From e3ec60d4d93f2eea2801e9d7fe8d71d5460a97de Mon Sep 17 00:00:00 2001 From: Johannes Soltwedel <38459088+jo-mueller@users.noreply.github.com> Date: Mon, 26 May 2025 22:08:39 +0200 Subject: [PATCH 1/5] flatten demo tree --- docs/01_code_usage/01_toolboxes/Readme.md | 3 -- .../02_example_workflows/Readme.md | 3 -- .../demo_analyze_everything.ipynb | 0 .../demo_analyze_everything_batch.ipynb | 0 .../demo_anisotropic_stresses.ipynb | 0 ..._droplet_reconstruction_toolbox_code.ipynb | 0 .../demo_fit_ellipsoid_code.ipynb | 0 .../demo_measure_intensity_on_surface.ipynb | 0 .../demo_measure_intensity_on_vectors.ipynb | 0 .../demo_measure_patch_fitted_curvature.ipynb | 0 .../demo_patch_fitting_reconstruction.ipynb | 0 .../demo_spherical_harmonics_code.ipynb | 0 .../demo_surface_reconstruction_code.ipynb | 0 .../demo_surface_tracing.ipynb | 0 .../reconstruction_settings.yaml | 0 .../01_toolboxes/Readme.md | 2 - .../02_example_workflows/Readme.md | 3 -- .../demo_droplet_reconstruction_toolbox.md | 0 .../demo_fit_ellipsoid_interactive.md | 0 .../demo_measure_curvature.md | 0 .../demo_spherical_harmonics_interactive.md | 0 .../demo_stress_toolbox_interactive.md | 0 ...demo_surface_reconstruction_interactive.md | 0 .../imgs/demo_fit_ellipsoid1.png | Bin .../imgs/demo_fit_ellipsoid2.png | Bin .../imgs/demo_fit_ellipsoid3.png | Bin .../imgs/demo_fit_ellipsoid5.png | Bin .../imgs/demo_fit_ellipsoid6.png | Bin .../imgs/demo_fit_ellipsoid7.png | Bin .../imgs/demo_fit_ellipsoid8.png | Bin .../imgs/demo_fit_spherical_harmonics1.png | Bin .../imgs/demo_measure_curvature1.png | Bin .../imgs/demo_measure_curvature2.png | Bin .../imgs/demo_measure_curvature3.png | Bin .../imgs/demo_reconstruction_toolbox1.png | Bin .../imgs/demo_reconstruction_toolbox2.png | Bin .../imgs/demo_reconstruction_toolbox3.png | Bin .../demo_reconstruction_toolbox_result1.png | Bin .../demo_reconstruction_toolbox_result2.png | Bin .../demo_reconstruction_toolbox_result3.png | Bin .../demo_reconstruction_toolbox_result4.png | Bin .../demo_reconstruction_toolbox_result5.png | Bin .../imgs/demo_stress_toolbox1.png | Bin .../imgs/demo_stress_toolbox2.png | Bin .../imgs/demo_stress_toolbox3.png | Bin .../imgs/demo_stress_toolbox4.png | Bin .../imgs/demo_stress_toolbox5.png | Bin .../imgs/demo_stress_toolbox6.png | Bin .../imgs/demo_stress_toolbox7.png | Bin .../imgs/demo_visualize_featureHistogram.png | Bin .../imgs/demo_visualize_featureHistogram2.png | Bin .../imgs/open_sample_droplet.png | Bin .../imgs/open_sample_droplet1.png | Bin .../imgs/open_terminal.png | Bin .../imgs/recipe_image_to_surface.png | Bin .../imgs/recipe_image_to_surface1.png | Bin .../imgs/recipe_image_to_surface10.png | Bin .../imgs/recipe_image_to_surface2.png | Bin .../imgs/recipe_image_to_surface3.png | Bin .../imgs/recipe_image_to_surface4.png | Bin .../imgs/recipe_image_to_surface5.png | Bin .../imgs/recipe_image_to_surface6.png | Bin .../imgs/recipe_image_to_surface7.png | Bin .../imgs/recipe_image_to_surface8.png | Bin .../imgs/recipe_image_to_surface8a.png | Bin .../imgs/recipe_image_to_surface9.png | Bin .../imgs/surface_to_curvature1.png | Bin .../imgs/surface_to_curvature2.png | Bin .../imgs/surface_to_curvature3.png | Bin .../imgs/surface_to_curvature4.png | Bin .../imgs/surface_to_curvature5.gif | Bin .../imgs/surface_to_curvature5.png | Bin .../imgs/surface_to_curvature5a.png | Bin .../imgs/surface_to_curvature5b.png | Bin .../imgs/surface_to_curvature6.png | Bin .../imgs/surface_to_curvature7.png | Bin .../imgs/surface_to_curvature8.png | Bin .../imgs/workflow.png | Bin .../imgs/workflow.svg | 0 .../imgs/workflow_surface_to_curvature.png | Bin .../visualize_measurements_in_viewer.md | 0 docs/_toc.yml | 48 +++++++----------- 82 files changed, 19 insertions(+), 40 deletions(-) delete mode 100644 docs/01_code_usage/01_toolboxes/Readme.md delete mode 100644 docs/01_code_usage/02_example_workflows/Readme.md rename docs/01_code_usage/{01_toolboxes => }/demo_analyze_everything.ipynb (100%) rename