napari-spatial-correlation-plotter 0.0.1__tar.gz → 0.0.3__tar.gz

{napari_spatial_correlation_plotter-0.0.1/src/napari_spatial_correlation_plotter.egg-info → napari_spatial_correlation_plotter-0.0.3}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.1
 Name: napari-spatial-correlation-plotter
-Version: 0.0.1
-Summary: A simple plugin to use FooBar segmentation within napari
+Version: 0.0.3
+Summary: A plugin to compute and display spatial correlation histograms in Napari
 Home-page: https://github.com/jules-vanaret/napari-spatial-correlation-plotter
 Author: Jules Vanaret
 Author-email: jules.vanaret@univ-amu.fr
@@ -31,6 +31,7 @@ Requires-Dist: matplotlib
 Requires-Dist: scikit-image
 Requires-Dist: qtpy
 Requires-Dist: pyclesperanto_prototype
+Requires-Dist: tapenade
 Provides-Extra: testing
 Requires-Dist: tox; extra == "testing"
 Requires-Dist: pytest; extra == "testing"
@@ -52,10 +53,10 @@ Requires-Dist: pyqt5; extra == "testing"
 
 A plugin to dynamically interact with the spatial correlation heatmap obtained by comparing two continuous fields of biophysical properties in 3D tissues.
 
-`napari-spatial-correlation-plotter` is a [napari] plugin that is part of the [Tapenade](https://github.com/GuignardLab/tapenade) project. Tapenade is a tool for the analysis of dense 3D tissues acquired with deep imaging microscopy. It is designed to be user-friendly and to provide a comprehensive analysis of the data.
-
 If you use this plugin for your research, please [cite us](https://github.com/GuignardLab/tapenade/blob/main/README.md#how-to-cite).
 
+`napari-spatial-correlation-plotter` is a [napari] plugin that is part of the [Tapenade](https://github.com/GuignardLab/tapenade) project. Tapenade is a tool for the analysis of dense 3D tissues acquired with deep imaging microscopy. It is designed to be user-friendly and to provide a comprehensive analysis of the data.
+
 ## Overview
 
 While working with large and dense 3D and 3D+time gastruloid datasets, we found that being able to visualise and interact with the data dynamically greatly helped processing it.
@@ -102,7 +103,15 @@ Steps:
 11. You can click on the `Save the figure` button to save the current plot (many formats are available, including .png, .svg, .jpeg).
 12. You can interact with the plot by manually drawing a region of interest directly on the plot to automatically select and display the corresponding cells in 3D on an independant Napari Labels layer `clustered labels`. By using a left click, you can draw an arbitrary shape. By using a right click, you can draw a rectangle. If `Shift` is pressed while drawing, several groups of cells can appear on the `clustered labels` layer, each with a different color.
 13. To trigger the grid view like in the example image, you can click on the `Toggle grid mode` button. This will display all layers in a grid view. By right clicking the button, you can parametrize the grid view (e.g number of columns, number of rows, etc).
-14. You can switch between 2D and 3D view at all time by clicking on the `Toggle 2D/3D view` button (it resembles a square when in 2D mode, or a cube when in 3D mode). 
+14. You can switch between 2D and 3D view at all time by clicking on the `Toggle 2D/3D view` button (it resembles a square when in 2D mode, or a cube when in 3D mode).
+
+## Acknowledgements
+
+The "napari-clusters-plotter" plugin [1] heavily inspired this plugin, most notably the `SelectFromCollection`, `MplCanvas` and `FigureToolbar` classes. The `PlotterWidget` class has been modified for the specific use case of this plugin, but the core functionalites have been adapted directly.
+napari-clusters-plotter source code is available [here](https://github.com/BiAPoL/napari-clusters-plotter/tree/main).
+
+
+[1] Zigutyte, L., Savill, R., Müller, J., Zoccoler, M., Wagner, T., & Haase, R. (2023). napari-clusters-plotter. Zenodo. https://doi.org/10.5281/zenodo.5884657
 
 ## Contributing
 

{napari_spatial_correlation_plotter-0.0.1 → napari_spatial_correlation_plotter-0.0.3}/README.md

@@ -11,10 +11,10 @@
 
 A plugin to dynamically interact with the spatial correlation heatmap obtained by comparing two continuous fields of biophysical properties in 3D tissues.
 
-`napari-spatial-correlation-plotter` is a [napari] plugin that is part of the [Tapenade](https://github.com/GuignardLab/tapenade) project. Tapenade is a tool for the analysis of dense 3D tissues acquired with deep imaging microscopy. It is designed to be user-friendly and to provide a comprehensive analysis of the data.
-
 If you use this plugin for your research, please [cite us](https://github.com/GuignardLab/tapenade/blob/main/README.md#how-to-cite).
 
