `subjects_list`.

    subjects_list: list of strings
        A list containing the subject identifiers in the same order as the data in `group_morphometry_data`. (If `subjects_detection_mode` is 'list' or 'file', the order in these is guaranteed to be preserved. But in mode 'search_dir' or 'auto' which may have chosen to fall back to 'search_dir' as a last resort, this is helpful: You can use the index of a subject in this list to find its data in `group_morphometry_data`, as it will have the same index. See the examples below.)

    group_meta_data: dictionary
        A dictionary containing detailed information on all subjects and files that were loaded. Each of its keys is a subject identifier. The data value is another dictionary that contains all meta data for this subject as returned by the `subject_avg` function.

    run_meta_data: dictionary
        A dictionary containing general information on the settings used when executing the function and determining which subjects to load.

    Raises
    ------
    ValueError
        If one of the parameters with a fixed set of values receives a value that is not allowed.

    Examples
    --------
    Load area data for all subjects in the directory defined by the environment variable SUBJECTS_DIR:

    >>> import brainload as bl
    >>> data, subjects, group_md, run_md = bl.group('area')

    Here, we load curv data for the right hemisphere, computed on the pial surface with smooting of 20:

    >>> data, subjects, group_md, run_md = bl.group('curv', hemi='rh', surf='pial', fwhm='20')

    We may want to be a but more explicit on which subjects are loaded from where:

    >>> import os
    >>> import brainload as bl
    >>> subjects_dir = os.path.join(os.getenv('HOME'), 'data', 'my_study_x')
    >>> subjects_list = ['subject1', 'subject4', 'subject8']
    >>> data, subjects, group_md, run_md = bl.group('curv', fwhm='20', subjects_dir=subjects_dir, subjects_list=subjects_list)

    Continuing the last example, we may want to have a look at the curv value of the vertex at index 100000 of the subject 'subject4':

    >>> subject4_idx = subjects.index('subject4')
    >>> print data[subject4_idx][100000]

    """


    if hemi not in ('lh', 'rh', 'both'):
        raise ValueError("ERROR: hemi must be one of {'lh', 'rh', 'both'} but is '%s'." % hemi)

    run_meta_data = {}

    if subjects_detection_mode not in ('auto', 'file', 'list', 'search_dir'):
        raise ValueError("ERROR: subjects_detection_mode must be one of {'auto', 'file', 'list', 'search_dir'} but is '%s'." % subjects_detection_mode)
    else:
        run_meta_data['subjects_detection_mode'] = subjects_detection_mode

    # supplying a list is only valid in modes 'auto' and 'list'
    if subjects_detection_mode in ('file', 'search_dir') and subjects_list is not None:
        raise ValueError("ERROR: subjects_detection_mode is set to '%s' but a subjects_list was given. Not supported in subjects_detection_mode 'file' and 'search_dir'." % subjects_detection_mode)

    if subjects_dir is None:
        subjects_dir = os.getenv('SUBJECTS_DIR', os.getcwd())

    if subjects_file_dir is None:
        subjects_file_dir = subjects_dir

    if group_meta_data is None:
        group_meta_data = {}

    run_meta_data['subjects_file_used'] = False
    if subjects_detection_mode == 'auto' and subjects_list is not None:
        run_meta_data['subjects_detection_mode_auto_used_method'] = 'list'  # just use the existing list
    elif subjects_detection_mode == 'list':
        if subjects_list is None:
            raise ValueError("ERROR: subjects_detection_mode is set to 'list' but the subjects_list parameter was not given.")
    elif subjects_detection_mode == 'search_dir':
        subjects_list = nit.detect_subjects_in_directory(subjects_dir, ignore_dir_names=[average_subject])
    else:
        # we are in modes 'auto' or 'file'
        subjects_file_with_path = os.path.join(subjects_file_dir, subjects_file)
        assumed_subjects_file_exists = os.path.isfile(subjects_file_with_path)

        # in file mode, the file has to exist.
        if subjects_detection_mode == 'file' and not assumed_subjects_file_exists:
            raise ValueError("ERROR: subjects_detection_mode is set to 'file' but the subjects_file '%s' does not exist." % subjects_file_with_path)

        auto_mode_done = False
        if assumed_subjects_file_exists:    # we are still in modes 'auto' or 'file', and the file exists.
            subjects_list = nit.read_subjects_file(subjects_file_with_path)
            run_meta_data['subjects_file_used'] = True
            run_meta_data['subjects_file'] = subjects_file_with_path
            if subjects_detection_mode == 'auto':   # in auto mode, we prefer/use the subject file if it exists. If it does not exist, we try to guess the list from the directory later.
                auto_mode_done = True
                run_meta_data['subjects_detection_mode_auto_used_method'] = 'file'

        if subjects_detection_mode == 'auto' and not auto_mode_done:            # last chance in auto mode: try to detect subjects from the contents of the subjects dir.
            run_meta_data['subjects_detection_mode_auto_used_method'] = 'search_dir'
            subjects_list = nit.detect_subjects_in_directory(subjects_dir, ignore_dir_names=[average_subject])

    if custom_morphometry_file_templates is not None:
        run_meta_data['custom_morphometry_file_templates_used'] = True
        run_meta_data['lh.custom_morphometry_file_template'] = custom_morphometry_file_templates['lh']
        run_meta_data['rh.custom_morphometry_file_template'] = custom_morphometry_file_templates['rh']
    else:
        run_meta_data['custom_morphometry_file_templates_used'] = False

    group_morphometry_data = []
    for subject_id in subjects_list:

        custom_morphometry_files = None
        subject_meta_data = {}
        if custom_morphometry_file_templates is not None:
            surf_file_part = _get_morphometry_data_suffix_for_surface(surf)
            substitution_dict_lh = {'MEASURE': measure, 'SURF_RAW': surf, 'SURF': surf_file_part, 'HEMI': 'lh', 'FWHM': fwhm, 'SUBJECT_ID': subject_id, 'AVERAGE_SUBJECT': average_subject}
            substitution_dict_rh = {'MEASURE': measure, 'SURF_RAW': surf, 'SURF': surf_file_part, 'HEMI': 'rh', 'FWHM': fwhm, 'SUBJECT_ID': subject_id, 'AVERAGE_SUBJECT': average_subject}
            custom_morphometry_file_lh = nit.fill_template_filename(custom_morphometry_file_templates['lh'], substitution_dict_lh)
            custom_morphometry_file_rh = nit.fill_template_filename(custom_morphometry_file_templates['rh'], substitution_dict_rh)
            custom_morphometry_files = {'lh': custom_morphometry_file_lh, 'rh': custom_morphometry_file_rh}

        # In the next function call, we discard the first two return values (vert_coords and faces), as these are None anyways because we did not load surface files.
        subject_morphometry_data, subject_meta_data = subject_avg(subject_id, measure=measure, surf=surf, hemi=hemi, fwhm=fwhm, subjects_dir=subjects_dir, average_subject=average_subject, meta_data=subject_meta_data, load_surface_files=False, custom_morphometry_files=custom_morphometry_files)[2:4]

        group_meta_data[subject_id] = subject_meta_data
        group_morphometry_data.append(subject_morphometry_data)
    group_morphometry_data = np.array(group_morphometry_data)
    return group_morphometry_data, subjects_list, group_meta_data, run_meta_data


def parse_talairach_file(file_name):
    """
    Parse a talairach matrix from a talairach.xfm file.

    Parse a talairach matrix from the mri/transforms/talairach.xfm file of a subject. Talairach space is a RAS space with the coordinate center at the Anterior Commisure. RAS (Right-Anterior-Superior) means X points to the right (from subjects point of view), Y points up out of the nose (subject is lying in scanner), and Z points out of the top of the head (so the axis is parallel to the floor). From the Freeurfer Wiki on coordinate systems: 'Note on Talairach: FreeSurfer does not report true "Talairach" coordinates. The coordinates listed unter "Talairach" are actually based on Matthew Brett's 10/8/98 non-linear transform from MNI305 space (see http://www.mrc-cbu.cam.ac.uk/Imaging/mnispace.html). FreeSurfer also reports "Talairach MNI" coordinates. These are MNI305 space.'

