def init(addon):
StreamingPanel.addon = addon
register()
StreamingPanel.cm = np.load(op.join(mu.file_fol(), 'color_maps', 'BuPu_YlOrRd.npy'))
StreamingPanel.fixed_data = fixed_data()
StreamingPanel.init = True
def init(addon):
if not bpy.data.objects.get("full_colorbar", None):
return
ColorbarPanel.addon = addon
colorbar_files = glob.glob(op.join(mu.file_fol(), "color_maps", "*.npy"))
if len(colorbar_files) == 0:
return None
files_names = [mu.namebase(fname).replace("_", "-") for fname in colorbar_files]
colorbar_items = [(c, c, "", ind) for ind, c in enumerate(files_names)]
bpy.types.Scene.colorbar_files = bpy.props.EnumProperty(
items=colorbar_items, description="colormaps files", update=colormap_update
)
bpy.context.scene.colorbar_files = files_names[0]
for space in mu.get_3d_spaces():
if space.lock_object and space.lock_object.name == "full_colorbar":
space.show_only_render = True
register()
ColorbarPanel.init = True
bpy.context.scene.show_cb_in_render = False
mu.select_hierarchy("colorbar_camera", False, False)
if not ColorbarPanel.colorbar_updated:
bpy.context.scene.colorbar_min = -1
bpy.context.scene.colorbar_max = 1
bpy.context.scene.colorbar_title = "MEG"
bpy.context.scene.colorbar_files = "BuPu-YlOrRd"
bpy.context.scene.colorbar_y = 0.18
bpy.context.scene.colorbar_text_y = -1.53
def init(addon):
cm_fname = op.join(mu.file_fol(), 'color_maps', 'BuPu_YlOrRd.npy')
if not op.isfile(cm_fname):
print("Streaming: Can't load without the cm file {}".format(cm_fname))
return
if not bpy.data.objects.get('Deep_electrodes'):
print('Streaming: No electrodes')
return
StreamingPanel.addon = addon
StreamingPanel.is_listening = False
StreamingPanel.is_streaming = False
StreamingPanel.first_time = True
StreamingPanel.electrodes_data = None
StreamingPanel.data_max, StreamingPanel.data_min = 0, 0
StreamingPanel.stim_exist = 'STIM' in _addon().settings.sections()
if StreamingPanel.stim_exist:
StreamingPanel.config = _addon().settings['STIM']
if 'STREAM' in _addon().settings.sections():
stream_con = _addon().settings['STREAM']
bpy.context.scene.streaming_buffer_size = int(
stream_con.get('buffer_size', 10))
bpy.context.scene.streaming_server = stream_con.get(
'server', 'localhost')
bpy.context.scene.multicast_group = stream_con.get(
'multicast_group', '1.1.1.1')
bpy.context.scene.multicast_group = stream_con.get(
'multicast_group', '1.1.1.1')
bpy.context.scene.streaming_server_port = int(
stream_con.get('port', 222))
bpy.context.scene.timeout = float(stream_con.get('timeout', 0.1))
streaming_items = [('udp', 'udp', '', 1)]
input_fol = op.join(mu.get_user_fol(), 'electrodes', 'streaming')
streaming_files = glob.glob(op.join(input_fol, '**',
'streaming_data_*.npy'),
recursive=True)
logs_dirs = [logs_dir.split(op.sep)[-1] for logs_dir in glob.glob(op.join(input_fol, '*.*')) if op.isdir(logs_dir) and \
len(glob.glob(op.join(input_fol, logs_dir, 'streaming_data_*.npy'))) > 0]
if len(streaming_files) > 0 and len(logs_dirs) > 0:
streaming_items.append(('offline', 'Offline recordings', '', 2))
bpy.types.Scene.logs_folders = bpy.props.EnumProperty(
items=[(f, f, '', ind + 1) for ind, f in enumerate(logs_dirs)],
update=logs_folders_update)
bpy.context.scene.logs_folders = logs_dirs[0]
bpy.types.Scene.stream_type = bpy.props.EnumProperty(
items=streaming_items, description='Type of stream listener')
bpy.context.scene.stream_type = 'udp'