+`napari-spatial-correlation-plotter` is a [napari] plugin that is part of the [Tapenade](https://github.com/GuignardLab/tapenade) project. Tapenade is a tool for the analysis of dense 3D tissues acquired with deep imaging microscopy. It is designed to be user-friendly and to provide a comprehensive analysis of the data.
+
 ## Overview
 
 While working with large and dense 3D and 3D+time gastruloid datasets, we found that being able to visualise and interact with the data dynamically greatly helped processing it.
@@ -61,7 +61,15 @@ Steps:
 11. You can click on the `Save the figure` button to save the current plot (many formats are available, including .png, .svg, .jpeg).
 12. You can interact with the plot by manually drawing a region of interest directly on the plot to automatically select and display the corresponding cells in 3D on an independant Napari Labels layer `clustered labels`. By using a left click, you can draw an arbitrary shape. By using a right click, you can draw a rectangle. If `Shift` is pressed while drawing, several groups of cells can appear on the `clustered labels` layer, each with a different color.
 13. To trigger the grid view like in the example image, you can click on the `Toggle grid mode` button. This will display all layers in a grid view. By right clicking the button, you can parametrize the grid view (e.g number of columns, number of rows, etc).
-14. You can switch between 2D and 3D view at all time by clicking on the `Toggle 2D/3D view` button (it resembles a square when in 2D mode, or a cube when in 3D mode). 
+14. You can switch between 2D and 3D view at all time by clicking on the `Toggle 2D/3D view` button (it resembles a square when in 2D mode, or a cube when in 3D mode).
+
+## Acknowledgements
+
+The "napari-clusters-plotter" plugin [1] heavily inspired this plugin, most notably the `SelectFromCollection`, `MplCanvas` and `FigureToolbar` classes. The `PlotterWidget` class has been modified for the specific use case of this plugin, but the core functionalites have been adapted directly.
+napari-clusters-plotter source code is available [here](https://github.com/BiAPoL/napari-clusters-plotter/tree/main).
+
+
+[1] Zigutyte, L., Savill, R., Müller, J., Zoccoler, M., Wagner, T., & Haase, R. (2023). napari-clusters-plotter. Zenodo. https://doi.org/10.5281/zenodo.5884657
 
 ## Contributing
 

{napari_spatial_correlation_plotter-0.0.1 → napari_spatial_correlation_plotter-0.0.3}/setup.cfg

@@ -1,7 +1,7 @@
 [metadata]
 name = napari-spatial-correlation-plotter
 version = attr: napari_spatial_correlation_plotter.__version__
-description = A simple plugin to use FooBar segmentation within napari
+description = A plugin to compute and display spatial correlation histograms in Napari
 long_description = file: README.md
 long_description_content_type = text/markdown
 url = https://github.com/jules-vanaret/napari-spatial-correlation-plotter
@@ -37,6 +37,7 @@ install_requires =
 	scikit-image
 	qtpy
 	pyclesperanto_prototype
+	tapenade
 python_requires = >=3.8
 include_package_data = True
 package_dir = 

{napari_spatial_correlation_plotter-0.0.1 → napari_spatial_correlation_plotter-0.0.3}/src/napari_spatial_correlation_plotter/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.0.1"
+__version__ = "0.0.3"
 from ._widget import PlotterWidget
 
 __all__ = (

{napari_spatial_correlation_plotter-0.0.1 → napari_spatial_correlation_plotter-0.0.3}/src/napari_spatial_correlation_plotter/_nice_colormap.py

@@ -1,3 +1,7 @@
+"""
+Copyright (c) 2022, DFG Cluster of Excellence "Physics of Life" TU Dresden: Robert Haase, Laura Zigutyte, Marcello Zoccoler, Ryan Savill, Johannes Müller and Max Planck Institute of Molecular Physiology Dortmund: Thorsten Wagner
+"""
+
 def get_nice_colormap():
     colours_w_old_colors = [
         "#ff7f0e",

{napari_spatial_correlation_plotter-0.0.1 → napari_spatial_correlation_plotter-0.0.3}/src/napari_spatial_correlation_plotter/_widget.py

@@ -1,3 +1,6 @@
+"""
+Copyright (c) 2022, DFG Cluster of Excellence "Physics of Life" TU Dresden: Robert Haase, Laura Zigutyte, Marcello Zoccoler, Ryan Savill, Johannes Müller and Max Planck Institute of Molecular Physiology Dortmund: Thorsten Wagner
+"""
 import os
 from pathlib import Path as PathL
 from time import time
@@ -28,6 +31,19 @@ from napari_spatial_correlation_plotter._nice_colormap import get_nice_colormap
 
 ICON_ROOT = PathL(__file__).parent / "icons"
 
+"""
+This widget takes HEAVY inspiration from the napari-clusters-plotter plugin [1],
+most notably the SelectFromCollection, MplCanvas and FigureToolbar classes.
+The PlotterWidget class has been modified for the specific use case of this
+plugin, but the core functionalites have been adapted directly.
+
+napari-clusters-plotter source code is available at
+https://github.com/BiAPoL/napari-clusters-plotter/tree/main
+
+
+[1] Zigutyte, L., Savill, R., Müller, J., Zoccoler, M., Wagner, T., & Haase, R. (2023).
+napari-clusters-plotter. Zenodo. https://doi.org/10.5281/zenodo.5884657
+"""
 
