Merge pull request #23 from haesleinhuepf/open3d-vedo-conversion

Open3d vedo conversion
haesleinhuepf · Feb 18, 2023 · 4300db3 · 4300db3
2 parents a6c9113 + 72d9c95
commit 4300db3
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diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml
@@ -51,7 +51,7 @@ jobs:
 
       # this runs the platform-specific tests declared in tox.ini
       - name: Test with tox
-        uses: GabrielBB/xvfb-action@v1
+        uses: aganders3/headless-gui@v1
         with:
           run: python -m tox
         env:

diff --git a/README.md b/README.md
@@ -8,7 +8,7 @@
 [![Development Status](https://img.shields.io/pypi/status/napari-process-points-and-surfaces.svg)](https://en.wikipedia.org/wiki/Software_release_life_cycle#Alpha)
 [![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-process-points-and-surfaces)](https://napari-hub.org/plugins/napari-process-points-and-surfaces)
 
-Process and analyze surfaces using [open3d](http://www.open3d.org/) and [vedo](https://vedo.embl.es/) in [napari].
+Process and analyze surfaces using [vedo](https://vedo.embl.es/) in [napari].
 
 ## Usage
 
@@ -21,12 +21,12 @@ The Standford Bunny example dataset has been taken from the [The Stanford 3D Sca
 
 For processing meshes in Python scripts, see the [demo notebook](https://github.com/haesleinhuepf/napari-process-points-and-surfaces/blob/main/docs/demo.ipynb). There you also learn how this screenshot is made:
 
-![img.png](https://github.com/haesleinhuepf/napari-process-points-and-surfaces/raw/main/docs/screenshot.png)
+![img.png](https://github.com/haesleinhuepf/napari-process-points-and-surfaces/raw/main/docs/screenshot1.png)
 
 For performing quantitative measurements of meshes in Python scripts, see the [demo notebook](https://github.com/haesleinhuepf/napari-process-points-and-surfaces/blob/main/docs/quality_measurements.ipynb). 
 There you also learn how this screenshot is made:
 
-![img.png](https://github.com/haesleinhuepf/napari-process-points-and-surfaces/raw/main/docs/screenshot2.png)
+![img.png](https://github.com/haesleinhuepf/napari-process-points-and-surfaces/raw/main/docs/screenshot4.png)
 
 ### Surface measurements and annotations
 
@@ -57,20 +57,28 @@ measurements and annotations side-by-side.
 
 ## Installation
 
-You can install `napari-process-points-and-surfaces` via [pip] and conda:
+You can install `napari-process-points-and-surfaces` via mamba/conda and pip:
 
 ```
-conda create -n nppas-env -c conda-forge -c open3d-admin python=3.9 open3d napari
-conda activate nppas-env
+mamba install vedo vtk libnetcdf=4.7.4 -c conda-forge
 pip install napari-process-points-and-surfaces
 ```
 
+f### Troubleshooting: Open3d installation
+
+Since version 0.4.0, `nppas` does no longer depend on [open3d](http://www.open3d.org/). 
+Some deprecated functions still use Open3d though. 
+Follow the installation instructions in the [open3d documentation](http://www.open3d.org/docs/release/getting_started.htm) to install it and keep using those functions.
+Also consider updating code and no longer using these deprecated functions. 
+See [release notes](https://github.com/haesleinhuepf/napari-process-points-and-surfaces/releases/tag/0.4.0) for details.
+
 ## See also
 
 There are other napari plugins with similar / overlapping functionality
 * [pymeshlab](https://www.napari-hub.org/plugins/napari-pymeshlab)
 * [morphometrics](https://www.napari-hub.org/plugins/morphometrics)  
 * [napari-pyclesperanto-assistant](https://www.napari-hub.org/plugins/napari-pyclesperanto-assistant)
+* [napari-stress](https://www.napari-hub.org/plugins/napari-stress)
 
 ## Contributing
 
@@ -82,6 +90,11 @@ the coverage at least stays the same before you submit a pull request.
 Distributed under the terms of the [BSD-3] license,
 "napari-process-points-and-surfaces" is free and open source software
 
+## Acknowledgements
+
+Some code snippets and example data were taken from the [vedo](https://vedo.embl.es/) and [open3d](http://www.open3d.org/) 
+repositories and documentation. See [thirdparty licenses](https://github.com/haesleinhuepf/napari-process-points-and-surfaces/tree/main/licenses_third_party) for licensing details.
+
 ## Issues
 
 If you encounter any problems, please create a thread on [image.sc] along with a detailed description and tag [@haesleinhuepf].

