Example #1
0
def load_connections_file():
    d, vertices, vertices_lookup = None, None, None
    conn_file_name = bpy.context.scene.connectivity_files.replace(' ', '_')
    connectivity_file = op.join(mu.get_user_fol(), 'connectivity', '{}.npz'.format(conn_file_name))
    vertices_file = op.join(mu.get_user_fol(), 'connectivity', '{}_vertices.pkl'.format(
        conn_file_name.replace('_static', '')))
    if op.isfile(connectivity_file):
        print('loading connectivity: {}'.format(connectivity_file))
        d = mu.Bag(np.load(connectivity_file))
        d.labels = [l.astype(str) for l in d.labels]
        d.hemis = [l.astype(str) for l in d.hemis]
        d.con_names = np.array([l.astype(str) for l in d.con_names], dtype=np.str)
        d.conditions = [l.astype(str) for l in d.conditions]
        if d.con_values.ndim == 2:
            d.con_values = d.con_values[:, :, np.newaxis]
        conditions_items = [(cond, cond, '', cond_ind) for cond_ind, cond in enumerate(d.conditions)]
        if len(d.conditions) > 1:
            diff_cond = '{}-{} difference'.format(d.conditions[0], d.conditions[1])
            conditions_items.append((diff_cond, diff_cond, '', len(d.conditions)))
        bpy.types.Scene.conditions = bpy.props.EnumProperty(items=conditions_items, description="Conditions")
        # bpy.context.scene.connections_max, bpy.context.scene.connections_min = d['data_max'], d['data_min']
    else:
        print('No connections file! {}'.format(connectivity_file))
    if op.isfile(vertices_file):
        vertices, vertices_lookup = mu.load(vertices_file)
    else:
        name_parts = mu.namebase(vertices_file).split('_')
        vertices_files = glob.glob(
            op.join(mu.get_parent_fol(vertices_file), '{}*_{}.pkl'.format(name_parts[0], name_parts[-1])))
        if len(vertices_files) == 1:
            vertices, vertices_lookup = mu.load(vertices_files[0])
        else:
            print('No vertices file! ({})'.format(vertices_file))
    ConnectionsPanel.d, ConnectionsPanel.vertices, ConnectionsPanel.vertices_lookup = d, vertices, vertices_lookup
Example #2
0
def init_electrodes_labeling(addon):
    #todo: this panel should work also without labeling file
    labeling_fname = '{}_{}_electrodes_cigar_r_*_l_*{}*.pkl'.format(
        mu.get_user(), bpy.context.scene.atlas,
        '_bipolar' if bpy.context.scene.bipolar else '')
    labling_files = glob.glob(
        op.join(mu.get_user_fol(), 'electrodes', labeling_fname))
    if not bpy.context.scene.bipolar:
        labling_files = [
            fname for fname in labling_files if 'bipolar' not in fname
        ]
    if len(labling_files) == 0:
        print("!!! Can't find any electrodes labeling file in {} !!!".format(
            op.join(mu.get_user_fol(), 'electrodes', labeling_fname)))
    else:
        files_names = [
            mu.namebase(fname) for fname in labling_files if mu.load(fname)
        ]
        labeling_items = [(c, c, '', ind) for ind, c in enumerate(files_names)]
        bpy.types.Scene.electrodes_labeling_files = bpy.props.EnumProperty(
            items=labeling_items,
            description='Labeling files',
            update=electrodes_labeling_files_update)
        bpy.context.scene.electrodes_labeling_files = files_names[0]
        # ElecsPanel.electrodes_locs = mu.load(labling_files[0])
        # ElecsPanel.lookup = create_lookup_table(ElecsPanel.electrodes_locs, ElecsPanel.electrodes)
    ElecsPanel.faces_verts = addon.get_faces_verts()
Example #3
0
def init_electrodes_labeling(addon):
    ela_code_fol = op.join(mu.get_parent_fol(mu.get_mmvt_code_root()),
                           'electrodes_rois')
    ElecsPanel.ela_code_exist = op.isfile(
        op.join(ela_code_fol, 'find_rois', 'find_rois.py'))
    ElecsPanel.labling_files = labling_files = find_elecrode_labeling_files()
    if len(labling_files) > 0:
        files_names = [
            mu.namebase(fname) for fname in labling_files if mu.load(fname)
        ]
        labeling_items = [(c, c, '', ind) for ind, c in enumerate(files_names)]
        bpy.types.Scene.electrodes_labeling_files = bpy.props.EnumProperty(
            items=labeling_items,
            description='Labeling files',
            update=electrodes_labeling_files_update)
        bpy.context.scene.electrodes_labeling_files = files_names[0]
        # ElecsPanel.electrodes_locs = mu.load(labling_files[0])
        # ElecsPanel.lookup = create_lookup_table(ElecsPanel.electrodes_locs, ElecsPanel.electrodes)
    ElecsPanel.faces_verts = addon.get_faces_verts()

