def save_open_dialogs_to_csv(self):
if not self.open_dialogs:
qtutil.info('No correlation matrix windows are open. ')
return
for i, dialog in enumerate(self.open_dialogs):
rois_names = [dialog.connectivity_dialog.model.rois[x].name for x in range(
len(dialog.connectivity_dialog.model.rois))]
file_name_avg = os.path.splitext(os.path.basename(dialog.windowTitle()))[0] + \
'_averaged_correlation_matrix.csv'
file_name_stdev = os.path.splitext(os.path.basename(dialog.windowTitle()))[0] + \
'_stdev_correlation_matrix.csv'
with open(os.path.join(self.project.path, file_name_avg), 'w', newline='') as csvfile:
writer = csv.writer(csvfile, delimiter=',')
writer.writerow(rois_names)
for row_ind in range(len(dialog.connectivity_dialog.model._data)):
row = dialog.connectivity_dialog.model._data[row_ind]
row = [row[x][0] for x in range(len(row))]
writer.writerow(row)
writer.writerow(['Selected videos:']+self.selected_videos)
# Do the standard deviation
with open(os.path.join(self.project.path, file_name_stdev), 'w', newline='') as csvfile:
writer = csv.writer(csvfile, delimiter=',')
writer.writerow(rois_names)
for row_ind in range(len(dialog.connectivity_dialog.model._data)):
row = dialog.connectivity_dialog.model._data[row_ind]
row = [row[x][1] for x in range(len(row))]
writer.writerow(row)
writer.writerow(['Selected videos:'] + self.selected_videos)
def import_file(self, filename):
if not filename.endswith('.npy'):
new_filename = self.to_npy(filename)
if not new_filename:
raise NotConvertedError()
else:
filename = new_filename
else:
new_filename = os.path.basename(filename)
new_filename = os.path.join(self.project.path, new_filename)
if os.path.normpath(filename) != os.path.normpath(new_filename):
qtutil.info('Copying .npy from '+ filename + ' to ' + new_filename +
'. You can do this manually for large files to see a progress bar')
copyfile(filename, new_filename)
filename = new_filename
if filename in [f['path'] for f in self.project.files]:
raise FileAlreadyInProjectError(filename)
name, ext = os.path.splitext(os.path.basename(filename))
self.project.files.append({
'name': name,
'path': filename,
'type': 'video',
'manipulations': []
})
self.project.save()
return filename
def execute_primary_function(self, input_paths=None):
'''Primary function of plugin'''
if not input_paths:
if not self.selected_videos:
return
else:
selected_videos = self.selected_videos
else:
selected_videos = input_paths
# use selected_videos which are the paths to stacks the user has selected or have been input from automation
# todo: insert functionality here
if not len(self.add_list.selectedIndexes()) == len(selected_videos):
qtutil.info('Select the same number of image stacks and additions to apply')
return
output_paths = []
for add_num_item, video_path in zip(self.add_list.selectedIndexes(), selected_videos):
frames = file_io.load_file(video_path)
frames = frames + int(add_num_item.data()) # note that memory mapping is recommended for large files.
