How to use the clinica.utils.atlas.AtlasAbstract function in clinica

    @staticmethod
    def get_atlas_map():
        import os
        FSLDIR = os.environ.get('FSLDIR', '')
        if not FSLDIR:
            raise Exception('FSLDIR variable from FSL software is not set')
        return os.path.join(FSLDIR, 'data', 'atlases', 'JHU', 'JHU-ICBM-FA-1mm.nii.gz')

    @staticmethod
    def get_tsv_roi():
        from os.path import join, split, realpath
        return join(split(realpath(__file__))[0], '../resources/atlases', 'JHUTract_FS_LUT_newformat.txt')


class JHUTracts252mm(AtlasAbstract):
    def __init__(self):
        AtlasAbstract.__init__(self)

    @staticmethod
    def get_name_atlas(): return "JHUTracts25"

    @staticmethod
    def get_atlas_labels():
        import os
        FSLDIR = os.environ.get('FSLDIR', '')
        if not FSLDIR:
            raise Exception('FSLDIR variable from FSL software is not set')
        return os.path.join(FSLDIR, 'data', 'atlases', 'JHU', 'JHU-ICBM-tracts-maxprob-thr25-2mm.nii.gz')

    @staticmethod
    def get_atlas_map():

if not os.path.exists(os.path.join(SPM_HOME, 'toolbox', 'cat12')):
            raise Exception('CAT12 not included in SPM_HOME/toolbox')
        return os.path.join(SPM_HOME, 'toolbox', 'cat12', 'templates_1.50mm', 'hammers.nii')

    @staticmethod
    def get_atlas_map():
        from os.path import join, split, realpath
        return join(split(realpath(__file__))[0], '../resources/atlases_spm', 'Template_MNI152.nii')

    @staticmethod
    def get_tsv_roi():
        from os.path import join, split, realpath
        return join(split(realpath(__file__))[0], '../resources/atlases_spm', 'lut_Hammers_newformat.txt')


class LPBA40(AtlasAbstract):
    def __init__(self):
        AtlasAbstract.__init__(self)

    @staticmethod
    def get_name_atlas(): return "LPBA40"

    @staticmethod
    def get_atlas_labels():
        import os
        import platform
        if "SPM_HOME" not in os.environ:
            raise Exception('SPM_HOME variable from SPM software is not set')
        else:
            if "SPMSTANDALONE_HOME" in os.environ:
                if platform.system() == 'Darwin':
                    SPM_HOME = os.environ['SPMSTANDALONE_HOME'] + "/spm12.app/Contents/MacOS/spm12_mcr"

def get_atlas_labels():
        from os.path import join, split, realpath
        return join(split(realpath(__file__))[0], '../resources/atlases_spm', 'AAL2.nii')

    @staticmethod
    def get_atlas_map():
        from os.path import join, split, realpath
        return join(split(realpath(__file__))[0], '../resources/atlases_spm', 'Template_MNI152.nii')

    @staticmethod
    def get_tsv_roi():
        from os.path import join, split, realpath
        return join(split(realpath(__file__))[0], '../resources/atlases_spm', 'lut_AAL2_newformat.txt')


class Hammers(AtlasAbstract):
    def __init__(self):
        AtlasAbstract.__init__(self)

    @staticmethod
    def get_name_atlas(): return "Hammers"

    @staticmethod
    def get_atlas_labels():
        import os
        import platform
        if "SPM_HOME" not in os.environ:
            raise Exception('SPM_HOME variable from SPM software is not set')
        else:
            if "SPMSTANDALONE_HOME" in os.environ:
                if platform.system() == 'Darwin':
                    SPM_HOME = os.environ['SPMSTANDALONE_HOME'] + "/spm12.app/Contents/MacOS/spm12_mcr"

    @staticmethod
    def get_atlas_map():
        import os
        FSLDIR = os.environ.get('FSLDIR', '')
        if not FSLDIR:
            raise Exception('FSLDIR variable from FSL software is not set')
        return os.path.join(FSLDIR, 'data', 'atlases', 'JHU', 'JHU-ICBM-FA-2mm.nii.gz')

    @staticmethod
    def get_tsv_roi():
        from os.path import join, split, realpath
        return join(split(realpath(__file__))[0], '../resources/atlases', 'JHUTract_FS_LUT_newformat.txt')


class JHUTracts501mm(AtlasAbstract):
    def __init__(self):
        AtlasAbstract.__init__(self)

    @staticmethod
    def get_name_atlas(): return "JHUTracts50"

    @staticmethod
    def get_atlas_labels():
        import os
        FSLDIR = os.environ.get('FSLDIR', '')
        if not FSLDIR:
            raise Exception('FSLDIR variable from FSL software is not set')
        return os.path.join(FSLDIR, 'data', 'atlases', 'JHU', 'JHU-ICBM-tracts-maxprob-thr50-1mm.nii.gz')

    @staticmethod
    def get_atlas_map():

