def plot_to_docks(self, video_path_to_plots_dict, area):
if not video_path_to_plots_dict:
return
roi_names = list(list(video_path_to_plots_dict.values())[0].keys())
video_paths = list(video_path_to_plots_dict.keys())
# regroup ROIs of same type together and add to Docks dynamically
plot_docks = range(len([i for i in self.area.docks.keys()]))
plot_docs_cycle = cycle(plot_docks)
for roi_name in roi_names:
warning_issued = False
plots_for_roi = []
source_names = []
for video_path in video_path_to_plots_dict.keys():
root, ext = os.path.splitext(video_path)
source_name = os.path.basename(root)
source_names = source_names + [source_name]
plots_for_roi = plots_for_roi + [video_path_to_plots_dict[video_path][roi_name]]
# put all plots from one ROI on a single plot and place on one of the 4 docs
next_dock = next(plot_docs_cycle)
d = Dock(roi_name, size=(500, 200), closable=True)
area.addDock(d, 'above', area.docks['d' + str(next_dock + 1)])
doc_window = pg.GraphicsWindow(title="Dock plot")
plot = doc_window.addPlot(title=roi_name)
plot.setLabel('bottom', "Image Frames")
plot.setLabel('left', "Activity")
plot.addLegend()
assert (len(plots_for_roi) == len(source_names))
for i, (p, source_name) in enumerate(zip(plots_for_roi, source_names)):
if i < len(brewer_colors):
color = brewer_colors[i].rgb
else:
if not warning_issued:
qtutil.warning('Perceptual distinctiveness limit (12) reached. Resorting to Kelly colours. '
'Please be careful with how you interpret your data')
warning_issued = True
if i < len(brewer_colors) + len(kelly_colors):
color = kelly_colors[i - len(brewer_colors)].rgb
else:
qtutil.critical(
'Colour limit reached. Please plot your data over multiple plots or output solely to csv')
return doc_window
plot.plot(p, pen=color, name=source_name)
d.addWidget(doc_window)
# Save plot to file (backup)
ps = [list(p) for p in plots_for_roi]
ps_rows = list(zip(*ps))
plot_out = os.path.join(os.path.dirname(video_paths[0]), roi_name + '_plots_backup.csv')
with open(plot_out, 'w', newline='') as csvfile:
writer = csv.writer(csvfile, delimiter=',',
quotechar='|', quoting=csv.QUOTE_MINIMAL)
writer.writerow(source_names)
for i, row in enumerate(ps_rows):
writer.writerow([str(p) for p in row])
# close placeholder docks
for plot_dock in plot_docks:
area.docks['d' + str(plot_dock + 1)].close()
def load_file(filename, progress_callback=None, segment=None):
file_size = os.path.getsize(filename)
available = list(psutil.virtual_memory())[1]
percent = list(psutil.virtual_memory())[2]
# [total, available, percent, used, free, active, inactive, buffers, cached, shared] = list(psutil.virtual_memory())
if file_size > available:
qtutil.critical('Not enough memory. File is of size ' +
str(file_size) + ' and available memory is: ' +
str(available))
raise MemoryError('Not enough memory. File is of size ' +
str(file_size) + ' and available memory is: ' +
str(available))
if percent > 95:
qtutil.warning('Your memory appears to be getting low.')
if filename.endswith('.npy'):
frames = load_npy(filename, progress_callback, segment)
# if frames.dtype == 'float64':
# qtutil.critical("FLOAT64")
# raise MemoryError("FLOAT64")
else:
raise UnknownFileFormatError()
return frames
def new_json(self):
self.video_list.model().clear()
fd = FileDialog()
fd.exec_()
fd.show()
dirnames = fd.selectedFiles()
if not dirnames or os.path.normpath(dirnames[0]) == os.path.normpath(
fd.directory().absolutePath()):
return
for project_dir in dirnames:
only_files = [
join(project_dir, f) for f in listdir(project_dir)
if isfile(join(project_dir, f))
]
json_paths = [f for f in only_files if f[-5:] == '.json']
if not json_paths:
qtutil.critical(
"Not a project directory. No JSON file found in " +
project_dir + ". Skipping.")
continue
self.project_list = self.project_list + [Project(project_dir)]
for project in self.project_list:
for f in project.files:
if f['type'] != 'video':
continue
self.video_list.model().appendRow(QStandardItem(f['name']))
self.project_at_ind = self.project_at_ind + [project]
self.video_list.setCurrentIndex(self.video_list.model().index(
0, 0))
def load_state(self):
filenames = QFileDialog.getOpenFileNames(
self, 'Load images',
QSettings().value('last_vis_path'),
'visualization window pickle (*.pkl)')[0]
if not filenames:
return
QSettings().setValue('last_vis_path', os.path.dirname(filenames[0]))
for filename in filenames:
try:
with open(filename, 'rb') as input:
[video_path_to_plots_dict, state] = pickle.load(input)
new_dw = DockWindowPlot(video_path_to_plots_dict,
parent=self.parent,
state=state,
title=os.path.basename(filename))
self.parent.open_dialogs.append(new_dw)
new_dw.show()
new_dw.saving_state[str].connect(
functools.partial(pfs.save_dock_window_to_project,
self.parent,
self.parent.Labels.window_type))
except:
qtutil.critical(filename + " failed to open. Aborting.")
return
def __init__(self, parent=None):
super(MainWindow, self).__init__(parent)
self.setWindowTitle(APPNAME)
self.setWindowFlags(Qt.Window | Qt.WindowContextHelpButtonHint |
Qt.WindowMinimizeButtonHint |
Qt.WindowMaximizeButtonHint |
Qt.WindowCloseButtonHint)
self.project = None
self.current_plugin = None
self.project_manager = ProjectManager(self)
self.plugins = self.load_plugins()
self.sidebar = Sidebar()
self.setup_ui()
self.setup_signals()
self.enable(False)
self.pipeline_model = PipelineModel()
self.sidebar.pl_list.setModel(self.pipeline_model)
self.pipeconf.pipeline_list.setModel(self.pipeline_model)
last = str(QSettings().value('path_of_last_project'))
if last:
quit_msg = "Load last project " + last + " ?"
reply = QMessageBox.question(self, 'Project Setup',
quit_msg, QMessageBox.Yes | QMessageBox.No)
if reply == QMessageBox.Yes:
if last:
try:
self.open_project(last)
except:
qtutil.critical('Previous project appears to have been corrupted.\n \n'
+ traceback.format_exc(), self)
#qtutil.critical("Previous project appears to have been corrupted. Please move or delete it.")
self.sidebar.setup_sidebar_values(self.project)
def connectivity_triggered(self):
cm_type = self.cm_comboBox.currentText()
progress = QProgressDialog('Generating Correlation Matrix...', 'Abort', 0, 100, self)
progress.setAutoClose(True)
progress.setMinimumDuration(0)
def callback(x):
progress.setValue(x * 100)
QApplication.processEvents()
indexes = self.roi_list.selectionModel().selectedIndexes()
roinames = [index.data(Qt.DisplayRole) for index in indexes]
rois = [self.view.vb.getRoi(roiname) for roiname in roinames]
if not self.view.vb.img:
qtutil.critical('Select video.')
elif not rois:
qtutil.critical('Select Roi(s).')
else:
win = ConnectivityDialog(self, roinames, cm_type, progress_callback=callback)
win.resize(900, 900)
callback(1)
# self.open_dialogs.append(win)
# todo: add matrices to docks
dock_window = DockWindowMat(win, parent=self)
self.open_dialogs.append(dock_window)
dock_window.show()
self.save_open_dialogs_to_csv()
def sub_clicked(self):
summed_filesize = 0
for path in self.selected_videos:
summed_filesize = summed_filesize + os.path.getsize(path)
available = list(psutil.virtual_memory())[1]
if summed_filesize > available:
qtutil.critical("Not enough memory. Total is of size "+str(summed_filesize) +\
" and available memory is: " + str(available))
raise MemoryError("Not enough memory. Total is of size "+str(summed_filesize) +\
" and available memory is: " + str(available))
paths = self.selected_videos
if len(paths) != 2:
qtutil.warning('Select two files to subtract.')