path = pfs.save_project(video_path, self.project, frames, 'custom-addition-'+add_num_item.data(),
'video')
output_paths = output_paths + [path]
# refresh_list can be used to refresh an input list that will have particular indices selected,
# specified content type shown as well as only showing content after a particular plugin manipulation
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])
# return the output path(s) of this function for automation
return output_paths
def save_open_dialogs_to_csv(self):
if not self.open_dialogs:
qtutil.info('No correlation matrix windows are open. ')
return
for i, dialog in enumerate(self.open_dialogs):
rois_names = [dialog.connectivity_dialog.model.rois[x].name for x in range(
len(dialog.connectivity_dialog.model.rois))]
file_name_avg = os.path.splitext(os.path.basename(dialog.windowTitle()))[0] + \
'_averaged_correlation_matrix.csv'
file_name_stdev = os.path.splitext(os.path.basename(dialog.windowTitle()))[0] + \
'_stdev_correlation_matrix.csv'
with open(os.path.join(self.project.path, file_name_avg), 'w', newline='') as csvfile:
writer = csv.writer(csvfile, delimiter=',')
writer.writerow(rois_names)
for row_ind in range(len(dialog.connectivity_dialog.model._data)):
row = dialog.connectivity_dialog.model._data[row_ind]
row = [row[x][0] for x in range(len(row))]
writer.writerow(row)
writer.writerow(['Selected videos:']+self.selected_videos)
# Do the standard deviation
with open(os.path.join(self.project.path, file_name_stdev), 'w', newline='') as csvfile:
writer = csv.writer(csvfile, delimiter=',')
writer.writerow(rois_names)
for row_ind in range(len(dialog.connectivity_dialog.model._data)):
row = dialog.connectivity_dialog.model._data[row_ind]
row = [row[x][1] for x in range(len(row))]
writer.writerow(row)
writer.writerow(['Selected videos:'] + self.selected_videos)
def execute_primary_function(self, input_paths=None):
'''Primary function of plugin'''
if not input_paths:
if not self.selected_videos:
return
else:
selected_videos = self.selected_videos
else:
selected_videos = input_paths
# use selected_videos which are the paths to stacks the user has selected or have been input from automation
# todo: insert functionality here
if not len(self.add_list.selectedIndexes()) == len(selected_videos):
qtutil.info(
'Select the same number of image stacks and additions to apply'
)
return
output_paths = []
for add_num_item, video_path in zip(self.add_list.selectedIndexes(),
selected_videos):
frames = file_io.load_file(video_path)
frames = frames + int(add_num_item.data(
)) # note that memory mapping is recommended for large files.
path = pfs.save_project(video_path, self.project, frames,
'custom-addition-' + add_num_item.data(),
'video')
output_paths = output_paths + [path]
# refresh_list can be used to refresh an input list that will have particular indices selected,
# specified content type shown as well as only showing content after a particular plugin manipulation
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])
# return the output path(s) of this function for automation
return output_paths
def export_bulk_clicked(self):
filetype = self.export_filetype_cb.currentText()
export_dir = str(QFileDialog.getExistingDirectory(self, "Select Directory"))
progress = MyProgressDialog('Export Progress', 'Exporting files...', self)
progress.show()
for i, selected_video in enumerate(self.selected_videos):
export_path = os.path.join(export_dir, os.path.basename(os.path.splitext(selected_video)[0]) + filetype)
progress.setValue((i / len(self.selected_videos)) * 100)
self.export_video(selected_video, export_path)
progress.close()
qtutil.info("Export to " + export_dir + " complete")
def export_bulk_clicked(self):
filetype = self.export_filetype_cb.currentText()
export_dir = str(QFileDialog.getExistingDirectory(self, "Select Directory"))
progress = MyProgressDialog('Export Progress', 'Exporting files...', self)
progress.show()
for i, selected_video in enumerate(self.selected_videos):
export_path = os.path.join(export_dir, os.path.basename(os.path.splitext(selected_video)[0]) + filetype)
progress.setValue((i / len(self.selected_videos)) * 100)
self.export_video(selected_video, export_path)
progress.close()
qtutil.info("Export to " + export_dir + " complete")
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 import_file(self, filename):
