cellects 0.1.0.dev1__py3-none-any.whl

cellects/__main__.py

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+#!/usr/bin/env python3
+"""Launcher of cellects software.
+
+ """
+import logging
+import sys
+import coloredlogs
+from PySide6 import QtWidgets, QtGui
+from cellects.core.cellects_paths import ICONS_DIR
+
+# These two lines allow the taskbar icon to be cellects_icon instead if python icon.
+if sys.platform.startswith('win'):
+    import ctypes
+    ctypes.windll.shell32.SetCurrentProcessExplicitAppUserModelID('company.app.1')
+
+
+LOGLEVEL = "INFO" #"DEBUG"
+
+def _initialize_coloredlogs(loglevel: str = 'DEBUG') -> None:
+    """Initialize logging parameters with coloredlogs library."""
+    coloredlogs.install(
+        logger=logging.basicConfig(),
+        level=loglevel,
+        fmt='[%(asctime)s] [%(levelname)s] %(message)s',
+        datefmt='%H:%M:%S')
+
+
+def run_cellects():
+    """Entry point of cellects software."""
+    _initialize_coloredlogs(LOGLEVEL)
+    from cellects.gui.cellects import CellectsMainWidget
+    app = QtWidgets.QApplication([])
+
+    # Add the icon file to the app
+    icon = QtGui.QIcon()
+    if sys.platform.startswith('win'):
+        icon.addPixmap(QtGui.QPixmap(ICONS_DIR / "cellects_icon.ico"))
+    else:
+        icon.addPixmap(QtGui.QPixmap(ICONS_DIR / "cellects_icon.icns"))
+    app.setWindowIcon(icon)
+    # Start session
+    session = CellectsMainWidget()
+    session.instantiate()
+    session.show()
+    sys.exit(app.exec())
+
+
+if __name__ == "__main__":
+    run_cellects()