return
frames = [file_io.load_file(f) for f in paths]
min_len = min([len(f) for f in frames])
frames = np.subtract(np.array(frames[0][0:min_len], dtype=np.float32),
np.array(frames[1][0:min_len], dtype=np.float32))
frames = np.array(frames, dtype=np.float32)
# First one has to take the name otherwise pfs.save_projects doesn't work
manip = 'channel_sub'
pfs.save_project(paths[0], self.project, frames, manip, 'video')
pfs.refresh_list(self.project, self.video_list,
self.params[self.Labels.video_list_indices_label],
self.Defaults.list_display_type,
self.params[self.Labels.last_manips_to_display_label])
def __init__(self, parent=None):
super(MainWindow, self).__init__(parent)
self.setWindowTitle(APPNAME)
self.setWindowFlags(Qt.Window | Qt.WindowContextHelpButtonHint |
Qt.WindowMinimizeButtonHint |
Qt.WindowMaximizeButtonHint |
Qt.WindowCloseButtonHint)
self.project = None
self.current_plugin = None
self.project_manager = ProjectManager(self)
self.plugins = self.load_plugins()
self.sidebar = Sidebar()
self.setup_ui()
self.setup_signals()
self.enable(False)
self.pipeline_model = PipelineModel()
self.sidebar.pl_list.setModel(self.pipeline_model)
self.pipeconf.pipeline_list.setModel(self.pipeline_model)
last = str(QSettings().value('path_of_last_project'))
if last:
quit_msg = "Load last project " + last + " ?"
reply = QMessageBox.question(self, 'Project Setup',
quit_msg, QMessageBox.Yes, QMessageBox.No)
if reply == QMessageBox.Yes:
if last:
try:
self.open_project(last)
except:
qtutil.critical('Previous project appears to have been corrupted.\n \n'
+ traceback.format_exc(), self)
#qtutil.critical("Previous project appears to have been corrupted. Please move or delete it.")
self.sidebar.setup_sidebar_values(self.project)
def remove_clicked(self):
rows = self.table.selectionModel().selectedRows()
if not rows:
return
fileinfos = [self.table.model().get_entry(row) for row in rows]
for fileinfo in fileinfos:
#fileinfo = self.table.model().get_entry(row)
dialog = RemoveDialog(fileinfo, self)
dialog.exec_()
if not dialog.action:
return
if dialog.action == 'remove':
try:
os.remove(fileinfo['path'])
except:
qtutil.critical('Could not delete file.')
return
# detach
self.project.files[:] = [
f for f in self.project.files
if f['path'] != fileinfo['path']
]
self.project.save()
self.reload_plugins.emit()
self.update(self.project)
def connectivity_triggered(self):
cm_type = self.cm_comboBox.currentText()
progress = QProgressDialog('Generating Correlation Matrix...', 'Abort', 0, 100, self)
progress.setAutoClose(True)
progress.setMinimumDuration(0)
def callback(x):
progress.setValue(x * 100)
QApplication.processEvents()
indexes = self.roi_list.selectionModel().selectedIndexes()
roinames = [index.data(Qt.DisplayRole) for index in indexes]
rois = [self.view.vb.getRoi(roiname) for roiname in roinames]
if not self.view.vb.img:
qtutil.critical('Select video.')
elif not rois:
qtutil.critical('Select Roi(s).')
else:
win = ConnectivityDialog(self, roinames, cm_type, progress_callback=callback)
win.resize(900, 900)
callback(1)
# self.open_dialogs.append(win)
# todo: add matrices to docks
dock_window = DockWindowMat(win, parent=self)
self.open_dialogs.append(dock_window)
dock_window.show()
self.save_open_dialogs_to_csv()
def export_raw(self, filepath, filename, export_dtype):
frames = file_io.load_file(filepath)
frames = frames.astype(export_dtype)
try:
frames.tofile(filename)
except:
qtutil.critical(filename + ' could not be written. Ensure that export dtype is properly set. '
'This fixes this issue in most cases.', self)
def export_raw(self, filepath, filename, export_dtype):
frames = file_io.load_file(filepath)
frames = frames.astype(export_dtype)
try:
frames.tofile(filename)
except:
qtutil.critical(filename + ' could not be written. Ensure that export dtype is properly set. '
'This fixes this issue in most cases.', self)
def save_state(self):
save_loc = super().save_state()
with open(save_loc, 'rb') as input:
state = pickle.load(input)
try:
with open(save_loc, 'wb') as output:
pickle.dump([self.video_path_to_plots_dict, state], output, -1)
except:
qtutil.critical(save_loc + " failed to save.")
return
def save_state(self):
save_loc = super().save_state()
with open(save_loc, 'rb') as input:
state = pickle.load(input)
try:
with open(save_loc, 'wb') as output:
pickle.dump([self.video_path_to_plots_dict, state], output, -1)
except:
qtutil.critical(save_loc + " failed to save.")
return
def convert_tif(self, filename):
rescale_value = float(self.scale_factor.value())
channel = int(self.channel.value())
new_filename = os.path.basename(filename)[:-4]
new_filename = os.path.join(self.project.path, new_filename) + '.npy'
if os.path.isfile(new_filename):
i = 1
path_after = new_filename
while os.path.isfile(path_after):
name_after = new_filename[:-4] + '(' + str(i) + ')' + '.npy'
path_after = os.path.join(self.project.path, name_after)
i = i + 1
path = path_after
else:
path = os.path.splitext(os.path.basename(filename))[0] + '.npy'
path = os.path.join(self.project.path, path)
progress = QProgressDialog('Converting tif to npy...', 'Abort', 0, 100,
self)
progress.setAutoClose(True)
progress.setMinimumDuration(0)
progress.setValue(0)
def callback(value):
progress.setValue(int(value * 100))
QApplication.processEvents()
try:
fileconverter.tif2npy(filename, path, callback)
except:
qtutil.critical('Converting tiff to npy failed.')
progress.close()
else:
ret_filename = path
with tiff.TiffFile(filename) as tif:
if rescale_value != 1.00:
w, h = tif[0].shape
rescale_width = int(w * rescale_value)
rescale_height = int(h * rescale_value)
no_frames = len(tif)
unscaled = np.load(path)
try:
scaled = self.bin_ndarray(
unscaled,
(no_frames, rescale_height, rescale_width),
callback,
operation='mean')
np.save(path, scaled)
except:
qtutil.critical(
'Rebinning tiff failed. We can only scale down from larger sized files to preserve data'
)
progress.close()
return ret_filename
def convert_coord_to_numpy_reference(self, coord, dim):
assert (dim == 'x' or dim == 'y')
if not self.project['origin']:
qtutil.critical("No origin set for project")
return
pix_per_mm = 1 / self.project['unit_per_pixel']
coord_pix = coord * pix_per_mm
if dim == 'x':
return self.project['origin'][0] + coord_pix
else:
return self.project['origin'][1] + coord_pix
def setData(self, index, value, role):
if role == Qt.EditRole:
value = str(value)
if value in self.rois[index.row()]:
pass
elif value in self.rois:
qtutil.critical('Roi name taken.')
else:
self.textChanged.emit(self.rois[index.row()], value)
self.rois[index.row()] = value
return True
return super(RoiItemModel, self).setData(index, value, role)
def save_state(self):
save_loc = super().save_state()
with open(save_loc, 'rb') as input:
state = pickle.load(input)
try:
with open(save_loc, 'wb') as output:
pickle.dump([self.connectivity_dialog.model._data, self.connectivity_dialog.model.roinames,
self.connectivity_dialog.selected_image_stacks,
state], output, -1)
except:
qtutil.critical(save_loc + " failed to save.")
return
def setData(self, index, value, role):
if role == Qt.EditRole:
value = str(value)
if value in self.rois[index.row()]:
pass
elif value in self.rois:
qtutil.critical('Roi name taken.')
else:
self.textChanged.emit(self.rois[index.row()], value)
self.rois[index.row()] = value
return True
return super(RoiItemModel, self).setData(index, value, role)
def save_state(self):
save_loc = super().save_state()
with open(save_loc, 'rb') as input:
state = pickle.load(input)
try:
with open(save_loc, 'wb') as output:
pickle.dump([self.connectivity_dialog.model._data, self.connectivity_dialog.model.roinames,
self.connectivity_dialog.selected_image_stacks,
state], output, -1)
except:
qtutil.critical(save_loc + " failed to save.")