    atlases = mu.get_annot_files()
    if len(atlases) > 0:
        ElecsPanel.atlases_exist = True
        atlases_items = [(c, c, '', ind) for ind, c in enumerate(atlases)]
        bpy.types.Scene.ela_atlas = bpy.props.EnumProperty(
            items=atlases_items, description='atlases')
        bpy.context.scene.ela_atlas = atlases[0]
    bpy.context.scene.ela_bipolar = bpy.context.scene.bipolar
    return len(labling_files) > 0
Example #4
0
def load_camera(camera_fname=''):
    if camera_fname == '':
        camera_fname = op.join(mu.get_user_fol(), 'camera',
                               '{}.pkl'.format(bpy.context.scene.camera_files))
    if op.isfile(camera_fname):
        camera_name = mu.namebase(camera_fname)
        for hemi in mu.HEMIS:
            if hemi in camera_name:
                _addon().show_hide_hemi(False, hemi)
                _addon().show_hide_hemi(True, mu.other_hemi(hemi))
        X_rotation, Y_rotation, Z_rotation, X_location, Y_location, Z_location = mu.load(
            camera_fname)
        RenderFigure.update_camera = False
        bpy.context.scene.X_rotation = X_rotation
        bpy.context.scene.Y_rotation = Y_rotation
        bpy.context.scene.Z_rotation = Z_rotation
        bpy.context.scene.X_location = X_location
        bpy.context.scene.Y_location = Y_location
        bpy.context.scene.Z_location = Z_location
        # print('Camera loaded: rotation: {},{},{} locatioin: {},{},{}'.format(
        #     X_rotation, Y_rotation, Z_rotation, X_location, Y_location, Z_location))
        # print('Camera loaded: {}'.format(camera_fname))
        RenderFigure.update_camera = True
        update_camera()
    else:
        pass
Example #5
0
def _electrodes_labeling_files_update():
    labeling_fname = op.join(
        mu.get_user_fol(), 'electrodes',
        '{}.pkl'.format(bpy.context.scene.electrodes_labeling_files))
    ElecsPanel.electrodes_locs = mu.load(labeling_fname)
    ElecsPanel.lookup = create_lookup_table(ElecsPanel.electrodes_locs,
                                            ElecsPanel.all_electrodes)
Example #6
0
def electrodes_labeling_files_update(self, context):
    # if ElecsPanel.init:
    # todo: How to get the other file names?
    # list(bpy.types.Scene.electrodes_labeling_files[1].items())[3][1]
    labeling_fname = op.join(mu.get_user_fol(), 'electrodes', '{}.pkl'.format(
        bpy.context.scene.electrodes_labeling_files))
    ElecsPanel.electrodes_locs = mu.load(labeling_fname)
    ElecsPanel.lookup = create_lookup_table(ElecsPanel.electrodes_locs, ElecsPanel.all_electrodes)
Example #7
0
def load_clusters_file(clusters_name=''):
    if clusters_name == '':
        clusters_name = bpy.context.scene.meg_clusters_labels_files
    fname = MEGPanel.clusters_labels_fnames[clusters_name]
    c = mu.Bag(mu.load(fname))
    for ind in range(len(c.values)):
        c.values[ind] = mu.Bag(c.values[ind])
    return c
Example #8
0
def init(addon):
    user_fol = mu.get_user_fol()
    # clusters_labels_files = glob.glob(op.join(user_fol, 'fmri', 'clusters_labels_*.pkl'))
    # old code was saving those files as npy instead of pkl
    # clusters_labels_files.extend(glob.glob(op.join(user_fol, 'fmri', 'clusters_labels_*.npy')))
    # fmri_blobs = glob.glob(op.join(user_fol, 'fmri', 'blobs_*_rh.npy'))
    fMRIPanel.addon = addon
    fMRIPanel.lookup, fMRIPanel.clusters_labels = {}, {}
    fMRIPanel.cluster_labels = {}
    files_names, clusters_labels_files, clusters_labels_items = get_clusters_files(
        user_fol)
    fMRIPanel.fMRI_clusters_files_exist = len(
        files_names) > 0  # and len(fmri_blobs) > 0
    if not fMRIPanel.fMRI_clusters_files_exist:
        register()
        fMRIPanel.init = True
        return
    # files_names = [mu.namebase(fname)[len('clusters_labels_'):] for fname in clusters_labels_files]
    fMRIPanel.clusters_labels_file_names = files_names
    bpy.types.Scene.fmri_clusters_labels_files = bpy.props.EnumProperty(
        items=clusters_labels_items,
        description="fMRI files",
        update=fmri_clusters_labels_files_update)
    bpy.context.scene.fmri_clusters_labels_files = files_names[0]
    bpy.context.scene.plot_fmri_cluster_contours = False

    for file_name, clusters_labels_file in zip(files_names,
                                               clusters_labels_files):
        # Check if the constrast files exist
        if all(
            [get_contrast_fname(file_name, hemi) != '' for hemi in mu.HEMIS]):
            key = file_name
            fMRIPanel.clusters_labels[key] = c = mu.Bag(
                mu.load(clusters_labels_file))
            for ind in range(len(c.values)):
                c.values[ind] = mu.Bag(c.values[ind])

            fMRIPanel.lookup[key] = create_lookup_table(
                fMRIPanel.clusters_labels[key])