 # TODO:
 # - add log scale to heatmap colors
@@ -712,6 +728,10 @@ class PlotterWidget(Container):
             )
         else:
             self.quantityX_smoothed_layer.data = blurredX
+            self.quantityX_smoothed_layer.contrast_limits = (
+                blurredX.min(), blurredX.max()
+            )
+            self.quantityX_smoothed_layer.refresh()
 
         if (
             self.quantityY_smoothed_layer is None
@@ -722,6 +742,10 @@ class PlotterWidget(Container):
             )
         else:
             self.quantityY_smoothed_layer.data = blurredY
+            self.quantityY_smoothed_layer.contrast_limits = (
+                blurredY.min(), blurredY.max()
+            )
+            self.quantityY_smoothed_layer.refresh()
 
     def _update_quantities_labels_choices(self, event):
 

{napari_spatial_correlation_plotter-0.0.1 → napari_spatial_correlation_plotter-0.0.3/src/napari_spatial_correlation_plotter.egg-info}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.1
 Name: napari-spatial-correlation-plotter
-Version: 0.0.1
-Summary: A simple plugin to use FooBar segmentation within napari
+Version: 0.0.3
+Summary: A plugin to compute and display spatial correlation histograms in Napari
 Home-page: https://github.com/jules-vanaret/napari-spatial-correlation-plotter
 Author: Jules Vanaret
 Author-email: jules.vanaret@univ-amu.fr
@@ -31,6 +31,7 @@ Requires-Dist: matplotlib
 Requires-Dist: scikit-image
 Requires-Dist: qtpy
 Requires-Dist: pyclesperanto_prototype
+Requires-Dist: tapenade
 Provides-Extra: testing
 Requires-Dist: tox; extra == "testing"
 Requires-Dist: pytest; extra == "testing"
@@ -52,10 +53,10 @@ Requires-Dist: pyqt5; extra == "testing"
 
 A plugin to dynamically interact with the spatial correlation heatmap obtained by comparing two continuous fields of biophysical properties in 3D tissues.
 
-`napari-spatial-correlation-plotter` is a [napari] plugin that is part of the [Tapenade](https://github.com/GuignardLab/tapenade) project. Tapenade is a tool for the analysis of dense 3D tissues acquired with deep imaging microscopy. It is designed to be user-friendly and to provide a comprehensive analysis of the data.
-
 If you use this plugin for your research, please [cite us](https://github.com/GuignardLab/tapenade/blob/main/README.md#how-to-cite).
 
+`napari-spatial-correlation-plotter` is a [napari] plugin that is part of the [Tapenade](https://github.com/GuignardLab/tapenade) project. Tapenade is a tool for the analysis of dense 3D tissues acquired with deep imaging microscopy. It is designed to be user-friendly and to provide a comprehensive analysis of the data.
+
 ## Overview
 
 While working with large and dense 3D and 3D+time gastruloid datasets, we found that being able to visualise and interact with the data dynamically greatly helped processing it.
@@ -102,7 +103,15 @@ Steps:
 11. You can click on the `Save the figure` button to save the current plot (many formats are available, including .png, .svg, .jpeg).
 12. You can interact with the plot by manually drawing a region of interest directly on the plot to automatically select and display the corresponding cells in 3D on an independant Napari Labels layer `clustered labels`. By using a left click, you can draw an arbitrary shape. By using a right click, you can draw a rectangle. If `Shift` is pressed while drawing, several groups of cells can appear on the `clustered labels` layer, each with a different color.
 13. To trigger the grid view like in the example image, you can click on the `Toggle grid mode` button. This will display all layers in a grid view. By right clicking the button, you can parametrize the grid view (e.g number of columns, number of rows, etc).
-14. You can switch between 2D and 3D view at all time by clicking on the `Toggle 2D/3D view` button (it resembles a square when in 2D mode, or a cube when in 3D mode). 
+14. You can switch between 2D and 3D view at all time by clicking on the `Toggle 2D/3D view` button (it resembles a square when in 2D mode, or a cube when in 3D mode).
+
+## Acknowledgements
+
+The "napari-clusters-plotter" plugin [1] heavily inspired this plugin, most notably the `SelectFromCollection`, `MplCanvas` and `FigureToolbar` classes. The `PlotterWidget` class has been modified for the specific use case of this plugin, but the core functionalites have been adapted directly.
+napari-clusters-plotter source code is available [here](https://github.com/BiAPoL/napari-clusters-plotter/tree/main).
+
+
+[1] Zigutyte, L., Savill, R., Müller, J., Zoccoler, M., Wagner, T., & Haase, R. (2023). napari-clusters-plotter. Zenodo. https://doi.org/10.5281/zenodo.5884657
 
 ## Contributing
 

{napari_spatial_correlation_plotter-0.0.1 → napari_spatial_correlation_plotter-0.0.3}/src/napari_spatial_correlation_plotter.egg-info/requires.txt

@@ -4,6 +4,7 @@ matplotlib
 scikit-image
 qtpy
 pyclesperanto_prototype
+tapenade
 
 [testing]
 tox