return
def set_shifts(self):
[reference_frame, not_reference_frames] = self.get_alignment_inputs()
if len(not_reference_frames) != 1:
qtutil.critical("Please select only one file to align to the reference frame to set the shift. Only one "
"file for setting shifts is supported for now")
return
frame_to_shift = file_io.load_file(not_reference_frames[0],
segment=[self.ref_no.value(), self.ref_no.value()+1])
shift = self.compute_shift(reference_frame, frame_to_shift[0])
self.tvec_x_sb.setValue(shift['tvec'][1]) # [Y,X] not [X,Y]
self.tvec_y_sb.setValue(shift['tvec'][0])
self.rotation_sb.setValue(shift['angle'])
self.scale_sb.setValue(shift['scale'])
def remove_clicked(self):
for path in self.selected_videos:
norm_path = os.path.normpath(path)
self.project.files[:] = [f for f in self.project.files if os.path.normpath(f['path']) != norm_path]
self.project.save()
for path in self.selected_videos:
try:
os.remove(path)
except:
qtutil.critical('Could not delete file ' + path)
return
pfs.refresh_list(self.project, self.video_list, self.video_list_indices,
self.Defaults.list_display_type, self.toolbutton_values)
def set_shifts(self):
[reference_frame, not_reference_frames] = self.get_alignment_inputs()
if len(not_reference_frames) != 1:
qtutil.critical("Please select only one file to align to the reference frame to set the shift. Only one "
"file for setting shifts is supported for now")
return
frame_to_shift = file_io.load_file(not_reference_frames[0],
segment=[self.ref_no.value(), self.ref_no.value()+1])
shift = self.compute_shift(reference_frame, frame_to_shift[0])
self.tvec_x_sb.setValue(shift['tvec'][1]) # [Y,X] not [X,Y]
self.tvec_y_sb.setValue(shift['tvec'][0])
self.rotation_sb.setValue(shift['angle'])
self.scale_sb.setValue(shift['scale'])
def remove_clicked(self):
for path in self.selected_videos:
norm_path = os.path.normpath(path)
self.project.files[:] = [f for f in self.project.files if os.path.normpath(f['path']) != norm_path]
self.project.save()
for path in self.selected_videos:
try:
os.remove(path)
except:
qtutil.critical('Could not delete file ' + path)
return
pfs.refresh_list(self.project, self.video_list, self.video_list_indices,
self.Defaults.list_display_type, self.toolbutton_values)
def import_files(self, filenames):
for filename in filenames:
if filename in [f['path'] for f in self.project.files]:
continue
try:
filename = self.import_file(filename)
except NotConvertedError:
qtutil.warning('Skipping file \'{}\' since not converted.'.format(filename))
except FileAlreadyInProjectError as e:
qtutil.warning('Skipping file \'{}\' since already in project.'.format(e.filename))
except:
qtutil.critical('Import of \'{}\' failed:\n'.format(filename) +\
traceback.format_exc())
else:
self.listview.model().appendRow(QStandardItem(filename))
def import_files(self, filenames):
imported_paths = []
for filename in filenames:
if filename in [f['path'] for f in self.project.files]:
continue
try:
imported_path = self.import_file(filename)
except NotConvertedError:
qtutil.warning('Skipping file \'{}\' since not converted.'.format(filename))
except:
qtutil.critical('Import of \'{}\' failed:\n'.format(filename) +\
traceback.format_exc())
else:
self.listview.model().appendRow(QStandardItem(imported_path))
imported_paths = imported_paths + [imported_path]
return imported_paths
def avg_mat_triggered(self):
qtutil.info("Please select all the matrices to be averaged. Matrices must have the same ROIs in the same "
"locations. You might find it easier to move all the matrix pkl files to the same folder before "
"performing this action.")
paths = QFileDialog.getOpenFileNames(
self, 'Load matrices', QSettings().value('last_vis_path'),
'visualization window pickle (*.pkl)')
dat = []
roinames_previous = []
path_previous = ''
for path in paths:
try:
with open(path, 'rb') as input:
[mat_data, roinames, selected_image_stacks, state] = \
pickle.load(input)
dat = dat + [[mat_data, roinames, selected_image_stacks, state]]
if roinames != roinames_previous and roinames_previous:
qtutil.critical(path + 'does not have the same ROI names as ' + path_previous)
return
roinames_previous = roinames
path_previous = path
except:
qtutil.critical(path + " failed to open. Aborting. Make sure this file is a MATRIX pkl file")
mat_datas = [[len(d[2]), d[0]] for d in dat]
ns_and_means_and_stdevs = [[[] for j in range(len(mat_datas[0][1][0]))] for i in range(len(mat_datas[0][1]))]
for row_no, row in enumerate(mat_datas[0][1]):
for col_no, col in enumerate(mat_datas[0][1][0]):
for mat_data in mat_datas:
ns_and_means_and_stdevs[row_no][col_no] = ns_and_means_and_stdevs[row_no][col_no] + \
[[mat_data[0]] + list(mat_data[1][row_no][col_no])]
result = [[[] for j in range(len(mat_datas[0][1][0]))] for i in range(len(mat_datas[0][1]))]
for row_no, row in enumerate(result):
for col_no, col in enumerate(result[0]):
result[row_no][col_no] = (combined_mean([x[:-1] for x in ns_and_means_and_stdevs[row_no][col_no]]),
combined_st_dev(ns_and_means_and_stdevs[row_no][col_no]))
cm_type = self.cm_comboBox.currentText()
win = ConnectivityDialog(self, roinames, cm_type, loaded_data=result)
new_dw = DockWindowMat(win, parent=self, state=state, title=os.path.basename(paths[0]) + ' ' + str(len(paths)) +
' other matrices averaged')
self.open_dialogs.append(new_dw)
new_dw.show()
new_dw.saving_state[str].connect(functools.partial(pfs.save_dock_window_to_project, self,
self.Defaults.window_type))
def avg_mat_triggered(self):
qtutil.info("Please select all the matrices to be averaged. Matrices must have the same ROIs in the same "
"locations. You might find it easier to move all the matrix pkl files to the same folder before "
"performing this action.")
paths = QFileDialog.getOpenFileNames(
self, 'Load matrices', QSettings().value('last_vis_path'),
'visualization window pickle (*.pkl)')
dat = []
roinames_previous = []
path_previous = ''
for path in paths:
try:
with open(path, 'rb') as input:
[mat_data, roinames, selected_image_stacks, state] = \
pickle.load(input)
dat = dat + [[mat_data, roinames, selected_image_stacks, state]]
if roinames != roinames_previous and roinames_previous:
qtutil.critical(path + 'does not have the same ROI names as ' + path_previous)
return
roinames_previous = roinames
path_previous = path
except:
qtutil.critical(path + " failed to open. Aborting. Make sure this file is a MATRIX pkl file")
mat_datas = [[len(d[2]), d[0]] for d in dat]
ns_and_means_and_stdevs = [[[] for j in range(len(mat_datas[0][1][0]))] for i in range(len(mat_datas[0][1]))]
for row_no, row in enumerate(mat_datas[0][1]):
for col_no, col in enumerate(mat_datas[0][1][0]):
for mat_data in mat_datas:
ns_and_means_and_stdevs[row_no][col_no] = ns_and_means_and_stdevs[row_no][col_no] + \
[[mat_data[0]] + list(mat_data[1][row_no][col_no])]
result = [[[] for j in range(len(mat_datas[0][1][0]))] for i in range(len(mat_datas[0][1]))]
for row_no, row in enumerate(result):
for col_no, col in enumerate(result[0]):
result[row_no][col_no] = (combined_mean([x[:-1] for x in ns_and_means_and_stdevs[row_no][col_no]]),
combined_st_dev(ns_and_means_and_stdevs[row_no][col_no]))
cm_type = self.cm_comboBox.currentText()
win = ConnectivityDialog(self, roinames, cm_type, loaded_data=result)
new_dw = DockWindowMat(win, parent=self, state=state, title=os.path.basename(paths[0]) + ' ' + str(len(paths)) +
' other matrices averaged')
self.open_dialogs.append(new_dw)
new_dw.show()
new_dw.saving_state[str].connect(functools.partial(pfs.save_dock_window_to_project, self,
self.Defaults.window_type))
def load_state(self):
filenames = QFileDialog.getOpenFileNames(
self, 'Load images', QSettings().value('last_vis_path'),
'visualization window pickle (*.pkl)')
if not filenames:
return
QSettings().setValue('last_vis_path', os.path.dirname(filenames[0]))
for filename in filenames:
try:
with open(filename, 'rb') as input:
state = pickle.load(input)
new_dw = DockWindow(state, os.path.basename(filename))
new_dw.show()
except:
qtutil.critical(filename + " failed to open. Aborting.")