    # bpy.context.scene.fmri_cluster_val_threshold = 2
    # bpy.context.scene.fmri_cluster_size_threshold = 20
    bpy.context.scene.search_closest_cluster_only_in_filtered = True
    bpy.context.scene.fmri_what_to_plot = 'blob'
    bpy.context.scene.fmri_how_to_sort = 'tval'
    bpy.context.scene.plot_current_cluster = True

    update_clusters()
    fMRIPanel.blobs_activity, _ = calc_blobs_activity(
        fMRIPanel.constrast, fMRIPanel.clusters_labels_filtered,
        fMRIPanel.colors_in_hemis)
    bpy.context.scene.plot_fmri_cluster_per_click = False
    fMRIPanel.dont_show_clusters_info = True
    # addon.clear_cortex()
    register()
    fMRIPanel.init = True
Example #9
0
def init(addon):
    import shutil
    ElecsPanel.addon = addon
    ElecsPanel.parent = bpy.data.objects.get('Deep_electrodes')
    if ElecsPanel.parent is None or len(ElecsPanel.parent.children) == 0:
        print("Can't register electrodes panel, no Deep_electrodes object")
        return
    mu.make_dir(op.join(mu.get_user_fol(), 'electrodes'))
    sorted_groups_fname = op.join(mu.get_user_fol(), 'electrodes',
                                  'sorted_groups.pkl')
    if not op.isfile(sorted_groups_fname):
        # Try to get the file from the subject's root folder
        if op.isfile(op.join(mu.get_user_fol(), 'sorted_groups.pkl')):
            shutil.move(op.join(mu.get_user_fol(), 'sorted_groups.pkl'),
                        sorted_groups_fname)
        else:
            print("Can't register electrodes panel, no sorted groups file")
            return
    # show_hide_electrodes(True)
    ElecsPanel.sorted_groups = mu.load(sorted_groups_fname)
    ElecsPanel.groups_hemi = create_groups_hemi_lookup(
        ElecsPanel.sorted_groups)
    ElecsPanel.all_electrodes = [el.name for el in ElecsPanel.parent.children]
    ElecsPanel.groups = create_groups_lookup_table(ElecsPanel.all_electrodes)
    ElecsPanel.groups_first_electrode = find_first_electrode_per_group(
        ElecsPanel.all_electrodes)
    ElecsPanel.groups_electrodes = create_groups_electrodes_lookup(
        ElecsPanel.all_electrodes)
    init_leads_list()
    init_electrodes_list()
    ret = init_electrodes_labeling(addon)
    if not ret:
        print('No electrodes labeling files.')
        return
    # addon.clear_colors_from_parent_childrens('Deep_electrodes')
    # addon.clear_cortex()
    bpy.context.scene.show_only_lead = False
    bpy.context.scene.listen_to_keyboard = False
    bpy.context.scene.listener_is_running = False
    bpy.context.scene.show_lh_electrodes = True
    bpy.context.scene.show_rh_electrodes = True
    _electrodes_labeling_files_update()
    if not ElecsPanel.electrodes_locs or not ElecsPanel.lookup:
        if not ElecsPanel.electrodes_locs:
            print(
                "!!! Can't find electrodes labeling files in user/electrdes!")
        if not ElecsPanel.lookup:
            print('No electrodes lookup table!')
        print("!!! Can't plot electrodes' probabilties !!!")
    if not ElecsPanel.groups or not ElecsPanel.groups_first_electrode or not ElecsPanel.sorted_groups or \
        not ElecsPanel.groups_hemi or not ElecsPanel.groups_electrodes:
        print('Error in electrodes panel init!')
    else:
        register()
        ElecsPanel.init = True
Example #10
0
def init(addon):
    from random import shuffle
    ColoringMakerPanel.addon = addon
    user_fol = mu.get_user_fol()
    ColoringMakerPanel.faces_verts = None
    labels_vertices_fname = op.join(user_fol, 'labels_vertices_{}.pkl'.format(bpy.context.scene.atlas))
    if not op.isfile(labels_vertices_fname):
        print("!!! Can't find {}!".format('labels_vertices_{}.pkl'.format(bpy.context.scene.atlas)))
        return None
    labels_names, labels_vertices = mu.load(labels_vertices_fname)
    ColoringMakerPanel.labels_vertices = dict(labels_names=labels_names, labels_vertices=labels_vertices)
    fmri_files = glob.glob(op.join(user_fol, 'fmri', 'fmri_*_lh.npy'))
    if len(fmri_files) > 0:
        files_names = [mu.namebase(fname)[5:-3] for fname in fmri_files]
        clusters_items = [(c, c, '', ind) for ind, c in enumerate(files_names)]
        bpy.types.Scene.fmri_files = bpy.props.EnumProperty(
            items=clusters_items, description="fMRI files", update=fmri_files_update)
        bpy.context.scene.fmri_files = files_names[0]
        for hemi in mu.HEMIS:
            ColoringMakerPanel.fMRI[hemi] = np.load('{}_{}.npy'.format(fmri_files[0][:-7], hemi))

    electrodes_source_files = glob.glob(op.join(user_fol, 'electrodes', '*_labels_*-rh.npz'))
    if len(electrodes_source_files) > 0:
        files_names = [mu.namebase(fname)[:-len('-rh')] for fname in electrodes_source_files]
        items = [(c, c, '', ind) for ind, c in enumerate(files_names)]
        bpy.types.Scene.electrodes_sources_files = bpy.props.EnumProperty(
            items=items, description="electrodes sources", update=electrodes_sources_files_update)
        bpy.context.scene.electrodes_sources_files = files_names[0]

