cellects 0.1.0__tar.gz → 0.1.3__tar.gz

{cellects-0.1.0/src/cellects.egg-info → cellects-0.1.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: cellects
-Version: 0.1.0
+Version: 0.1.3
 Summary: Cell Expansion Computer Tracking Software.
 Author: Aurèle Boussard
 Project-URL: Homepage, https://github.com/Aurele-B/Cellects
@@ -8,7 +8,7 @@ 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
+Requires-Python: <3.14,>=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE.odt
 Requires-Dist: coloredlogs
@@ -48,40 +48,84 @@ automated computation of a variety of geometrical descriptors, easy installation
 
 
 ---
-
 ## 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 />
 
-⚠️ **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`).
+### 2. Using pip (Mac, Windows or Linux)
+- Install [python 3.13](https://www.python.org/downloads/release/python-3139/)
 
-Once these prerequisites are installed, you can set up Cellects as follows:
+- 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
-# Clone the repository
-git clone https://github.com/Aurele-B/Cellects.git
-cd Cellects
+pip install cellects
+```
 
-# Create and activate the environment
-conda env create -f conda/env.yml
-conda activate cellects-dev
+- Run Cellects:
+```bash
+Cellects
+```
 
-# Install the package in editable mode
+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 .
 ```
-
-Launch the application:
+Run Cellects:
 ```bash
 Cellects
 ```
 
----
-
 ## Developer Guide
 
 ### Run Tests

cellects-0.1.3/README.md

@@ -0,0 +1,138 @@
+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)

{cellects-0.1.0 → cellects-0.1.3}/pyproject.toml

@@ -4,11 +4,11 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "cellects"
-version = "0.1.0"
+version = "0.1.3"
 description = "Cell Expansion Computer Tracking Software."
 readme = "README.md"
 license = { file = "LICENSE" }
-requires-python = ">=3.11,<3.13"
+requires-python = ">=3.11,<3.14"
 authors = [{ name = "Aurèle Boussard" }]
 classifiers = [
   "Programming Language :: Python :: 3",

{cellects-0.1.0 → cellects-0.1.3}/src/cellects/config/all_vars_dict.py

@@ -12,7 +12,7 @@ from cellects.image_analysis.shape_descriptors import descriptors_categories, de
 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
+from cellects.core.cellects_paths import EXPERIMENTS_DIR
 
 
 class DefaultDicts:
@@ -46,7 +46,7 @@ class DefaultDicts:
             'first_folder_sample_number': 1,
             'first_move_threshold_in_mm²': 10,
             'folder_list': [],
-            'global_pathway': str(TEST_DIR / "experiment"),
+            'global_pathway': str(EXPERIMENTS_DIR),
             'im_or_vid': 0,
             'image_horizontal_size_in_mm': 700,
             'minimal_appearance_size': 10,

{cellects-0.1.0 → cellects-0.1.3}/src/cellects/core/cellects_paths.py

@@ -20,10 +20,11 @@ IMAGE_ANALYSIS_DIR = CELLECTS_DIR / "image_analysis"
 UTILS_DIR = CELLECTS_DIR / "utils"
 
 # Repo root (src/..)
-REPO_ROOT = CELLECTS_DIR.parent
+REPO_ROOT = CELLECTS_DIR.parent.parent
 
 # Repo-level dirs
 DATA_DIR = REPO_ROOT / "data"
+EXPERIMENTS_DIR = DATA_DIR / "experiment"
 TEST_DIR = REPO_ROOT / "tests"
 
 # Example packaged file

{cellects-0.1.0 → cellects-0.1.3}/src/cellects/gui/advanced_parameters.py

@@ -214,9 +214,23 @@ class AdvancedParameters(WindowType):
         # self.min_size_for_connection.setVisible(do_use_min_size)
         # self.min_size_for_connection_label.setVisible(do_use_min_size)
 
-        self.use_min_size.setStyleSheet("margin-left:100%; margin-right:0%;")
+        self.use_min_size.setStyleSheet("QCheckBox::indicator {width: 12px;height: 12px;background-color: transparent;"
+                            "border-radius: 5px;border-style: solid;border-width: 1px;"
+                            "border-color: rgb(100,100,100);}"
+                            "QCheckBox::indicator:checked {background-color: rgb(70,130,180);}"
+                            "QCheckBox:checked, QCheckBox::indicator:checked {border-color: black black white white;}"
+                            "QCheckBox:checked {background-color: transparent;}"