return
return filenames
def export_avi(self, filepath, filename, export_dtype, export_framerate):
progress = MyProgressDialog('File Exporter', 'Writing to avi...', self)
try:
frames = file_io.load_file(filepath)
frames = frames.astype(export_dtype)
video = cv2.VideoWriter(
filename, cv2.VideoWriter_fourcc(*'DIVX'), export_framerate,
(frames.shape[1], frames.shape[2]), False
)
for i, frame in enumerate(frames):
progress.setValue(100 * i / float(len(frames)-1))
video.write(frame)
cv2.destroyAllWindows()
video.release()
except:
progress.close()
qtutil.critical(filename + ' could not be written. Ensure that dtype and framerate are properly set above. '
'This fixes this issue in most cases.', self)
def export_avi(self, filepath, filename, export_dtype, export_framerate):
progress = MyProgressDialog('File Exporter', 'Writing to avi...', self)
try:
frames = file_io.load_file(filepath)
frames = frames.astype(export_dtype)
video = cv2.VideoWriter(
filename, cv2.VideoWriter_fourcc(*'DIVX'), export_framerate,
(frames.shape[1], frames.shape[2]), False
)
for i, frame in enumerate(frames):
progress.setValue(100 * i / float(len(frames)-1))
video.write(frame)
cv2.destroyAllWindows()
video.release()
except:
progress.close()
qtutil.critical(filename + ' could not be written. Ensure that dtype and framerate are properly set above. '
'This fixes this issue in most cases.', self)
def load_state(self):
filenames = QFileDialog.getOpenFileNames(
self, 'Load images',
QSettings().value('last_vis_path'),
'visualization window pickle (*.pkl)')
if not filenames:
return
QSettings().setValue('last_vis_path', os.path.dirname(filenames[0]))
for filename in filenames:
try:
with open(filename, 'rb') as input:
state = pickle.load(input)
new_dw = DockWindow(state, os.path.basename(filename))
new_dw.show()
except:
qtutil.critical(filename + " failed to open. Aborting.")
return
return filenames
def export_avi(self, filepath, filename):
progress = MyProgressDialog('File Exporter', 'Writing to avi...', self)
try:
frames = fileloader.load_file(filepath)
if frames.dtype != np.uint8:
frames = frames.astype(np.uint8)
# todo: 30 = export framerate needs to be user-decided
video = cv2.VideoWriter(
filename, cv2.VideoWriter_fourcc(*'DIVX'), 30,
(frames.shape[1], frames.shape[2]), False
)
for i, frame in enumerate(frames):
progress.setValue(100 * i / float(len(frames)-1))
video.write(frame)
cv2.destroyAllWindows()
video.release()
except:
progress.close()
qtutil.critical('Video file could not be written.', self)
def open_project(self, path=''):
if not path:
dialog = QFileDialog(self.mainwindow, 'Select project location', str(QSettings().value('projects_path')))
dialog.setFileMode(QFileDialog.Directory)
dialog.setOption(QFileDialog.DontUseNativeDialog)
dialog.setOption(QFileDialog.ShowDirsOnly, True)
if dialog.exec_():
path = str(dialog.selectedFiles()[0])
if path:
if not os.path.isfile(os.path.join(path, 'mbeproject.json')):
qtutil.critical('Directory is not a project.')
return None
parent = os.path.abspath(os.path.join(path, os.pardir))
QSettings().setValue('projects_path', parent)
if os.path.isdir(path) and os.path.isfile(os.path.join(path, 'mbeproject.json')):
return self.redefine_paths(Project(path))
else:
return None
def import_files(self, filenames):
for filename in filenames:
if filename in [f['path'] for f in self.project.files]:
continue
try:
filename = self.import_file(filename)
except NotConvertedError:
qtutil.warning(
'Skipping file \'{}\' since not converted.'.format(
filename))
except FileAlreadyInProjectError as e:
qtutil.warning(
'Skipping file \'{}\' since already in project.'.format(
e.filename))
except:
qtutil.critical('Import of \'{}\' failed:\n'.format(filename) + \
traceback.format_exc())
else:
self.listview.model().appendRow(QStandardItem(filename))
def load_state(self):
filenames = QFileDialog.getOpenFileNames(
self, 'Load images', QSettings().value('last_vis_path'),
'visualization window pickle (*.pkl)')
if not filenames:
return
QSettings().setValue('last_vis_path', os.path.dirname(filenames[0]))
for filename in filenames:
try:
with open(filename, 'rb') as input:
[video_path_to_plots_dict, state] = pickle.load(input)
new_dw = DockWindowPlot(video_path_to_plots_dict, parent=self.parent,
state=state, title=os.path.basename(filename))
self.parent.open_dialogs.append(new_dw)
new_dw.show()
new_dw.saving_state[str].connect(functools.partial(pfs.save_dock_window_to_project, self.parent,
self.parent.Labels.window_type))
except:
qtutil.critical(filename + " failed to open. Aborting.")
return
def execute_primary_function(self, input_paths=None):
if not input_paths:
if not self.selected_videos:
return
else:
selected_videos = self.selected_videos
else:
selected_videos = input_paths
summed_filesize = 0
for path in self.selected_videos:
summed_filesize = summed_filesize + os.path.getsize(path)
available = list(psutil.virtual_memory())[1]
if summed_filesize > available:
qtutil.critical("Not enough memory. Concatenated file is of size ~"+str(summed_filesize) +\
" and available memory is: " + str(available))
raise MemoryError("Not enough memory. Concatenated file is of size ~"+str(summed_filesize) +\
" and available memory is: " + str(available))
paths = selected_videos
if len(paths) < 2:
qtutil.warning('Select multiple files to concatenate.')
return
frames = [file_io.load_file(f) for f in paths]
progress = MyProgressDialog('Concatenation', 'Concatenating files...',
self)
progress.show()
progress.setValue(1)
frames = np.concatenate(frames)
progress.setValue(99)
# First one has to take the name otherwise pfs.save_projects doesn't work
filenames = [os.path.basename(path) for path in paths]
manip = 'concat-' + str(len(filenames))
output_path = pfs.save_project(paths[0], self.project, frames, manip,
'video')
pfs.refresh_list(self.project, self.video_list,
self.params[self.Labels.video_list_indices_label],
self.Defaults.list_display_type,
self.params[self.Labels.last_manips_to_display_label])
progress.close()
return [output_path]
def load_state(self):
filenames = QFileDialog.getOpenFileNames(
self, 'Load matrix', QSettings().value('last_vis_path'),
'visualization window pickle (*.pkl)')[0]
if not filenames:
return
QSettings().setValue('last_vis_path', os.path.dirname(filenames[0]))
for filename in filenames:
try:
with open(filename, 'rb') as input:
[mat_data, roinames, selected_image_stacks, state] = pickle.load(input)
cm_type = self.parent.cm_comboBox.currentText()
win = ConnectivityDialog(self.parent, roinames, cm_type, mat_data)
new_dw = DockWindowMat(win, parent=self.parent, state=state, title=os.path.basename(filename))
self.parent.open_dialogs.append(new_dw)
new_dw.show()
new_dw.saving_state[str].connect(functools.partial(pfs.save_dock_window_to_project, self.parent,
self.parent.Defaults.window_type))
except:
qtutil.critical(filename + " failed to open. Aborting.")
return
def load_state(self):
filenames = QFileDialog.getOpenFileNames(
self, 'Load matrix', QSettings().value('last_vis_path'),
'visualization window pickle (*.pkl)')
if not filenames:
return
QSettings().setValue('last_vis_path', os.path.dirname(filenames[0]))
for filename in filenames:
try:
with open(filename, 'rb') as input:
[mat_data, roinames, selected_image_stacks, state] = pickle.load(input)
cm_type = self.parent.cm_comboBox.currentText()
win = ConnectivityDialog(self.parent, roinames, cm_type, mat_data)
new_dw = DockWindowMat(win, parent=self.parent, state=state, title=os.path.basename(filename))
self.parent.open_dialogs.append(new_dw)
new_dw.show()
new_dw.saving_state[str].connect(functools.partial(pfs.save_dock_window_to_project, self.parent,
self.parent.Defaults.window_type))
except:
qtutil.critical(filename + " failed to open. Aborting.")