    mu.make_dir(op.join(user_fol, 'coloring'))
    manually_color_files = glob.glob(op.join(user_fol, 'coloring', '*.csv'))
    if len(manually_color_files) > 0:
        files_names = [mu.namebase(fname) for fname in manually_color_files]
        coloring_items = [(c, c, '', ind) for ind, c in enumerate(files_names)]
        bpy.types.Scene.coloring_files = bpy.props.EnumProperty(items=coloring_items, description="Coloring files")
        bpy.context.scene.coloring_files = files_names[0]
    vol_color_files = glob.glob(op.join(user_fol, 'coloring', 'volumetric', '*.csv'))
    if len(vol_color_files) > 0:
        files_names = [mu.namebase(fname) for fname in vol_color_files]
        coloring_items = [(c, c, '', ind) for ind, c in enumerate(files_names)]
        bpy.types.Scene.vol_coloring_files = bpy.props.EnumProperty(
            items=coloring_items, description="Volumetric Coloring files")
        bpy.context.scene.vol_coloring_files = files_names[0]

    ColoringMakerPanel.colors = list(set(list(cu.NAMES_TO_HEX.keys())) - set(['black']))
    shuffle(ColoringMakerPanel.colors)
    ColoringMakerPanel.labels_groups = read_groups_labels(ColoringMakerPanel.colors)
    if len(ColoringMakerPanel.labels_groups) > 0:
        groups_items = [(gr, gr, '', ind) for ind, gr in enumerate(list(ColoringMakerPanel.labels_groups.keys()))]
        bpy.types.Scene.labels_groups = bpy.props.EnumProperty(
            items=groups_items, description="Groups")