+                            "QCheckBox:margin-left {100%}"
+                            "QCheckBox:margin-right {0%}")
         self.min_size_for_connection_label.setAlignment(QtCore.Qt.AlignRight)
-        self.use_max_size.setStyleSheet("margin-left:100%; margin-right:0%;")
+        self.use_max_size.setStyleSheet("QCheckBox::indicator {width: 12px;height: 12px;background-color: transparent;"
+                            "border-radius: 5px;border-style: solid;border-width: 1px;"
+                            "border-color: rgb(100,100,100);}"
+                            "QCheckBox::indicator:checked {background-color: rgb(70,130,180);}"
+                            "QCheckBox:checked, QCheckBox::indicator:checked {border-color: black black white white;}"
+                            "QCheckBox:checked {background-color: transparent;}"
+                            "QCheckBox:margin-left {100%}"
+                            "QCheckBox:margin-right {0%}")
         self.max_size_for_connection_label.setAlignment(QtCore.Qt.AlignRight)
 
         # II/D/ Arrange widgets in the box
@@ -838,7 +852,14 @@ class AdvancedParameters(WindowType):
         self.more_than_2_colors_widget = QtWidgets.QWidget()
         self.more_than_2_colors_layout = QtWidgets.QHBoxLayout()
         self.more_than_two_colors = Checkbox(self.parent().po.all["more_than_two_colors"])
-        self.more_than_two_colors.setStyleSheet("margin-left:0%; margin-right:-10%;")
+        self.more_than_two_colors.setStyleSheet("QCheckBox::indicator {width: 12px;height: 12px;background-color: transparent;"
+                            "border-radius: 5px;border-style: solid;border-width: 1px;"
+                            "border-color: rgb(100,100,100);}"
+                            "QCheckBox::indicator:checked {background-color: rgb(70,130,180);}"
+                            "QCheckBox:checked, QCheckBox::indicator:checked {border-color: black black white white;}"
+                            "QCheckBox:checked {background-color: transparent;}"
+                            "QCheckBox:margin-left {0%}"
+                            "QCheckBox:margin-right {-10%}")
         self.more_than_two_colors.stateChanged.connect(self.display_more_than_two_colors_option)
 
         self.more_than_two_colors_label = FixedText("Heterogeneous back",

{cellects-0.1.0 → cellects-0.1.3}/src/cellects/gui/custom_widgets.py

@@ -65,30 +65,12 @@ class WindowType(QtWidgets.QWidget):
         self.frame = QtWidgets.QFrame(self)
         self.frame.setGeometry(QtCore.QRect(0, 0, self.parent().screen_width, self.parent().screen_height))
         self.display_image = None
-        # self.setFont(QFont(textfont, textsize, QFont.Medium))
-        # self.setStyleSheet("background-color: %s; color: %s; font: %s; border-color: %s; selection-color: %s; selection-background-color: %s" % (backgroundcolor, textColor, f"{textsize}pt {textfont};", bordercolor, selectioncolor, selectionbackgroundcolor))
-        # self.setStyleSheet("background-color: %s; color: %s; border-color: %s; selection-color: %s; selection-background-color: %s" % (backgroundcolor, textColor, bordercolor, selectioncolor, selectionbackgroundcolor))
-
         self.setFont(QFont(textfont, textsize, QFont.Medium))
         self.night_mode_switch(night_mode)
-        # self.setStyleSheet("background-color: rgb(50,50,65);"
-        #                    "color: rgb(255, 255, 255);\n" # 213, 251, 255
-        #                    "font: 15pt \"Calibri\";\n"
-        #                    "border-color: rgb(50,50,65);\n"
-        #                    # "border-color: rgb(0, 150, 75);\n"
-        #                    "selection-color: rgb(1, 152, 117);\n" # 0, 150, 75  0, 132, 66  0, 120, 215
-        #                    "selection-background-color:rgb(50,50,65);\n"  # jsp
-        #                    )
-                           # "selection-background-color:rgb(60, 60, 60);\n"  # jsp
-                           # "alternate-background-color: rgb(54, 54, 54);\n"  # jsp
-                           # "QToolTip { color:  rgb(1, 152, 117); background-color: rgb(64,64,64); border: 0px; };\n"
