diff --git a/2d_spots_in_fibers.py b/2d_spots_in_fibers.py index 036a2986c5917ffacf1c8ec1034e6c4014952b04..18161e8e6d97bd6796063dc021df1ea18bb1d2fe 100644 --- a/2d_spots_in_fibers.py +++ b/2d_spots_in_fibers.py @@ -31,7 +31,7 @@ from inra.ijpb.binary import BinaryImages # BIOP imports from ch.epfl.biop.ij2command import Labels2Rois # python imports -import os +import os, operator def get_parentdir_filename_ext_from_path(path): @@ -520,17 +520,16 @@ for index, channel in enumerate(processing_channels): save_labelimage_as_ijroiset(spots_label_imp, rm, filename, "spots_ch" + str(channel), parent_dir) spots_binary_imp = convert_labelimage_to_binary(spots_label_imp) dapi_positive_spots_binary = ImageCalculator.run(spots_binary_imp, dapi_binary, "Multiply create") - dapi_negative_spots_binary = ImageCalculator.run(spots_binary_imp, dapi_positive_spots_binary, "Subtract create") load_rois_from_zip(fiber_segmentation_roiset, rm) _, n_spots_per_fiber = measure_intensity_sum(spots_binary_imp, rm) _, n_dapi_positive_spots_per_fiber = measure_intensity_sum(dapi_positive_spots_binary, rm) - _, n_dapi_negative_spots_per_fiber = measure_intensity_sum(dapi_negative_spots_binary, rm) + n_dapi_negative_spots_per_fiber = map(operator.sub, n_spots_per_fiber, n_dapi_positive_spots_per_fiber) add_results_to_resultstable(results_table, "n spots channel " + str(channel), n_spots_per_fiber) add_results_to_resultstable(results_table, "n spots dapi positive channel " + str(channel), n_dapi_positive_spots_per_fiber) add_results_to_resultstable(results_table, "n spots dapi negative channel " + str(channel), n_dapi_negative_spots_per_fiber) - close_images([spots_channel, spots_label_imp, spots_binary_imp, spots_binary_imp, dapi_binary, dapi_positive_spots_binary, dapi_negative_spots_binary]) + close_images([spots_channel, spots_label_imp, spots_binary_imp, spots_binary_imp, dapi_binary, dapi_positive_spots_binary]) results_table.show("Spots") save_results_table(results_table, filename, "Spots", parent_dir)