docs/01_code_usage/{01_toolboxes => }/demo_analyze_everything_batch.ipynb (100%) rename docs/01_code_usage/{01_toolboxes => }/demo_anisotropic_stresses.ipynb (100%) rename docs/01_code_usage/{01_toolboxes => }/demo_droplet_reconstruction_toolbox_code.ipynb (100%) rename docs/01_code_usage/{02_example_workflows => }/demo_fit_ellipsoid_code.ipynb (100%) rename docs/01_code_usage/{02_example_workflows => }/demo_measure_intensity_on_surface.ipynb (100%) rename docs/01_code_usage/{02_example_workflows => }/demo_measure_intensity_on_vectors.ipynb (100%) rename docs/01_code_usage/{02_example_workflows => }/demo_measure_patch_fitted_curvature.ipynb (100%) rename docs/01_code_usage/{02_example_workflows => }/demo_patch_fitting_reconstruction.ipynb (100%) rename docs/01_code_usage/{02_example_workflows => }/demo_spherical_harmonics_code.ipynb (100%) rename docs/01_code_usage/{02_example_workflows => }/demo_surface_reconstruction_code.ipynb (100%) rename docs/01_code_usage/{02_example_workflows => }/demo_surface_tracing.ipynb (100%) rename docs/01_code_usage/{01_toolboxes => }/reconstruction_settings.yaml (100%) delete mode 100644 docs/02_interactive_usage/01_toolboxes/Readme.md delete mode 100644 docs/02_interactive_usage/02_example_workflows/Readme.md rename docs/02_interactive_usage/{01_toolboxes => }/demo_droplet_reconstruction_toolbox.md (100%) rename docs/02_interactive_usage/{02_example_workflows => }/demo_fit_ellipsoid_interactive.md (100%) rename docs/02_interactive_usage/{02_example_workflows => }/demo_measure_curvature.md (100%) rename docs/02_interactive_usage/{02_example_workflows => }/demo_spherical_harmonics_interactive.md (100%) rename docs/02_interactive_usage/{01_toolboxes => }/demo_stress_toolbox_interactive.md (100%) rename docs/02_interactive_usage/{02_example_workflows => }/demo_surface_reconstruction_interactive.md (100%) rename docs/02_interactive_usage/{02_example_workflows => 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rename docs/02_interactive_usage/{02_example_workflows => }/imgs/surface_to_curvature6.png (100%) rename docs/02_interactive_usage/{02_example_workflows => }/imgs/surface_to_curvature7.png (100%) rename docs/02_interactive_usage/{02_example_workflows => }/imgs/surface_to_curvature8.png (100%) rename docs/02_interactive_usage/{02_example_workflows => }/imgs/workflow.png (100%) rename docs/02_interactive_usage/{02_example_workflows => }/imgs/workflow.svg (100%) rename docs/02_interactive_usage/{02_example_workflows => }/imgs/workflow_surface_to_curvature.png (100%) rename docs/02_interactive_usage/{02_example_workflows => }/visualize_measurements_in_viewer.md (100%) diff --git a/docs/01_code_usage/01_toolboxes/Readme.md b/docs/01_code_usage/01_toolboxes/Readme.md deleted file mode 100644 index 79fc140f..00000000 --- a/docs/01_code_usage/01_toolboxes/Readme.md +++ /dev/null @@ -1,3 +0,0 @@ -(topic:01_code_usage:toolboxes)= - -# Toolboxes diff --git a/docs/01_code_usage/02_example_workflows/Readme.md b/docs/01_code_usage/02_example_workflows/Readme.md deleted file mode 100644 index 6afd0fae..00000000 --- a/docs/01_code_usage/02_example_workflows/Readme.md +++ /dev/null @@ -1,3 +0,0 @@ -# Other example workflows - -The functions in napari-stress can be used to do a set of typical tasks and workflows, some of which shall be summarized in this section. diff --git a/docs/01_code_usage/01_toolboxes/demo_analyze_everything.ipynb b/docs/01_code_usage/demo_analyze_everything.ipynb similarity index 100% rename from docs/01_code_usage/01_toolboxes/demo_analyze_everything.ipynb rename to docs/01_code_usage/demo_analyze_everything.ipynb diff --git a/docs/01_code_usage/01_toolboxes/demo_analyze_everything_batch.ipynb b/docs/01_code_usage/demo_analyze_everything_batch.ipynb similarity index 100% rename from docs/01_code_usage/01_toolboxes/demo_analyze_everything_batch.ipynb rename to docs/01_code_usage/demo_analyze_everything_batch.ipynb diff --git a/docs/01_code_usage/01_toolboxes/demo_anisotropic_stresses.ipynb