bpy.context.scene.multicast = False
register()
StreamingPanel.cm = np.load(cm_fname)
# StreamingPanel.fixed_data = fixed_data()
StreamingPanel.electrodes_objs_names = [
l.name for l in bpy.data.objects['Deep_electrodes'].children
]
bpy.context.scene.streaming_electrodes_num = len(
StreamingPanel.electrodes_objs_names)
StreamingPanel.minmax_vals = []
StreamingPanel.max_steps = _addon().get_max_time_steps()
StreamingPanel.init = True
def init(addon):
cm_fname = op.join(mu.file_fol(), 'color_maps', 'BuPu_YlOrRd.npy')
if not op.isfile(cm_fname):
return
StreamingPanel.addon = addon
register()
StreamingPanel.cm = np.load(cm_fname)
StreamingPanel.fixed_data = fixed_data()
StreamingPanel.init = True
def load_colormap():
colormap_fname = op.join(mu.file_fol(), 'color_maps', '{}.npy'.format(
bpy.context.scene.colorbar_files)) # .replace('-', '_')
colormap = np.load(colormap_fname)
ColorbarPanel.cm = colormap
for ind in range(colormap.shape[0]):
cb_obj_name = 'cb.{0:0>3}'.format(ind)
cb_obj = bpy.data.objects[cb_obj_name]
cur_mat = cb_obj.active_material
cur_mat.diffuse_color = colormap[ind]
def load_colormap():
colormap_fname = op.join(
mu.file_fol(), "color_maps", "{}.npy".format(bpy.context.scene.colorbar_files.replace("-", "_"))
)
colormap = np.load(colormap_fname)
ColorbarPanel.cm = colormap
for ind in range(colormap.shape[0]):
cb_obj_name = "cb.{0:0>3}".format(ind)
cb_obj = bpy.data.objects[cb_obj_name]
cur_mat = cb_obj.active_material
cur_mat.diffuse_color = colormap[ind]
def init(addon):
try:
trans_fname = op.join(mu.get_user_fol(), 'orig_trans.npz')
volumes = glob.glob(
op.join(mu.get_user_fol(), 'freeview', '*+aseg.npy'))
luts = glob.glob(
op.join(mu.get_user_fol(), 'freeview', '*ColorLUT.npz'))
if op.isfile(trans_fname):
WhereAmIPanel.subject_orig_trans = mu.Bag(np.load(trans_fname))
for atlas_vol_fname, atlas_vol_lut_fname in zip(volumes, luts):
atlas = mu.namebase(atlas_vol_fname)[:-len('+aseg')]
WhereAmIPanel.vol_atlas[atlas] = np.load(atlas_vol_fname)
WhereAmIPanel.vol_atlas_lut[atlas] = np.load(atlas_vol_lut_fname)
subjects_dir = mu.get_link_dir(mu.get_links_dir(), 'subjects')
annot_files = glob.glob(
op.join(subjects_dir, mu.get_user(), 'label', 'rh.*.annot'))
if len(annot_files) > 0:
files_names = [mu.namebase(fname)[3:] for fname in annot_files]
items = [(c, c, '', ind) for ind, c in enumerate(files_names)]
bpy.types.Scene.subject_annot_files = bpy.props.EnumProperty(
items=items)
bpy.context.scene.subject_annot_files = files_names[0]
else:
bpy.types.Scene.subject_annot_files = bpy.props.EnumProperty(
items=[])
# bpy.context.scene.subject_annot_files = ''
bpy.context.scene.closest_label_output = ''
bpy.context.scene.new_label_r = 5
mri_data_fname = op.join(mu.get_user_fol(), 'freeview',
'{}_data.npz'.format('mri'))
if op.isfile(mri_data_fname):
WhereAmIPanel.mri_data = mu.Bag(np.load(mri_data_fname))
gray_colormap_fname = op.join(mu.file_fol(), 'color_maps', 'gray.npy')
if op.isfile(gray_colormap_fname):
WhereAmIPanel.gray_colormap = np.load(gray_colormap_fname)
WhereAmIPanel.addon = addon
WhereAmIPanel.init = True
WhereAmIPanel.run_slices_listener = False
init_slices()
if WhereAmIPanel.run_slices_listener:
start_slicer_server()
else:
WhereAmIPanel.slicer_state = slicer.init('mri')
create_slices('mri', bpy.context.scene.cursor_location)
save_slices_cursor_pos()
register()
except:
print("Can't init where-am-I panel!")
