def invoke(self, context, event=None):
cmd = '{} -m src.preproc.anatomy_preproc -s {} -a {}'.format(
bpy.context.scene.python_cmd, mu.get_user(),
bpy.context.scene.atlas)
print('Running {}'.format(cmd))
mu.run_command_in_new_thread(cmd, False)
return {"FINISHED"}
def invoke(self, context, event=None):
packetsender_cmd = StreamingPanel.config['packetsender']
ip = StreamingPanel.config['ip']
port = StreamingPanel.config['port']
num = StreamingPanel.config['num']
mu.run_command_in_new_thread('{} -a -u {} {} "stim {}"'.format(packetsender_cmd, ip, port, num),
queues=False, shell=True, read_stdin=False, read_stdout=False, read_stderr=False)
return {"FINISHED"}
def create_movie():
output_file = op.join(bpy.context.scene.output_path, 'combine_images_cmd.txt')
if op.isfile(output_file):
os.remove(output_file)
cmd = '{} -m src.utils.movies_utils --fol {} --copy_files 1 --frame_rate {}'.format(
bpy.context.scene.python_cmd, bpy.context.scene.output_path, bpy.context.scene.frames_num)
print('Running {}'.format(cmd))
mu.run_command_in_new_thread(cmd, False)
def invoke(self, context, event=None):
electrodes_pos_fname = op.join(mu.get_user_fol(), 'electrodes', 'electrodes{}_positions.npz'.format(
'_bipolar' if bpy.context.scene.bipolar else ''))
cmd = '{} -m src.preproc.freeview -s {} -a {} -b {} --electrodes_pos_fname {} --ignore_missing 1'.format(
bpy.context.scene.python_cmd, mu.get_user(), bpy.context.scene.atlas,
bpy.context.scene.bipolar, electrodes_pos_fname)
mu.run_command_in_new_thread(cmd, False)
bpy.context.scene.freeview_messages = 'Preparing...'
return {"FINISHED"}
def run_hnn():
hnn_folder = op.abspath(bpy.path.abspath(bpy.context.scene.hnn_folder))
hnn_cmd = '{} -dataf {} -paramf {}'.format(
op.join(hnn_folder, 'hnn.sh'),
op.join(hnn_folder, 'data',
'{}.txt'.format(bpy.context.scene.hnn_data_files)),
op.join(hnn_folder, 'param',
'{}.param'.format(bpy.context.scene.hnn_param_files)))
mu.run_command_in_new_thread(hnn_cmd, False, cwd=hnn_folder)
def open_freeview():
root = mu.get_user_fol()
sig_cmd = ''
if bpy.context.scene.fMRI_files_exist and bpy.context.scene.freeview_load_fMRI:
sig_fnames = glob.glob(op.join(root, 'freeview', '*{}*.mgz'.format(bpy.context.scene.fmri_files))) + \
glob.glob(op.join(root, 'freeview', '*{}*.nii'.format(bpy.context.scene.fmri_files)))
if len(sig_fnames) > 0:
sig_fname = sig_fnames[0]
sig_cmd = '-v "{}":colormap=heat:heatscale=2,3,6 '.format(
sig_fname) if op.isfile(sig_fname) else ''
ct_cmd = ''
if bpy.context.scene.freeview_load_CT:
mmvt_ct_fname = op.join(root, 'ct', 'ct_reg_to_mr.mgz')
if FreeviewPanel.CT_files_exist:
ct_cmd = '-v "{}":opacity=0 '.format(mmvt_ct_fname)
else:
print("Can't find CT {}!".format(mmvt_ct_fname))
dura_cmd = ''
if bpy.context.scene.freeview_load_dura:
dura_fname = FreeviewPanel.dura_srf_fname
if FreeviewPanel.dura_srf_exist:
dura_cmd = '-f "{}":edgecolor=blue "{}":edgecolor=blue '.format(
dura_fname.format(hemi='rh'), dura_fname.format(hemi='lh'))
T1 = op.join(root, 'freeview', 'T1.mgz') # sometimes 'orig.mgz' is better
if not op.isfile(T1):
T1 = op.join(root, 'freeview', 'orig.mgz')
if not op.isfile(T1):
print(
'No T1 / orig files in freeview folder. Running preproc.freeview')
bpy.context.scene.freeview_messages = 'Preparing... Try to run again'
cmd = '{} -m src.preproc.freeview -s {} -a {} -b {} --ignore_missing 1'.format(
bpy.context.scene.python_cmd, mu.get_user(),