if not filename.endswith('.npy'):
new_filename = self.to_npy(filename)
if not new_filename:
raise NotConvertedError()
else:
filename = new_filename
else:
new_filename = os.path.basename(filename)
new_filename = os.path.join(self.project.path, new_filename)
if os.path.normpath(filename) != os.path.normpath(new_filename):
qtutil.info(
'Copying .npy from ' + filename + ' to ' + new_filename +
'. We recommend doing this manually for large files')
copyfile_progress = QProgressDialog(
'Progress Copying ' + filename + ' to ' + new_filename,
'Abort', 0, 100, self)
copyfile_progress.setAutoClose(True)
copyfile_progress.setMinimumDuration(0)
def callback(x):
copyfile_progress.setValue(x * 100)
QApplication.processEvents()
callback(0.0)
if copyfile_progress.wasCanceled():
return
copyfile(filename, new_filename)
if copyfile_progress.wasCanceled():
return
callback(1.0)
filename = new_filename
if filename in [f['path'] for f in self.project.files]:
return filename
# raise FileAlreadyInProjectError(filename)
name, ext = os.path.splitext(os.path.basename(filename))
self.project.files.append({
'name': name,
'path': filename,
'type': 'video',
'manipulations': []
})
self.project.save()
return filename
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 execute_primary_function(self, input_paths=None):
'''Primary function of plugin'''
if not input_paths:
if not self.selected_videos:
return
else:
selected_videos = self.selected_videos
else:
selected_videos = input_paths
# use selected_videos which are the paths to stacks the user has selected or have been input from automation
qtutil.info('This is only a template. Use it to code from. \n'
'Value of spinbox is: ' + str(self.example_sb.value()))
# todo: insert functionality here
# refresh_list can be used to refresh an input list that will have particular indices selected,
# specified content type shown as well as only showing content after a particular plugin manipulation
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 execute_primary_function(self, input_paths=None):
'''Primary function of plugin'''
if not input_paths:
if not self.selected_videos:
return
else:
selected_videos = self.selected_videos
else:
selected_videos = input_paths
# use selected_videos which are the paths to stacks the user has selected or have been input from automation
qtutil.info('This is only a template. Use it to code from. \n'
'Value of spinbox is: ' + str(self.example_sb.value()))
# todo: insert functionality here
# refresh_list can be used to refresh an input list that will have particular indices selected,
# specified content type shown as well as only showing content after a particular plugin manipulation
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 export_clicked(self):
"""Retrieve fileinfo and call export"""
progress = MyProgressDialog('Export Progress', 'Exporting files...', self)
progress.show()
for i, selected_video in enumerate(self.selected_videos):
progress.setValue((i/len(self.selected_videos)) * 100)
filters = {
# '.mp4': 'MP4 file (*.mp4)',
'.avi': 'AVI file (*.avi)',
'.tif': 'TIF file (*.tif)',
'.raw': 'RAW file (*.raw)'
}
default = os.path.basename(selected_video) or 'untitled'
# default = 'name' in fileinfo and fileinfo['name'] or 'untitled'
filename = self.filedialog(default, filters)
if not filename:
return
self.export_video(selected_video, filename)
progress.close()
qtutil.info("File export for selected files complete")
def export_clicked(self):
"""Retrieve fileinfo and call export"""
progress = MyProgressDialog('Export Progress', 'Exporting files...', self)
progress.show()
for i, selected_video in enumerate(self.selected_videos):
progress.setValue((i/len(self.selected_videos)) * 100)
filters = {
# '.mp4': 'MP4 file (*.mp4)',
'.avi': 'AVI file (*.avi)',
'.tif': 'TIF file (*.tif)',
'.raw': 'RAW file (*.raw)'
}
default = os.path.basename(selected_video) or 'untitled'
# default = 'name' in fileinfo and fileinfo['name'] or 'untitled'
filename = self.filedialog(default, filters)
if not filename:
return
self.export_video(selected_video, filename)
progress.close()
qtutil.info("File export for selected files complete")
def load_triggered(self):
paths = [p['path'] for p in self.project.files if p['type'] == self.Defaults.window_type]
if not paths:
qtutil.info("Your project has no correlation matrices. Make and save some!")