-                           # "")
-        # self.titles_font = "font: 24pt"
         self.horizontal_space = QtWidgets.QSpacerItem(1, 1, QtWidgets.QSizePolicy.MinimumExpanding,
                                               QtWidgets.QSizePolicy.Maximum)
         self.vertical_space = QtWidgets.QSpacerItem(1, 1, QtWidgets.QSizePolicy.Maximum,
                                               QtWidgets.QSizePolicy.MinimumExpanding)
-        # self.resized.connect(self.center_window)
 
     def resizeEvent(self, event):
         '''
@@ -116,13 +98,13 @@ class WindowType(QtWidgets.QWidget):
     def night_mode_switch(self, night_mode):
         if night_mode:
             self.setStyleSheet(
-                "background-color: %s; color: %s; font: %s; border-color: %s; selection-color: %s; selection-background-color: %s" % (
-                night_background_color, night_text_Color, f"{textsize}pt {textfont};", night_border_color,
+                "background-color: %s; color: %s; font: %s; selection-color: %s; selection-background-color: %s" % (
+                night_background_color, night_text_Color, f"{textsize}pt {textfont};",
                 night_selection_color, night_selection_background_color))
         else:
             self.setStyleSheet(
-                "background-color: %s; color: %s; font: %s; border-color: %s; selection-color: %s; selection-background-color: %s" % (
-                backgroundcolor, textColor, f"{textsize}pt {textfont};", bordercolor, selectioncolor,
+                "background-color: %s; color: %s; font: %s; selection-color: %s; selection-background-color: %s" % (
+                backgroundcolor, textColor, f"{textsize}pt {textfont};", selectioncolor,
                 selectionbackgroundcolor))
 
 
@@ -487,12 +469,6 @@ class Spinbox(QtWidgets.QWidget):
                 "background-color: %s; color: %s; border-color: %s; border: %s; border-radius: %s" % (
                     backgroundcolor, textColor, bordercolor, rollingborder, rollingangles))
 
-        # self.setStyleSheet("background-color: rgb(50,50,65);\n"
-        #                    "font: 16pt \"Calibri\";\n"
-        #                    "border-color: rgb(50,50,65);\n"
-        #                    # "border-color: rgb(255, 255, 255);\n"
-        #                    "color: rgb(213, 251, 255);\n")
-
 
 class Combobox(QtWidgets.QComboBox):
     def __init__(self, items_list, current_idx=None, night_mode=False):
@@ -530,8 +506,14 @@ class Checkbox(QtWidgets.QCheckBox):
         self.setChecked(set_checked)
         self.setSizePolicy(QtWidgets.QSizePolicy.Maximum, QtWidgets.QSizePolicy.Maximum)
         self.setMinimumWidth(75)
-        # self.setStyleSheet("padding:5px")
-        self.setStyleSheet("margin-left:50%; margin-right:50%;")
+        self.setStyleSheet("QCheckBox::indicator {width: 12px;height: 12px;background-color: transparent;"
+                            "border-radius: 5px;border-style: solid;border-width: 1px;"
+                            "border-color: rgb(100,100,100);}"
+                            "QCheckBox::indicator:checked {background-color: rgb(70,130,180);}"
+                            "QCheckBox:checked, QCheckBox::indicator:checked {border-color: black black white white;}"
+                            "QCheckBox:checked {background-color: transparent;}"
+                            "QCheckBox:margin-left {50%}"
+                            "QCheckBox:margin-right {50%}")
         self.setCursor(QtCore.Qt.CursorShape.PointingHandCursor)
 
 

{cellects-0.1.0 → cellects-0.1.3}/src/cellects/gui/image_analysis_window.py

@@ -1156,7 +1156,14 @@ class ImageAnalysisWindow(MainTabsType):
         self.advanced_mode_widget = QtWidgets.QWidget()
         self.advanced_mode_layout = QtWidgets.QHBoxLayout()
         self.advanced_mode_cb = Checkbox(self.parent().po.all['expert_mode'])
-        self.advanced_mode_cb.setStyleSheet("margin-left:0%; margin-right:0%;")
+        self.advanced_mode_cb.setStyleSheet("QCheckBox::indicator {width: 12px;height: 12px;background-color: transparent;"
+                            "border-radius: 5px;border-style: solid;border-width: 1px;"