bpy.context.scene.atlas, bpy.context.scene.bipolar)
mu.run_command_in_new_thread(cmd, False)
return {'RUNNING_MODAL'}
bpy.context.scene.freeview_messages = ''
aseg = op.join(root, 'freeview',
'{}+aseg.mgz'.format(bpy.context.scene.atlas))
if op.isfile(aseg):
lut = op.join(root, 'freeview',
'{}ColorLUT.txt'.format(bpy.context.scene.atlas))
aseg_cmd = '"{}":opacity=0.05:colormap=lut:lut="{}"'.format(aseg, lut)
else:
aseg_cmd = ''
electrodes_cmd = get_electrodes_command(root)
cmd = '{} "{}":opacity=0.5 {}{}{}{}{}{}{}'.format(
FreeviewPanel.addon_prefs.freeview_cmd, T1, aseg_cmd, electrodes_cmd,
sig_cmd, ct_cmd, dura_cmd,
' -verbose' if FreeviewPanel.addon_prefs.freeview_cmd_verbose else '',
' -stdin' if FreeviewPanel.addon_prefs.freeview_cmd_stdin else '')
print(cmd)
FreeviewPanel.freeview_in_queue, FreeviewPanel.freeview_out_queue = mu.run_command_in_new_thread(
cmd
) #, read_stderr=reading_freeview_stderr_func, read_stdin=reading_freeview_stdin_func,
def grow_a_label():
closest_mesh_name, vertex_ind, _, _ = \
_addon().find_vertex_index_and_mesh_closest_to_cursor(use_shape_keys=True)
hemi = closest_mesh_name[len('infalted_'):] if _addon().is_inflated(
) else closest_mesh_name
subject, atlas = mu.get_user(), bpy.context.scene.subject_annot_files
label_name, label_r = bpy.context.scene.new_label_name, bpy.context.scene.new_label_r
cmd = '{} -m src.preproc.anatomy -s {} -a {} -f grow_label '.format(
bpy.context.scene.python_cmd, subject, atlas)
cmd += '--vertice_indice {} --hemi {} --label_name {} --label_r {}'.format(
vertex_ind, hemi, label_name, label_r)
mu.run_command_in_new_thread(cmd, False)
def invoke(self, context, event=None):
self._time = time.time()
self._obj = bpy.data.objects['LMF6']
if StreamingPanel.first_time:
StreamingPanel.first_time = False
context.window_manager.modal_handler_add(self)
self._timer = context.window_manager.event_timer_add(0.01, context.window)
StreamingPanel.is_streaming = not StreamingPanel.is_streaming
print(__name__)
script = 'src.mmvt_addon.streaming_panel'
cmd = '{} -m {} -s {}'.format(bpy.context.scene.python_cmd, script)
FreeviewPanel.freeview_in_queue, FreeviewPanel.freeview_out_queue mu.run_command_in_new_thread(cmd, queues=True)
return {'RUNNING_MODAL'}
def render_image(image_name='',
image_fol='',
quality=0,
use_square_samples=None,
render_background=None):
bpy.context.scene.render.resolution_percentage = bpy.context.scene.quality if quality == 0 else quality
bpy.context.scene.cycles.use_square_samples = bpy.context.scene.smooth_figure if use_square_samples is None \
else use_square_samples
if not render_background is None:
bpy.context.scene.render_background = render_background
# print('@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@')
print('use_square_samples: {}'.format(use_square_samples))
# print('@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@')
cur_frame = bpy.context.scene.frame_current
if image_name == '':
image_name = 't{}'.format(cur_frame)
image_fol = bpy.path.abspath(
bpy.context.scene.output_path) if image_fol == '' else image_fol
print('file name: {}'.format(op.join(image_fol, image_name)))
bpy.context.scene.render.filepath = op.join(image_fol, image_name)
# Render and save the rendered scene to file. ------------------------------
print('Image quality:')
print(bpy.context.scene.render.resolution_percentage)
print("Rendering...")
