コード例 #1
0
def run_makespec_bothhemis(config, env):
    refdir = config['refdir']
    overwrite = config['overwrite']
    icolds, hemis = _get_hemis_icolds(config)

    if hemis != ['l', 'r']:
        raise ValueError("Cannot run without left and right hemisphere")

    for icold in icolds:
        specs = []
        for hemi in hemis:
            #surfprefix = '%s%sh' % (config['mi_icopat'] % icold, hemi)
            specfn = afni_suma_spec.canonical_filename(icold, hemi,
                                                       config['alsuffix'])
            specpathfn = os.path.join(refdir, specfn)
            specs.append(afni_suma_spec.read(specpathfn))

        specs = afni_suma_spec.hemi_pairs_add_views(specs,
                                                    'inflated',
                                                    refdir,
                                                    overwrite=overwrite)
        specs = afni_suma_spec.hemi_pairs_add_views(specs,
                                                    'sphere.reg',
                                                    refdir,
                                                    overwrite=overwrite)

        spec_both = afni_suma_spec.combine_left_right(specs)

        # generate spec files for both hemispheres
        hemiboth = 'b'
        specfn = afni_suma_spec.canonical_filename(icold, hemiboth,
                                                   config['alsuffix'])
        specpathfn = os.path.join(refdir, specfn)
        spec_both.write(specpathfn, overwrite=overwrite)

        # merge left and right into one surface
        # and generate the spec files as well
        hemimerged = 'm'
        specfn = afni_suma_spec.canonical_filename(icold, hemimerged,
                                                   config['alsuffix'])
        specpathfn = os.path.join(refdir, specfn)

        if config['overwrite'] or not os.path.exists(specpathfn):
            spec_merged, surfs_to_join = afni_suma_spec.merge_left_right(
                spec_both)
            spec_merged.write(specpathfn, overwrite=overwrite)

            full_path = lambda x: os.path.join(refdir, x)
            for fn_out, fns_in in surfs_to_join.iteritems():
                surfs_in = [surf_fs_asc.read(full_path(fn)) for fn in fns_in]
                surf_merged = surf.merge(*surfs_in)
                if config['overwrite'] or not os.path.exists(
                        full_path(fn_out)):
                    surf_fs_asc.write(surf_merged,
                                      full_path(fn_out),
                                      overwrite=overwrite)
                    print "Merged surfaces written to %s" % fn_out
コード例 #2
0
def run_makespec_bothhemis(config, env):
    refdir = config['refdir']
    overwrite = config['overwrite']
    icolds, hemis = _get_hemis_icolds(config)

    if hemis != ['l', 'r']:
        raise ValueError("Cannot run without left and right hemisphere")

    for icold in icolds:
        specs = []
        for hemi in hemis:
            #surfprefix = '%s%sh' % (config['mi_icopat'] % icold, hemi)
            specfn = afni_suma_spec.canonical_filename(icold, hemi,
                                                       config['alsuffix'])
            specpathfn = os.path.join(refdir, specfn)
            specs.append(afni_suma_spec.read(specpathfn))

        specs = afni_suma_spec.hemi_pairs_add_views(specs,
                            'inflated', refdir, overwrite=overwrite)
        specs = afni_suma_spec.hemi_pairs_add_views(specs,
                            'sphere.reg', refdir, overwrite=overwrite)


        spec_both = afni_suma_spec.combine_left_right(specs)


        # generate spec files for both hemispheres
        hemiboth = 'b'
        specfn = afni_suma_spec.canonical_filename(icold, hemiboth, config['alsuffix'])
        specpathfn = os.path.join(refdir, specfn)
        spec_both.write(specpathfn, overwrite=overwrite)

        # merge left and right into one surface
        # and generate the spec files as well
        hemimerged = 'm'
        specfn = afni_suma_spec.canonical_filename(icold, hemimerged, config['alsuffix'])
        specpathfn = os.path.join(refdir, specfn)

        if config['overwrite'] or not os.path.exists(specpathfn):
            spec_merged, surfs_to_join = afni_suma_spec.merge_left_right(spec_both)
            spec_merged.write(specpathfn, overwrite=overwrite)

            full_path = lambda x:os.path.join(refdir, x)
            for fn_out, fns_in in surfs_to_join.iteritems():
                surfs_in = [surf_fs_asc.read(full_path(fn)) for fn in fns_in]
                surf_merged = surf.merge(*surfs_in)
                if config['overwrite'] or not os.path.exists(full_path(fn_out)):
                    surf_fs_asc.write(surf_merged, full_path(fn_out),
                                                overwrite=overwrite)
                    print "Merged surfaces written to %s" % fn_out
コード例 #3
0
ファイル: lib_prep_afni_surf.py プロジェクト: neurosbh/PyMVPA
def run_makespec_bothhemis(config, env):
    refdir = config['refdir']
    overwrite = config['overwrite']
    icolds, hemis = _get_hemis_icolds(config)

    ext = format2extension(config)

    if hemis != ['l', 'r']:
        raise ValueError("Cannot run without left and right hemisphere")

    for icold in icolds:
        specs = []
        for hemi in hemis:
            #surfprefix = '%s%sh' % (config['mi_icopat'] % icold, hemi)
            specfn = afni_suma_spec.canonical_filename(icold, hemi,
                                                       config['alsuffix'])
            specpathfn = os.path.join(refdir, specfn)
            s = afni_suma_spec.read(specpathfn)