return
for pickle_path in paths:
try:
with open(pickle_path, 'rb') as input:
(title, roinames, dat) = pickle.load(input)
except:
del_msg = pickle_path + " could not be loaded. If this file exists, " \
"ensure MBE has read access to this " \
"location and that another program isn't using this file " \
"" \
"\n \nOtherwise, would you like to detatch this file from your project? "
reply = QMessageBox.question(self, 'File Load Error',
del_msg, QMessageBox.Yes, QMessageBox.No)
if reply == QMessageBox.Yes:
norm_path = os.path.normpath(pickle_path)
self.project.files[:] = [f for f in self.project.files if
os.path.normpath(f['path']) != norm_path]
self.project.save()
load_msg = pickle_path + " detatched from your project." \
"" \
"\n \n Would you like to continue loading the " \
"remaining project matrices?"
reply = QMessageBox.question(self, 'Continue?',
load_msg, QMessageBox.Yes, QMessageBox.No)
if reply == QMessageBox.No:
return
continue
main_window = ConnectivityDialog(self, roinames, self.cm_comboBox.currentText(), dat)
main_window.setWindowTitle(title)
main_window.resize(900, 900)
main_window.show()
self.open_dialogs.append(main_window)
def load_triggered(self):
paths = [p['path'] for p in self.project.files if p['type'] == self.Defaults.window_type]
if not paths:
qtutil.info("Your project has no correlation matrices. Make and save some!")
return
for pickle_path in paths:
try:
with open(pickle_path, 'rb') as input:
(title, roinames, dat) = pickle.load(input)
except:
del_msg = pickle_path + " could not be loaded. If this file exists, " \
"ensure MBE has read access to this " \
"location and that another program isn't using this file " \
"" \
"\n \nOtherwise, would you like to detatch this file from your project? "
reply = QMessageBox.question(self, 'File Load Error',
del_msg, QMessageBox.Yes | QMessageBox.No)
if reply == QMessageBox.Yes:
norm_path = os.path.normpath(pickle_path)
self.project.files[:] = [f for f in self.project.files if
os.path.normpath(f['path']) != norm_path]
self.project.save()
load_msg = pickle_path + " detatched from your project." \
"" \
"\n \n Would you like to continue loading the " \
"remaining project matrices?"
reply = QMessageBox.question(self, 'Continue?',
load_msg, QMessageBox.Yes | QMessageBox.No)
if reply == QMessageBox.No:
return
continue
main_window = ConnectivityDialog(self, roinames, self.cm_comboBox.currentText(), dat)
main_window.setWindowTitle(title)
main_window.resize(900, 900)
main_window.show()
self.open_dialogs.append(main_window)
def save_open_dialogs_to_csv(self):
progress = QProgressDialog('Generating csv files...',
'Abort', 0, 100, self)
progress.setAutoClose(True)
progress.setMinimumDuration(0)
def callback(x):
progress.setValue(x * 100)
QApplication.processEvents()
for i, dialog in enumerate(self.open_dialogs):
callback(i / len(self.open_dialogs))
rois_names = [dialog.model.rois[x].name for x in range(len(dialog.model.rois))]
unique_id = str(uuid.uuid4())
file_name_avg = self.project.name + '_averaged_connectivity_matrix_' + unique_id + '.csv'
file_name_stdev = self.project.name + '_stdev_connectivity_matrix_' + unique_id + '.csv'
with open(os.path.join(self.project.path, file_name_avg), 'w', newline='') as csvfile:
writer = csv.writer(csvfile, delimiter=',')
writer.writerow(rois_names)
for row_ind in range(len(dialog.model._data)):
row = dialog.model._data[row_ind]
row = [row[x][0] for x in range(len(row))]
writer.writerow(row)
writer.writerow(['Selected videos:']+self.selected_videos)
# Do the standard deviation
with open(os.path.join(self.project.path, file_name_stdev), 'w', newline='') as csvfile:
writer = csv.writer(csvfile, delimiter=',')
writer.writerow(rois_names)