if not bpy.context.scene.render_background:
bpy.ops.render.render(write_still=True)
else:
grab_camera()
mu.change_fol_to_mmvt_root()
electrode_marked = RenderingMakerPanel.addon.is_current_electrode_marked(
)
script = 'src.mmvt_addon.scripts.render_image'
cmd = '{} -m {} -s {} -a {} -q {} -b {} '.format(
bpy.context.scene.python_cmd, script, mu.get_user(), bpy.context.scene.atlas,
bpy.context.scene.render.resolution_percentage, bpy.context.scene.bipolar) + \
'--hide_lh {} --hide_rh {} --hide_subs {} --show_elecs {} --curr_elec {} --show_only_lead {} '.format(
bpy.context.scene.objects_show_hide_lh, bpy.context.scene.objects_show_hide_rh,
bpy.context.scene.objects_show_hide_sub_cortical, bpy.context.scene.appearance_show_electrodes_layer,
bpy.context.scene.electrodes if electrode_marked else None,
bpy.context.scene.show_only_lead if electrode_marked else None) + \
'--show_connections {}'.format(
RenderingMakerPanel.addon.connections_visible())
print('Running {}'.format(cmd))
mu.save_blender_file()
mu.run_command_in_new_thread(cmd, queues=False)
print("Finished")
def combine_four_brain_perspectives():
data_min, data_max = _addon().get_colorbar_max_min()
background = bpy.context.scene.background_color
figure_name = 'splitted_lateral_medial_{}_{}.png'.format(
'inflated' if _addon().is_inflated() else 'pial', background)
figure_fname = op.join(mu.get_user_fol(), 'figures', figure_name)
colors_map = _addon().get_colormap_name().replace('-', '_')
x_left_crop, x_right_crop, y_top_crop, y_buttom_crop = (300, 300, 0, 0)
w_fac, h_fac = (1.5, 1)
cmd = '{} -m src.utils.figures_utils '.format(bpy.context.scene.python_cmd) + \
'-f combine_four_brain_perspectives,combine_brain_with_color_bar --fol {} --data_max {} --data_min {} '.format(
op.join(mu.get_user_fol(), 'figures'), data_max, data_min) + \
'--figure_fname {} --colors_map {} --x_left_crop {} --x_right_crop {} --y_top_crop {} --y_buttom_crop {} '.format(
figure_fname, colors_map, x_left_crop, x_right_crop, y_top_crop, y_buttom_crop) + \
'--w_fac {} --h_fac {} --facecolor {}'.format(w_fac, h_fac, background)
mu.run_command_in_new_thread(cmd, False)
def render_in_background(image_name,
image_fol,
camera_fname,
hide_subcorticals,
overwrite=True):
hide_subs_in_background = True if hide_subcorticals else bpy.context.scene.objects_show_hide_sub_cortical
mu.change_fol_to_mmvt_root()
electrode_marked = _addon().is_current_electrode_marked()
script = 'src.mmvt_addon.scripts.render_image'
cmd = '{} -m {} -s {} -a {} -i {} -o {} -q {} -b {} -c "{}"'.format(
bpy.context.scene.python_cmd, script, mu.get_user(), bpy.context.scene.atlas,
image_name, image_fol, bpy.context.scene.render.resolution_percentage,
bpy.context.scene.bipolar, camera_fname) + \
' --hide_lh {} --hide_rh {} --hide_subs {} --show_elecs {} --curr_elec {} --show_only_lead {}'.format(
bpy.context.scene.objects_show_hide_lh, bpy.context.scene.objects_show_hide_rh,
hide_subs_in_background, bpy.context.scene.show_hide_electrodes,
bpy.context.scene.electrodes if electrode_marked else None,
bpy.context.scene.show_only_lead if electrode_marked else None) + \