            specs.append(afni_suma_spec.read(specpathfn))

        add_states = ['inflated', 'full.patch.flat', 'sphere.reg']
        add_states_required = [True, False, True]  # flat surface is optional
        for add_state, is_req in zip(add_states, add_states_required):
            has_state = all([
                len(spec.find_surface_from_state(add_state)) == 1
                for spec in specs
            ])

            if not has_state:
                if is_req:
                    error('cannot find state %s' % add_state)
                else:
                    # skip this state
                    print "Optional state %s not found - skipping" % add_state
                    continue

            specs = afni_suma_spec.hemi_pairs_add_views(specs,
                                                        add_state,
                                                        ext,
                                                        refdir,
                                                        overwrite=overwrite)

        spec_both = afni_suma_spec.combine_left_right(specs)

        # generate spec files for both hemispheres
        hemiboth = 'b'
        specfn = afni_suma_spec.canonical_filename(icold, hemiboth,
                                                   config['alsuffix'])
        specpathfn = os.path.join(refdir, specfn)
        spec_both.write(specpathfn, overwrite=overwrite)

        # merge left and right into one surface
        # and generate the spec files as well
        hemimerged = 'm'
        specfn = afni_suma_spec.canonical_filename(icold, hemimerged,
                                                   config['alsuffix'])
        specpathfn = os.path.join(refdir, specfn)

        if config['overwrite'] or not os.path.exists(specpathfn):
            spec_merged, surfs_to_join = afni_suma_spec.merge_left_right(
                spec_both)
            spec_merged.write(specpathfn, overwrite=overwrite)

            full_path = lambda x: os.path.join(refdir, x)
            for fn_out, fns_in in surfs_to_join.iteritems():
                surfs_in = [surf.read(full_path(fn)) for fn in fns_in]

                if all(['full.patch.flat' in fn for fn in fns_in]):
                    # left hemi of flat; rotate 180 degrees, reposition again
                    surfs_in[0] = surfs_in[0] * [-1, -1, 1]
                    surfs_in = surf.reposition_hemisphere_pairs(
                        surfs_in[0], surfs_in[1], 'm')

                surf_merged = surf.merge(*surfs_in)

                if config['overwrite'] or not os.path.exists(
                        full_path(fn_out)):
                    surf.write(full_path(fn_out), surf_merged)
                    print "Merged surfaces written to %s" % fn_out
コード例 #4
0
def run_makespec_bothhemis(config, env):
    refdir = config['refdir']
    overwrite = config['overwrite']
    icolds, hemis = _get_hemis_icolds(config)

    ext = format2extension(config)

    if hemis != ['l', 'r']:
        raise ValueError("Cannot run without left and right hemisphere")

    for icold in icolds:
        specs = []
        for hemi in hemis:
            #surfprefix = '%s%sh' % (config['mi_icopat'] % icold, hemi)
            specfn = afni_suma_spec.canonical_filename(icold, hemi,
                                                       config['alsuffix'])
            specpathfn = pathjoin(refdir, specfn)
            s = afni_suma_spec.read(specpathfn)

            specs.append(afni_suma_spec.read(specpathfn))

        add_states = ['inflated', 'full.patch.flat', 'sphere.reg']
        add_states_required = [True, False, True] # flat surface is optional
        for add_state, is_req in zip(add_states, add_states_required):
            has_state = all([len(spec.find_surface_from_state(add_state)) == 1
                                    for spec in specs])

            if not has_state:
                if is_req:
                    error('cannot find state %s' % add_state)
                else:
                    # skip this state
                    print "Optional state %s not found - skipping" % add_state
                    continue

            specs = afni_suma_spec.hemi_pairs_add_views(specs,
                            add_state, ext, refdir, overwrite=overwrite)


        spec_both = afni_suma_spec.combine_left_right(specs)


        # generate spec files for both hemispheres
        hemiboth = 'b'
        specfn = afni_suma_spec.canonical_filename(icold, hemiboth, config['alsuffix'])
        specpathfn = pathjoin(refdir, specfn)
        spec_both.write(specpathfn, overwrite=overwrite)

        # merge left and right into one surface
        # and generate the spec files as well
        hemimerged = 'm'
        specfn = afni_suma_spec.canonical_filename(icold, hemimerged, config['alsuffix'])
        specpathfn = pathjoin(refdir, specfn)

        if config['overwrite'] or not os.path.exists(specpathfn):
            spec_merged, surfs_to_join = afni_suma_spec.merge_left_right(spec_both)
            spec_merged.write(specpathfn, overwrite=overwrite)

            full_path = lambda x:pathjoin(refdir, x)
            for fn_out, fns_in in surfs_to_join.iteritems():
                surfs_in = [surf.read(full_path(fn)) for fn in fns_in]

                if all(['full.patch.flat' in fn for fn in fns_in]):
                    # left hemi of flat; rotate 180 degrees, reposition again
                    surfs_in[0] = surfs_in[0] * [-1, -1, 1]
                    surfs_in = surf.reposition_hemisphere_pairs(surfs_in[0], surfs_in[1], 'm')

                surf_merged = surf.merge(*surfs_in)

                if config['overwrite'] or not os.path.exists(full_path(fn_out)):
                    surf.write(full_path(fn_out), surf_merged)
                    print "Merged surfaces written to %s" % fn_out