    ColoringMakerPanel.faces_verts = load_faces_verts()
    register()
Example #11
0
def electrodes_labeling_files_update(self, context):
    # if ElecsPanel.init:
    # todo: How to get the other file names?
    # list(bpy.types.Scene.electrodes_labeling_files[1].items())[3][1]
    if ElecsPanel.init:
        labeling_fname = op.join(
            mu.get_user_fol(), 'electrodes',
            '{}.pkl'.format(bpy.context.scene.electrodes_labeling_files))
        ElecsPanel.electrodes_locs = mu.load(labeling_fname)
        ElecsPanel.lookup = create_lookup_table(ElecsPanel.electrodes_locs,
                                                ElecsPanel.all_electrodes)
Example #12
0
def init_sorted_groups():
    import shutil
    sorted_groups_fname = op.join(mu.get_user_fol(), 'electrodes', 'sorted_groups.pkl')
    if not op.isfile(sorted_groups_fname):
        # Try to get the file from the subject's root folder
        if op.isfile(op.join(mu.get_user_fol(), 'sorted_groups.pkl')):
            shutil.move(op.join(mu.get_user_fol(), 'sorted_groups.pkl'), sorted_groups_fname)
        else:
            print("electrodes_panel: no sorted groups file")
            # return
    if op.isfile(sorted_groups_fname):
        ElecsPanel.sorted_groups = mu.load(sorted_groups_fname)
Example #13
0
def fmri_files_update(self, context):
    #todo: there are two frmi files list (the other one in fMRI panel)
    user_fol = mu.get_user_fol()
    for hemi in mu.HEMIS:
        fname = op.join(user_fol, 'fmri', 'fmri_{}_{}.npy'.format(bpy.context.scene.fmri_files, hemi))
        ColoringMakerPanel.fMRI[hemi] = np.load(fname)
    fmri_data_maxmin_fname = op.join(mu.get_user_fol(), 'fmri', 'fmri_activity_map_minmax_{}.pkl'.format(
        bpy.context.scene.fmri_files))
    if op.isfile(fmri_data_maxmin_fname):
        data_min, data_max = mu.load(fmri_data_maxmin_fname)
        ColoringMakerPanel.fmri_activity_colors_ratio = 256 / (data_max - data_min)
        ColoringMakerPanel.fmri_activity_data_min = data_min
        ColoringMakerPanel.fmri_activity_data_max = data_max
Example #14
0
def plot_pathway(self, context, layers_dti, pathway_name, pathway_type):
    if pathway_type == TRACULA:
        pkl_fname = op.join(SUBJECT_DTI_FOL, TRACULA, '{}{}.pkl'.format(pathway_name, TRACULA_POSTFIX))
        mu.create_empty_if_doesnt_exists(pathway_name, DTIPanel.addon.CONNECTIONS_LAYER, None, PARENT_OBJ)
        parent_obj = bpy.data.objects[pathway_name]
        tracks = mu.load(pkl_fname)
        N = len(tracks)
        now = time.time()
        for ind, track in enumerate(tracks[:1000]):
            mu.time_to_go(now, ind, N, 100)
            track = track * 0.1
            # pprint(track)
            cur_obj = mu.create_spline(track, layers_dti, bevel_depth=0.01)
            # cur_obj.scale = [0.1] * 3
            cur_obj.name = '{}_{}'.format(pathway_name, ind)
            cur_obj.parent = parent_obj
Example #15
0
def load_camera(camera_fname=''):
    if camera_fname == '':
        camera_fname = op.join(bpy.path.abspath(bpy.context.scene.output_path), 'camera.pkl')
    if op.isfile(camera_fname):
        X_rotation, Y_rotation, Z_rotation, X_location, Y_location, Z_location = mu.load(camera_fname)
        RenderFigure.update_camera = False
        bpy.context.scene.X_rotation = X_rotation
        bpy.context.scene.Y_rotation = Y_rotation
        bpy.context.scene.Z_rotation = Z_rotation
        bpy.context.scene.X_location = X_location
        bpy.context.scene.Y_location = Y_location
        bpy.context.scene.Z_location = Z_location
        RenderFigure.update_camera = True
        update_camera()
    else:
        print('No camera file was found in {}!'.format(camera_fname))
Example #16
0
def init_electrodes_labeling(addon):
    #todo: this panel should work also without labeling file
    labling_files = find_elecrode_labeling_files()
    if len(labling_files) > 0:
        files_names = [
            mu.namebase(fname) for fname in labling_files if mu.load(fname)
        ]
        labeling_items = [(c, c, '', ind) for ind, c in enumerate(files_names)]
        bpy.types.Scene.electrodes_labeling_files = bpy.props.EnumProperty(
            items=labeling_items,
            description='Labeling files',
            update=electrodes_labeling_files_update)
        bpy.context.scene.electrodes_labeling_files = files_names[0]
        # ElecsPanel.electrodes_locs = mu.load(labling_files[0])
        # ElecsPanel.lookup = create_lookup_table(ElecsPanel.electrodes_locs, ElecsPanel.electrodes)
    ElecsPanel.faces_verts = addon.get_faces_verts()
    return len(labling_files) > 0
Example #17
0
def init(addon):
    import shutil
    ElecsPanel.addon = addon
    ElecsPanel.parent = bpy.data.objects.get('Deep_electrodes')
    if ElecsPanel.parent is None or len(ElecsPanel.parent.children) == 0:
        print("!!!! Can't register electrodes panel, no Deep_electrodes object!!!!")
        return
    mu.make_dir(op.join(mu.get_user_fol(), 'electrodes'))
    sorted_groups_fname = op.join(mu.get_user_fol(), 'electrodes', 'sorted_groups.pkl')
    if not op.isfile(sorted_groups_fname):
        # Try to get the file from the subject's root folder
        if op.isfile(op.join(mu.get_user_fol(), 'sorted_groups.pkl')):
            shutil.move(op.join(mu.get_user_fol(), 'sorted_groups.pkl'), sorted_groups_fname)
        else:
            print("!!!! Can't register electrodes panel, no sorted groups file!!!!")
            return
    ElecsPanel.sorted_groups = mu.load(sorted_groups_fname)
    ElecsPanel.groups_hemi = create_groups_hemi_lookup(ElecsPanel.sorted_groups)
    ElecsPanel.all_electrodes = [el.name for el in ElecsPanel.parent.children]
    ElecsPanel.groups = create_groups_lookup_table(ElecsPanel.all_electrodes)
    ElecsPanel.groups_first_electrode = find_first_electrode_per_group(ElecsPanel.all_electrodes)
    ElecsPanel.groups_electrodes = create_groups_electrodes_lookup(ElecsPanel.all_electrodes)
    init_leads_list()
    init_electrodes_list()
    init_electrodes_labeling(addon)
    addon.clear_colors_from_parent_childrens('Deep_electrodes')
    addon.clear_cortex()
    bpy.context.scene.show_only_lead = False
    bpy.context.scene.listen_to_keyboard = False
    bpy.context.scene.listener_is_running = False
    bpy.context.scene.show_lh_electrodes = True
    bpy.context.scene.show_rh_electrodes = True
    _electrodes_labeling_files_update()
    if not ElecsPanel.electrodes_locs or not ElecsPanel.lookup:
        if not ElecsPanel.electrodes_locs:
            print("!!! Can't find electrodes labeling files in user/electrdes!")
        if not ElecsPanel.lookup:
            print('No electrodes lookup table!')
        print("!!! Can't plot electrodes' probabilties !!!")
    if not ElecsPanel.groups or not ElecsPanel.groups_first_electrode or not ElecsPanel.sorted_groups or \
        not ElecsPanel.groups_hemi or not ElecsPanel.groups_electrodes:
            print('Error in electrodes panel init!')
    else:
        register()
        ElecsPanel.init = True
Example #18
0
def load_camera(camera_fname=''):
    if camera_fname == '':
        camera_fname = op.join(bpy.path.abspath(bpy.context.scene.output_path),
                               'camera.pkl')
    if op.isfile(camera_fname):
        X_rotation, Y_rotation, Z_rotation, X_location, Y_location, Z_location = mu.load(
            camera_fname)
        RenderFigure.update_camera = False
        bpy.context.scene.X_rotation = X_rotation
        bpy.context.scene.Y_rotation = Y_rotation
        bpy.context.scene.Z_rotation = Z_rotation
        bpy.context.scene.X_location = X_location
        bpy.context.scene.Y_location = Y_location
        bpy.context.scene.Z_location = Z_location
        RenderFigure.update_camera = True
        update_camera()
    else:
        print('No camera file was found in {}!'.format(camera_fname))
Example #19
0
def init_electrodes_labeling(addon):
    #todo: this panel should work also without labeling file
    labeling_fname = '{}_{}_electrodes_cigar_r_*_l_*{}*.pkl'.format(mu.get_user(), bpy.context.scene.atlas,
        '_bipolar' if bpy.context.scene.bipolar else '')
    labling_files = glob.glob(op.join(mu.get_user_fol(), 'electrodes', labeling_fname))
    if not bpy.context.scene.bipolar:
        labling_files = [fname for fname in labling_files if 'bipolar' not in fname]
    if len(labling_files) == 0:
        print("!!! Can't find any electrodes labeling file in {} !!!".format(
            op.join(mu.get_user_fol(), 'electrodes', labeling_fname)))
    else:
        files_names = [mu.namebase(fname) for fname in labling_files if mu.load(fname)]
        labeling_items = [(c, c, '', ind) for ind, c in enumerate(files_names)]
        bpy.types.Scene.electrodes_labeling_files = bpy.props.EnumProperty(
            items=labeling_items, description='Labeling files', update=electrodes_labeling_files_update)
        bpy.context.scene.electrodes_labeling_files = files_names[0]
        # ElecsPanel.electrodes_locs = mu.load(labling_files[0])
        # ElecsPanel.lookup = create_lookup_table(ElecsPanel.electrodes_locs, ElecsPanel.electrodes)
    ElecsPanel.faces_verts = addon.get_faces_verts()
Example #20
0
def find_elecrode_labeling_files():
    files = []
    blender_electrodes_names = set([o.name for o in bpy.data.objects['Deep_electrodes'].children])
    # labeling_template = '{}_{}_electrodes_cigar_r_*_l_*.pkl'.format(mu.get_user(), bpy.context.scene.atlas)
    labeling_template = '{}_*_electrodes_cigar_r_*_l_*.pkl'.format(mu.get_user(), bpy.context.scene.atlas)
    labling_files = glob.glob(op.join(mu.get_user_fol(), 'electrodes', labeling_template))
    for labling_file in labling_files:
        try:
            d = mu.load(labling_file)
            electrodes_names = set([e['name'] for e in d])
            # todo: find what is the problem... (mg96)
            # if len(electrodes_names - blender_electrodes_names) == 0:
            files.append(labling_file)
        except:
            print('Error reading {}'.format(labling_file))
            continue
    if len(files) == 0:
        print("Can't find any labeling file that match the electrodes names in{}!".format(
            op.join(mu.get_user_fol(), 'electrodes')))
    return files
Example #21
0
def plot_tracks():
    tracks_name = bpy.context.scene.dti_tracks
    tracks_fname = op.join(SUBJECT_DTI_FOL, '{}_tracks.npy'.format(tracks_name))
    tracks_header = op.join(SUBJECT_DTI_FOL, '{}_header.pkl'.format(tracks_name))
    world_matrix = mu.get_matrix_world()
    tracks = np.load(tracks_fname) * 0.1
    header = mu.load(tracks_header)