' --show_connections {} --interactive 0 --overwrite {}'.format(
_addon().connections_visible(), overwrite)
print('Running {}'.format(cmd))
RenderingMakerPanel.background_rendering = True
mu.save_blender_file()
_, RenderingMakerPanel.render_in_queue = mu.run_command_in_new_thread(
cmd,
read_stderr=False,
read_stdin=False,
stdout_func=reading_from_rendering_stdout_func)
def invoke(self, context, event=None):
root = mu.get_user_fol()
if bpy.context.scene.fMRI_files_exist and bpy.context.scene.freeview_load_fMRI:
sig_fnames = glob.glob(
op.join(root, 'freeview',
'*{}*.mgz'.format(bpy.context.scene.fmri_files)))
if len(sig_fnames) > 0:
sig_fname = sig_fnames[0]
sig_cmd = '-v "{}":colormap=heat:heatscale=2,3,6'.format(
sig_fname) if op.isfile(sig_fname) else ''
else:
sig_cmd = ''
else:
sig_cmd = ''
T1 = op.join(root, 'freeview',
'T1.mgz') # sometimes 'orig.mgz' is better
aseg = op.join(root, 'freeview',
'{}+aseg.mgz'.format(bpy.context.scene.atlas))
lut = op.join(root, 'freeview',
'{}ColorLUT.txt'.format(bpy.context.scene.atlas))
electrodes_cmd = self.get_electrodes_command(root)
cmd = '{} {} "{}":opacity=0.3 "{}":opacity=0.05:colormap=lut:lut="{}"{}{}{}'.format(
FreeviewPanel.addon_prefs.freeview_cmd, sig_cmd, T1, aseg, lut,
electrodes_cmd, ' -verbose'
if FreeviewPanel.addon_prefs.freeview_cmd_verbose else '',
' -stdin' if FreeviewPanel.addon_prefs.freeview_cmd_stdin else '')
print(cmd)
FreeviewPanel.freeview_in_queue, FreeviewPanel.freeview_out_queue = mu.run_command_in_new_thread(
cmd)
context.window_manager.modal_handler_add(self)
self._updating = False
self._timer = context.window_manager.event_timer_add(
0.1, context.window)
return {'RUNNING_MODAL'}
def invoke(self, context, event=None):
root = mu.get_user_fol()
if bpy.context.scene.fMRI_files_exist and bpy.context.scene.freeview_load_fMRI:
sig_fnames = glob.glob(op.join(root, 'freeview', '*{}*.mgz'.format(bpy.context.scene.fmri_files))) + \
glob.glob(op.join(root, 'freeview', '*{}*.nii'.format(bpy.context.scene.fmri_files)))
if len(sig_fnames) > 0:
sig_fname = sig_fnames[0]
sig_cmd = '-v "{}":colormap=heat:heatscale=2,3,6'.format(sig_fname) if op.isfile(sig_fname) else ''
else:
sig_cmd = ''
else:
sig_cmd = ''
T1 = op.join(root, 'freeview', 'T1.mgz') # sometimes 'orig.mgz' is better
aseg = op.join(root, 'freeview', '{}+aseg.mgz'.format(bpy.context.scene.atlas))
lut = op.join(root, 'freeview', '{}ColorLUT.txt'.format(bpy.context.scene.atlas))
electrodes_cmd = self.get_electrodes_command(root)
cmd = '{} {} "{}":opacity=0.3 "{}":opacity=0.05:colormap=lut:lut="{}"{}{}{}'.format(
FreeviewPanel.addon_prefs.freeview_cmd, sig_cmd, T1, aseg, lut, electrodes_cmd,
' -verbose' if FreeviewPanel.addon_prefs.freeview_cmd_verbose else '',
' -stdin' if FreeviewPanel.addon_prefs.freeview_cmd_stdin else '')
print(cmd)
FreeviewPanel.freeview_in_queue, FreeviewPanel.freeview_out_queue = mu.run_command_in_new_thread(cmd)
context.window_manager.modal_handler_add(self)
self._updating = False
self._timer = context.window_manager.event_timer_add(0.1, context.window)
return {'RUNNING_MODAL'}
def combine_four_brain_perspectives():