b/docs/01_code_usage/demo_anisotropic_stresses.ipynb similarity index 100% rename from docs/01_code_usage/01_toolboxes/demo_anisotropic_stresses.ipynb rename to docs/01_code_usage/demo_anisotropic_stresses.ipynb diff --git a/docs/01_code_usage/01_toolboxes/demo_droplet_reconstruction_toolbox_code.ipynb b/docs/01_code_usage/demo_droplet_reconstruction_toolbox_code.ipynb similarity index 100% rename from docs/01_code_usage/01_toolboxes/demo_droplet_reconstruction_toolbox_code.ipynb rename to docs/01_code_usage/demo_droplet_reconstruction_toolbox_code.ipynb diff --git a/docs/01_code_usage/02_example_workflows/demo_fit_ellipsoid_code.ipynb b/docs/01_code_usage/demo_fit_ellipsoid_code.ipynb similarity index 100% rename from docs/01_code_usage/02_example_workflows/demo_fit_ellipsoid_code.ipynb rename to docs/01_code_usage/demo_fit_ellipsoid_code.ipynb diff --git a/docs/01_code_usage/02_example_workflows/demo_measure_intensity_on_surface.ipynb b/docs/01_code_usage/demo_measure_intensity_on_surface.ipynb similarity index 100% rename from docs/01_code_usage/02_example_workflows/demo_measure_intensity_on_surface.ipynb rename to docs/01_code_usage/demo_measure_intensity_on_surface.ipynb diff --git a/docs/01_code_usage/02_example_workflows/demo_measure_intensity_on_vectors.ipynb b/docs/01_code_usage/demo_measure_intensity_on_vectors.ipynb similarity index 100% rename from docs/01_code_usage/02_example_workflows/demo_measure_intensity_on_vectors.ipynb rename to docs/01_code_usage/demo_measure_intensity_on_vectors.ipynb diff --git a/docs/01_code_usage/02_example_workflows/demo_measure_patch_fitted_curvature.ipynb b/docs/01_code_usage/demo_measure_patch_fitted_curvature.ipynb similarity index 100% rename from docs/01_code_usage/02_example_workflows/demo_measure_patch_fitted_curvature.ipynb rename to docs/01_code_usage/demo_measure_patch_fitted_curvature.ipynb diff --git a/docs/01_code_usage/02_example_workflows/demo_patch_fitting_reconstruction.ipynb b/docs/01_code_usage/demo_patch_fitting_reconstruction.ipynb similarity index 100% rename from docs/01_code_usage/02_example_workflows/demo_patch_fitting_reconstruction.ipynb rename to docs/01_code_usage/demo_patch_fitting_reconstruction.ipynb diff --git a/docs/01_code_usage/02_example_workflows/demo_spherical_harmonics_code.ipynb b/docs/01_code_usage/demo_spherical_harmonics_code.ipynb similarity index 100% rename from docs/01_code_usage/02_example_workflows/demo_spherical_harmonics_code.ipynb rename to docs/01_code_usage/demo_spherical_harmonics_code.ipynb diff --git a/docs/01_code_usage/02_example_workflows/demo_surface_reconstruction_code.ipynb b/docs/01_code_usage/demo_surface_reconstruction_code.ipynb similarity index 100% rename from docs/01_code_usage/02_example_workflows/demo_surface_reconstruction_code.ipynb rename to docs/01_code_usage/demo_surface_reconstruction_code.ipynb diff --git a/docs/01_code_usage/02_example_workflows/demo_surface_tracing.ipynb b/docs/01_code_usage/demo_surface_tracing.ipynb similarity index 100% rename from docs/01_code_usage/02_example_workflows/demo_surface_tracing.ipynb rename to docs/01_code_usage/demo_surface_tracing.ipynb diff --git a/docs/01_code_usage/01_toolboxes/reconstruction_settings.yaml b/docs/01_code_usage/reconstruction_settings.yaml similarity index 100% rename from docs/01_code_usage/01_toolboxes/reconstruction_settings.yaml rename to docs/01_code_usage/reconstruction_settings.yaml diff --git a/docs/02_interactive_usage/01_toolboxes/Readme.md b/docs/02_interactive_usage/01_toolboxes/Readme.md deleted file mode 100644 index dab2f2b3..00000000 --- a/docs/02_interactive_usage/01_toolboxes/Readme.md +++ /dev/null @@ -1,2 +0,0 @@ -(topic:interactive_usage:toolboxes)= -# Toolboxes diff --git a/docs/02_interactive_usage/02_example_workflows/Readme.md b/docs/02_interactive_usage/02_example_workflows/Readme.md deleted file mode 100644 index f71c194e..00000000 --- a/docs/02_interactive_usage/02_example_workflows/Readme.md +++ /dev/null @@ -1,3 +0,0 @@ -# Other