+                            "border-color: rgb(100,100,100);}"
+                            "QCheckBox::indicator:checked {background-color: rgb(70,130,180);}"
+                            "QCheckBox:checked, QCheckBox::indicator:checked {border-color: black black white white;}"
+                            "QCheckBox:checked {background-color: transparent;}"
+                            "QCheckBox:margin-left {0%}"
+                            "QCheckBox:margin-right {0%}")
         self.advanced_mode_cb.stateChanged.connect(self.advanced_mode_check)
         self.advanced_mode_label = FixedText('Advanced mode', halign='l',
                                              tip="Display the color space combination corresponding to the selected option",
@@ -1380,7 +1387,14 @@ class ImageAnalysisWindow(MainTabsType):
         except KeyError:
             self.parent().po.vars["grid_segmentation"] = False
         self.grid_segmentation = Checkbox(self.parent().po.vars["grid_segmentation"])
-        self.grid_segmentation.setStyleSheet("margin-left:0%; margin-right:-10%;")
+        self.grid_segmentation.setStyleSheet("QCheckBox::indicator {width: 12px;height: 12px;background-color: transparent;"
+                            "border-radius: 5px;border-style: solid;border-width: 1px;"
+                            "border-color: rgb(100,100,100);}"
+                            "QCheckBox::indicator:checked {background-color: rgb(70,130,180);}"
+                            "QCheckBox:checked, QCheckBox::indicator:checked {border-color: black black white white;}"
+                            "QCheckBox:checked {background-color: transparent;}"
+                            "QCheckBox:margin-left {0%}"
+                            "QCheckBox:margin-right {-10%}")
         self.grid_segmentation.stateChanged.connect(self.grid_segmentation_option)
 
         self.grid_segmentation_label = FixedText("Grid segmentation",
@@ -1399,7 +1413,14 @@ class ImageAnalysisWindow(MainTabsType):
         self.more_than_2_colors_widget = QtWidgets.QWidget()
         self.more_than_2_colors_layout = QtWidgets.QHBoxLayout()
         self.more_than_two_colors = Checkbox(self.parent().po.all["more_than_two_colors"])
-        self.more_than_two_colors.setStyleSheet("margin-left:0%; margin-right:-10%;")
+        self.more_than_two_colors.setStyleSheet("QCheckBox::indicator {width: 12px;height: 12px;background-color: transparent;"
+                            "border-radius: 5px;border-style: solid;border-width: 1px;"
+                            "border-color: rgb(100,100,100);}"
+                            "QCheckBox::indicator:checked {background-color: rgb(70,130,180);}"
+                            "QCheckBox:checked, QCheckBox::indicator:checked {border-color: black black white white;}"
+                            "QCheckBox:checked {background-color: transparent;}"
+                            "QCheckBox:margin-left {0%}"
+                            "QCheckBox:margin-right {-10%}")
         self.more_than_two_colors.stateChanged.connect(self.display_more_than_two_colors_option)
 
         self.more_than_two_colors_label = FixedText("More than two colors",

{cellects-0.1.0 → cellects-0.1.3}/src/cellects/gui/required_output.py

@@ -4,12 +4,12 @@ This module contains the widget allowing the user to set which variables Cellect
 A first kind of variable is raw data: presence/absence coordinates of the specimens, network, oscillating pixels
 A second kind of variable describe the specimen at each time frame and for each arena of the image stack or video
 """
-
+import numpy as np
 from PySide6 import QtWidgets, QtCore
 import logging
 from cellects.gui.custom_widgets import (
     WindowType, PButton, Checkbox, FixedText)
-from cellects.image_analysis.shape_descriptors import descriptors_names_to_display
+from cellects.image_analysis.shape_descriptors import descriptors_names_to_display, descriptors_categories
 
 
 class RequiredOutput(WindowType):
@@ -136,6 +136,9 @@ class RequiredOutput(WindowType):
             showing the presence/absence of the cell/colony at one time frame.