diff --git a/docs/branchoid.ipynb b/docs/branchoid.ipynb
diff --git a/docs/branchoid2.ipynb b/docs/branchoid2.ipynb
diff --git a/docs/creating_surfaces.ipynb b/docs/creating_surfaces.ipynb
diff --git a/docs/curvature_measurement.ipynb b/docs/curvature_measurement.ipynb
diff --git a/docs/demo.ipynb b/docs/demo.ipynb
diff --git a/docs/quality_measurements.ipynb b/docs/quality_measurements.ipynb
diff --git a/docs/screenshot.png b/docs/screenshot.png
diff --git a/docs/screenshot1.png b/docs/screenshot1.png
diff --git a/docs/screenshot4.png b/docs/screenshot4.png
diff --git a/docs/surface_vertex_classification.ipynb b/docs/surface_vertex_classification.ipynb
diff --git a/docs/table_row_classifier.cl b/docs/table_row_classifier.cl
@@ -0,0 +1,116 @@
+/*
+OpenCL RandomForestClassifier
+classifier_class_name = TableRowClassifier
+feature_specification = Quality.AREA Quality.ASPECT_RATIO Quality.GAUSS_CURVATURE Quality.MEAN_CURVATURE Quality.SPHERE_FITTED_CURVATURE_HECTA_VOXEL Quality.SPHERE_FITTED_CURVATURE_KILO_VOXEL
+num_ground_truth_dimensions = 1
+num_classes = 2
+num_features = 6
+max_depth = 2
+num_trees = 10
+feature_importances = 0.014774211871627363,0.045757080610021775,0.4964465603808598,0.10980786142320526,0.3332142857142857,0.0
+apoc_version = 0.12.0
+*/
+__kernel void predict (IMAGE_in0_TYPE in0, IMAGE_in1_TYPE in1, IMAGE_in2_TYPE in2, IMAGE_in3_TYPE in3, IMAGE_in4_TYPE in4, IMAGE_in5_TYPE in5, IMAGE_out_TYPE out) {
+ sampler_t sampler = CLK_NORMALIZED_COORDS_FALSE | CLK_ADDRESS_CLAMP_TO_EDGE | CLK_FILTER_NEAREST;
+ const int x = get_global_id(0);
+ const int y = get_global_id(1);
+ const int z = get_global_id(2);
+ float i0 = READ_IMAGE(in0, sampler, POS_in0_INSTANCE(x,y,z,0)).x;
+ float i1 = READ_IMAGE(in1, sampler, POS_in1_INSTANCE(x,y,z,0)).x;
+ float i2 = READ_IMAGE(in2, sampler, POS_in2_INSTANCE(x,y,z,0)).x;
+ float i3 = READ_IMAGE(in3, sampler, POS_in3_INSTANCE(x,y,z,0)).x;
+ float i4 = READ_IMAGE(in4, sampler, POS_in4_INSTANCE(x,y,z,0)).x;
+ float i5 = READ_IMAGE(in5, sampler, POS_in5_INSTANCE(x,y,z,0)).x;
+ float s0=0;
+ float s1=0;
+if(i2<0.01253616251051426){
+ s0+=13.0;
+} else {
+ if(i1<1.5743114948272705){
+  s1+=16.0;
+ } else {
+  s0+=2.0;
+ }
+}
+if(i2<0.013402309268712997){
+ if(i2<0.007590430788695812){
+  s0+=13.0;
+ } else {
+  s0+=2.0;
+  s1+=1.0;
+ }
+} else {
+ s1+=15.0;
+}
+if(i2<0.00794646143913269){
+ s0+=21.0;
+} else {
+ s1+=10.0;
+}
+if(i4<0.00028659982490353286){
+ s0+=17.0;
+} else {
+ s1+=14.0;
+}
+if(i3<9.934128320310265e-05){
+ if(i1<1.3991124629974365){
+  s0+=9.0;
+ } else {
+  s0+=3.0;
+  s1+=4.0;
+ }
+} else {
+ s1+=15.0;
+}
+if(i4<0.00029376597376540303){
+ s0+=21.0;
+} else {
+ s1+=10.0;
+}
+if(i3<9.934128320310265e-05){
+ if(i2<0.007590430788695812){
+  s0+=16.0;
+ } else {
+  s0+=1.0;
+  s1+=3.0;
+ }
+} else {
+ if(i2<0.04185527563095093){
+  s0+=1.0;
+  s1+=7.0;
+ } else {
+  s0+=3.0;
+ }
+}
+if(i4<0.00028545514214783907){
+ s0+=14.0;
+} else {
+ s1+=17.0;
+}
+if(i2<0.006332993507385254){
+ s0+=11.0;
+} else {
+ if(i4<0.00028545514214783907){
+  s0+=3.0;
+ } else {
+  s1+=17.0;
+ }
+}
+if(i0<26.780094146728516){
+ s1+=3.0;
+} else {
+ if(i2<0.011249952018260956){
+  s0+=16.0;
+ } else {
+  s0+=1.0;
+  s1+=11.0;
+ }
+}
+ float max_s=s0;
+ int cls=1;
+ if (max_s < s1) {
+  max_s = s1;
+  cls=2;
+ }
+ WRITE_IMAGE (out, POS_out_INSTANCE(x,y,z,0), cls);
+}
diff --git a/docs/tabular_quality_measurements.ipynb b/docs/tabular_quality_measurements.ipynb
diff --git a/docs/visualizing_surfaces.ipynb b/docs/visualizing_surfaces.ipynb