data_min, data_max = _addon().get_colorbar_max_min()
background = bpy.context.scene.background_color
figure_name = 'splitted_lateral_medial_{}_{}.png'.format(
'inflated' if _addon().is_inflated() else 'pial', background)
figure_fname = op.join(mu.get_user_fol(), 'figures', figure_name)
colors_map = _addon().get_colormap_name().replace('-', '_')
x_left_crop, x_right_crop, y_top_crop, y_buttom_crop = (300, 300, 0, 0)
w_fac, h_fac = (1.5, 1)
cmd = '{} -m src.utils.figures_utils '.format(bpy.context.scene.python_cmd) + \
'-f combine_four_brain_perspectives,combine_brain_with_color_bar --fol {} --data_max {} --data_min {} '.format(
op.join(mu.get_user_fol(), 'figures'), data_max, data_min) + \
'--figure_fname {} --colors_map {} --x_left_crop {} --x_right_crop {} --y_top_crop {} --y_buttom_crop {} '.format(
figure_fname, colors_map, x_left_crop, x_right_crop, y_top_crop, y_buttom_crop) + \
'--w_fac {} --h_fac {} --facecolor {}'.format(w_fac, h_fac, background)
mu.run_command_in_new_thread(cmd, False)
def load_surf_files(nii_fname):
fmri_file_template = ''
user_fol = mu.get_user_fol()
nii_fol = mu.get_fname_folder(nii_fname)
fmri_hemis = mu.get_both_hemis_files(nii_fname)
hemi = mu.get_hemi_from_full_fname(nii_fname)
local_fname = build_local_fname(nii_fname, user_fol)
mu.make_dir(op.join(user_fol, 'fmri'))
if nii_fol != op.join(user_fol, 'fmri'):
mu.make_link(nii_fname, local_fname, True)
other_hemi = mu.other_hemi(hemi)
other_hemi_fname = fmri_hemis[other_hemi]
if op.isfile(other_hemi_fname):
local_other_hemi_fname = build_local_fname(other_hemi_fname, user_fol)
if nii_fol != op.join(user_fol, 'fmri'):
mu.make_link(other_hemi_fname, local_other_hemi_fname, True)
fmri_file_template = mu.get_template_hemi_label_name(mu.namesbase_with_ext(local_fname))
cmd = '{} -m src.preproc.fMRI -s {} -f load_surf_files --fmri_file_template "{}"'.format(
bpy.context.scene.python_cmd, mu.get_user(), fmri_file_template)
mu.run_command_in_new_thread(cmd, False)
return fmri_file_template, hemi
def render_image(image_name='', image_fol='', quality=0, use_square_samples=None, render_background=None):
bpy.context.scene.render.resolution_percentage = bpy.context.scene.quality if quality == 0 else quality
bpy.context.scene.cycles.use_square_samples = bpy.context.scene.smooth_figure if use_square_samples is None \
else use_square_samples
if not render_background is None:
bpy.context.scene.render_background = render_background
# print('@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@')
print('use_square_samples: {}'.format(use_square_samples))
# print('@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@')
cur_frame = bpy.context.scene.frame_current
if image_name == '':
image_name = 't{}'.format(cur_frame)
image_fol = bpy.path.abspath(bpy.context.scene.output_path) if image_fol == '' else image_fol
print('file name: {}'.format(op.join(image_fol, image_name)))
bpy.context.scene.render.filepath = op.join(image_fol, image_name)
# Render and save the rendered scene to file. ------------------------------
print('Image quality:')
print(bpy.context.scene.render.resolution_percentage)
print("Rendering...")