example workflows - -Test 123 diff --git a/docs/02_interactive_usage/01_toolboxes/demo_droplet_reconstruction_toolbox.md b/docs/02_interactive_usage/demo_droplet_reconstruction_toolbox.md similarity index 100% rename from docs/02_interactive_usage/01_toolboxes/demo_droplet_reconstruction_toolbox.md rename to docs/02_interactive_usage/demo_droplet_reconstruction_toolbox.md diff --git a/docs/02_interactive_usage/02_example_workflows/demo_fit_ellipsoid_interactive.md b/docs/02_interactive_usage/demo_fit_ellipsoid_interactive.md similarity index 100% rename from docs/02_interactive_usage/02_example_workflows/demo_fit_ellipsoid_interactive.md rename to docs/02_interactive_usage/demo_fit_ellipsoid_interactive.md diff --git a/docs/02_interactive_usage/02_example_workflows/demo_measure_curvature.md b/docs/02_interactive_usage/demo_measure_curvature.md similarity index 100% rename from docs/02_interactive_usage/02_example_workflows/demo_measure_curvature.md rename to docs/02_interactive_usage/demo_measure_curvature.md diff --git a/docs/02_interactive_usage/02_example_workflows/demo_spherical_harmonics_interactive.md b/docs/02_interactive_usage/demo_spherical_harmonics_interactive.md similarity index 100% rename from docs/02_interactive_usage/02_example_workflows/demo_spherical_harmonics_interactive.md rename to docs/02_interactive_usage/demo_spherical_harmonics_interactive.md diff --git a/docs/02_interactive_usage/01_toolboxes/demo_stress_toolbox_interactive.md b/docs/02_interactive_usage/demo_stress_toolbox_interactive.md similarity index 100% rename from docs/02_interactive_usage/01_toolboxes/demo_stress_toolbox_interactive.md rename to docs/02_interactive_usage/demo_stress_toolbox_interactive.md diff 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a/docs/02_interactive_usage/02_example_workflows/imgs/workflow.png b/docs/02_interactive_usage/imgs/workflow.png similarity index 100% rename from docs/02_interactive_usage/02_example_workflows/imgs/workflow.png rename to docs/02_interactive_usage/imgs/workflow.png diff --git a/docs/02_interactive_usage/02_example_workflows/imgs/workflow.svg b/docs/02_interactive_usage/imgs/workflow.svg similarity index 100% rename from docs/02_interactive_usage/02_example_workflows/imgs/workflow.svg rename to docs/02_interactive_usage/imgs/workflow.svg diff --git a/docs/02_interactive_usage/02_example_workflows/imgs/workflow_surface_to_curvature.png b/docs/02_interactive_usage/imgs/workflow_surface_to_curvature.png similarity index 100% rename from docs/02_interactive_usage/02_example_workflows/imgs/workflow_surface_to_curvature.png rename to docs/02_interactive_usage/imgs/workflow_surface_to_curvature.png diff --git a/docs/02_interactive_usage/02_example_workflows/visualize_measurements_in_viewer.md b/docs/02_interactive_usage/visualize_measurements_in_viewer.md similarity index 100% rename from docs/02_interactive_usage/02_example_workflows/visualize_measurements_in_viewer.md rename to docs/02_interactive_usage/visualize_measurements_in_viewer.md diff --git a/docs/_toc.yml b/docs/_toc.yml index e61c2c7d..3c6ee77e 100644 --- a/docs/_toc.yml +++ b/docs/_toc.yml @@ -13,38 +13,28 @@ parts: chapters: - file: 01_code_usage/code_usage sections: - - file: 01_code_usage/01_toolboxes/Readme - sections: - - file: 01_code_usage/01_toolboxes/demo_droplet_reconstruction_toolbox_code - - file: 01_code_usage/01_toolboxes/demo_anisotropic_stresses - - file: 01_code_usage/01_toolboxes/demo_analyze_everything - - file: 01_code_usage/01_toolboxes/demo_analyze_everything_batch - - - file: 01_code_usage/02_example_workflows/Readme - sections: - - file: 01_code_usage/02_example_workflows/demo_fit_ellipsoid_code - - file: 01_code_usage/02_example_workflows/demo_measure_patch_fitted_curvature - - file: 01_code_usage/02_example_workflows/demo_surface_reconstruction_code - - file: 01_code_usage/02_example_workflows/demo_surface_tracing - - file: 01_code_usage/02_example_workflows/demo_patch_fitting_reconstruction - - file: 