print(traceback.format_exc())
def init(modality, modality_data=None, colormap=None, subject='', mmvt_dir=''):
if subject == '':
subject = mu.get_user()
if mmvt_dir == '':
mmvt_dir = mu.file_fol()
if modality_data is None:
if modality == 'mri':
fname = op.join(mmvt_dir, subject, 'freeview', 'mri_data.npz')
elif modality == 't2':
fname = op.join(mmvt_dir, subject, 'freeview', 't2_data.npz')
elif modality == 'ct':
fname = op.join(mmvt_dir, subject, 'ct', 'ct_data.npz'.format(modality))
if op.isfile(fname):
modality_data = mu.Bag(np.load(fname))
else:
print('To see the slices the following command is being called:'.format(modality))
print('python -m src.preproc.anatomy -s {} -f save_images_data_and_header'.format(mu.get_user()))
mu.run_mmvt_func('src.preproc.anatom', 'save_subject_orig_trans,save_images_data_and_header')
# cmd = '{} -m src.preproc.anatomy -s {} -f save_subject_orig_trans,save_images_data_and_header --ignore_missing 1'.format(
# bpy.context.scene.python_cmd, mu.get_user())
# mu.run_command_in_new_thread(cmd, False, cwd=mu.get_mmvt_code_root())
return None
if colormap is None:
if op.isfile(op.join(mmvt_dir, 'color_maps', 'gray.npy')):
colormap_fname = op.join(mmvt_dir, 'color_maps', 'gray.npy')
print("Can't find The gray colormap!")
else:
colormap_fname = glob.glob(op.join(mmvt_dir, 'color_maps', '*.npy'))[0]
colormap = np.load(colormap_fname)
affine = np.array(modality_data.affine, float)
data = modality_data.data
clim = modality_data.precentiles
if IN_BLENDER:
bpy.context.scene.slices_x_min, bpy.context.scene.slices_x_max = clim
colors_ratio = modality_data.colors_ratio
codes = axcodes2ornt(aff2axcodes(affine))
order = np.argsort([c[0] for c in codes])
print(modality, order)
flips = np.array([c[1] < 0 for c in codes])[order]
flips[0] = not flips[0]
sizes = [data.shape[order] for order in order]
scalers = voxel_sizes(affine)
r = [scalers[order[2]] / scalers[order[1]],
scalers[order[2]] / scalers[order[0]],
scalers[order[1]] / scalers[order[0]]]
extras = [0] * 3
pial_vol_mask_fname = op.join(mmvt_dir, subject, 'freeview', 'pial_vol_mask.npy')
pial_vol_mask = np.load(pial_vol_mask_fname) if op.isfile(pial_vol_mask_fname) else None
self = mu.Bag(dict(
data=data, affine=affine, order=order, sizes=sizes, flips=flips, clim=clim, r=r, colors_ratio=colors_ratio,
colormap=colormap, coordinates=[], modality=modality, extras=extras, pial_vol_mask=pial_vol_mask))
return self
def init(modality, modality_data=None, colormap=None):
if modality_data is None:
fname = op.join(mu.get_user_fol(), 'freeview',
'{}_data.npz'.format(modality))
if op.isfile(fname):
modality_data = mu.Bag(np.load(fname))
else:
print(
'To see the slices you need to create the file {}_data.npz by calling:'
.format(modality))
print(
'python -m src.preproc.anatomy -s {} -f save_images_data_and_header'
.format(mu.get_user()))
return None
if colormap is None:
colormap_fname = op.join(mu.file_fol(), 'color_maps', 'gray.npy')
colormap = np.load(colormap_fname)
affine = np.array(modality_data.affine, float)
data = modality_data.data
clim = modality_data.precentiles
colors_ratio = modality_data.colors_ratio
codes = axcodes2ornt(aff2axcodes(affine))
order = np.argsort([c[0] for c in codes])
flips = np.array([c[1] < 0 for c in codes])[order]
flips[0] = not flips[0]