    Parameters
    ----------
    file_name: str
        Path to the file, usually SUBJECT/mri/transforms/talairach.xfm

    Returns
    -------
    numpy 2D array
        The matrix, a float array with shape (3, 4).
    """
    with open(file_name, 'r') as fh:
        lines = [line.rstrip('\n') for line in fh]
    if len(lines) == 8:
        return _parse_talairach_matrix_lines(lines[5:8])
    else:
        raise ValueError("Expected talairach file with 8 lines, got %d." % (len(lines)))


def _parse_talairach_matrix_lines(matrix_lines):
    """
    Parse a 3x4 talairach matrix.

    Parse a talairach matrix from the 3 lines representing it in the mri/transforms/talairach.xfm file of a subject.

    Parameters
    ----------
    matrix_lines: list of str
        The 3 matrix lines of a file in talairach.xfm format. Each line must contain 4 floats, separated by spaces. The last line may end with an ';', which will be removed by this function.

    Returns
    -------
    2D numpy array of floats
        The parsed matrix, with dimension (3, 4).
    """
    if len(matrix_lines) != 3:
        raise ValueError("Talairach matrix has wrong line count. Expected exactly 3 lines, got %d." % len(matrix_lines))

    last_line = matrix_lines[2]
    if last_line.endswith(';'):
        matrix_lines[2] = last_line[:-1]

    tal_matrix = np.zeros((3, 4))
    for idx, line in enumerate(matrix_lines):
        tal_matrix[idx] = np.fromstring(line, dtype=np.float_, sep=' ')
    return tal_matrix