if not bpy.context.scene.render_background:
bpy.ops.render.render(write_still=True)
else:
mu.change_fol_to_mmvt_root()
electrode_marked = RenderingMakerPanel.addon.is_current_electrode_marked()
script = 'src.mmvt_addon.scripts.render_image'
cmd = '{} -m {} -s {} -a {} -q {} -b {} --hide_lh {} --hide_rh {} --hide_subs {} --show_elecs {} --curr_elec {} --show_only_lead {}'.format(
bpy.context.scene.python_cmd, script, mu.get_user(), bpy.context.scene.atlas,
bpy.context.scene.render.resolution_percentage, bpy.context.scene.bipolar,
bpy.context.scene.objects_show_hide_lh, bpy.context.scene.objects_show_hide_rh,
bpy.context.scene.objects_show_hide_sub_cortical, bpy.context.scene.appearance_show_electrodes_layer,
bpy.context.scene.electrodes if electrode_marked else None,
bpy.context.scene.show_only_lead if electrode_marked else None)
print('Running {}'.format(cmd))
mu.save_blender_file()
mu.run_command_in_new_thread(cmd, queues=False)
print("Finished")
def invoke(self, context, event=None):
subject = mu.get_user()
threshold = bpy.context.scene.fmri_clustering_threshold
contrast = bpy.context.scene.fmri_clusters_labels_files
atlas = bpy.context.scene.atlas
task = contrast.split('_')[0]
context.window_manager.modal_handler_add(self)
self._timer = context.window_manager.event_timer_add(0.1, context.window)
mu.change_fol_to_mmvt_root()
cmd = '{} -m src.preproc.fMRI_preproc -s {} -T {} -c {} -t {} -a {} -f find_clusters'.format(
bpy.context.scene.python_cmd, subject, task, contrast, threshold, atlas)
print('Running {}'.format(cmd))
self.in_q, self.out_q = mu.run_command_in_new_thread(cmd)
return {'RUNNING_MODAL'}
def invoke(self, context, event=None):
self._time = time.time()
self._obj = bpy.data.objects['LMF6']
if StreamingPanel.first_time:
StreamingPanel.first_time = False
context.window_manager.modal_handler_add(self)
self._timer = context.window_manager.event_timer_add(0.01, context.window)
# script = op.join(mu.get_mmvt_code_root(), 'src', 'misc', 'udp_listener.py')
script = 'src.misc.udp_listener'
cmd = '{} -m {}'.format(bpy.context.scene.python_cmd, script)
StreamingPanel.in_queue, StreamingPanel.out_queue = mu.run_command_in_new_thread(cmd, queues=True)
StreamingPanel.is_streaming = not StreamingPanel.is_streaming
return {'RUNNING_MODAL'}
def invoke(self, context, event=None):
subject = mu.get_user()
threshold = bpy.context.scene.fmri_clustering_threshold
contrast = bpy.context.scene.fmri_clusters_labels_files
atlas = bpy.context.scene.atlas
task = contrast.split('_')[0]
context.window_manager.modal_handler_add(self)
self._timer = context.window_manager.event_timer_add(0.1, context.window)
mu.change_fol_to_mmvt_root()
cmd = '{} -m src.preproc.fMRI_preproc -s {} -T {} -c {} -t {} -a {} -f find_clusters'.format(
bpy.context.scene.python_cmd, subject, task, contrast, threshold, atlas)
print('Running {}'.format(cmd))
self.in_q, self.out_q = mu.run_command_in_new_thread(cmd)
return {'RUNNING_MODAL'}
def color_manually():
ColoringMakerPanel.what_is_colored.add(WIC_MANUALLY)
init_activity_map_coloring('FMRI')
subject_fol = mu.get_user_fol()
objects_names, colors, data = defaultdict(list), defaultdict(list), defaultdict(list)
for line in mu.csv_file_reader(op.join(subject_fol, 'coloring', '{}.csv'.format(bpy.context.scene.coloring_files))):
obj_name, color_name = line[0], line[1:]
if obj_name[0] == '#':
continue
if isinstance(color_name, list) and len(color_name) == 1:
color_name = color_name[0]
obj_type = mu.check_obj_type(obj_name)
if isinstance(color_name, str) and color_name.startswith('mark'):
import filter_panel
filter_panel.filter_roi_func(obj_name, mark=color_name)
else:
if isinstance(color_name, str):
color_rgb = cu.name_to_rgb(color_name)
# Check if the color is already in RBG
elif len(color_name) == 3:
color_rgb = color_name
else:
print('Unrecognize color! ({})'.format(color_name))
continue
color_rgb = list(map(float, color_rgb))
if obj_type is not None:
objects_names[obj_type].append(obj_name)
colors[obj_type].append(color_rgb)
data[obj_type].append(1.)