    layers_dti = [False] * 20
    dti_layer = DTIPanel.addon.CONNECTIONS_LAYER
    layers_dti[dti_layer] = True
    mu.create_empty_if_doesnt_exists(tracks_name, DTIPanel.addon.CONNECTIONS_LAYER, None, PARENT_OBJ)
    parent_obj = bpy.data.objects[tracks_name]

    # N = len(tracks)
    # now = time.time()
    # for ind, track in enumerate(tracks):
    #     mu.time_to_go(now, ind, N, 100)
    cur_obj = mu.create_spline(tracks, layers_dti, bevel_depth=0.01)
    cur_obj.name = tracks_name
    cur_obj.parent = parent_obj
Example #22
0
def load_camera(camera_fname=''):
    if camera_fname == '':
        camera_fname = op.join(mu.get_user_fol(), 'camera', '{}.pkl'.format(bpy.context.scene.camera_files))
    if op.isfile(camera_fname):
        camera_name = mu.namebase(camera_fname)
        for hemi in mu.HEMIS:
            if hemi in camera_name:
                _addon().show_hide_hemi(False, hemi)
                _addon().show_hide_hemi(True, mu.other_hemi(hemi))
        X_rotation, Y_rotation, Z_rotation, X_location, Y_location, Z_location = mu.load(camera_fname)
        RenderFigure.update_camera = False
        bpy.context.scene.X_rotation = X_rotation
        bpy.context.scene.Y_rotation = Y_rotation
        bpy.context.scene.Z_rotation = Z_rotation
        bpy.context.scene.X_location = X_location
        bpy.context.scene.Y_location = Y_location
        bpy.context.scene.Z_location = Z_location
        RenderFigure.update_camera = True
        update_camera()
    else:
        print('No camera file was found in {}!'.format(camera_fname))
Example #23
0
def find_point_thickness():
    vertex_ind, closest_mesh_name = _addon().snap_cursor()
    vertex_co = bpy.data.objects['inner_skull'].data.vertices[vertex_ind].co
    distances = np.load(op.join(mu.get_user_fol(), 'skull', 'ray_casts.npy'))
    rays_info = mu.load(
        op.join(mu.get_user_fol(), 'skull', 'ray_casts_info.pkl'))
    # closest_mesh_name, vertex_ind, vertex_co, _ = _addon().find_vertex_index_and_mesh_closest_to_cursor(
    #     objects_names=['inner_skull'])
    # distance = np.linalg.norm(f.intersections[vertex_ind, 0] - f.intersections[vertex_ind, 1])
    distance = distances[vertex_ind][0]
    (hit, loc, norm, index) = rays_info[vertex_ind]