Functions for loading FreeSurfer data on different levels.  The high-level functions are available directly in the package namespace. Using the functions in here should not be necessary. # for matrix inversion # for reading binary data Read a file in FreeSurfer m3z format.      Read a file in FreeSurfer m3z format, usually mri/transforms/talairach.m3z of a subject. An m3z file is a gzipped binary file containing a dense vector field that describes a 3D registration between two volumes/images. This implementation follows the Matlab implementation from the FreeSurfer source repository at github, see https://github.com/freesurfer/freesurfer/blob/dev/matlab/mris_read_m3z.m. This function is released under the Freesurfer license: https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense      Parameters     ----------     m3z_file: str         Path to a file in m3z format      Returns     -------     vol_orig: numpy 4D array         Array of np.single, containing 3 numbers per voxel. The shape is (width, height, depth, 3), where width, height, and depth are the dimensions of the source volume.      vol_dest: numpy 4D array         Array of np.single, containing 3 numbers per voxel. The shape is (width, height, depth, 3), where width, height, and depth are the dimensions of the destination volume.      vol_ind0: numpy 4D array         Array of np.int32, containing 3 numbers per voxel. The shape is (width, height, depth, 3).      meta_data: dictionary         Contains meta data on the registration. The following keys are included:             - version: float, File format version             - width: int, Volume width             - height: int, Volume height             - depth: int, Volume depth             - spacing: int, voxel spacing of the volume             - exp_k: float, exp_k of the volume      Examples     --------     Read a talairach.m3z file that has been generated by FreeSurfer's ```recon-all``` command.      >>> import brainload.freesurferdata as fsd     >>> import os     >>> m3z_file = os.path.join(os.getenv('HOME'), 'my_study_data', 'subject1', 'mri', 'transforms', 'talairach.m3z')     >>> vol_orig, vol_dest, vol_ind0, meta_data = fsd.read_m3z_file(m3z_file) # read the whole file contents # Read the file header # vol_data is a tuple # the first 4 bytes after the data are an integer tag, that holds information on what kind of data follows. We do not read that data but check the tag here. # create indices into the vol_data where data resides # Extract the three interleaved volumes and permute the result to match the original looped read. Start with viol_orig. # OK, vol_orig is reconstructed. Now for vol_dest # now for vol_ind0 Read a FreeSurfer lookup table file in text format.      Read a FreeSurfer lookup table file in text format, this is used for the FreeSurferColorLUT.txt file.      Parameters     ----------     lookup_file: str         Path to the FreeSurferColorLUT.txt file. It comes with FreeSurfer and can be found directly in $FREESURFER_HOME for v6.      Returns     -------     numpy 2D str array         Array with shape (n, 6) for a file with n relevant lines. A relevant line is a line describing a segmentation in 6 fields (seg_code, structure_name, color_red, color_green, color_blue, color_alpha). There are 2 types of ignored lines in the file: empty lines and those starting with the comment character '#'. All other lines are considered relevant and split into the 6 parts. Load the vox2ras and ras2vox matrices from a nifti file header.      Load the vox2ras and ras2vox matrices from a nifti file header. The file can be in nifti (.nii) or gzipped nifti (.nii.gz) format. To understand qform and sform, read the nibabel docs or better https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Orientation%20Explained.      Parameters     ----------     nifti_file: str         Path to a nifti or gzipped nifti file.      use_sform: bool, optional         Whether to report the sform matrix or qform matrix from the nifti header. Defaults to True (=sform). If set to False, the qform will be used.      Returns     -------     vox2ras: 2D numpy array         The sform or qform matrix      ras2vox: 2D numpy array         The inverse of the vox2ras matrix.      Examples     --------     >>> import brainload.freesurferdata as fsd     >>> vox2ras, ras2vox = fsd.get_vox2ras_and_ras2vox_from_nifti_file("mni152_volume.nii.gz") Read the 3 affine transformation matrices from a MGH file header.      Read the 3 affine transformation matrices ras2vox, vox2ras, and vox2ras_tkr from a MGH file header. The input file is assumed to be gzipped (and extracted appropriately) if the file name ends with '.mgz' or '.mgh.gz'. See the FreeSurfer wiki on coordinate systems for details on what these matrices are. In short, RAS coordinates are used to specify positions of vertices in FreeSurfer surface files.      In short, VOX is the voxel index and the RAS coordinate is used for the surface coordinate of a vertex.      VOX: After FreeSurfer pre-processing, this is a triplet of integers in range 0 - 255 for 3D images. Note though that the original T1 images (before pre-processing) from a study can - and usually will - have different numbers of voxels (both different between the axes of a single image as well as between subjects). The VOX is sometimes called CRS for voxel column, row, slice.      RAS: Right-Anterior-Superior (anatomical coordinates). According to http://www.grahamwideman.com/gw/brain/fs/coords/fscoords.htm, the RAS coordinate origin (0, 0, 0) is the center of the voxel (128, 128, 128). Note that this voxel could or could NOT be the center of the MRI volume.      Parameters     ----------     mgh_file_name: string         Path to a file in MGH format. The input file is assumed to be gzipped (and extracted appropriately) if the file name ends with '.mgz' or '.mgh.gz'.      Returns     -------     ras2vox: numpy array         2D numpy array with shape (4, 4). Transformation matrix from RAS coordinate to voxel index.      vox2ras: numpy array         2D numpy array with shape (4, 4). Transformation matrix from voxel index to RAS coordinate.      vox2ras_tkr: numpy array         2D numpy array with shape (4, 4). Transformation matrix from voxel index to (tkregister) surface RAS coordinate. This is a RAS coordinate of a vertex on the surface.      Examples     --------     >>> import os; import brainload.freesurferdata as fsd     >>> mgh_file = os.path.join(TEST_DATA_DIR, 'subject1', 'mri', 'orig.mgh')     >>> ras2vox, vox2ras, vox2ras_tkr = fsd.read_mgh_header_matrices(mgh_file) Read data from a FreeSurfer output file in mgh format.      Read all data from the MGH file and return it as a numpy array. Optionally, collect meta data from the mgh file header.      Parameters     ----------     mgh_file_name: string         A string representing a full path to a file in FreeSurfer MGH file format. If the file name end with '.mgz' or '.mgh.gz', the file is assumed to be in gzipped MGH format.      collect_meta_data: bool, optional         Whether or not to collect meta data from the MGH file header. Defaults to True.      collect_data: bool, optional         Whether or not to collect the file data (voxel values) from the MGH file. Defaults to True.      Returns     -------     mgh_data: numpy array         The data from the MGH file, usually one scalar value per voxel.      mgh_meta_data: dictionary         The meta data collected from the header, or an empty dictionary if the argument `collect_meta_data` was 'False'. The keys correspond to the names of the respective nibabel function used to retrieve the data. The values are the data as returned by nibabel.      Examples     --------     Read a file in MGH format from the surf dir of a subject:      >>> import os     >>> import brainload.freesurferdata as fsd     >>> mgh_file = os.path.join('my_subjects_dir', 'subject1', 'surf', 'rh.area.fsaverage.mgh')     >>> mgh_data, mgh_meta_data = fsd.read_mgh_file(mgh_file)      See also     --------         - https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems         - https://github.com/nipy/nibabel/blob/master/nibabel/freesurfer/mghformat.py         - https://surfer.nmr.mgh.harvard.edu/fswiki/FileFormats # identical to get_affine for MGH format # MGH format has a header, then data, then a footer # the voxel dimensions (along all 3 axes in space) Return the number of vertices per fsaverage hemisphere.      Returns     -------     vertcount: int          The number of vertices per fsaverage hemisphere. Merge morphometry data horizontally.      Merge morphometry data read from several meshes of the same subject horizontally. This is used to merge data from the left and right hemispheres.      Parameters     ----------     morphometry_data_arrays: 2D array         An array of arrays, each of which represents morphometry data from different hemispheres of the same subject.      dtype: data type, optional         Data type for the output numpy array. Defaults to float.      Returns     -------     numpy array         Horizontally stacked array containing the data from all arrays in the input array.      Examples     --------     Merge some data:      >>> lh_morphometry_data = np.array([0.0, 0.1, 0.2, 0.3])   # some fake data     >>> rh_morphometry_data = np.array([0.5, 0.6])     >>> merged_data = fsd.merge_morphometry_data(np.array([lh_morphometry_data, rh_morphometry_data]))     >>> print merged_data.shape     (6, )      Typically, the `lh_morphometry_data` and `rh_morphometry_data` come from calls to `read_fs_morphometry_data_file_and_record_meta_data` as shown here:      >>> lh_morphometry_data, meta_data = read_fs_morphometry_data_file_and_record_meta_data(lh_morphometry_data_file, 'lh')     >>> rh_morphometry_data, meta_data = read_fs_morphometry_data_file_and_record_meta_data(rh_morphometry_data_file, 'rh', meta_data=meta_data)     >>> both_hemis_morphometry_data = merge_morphometry_data(np.array([lh_morphometry_data, rh_morphometry_data])) Determine FreeSurfer surface representation string.      Determine the substring representing the given surface in a FreeSurfer output curv file. For FreeSurfer's default surface 'white', the surface is not represented in the output file name pattern. For all others, it is represented by a dot followed by the name.      Parameters     ----------     surf: string         A string representing a FreeSurfer surface, e.g., 'white' or 'pial'.      Returns     -------     string         The empty string if `surf` is 'white'. A dot followed by the string in the input argument `surf` otherwise.      