cellects 0.1.3__py3-none-any.whl → 0.2.6__py3-none-any.whl

cellects/image_analysis/cluster_flux_study.py

@@ -1,102 +0,0 @@
-#!/usr/bin/env python3
-"""
-This script contains the class for studying oscillating clusters on videos in 2D
-"""
-import cv2
-import numpy as np
-from numpy import (
-    append, float32, sum, mean, zeros, empty, array, nonzero, unique,
-    isin, logical_or, logical_not, greater, uint8,
-    uint32, min, any, zeros)
-from cellects.image_analysis.morphological_operations import cross_33, get_minimal_distance_between_2_shapes
-
-
-class ClusterFluxStudy:
-    """
-
-    """
-    def __init__(self, dims):
-        self.dims = dims
-
-        self.pixels_data = np.empty((4, 0), dtype=np.uint32)
-        self.clusters_id = np.zeros(self.dims[1:], dtype=np.uint32)
-        # self.alive_clusters_in_flux = np.empty(0, dtype=np.uint32)#list()
-        self.cluster_total_number = 0
-
-    def update_flux(self, t, contours, current_flux, period_tracking, clusters_final_data):
-        # Save the data from pixels that are not anymore in efflux
-        lost = np.greater(self.clusters_id > 0, current_flux > 0)
-        # Some pixels of that cluster faded, save their data
-        lost_data = np.nonzero(lost)
-        lost_data = np.array((period_tracking[lost],  # lost_coord[0], lost_coord[1],
-                      self.clusters_id[lost], lost_data[0], lost_data[1]), dtype=np.uint32)
-        # Add this to the array containing the data of each cluster that are still alive
-        self.pixels_data = np.append(self.pixels_data, lost_data, axis=1)
-        # Stop considering these pixels in period_tracking because they switched
-        period_tracking[lost] = 0
-        current_period_tracking = np.zeros(self.dims[1:], dtype=bool)
-        for curr_clust_id in np.unique(current_flux)[1:]:
-            # Get all pixels that were in the same flux previously
-            curr_clust = current_flux == curr_clust_id
-            already = self.clusters_id * curr_clust
-            new = np.greater(curr_clust, self.clusters_id > 0)
-
-            if not np.any(already):
-                # It is an entirely new cluster:
-                cluster_pixels = new
-                self.cluster_total_number += 1
-                cluster_name = self.cluster_total_number
-            else:
-                # Check whether parts of that cluster correspond to several clusters in clusters_id
-                cluster_names = np.unique(already)[1:]
-                # keep only one cluster name to gather clusters that just became connected
-                cluster_name = np.min(cluster_names)
-                # Put the same cluster name for new ones and every pixels that were
-                # a part of a cluster touching the current cluster
-                cluster_pixels = np.logical_or(np.isin(self.clusters_id, cluster_names), new)
-                # If they are more than one,
-                if len(cluster_names) > 1:
-                    # Update these cluster names in pixels_data
-                    self.pixels_data[1, np.isin(self.pixels_data[1, :], cluster_names)] = cluster_name
-            # Update clusters_id
-            self.clusters_id[cluster_pixels] = cluster_name
-            # Update period_tracking
-            current_period_tracking[curr_clust] = True
-
-        period_tracking[current_period_tracking] += 1
-        # Remove lost pixels from clusters_id
-        self.clusters_id[lost] = 0
-        # Find out which clusters are still alive or not
-        still_alive_clusters = np.isin(self.pixels_data[1, :], np.unique(self.clusters_id))
-        clusters_to_archive = np.unique(self.pixels_data[1, np.logical_not(still_alive_clusters)])
-        # store their data in clusters_final_data
-        clusters_data = np.zeros((len(clusters_to_archive), 6), dtype=np.float32)
-        for clust_i, cluster in enumerate(clusters_to_archive):
-            cluster_bool = self.pixels_data[1, :] == cluster
-            cluster_size = np.sum(cluster_bool)
-            cluster_img = np.zeros(self.dims[1:], dtype=np.uint8)
-            cluster_img[self.pixels_data[2, cluster_bool], self.pixels_data[3, cluster_bool]] = 1
-            nb, im, stats, centro = cv2.connectedComponentsWithStats(cluster_img)
-            if np.any(cv2.dilate(cluster_img, kernel=cross_33, borderType=cv2.BORDER_CONSTANT, borderValue=0) * contours):
-                minimal_distance = 1
-            else:
-                if cluster_size > 200:
-
-                    eroded_cluster_img = cv2.erode(cluster_img, cross_33)
-                    cluster_img = np.nonzero(cluster_img - eroded_cluster_img)
-                    contours[cluster_img] = 2
-                else:
-                    contours[self.pixels_data[2, cluster_bool], self.pixels_data[3, cluster_bool]] = 2
-                # Get the minimal distance between the border of the cell(s) (noted 1 in contours)
-                # and the border of the cluster in the cell(s) (now noted 2 in contours)
-                minimal_distance = get_minimal_distance_between_2_shapes(contours)
-            data_to_save = np.array([[np.mean(self.pixels_data[0, cluster_bool]), t,
-                                   cluster_size, minimal_distance, centro[1, 0], centro[1, 1]]], dtype=np.float32)
-            clusters_data[clust_i,:] = data_to_save
-        # and remove their data from pixels_data
-        clusters_final_data = np.append(clusters_final_data, clusters_data, axis=0)
-        self.pixels_data = self.pixels_data[:, still_alive_clusters]
-
-        return period_tracking, clusters_final_data
-
-

