cellects 0.1.0.dev1__py3-none-any.whl

cellects/core/script_based_run.py

@@ -0,0 +1,154 @@
+#!/usr/bin/env python3
+"""This file contains lines to run Cellects without user interface"""
+
+import logging
+import os
+from pathlib import Path
+import numpy as np
+import pandas as pd
+import cv2
+from cellects.core.program_organizer import ProgramOrganizer
+from cellects.utils.utilitarian import insensitive_glob
+from cellects.core.one_video_per_blob import OneVideoPerBlob
+from cellects.core.motion_analysis import MotionAnalysis
+from cellects.config.all_vars_dict import DefaultDicts
+from cellects.utils.load_display_save import show
+
+
+def load_one_folder(pathway, sample_number):
+    po = ProgramOrganizer()
+    po.load_variable_dict()
+    # dd = DefaultDicts()
+    # po.all = dd.all
+    # po.vars = dd.vars
+    po.all['global_pathway'] = pathway
+    po.all['first_folder_sample_number'] = sample_number
+    # po.all['first_folder_sample_number'] = 6
+    # po.all['radical'] = "IMG"
+    # po.all['extension'] = ".jpg"
+    # po.all['im_or_vid'] = 0
+    po.look_for_data()
+    po.load_data_to_run_cellects_quickly()
+    return po
+
+def run_image_analysis(po):
+    if not po.first_exp_ready_to_run:
+        po.get_first_image()
+        po.fast_image_segmentation(True)
+        # po.first_image.find_first_im_csc(sample_number=po.sample_number,
+        #                                    several_blob_per_arena=None,
+        #                                    spot_shape=None, spot_size=None,
+        #                                    kmeans_clust_nb=2,
+        #                                    biomask=None, backmask=None,
+        #                                    color_space_dictionaries=None,
+        #                                    carefully=True)
+        po.cropping(is_first_image=True)
+        po.get_average_pixel_size()
+        po.delineate_each_arena()
+        po.get_background_to_subtract()
+        po.get_origins_and_backgrounds_lists()
+        po.get_last_image()
+        po.fast_image_segmentation(is_first_image=False)
+        po.find_if_lighter_background()
+        po.extract_exif()
+    else:
+        print('Image analysis already done, run video analysis')
+    return po
+
+
+def write_videos(po):
+    po.update_output_list()
+    look_for_existing_videos = insensitive_glob('ind_' + '*' + '.npy')
+    there_already_are_videos = len(look_for_existing_videos) == len(po.vars['analyzed_individuals'])
+    logging.info(
+        f"{len(look_for_existing_videos)} .npy video files found for {len(po.vars['analyzed_individuals'])} arenas to analyze")
+    do_write_videos = not there_already_are_videos or (
+            there_already_are_videos and po.all['overwrite_unaltered_videos'])
+    if do_write_videos:
+        po.videos = OneVideoPerBlob(po.first_image, po.starting_blob_hsize_in_pixels, po.all['raw_images'])
+        po.videos.left = po.left
+        po.videos.right = po.right
+        po.videos.top = po.top
+        po.videos.bot = po.bot
+        po.videos.first_image.shape_number = po.sample_number
+        po.videos.write_videos_as_np_arrays(
+            po.data_list, po.vars['min_ram_free'], not po.vars['already_greyscale'], po.reduce_image_dim)
+    po.instantiate_tables()
+    return po
+
+
+def run_one_video_analysis(po):
+    i=0
+    show_seg= False
+    # if os.path.isfile(f"coord_specimen{i + 1}_t720_y1475_x1477.npy"):
+    #     binary_coord = np.load(f"coord_specimen{i + 1}_t720_y1475_x1477.npy")
+    #     l = [i, i + 1, po.vars, False, False, show_seg, None]
+    #     MA = MotionAnalysis(l)
+    #     MA.binary = np.zeros((720, 1475, 1477), dtype=np.uint8)
+    #     MA.binary[binary_coord[0, :], binary_coord[1, :], binary_coord[2, :]] = 1
+    # else:
+    l = [i, i + 1, po.vars, True, False, show_seg, None]
+    MA = MotionAnalysis(l)
+    MA.get_descriptors_from_binary()
+    MA.detect_growth_transitions()
+    MA.networks_detection(show_seg)
+    MA.study_cytoscillations(show_seg)
+    return MA
+
+
+def run_all_arenas(po):
+    po.instantiate_tables()
+    for i, arena in enumerate(po.vars['analyzed_individuals']):
+        l = [i, arena, po.vars, True, True, False, None]
+        analysis_i = MotionAnalysis(l)
+        po.add_analysis_visualization_to_first_and_last_images(i, analysis_i.efficiency_test_1,
+                                                                    analysis_i.efficiency_test_2)
+        if not po.vars['several_blob_per_arena']:
+            # Save basic statistics
+            po.update_one_row_per_arena(i, analysis_i.one_descriptor_per_arena)
+
+            # Save descriptors in long_format
+            po.update_one_row_per_frame(i * po.vars['img_number'],
+                                                      arena * po.vars['img_number'],
+                                                      analysis_i.one_row_per_frame)
+            # Save cytosol_oscillations
+        if not pd.isna(analysis_i.one_descriptor_per_arena["first_move"]):
+            if po.vars['oscilacyto_analysis']:
+                oscil_i = pd.DataFrame(
+                    np.c_[np.repeat(arena,
+                                    analysis_i.clusters_final_data.shape[0]), analysis_i.clusters_final_data],
+                    columns=['arena', 'mean_pixel_period', 'phase', 'cluster_size', 'edge_distance', 'coord_y',
+                             'coord_x'])
+                if po.one_row_per_oscillating_cluster is None:
+                    po.one_row_per_oscillating_cluster = oscil_i
+                else:
+                    po.one_row_per_oscillating_cluster = pd.concat((po.one_row_per_oscillating_cluster, oscil_i))
+    po.save_tables()
+    cv2.imwrite(f"Analysis efficiency, last image.jpg", po.last_image.bgr)
+    cv2.imwrite(f"Analysis efficiency, {np.ceil(po.vars['img_number'] / 10).astype(np.uint64)}th image.jpg",
+        po.first_image.bgr)
+
+
+
+if __name__ == "__main__":
+    po = load_one_folder(Path("/data/experiment"), 1)
+    po = run_image_analysis(po)
+    po = write_videos(po)
+    # MA = run_one_video_analysis(po)
+    run_all_arenas(po)
+
+    # MA.one_row_per_frame.to_csv(
+    #     "/Users/Directory/Scripts/python/Cellects/tests/data/experiment/motion_analysis_thresh.csv")
+
+    # path = Path("/Users/Directory/Scripts/python/Cellects/tests/data/experiment")
+    # po.load_variable_dict()
+    # run_image_analysis(po)
+    # os.chdir(path)
+    # from glob import glob
+    # from cellects.utils.load_display_save import readim
+    # im_names = np.sort(glob("*.JPG"))
+    # for i, im_name in enumerate(im_names): #  im_name = im_names[-1]
+    #     im = readim(im_name)
+    #     cv2.imwrite(f"image{i + 1}.tif", im[2925:3170, 1200:1500, :])
+    #
+    #     show(im[2925:3170,1200:1500, :])