Examples     --------     >>> import brainload.freesurferdata as fsd     >>> print fsd._get_morphometry_data_suffix_for_surface('pial')     .pial Read a surface file and record meta data on it.      Read a surface file and record meta data on it. A surface file is a mesh file in FreeSurfer format, e.g., 'lh.white'. It contains vertices and 3-faces made out of them.      Parameters     ----------     surf_file: string         A string representing an absolute path to a surface (or 'mesh') file (e.g., the path to 'lh.white').      hemisphere_label: {'lh' or 'rh'}         A string representing the hemisphere this file belongs to. This is used to write the correct meta data.      meta_data: dictionary | None, optional         Meta data to merge into the output `meta_data`. Defaults to the empty dictionary.      Returns     -------     vert_coords: numpy array         A 2D array containing 3 coordinates for each vertex in the `surf_file`.      faces: numpy array         A 2D array containing 3 vertex indices per face. Look at the respective indices in `vert_coords` to get the vertex coordinates.      meta_data: dictionary         Contains detailed information on the data that was loaded. The following keys are available (replace `?h` with the value of the argument `hemisphere_label`, which must be 'lh' or 'rh').             - `?h.num_vertices` : number of vertices in the loaded mesh             - `?h.num_faces` : number of faces in the loaded mesh             - `?lh.surf_file` : value of the `surf_file` argument: the mesh file that was loaded      Examples     --------     >>> vert_coords, faces, meta_data = fsd.read_fs_surface_file_and_record_meta_data(surf_file, 'lh')     >>> print meta_data['lh.num_vertices']     121567                  # arbitrary number, depends on the subject mesh Guess a hemisphere label from a file path.      Guess a hemisphere label, i.e., one of ```lh``` or ```rh```, from a file path like ```/some/path/to/subjects/subject1/surf/lh.area```.      Parameters     ----------     file_path: str         The full path to a file.      default: str         What to return if the function cannot deduce the information from the given file_path.      Returns     -------     hemi: str         The hemisphere label      is_default: boolean         True if the file_path contained no information to deduce the hemisphere label, and the returned ```hemi``` value thus is the one from the ```default``` parameter. Read a morphometry file and record meta data on it.      Read a morphometry file and record meta data on it. A morphometry file is file containing a scalar value for each vertex on the surface of a FreeSurfer mesh. An example is the file 'lh.area', which contains the area values for all vertices of the left hemisphere of the white surface. Such a file can be in two different formats: 'curv' or 'mgh'. The former is used when the data refers to the surface mesh of the original subject, the latter when it has been mapped to a standard subject like fsaverage.      Parameters     ----------     curv_file: string         A string representing a path to a morphometry file (e.g., the path to 'lh.area').      hemisphere_label: {'lh' or 'rh'}         A string representing the hemisphere this file belongs to. This is used to write the correct meta data.      meta_data: dictionary | None, optional         Meta data to merge into the output `meta_data`. Defaults to the empty dictionary.      format: {'curv', 'mgh'}, optional         The file format for the files that are to be loaded. Defaults to 'curv'.      Returns     -------     per_vertex_data: numpy array         A 1D array containing one scalar value per vertex.      meta_data: dictionary         Contains detailed information on the data that was loaded. The following keys are available (replace `?h` with the value of the argument `hemisphere_label`, which must be 'lh' or 'rh').             - `?h.num_data_points` : the number of data points loaded.             - `?h.morphometry_file` : the value of the `curv_file` argument (data file that was loaded)             - `?h.morphometry_file_format` : the value for `format` that was used      Examples     --------     >>> import brainload.freesurferdata as fsd; import os     >>> lh_morphometry_file = os.path.join('my_subjects_dir', 'subject1', 'surf', 'lh.area')     >>> lh_morphometry_data, meta_data = read_fs_morphometry_data_file_and_record_meta_data(lh_morphometry_file, 'lh')     >>> print meta_data['lh.num_data_points']     121567                  # arbitrary number, depends on the subject mesh     >>> print meta_data['lh.morphometry_file']     my_subjects_dir/subject1/surf/lh.area             # on UNIX-like systems Load mesh files for a subject.      Load one or two mesh files for a subject. Which of the two files `lh_surf_file` and `rh_surf_file` are actually loaded is determined by the `hemi` parameter.      Parameters     ----------     lh_surf_file: string | None         A string representing an absolute path to a mesh file for the left hemisphere (e.g., the path to 'lh.white'). If `hemi` is 'rh', this will be ignored and can thus be None.      rh_surf_file: string | None         A string representing an absolute path to a mesh file for the right hemisphere (e.g., the path to 'rh.white'). If `hemi` is 'lh', this will be ignored and can thus be None.      hemi: {'both', 'lh', 'rh'}, optional         The hemisphere for which data should actually be loaded. Defaults to 'both'.      meta_data: dictionary | None, optional         Meta data to merge into the output `meta_data`. Defaults to the empty dictionary.      Returns     -------     vert_coords: numpy array of floats         A 2D array containing 3 coordinates for each vertex. Dimension is (n, 3) for n vertices. If the argument `hemi` was 'both', this includes vertices from several meshes. You can check the `meta_data` return values to get the border between meshes, see `meta_data['lh.num_vertices']` and  `meta_data['rh.num_vertices']`.      faces: numpy array of integers         A 2D array containing 3 vertex indices per face. Dimension is (m, 3) for m faces. Look at the respective indices in `vert_coords` to get the vertex coordinates. If the argument `hemi` was 'both', this includes faces from several meshes. You can check the `meta_data` return values to get the border between meshes, see `meta_data['lh.num_faces']` and  `meta_data['rh.num_faces']`.      meta_data: dictionary         Contains detailed information on the data that was loaded. The following keys are available (depending on the value of the `hemi` argument, you can replace ?h with 'lh' or 'rh' or both 'lh' and 'rh'):             - `?h.num_vertices` : number of vertices in the loaded mesh             - `?h.num_faces` : number of faces in the loaded mesh             - `?h.surf_file` : the mesh file that was loaded for this hemisphere      Examples     --------     >>> import brainload.freesurferdata as fsd; import os     >>> lh_surf_file = os.path.join('my_subjects_dir', 'subject1', 'surf', 'lh.white')     >>> rh_surf_file = os.path.join('my_subjects_dir', 'subject1', 'surf', 'rh.white')     >>> vert_coords, faces, meta_data = fsd.load_subject_mesh_files(lh_surf_file, rh_surf_file) Computes the absolute data index given an index relative to the right hemisphere.      This function makes sense only given a `morphometry_data` and associated `meta_data` that contains data on two hemispheres (even though the `morphometry_data` array itself is not passed to this function). E.g., the return value of a function like `subject()` or `subject_avg()` when called with `hemi='both'`. For such data, it computes the absolute index in the data given a request index relative to the right hemisphere. The name is short for 'right hemisphere index'.      Parameters     ----------     rh_relative_index: int         An index relative to the right hemisphere. E.g., `0` if you want to get the index of the first vertex of the right hemisphere. Its absolute value must be between 0 and the number of vertices of the right hemisphere. Negative values are allowed, and `-1` will get you the second-to-last possible index, `-2` the third-to-last, and so on.      meta_data: dictionary         The meta data dictionary returned for your data. It must contain the keys 'lh.num_data_points' and 'rh.num_data_points'.      Returns     -------     The absolute index into the data for the given `rh_relative_index`.      Examples     --------     >>> import brainload as bl     >>> morphometry_data, meta_data = bl.subject('heinz', hemi='both')[2:4]     >>> print "rh value at index 10, relative to start of right hemisphere: %d." % morphometry_data[bl.rhi(10, meta_data)] Compute start and end index in the hemisphere data for the given hemisphere.      Parameters     ----------     morphometry_meta_data: dictionary as returned by the functions that read morphometry data (e.g., ```subject_data_native```).      hemi: string, one of 'lh' or 'rh'. The hemisphere you want to get the start and end index for.      Returns     -------     start_index: integer         The start index of the lh data.      end_index: integer         The end index of the lh data.      Examples     --------     >>> import brainload as bl     >>> morphometry_data, meta_data = bl.subject_data_native('subject1', '/mnt/study1_data', 'thickness', 'both')     >>> s, e = bl.hemi_range(meta_data, 'lh')     >>> print("Mean lh thickness value is: %f" % (np.mean(morphometry_data[s:e]))) Returns the value in `morphometry_data` at an index relative to the right hemisphere.      This function makes sense only given a `morphometry_data` and associated `meta_data` that contains data on two hemispheres. E.g., the return value of a function like `subject()` or `subject_avg()` when called with `hemi='both'`. For such data, it returns the value in `morphometry_data` at a request index given relative to the right hemisphere. The name is short for 'right hemisphere value'.      Parameters     ----------     rh_relative_index: int         An index relative to the start of the right hemisphere in the data. E.g., `0` if you want to get the value for the first vertex of the right hemisphere. Its absolute value must be between 0 and the number of vertices of the right hemisphere. Negative values are allowed, and `-1` will get you the last possible value, `-2` the second-to-last, and so on.      morphometry_data: numpy array         The morphometry data array, must represent data for both hemispheres.      