return
def convert_raw(self, filename):
rescale_value = float(self.scale_factor.value())
dtype = str(self.cb_dtype.currentText())
width = int(self.sb_width.value())
height = int(self.sb_height.value())
rescale_width = int(width * rescale_value)
rescale_height = int(height * rescale_value)
channels = int(self.sb_channel.value())
channel = int(self.channel.value())
path = os.path.splitext(os.path.basename(filename))[0] + '_channel_' + str(channel) + '.npy'
path = os.path.join(self.project.path, path)
progress = QProgressDialog('Converting raw to npy...', 'Abort', 0, 100, self)
progress.setAutoClose(True)
progress.setMinimumDuration(0)
progress.setValue(0)
def callback(value):
progress.setValue(int(value * 100))
QApplication.processEvents()
try:
fileconverter.raw2npy(filename, path, dtype, width, height,
channels, channel, callback)
except:
qtutil.critical('Converting raw to npy failed.')
progress.close()
else:
ret_filename = path
if rescale_value != 1.00:
unscaled = np.load(path)
no_frames = len(unscaled)
try:
scaled = self.bin_ndarray(unscaled, (no_frames, rescale_height,
rescale_width), callback, operation='mean')
np.save(path, scaled)
except:
qtutil.critical('Rebinning raw failed. We can only scale down from larger sized files to preserve data')
progress.close()
return ret_filename
def compute_ref_frame(self):
if not self.selected_videos:
qtutil.critical("No files selected")
return
if len(self.selected_videos) > 1:
qtutil.critical(
"Select only one file to compute the reference frame from")
return
if 'ref_frame' in self.selected_videos[0]:
qtutil.critical(
"Cannot compute reference frame of reference frame")
return
# find size, assuming all files in project have the same size
ref_no_min = self.ref_no_min.value()
ref_no_max = self.ref_no_max.value()
frames_mmap = np.load(self.shown_video_path, mmap_mode='c')
reference_frame_range = np.array(frames_mmap[ref_no_min:ref_no_max])
ref_frames = self.spatial_filter(reference_frame_range)
ref_frames = self.crop_border(ref_frames)
if not ref_frames.any():
return
self.reference_frame = np.mean(ref_frames, axis=0, dtype=np.float32)
frames_mmap = np.load(self.shown_video_path, mmap_mode='c')
frame_no, h, w = frames_mmap.shape
self.reference_frame = np.reshape(self.reference_frame, (1, h, w))
pfs.save_project(self.selected_videos[0], self.project,
self.reference_frame, 'ref_frame', 'ref_frame')
pfs.refresh_list(self.project, self.video_list,
self.params[self.Labels.video_list_indices_label],
self.Defaults.list_display_type,
self.params[self.Labels.last_manips_to_display_label])
def div_clicked(self):
summed_filesize = 0
for path in self.selected_videos:
summed_filesize = summed_filesize + os.path.getsize(path)
available = list(psutil.virtual_memory())[1]
if summed_filesize > available:
qtutil.critical("Not enough memory. Total is of size "+str(summed_filesize) +\
" and available memory is: " + str(available))
raise MemoryError("Not enough memory. Total is of size "+str(summed_filesize) +\
" and available memory is: " + str(available))
paths = self.selected_videos
if len(paths) != 2:
qtutil.warning('Select 2 files to divide.')
return
frames = [file_io.load_file(f) for f in paths]
min_len = min([len(f) for f in frames])
frames = np.divide(np.array(frames[0][0:min_len], dtype=np.float32),
np.array(frames[1][0:min_len], dtype=np.float32))
if np.isinf(frames).any():
qtutil.critical("Infinite values detected. Are you sure you are dividing appropriate image stacks?")
qtutil.critical('Output will appear blank. Output is too small when scaled against infinite')
frames[np.isnan(frames)] = 0 # todo: is this okay?
frames = np.array(frames, dtype=np.float32)
# First one has to take the name otherwise pfs.save_projects doesn't work
manip = 'channel_div'
pfs.save_project(paths[0], self.project, frames, manip, 'video')
pfs.refresh_list(self.project, self.video_list,
self.params[self.Labels.video_list_indices_label],
self.Defaults.list_display_type,
self.params[self.Labels.last_manips_to_display_label])
def get_alignment_inputs(self, input_files=None):
if not input_files:
filenames = self.selected_videos
reference_frame_file = [path for path in filenames if self.Defaults.secondary_manip in path]
else:
filenames = input_files
reference_frame_file = self.selected_videos
if len(reference_frame_file) != 1:
qtutil.critical("Please only select a single reference frame for each alignment plugin used."
" Automation will now close.")
raise ValueError("Please only select a single reference frame for each alignment plugin used")
if len(reference_frame_file) == 0:
qtutil.critical("No reference frame selected")
raise ValueError("No reference frame selected")
if len(reference_frame_file) > 1:
qtutil.critical("Multiple reference frames selected. Please only pick one")
raise ValueError("Multiple reference frames selected. Please only pick one")
assert(len(reference_frame_file) == 1)
reference_frame_file = reference_frame_file[0]
assert ('ref_frame' in reference_frame_file)
reference_frame = np.load(reference_frame_file)[0]
not_reference_frames = [path for path in filenames if self.Defaults.secondary_manip not in path]
return [reference_frame, not_reference_frames]
def compute_ref_frame(self):
if not self.selected_videos:
qtutil.critical("No files selected")
return
if len(self.selected_videos) > 1:
qtutil.critical("Select only one file to compute the reference frame from")
return
if 'ref_frame' in self.selected_videos[0]:
qtutil.critical("Cannot compute reference frame of reference frame")
return
# find size, assuming all files in project have the same size
ref_no_min = self.ref_no_min.value()
ref_no_max = self.ref_no_max.value()
frames_mmap = np.load(self.shown_video_path, mmap_mode='c')
reference_frame_range = np.array(frames_mmap[ref_no_min:ref_no_max])
ref_frames = self.spatial_filter(reference_frame_range)
ref_frames = self.crop_border(ref_frames)
if not ref_frames.any():
return
self.reference_frame = np.mean(ref_frames, axis=0, dtype=np.float32)
frames_mmap = np.load(self.shown_video_path, mmap_mode='c')
frame_no, h, w = frames_mmap.shape
self.reference_frame = np.reshape(self.reference_frame, (1, h, w))
pfs.save_project(self.selected_videos[0], self.project, self.reference_frame, 'ref_frame', 'ref_frame')
pfs.refresh_list(self.project, self.video_list,
self.params[self.Labels.video_list_indices_label],
self.Defaults.list_display_type,
self.params[self.Labels.last_manips_to_display_label])
def get_alignment_inputs(self, input_files=None):
if not input_files:
filenames = self.selected_videos
reference_frame_file = [path for path in filenames if self.Defaults.secondary_manip in path]
else:
filenames = input_files
reference_frame_file = self.selected_videos
if len(reference_frame_file) != 1:
qtutil.critical("Please only select a single reference frame for each alignment plugin used."
