cellects 0.1.0.dev1__tar.gz

cellects-0.1.0.dev1/PKG-INFO

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+Metadata-Version: 2.2
+Name: cellects
+Version: 0.1.0.dev1
+Summary: Cell Expansion Computer Tracking Software.
+Author: Aurèle Boussard
+Project-URL: Homepage, https://github.com/Aurele-B/Cellects
+Project-URL: Issues, https://github.com/Aurele-B/Cellects/issues
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
+Classifier: Operating System :: OS Independent
+Requires-Python: <3.13,>=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE.odt
+Requires-Dist: coloredlogs
+Requires-Dist: exif
+Requires-Dist: ExifRead
+Requires-Dist: numba
+Requires-Dist: opencv-python
+Requires-Dist: pandas
+Requires-Dist: psutil
+Requires-Dist: PySide6>=6.5
+Requires-Dist: scipy
+Requires-Dist: screeninfo
+Requires-Dist: numpy>=1.26
+Requires-Dist: scikit-image
+Requires-Dist: tqdm
+Requires-Dist: h5py
+Requires-Dist: matplotlib
+Requires-Dist: natsort
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Provides-Extra: doc
+Requires-Dist: mkdocs; extra == "doc"
+Requires-Dist: mkdocs-material; extra == "doc"
+Requires-Dist: pymdown-extensions; extra == "doc"
+
+Cellects: Cell Expansion Computer Tracking Software
+===================================================
+
+Description
+-----------
+
+Cellects is a tracking software for organisms whose shape and size change over time. 
+Cellects’ main strengths are its broad scope of action, 
+automated computation of a variety of geometrical descriptors, easy installation and user-friendly interface.
+
+
+---
+
+## Quick Start
+
+
+⚠️ **Note:** At this stage, Cellects is available **only from source**.  
+You will need **Miniconda3** and **git** installed on your system.
+
+- Install [Miniconda3](https://docs.conda.io/en/latest/miniconda.html)  
+  (choose the installer for your operating system).  
+- Install [git](https://git-scm.com/downloads)  
+  (also available through package managers like `apt`, `brew`, or `choco`).
+
+Once these prerequisites are installed, you can set up Cellects as follows:
+
+```bash
+# Clone the repository
+git clone https://github.com/Aurele-B/Cellects.git
+cd Cellects
+
+# Create and activate the environment
+conda env create -f conda/env.yml
+conda activate cellects-dev
+
+# Install the package in editable mode
+pip install -e .
+```
+
+Launch the application:
+```bash
+Cellects
+```
+
+---
+
+## Developer Guide
+
+### Run Tests
+Cellects uses `pytest` + `pytest-cov`.  
+Install test dependencies:
+
+```bash
+pip install -e ".[test]"
+```
+
+Run the test suite (with coverage enabled by default via `pyproject.toml`):
+
+```bash
+pytest
+```
+
+You can access the coverage report with `coverage html` and open `htmlcov/index.html` in your browser.
+
+```bash
+open htmlcov/index.html        # macOS
+xdg-open htmlcov/index.html    # Linux
+start htmlcov\index.html       # Windows (PowerShell)
+```
+
+Or explicitly:
+```bash
+pytest --cov=src/cellects --cov-report=term-missing
+```
+
+### Build Documentation
+Install doc dependencies:
+
+```bash
+pip install -e ".[doc]"
+```
+
+Serve the docs locally:
+```bash
+mkdocs serve
+```
+
+Open [http://127.0.0.1:8000](http://127.0.0.1:8000) in your browser.
+
+---
+
+## Resources
+- [User manual](https://github.com/Aurele-B/Cellects/blob/main/_old_doc/UserManual.md)  
+- [Usage example (video)](https://www.youtube.com/watch?v=N-k4p_aSPC0)