meta_data: dictionary         The meta data dictionary returned for your data. It must contain the keys 'lh.num_data_points' and 'rh.num_data_points'.      Returns     -------     The value at the given index that is relative to the start of the right hemisphere in the data.      Examples     --------     >>> import brainload as bl     >>> morphometry_data, meta_data = bl.subject('heinz', hemi='both')[2:4]     >>> print "rh value at index 10, relative to start of right hemisphere: %d." % bl.rhv(10, morphometry_data, meta_data) Load morphometry data files for a subject.      Load one or two morphometry data files for a subject. Which of the two files `lh_morphometry_data_file` and `rh_morphometry_data_file` are actually loaded is determined by the `hemi` parameter.      Parameters     ----------     lh_morphometry_data_file: string | None         A string representing an absolute path to a morphometry data file for the left hemisphere. If `hemi` is 'rh', this will be ignored and can thus be None.      rh_morphometry_data_file: string | None         A string representing an absolute path to a morphometry data file for the right hemisphere. If `hemi` is 'lh', this will be ignored and can thus be None.      hemi: {'both', 'lh', 'rh'}, optional         The hemisphere for which data should actually be loaded. Defaults to 'both'.      format: {'curv', 'mgh'}, optional         The file format for the files that are to be loaded. Defaults to 'curv'.      meta_data: dictionary | None, optional         Meta data to merge into the output `meta_data`. Defaults to the empty dictionary.      Returns     -------     morphometry_data: numpy array         An array containing the scalar per-vertex data loaded from the file(s).      meta_data: dictionary         Contains detailed information on the data that was loaded. The following keys are available (depending on the value of the `hemi` argument, you can replace ?h with 'lh' or 'rh' or both 'lh' and 'rh'):             - `?h.num_data_points` : the number of data points loaded.             - `?h.morphometry_file` : the value of the `?h_morphometry_data_file` argument (data file that was loaded)             - `?h.morphometry_file_format` : the value for `format` that was used      Examples     --------     Load the lh and rh area files for subject1.      >>> import brainload.freesurferdata as fsd; import os     >>> lh_morphometry_file = os.path.join('path', 'to', 'subjects_dir', 'subject1', 'surf', 'lh.area')     >>> rh_morphometry_file = os.path.join('path', 'to', 'subjects_dir', 'subject1', 'surf', 'rh.area')     >>> morphometry_data, meta_data = fsd.load_subject_morphometry_data_files(lh_morphometry_file, rh_morphometry_file)      Now let's look at the area value for the vertex at index 10:      >>> print "lh value at index 10: %d." % morphometry_data[10]      But what about the value of vertex 10 at the right hemisphere? We loaded 2 hemispheres, so the data is concatinated. But you can use the `meta_data` to get the correct index relative to the right hemisphere:      >>> print "rh value at index 10: %d." % morphometry_data[fsd.rhi(10, meta_data)]      You could also get the value directly using the `rhv` function:      >>> print "rh value at index 10: %d." % fsd.rhv(10, morphometry_data, meta_data) Load a surface mesh of a subject.      Convenience function to load a FreeSurfer surface mesh of a subject.      Parameters     ----------     subject_id: string         The subject identifier of the subject.      surf : string, optional         The brain surface where the data has been measured, e.g., 'white' or 'pial'. This will become part of the file name that is loaded. Defaults to 'white'.      hemi : {'both', 'lh', 'rh'}, optional         The hemisphere that should be loaded. Defaults to 'both'.      subjects_dir: string         A string representing the full path to a directory. This should be the directory containing all subjects of your study.      Returns     -------     vert_coords: numpy array         A 2-dimensional array containing the vertices of the mesh(es) of the subject. Each vertex entry contains 3 coordinates. Each coordinate describes a 3D position in a FreeSurfer surface file (e.g., 'lh.white'), as returned by the `nibabel` function `nibabel.freesurfer.io.read_geometry`.      faces: numpy array         A 2-dimensional array containing the 3-faces of the mesh(es) of the subject. Each face entry contains 3 indices. Each index references the respective vertex in the `vert_coords` array.      meta_data: dictionary         A dictionary containing detailed information on all files that were loaded and used settings. The following keys are available (depending on the value of the `hemi` argument, you can replace ?h with 'lh' or 'rh' or both 'lh' and 'rh'):             - `?h.num_vertices` : number of vertices in the loaded mesh             - `?h.num_faces` : number of faces in the loaded mesh             - `?lh.surf_file` : the mesh file that was loaded for this hemisphere      Raises     ------     ValueError         If one of the parameters with a fixed set of values receives a value that is not allowed.      Examples     --------     Load the pial surface mesh for both hemispheres of the Freeurfer example subject bert:      >>> import brainload as bl, import os     >>> subjects_dir = os.path.join('Applications', 'freesurfer', 'subjects')     >>> verts, faced, meta_data = bl.subject_mesh('bert', subjects_dir, surf='pial') Load a surface mesh of the fsaverage subject.      Convenience function to load a FreeSurfer surface mesh of the fsaverage subject. Use the subject_mesh function to load the mesh of any other subject.      Parameters     ----------     subject_id: string, optional         The subject identifier of the subject. Defaults to 'fsaverage'.      surf : string, optional         The brain surface where the data has been measured, e.g., 'white' or 'pial'. This will become part of the file name that is loaded. Defaults to 'white'.      hemi : {'both', 'lh', 'rh'}, optional         The hemisphere that should be loaded. Defaults to 'both'.      subjects_dir: string, optional         A string representing the full path to a directory. This should be the directory containing all subjects of your study. Defaults to the environment variable SUBJECTS_DIR if omitted. If that is not set, used the current working directory instead. This is the directory from which the application was executed.      use_freesurfer_home_if_missing: boolean, optional         If set to True, first checks whether the directory for the given subject exists in the `subjects_dir`. If it does not, it will reset the `subjects_dir` to '${FREESURFER_HOME}/subjects' before proceeding.      Returns     -------     vert_coords: numpy array         A 2-dimensional array containing the vertices of the mesh(es) of the subject. Each vertex entry contains 3 coordinates. Each coordinate describes a 3D position in a FreeSurfer surface file (e.g., 'lh.white'), as returned by the `nibabel` function `nibabel.freesurfer.io.read_geometry`.      faces: numpy array         A 2-dimensional array containing the 3-faces of the mesh(es) of the subject. Each face entry contains 3 indices. Each index references the respective vertex in the `vert_coords` array.      meta_data: dictionary         A dictionary containing detailed information on all files that were loaded and used settings. The following keys are available (depending on the value of the `hemi` argument, you can replace ?h with 'lh' or 'rh' or both 'lh' and 'rh'):             - `?h.num_vertices` : number of vertices in the loaded mesh             - `?h.num_faces` : number of faces in the loaded mesh             - `?lh.surf_file` : the mesh file that was loaded for this hemisphere      Raises     ------     ValueError         If one of the parameters with a fixed set of values receives a value that is not allowed.      Examples     --------     Load area data for both hemispheres and white surface of subject1 in the directory defined by the environment variable SUBJECTS_DIR:      >>> import brainload as bl     >>> verts, faced, meta_data = bl.fsaverage_mesh() Load native space morphometry data for a subject (e.g., lh.area).      Parameters     ----------     subject_id: string         The subject identifier of the subject. As always, it is assumed that this is the name of the directory containing the subject's data, relative to `subjects_dir`. Example: 'subject33'.      measure : string         The measure to load, e.g., 'area' or 'curv'. Defaults to 'area'.      surf : string, optional         The brain surface where the data has been measured, e.g., 'white' or 'pial'. This will become part of the file name that is loaded. For white, nothing will be added. Defaults to 'white'.      hemi : {'both', 'lh', 'rh'}         The hemisphere that should be loaded.      subjects_dir: string         A string representing the full path to a directory. This should be the directory containing all subjects of your study.      Returns     -------     morphometry_data: numpy array         A numpy array with as many entries as there are vertices in the subject. If you load two hemispheres instead of one, the length doubles. You can get the start indices for data of the hemispheres in the returned `meta_data`, see `meta_data['lh.num_vertices']` and `meta_data['rh.num_vertices']`. You can be sure that the data for the left hemisphere will always come first (if both were loaded). Indices start at 0, of course. So if the left hemisphere has `n` vertices, the data for them are at indices `0..n-1`, and the data for the right hemisphere start at index `n`. Note that the two hemispheres do in general NOT have the same number of vertices.      meta_data: dictionary         A dictionary containing detailed information on all files that were loaded and used settings. The following keys are available (depending on the value of the `hemi` argument, you can replace ?h with 'lh' or 'rh' or both 'lh' and 'rh'):             - `?h.num_data_points` : the number of data points loaded.             - `?h.morphometry_file` : the value of the `?h_morphometry_data_file` argument (data file that was loaded)             - `?h.morphometry_file_format` : the value for `format` that was used             - `subject_id` : the subject id             - `subjects_dir` : the subjects dir that was used             - `surf` : the surf that was used, e.g., 'white'             - `measure` : the measure that was loaded as morphometry data, e.g., 'area'             - `space` : always the string 'subject'. This means that the data loaded represent morphometry data taken from the subject's surface (as opposed to data mapped to a common or average subject).             - `hemi` : the `hemi` value that was used      Examples     --------     >>> import brainload as bl     >>> morphometry_data, meta_data = bl.subject_data_native('subject1', '/mnt/study1_data', 'thickness', 'both') Load standard space data for a subject (e.g., lh.area.fwhm10.fsaverage.mgh).      Parameters     ----------     subject_id: string         The subject identifier of the subject. As always, it is assumed that this is the name of the directory containing the subject's data, relative to `subjects_dir`. Example: 'subject33'.      measure : string         The measure to load, e.g., 'area' or 'curv'.      surf : string, optional         The brain surface where the data has been measured, e.g., 'white' or 'pial'. This will become part of the file name that is loaded. Defaults to 'white'.      hemi : {'both', 'lh', 'rh'}         The hemisphere that should be loaded.      fwhm : string or None         Which averaging version of the data should be loaded. FreeSurfer usually generates different standard space files with a number of smoothing settings. If None is passed, the `.fwhmX` part is omitted from the file name completely. Set this to '0' to get the unsmoothed version.      subjects_dir: string         A string representing the full path to a directory. This should be the directory containing all subjects of your study.      average_subject: string, optional         The name of the average subject to which the data was mapped. Defaults to 'fsaverage'.      Returns     -------     morphometry_data: numpy array         A numpy array with as many entries as there are vertices in the subject. If you load two hemispheres instead of one, the length doubles. You can get the start indices for data of the hemispheres in the returned `meta_data`, see `meta_data['lh.num_vertices']` and `meta_data['rh.num_vertices']`. You can be sure that the data for the left hemisphere will always come first (if both were loaded). Indices start at 0, of course. So if the left hemisphere has `n` vertices, the data for them are at indices `0..n-1`, and the data for the right hemisphere start at index `n`. Note that the two hemispheres do in general NOT have the same number of vertices.      meta_data: dictionary         A dictionary containing detailed information on all files that were loaded and used settings. The following keys are available (depending on the value of the `hemi` argument, you can replace ?h with 'lh' or 'rh' or both 'lh' and 'rh'):             - `?h.num_data_points` : the number of data points loaded.             - `?h.morphometry_file` : the value of the `?h_morphometry_data_file` argument (data file that was loaded)             - `?h.morphometry_file_format` : the value for `format` that was used             - `subject_id` : the subject id             - `subjects_dir` : the subjects dir that was used             - `surf` : the surf that was used, e.g., 'white'             - `measure` : the measure that was loaded as morphometry data, e.g., 'area'             - `space` : always the string 'common'. This means that the data loaded represent morphometry data that has been mapped to a common or average subject.             - `hemi` : the `hemi` value that was used Load FreeSurfer brain morphometry and/or mesh data for a single subject.      High-level interface to load FreeSurfer brain data for a single space. This parses the data for the surfaces of this subject. If you want to load data that has been mapped to an average subject like 'fsaverage', use `subject_avg` instead.      Parameters     ----------     subject_id: string         The subject identifier of the subject. As always, it is assumed that this is the name of the directory containing the subject's data, relative to `subjects_dir`. Example: 'subject33'.      measure : string, optional         The measure to load, e.g., 'area' or 'curv'. Defaults to 'area'.      surf : string, optional         The brain surface where the data has been measured, e.g., 'white' or 'pial'. This will become part of the file name that is loaded. Defaults to 'white'.      hemi : {'both', 'lh', 'rh'}, optional         The hemisphere that should be loaded. Defaults to 'both'.      subjects_dir: string, optional         A string representing the full path to a directory. This should be the directory containing all subjects of your study. Defaults to the environment variable SUBJECTS_DIR if omitted. If that is not set, used the current working directory instead. This is the directory from which the application was executed.      meta_data: dictionary, optional         A dictionary that should be merged into the return value `meta_data`. Defaults to the empty dictionary if omitted.      load_surface_files: boolean, optional         Whether to load mesh data. If set to `False`, the first return values `vert_coords` and `faces` will be `None`. Defaults to `True`.      load_morphometry_data: boolean, optional         Whether to load morphometry data. If set to `False`, the first return value `morphometry_data` will be `None`. Defaults to `True`.      Returns     -------     vert_coords: numpy array         A 2-dimensional array containing the vertices of the mesh(es) of the subject. Each vertex entry contains 3 coordinates. Each coordinate describes a 3D position in a FreeSurfer surface file (e.g., 'lh.white'), as returned by the `nibabel` function `nibabel.freesurfer.io.read_geometry`.      faces: numpy array         A 2-dimensional array containing the 3-faces of the mesh(es) of the subject. Each face entry contains 3 indices. Each index references the respective vertex in the `vert_coords` array.      morphometry_data: numpy array         A numpy array with as many entries as there are vertices in the subject. If you load two hemispheres instead of one, the length doubles. You can get the start indices for data of the hemispheres in the returned `meta_data`, see `meta_data['lh.num_vertices']` and `meta_data['rh.num_vertices']`. You can be sure that the data for the left hemisphere will always come first (if both were loaded). Indices start at 0, of course. So if the left hemisphere has `n` vertices, the data for them are at indices `0..n-1`, and the data for the right hemisphere start at index `n`. Note that the two hemispheres do in general NOT have the same number of vertices.      meta_data: dictionary         A dictionary containing detailed information on all files that were loaded and used settings. The following keys are available (depending on the value of the `hemi` argument, you can replace ?h with 'lh' or 'rh' or both 'lh' and 'rh'):             - `?h.num_data_points` : the number of data points loaded.             - `?h.morphometry_file` : the value of the `?h_morphometry_data_file` argument (data file that was loaded)             - `?h.morphometry_file_format` : the value for `format` that was used             - `?h.num_vertices` : number of vertices in the loaded mesh             - `?h.num_faces` : number of faces in the loaded mesh             - `?lh.surf_file` : the mesh file that was loaded for this hemisphere             - `subject_id` : the subject id             - `subjects_dir` : the subjects dir that was used             - `surf` : the surf that was used, e.g., 'white'             - `measure` : the measure that was loaded as morphometry data, e.g., 'area'             - `space` : always the string 'subject'. This means that the data loaded represent morphometry data taken from the subject's surface (as opposed to data mapped to a common or average subject).             - `hemi` : the `hemi` value that was used      Raises     ------     ValueError         If one of the parameters with a fixed set of values receives a value that is not allowed.      Examples     --------     Load area data for both hemispheres and white surface of subject1 in the directory defined by the environment variable SUBJECTS_DIR:      >>> import brainload as bl     >>> vertices, faces, data, md = bl.subject('subject1')      Here, we are a bit more explicit about what we want to load:      >>> import os     >>> user_home = os.getenv('HOME')     >>> subjects_dir = os.path.join(user_home, 'data', 'my_study_x')     >>> vertices, faces, data, md = bl.subject('subject1', hemi='lh', measure='curv', subjects_dir=subjects_dir)      Sometimes we do not care for the mesh, e.g., we only want the morphometry data:      >>> data, md = bl.subject('subject1', hemi='rh', load_surface_files=False)[2:4]      ...or the other way around (mesh only, no morphometry data):      >>> vertices, faces = bl.subject('subject1', hemi='rh', load_morphometry_data=False)[0:2] Determine the path to a surface file, e.g., `lh.white`. Determine the path to a standard space morphometry file, e.g., `lh.area.fwhm10.fsaverage.mgh`. Determine the path to a native space morphometry file, e.g., `lh.area`. Merge several meshes into a single one.      Merge a list of meshes into a single one. Each mesh is given by a vertex list and a face list. The merged vertex list is just a vstack of the individual lists, and the vertex coordinates are not altered in any way. As a face id defined by the indices of its 3 vertices, these indices get adjusted for all meshes but the first one.      Parameters     ----------     meshes: array-like         A array of meshes. Each mesh is represented as an array of length 2, where the entry at index 0 is the vertex list, and the one at index 2 is the face list.      Returns     -------     all_vert_coords: numpy array         An array of vertex coordinates with shape(3, n), where n is the sum of the vertex counts of all input meshes.      all_faces: numpy_array (2d)         An array of faces with shape(3, m), where m is the sum of the face counts of all input meshes. For each face, each of its 3 values represent the vertex at the respective index in the `all_vert_coords` array. # Keep track of the total number of vertices we had *before* adding the new ones. This is the shift we need for the faces. Load morphometry data that has been mapped to an average subject for a subject, i.e., standard space data.      Load data for a single subject that has been mapped to an average subject like the `fsaverage` subject from FreeSurfer. Can also load the mesh of an arbitrary surface for the average subject.      