" Automation will now close.")
raise ValueError("Please only select a single reference frame for each alignment plugin used")
if len(reference_frame_file) == 0:
qtutil.critical("No reference frame selected")
raise ValueError("No reference frame selected")
if len(reference_frame_file) > 1:
qtutil.critical("Multiple reference frames selected. Please only pick one")
raise ValueError("Multiple reference frames selected. Please only pick one")
assert(len(reference_frame_file) == 1)
reference_frame_file = reference_frame_file[0]
assert ('ref_frame' in reference_frame_file)
reference_frame = np.load(reference_frame_file)[0]
not_reference_frames = [path for path in filenames if self.Defaults.secondary_manip not in path]
return [reference_frame, not_reference_frames]
def open_project(self, path=''):
if not path:
dialog = QFileDialog(self.mainwindow, 'Select project location',
str(QSettings().value('projects_path')))
dialog.setFileMode(QFileDialog.Directory)
dialog.setOption(QFileDialog.DontUseNativeDialog)
dialog.setOption(QFileDialog.ShowDirsOnly, True)
if dialog.exec_():
path = str(dialog.selectedFiles()[0])
if path:
if not os.path.isfile(os.path.join(path,
'mbeproject.json')):
qtutil.critical('Directory is not a project.')
return None
parent = os.path.abspath(os.path.join(path, os.pardir))
QSettings().setValue('projects_path', parent)
if os.path.isdir(path) and os.path.isfile(
os.path.join(path, 'mbeproject.json')):
return self.redefine_paths(Project(path))
else:
return None
def connectivity_triggered(self):
progress = QProgressDialog('Generating Connectivity Matrix...', 'Abort', 0, 100, self)
progress.setAutoClose(True)
progress.setMinimumDuration(0)
def callback(x):
progress.setValue(x * 100)
QApplication.processEvents()
indexes = self.roi_list.selectionModel().selectedIndexes()
roinames = [index.data(Qt.DisplayRole) for index in indexes]
rois = [self.view.vb.getRoi(roiname) for roiname in roinames]
if not self.view.vb.img:
qtutil.critical('Select video.')
elif not rois:
qtutil.critical('Select Roi(s).')
else:
win = ConnectivityDialog(self.selected_videos, self.view.vb.img,
rois, self.cm_type, self, callback)
callback(1)
win.show()
self.open_dialogs.append(win)
def convert_tif(self, filename):
rescale_value = float(self.scale_factor.value())
#channel = int(self.channel.value())
path = os.path.splitext(os.path.basename(filename))[0] + '.npy'
path = os.path.join(self.project.path, path)
progress = QProgressDialog('Converting tif to npy...', 'Abort', 0, 100, self)
progress.setAutoClose(True)
progress.setMinimumDuration(0)
progress.setValue(0)
def callback(value):
progress.setValue(int(value * 100))
QApplication.processEvents()
try:
fileconverter.tif2npy(filename, path, callback)
except:
qtutil.critical('Converting tiff to npy failed.')
progress.close()
else:
ret_filename = path
with tiff.TiffFile(filename) as tif:
if rescale_value != 1.00:
w, h = tif[0].shape
rescale_width = int(w * rescale_value)
rescale_height = int(h * rescale_value)
no_frames = len(tif)
unscaled = np.load(path)
try:
scaled = self.bin_ndarray(unscaled, (no_frames, rescale_height,
rescale_width), callback, operation='mean')
np.save(path, scaled)
except:
qtutil.critical('Rebinning tiff failed. We can only scale down from larger sized files to preserve data')
progress.close()
return ret_filename
def save_file(path, data):
file_size = data.nbytes
available = list(psutil.virtual_memory())[1]
percent = list(psutil.virtual_memory())[2]
# [total, available, percent, used, free, active, inactive, buffers, cached, shared] = list(psutil.virtual_memory())
if file_size > available:
qtutil.critical('Memory warning. File is of size ' + str(file_size) +
' and available memory is: ' + str(available))
# del_msg = path + " might not be saved due to insufficient memory. " \
# "If you attempt to save it, it may cause system instability. If you do abort then this file" \
# "will be lost. Note that only this one file will be lost. Proceed?"
# reply = QMessageBox.question(widget, 'File Save Error',
# del_msg, QMessageBox.Yes, QMessageBox.No)
# if reply == QMessageBox.No:
# raise MemoryError('Not enough memory. File is of size ' + str(file_size) +
# ' and available memory is: ' + str(available))
if percent > 95:
qtutil.warning('Your memory appears to be getting low.')
# total, used, free = psutil.disk_usage(os.path.dirname(path))
# if data.nbytes > free:
# qtutil.critical('Not enough space on drive. File is of size ' + str(data.nbytes) +
# ' and available space is: ' + str(free))
# raise IOError('Not enough space on drive. File is of size ' + str(data.nbytes) +
# ' and available space is: ' + str(free))
if os.path.isfile(path):
os.remove(path)
try:
# if data.dtype == 'float64':
# qtutil.critical("FLOAT64")
# raise MemoryError("FLOAT64")
np.save(path, data)
except:
qtutil.critical(
'Could not save ' + path +
'. This is likely due to running out of space on the drive')
def get_video_path_to_plots_dict(self):
'''Collect ROI activities for each selected vid'''
indexes = self.roi_list.selectionModel().selectedIndexes()
roinames = [index.data(Qt.DisplayRole) for index in indexes]
rois = [self.view.vb.getRoi(roiname) for roiname in roinames]
video_paths = self.selected_videos
image = self.view.vb.img
if not rois:
qtutil.critical("No ROI selected.")
return
if not video_paths:
qtutil.critical("No image stack selected")
return
progress_load = QProgressDialog(
'Loading files and collecting ROI data. This may take a while '
'for large files.', 'Abort', 0, 100)
progress_load.setAutoClose(True)
progress_load.setMinimumDuration(0)
def callback_load(x):
progress_load.setValue(x * 100)
QApplication.processEvents()
video_path_to_plots_dict = {}
for i, video_path in enumerate(video_paths):
callback_load(i / len(video_paths))
if progress_load.wasCanceled():
return
frames = file_io.load_file(video_path)
roi_activity_dict = {}
for j, roi in enumerate(rois):
mask = roi.getROIMask(frames, image, axes=(1, 2))
size = np.count_nonzero(mask)
if size <= 0:
qtutil.critical(
"No ROI selected. If you do have ROIs selected then the most likely cause is that "
"you have modified the unit per pixel and not updated the size of the ROIs which "
"don't adjust automatically. So for example any ROI with length 1 might now be less "
"than 1 pixel after you changed the unit per pixel. To update the ROIs against your "
"new unit per pixel, go to the import ROI plugin and press the 'Update Table' button"
)
return
roi_frames = frames * mask[np.newaxis, :, :]
roi_frames = np.ndarray.sum(np.ndarray.sum(roi_frames, axis=1),
axis=1)
p = roi_frames / size
roi_activity_dict[roi.name] = p
video_path_to_plots_dict[video_path] = roi_activity_dict
callback_load(1)
return video_path_to_plots_dict
def get_video_path_to_spc_dict(self):
# retrieve ROIs in view and their coordinates
if 'roi_table' not in [self.project.files[x]['type'] for x in range(len(self.project.files))]:
qtutil.critical("There's no ROI table associated with this project. "
"ROIs coordinates are used as seeds to create seed pixel correlation maps")
return
text_file_path = [self.project.files[x]['path'] for x in range(len(self.project.files))
if self.project.files[x]['type'] == 'roi_table']
assert (len(text_file_path) == 1)
text_file_path = text_file_path[0]
roi_table = []
with open(text_file_path, 'rt', encoding='ascii') as csvfile:
roi_table_it = csv.reader(csvfile, delimiter=',')
for row in roi_table_it:
roi_table = roi_table + [row]
roi_table = np.array(roi_table)
roi_table_range = range(len(roi_table))[1:]
roi_names = [roi_table[x, 0] for x in roi_table_range]
roi_coord_x = [float(roi_table[x, 2]) for x in roi_table_range]
roi_coord_y = [float(roi_table[x, 3]) for x in roi_table_range]
roi_coord_x = [self.convert_coord_to_numpy_reference(x, 'x') for x in roi_coord_x]
roi_coord_y = [self.convert_coord_to_numpy_reference(y, 'y') for y in roi_coord_y]
rois_in_view = [self.view.vb.rois[x].name for x in range(len(self.view.vb.rois))]
selected_videos = self.selected_videos
if not rois_in_view:
qtutil.critical("No ROI(s) selected as seed(s)")
return
if not selected_videos:
qtutil.critical("No image stack selected")
return
progress_load = MyProgressDialog('Processing...', 'Loading files and processing Seed Pixel Correlation maps. '
'This may take a while for large files.', parent=self)
video_path_to_plots_dict = {}
progress = MyProgressDialog('SPC Map', 'Generating correlation map...', self)
for selected_vid_no, video_path in enumerate(selected_videos):
frames = file_io.load_file(video_path)
roi_activity_dict = {}
for i, roi_name in enumerate(roi_names):
if progress_load.wasCanceled():
return
progress_load.setValue((selected_vid_no * i) / (len(selected_videos) * len(roi_names)) * 100)
if roi_name in rois_in_view:
x = roi_coord_x[i]
y = roi_coord_y[i]
spc = calc_spc(frames, x, y, progress)
roi_activity_dict[roi_name] = spc
video_path_to_plots_dict[video_path] = roi_activity_dict
progress.close()
progress_load.close()
return video_path_to_plots_dict
def get_video_path_to_plots_dict(self):
'''Collect ROI activities for each selected vid'''
indexes = self.roi_list.selectionModel().selectedIndexes()
roinames = [index.data(Qt.DisplayRole) for index in indexes]
rois = [self.view.vb.getRoi(roiname) for roiname in roinames]
video_paths = self.selected_videos
image = self.view.vb.img
if not rois:
qtutil.critical("No ROI selected.")