    # bpy.context.scene.cursor_location = vertex_co
    print(closest_mesh_name, vertex_ind, vertex_co, distance, loc)
    SkullPanel.vertex_skull_thickness = distance
    if not bpy.context.scene.thickness_arrows and bpy.context.scene.show_point_arrow:
        if SkullPanel.prev_vertex_arrow is not None:
            SkullPanel.prev_vertex_arrow.hide = True
        vertex_arrow = bpy.data.objects.get('mt_{}'.format(vertex_ind), None)
        if vertex_arrow is not None:
            vertex_arrow.hide = False
            SkullPanel.prev_vertex_arrow = vertex_arrow
Example #24
0
def init(addon):
    from random import shuffle
    ColoringMakerPanel.addon = addon
    user_fol = mu.get_user_fol()
    ColoringMakerPanel.faces_verts = None
    labels_vertices_fname = op.join(user_fol, 'labels_vertices_{}.pkl'.format(bpy.context.scene.atlas))
    if not op.isfile(labels_vertices_fname):
        print("!!! Can't find {}!".format('labels_vertices_{}.pkl'.format(bpy.context.scene.atlas)))
        return None
    labels_names, labels_vertices = mu.load(labels_vertices_fname)
    ColoringMakerPanel.labels_vertices = dict(labels_names=labels_names, labels_vertices=labels_vertices)
    ColoringMakerPanel.max_labels_vertices_num = {}

    meg_files_exist = mu.hemi_files_exists(op.join(user_fol, 'activity_map_{hemi}', 't0.npy'))
    meg_data_maxmin_fname = op.join(mu.get_user_fol(), 'meg_activity_map_minmax.pkl')
    if meg_files_exist and op.isfile(meg_data_maxmin_fname):
        data_min, data_max = mu.load(meg_data_maxmin_fname)
        ColoringMakerPanel.meg_activity_colors_ratio = 256 / (data_max - data_min)
        ColoringMakerPanel.meg_activity_data_min = data_min
        ColoringMakerPanel.meg_activity_data_max = data_max
        print('data meg: {}-{}'.format(data_min, data_max))
        _addon().set_colorbar_max_min(data_max, data_min, True)
        _addon().set_colorbar_title('MEG')

    fmri_files = glob.glob(op.join(user_fol, 'fmri', 'fmri_*_lh.npy'))
    if len(fmri_files) > 0:
        files_names = [mu.namebase(fname)[5:-3] for fname in fmri_files]
        clusters_items = [(c, c, '', ind) for ind, c in enumerate(files_names)]
        bpy.types.Scene.fmri_files = bpy.props.EnumProperty(
            items=clusters_items, description="fMRI files", update=fmri_files_update)
        bpy.context.scene.fmri_files = files_names[0]
        for hemi in mu.HEMIS:
            ColoringMakerPanel.fMRI[hemi] = np.load('{}_{}.npy'.format(fmri_files[0][:-7], hemi))
        # Check separately for each contrast
        fmri_data_maxmin_fname = op.join(mu.get_user_fol(), 'fmri', 'fmri_activity_map_minmax.pkl')
        if op.isfile(fmri_data_maxmin_fname):
            data_min, data_max = mu.load(fmri_data_maxmin_fname)
            ColoringMakerPanel.fmri_activity_colors_ratio = 256 / (data_max - data_min)
            ColoringMakerPanel.fmri_activity_data_min = data_min
            ColoringMakerPanel.fmri_activity_data_max = data_max

    electrodes_source_files = glob.glob(op.join(user_fol, 'electrodes', '*_labels_*-rh.npz'))
    if len(electrodes_source_files) > 0:
        files_names = [mu.namebase(fname)[:-len('-rh')] for fname in electrodes_source_files]
        items = [(c, c, '', ind) for ind, c in enumerate(files_names)]
        bpy.types.Scene.electrodes_sources_files = bpy.props.EnumProperty(
            items=items, description="electrodes sources", update=electrodes_sources_files_update)
        bpy.context.scene.electrodes_sources_files = files_names[0]

    mu.make_dir(op.join(user_fol, 'coloring'))
    manually_color_files = glob.glob(op.join(user_fol, 'coloring', '*.csv'))
    if len(manually_color_files) > 0:
        files_names = [mu.namebase(fname) for fname in manually_color_files]
        coloring_items = [(c, c, '', ind) for ind, c in enumerate(files_names)]
        bpy.types.Scene.coloring_files = bpy.props.EnumProperty(items=coloring_items, description="Coloring files")
        bpy.context.scene.coloring_files = files_names[0]
    vol_color_files = glob.glob(op.join(user_fol, 'coloring', 'volumetric', '*.csv'))
    if len(vol_color_files) > 0:
        files_names = [mu.namebase(fname) for fname in vol_color_files]
        coloring_items = [(c, c, '', ind) for ind, c in enumerate(files_names)]
        bpy.types.Scene.vol_coloring_files = bpy.props.EnumProperty(
            items=coloring_items, description="Volumetric Coloring files")
        bpy.context.scene.vol_coloring_files = files_names[0]

    ColoringMakerPanel.colors = list(set(list(cu.NAMES_TO_HEX.keys())) - set(['black']))
    shuffle(ColoringMakerPanel.colors)
    ColoringMakerPanel.labels_groups = read_groups_labels(ColoringMakerPanel.colors)
    if len(ColoringMakerPanel.labels_groups) > 0:
        groups_items = [(gr, gr, '', ind) for ind, gr in enumerate(list(ColoringMakerPanel.labels_groups.keys()))]
        bpy.types.Scene.labels_groups = bpy.props.EnumProperty(
            items=groups_items, description="Groups")