Parameters     ----------     subject_id: string         The subject identifier of the subject. As always, it is assumed that this is the name of the directory containing the subject's data, relative to `subjects_dir`. Example: 'subject33'.      measure : string, optional         The measure to load, e.g., 'area' or 'curv'. Defaults to 'area'.      surf : string, optional         The brain surface where the data has been measured, e.g., 'white' or 'pial'. This will become part of the file name that is loaded. Defaults to 'white'.      hemi : {'both', 'lh', 'rh'}, optional         The hemisphere that should be loaded. Defaults to 'both'.      fwhm : string or None, optional         Which averaging version of the data should be loaded. FreeSurfer usually generates different standard space files with a number of smoothing settings. Defaults to '10'. If None is passed, the `.fwhmX` part is omitted from the file name completely. Set this to '0' to get the unsmoothed version.      subjects_dir: string, optional         A string representing the full path to a directory. This should be the directory containing all subjects of your study. Defaults to the environment variable SUBJECTS_DIR if omitted. If that is not set, used the current working directory instead. This is the directory from which the application was executed.      average_subject: string, optional         The name of the average subject to which the data was mapped. Defaults to 'fsaverage'.      display_surf: string, optional         The surface of the average subject for which the mesh should be loaded, e.g., 'white', 'pial', 'inflated', or 'sphere'. Defaults to 'white'. Ignored if `load_surface_files` is `False`.      subjects_dir_for_average_subject: string, optional         A string representing the full path to a directory. This can be used if the average subject is not in the same directory as all your study subjects. Defaults to the setting of `subjects_dir`.      meta_data: dictionary, optional         A dictionary that should be merged into the return value `meta_data`. Defaults to the empty dictionary if omitted.      load_surface_files: boolean, optional         Whether to load mesh data. If set to `False`, the first return values `vert_coords` and `faces` will be `None`. Defaults to `True`.      load_morphometry_data: boolean, optional         Whether to load morphometry data. If set to `False`, the first return value `morphometry_data` will be `None`. Defaults to `True`.      custom_morphometry_files: dictionary, optional         Cutom filenames for the left and right hemispjere data files that should be loaded. A dictionary of strings with exactly the following two keys: `lh` and `rh`. The value strings must contain hardcoded file names or template strings for them. As always, the files will be loaded relative to the `surf/` directory of the respective subject. Example: `{'lh': 'lefthemi.nonstandard.mymeasure44.mgh', 'rh': 'righthemi.nonstandard.mymeasure44.mgh'}`.      Returns     -------     vert_coords: numpy array         A 2-dimensional array containing the vertices of the mesh(es) of the average subject. Each vertex entry contains 3 coordinates. Each coordinate describes a 3D position in a FreeSurfer surface file (e.g., 'lh.white'), as returned by the `nibabel` function `nibabel.freesurfer.io.read_geometry`.      faces: numpy array         A 2-dimensional array containing the 3-faces of the mesh(es) of the average subject. Each face entry contains 3 indices. Each index references the respective vertex in the `vert_coords` array.      morphometry_data: numpy array         A numpy array with as many entries as there are vertices in the average subject. If you load two hemispheres instead of one, the length doubles. You can get the start indices for data of the hemispheres in the returned `meta_data`, see `meta_data['lh.num_vertices']` and `meta_data['rh.num_vertices']`. You can be sure that the data for the left hemisphere will always come first (if both were loaded). Indices start at 0, of course. So if the left hemisphere has `n` vertices, the data for them are at indices `0..n-1`, and the data for the right hemisphere start at index `n`. In many cases, your average subject will have the same number of vertices for both hemispheres and you will know this number beforehand, so you may not have to worry about this at all.      meta_data: dictionary         A dictionary containing detailed information on all files that were loaded and used settings. The following keys are available (depending on the value of the `hemi` argument, you can replace ?h with 'lh' or 'rh' or both 'lh' and 'rh'):             - `?h.num_data_points` : the number of data points loaded.             - `?h.morphometry_file` : the value of the `?h_morphometry_data_file` argument (data file that was loaded)             - `?h.morphometry_file_format` : the value for `format` that was used             - `?h.num_vertices` : number of vertices in the loaded mesh             - `?h.num_faces` : number of faces in the loaded mesh             - `?lh.surf_file` : the mesh file that was loaded for this hemisphere             - `subject_id` : the subject id             - `subjects_dir` : the subjects dir that was used             - `surf` : the surf that was used, e.g., 'white'             - `measure` : the measure that was loaded as morphometry data, e.g., 'area'             - `space` : always the string 'common'. This means that the data loaded represent morphometry data that has been mapped to a common or average subject.             - `hemi` : the `hemi` value that was used             - `display_subject` : the name of the common or average subject. This is the subject the surface meshes originate from. Ususally 'fsaverage'.             - `display_surf` : the surface of the common subject that has been loaded. Something like 'pial', 'white', or 'inflated'.      Raises     ------     ValueError         If one of the parameters with a fixed set of values receives a value that is not allowed.      Examples     --------     Load area data for both hemispheres and white surface of subject1 in the directory defined by the environment variable SUBJECTS_DIR, mapped to fsaverage:      >>> import brainload as bl     >>> v, f, data, md = bl.subject_avg('subject1')     >>> print md['surf']     white      Here, we are a bit more picky and explicit about what we want to load:      >>> import os     >>> import brainload as bl     >>> user_home = os.getenv('HOME')     >>> subjects_dir = os.path.join(user_home, 'data', 'my_study_x')     >>> v, f, data, md = bl.subject_avg('subject1', hemi='lh', measure='curv', fwhm='15', display_surf='inflated', subjects_dir=subjects_dir)      Sometime we do not care for the mesh, e.g., we only want the morphometry data:      >>> import brainload as bl     >>> data, md = bl.subject_avg('subject1', hemi='rh', fwhm='15', load_surface_files=False)[2:4] # Retrieve the surface mesh on which to display the data. This is the average subject's surface. # Parse the subject's morphometry data, mapped to standard space by FreeSurfer's recon-all. Load native space morphometry data for a number of subjects.      Load native space group data, i.e., morphometry data for all subjects in a study.     The information given in the parameters `measure`, `surf`, and `hemi` are used to construct the file name that will be loaded by default. This function will NOT load the meshes.      Parameters     ----------     measure : string         The measure to load, e.g., 'area' or 'curv'. Data files for this measure have to exist for all subjects.      surf : string, optional         The brain surface where the data has been measured, e.g., 'white' or 'pial'. Defaults to 'white'. Will be added after the measure name unless left at default.      hemi : {'both', 'lh', 'rh'}, optional         The hemisphere that should be loaded. Defaults to 'both'.      subjects_dir: string, optional         A string representing the full path to a directory. Defaults to the environment variable SUBJECTS_DIR if omitted. If that is not set, used the current working directory instead. This is the directory from which the application was executed.      subjects_list: list of strings, optional (unless `subjects_detection_mode` is set to `list`)         A list of subject identifiers or directory names that should be loaded from the `subjects_dir`. Example list: `['subject1', 'subject2']`. Defaults to None. Only allowed if `subjects_detection_mode` is `auto` or `list`. In `auto` mode, this takes         precedence over all other options, i.e., if a `subjects_list` *and* the (default or custom) `subjects_file` are given, the `subjects_list` will be used.      Returns     -------     morphdata_by_subject: dictionary         A dictionary containing the morphometry data. Keys are subject identifiers, and values are the morphometry data numpy 1D arrays.      metadata_by_subject: dictionary         A dictionary containing detailed information on all subjects and files that were loaded. Each of its keys is a subject identifier. The data value is another dictionary that contains all meta data for this subject. Load standard space morphometry data for a number of subjects.      Load group data, i.e., morphometry data for all subjects in a study that has already been mapped to standard space and is ready for group analysis.     The information given in the parameters `measure`, `surf`, `hemi`, and `fwhm` are used to construct the file name that will be loaded by default. This function will NOT load the meshes.      Parameters     ----------     measure : string         The measure to load, e.g., 'area' or 'curv'. Data files for this measure have to exist for all subjects.      surf : string, optional         The brain surface where the data has been measured, e.g., 'white' or 'pial'. Defaults to 'white'.      hemi : {'both', 'lh', 'rh'}, optional         The hemisphere that should be loaded. Defaults to 'both'.      fwhm : string or None, optional         Which averaging version of the data should be loaded. FreeSurfer usually generates different standard space files with a number of smoothing settings. Defaults to '10'. If None is passed, the `.fwhmX` part is omitted from the file name completely. Set this to '0' to get the unsmoothed version.      subjects_dir: string, optional         A string representing the full path to a directory. Defaults to the environment variable SUBJECTS_DIR if omitted. If that is not set, used the current working directory instead. This is the directory from which the application was executed.      