color_objects(objects_names, colors, data)
if op.isfile(op.join(subject_fol, 'coloring', '{}_legend.jpg'.format(bpy.context.scene.coloring_files))):
cmd = '{} -m src.preproc.electrodes_preproc -s {} -a {} -f show_labeling_coloring'.format(
bpy.context.scene.python_cmd, mu.get_user(), bpy.context.scene.atlas)
print('Running {}'.format(cmd))
mu.run_command_in_new_thread(cmd, False)
def color_manually():
ColoringMakerPanel.what_is_colored.add(WIC_MANUALLY)
init_activity_map_coloring('FMRI')
subject_fol = mu.get_user_fol()
objects_names, colors, data = defaultdict(list), defaultdict(list), defaultdict(list)
for line in mu.csv_file_reader(op.join(subject_fol, 'coloring', '{}.csv'.format(bpy.context.scene.coloring_files))):
obj_name, color_name = line[0], line[1:]
if obj_name[0] == '#':
continue
if isinstance(color_name, list) and len(color_name) == 1:
color_name = color_name[0]
obj_type = mu.check_obj_type(obj_name)
if isinstance(color_name, str) and color_name.startswith('mark'):
import filter_panel
filter_panel.filter_roi_func(obj_name, mark=color_name)
else:
if isinstance(color_name, str):
color_rgb = cu.name_to_rgb(color_name)
# Check if the color is already in RBG
elif len(color_name) == 3:
color_rgb = color_name
else:
print('Unrecognize color! ({})'.format(color_name))
continue
color_rgb = list(map(float, color_rgb))
if obj_type is not None:
objects_names[obj_type].append(obj_name)
colors[obj_type].append(color_rgb)
data[obj_type].append(1.)
color_objects(objects_names, colors, data)
if op.isfile(op.join(subject_fol, 'coloring', '{}_legend.jpg'.format(bpy.context.scene.coloring_files))):
cmd = '{} -m src.preproc.electrodes_preproc -s {} -a {} -f show_labeling_coloring'.format(
bpy.context.scene.python_cmd, mu.get_user(), bpy.context.scene.atlas)
print('Running {}'.format(cmd))
mu.run_command_in_new_thread(cmd, False)
def render_in_background(image_name, image_fol, camera_fname, hide_subcorticals, overwrite=True):
hide_subs_in_background = True if hide_subcorticals else bpy.context.scene.objects_show_hide_sub_cortical
mu.change_fol_to_mmvt_root()
electrode_marked = _addon().is_current_electrode_marked()
script = 'src.mmvt_addon.scripts.render_image'
cmd = '{} -m {} -s {} -a {} -i {} -o {} -q {} -b {} -c "{}"'.format(
bpy.context.scene.python_cmd, script, mu.get_user(), bpy.context.scene.atlas,
image_name, image_fol, bpy.context.scene.render.resolution_percentage,
bpy.context.scene.bipolar, camera_fname) + \
' --hide_lh {} --hide_rh {} --hide_subs {} --show_elecs {} --curr_elec {} --show_only_lead {}'.format(
bpy.context.scene.objects_show_hide_lh, bpy.context.scene.objects_show_hide_rh,
hide_subs_in_background, bpy.context.scene.show_hide_electrodes,
bpy.context.scene.electrodes if electrode_marked else None,
bpy.context.scene.show_only_lead if electrode_marked else None) + \
' --show_connections {} --interactive 0 --overwrite {}'.format(
_addon().connections_visible(), overwrite)
print('Running {}'.format(cmd))
RenderingMakerPanel.background_rendering = True
mu.save_blender_file()
_, RenderingMakerPanel.render_in_queue = mu.run_command_in_new_thread(
cmd, read_stderr=False, read_stdin=False, stdout_func=reading_from_rendering_stdout_func)
def start_slicer_server():
cmd = '{} -m src.listeners.slicer_listener'.format(bpy.context.scene.python_cmd)
mu.run_command_in_new_thread(cmd, False)
def start_listener():
cmd = 'python {}'.format(
op.join(mmvt_utils.current_path(), 'addon_listener.py'))
listener_in_queue, listener_out_queue = mmvt_utils.run_command_in_new_thread(
cmd)
return listener_in_queue, listener_out_queue
def invoke(self, context, event=None):
cmd = '{} -m src.preproc.anatomy_preproc -s {} -a {}'.format(
bpy.context.scene.python_cmd, mu.get_user(), bpy.context.scene.atlas)
print('Running {}'.format(cmd))
mu.run_command_in_new_thread(cmd, False)
return {"FINISHED"}
def start_listener():
cmd = 'python {}'.format(op.join(mmvt_utils.current_path(), 'addon_listener.py'))
listener_in_queue, listener_out_queue = mmvt_utils.run_command_in_new_thread(cmd)
return listener_in_queue, listener_out_queue
