Merge pull request #330 from jo-mueller/replace-pointcloud-visualizat…

…ion-with-napari-matplotlib Replace pointcloud visualization with napari matplotlib
campaslab · Oct 5, 2023 · 38f6be5 · 38f6be5
2 parents 49fa279 + 0355b2f
commit 38f6be5
Show file tree

Hide file tree

Showing 16 changed files with 16 additions and 432 deletions.
diff --git a/docs/02_interactive_usage/02_example_workflows/demo_fit_ellipsoid_interactive.md b/docs/02_interactive_usage/02_example_workflows/demo_fit_ellipsoid_interactive.md
@@ -47,7 +47,7 @@ Lastly, you can measure mean curvature on the surface of this ellipse. To do so,
 
 ![](imgs/demo_fit_ellipsoid7.png)
 
-You can also use the built-in [feature visualization widget](utility:visualize_features) to show, for instance, a hiostogram of the curvature on the surface.
+You can also use [napari-matplotlib](https://napari-matplotlib.github.io/index.html) [feature visualization widget](point_and_click:visualize_features) to show, for instance, a hiostogram of the curvature on the surface.
 
 (fit_ellipsoid:normal_vectors)=
 ## Distances between pointcloud and approximation

diff --git a/docs/02_interactive_usage/02_example_workflows/demo_visualize_features.md b/docs/02_interactive_usage/02_example_workflows/demo_visualize_features.md
diff --git a/...interactive_usage/02_example_workflows/imgs/demo_visualize_featureHistogram.png b/...interactive_usage/02_example_workflows/imgs/demo_visualize_featureHistogram.png
diff --git a/...nteractive_usage/02_example_workflows/imgs/demo_visualize_featureHistogram2.png b/...nteractive_usage/02_example_workflows/imgs/demo_visualize_featureHistogram2.png
diff --git a/docs/02_interactive_usage/02_example_workflows/imgs/demo_visualize_features1.png b/docs/02_interactive_usage/02_example_workflows/imgs/demo_visualize_features1.png
diff --git a/docs/02_interactive_usage/02_example_workflows/imgs/demo_visualize_features2.png b/docs/02_interactive_usage/02_example_workflows/imgs/demo_visualize_features2.png
diff --git a/docs/02_interactive_usage/02_example_workflows/imgs/demo_visualize_features3.png b/docs/02_interactive_usage/02_example_workflows/imgs/demo_visualize_features3.png
diff --git a/docs/02_interactive_usage/02_example_workflows/imgs/demo_visualize_features4.png b/docs/02_interactive_usage/02_example_workflows/imgs/demo_visualize_features4.png
diff --git a/docs/02_interactive_usage/02_example_workflows/imgs/demo_visualize_features5.png b/docs/02_interactive_usage/02_example_workflows/imgs/demo_visualize_features5.png
diff --git a/docs/02_interactive_usage/02_example_workflows/visualize_measurements_in_viewer.md b/docs/02_interactive_usage/02_example_workflows/visualize_measurements_in_viewer.md
@@ -0,0 +1,12 @@
+(point_and_click:visualize_features)=
+# Visualize measurements
+
+Napari-stress (and the [measurement toolbox](toolboxes:stress_toolbox:stress_toolbox_interactive), in partciular) generate a number of measurements that can be visualized using the [napari-matplotlib](https://napari-matplotlib.github.io/) plugin. It is automatically installed with napari-stress and can be activated from the plugins menu (`Plugins > napari Matplotlib`).
+
+In order to use it, check out the documentation on the [napari-matplotlib page](https://napari-matplotlib.github.io/). In the scope of napari-stress, what you will need, is the Features Histogram (`Plugins > napari Matplotlib > FeaturesHistogram`).
+
+![](./imgs/demo_visualize_featureHistogram.png)
+
+To display measurements, select a layer of interest and the dropdown in the newly created Histogram widget will show all possible features for you to highlight.
+
+![](./imgs/demo_visualize_featureHistogram2.png)
diff --git a/docs/_toc.yml b/docs/_toc.yml
@@ -27,6 +27,7 @@ parts:
         - file: 01_code_usage/02_example_workflows/demo_spherical_harmonics_code
         - file: 01_code_usage/02_example_workflows/demo_timelapse_processing
         - file: 01_code_usage/02_example_workflows/demo_measure_intensity_on_surface
+        - file: 01_code_usage/02_example_workflows/demo_measure_intensity_on_vectors
 
     - file: 02_interactive_usage/interactive_usage
       sections:
@@ -41,7 +42,7 @@ parts:
         - file: 02_interactive_usage/02_example_workflows/demo_surface_reconstruction_interactive
         - file: 02_interactive_usage/02_example_workflows/demo_spherical_harmonics_interactive
         - file: 02_interactive_usage/02_example_workflows/demo_measure_curvature
-        - file: 02_interactive_usage/02_example_workflows/demo_visualize_features
+        - file: 02_interactive_usage/02_example_workflows/visualize_measurements_in_viewer
 
   - caption: Glossary
     chapters:

diff --git a/setup.cfg b/setup.cfg
@@ -34,10 +34,9 @@ install_requires =
     dask
     distributed
     joblib
-    matplotlib
     mpmath
     napari
-    napari-matplotlib==0.2.0
+    napari-matplotlib>=1.1.0
     napari-process-points-and-surfaces>=0.4.0
     napari-segment-blobs-and-things-with-membranes
     napari-tools-menu>=0.1.15

diff --git a/src/napari_stress/__init__.py b/src/napari_stress/__init__.py
@@ -24,7 +24,5 @@
 
 from ._sample_data.sample_data import get_droplet_point_cloud, get_droplet_point_cloud_4d, get_droplet_4d
 
-from ._plotting.features_histogram import FeaturesHistogramWidget
-
 from . import types
 from . import _vectors as vectors