cellects-0.1.3.dist-info/METADATA

@@ -1,176 +0,0 @@
-Metadata-Version: 2.2
-Name: cellects
-Version: 0.1.3
-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: <3.14,>=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-env; 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
-### 1. With Cellects_installer.exe (windows)
-- Download [Cellects_installer.exe](https://drive.google.com/file/d/1v2ppaln0LJ5QhXXq1D-zduhfun5D2ZXX/view?usp=drive_link)
-- Double-click on the Cellects_installer.exe file to start installation
-Note 1: Windows may warn you that it's unsafe; that's normal, because we are not a registered developer. Click "More info" and "Run Anyway".
-Note 2: For the same reason, some antivirus software can prevent installation.
-
-- To run Cellects, explore the newly created folder to find and execute Cellects.exe
-<br />
-
-### 2. Using pip (Mac, Windows or Linux)
-- Install [python 3.13](https://www.python.org/downloads/release/python-3139/)
-
-- Best practice(optional): create and activate a python environment
-Use a terminal to create the environment:
-```bash
-cd path/toward/an/existing/folder/
-python -m venv ./cellects_env
-```
-Activation on Windows:
-```bash
-cellects_env\Scripts\activate
-```
-Activation on Unix or MacOS:
-```bash
-source cellects_env/bin/activate
-```
-
-- Installation:
-```bash
-pip install cellects
-```
-
-- Run Cellects:
-```bash
-Cellects
-```
-
-To uninstall, use:
-```bash
-pip uninstall cellects
-```
-Note: creating a python environment avoids compatibilities issues with other python scripts.
-However, the user have to activate this environment every time before running Cellects.
-
-### 3. To access the source code (Mac, Windows or Linux)
-- Install [python 3.13](https://www.python.org/downloads/release/python-3139/)
-- Install [git](https://git-scm.com/downloads)
-- On Mac: also install [brew](https://brew.sh/)
-- Choose a place to install Cellects and use a terminal to write:
-```bash
-cd path/toward/an/existing/folder/
-```
-Note: The repository will be cloned to that folder; if updating an existing project, use a different folder name and rename it after verifying the new version.
-- Clone [Cellects repository](https://github.com/Aurele-B/Cellects.git) in terminal (or any IDE) with:
-```bash
-git clone https://github.com/Aurele-B/Cellects.git
-cd ./Cellects
-pip install --upgrade pip
-python -m venv ./cellects_env
-```
-On Windows, run:
-```bash
-cellects_env\Scripts\activate
-```
-On Unix or MacOS, run:
-```bash
-source cellects_env/bin/activate
-```
-Install Cellects dependencies in editable mode:
-```bash
-pip install -e .
-```
-Run Cellects:
-```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)

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