def headless(directory, output, processes=-1):
"""
run the full pipeline on a directory without a gui
parameters:
directory: input directory with ps2 data
output: output directory
processes: max number of multiprocesses. default: max available
1. convert bins to pngs
2. do image segmentation (this is where the imagej macro
would go, but it has been rewritten)
3. get ps2 offsets
4. generate aggregate files
5. generate fluorescence file
"""
print("Converting bins to pngs")
bin_conversion.convert_dirs(
directory,
processes=processes) # converting all images in a dir from bin to png
print("segmenting images")
# imagej_macro(args.macro, args.directory) # old fiji macro
image_segmentation.process_collection(directory) # new python macro
# getting offsets
with open(
os.path.join(this_dir, "static", "ps2",
"sensor_fixed_metadata.json"), 'r') as f:
ps2_dict = json.load(f)
ps2_x = float(ps2_dict[0]['location_in_camera_box_m']['x'])
ps2_y = float(ps2_dict[0]['location_in_camera_box_m']['y'])
print("generating aggregates")
fluorescence_aggregation.generate_aggregate(
directory, output,
os.path.join(this_dir, "static", 'S10_Plot_boundaries.csv'),
os.path.join(this_dir, "static", 'multithresh.json'), ps2_x,
ps2_y) # generating aggregates
fluorescence_aggregation.generate_fluorescence(
directory, output, True) # generate fluorescence files
print("Finished processing", directory)
def headless(directory):
"""run the full pipeline on a directory without a gui"""
bin_conversion.convert_dirs(directory) # converting all images in a dir from bin to png
# imagej_macro(args.macro, args.directory) # old fiji macro
image_segmentation.process_collection(directory) # new python macro
# getting offsets
with open(os.path.join(this_dir, "static", "ps2", "sensor_fixed_metadata.json"), 'r') as f:
ps2_dict = json.load(f)
ps2_x = float(ps2_dict[0]['location_in_camera_box_m']['x'])
ps2_y = float(ps2_dict[0]['location_in_camera_box_m']['y'])
fluorescence_aggregation.generate_aggregate(
directory,
os.path.join(this_dir, "static", 'Plot boundaries.xlsx'),
os.path.join(this_dir, "static", 'multithresh.json'),
ps2_x,
ps2_y
) # generating aggregates
fluorescence_aggregation.generate_fluorescence(directory, True) # generate fluorescence files
print("Finished processing", directory)