01_code_usage/02_example_workflows/demo_spherical_harmonics_code - - 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: 01_code_usage/demo_droplet_reconstruction_toolbox_code + - file: 01_code_usage/demo_anisotropic_stresses + - file: 01_code_usage/demo_analyze_everything + - file: 01_code_usage/demo_analyze_everything_batch + - file: 01_code_usage/demo_fit_ellipsoid_code + - file: 01_code_usage/demo_measure_patch_fitted_curvature + - file: 01_code_usage/demo_surface_reconstruction_code + - file: 01_code_usage/demo_surface_tracing + - file: 01_code_usage/demo_patch_fitting_reconstruction + - file: 01_code_usage/demo_spherical_harmonics_code + - file: 01_code_usage/demo_measure_intensity_on_surface + - file: 01_code_usage/demo_measure_intensity_on_vectors - file: 02_interactive_usage/interactive_usage sections: - - file: 02_interactive_usage/01_toolboxes/Readme - sections: - - file: 02_interactive_usage/01_toolboxes/demo_droplet_reconstruction_toolbox - - file: 02_interactive_usage/01_toolboxes/demo_stress_toolbox_interactive - - - file: 02_interactive_usage/02_example_workflows/Readme - sections: - - file: 02_interactive_usage/02_example_workflows/demo_fit_ellipsoid_interactive - - 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/visualize_measurements_in_viewer + - file: 02_interactive_usage/demo_droplet_reconstruction_toolbox + - file: 02_interactive_usage/demo_stress_toolbox_interactive + - file: 02_interactive_usage/demo_fit_ellipsoid_interactive + - file: 02_interactive_usage/demo_surface_reconstruction_interactive + - file: 02_interactive_usage/demo_spherical_harmonics_interactive + - file: 02_interactive_usage/demo_measure_curvature + - file: 02_interactive_usage/visualize_measurements_in_viewer - caption: Glossary chapters: From e1ba5ee138281b62ac0d22df9208f05ea999d9e2 Mon Sep 17 00:00:00 2001 From: Johannes Soltwedel <38459088+jo-mueller@users.noreply.github.com> Date: Mon, 26 May 2025 22:35:48 +0200 Subject: [PATCH 2/5] fixed links --- .../demo_fit_ellipsoid_interactive.md | 4 ++-- .../demo_spherical_harmonics_interactive.md | 14 +++++++------- .../demo_surface_reconstruction_interactive.md | 14 +++++++------- docs/intro.md | 4 ++-- 4 files changed, 18 insertions(+), 18 deletions(-) diff --git a/docs/02_interactive_usage/demo_fit_ellipsoid_interactive.md b/docs/02_interactive_usage/demo_fit_ellipsoid_interactive.md index cd18cfa9..48b0e1a5 100644 --- a/docs/02_interactive_usage/demo_fit_ellipsoid_interactive.md +++ b/docs/02_interactive_usage/demo_fit_ellipsoid_interactive.md @@ -11,8 +11,8 @@ This tutorial shows how to handle ellipse-fitting in napari-stress. It covers th To get started, create a pointcloud according to the workflow suggestions in this repository or load the sample data from napari-stress (`File > Open Sample > napari-stress: Dropplet pointcloud`). -![](../../imgs/viewer_screenshots/open_sample_droplet.png) -![](../../imgs/viewer_screenshots/open_sample_droplet1.png) +![](../imgs/viewer_screenshots/open_sample_droplet.png) +![](../imgs/viewer_screenshots/open_sample_droplet1.png) (fit_ellipsoid:major_minor_axes)= ## Finding the major and minor axes diff --git a/docs/02_interactive_usage/demo_spherical_harmonics_interactive.md b/docs/02_interactive_usage/demo_spherical_harmonics_interactive.md index 30cb969d..b2afef8b 100644 --- a/docs/02_interactive_usage/demo_spherical_harmonics_interactive.md +++ b/docs/02_interactive_usage/demo_spherical_harmonics_interactive.md @@ -4,14 +4,14 @@ This tutorial will explain how to perform a spherical harmonics surface expansion with napari-stress interactively from the napari viewer. To get started, open your own data or use the provided sample data from napari-stress ([raw data source](https://github.com/campaslab/STRESS)): -![](../../imgs/viewer_screenshots/open_sample_droplet.png) -![](../../imgs/viewer_screenshots/open_sample_droplet1.png) +![](../imgs/viewer_screenshots/open_sample_droplet.png) +![](../imgs/viewer_screenshots/open_sample_droplet1.png) You can