# ensure consistent preference settings

Prefs.blackBackground = False;

# get locations for previous and new outputs

params = Parameters();

params.loadLastParams();

output_folder_old, output_folder = mbio.rerun_location_chooser(params.input_image_path);

params.loadParametersFromJson(os.path.join(output_folder_old, 'parameters used.json'));

params.setOutputPath(output_folder);

# present user with the familiar setup UI, with options that don't make sense/aren't yet implemented disabled

params = mbui.analysis_parameters_gui(rerun_analysis=True, params=params);

# get original image file (for overlays etc.)

if not os.path.isfile(params.input_image_path):

mbui.warning_dialog(["The original data can't be found at the location specified in saved parameters. ",

"(Possibly something as simple as a change in network drive mapping has occurred)",

"Please specify the location of the original image file..."]);

params.setInputImagePath(mbio.input_file_location_chooser(params.output_path));

import_opts, params = mbui.choose_series(params.input_image_path, params);

imps = bf.openImagePlus(import_opts);

imp = imps[0];

if imp.getNSlices() > 1:

mbui.warning_dialog(["More than one Z plane detected.",

"I will do a maximum projection before proceeding",

"Continue?"]);

imp = ZProjector.run(imp,"max all");

params = mbio.get_metadata(params);

params.setCurvatureLengthUm(round(params.curvature_length_um / params.pixel_physical_size) * params.pixel_physical_size);

params.persistParameters();

IJ.run(imp, "Set Scale...", "distance=0 known=0 pixel=1 unit=pixel");

imp.show();

if imp.getNChannels() > 1:

imp.setPosition(params.membrane_channel_number, 1, 1);

mbui.autoset_zoom(imp);

IJ.run("Enhance Contrast", "saturated=0.35");

# prompt user to select ROI

original_imp = Duplicator().run(imp);

_, crop_params = mbui.crop_to_ROI(imp, params);

imp.show();

if crop_params is not None:

params.perform_spatial_crop = True;

mbui.autoset_zoom(imp);

imp.updateAndDraw();

review_crop = mb.check_cropping(output_folder_old, params);

keep_crop = not review_crop;

if review_crop:

keep_crop = mbui.crop_review();

if not keep_crop:

imp.changes = False;

imp.close();

imp = original_imp;

else:

original_imp.close();

else:

original_imp.close();

# prompt user to do time cropping

imp, start_end_tuple = mbui.time_crop(imp, params);

params.setTimeCropStartEnd(start_end_tuple);

# import edges

membrane_edges = mbio.load_qcd_edges2(os.path.join(output_folder_old, "user_defined_edges.zip"));

mbio.save_qcd_edges2(membrane_edges, params.output_path);

calculated_objects = CalculatedObjects();

calculated_objects.membrane_edges = membrane_edges;

if params.time_crop_start_end[0] is not None:

calculated_objects.timelist = [idx * params.frame_interval for idx in range(params.time_crop_start_end[0], params.time_crop_start_end[1]+1)]

else:

calculated_objects.timelist = [idx * params.frame_interval for idx in range(imp.getNFrames())];

split_channels = mbfs.split_image_plus(imp, params)

membrane_channel_imp = split_channels[0];

actin_channel_imp = split_channels[1];

segmentation_channel_imp = None;

if params.photobleaching_correction:

if os.path.isfile(os.path.join(output_folder_old, 'binary_membrane_stack.tif')):

segmentation_binary_path = os.path.join(output_folder_old, 'binary_membrane_stack.tif');

segmentation_channel_imp = IJ.openImage(segmentation_binary_path);

else:

segmentation_channel_imp = split_channels[2];

segmentation_channel_imp = mb.make_and_clean_binary(segmentation_channel_imp, params.threshold_method)

split_channels[2] = segmentation_channel_imp;

calculated_objects = mbfs.calculate_outputs(params,

calculated_objects,

split_channels);

# output colormapped images and kymographs

fig_imp_list = mbfs.generate_and_save_figures(imp, calculated_objects, params, membrane_channel_imp, segmentation_channel_imp);

mbfs.save_csvs(calculated_objects, params);

params.saveParametersToJson(os.path.join(params.output_path, "parameters used.json"));

imp.changes = False;

IJ.setTool("zoom");

if params.close_on_completion:

for fig_imp in fig_imp_list:

fig_imp.close();

imp.close();