             This function
         """
+        if not np.array_equal(self.parent().po.all['descriptors'], list(descriptors_categories.keys())):
+            self.parent().po.all['descriptors'] = descriptors_categories
+
         descriptor_names = self.parent().po.all['descriptors']
 
         for i, name in enumerate(descriptor_names):

{cellects-0.1.0 → cellects-0.1.3}/src/cellects/gui/video_analysis_window.py

@@ -190,7 +190,14 @@ class VideoAnalysisWindow(MainTabsType):
                                                    tip='Uncheck to do a Post processing on only one option and earn computation time\nSelecting one of the remaining options will display the result from a Detection',
                                                    night_mode=self.parent().po.all['night_mode'])
         self.compute_all_options_cb = Checkbox(self.parent().po.all['compute_all_options'])
-        self.compute_all_options_cb.setStyleSheet("margin-left:0%; margin-right:0%;")
+        self.compute_all_options_cb.setStyleSheet("QCheckBox::indicator {width: 12px;height: 12px;background-color: transparent;"
+                            "border-radius: 5px;border-style: solid;border-width: 1px;"
+                            "border-color: rgb(100,100,100);}"
+                            "QCheckBox::indicator:checked {background-color: rgb(70,130,180);}"
+                            "QCheckBox:checked, QCheckBox::indicator:checked {border-color: black black white white;}"
+                            "QCheckBox:checked {background-color: transparent;}"
+                            "QCheckBox:margin-left {0%}"
+                            "QCheckBox:margin-right {0%}")
         self.compute_all_options_cb.stateChanged.connect(self.compute_all_options_check)
         self.all_options_row_widget = QtWidgets.QWidget()
         self.all_options_row_layout = QtWidgets.QHBoxLayout()
@@ -234,7 +241,14 @@ class VideoAnalysisWindow(MainTabsType):
         self.fading_widget = QtWidgets.QWidget()
         self.fading_layout = QtWidgets.QHBoxLayout()
         self.do_fading = Checkbox(self.parent().po.vars['do_fading'])
-        self.do_fading.setStyleSheet("margin-left:0%; margin-right:0%;")
+        self.do_fading.setStyleSheet("QCheckBox::indicator {width: 12px;height: 12px;background-color: transparent;"
+                            "border-radius: 5px;border-style: solid;border-width: 1px;"
+                            "border-color: rgb(100,100,100);}"
+                            "QCheckBox::indicator:checked {background-color: rgb(70,130,180);}"
+                            "QCheckBox:checked, QCheckBox::indicator:checked {border-color: black black white white;}"
+                            "QCheckBox:checked {background-color: transparent;}"
+                            "QCheckBox:margin-left {0%}"
+                            "QCheckBox:margin-right {0%}")
         self.do_fading.stateChanged.connect(self.do_fading_check)
         self.fading = Spinbox(min=- 1, max=1, val=self.parent().po.vars['fading'], decimals=2,
                                night_mode=self.parent().po.all['night_mode'])
@@ -274,24 +288,6 @@ class VideoAnalysisWindow(MainTabsType):
         self.last_options_layout = QtWidgets.QHBoxLayout()
         self.last_options_layout.addItem(self.horizontal_space)
 
-        # #  advanced mode widget
-        # self.advanced_mode_widget = QtWidgets.QWidget()
-        # self.advanced_mode_layout = QtWidgets.QHBoxLayout()
-        # advanced_mode = self.parent().po.all['expert_mode']
-        # self.advanced_mode_cb = Checkbox(self.parent().po.all['expert_mode'])
-        # self.advanced_mode_cb.setStyleSheet("margin-left:0%; margin-right:0%;")
-        # self.advanced_mode_cb.stateChanged.connect(self.advanced_mode_check)
-        # self.advanced_mode_label = FixedText('Go to step 2 directly', align='l',
-        #                                      tip="Allow the user to try Post processing before having tuned the parameters related to Detection.",
-        #                                      night_mode=self.parent().po.all['night_mode'])
-        # # self.advanced_mode_label.setAlignment(QtCore.Qt.AlignTop)
-        # self.advanced_mode_layout.addWidget(self.advanced_mode_cb)
-        # self.advanced_mode_layout.addWidget(self.advanced_mode_label)
-        # self.advanced_mode_layout.addItem(self.horizontal_space)
-        # self.advanced_mode_layout.setAlignment(QtCore.Qt.AlignHCenter)
-        # self.advanced_mode_widget.setLayout(self.advanced_mode_layout)
-        # self.last_options_layout.addWidget(self.advanced_mode_widget)
-
         self.advanced_parameters = PButton('Advanced Parameters', night_mode=self.parent().po.all['night_mode'])
         self.advanced_parameters.clicked.connect(self.advanced_parameters_is_clicked)
         self.last_options_layout.addWidget(self.advanced_parameters)

{cellects-0.1.0 → cellects-0.1.3}/src/cellects/utils/load_display_save.py

@@ -220,10 +220,6 @@ class PickleRick:
         Examples
         --------
         >>> PickleRick().read_file("example.pkl")
-        Some content
-
-        >>> read_file("non_existent_file.pkl")
-        None
         """
         self.counter += 1
         if self.counter < 1000:
@@ -919,7 +915,8 @@ def save_fig(img: NDArray, full_path, cmap=None):
     else:
         ax.imshow(img, cmap=cmap, interpolation="none")
     plt.axis('off')
-    fig.tight_layout()
+    if np.min(img.shape) > 50:
+        fig.tight_layout()
 
     fig.savefig(full_path, bbox_inches='tight', pad_inches=0., transparent=True, dpi=500)
     plt.close(fig)