cellects-0.1.0.dev1/README.md

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+Cellects: Cell Expansion Computer Tracking Software
+===================================================
+
+Description
+-----------
+
+Cellects is a tracking software for organisms whose shape and size change over time. 
+Cellects’ main strengths are its broad scope of action, 
+automated computation of a variety of geometrical descriptors, easy installation and user-friendly interface.
+
+
+---
+
+## Quick Start
+
+
+⚠️ **Note:** At this stage, Cellects is available **only from source**.  
+You will need **Miniconda3** and **git** installed on your system.
+
+- Install [Miniconda3](https://docs.conda.io/en/latest/miniconda.html)  
+  (choose the installer for your operating system).  
+- Install [git](https://git-scm.com/downloads)  
+  (also available through package managers like `apt`, `brew`, or `choco`).
+
+Once these prerequisites are installed, you can set up Cellects as follows:
+
+```bash
+# Clone the repository
+git clone https://github.com/Aurele-B/Cellects.git
+cd Cellects
+
+# Create and activate the environment
+conda env create -f conda/env.yml
+conda activate cellects-dev
+
+# Install the package in editable mode
+pip install -e .
+```
+
+Launch the application:
+```bash
+Cellects
+```
+
+---
+
+## Developer Guide
+
+### Run Tests
+Cellects uses `pytest` + `pytest-cov`.  
+Install test dependencies:
+
+```bash
+pip install -e ".[test]"
+```
+
+Run the test suite (with coverage enabled by default via `pyproject.toml`):
+
+```bash
+pytest
+```
+
+You can access the coverage report with `coverage html` and open `htmlcov/index.html` in your browser.
+
+```bash
+open htmlcov/index.html        # macOS
+xdg-open htmlcov/index.html    # Linux
+start htmlcov\index.html       # Windows (PowerShell)
+```
+
+Or explicitly:
+```bash
+pytest --cov=src/cellects --cov-report=term-missing
+```
+
+### Build Documentation
+Install doc dependencies:
+
+```bash
+pip install -e ".[doc]"
+```
+
+Serve the docs locally:
+```bash
+mkdocs serve
+```
+
+Open [http://127.0.0.1:8000](http://127.0.0.1:8000) in your browser.
+
+---
+
+## Resources
+- [User manual](https://github.com/Aurele-B/Cellects/blob/main/_old_doc/UserManual.md)  
+- [Usage example (video)](https://www.youtube.com/watch?v=N-k4p_aSPC0)

cellects-0.1.0.dev1/pyproject.toml

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+[build-system]
+requires = ["setuptools==76.1.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "cellects"
+version = "0.1.0.dev1"
+description = "Cell Expansion Computer Tracking Software."
+readme = "README.md"
+license = { file = "LICENSE" }
+requires-python = ">=3.11,<3.13"
+authors = [{ name = "Aurèle Boussard" }]
+classifiers = [
+  "Programming Language :: Python :: 3",
+  "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+  "Operating System :: OS Independent",
+]
+
+dependencies = [
+  "coloredlogs",
+  "exif",
+  "ExifRead",
+  "numba",
+  "opencv-python",
+  "pandas",
+  "psutil",
+  "PySide6>=6.5",
+  "scipy",
+  "screeninfo",
+  "numpy>=1.26",
+  "scikit-image",
+  "tqdm",
+  "h5py",
+  "matplotlib",
+  "natsort",
+]
+
+[project.scripts]
+Cellects = "cellects.__main__:run_cellects"
+
+[project.optional-dependencies]
+test = [
+  "pytest",
+  "pytest-cov",
+]
+doc = [
+  "mkdocs",
+  "mkdocs-material",
+  "pymdown-extensions",
+]
+
+[project.urls]
+Homepage = "https://github.com/Aurele-B/Cellects"
+Issues = "https://github.com/Aurele-B/Cellects/issues"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+exclude = ["tests*"]
+
+[tool.setuptools.package-data]
+cellects = ["icons/**"]
+
+[tool.setuptools]
+package-dir = {"" = "src"}
+include-package-data = true
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+addopts = "--cov=src/cellects --cov-report=term-missing --cov-report=html"

cellects-0.1.0.dev1/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

cellects-0.1.0.dev1/src/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-0.1.0.dev1/src/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-0.1.0.dev1/src/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"