    ColoringMakerPanel.faces_verts = load_faces_verts()
    bpy.context.scene.coloring_meg_subcorticals = False
    # ColoringMakerPanel.cm = np.load(op.join(mu.file_fol(), 'color_maps', 'BuPu_YlOrRd.npy'))
    register()
Example #25
0
def init(addon):
    from random import shuffle
    ColoringMakerPanel.addon = addon
    user_fol = mu.get_user_fol()
    ColoringMakerPanel.faces_verts = None
    labels_vertices_fname = op.join(user_fol, 'labels_vertices_{}.pkl'.format(bpy.context.scene.atlas))
    if not op.isfile(labels_vertices_fname):
        print("!!! Can't find {}!".format('labels_vertices_{}.pkl'.format(bpy.context.scene.atlas)))
        return None
    labels_names, labels_vertices = mu.load(labels_vertices_fname)
    ColoringMakerPanel.labels_vertices = dict(labels_names=labels_names, labels_vertices=labels_vertices)

    meg_files_exist = mu.hemi_files_exists(op.join(user_fol, 'activity_map_{hemi}', 't0.npy'))
    if meg_files_exist:
        data_min, data_max = mu.load(op.join(mu.get_user_fol(), 'meg_activity_map_minmax.pkl'))
        ColoringMakerPanel.meg_activity_colors_ratio = 256 / (data_max - data_min)
        ColoringMakerPanel.meg_activity_data_min = data_min
        print('data meg: {}-{}'.format(data_min, data_max))

    fmri_files = glob.glob(op.join(user_fol, 'fmri', 'fmri_*_lh.npy'))
    if len(fmri_files) > 0:
        files_names = [mu.namebase(fname)[5:-3] for fname in fmri_files]
        clusters_items = [(c, c, '', ind) for ind, c in enumerate(files_names)]
        bpy.types.Scene.fmri_files = bpy.props.EnumProperty(
            items=clusters_items, description="fMRI files", update=fmri_files_update)
        bpy.context.scene.fmri_files = files_names[0]
        for hemi in mu.HEMIS:
            ColoringMakerPanel.fMRI[hemi] = np.load('{}_{}.npy'.format(fmri_files[0][:-7], hemi))

    electrodes_source_files = glob.glob(op.join(user_fol, 'electrodes', '*_labels_*-rh.npz'))
    if len(electrodes_source_files) > 0:
        files_names = [mu.namebase(fname)[:-len('-rh')] for fname in electrodes_source_files]
        items = [(c, c, '', ind) for ind, c in enumerate(files_names)]
        bpy.types.Scene.electrodes_sources_files = bpy.props.EnumProperty(
            items=items, description="electrodes sources", update=electrodes_sources_files_update)
        bpy.context.scene.electrodes_sources_files = files_names[0]

    mu.make_dir(op.join(user_fol, 'coloring'))
    manually_color_files = glob.glob(op.join(user_fol, 'coloring', '*.csv'))
    if len(manually_color_files) > 0:
        files_names = [mu.namebase(fname) for fname in manually_color_files]
        coloring_items = [(c, c, '', ind) for ind, c in enumerate(files_names)]
        bpy.types.Scene.coloring_files = bpy.props.EnumProperty(items=coloring_items, description="Coloring files")
        bpy.context.scene.coloring_files = files_names[0]
    vol_color_files = glob.glob(op.join(user_fol, 'coloring', 'volumetric', '*.csv'))
    if len(vol_color_files) > 0:
        files_names = [mu.namebase(fname) for fname in vol_color_files]
        coloring_items = [(c, c, '', ind) for ind, c in enumerate(files_names)]
        bpy.types.Scene.vol_coloring_files = bpy.props.EnumProperty(
            items=coloring_items, description="Volumetric Coloring files")
        bpy.context.scene.vol_coloring_files = files_names[0]

    ColoringMakerPanel.colors = list(set(list(cu.NAMES_TO_HEX.keys())) - set(['black']))
    shuffle(ColoringMakerPanel.colors)
    ColoringMakerPanel.labels_groups = read_groups_labels(ColoringMakerPanel.colors)
    if len(ColoringMakerPanel.labels_groups) > 0:
        groups_items = [(gr, gr, '', ind) for ind, gr in enumerate(list(ColoringMakerPanel.labels_groups.keys()))]
        bpy.types.Scene.labels_groups = bpy.props.EnumProperty(
            items=groups_items, description="Groups")

    ColoringMakerPanel.faces_verts = load_faces_verts()
    ColoringMakerPanel.cm = np.load(op.join(mu.file_fol(), 'color_maps', 'BuPu_YlOrRd.npy'))
    register()
Example #26
0
def _electrodes_labeling_files_update():
    labeling_fname = op.join(mu.get_user_fol(), 'electrodes', '{}.pkl'.format(
        bpy.context.scene.electrodes_labeling_files))
    ElecsPanel.electrodes_locs = mu.load(labeling_fname)
    ElecsPanel.lookup = create_lookup_table(ElecsPanel.electrodes_locs, ElecsPanel.all_electrodes)