then approximate this pointcloud with a [](spherical_harmonics:mathematical_basics) expansion. In brief, this fits a set of basis functions to the input pointcloud and returns an analytical representation of the points on the surface. This then allows to sample any number of points on the approximated surface and derive further characteristic surface parameters. Select the spherical harmonics expansion from the tools menu (`Tools > Points > Fit spherical harmonics (n-STRESS)`): -![](../../imgs/viewer_screenshots/fit_spherical_harmonics.png) +![](../imgs/viewer_screenshots/fit_spherical_harmonics.png) This will bring up a dialogue with the available options: @@ -25,21 +25,21 @@ This will bring up a dialogue with the available options: Applying a spherical harmonics expansion of `max_degree = 5` will lead to the following result. The colorcoding of the fitted points corresponds to the fit remainder of the spherical harmonics expansion. -![](../../imgs/viewer_screenshots/fit_spherical_harmonics2.png) +![](../imgs/viewer_screenshots/fit_spherical_harmonics2.png) Lowering the value to `max_degree = 1` will lead to only the first *mode* of spherical harmonics being used, which corresponds to fitting a sphere to the pointcloud: -![](../../imgs/viewer_screenshots/fit_spherical_harmonics3.png) +![](../imgs/viewer_screenshots/fit_spherical_harmonics3.png) **Layer display settings** napari may default to innapropriate settings for the pointcloud (e.g., inproper point size or color). To change this, select the malformated layer, click the `select_points` icon in the top left: -![](../../imgs/viewer_screenshots/change_layer_settings.png) +![](../imgs/viewer_screenshots/change_layer_settings.png) Then, drag a box over all points and change the point size and face color with the slider and the color selecter, respectively. Alternatively, you can also open the code terminal with the icon in the bottom-left: -![](../../imgs/viewer_screenshots/open_terminal.png) +![](../imgs/viewer_screenshots/open_terminal.png) and type: diff --git a/docs/02_interactive_usage/demo_surface_reconstruction_interactive.md b/docs/02_interactive_usage/demo_surface_reconstruction_interactive.md index 007fbbbe..945af963 100644 --- a/docs/02_interactive_usage/demo_surface_reconstruction_interactive.md +++ b/docs/02_interactive_usage/demo_surface_reconstruction_interactive.md @@ -3,29 +3,29 @@ This tutorial will explain how to perform a surface reconstruction with napari-stress interactively from the napari viewer. This plugin implements the [respective function](https://vedo.embl.es/autodocs/content/vedo/pointcloud.html#vedo.pointcloud.Points.reconstructSurface) from the [vedo](https://vedo.embl.es) library. To get started, open your own data or use the provided sample data from napari-stress ([raw data source](https://github.com/campaslab/STRESS)): -![](../../imgs/viewer_screenshots/open_sample_droplet.png) -![](../../imgs/viewer_screenshots/open_sample_droplet1.png) +![](../imgs/viewer_screenshots/open_sample_droplet.png) +![](../imgs/viewer_screenshots/open_sample_droplet1.png) Select the `Reconstruct surface` function from the plugin menu: -![](../../imgs/viewer_screenshots/reconstruct_surface.png) +![](../imgs/viewer_screenshots/reconstruct_surface.png) This will bring up the plugin widget: -![](../../imgs/viewer_screenshots/reconstruct_surface1.png) +![](../imgs/viewer_screenshots/reconstruct_surface1.png) ## Results The `radius` controls the search radius of the algorithm: To reconstruct a surface, the function finds all neighboring points for a given point in the pointcloud to be considered for a surface. Setting this value too low will result in a leaky surface: -![](../../imgs/viewer_screenshots/reconstruct_surface2.png) +![](../imgs/viewer_screenshots/reconstruct_surface2.png) In creasing the value will fix this issue: -![](../../imgs/viewer_screenshots/reconstruct_surface3.png) +![](../imgs/viewer_screenshots/reconstruct_surface3.png) Such surfaces typically consist