average_subject: string, optional         The name of the average subject to which the data was mapped. Defaults to 'fsaverage'.      group_meta_data: dictionary, optional         A dictionary that should be merged into the return value `group_meta_data`. Defaults to the empty dictionary if omitted.      subjects_list: list of strings, optional (unless `subjects_detection_mode` is set to `list`)         A list of subject identifiers or directory names that should be loaded from the `subjects_dir`. Example list: `['subject1', 'subject2']`. Defaults to None. Only allowed if `subjects_detection_mode` is `auto` or `list`. In `auto` mode, this takes         precedence over all other options, i.e., if a `subjects_list` *and* the (default or custom) `subjects_file` are given, the `subjects_list` will be used.      subjects_file_dir: string, optional         A string representing the full path to a directory. This directory must contain the `subjects_file` (see below). Defaults to the `subjects_dir`.      subjects_file: string, optional         The name of the subjects file, relative to the `subjects_file_dir`. Defaults to 'subjects.txt'. The file must be a simple text file that contains one `subject_id` per line. It can be a CSV file that has other data following, but the `subject_id` has to be the first item on each line and the separator must be a comma. So a line is allowed to look like this: `subject1, 35, center1, 147`. No header is allowed. If you have a different format, consider reading the file yourself and pass the result as `subjects_list` instead.      custom_morphometry_file_templates: dictionary, optional         Cutom filenames for the left and right hemisphere data files that should be loaded. A dictionary of strings with exactly the following two keys: `lh` and `rh`. The value strings can contain hardcoded file names or template strings for them. As always, the files will be loaded relative to the `surf/` directory of the respective subject. Example for hard-coded files: `{'lh': 'lefthemi.nonstandard.mymeasure44.mgh', 'rh': 'righthemi.nonstandard.mymeasure44.mgh'}`. The strings may contain any of the following variabes, which will be replaced by what you supplied to the other arguments of this function:             - `${MEASURE}` will be replaced with the value of `measure`.             - `${SURF}` will be replaced with the FreeSurfer file name part for the surface `surf`. This is the empty string if `surf` is 'white', and a dot followed by the value of `surf` for all other settings of surf. Examples: when `surf` is 'pial', this will be replaced with '.pial' (Note the dot!). If `surf` is 'white', this will be replaced with the empty string.             - `${SURF_RAW}` will be replaced with the value of `surf`.             - `${HEMI}` will be replaced with 'lh' for the left hemisphere, and with 'rh' for the right hemisphere.             - `${FWHM}` will be replaced with the value of `fwhm`, so something like '10'.             - `${SUBJECT_ID}` will be replaced by the id of the subject that is being loaded, e.g., 'subject3'.             - `${AVERAGE_SUBJECT}` will be replaced by the value of `average_subject`.              Note that only `${SURF}` and `${HEMI}` are usually needed, everything else can be hardcoded (or is not part of typical FreeSurfer file names at all, like `${SUBJECT_ID}`).             Example template string: `subj_${SUBJECT_ID}_hemi_${HEMI}.alsononstandard.mgh`. Complete example for template strings in dictionary: `{'lh': 'subj_${SUBJECT_ID}_hemi_${HEMI}.alsononstandard.mgh', 'rh': 'subj_${SUBJECT_ID}_hemi_${HEMI}.alsononstandard.mgh'}`.      subjects_detection_mode: {'auto', 'list', 'file', 'search_dir'}, optional         The method used to determine the subjects that should be loaded. Defaults to 'auto'. You can always see which mode was used by looking at the returned `run_meta_data`, see `run_meta_data['subjects_detection_mode']`.             - 'auto': In this mode, all available methods will be tried in the following order: If a `subjects_list` is given, it is used. Then, the `subjects_file` is used if it exists. Note that this may be the default file, '$SUBJECTS_DIR/subject_surf_dir.txt', or another if one has explicitely been defined by setting `subjects_file` and/or `subjects_file_dir`. If the file does not exist, the directory is searched for directories containing FreeSurfer data as defined in the section for 'search_dir' mode below. You can always see which method was used in auto mode by looking at the returned `run_meta_data`, see `run_meta_data['subjects_detection_mode_auto_used_method']`.              - 'list': In this mode, the given `subjects_list` is used, and you have to supply one. If not, an error is raised. You are not allowed to supply a `subjects_file` in this mode, or an error will be raised.              - 'file': In this mode, the subjects file is used. Note that this may be the default file, '$SUBJECTS_DIR/subjects.txt', or another if one has explicitely been defined by setting `subjects_file` and/or `subjects_file_dir`. If the file does not exist, an error is raised. You can see which file was used by looking at the returned `run_meta_data`, see `run_meta_data['subjects_file']`. You are not allowed to supply a `subjects_list` in this mode, or an error will be raised.              - 'search_dir': In this mode, the `subjects_dir` (default or explicitely given) is searched for sub directories which look as if they could contain FreeSurfer data. The latter means that they contain a sub directory named 'surf'. There is one exception though: if the name of one such directory equals the name of the `average_subject`, the directory is skipped. You are not allowed to supply a `subjects_list` in this mode, or an error will be raised.      Returns     -------     group_morphometry_data: numpy array         An array filled with the morphometry data for the subjects. The array has shape `(n, m)` where `n` is the number of subjects, and `m` is the number of vertices of the standard subject. (If you load both hemispheres instead of one, m doubles.) To get the subject id for the entries, look at the respective index in the returned `subjects_list`.      subjects_list: list of strings         A list containing the subject identifiers in the same order as the data in `group_morphometry_data`. (If `subjects_detection_mode` is 'list' or 'file', the order in these is guaranteed to be preserved. But in mode 'search_dir' or 'auto' which may have chosen to fall back to 'search_dir' as a last resort, this is helpful: You can use the index of a subject in this list to find its data in `group_morphometry_data`, as it will have the same index. See the examples below.)      group_meta_data: dictionary         A dictionary containing detailed information on all subjects and files that were loaded. Each of its keys is a subject identifier. The data value is another dictionary that contains all meta data for this subject as returned by the `subject_avg` function.      run_meta_data: dictionary         A dictionary containing general information on the settings used when executing the function and determining which subjects to load.      Raises     ------     ValueError         If one of the parameters with a fixed set of values receives a value that is not allowed.      Examples     --------     Load area data for all subjects in the directory defined by the environment variable SUBJECTS_DIR:      >>> import brainload as bl     >>> data, subjects, group_md, run_md = bl.group('area')      Here, we load curv data for the right hemisphere, computed on the pial surface with smooting of 20:      >>> data, subjects, group_md, run_md = bl.group('curv', hemi='rh', surf='pial', fwhm='20')      We may want to be a but more explicit on which subjects are loaded from where:      >>> import os     >>> import brainload as bl     >>> subjects_dir = os.path.join(os.getenv('HOME'), 'data', 'my_study_x')     >>> subjects_list = ['subject1', 'subject4', 'subject8']     >>> data, subjects, group_md, run_md = bl.group('curv', fwhm='20', subjects_dir=subjects_dir, subjects_list=subjects_list)      Continuing the last example, we may want to have a look at the curv value of the vertex at index 100000 of the subject 'subject4':      >>> subject4_idx = subjects.index('subject4')     >>> print data[subject4_idx][100000] # supplying a list is only valid in modes 'auto' and 'list' # just use the existing list # we are in modes 'auto' or 'file' # in file mode, the file has to exist. # we are still in modes 'auto' or 'file', and the file exists. # in auto mode, we prefer/use the subject file if it exists. If it does not exist, we try to guess the list from the directory later. # last chance in auto mode: try to detect subjects from the contents of the subjects dir. # In the next function call, we discard the first two return values (vert_coords and faces), as these are None anyways because we did not load surface files. Parse a talairach matrix from a talairach.xfm file.      Parse a talairach matrix from the mri/transforms/talairach.xfm file of a subject. Talairach space is a RAS space with the coordinate center at the Anterior Commisure. RAS (Right-Anterior-Superior) means X points to the right (from subjects point of view), Y points up out of the nose (subject is lying in scanner), and Z points out of the top of the head (so the axis is parallel to the floor). From the Freeurfer Wiki on coordinate systems: 'Note on Talairach: FreeSurfer does not report true "Talairach" coordinates. The coordinates listed unter "Talairach" are actually based on Matthew Brett's 10/8/98 non-linear transform from MNI305 space (see http://www.mrc-cbu.cam.ac.uk/Imaging/mnispace.html). FreeSurfer also reports "Talairach MNI" coordinates. These are MNI305 space.'      Parameters     ----------     file_name: str         Path to the file, usually SUBJECT/mri/transforms/talairach.xfm      Returns     -------     numpy 2D array         The matrix, a float array with shape (3, 4). Parse a 3x4 talairach matrix.      Parse a talairach matrix from the 3 lines representing it in the mri/transforms/talairach.xfm file of a subject.      Parameters     ----------     matrix_lines: list of str         The 3 matrix lines of a file in talairach.xfm format. Each line must contain 4 floats, separated by spaces. The last line may end with an ';', which will be removed by this function.      Returns     -------     2D numpy array of floats         The parsed matrix, with dimension (3, 4).