return
if not video_paths:
qtutil.critical("No image stack selected")
return
progress_load = QProgressDialog('Loading files and collecting ROI data. This may take a while '
'for large files.', 'Abort', 0, 100)
progress_load.setAutoClose(True)
progress_load.setMinimumDuration(0)
def callback_load(x):
progress_load.setValue(x * 100)
QApplication.processEvents()
video_path_to_plots_dict = {}
for i, video_path in enumerate(video_paths):
callback_load(i / len(video_paths))
if progress_load.wasCanceled():
return
frames = file_io.load_file(video_path)
roi_activity_dict = {}
for j, roi in enumerate(rois):
mask = roi.getROIMask(frames, image, axes=(1, 2))
size = np.count_nonzero(mask)
if size <= 0:
qtutil.critical("No ROI selected. If you do have ROIs selected then the most likely cause is that "
"you have modified the unit per pixel and not updated the size of the ROIs which "
"don't adjust automatically. So for example any ROI with length 1 might now be less "
"than 1 pixel after you changed the unit per pixel. To update the ROIs against your "
"new unit per pixel, go to the import ROI plugin and press the 'Update Table' button")
return
roi_frames = frames * mask[np.newaxis, :, :]
roi_frames = np.ndarray.sum(np.ndarray.sum(roi_frames, axis=1), axis=1)
p = roi_frames / size
roi_activity_dict[roi.name] = p
video_path_to_plots_dict[video_path] = roi_activity_dict
callback_load(1)
return video_path_to_plots_dict
def go(self):
path = str(self.final_path_edit.text())
if not path:
qtutil.critical('Choose project location.')
elif os.path.isdir(path):
qtutil.critical('Directory already exists.')
else:
try:
os.makedirs(path)
except Exception:
qtutil.critical(traceback.format_exc())
else:
self.path = path
self.name = str(self.project_name_edit.text())
self.close()
return
self.path = None
self.name = None
def go(self):
path = str(self.final_path_edit.text())
if not path:
qtutil.critical('Choose project location.')
elif os.path.isdir(path):
qtutil.critical('Directory already exists.')
else:
try:
os.makedirs(path)
except Exception:
qtutil.critical(traceback.format_exc())
else:
self.path = path
self.name = str(self.project_name_edit.text())
self.close()
return
self.path = None
self.name = None
def div_clicked(self):
summed_filesize = 0
for path in self.selected_videos:
summed_filesize = summed_filesize + os.path.getsize(path)
available = list(psutil.virtual_memory())[1]
if summed_filesize > available:
qtutil.critical("Not enough memory. Total is of size "+str(summed_filesize) +\
" and available memory is: " + str(available))
raise MemoryError("Not enough memory. Total is of size "+str(summed_filesize) +\
" and available memory is: " + str(available))
paths = self.selected_videos
if len(paths) != 2:
qtutil.warning('Select 2 files to divide.')
return
frames = [file_io.load_file(f) for f in paths]
min_len = min([len(f) for f in frames])
frames = np.divide(np.array(frames[0][0:min_len], dtype=np.float32),
np.array(frames[1][0:min_len], dtype=np.float32))
if np.isinf(frames).any():
qtutil.critical(
"Infinite values detected. Are you sure you are dividing appropriate image stacks?"
)
qtutil.critical(
'Output will appear blank. Output is too small when scaled against infinite'
)
frames[np.isnan(frames)] = 0 # todo: is this okay?
frames = np.array(frames, dtype=np.float32)
# First one has to take the name otherwise pfs.save_projects doesn't work
manip = 'channel_div'
pfs.save_project(paths[0], self.project, frames, manip, 'video')
pfs.refresh_list(self.project, self.video_list,
self.params[self.Labels.video_list_indices_label],
self.Defaults.list_display_type,
self.params[self.Labels.last_manips_to_display_label])
def sub_mat_triggered(self):
qtutil.info("Please select the matrix that will act as the minuend")
minuend_path = QFileDialog.getOpenFileName(
self, 'Load matrix', QSettings().value('last_vis_path'),
'visualization window pickle (*.pkl)')
if not minuend_path:
return
qtutil.info("Please select the matrix that will act as the subtrahend. This second matrix must have the "
"same dimensions and ROIs in the same locations as the minuend matrix")
subtrahand_path = QFileDialog.getOpenFileName(
self, 'Load matrix', QSettings().value('last_vis_path'),
'visualization window pickle (*.pkl)')
if not subtrahand_path:
return
QSettings().setValue('last_vis_path', os.path.dirname(subtrahand_path))
try:
with open(minuend_path, 'rb') as input:
[minuend_mat_data, minuend_roinames, minuend_selected_image_stacks, minuend_state] = pickle.load(input)
except:
qtutil.critical(minuend_path + " failed to open. Aborting. Make sure this file is a MATRIX pkl file")
try:
with open(subtrahand_path, 'rb') as input:
[subtrahand_mat_data, subtrahand_roinames, subtrahand_selected_image_stacks,
subtrahand_state] = pickle.load(input)
except:
qtutil.critical(subtrahand_path + " failed to open. Aborting. Make sure this file is a MATRIX pkl file")
if subtrahand_roinames != minuend_roinames:
qtutil.critical('roi names do not match. The same roi names and same order is required. Aborting.')
return
minuend_number = len(minuend_selected_image_stacks)
subtrahand_number = len(subtrahand_selected_image_stacks)
altogether = minuend_number + subtrahand_number
# minus one = Bessel correction.
# See https://stats.stackexchange.com/questions/55999/is-it-possible-to-find-the-combined-standard-deviation
ns_and_means_and_stdevs = [[[] for j in range(len(subtrahand_mat_data))]
for i in range(len(subtrahand_mat_data[0]))]
for row_no, row in enumerate(ns_and_means_and_stdevs):
for col_no, col in enumerate(ns_and_means_and_stdevs[0]):
ns_and_means_and_stdevs[row_no][col_no] = [[minuend_number] + list(minuend_mat_data[row_no][col_no]),
[subtrahand_number] +
list(subtrahand_mat_data[row_no][col_no])]
sub_mat = [[[] for j in range(len(subtrahand_mat_data[0]))] for i in range(len(subtrahand_mat_data))]
for row_no, row in enumerate(sub_mat):
for col_no, col in enumerate(sub_mat[0]):
sub_mat[row_no][col_no] = (minuend_mat_data[row_no][col_no][0]-subtrahand_mat_data[row_no][col_no][0],
combined_st_dev(ns_and_means_and_stdevs[row_no][col_no]))
cm_type = self.cm_comboBox.currentText()
win = ConnectivityDialog(self, minuend_roinames, cm_type, sub_mat)
new_dw = DockWindowMat(win, parent=self, state=minuend_state, title=os.path.basename(minuend_path) +
' - ' + os.path.basename(subtrahand_path))
self.open_dialogs.append(new_dw)
new_dw.show()
new_dw.saving_state[str].connect(functools.partial(pfs.save_dock_window_to_project, self,
self.Defaults.window_type))
def save_triggered(self):
if not self.open_dialogs:
qtutil.info('No correlation matrix windows are open. ')
return
self.save_open_dialogs_to_csv()
qtutil.info('csvs saved to project directory')
return
#todo: improve general user experience (saving,loading etc). Look at below
continue_msg = "All Correlation Matrices will be closed after saving, *including* ones you have not saved. \n" \
"\n" \
"Continue?"