of a large ammount of vertices. This behaviour can be control with the `padding` parameter: Increasing it will simplify the obtained surface representation: -![](../../imgs/viewer_screenshots/reconstruct_surface4.png) +![](../imgs/viewer_screenshots/reconstruct_surface4.png) If you are interested in doing this from code, check out this [example notebook](glossary:surface_reconstruction:code)= diff --git a/docs/intro.md b/docs/intro.md index 9ae3add9..eccd3104 100644 --- a/docs/intro.md +++ b/docs/intro.md @@ -14,9 +14,9 @@ Welcome to the documentation for napari-stress! This ressource provides informat ## Contents -- [Usage from code](topic:01_code_usage): Overview about modular functions in napari-stress and how to use them from code or interactively from the napari viewer. Among others, you'll find examples for how to use [toolbox functions](topic:01_code_usage:toolboxes), which bundle up many functionalities of the STRESS workflow in few lines of code. +- [Usage from code](topic:01_code_usage): Overview about modular functions in napari-stress and how to use them from code or interactively from the napari viewer. Among others, you'll find examples for how to use toolbox functions, which bundle up many functionalities of the STRESS workflow in few lines of code. See demo notebook for [reconstruction and analysis](toolboxes:analyze_everything) -- [Interactive usage](topic:interactive_usage): If you want to do the analysis in an interactive fashion, you can do so directly in the napari viewer. Again, the provided [toolboxes](topic:interactive_usage:toolboxes). +- [Interactive usage](topic:interactive_usage): If you want to do the analysis in an interactive fashion, you can do so directly in the napari viewer. Again, the provided toolboxes for [reconstruction](glossary:surface_reconstruction:interactive) and [measurement](toolboxes:stress_toolbox:stress_toolbox_interactive) should come in handy. ![](imgs/viewer_screenshots/all_outputs.png) From 6b23e7c1a2568536342c60313a03a45030f71e3e Mon Sep 17 00:00:00 2001 From: Johannes Soltwedel <38459088+jo-mueller@users.noreply.github.com> Date: Mon, 26 May 2025 22:35:57 +0200 Subject: [PATCH 3/5] added _build to ignored files --- .gitignore | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.gitignore b/.gitignore index 97c6427b..fd68a3a4 100644 --- a/.gitignore +++ b/.gitignore @@ -96,3 +96,6 @@ venv/ # Dask dask-worker-space/ + +# MyST build outputs +_build From e5d399187adb90467a87f70293ec0af61fdceed2 Mon Sep 17 00:00:00 2001 From: Johannes Soltwedel <38459088+jo-mueller@users.noreply.github.com> Date: Mon, 26 May 2025 22:36:05 +0200 Subject: [PATCH 4/5] codestyle --- docs/_toc.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/_toc.yml b/docs/_toc.yml index 3c6ee77e..014dcff5 100644 --- a/docs/_toc.yml +++ b/docs/_toc.yml @@ -8,7 +8,6 @@ options: numbered: False parts: - - caption: Usage chapters: - file: 01_code_usage/code_usage From bcc718da3f0764cdec2482a1d2151d06283df25e Mon Sep 17 00:00:00 2001 From: Johannes Soltwedel <38459088+jo-mueller@users.noreply.github.com> Date: Mon, 26 May 2025 22:36:10 +0200 Subject: [PATCH 5/5] Delete demo_register_napari_stress_types.ipynb --- .../demo_register_napari_stress_types.ipynb | 371 ------------------ 1 file changed, 371 deletions(-) delete mode 100644 docs/tutorials/demo/demo_register_napari_stress_types.ipynb diff --git a/docs/tutorials/demo/demo_register_napari_stress_types.ipynb b/docs/tutorials/demo/demo_register_napari_stress_types.ipynb deleted file mode 100644 index 93ef1118..00000000 --- a/docs/tutorials/demo/demo_register_napari_stress_types.ipynb +++ /dev/null @@ -1,371 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 14, - "id": "77c64789-a07e-4c6c-9415-f7937904e37c", - "metadata": {}, - "outputs": [], - "source": [ - "import napari\n", - "from napari import layers\n", - "from typing import NewType, List, Tuple, Any, Optional, Type, Union\n", - "import numpy as np\n", - "\n", - "import magicgui\n", - "from magicgui