cellects/config/all_vars_dict.py

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+#!/usr/bin/env python3
+"""
+This script generates the default parameters of the GUI of Cellects.
+It can be used to write these parameters in a file named all_vars_dict.
+Then, the gui updates this file as users adjust the GUI parameters.
+These parameters are stored in a dictionary with keys corresponding to the parameter's name and values to its tunable
+ value.
+"""
+
+import os
+from cellects.image_analysis.shape_descriptors import descriptors_categories, descriptors
+import numpy as np
+from cellects.core.cellects_paths import ALL_VARS_PKL_FILE
+from cellects.utils.load_display_save import PickleRick
+from cellects.core.cellects_paths import TEST_DIR
+
+
+class DefaultDicts:
+    def __init__(self):
+        # po.load_variable_dict()
+        self.all = {
+            # Interface settings:
+            'compute_all_options': True,
+            'expert_mode': False,
+            'is_auto': False,
+            'night_mode': False,
+            'arena': 1,
+            'video_option': 0,
+
+            # Analysis settings:
+            'are_gravity_centers_moving': 0,
+            'are_zigzag': 'columns',
+            'automatic_size_thresholding': True,
+            'color_number': 2,
+            'cores': 1,
+            'automatically_crop': False,
+            'descriptors': descriptors_categories,
+            'display_shortcuts': False,
+            'connect_distant_shape_during_segmentation': False,
+            'all_specimens_have_same_direction': True,
+            'extract_time_interval': True,
+            'do_multiprocessing': False,
+            'extension': '.tif',
+            'first_detection_frame': 1,
+            'folder_number': 1,
+            'first_folder_sample_number': 1,
+            'first_move_threshold_in_mm²': 10,
+            'folder_list': [],
+            'global_pathway': str(TEST_DIR / "experiment"),
+            'im_or_vid': 0,
+            'image_horizontal_size_in_mm': 700,
+            'minimal_appearance_size': 10,
+            'more_than_two_colors': False,
+            'bio_mask': None,
+            'back_mask': None,
+            'keep_cell_and_back_for_all_folders': False,
+
+            # 'overwrite_cellects_data': True,
+            'overwrite_unaltered_videos': False,
+            'radical': 'im',
+            'raw_images': False,
+            'sample_number_per_folder': [1],
+            'scale_with_image_or_cells': 1,
+            'set_spot_shape': True,
+            'set_spot_size': True,
+            'starting_blob_hsize_in_mm': 15,
+            'starting_blob_shape': None
+        }
+
+        self.vars = {
+            'analyzed_individuals': np.empty(0, dtype=np.uint16),
+            'arena_shape': 'rectangle', # 'circle',
+            'bio_label': 1,
+            'bio_label2': 1,
+            'color_number': 2,
+            'convert_for_motion': {
+                'lab': np.array((0, 0, 1), np.int8),
+                'logical': 'None'},
+            'convert_for_origin': {
+                'lab': np.array((0, 0, 1), np.int8),
+                'logical': 'None'},
+            'detection_range_factor': 2,
+            'first_move_threshold': None,
+            'img_number': 0,
+            'iso_digi_analysis': True,
+            'luminosity_threshold': 127,
+            'max_size_for_connection': 300,
+            'min_size_for_connection': 20,
+            'origin_state': 'fluctuating',
+            'oscilacyto_analysis': False,
+            'network_analysis': False,
+            'graph_extraction': False,
+            'network_detection_threshold': 20,
+            'network_mesh_side_length': 8,
+            'network_mesh_step_length': 2,
+            'fractal_analysis': False,
+            'fractal_box_side_threshold': 32,
+            'fractal_zoom_step': 0,
+            'subtract_background': False,
+            'correct_errors_around_initial': False,
+            'prevent_fast_growth_near_periphery': False,
+            'periphery_width': 40,
+            'max_periphery_growth': 20,
+            # According to Smith and Saldana (1992),
+            # P. polycephalum shuttle streaming has a period of 100-200s
+            'already_greyscale': False,
+            'descriptors_in_long_format': True,
+            'do_slope_segmentation': False,
+            'do_threshold_segmentation': True,
+            'drift_already_corrected': False,
+            'appearance_detection_method': 'largest',
+            'frame_by_frame_segmentation': False,
+            'repeat_video_smoothing': 1,
+            'keep_unaltered_videos': False,
+            'maximal_growth_factor': 0.05,
+            'min_ram_free': 0.87,
+            'expected_oscillation_period': 2,  # (min)
+            'minimal_oscillating_cluster_size': 10,  # (pixels)
+            'output_in_mm': True,
+            'save_processed_videos': True,
+            'several_blob_per_arena': False,
+            'time_step': 1,
+            'true_if_use_light_AND_slope_else_OR': False,
+            'do_fading': False,
+            'fading': 0,
+            'video_fps': 60,
+            'videos_extension': '.mp4',
+            'exif': [],
+            'lose_accuracy_to_save_memory': True,
+            'save_coord_specimen': False,
+            'save_coord_contour': False,
+            'save_coord_thickening_slimming': False,
+            'save_coord_network': False,
+            'grid_segmentation': False,
+            # Data stored during analysis:
+            'descriptors': descriptors,
+        }
+
+    def save_as_pkl(self, po=None):
+        if po is None:
+            if os.path.isfile('PickleRick0.pkl'):
+                os.remove('PickleRick0.pkl')
+            pickle_rick = PickleRick(0)
+            pickle_rick.write_file(self.all, ALL_VARS_PKL_FILE)
+        else:
+            po = po
+            po.all = self.all
+            po.vars = self.vars
+            po.save_variable_dict()
+
+
+
+if __name__ == "__main__":
+    DefaultDicts().save_as_pkl()

cellects/core/cellects_paths.py

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+#!/usr/bin/env python3
+"""
+Generate the different paths used by cellects.
+Adjust the path names according to the current position of the software.
+"""
+
+import os
+from pathlib import Path
+
+# Current file -> src/cellects/cellect_paths.py
+CURR_DIR = Path(os.path.dirname(os.path.realpath(__file__)))
+CELLECTS_DIR = CURR_DIR.parent  # = src/cellects
+
+# Package-internal dirs
+CONFIG_DIR = CELLECTS_DIR / "config"
+CORE_DIR = CELLECTS_DIR / "core"
+GUI_DIR = CELLECTS_DIR / "gui"
+ICONS_DIR = CELLECTS_DIR / "icons"
+IMAGE_ANALYSIS_DIR = CELLECTS_DIR / "image_analysis"
+UTILS_DIR = CELLECTS_DIR / "utils"
+
+# Repo root (src/..)
+REPO_ROOT = CELLECTS_DIR.parent
+
+# Repo-level dirs
+DATA_DIR = REPO_ROOT / "data"
+TEST_DIR = REPO_ROOT / "tests"
+
+# Example packaged file
+ALL_VARS_PKL_FILE = CONFIG_DIR / "all_vars.pkl"