reply = QMessageBox.question(self, 'Save All',
continue_msg, QMessageBox.Yes, QMessageBox.No)
if reply == QMessageBox.No:
return
qtutil.info(
'There are ' + str(len(self.open_dialogs)) + ' correlation matrices in memory. We will now choose a path '
'to save each one to. Simply don\'t save ones you have '
'purposefully closed. Though, good news, you now have '
'one last chance to save and recover any matrices you '
'accidentally closed')
for dialog in self.open_dialogs:
win_title = dialog.windowTitle()
filters = {
'.pkl': 'Python pickle file (*.pkl)'
}
default = win_title
pickle_path = self.filedialog(default, filters)
if pickle_path:
self.project.files.append({
'path': pickle_path,
'type': self.Defaults.window_type,
'name': os.path.basename(pickle_path)
})
self.project.save()
# for row in dialog.model._data:
# for cell in row:
# if math.isnan(cell[0]) or math.isnan(cell[0]):
# qtutil.warning("File might not save properly since it has nan values. Make sure all your "
# "ROIs are inside your mask.")
# break
# Now save the actual file
title = os.path.basename(pickle_path)
matrix_output_data = (title, dialog.connectivity_dialog.model.roinames,
dialog.connectivity_dialog.model._data)
try:
with open(pickle_path, 'wb') as output:
pickle.dump(matrix_output_data, output, -1)
except:
qtutil.critical(
pickle_path + " could not be saved. Ensure MBE has write access to this location and "
"that another program isn't using this file.")
qtutil.info("All files have been saved")
csv_msg = "Save csv files of all open Correlation Matrix windows as well?"
reply = QMessageBox.question(self, 'Save All',
csv_msg, QMessageBox.Yes, QMessageBox.No)
if reply == QMessageBox.Yes:
self.save_open_dialogs_to_csv()
for dialog in self.open_dialogs:
dialog.close()
self.open_dialogs = []
def load_ROI_table(self, text_file_path=None):
if not self.isActiveWindow():
return
if not text_file_path:
text_file_path = QFileDialog.getOpenFileName(
self, 'Load images', QSettings().value('last_load_text_path'),
'Video files (*.csv *.txt)')
if not text_file_path:
return
QSettings().setValue('last_load_text_path', os.path.dirname(text_file_path))
self.text_file_path = text_file_path
# Remove all ROI's from list
rois = [r for r in self.roi_list.model().rois]
for roi in rois:
self.roi_list.model().removeRow(roi)
# Delete all auto_ROIs from file
for auto_roi in [fileinfo for fileinfo in self.project.files if fileinfo['type'] == 'auto_roi']:
try:
os.remove(auto_roi['path'])
except:
qtutil.critical('Could not delete previous ROI '
+ auto_roi['path'] + '. Please delete manually before continuing')
return
# detach
self.project.files[:] = [
f for f in self.project.files
if f['path'] != auto_roi['path']
]
self.project.save()
roi_table = [] # numpy way: np.empty(shape=(4, ))
with open(text_file_path, 'rt', encoding='ascii') as csvfile:
roi_table_it = csv.reader(csvfile, delimiter=',')
for row in roi_table_it:
roi_table = roi_table + [row]
roi_table = np.array(roi_table)
self.headers = [str.strip(x) for x in roi_table[0, ]]
roi_table_range = range(len(roi_table))[1:]
roi_names = [str(roi_table[x, 0]) for x in roi_table_range]
roi_sizes = [int(roi_table[x, 1]) for x in roi_table_range]
roi_coord_x = [float(roi_table[x, 2]) for x in roi_table_range]
roi_coord_y = [float(roi_table[x, 3]) for x in roi_table_range]
self.data = {self.headers[0]: roi_names, self.headers[1]: roi_sizes,
self.headers[2]: roi_coord_x, self.headers[3]: roi_coord_y}
text_file_path_for_project = os.path.join(self.project.path, os.path.basename(text_file_path))
# for now only support having one roi_table associated per project
if 'roi_table' not in [self.project.files[x]['type'] for x in range(len(self.project.files))]:
# if text_file_path not in [self.project.files[x]['path'] for x in range(len(self.project.files))]:
try:
copyfile(text_file_path, text_file_path_for_project)
except:
qtutil.critical('Could not copy '
+ text_file_path + ' to ' + text_file_path_for_project +
'. Please do this manually and try again')
self.project.files.append({
'path': text_file_path_for_project,
'type': 'roi_table',
'name': os.path.basename(text_file_path)
})
else:
# Replace old table with new one
if not (os.path.normpath(text_file_path) ==
os.path.normpath(text_file_path_for_project)):
try:
copyfile(text_file_path, text_file_path_for_project)
except:
qtutil.critical('Could not copy '
+ text_file_path + ' to ' + text_file_path_for_project +
'. Please do this manually and try again')
for i, item in enumerate(self.project.files):
if item['type'] == 'roi_table':
self.project.files[i] = {
'path': text_file_path_for_project,
'type': 'roi_table',
'name': os.path.basename(text_file_path)
}
self.table_widget.clear()
self.table_widget.setRowCount(len(self.data[self.headers[0]]))
self.table_widget.update(self.data)
self.auto_ROI()
def plot_triggered(self):
# main_window = QMainWindow()
# area = self.setup_docks()
# main_window.setCentralWidget(area)
# main_window.resize(2000, 900)
# main_window.setWindowTitle("Window ID - " + str(uuid.uuid4()) +
# ". Click Shift+F1 for help")
# main_window.setWhatsThis("Use View All to reset a view\n"
# "\n"
# "The blue tabs have the name of the ROI for a particular plot. These tabs can be dragged "
# "around to highlighted regions to the side of other tabs to split the dock or on top of "
# "other plots to place the tab in that dock. \n"
# "\n"
# "right click any plot to see more options. One important one is mouse mode. In Mouse "
# "mode 3 you can hold the left mouse button to pan and "
# "In mouse mode 1 you can zoom in on a particular region by creating cropping it with the "
# "left mouse button. In either mode the right mouse button can be used to adjust the shape "
# "of the plot and the mouse wheel for zoom \n"
# "\n"
# "Use Export to save a particular plot's data to csv or save as an image after you are "
# "satisfied with how graphical elements (see 'plot options') are arranged. "
# "Note that backups csv's of all plots are made automatically and can be found in your "
# "project directory")
video_path_to_plots_dict = self.get_video_path_to_plots_dict()
if len(video_path_to_plots_dict.keys()) == 1:
# area = DockArea()
# d1 = Dock("d1", size=(500, 200), closable=True)
# area.addDock(d1)
video_path = list(video_path_to_plots_dict.keys())[0]
plot_title, ext = os.path.splitext(video_path)
# d = Dock(video_path, size=(500, 200), closable=True)
# area.addDock(d, 'above', area.docks['d1'])
win = pg.GraphicsWindow(title="Single Image Stack Plot")
plot = win.addPlot(title=plot_title)
plot.setLabel('bottom', "Image Frames")
plot.setLabel('left', "Activity")
plot.addLegend()
roi_names = list(video_path_to_plots_dict[video_path].keys())
warning_issued = False
for i, roi_name in enumerate(roi_names):
p = video_path_to_plots_dict[video_path][roi_name]
if i < len(brewer_colors):
color = brewer_colors[i].rgb
else:
if not warning_issued:
qtutil.warning('Perceptual distinctiveness limit (12) reached. Resorting to Kelly colours. '
'Please be careful with how you interpret your data')
warning_issued = True
if i < len(brewer_colors) + len(kelly_colors):
color = kelly_colors[i - len(brewer_colors)].rgb
else:
qtutil.critical(
'Colour limit reached. Outputting to csv instead.')
# Save plot to file (backup)
ps = [list(p) for p in list(video_path_to_plots_dict[video_path].values())]
ps_rows = list(zip(*ps))
plot_out = os.path.join(os.path.dirname(video_path), roi_name + '_plots.csv')
with open(plot_out, 'w', newline='') as csvfile:
writer = csv.writer(csvfile, delimiter=',',
quotechar='|', quoting=csv.QUOTE_MINIMAL)
writer.writerow(roi_names)
for i, row in enumerate(ps_rows):
writer.writerow([str(p) for p in row])
plot.plot(p, pen=color, name=roi_name)
self.open_dialogs.append(win)
# d.addWidget(doc_window)
else:
# self.plot_to_docks(video_path_to_plots_dict, area)
dock_window = DockWindowPlot(video_path_to_plots_dict, parent=self)
dock_window.show()
self.open_dialogs.append(dock_window)