import register_type\n", - "from magicgui.widgets._bases import CategoricalWidget\n", - "from magicgui.widgets import FunctionGui\n", - "\n", - "from napari.utils._magicgui import find_viewer_ancestor" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "id": "56f74038-19ff-45f2-922f-b0b8c0667558", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - ".new_type(x)>" - ] - }, - "execution_count": 2, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "curvature = NewType(\"mean_curvature\", np.ndarray)\n", - "curvature" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "id": "16d2be94-a5be-4ddb-8696-6c7c7fb46450", - "metadata": {}, - "outputs": [], - "source": [ - "def get_layers_features(gui: CategoricalWidget) -> List[layers.Layer]:\n", - " \"\"\"Retrieve layers matching gui.annotation, from the Viewer the gui is in.\n", - " Parameters\n", - " ----------\n", - " gui : magicgui.widgets.Widget\n", - " The instantiated MagicGui widget. May or may not be docked in a\n", - " dock widget.\n", - " Returns\n", - " -------\n", - " tuple\n", - " Tuple of layers of type ``gui.annotation``\n", - " Examples\n", - " --------\n", - " This allows the user to do this, and get a dropdown box in their GUI\n", - " that shows the available image layers.\n", - " >>> @magicgui\n", - " ... def get_layer_mean(layer: napari.layers.Image) -> float:\n", - " ... return layer.data.mean()\n", - " \"\"\"\n", - " if not (viewer := find_viewer_ancestor(gui.native)):\n", - " return ()\n", - "\n", - " search_key = gui.annotation.__name__\n", - " search_fields = list(layer.features.keys()) + list(layer.metadata.keys())\n", - " \n", - " return [layer for layer in viewer.layers if search_key in search_fields]" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "id": "83f5991f-84a7-4569-b79e-1df1370186db", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - ".new_type(x)>" - ] - }, - "execution_count": 4, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "register_type(\n", - " curvature,\n", - " choices = get_layers_features\n", - ")" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "id": "2ea1d2e9-1ce1-4ab9-962c-6f0189f7ed39", - "metadata": {}, - "outputs": [], - "source": [ - "def test_function(mean_curvature: curvature) -> curvature:\n", - " \n", - " layer = None\n", - " if isinstance(mean_curvature, layers.Layer):\n", - " layer = mean_curvature\n", - " mean_curvature = np.asarray(mean_curvature.features[curvature.__name__])\n", - " \n", - " result = mean_curvature * 10\n", - " if layer is not None:\n", - " layer.features['new_result'] = result\n", - " return result" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "id": "ff432579-c860-41fb-9a30-37c922bf730c", - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "WARNING: DirectWrite: CreateFontFaceFromHDC() failed (Indicates an error in an input file such as a font file.) for QFontDef(Family=\"8514oem\", pointsize=12, pixelsize=20, styleHint=5, weight=50, stretch=100, hintingPreference=0) LOGFONT(\"8514oem\", lfWidth=0, lfHeight=-20) dpi=192\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Assistant skips harvesting pyclesperanto as it's not installed.\n" - ] - } - ], - "source": [ - "viewer = napari.Viewer()" - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "id": "b0148d82-a4ea-493f-89ee-66710dea1ce0", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "" - ] - }, - "execution_count": 7, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "viewer.add_points(np.random.random((100,3)), features = {'mean_curvature': np.ones(100)})" - ] - }, - { - "cell_type": "code", - "execution_count": 8, - "id": "c8c4d6e1-8544-4cda-8943-431526ae9ac1", - "metadata": {}, - "outputs": [], - "source": [ - "widget = magicgui.magicgui(test_function)\n", - "widget = viewer.window.add_dock_widget(widget)" - ] - }, - { - "cell_type": "code", - "execution_count": 10, - "id": "9ac09316-db11-41b4-ae5b-532da791a12b", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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