for row_ind in range(len(dialog.model._data)):
row = dialog.model._data[row_ind]
row = [row[x][1] for x in range(len(row))]
writer.writerow(row)
writer.writerow(['Selected videos:'] + self.selected_videos)
callback(1)
qtutil.info("All matrices saved to project directory")
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 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 automate_pipeline(self):
# order by index
ordered_q_model_indexes = sorted(self.sidebar.pl_list.selectedIndexes(), key=lambda x: x.row(), reverse=False)
if not ordered_q_model_indexes:
qtutil.info("Select all the plugins you want to process through. Use shift or ctrl to select multiple")
import_plugin_indexes = [ind for ind in range(len(ordered_q_model_indexes)) if
self.plugins[ordered_q_model_indexes[ind].data(Qt.UserRole)].name in
constants.IMPORT_PLUGINS]
if not import_plugin_indexes:
p = self.plugins[ordered_q_model_indexes[0].data(Qt.UserRole)]
if p.name not in constants.IMPORT_PLUGINS:
number_of_outputs = p.output_number_expected() # find the number of files outputted by the first plugin
for q_model_index in ordered_q_model_indexes:
p = self.plugins[q_model_index.data(Qt.UserRole)]
if p.name not in constants.IMPORT_PLUGINS:
number_of_outputs = p.output_number_expected()
if not p.check_ready_for_automation(number_of_outputs):
qtutil.critical(p.automation_error_message())
return
number_of_outputs = p.output_number_expected(number_of_outputs) # find the number of outputs
p = self.plugins[ordered_q_model_indexes[0].data(Qt.UserRole)]
input_paths = p.get_input_paths()
if not input_paths:
qtutil.critical("The first plugin in the pipeline does not have a set of input files selected")
return
for q_model_index in ordered_q_model_indexes:
p = self.plugins[q_model_index.data(Qt.UserRole)]
output_paths = p.run(input_paths)
input_paths = output_paths
ordered_q_model_indexes_segments = []
for i, import_ind in enumerate(import_plugin_indexes):
if i < len(import_plugin_indexes)-1:
# ordered_q_model_indexes are the indices in the GUI.
# retrieve the indices from where this import plugin is (import_ind) to
# the index right before the next import plugin
ordered_q_model_indexes_segment = ordered_q_model_indexes[import_ind:(import_plugin_indexes[i+1])]
else:
ordered_q_model_indexes_segment = ordered_q_model_indexes[import_ind:]
ordered_q_model_indexes_segments = ordered_q_model_indexes_segments + [ordered_q_model_indexes_segment]
import_paths = []
for i, ordered_q_model_indexes_segment in enumerate(ordered_q_model_indexes_segments):
import_plugin = self.plugins[ordered_q_model_indexes_segment[0].data(Qt.UserRole)]
qtutil.info("Please select all your files for the pipeline starting from import plugin " + str(i))
input_paths = import_plugin.get_input_paths()
import_paths = import_paths + [input_paths]
if not input_paths:
qtutil.critical("import plugin " + str(i) + " in the pipeline does not have a set of input files selected")
return
# ensure all selected plugins are ready for automation
for i, ordered_q_model_indexes_segment in enumerate(ordered_q_model_indexes_segments):
not_import_plugins = [self.plugins[ordered_q_model_indexes_segment[j].data(Qt.UserRole)] for j in
range(1, len(ordered_q_model_indexes_segment))]
number_of_outputs = len(import_paths[i])
for not_import_plugin in not_import_plugins:
if not not_import_plugin.check_ready_for_automation(number_of_outputs):
qtutil.critical(not_import_plugin.automation_error_message())
return
number_of_outputs = not_import_plugin.output_number_expected(number_of_outputs)
for i, ordered_q_model_indexes_segment in enumerate(ordered_q_model_indexes_segments):
input_paths = import_paths[i]
for q_model_index in ordered_q_model_indexes_segment:
p = self.plugins[q_model_index.data(Qt.UserRole)]
output_paths = p.run(input_paths)
input_paths = output_paths
def automate_pipeline(self):
# order by index
ordered_q_model_indexes = sorted(
self.sidebar.pl_list.selectedIndexes(),
key=lambda x: x.row(),
reverse=False)
if not ordered_q_model_indexes:
qtutil.info(
"Select all the plugins you want to process through. Use shift or ctrl to select multiple"
)
import_plugin_indexes = [
ind for ind in range(len(ordered_q_model_indexes))
if self.plugins[ordered_q_model_indexes[ind].data(
Qt.UserRole)].name in constants.IMPORT_PLUGINS
]
if not import_plugin_indexes:
p = self.plugins[ordered_q_model_indexes[0].data(Qt.UserRole)]
if p.name not in constants.IMPORT_PLUGINS:
number_of_outputs = p.output_number_expected(
) # find the number of files outputted by the first plugin
for q_model_index in ordered_q_model_indexes:
p = self.plugins[q_model_index.data(Qt.UserRole)]
if p.name not in constants.IMPORT_PLUGINS:
number_of_outputs = p.output_number_expected()
if not p.check_ready_for_automation(number_of_outputs):
qtutil.critical(p.automation_error_message())
return
number_of_outputs = p.output_number_expected(
number_of_outputs) # find the number of outputs
p = self.plugins[ordered_q_model_indexes[0].data(Qt.UserRole)]
input_paths = p.get_input_paths()
if not input_paths:
qtutil.critical(
"The first plugin in the pipeline does not have a set of input files selected"
)
return
for q_model_index in ordered_q_model_indexes:
p = self.plugins[q_model_index.data(Qt.UserRole)]
output_paths = p.run(input_paths)
input_paths = output_paths
ordered_q_model_indexes_segments = []
for i, import_ind in enumerate(import_plugin_indexes):
if i < len(import_plugin_indexes) - 1:
# ordered_q_model_indexes are the indices in the GUI.
# retrieve the indices from where this import plugin is (import_ind) to
# the index right before the next import plugin
ordered_q_model_indexes_segment = ordered_q_model_indexes[
import_ind:(import_plugin_indexes[i + 1])]
else:
ordered_q_model_indexes_segment = ordered_q_model_indexes[
import_ind:]
ordered_q_model_indexes_segments = ordered_q_model_indexes_segments + [
ordered_q_model_indexes_segment
]
import_paths = []
for i, ordered_q_model_indexes_segment in enumerate(
ordered_q_model_indexes_segments):
import_plugin = self.plugins[
ordered_q_model_indexes_segment[0].data(Qt.UserRole)]
qtutil.info(
"Please select all your files for the pipeline starting from import plugin "
+ str(i))
input_paths = import_plugin.get_input_paths()
import_paths = import_paths + [input_paths]
if not input_paths:
qtutil.critical(
"import plugin " + str(i) +
" in the pipeline does not have a set of input files selected"
)
return
# ensure all selected plugins are ready for automation
for i, ordered_q_model_indexes_segment in enumerate(
ordered_q_model_indexes_segments):
not_import_plugins = [
self.plugins[ordered_q_model_indexes_segment[j].data(
Qt.UserRole)]
for j in range(1, len(ordered_q_model_indexes_segment))
]
number_of_outputs = len(import_paths[i])
for not_import_plugin in not_import_plugins:
if not not_import_plugin.check_ready_for_automation(
number_of_outputs):
qtutil.critical(
not_import_plugin.automation_error_message())
return
number_of_outputs = not_import_plugin.output_number_expected(
number_of_outputs)
for i, ordered_q_model_indexes_segment in enumerate(
ordered_q_model_indexes_segments):
input_paths = import_paths[i]
for q_model_index in ordered_q_model_indexes_segment:
p = self.plugins[q_model_index.data(Qt.UserRole)]
output_paths = p.run(input_paths)
input_paths = output_paths
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)')[0]
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))