sizes = [data.shape[order] for order in order]
scalers = voxel_sizes(affine)
r = [
scalers[order[2]] / scalers[order[1]],
scalers[order[2]] / scalers[order[0]],
scalers[order[1]] / scalers[order[0]]
]
self = mu.Bag(
dict(data=data,
affine=affine,
order=order,
sizes=sizes,
flips=flips,
clim=clim,
r=r,
colors_ratio=colors_ratio,
colormap=colormap))
return self
def init(addon):
try:
t1_trans_fname = op.join(mu.get_user_fol(), 't1_trans.npz')
if not op.isfile(t1_trans_fname):
# backward compatibility
t1_trans_fname = op.join(mu.get_user_fol(), 'orig_trans.npz')
t2_trans_fname = op.join(mu.get_user_fol(), 't2_trans.npz')
ct_trans_fname = op.join(mu.get_user_fol(), 'ct', 'ct_trans.npz')
volumes = glob.glob(op.join(mu.get_user_fol(), 'freeview', '*+aseg.npy'))
luts = glob.glob(op.join(mu.get_user_fol(), 'freeview', '*ColorLUT.npz'))
if op.isfile(t1_trans_fname):
WhereAmIPanel.subject_t1_trans = mu.Bag(np.load(t1_trans_fname))
if op.isfile(t2_trans_fname):
WhereAmIPanel.subject_t2_trans = mu.Bag(np.load(t2_trans_fname))
if op.isfile(ct_trans_fname):
WhereAmIPanel.subject_ct_trans = mu.Bag(np.load(ct_trans_fname))
for atlas_vol_fname, atlas_vol_lut_fname in zip(volumes, luts):
atlas = mu.namebase(atlas_vol_fname)[:-len('+aseg')]
WhereAmIPanel.vol_atlas[atlas] = np.load(atlas_vol_fname)
WhereAmIPanel.vol_atlas_lut[atlas] = np.load(atlas_vol_lut_fname)
try:
subjects_dir = mu.get_link_dir(mu.get_links_dir(), 'subjects')
annot_files = [mu.namebase(fname)[3:] for fname in glob.glob(
op.join(subjects_dir, mu.get_user(), 'label', 'rh.*.annot'))]
annot_files += [mu.namebase(fname)[3:] for fname in glob.glob(
op.join(mu.get_user_fol(), 'labels', 'rh.*.annot'))]
WhereAmIPanel.annot_files = annot_files = list(set(annot_files))
if len(annot_files) > 0:
items = [(c, c, '', ind) for ind, c in enumerate(annot_files)]
bpy.types.Scene.subject_annot_files = bpy.props.EnumProperty(
items=items, update=subject_annot_files_update, description='List of different atlases.\n\nCurrent atlas')
ind = mu.index_in_list(bpy.context.scene.atlas, annot_files, 0)
bpy.context.scene.subject_annot_files = annot_files[ind]
else:
bpy.types.Scene.subject_annot_files = bpy.props.EnumProperty(items=[])
# bpy.context.scene.subject_annot_files = ''
except:
bpy.types.Scene.subject_annot_files = bpy.props.EnumProperty(items=[])
bpy.context.scene.closest_label_output = ''
bpy.context.scene.new_label_r = 5
bpy.context.scene.find_closest_label_on_click = False
bpy.context.scene.plot_closest_label_contour = False
mri_data_fname = op.join(mu.get_user_fol(), 'freeview', 'mri_data.npz')
if op.isfile(mri_data_fname):
WhereAmIPanel.mri_data = mu.Bag(np.load(mri_data_fname))
gray_colormap_fname = op.join(mu.file_fol(), 'color_maps', 'gray.npy')
if op.isfile(gray_colormap_fname):
WhereAmIPanel.gray_colormap = np.load(gray_colormap_fname)
WhereAmIPanel.addon = addon
WhereAmIPanel.init = True
WhereAmIPanel.run_slices_listener = False
init_slices()
if WhereAmIPanel.run_slices_listener:
start_slicer_server()
else:
WhereAmIPanel.slicer_state = mu.Bag({})
WhereAmIPanel.slicer_state['mri'] = slicer.init(_addon(), 'mri')
create_slices(None, bpy.context.scene.cursor_location)
save_slices_cursor_pos()
register()
except:
print("Can't init where-am-I panel!")
print(traceback.format_exc())
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()