    @staticmethod
    def get_atlas_map():
        import os
        FSLDIR = os.environ.get('FSLDIR', '')
        if not FSLDIR:
            raise Exception('FSLDIR variable from FSL software is not set')
        return os.path.join(FSLDIR, 'data', 'atlases', 'JHU', 'JHU-ICBM-FA-2mm.nii.gz')

    @staticmethod
    def get_tsv_roi():
        from os.path import join, split, realpath
        return join(split(realpath(__file__))[0], '../resources/atlases', 'JHUTract_FS_LUT_newformat.txt')


class AAL2(AtlasAbstract):
    def __init__(self):
        AtlasAbstract.__init__(self)

    @staticmethod
    def get_name_atlas(): return "AAL2"

    @staticmethod
    def get_atlas_labels():
        from os.path import join, split, realpath
        return join(split(realpath(__file__))[0], '../resources/atlases_spm', 'AAL2.nii')

    @staticmethod
    def get_atlas_map():
        from os.path import join, split, realpath
        return join(split(realpath(__file__))[0], '../resources/atlases_spm', 'Template_MNI152.nii')

in_atlas (:obj: AbstractClass): An atlas with a set of ROI. These ROI
            are used to compute statistics.
        out_file (Optional[str]): Name of the output file.

    Returns:
        out_file (str): TSV file containing the statistics (content of the
            columns: label, mean scalar, std of the scalar', number of voxels).
    """
    from clinica.utils.atlas import AtlasAbstract
    import nibabel as nib
    import numpy as np
    import pandas
    import os.path as op
    from clinica.utils.stream import cprint

    if not isinstance(in_atlas, AtlasAbstract):
        raise Exception("Atlas element must be an AtlasAbstract type")

    if out_file is None:
        fname, ext = op.splitext(op.basename(in_normalized_map))
        if ext == ".gz":
            fname, ext2 = op.splitext(fname)
            ext = ext2 + ext
        out_file = op.abspath("%s_statistics_%s.tsv"
                              % (fname, in_atlas.get_name_atlas()))

    atlas_labels = nib.load(in_atlas.get_atlas_labels())
    atlas_labels_data = atlas_labels.get_data()

    img = nib.load(in_normalized_map)
    img_data = img.get_data()

"""
        pass

    def get_index(self):
        import nibabel as nib
        import numpy as np
        img_labels = nib.load(self.get_atlas_labels())
        img_labels = img_labels.get_data()
        labels = list(set(img_labels.ravel()))
        index_vector = np.zeros(len(labels))
        for index, n in enumerate(labels):
            index_vector[index] = index
        return index_vector


class JHUDTI812mm(AtlasAbstract):
    def __init__(self):
        AtlasAbstract.__init__(self)

    @staticmethod
    def get_name_atlas(): return "JHUDTI81"

    @staticmethod
    def get_atlas_labels():
        import os
        FSLDIR = os.environ.get('FSLDIR', '')
        if not FSLDIR:
            raise Exception('FSLDIR variable from FSL software is not set')
        return os.path.join(FSLDIR, 'data', 'atlases', 'JHU', 'JHU-ICBM-labels-2mm.nii.gz')

    @staticmethod
    def get_atlas_map():

out_md_statistics (str): Statistics of the MD-map on .
        out_ad_statistics (str): Statistics of the AD-map on .
        out_rd_statistics (str): Statistics of the RD-map on .
    """
    import tempfile
    import os
    import nipype.interfaces.io as nio
    import nipype.interfaces.utility as niu
    import nipype.pipeline.engine as pe
    from clinica.utils.atlas import AtlasAbstract
    from clinica.utils.mri_registration import ants_registration_syn_quick
    from clinica.utils.mri_registration import apply_ants_registration_syn_quick_transformation
    from clinica.utils.statistics import statistics_on_atlas


    if not isinstance(atlas, AtlasAbstract):
        raise Exception("Atlas element must be an AtlasAbstract type")

    if working_directory is None:
        working_directory = tempfile.mkdtemp()

    inputnode = pe.Node(niu.IdentityInterface(
        fields=['in_fa', 'in_md', 'in_ad', 'in_rd', 'in_atlas_scalar_image', 'in_atlas_labels']),
        name='inputnode')
    inputnode.inputs.in_atlas_scalar_image=atlas.get_atlas_map()
    inputnode.inputs.in_atlas_labels=atlas.get_atlas_labels()

    ants_registration = pe.Node(interface=niu.Function(
        input_names=['fixe_image', 'moving_image', 'prefix_output'],
        output_names=['image_warped', 'affine_matrix', 'warp', 'inverse_warped', 'inverse_warp'],
        function=ants_registration_syn_quick), name='ants_registration')

def __init__(self):
        AtlasAbstract.__init__(self)

def add_atlas(self, atlas):
        if not isinstance(atlas, AtlasAbstract):
            raise Exception("Atlas element must be an AtlasAbstract type")