don't return rescaled image

.github/pull_request_template.md

@@ -38,4 +38,4 @@ Fixes #issue_number
 
 ## Additional Context
 
-<!-- Include any additional information about the PR here. -->
+<!-- Include any additional information about the PR here. -->

.gitignore

@@ -7,7 +7,7 @@ __pycache__/
 /data
 
 # STRESS outputs
-*.pdf  
+*.pdf
 *.vtp
 *.mat
 results_*/
@@ -94,6 +94,5 @@ venv/
 # written by setuptools_scm
 **/_version.py
 
-# Dask 
+# Dask
 dask-worker-space/
-

.napari/DESCRIPTION.md

@@ -5,18 +5,18 @@ the functionality of your plugin. Its content will be rendered on your plugin's
 napari hub page.
 
 The sections below are given as a guide for the flow of information only, and
-are in no way prescriptive. You should feel free to merge, remove, add and 
-rename sections at will to make this document work best for your plugin. 
+are in no way prescriptive. You should feel free to merge, remove, add and
+rename sections at will to make this document work best for your plugin.
 
 # Description
 
-This should be a detailed description of the context of your plugin and its 
+This should be a detailed description of the context of your plugin and its
 intended purpose.
 
 If you have videos or screenshots of your plugin in action, you should include them
-here as well, to make them front and center for new users. 
+here as well, to make them front and center for new users.
 
-You should use absolute links to these assets, so that we can easily display them 
+You should use absolute links to these assets, so that we can easily display them
 on the hub. The easiest way to include a video is to use a GIF, for example hosted
 on imgur. You can then reference this GIF as an image.
 
@@ -59,7 +59,7 @@ anywhere, feel free to also include this information here.
 This section should go through step-by-step examples of how your plugin should be used.
 Where your plugin provides multiple dock widgets or functions, you should split these
 out into separate subsections for easy browsing. Include screenshots and videos
-wherever possible to elucidate your descriptions. 
+wherever possible to elucidate your descriptions.
 
 Ideally, this section should start with minimal examples for those who just want a
 quick overview of the plugin's functionality, but you should definitely link out to
@@ -72,8 +72,8 @@ for the majority of plugins. They will include instructions to pip install, and
 to install via napari itself.
 
 Most plugins can be installed out-of-the-box by just specifying the package requirements
-over in `setup.cfg`. However, if your plugin has any more complex dependencies, or 
-requires any additional preparation before (or after) installation, you should add 
+over in `setup.cfg`. However, if your plugin has any more complex dependencies, or
+requires any additional preparation before (or after) installation, you should add
 this information here.
 
 # Getting Help

README.md

@@ -10,8 +10,8 @@
 
 # napari-stress
 
-This plugin provides tools for the analysis of surfaces in Napari, such as utilities to determine and refine the surface-representation of objects using a ray-casting approach and calculate the curvature of surfaces. 
-It re-implements code in Napari that was written for [Gross et al. (2021): STRESS, an automated geometrical characterization of deformable particles for in vivo measurements of cell and tissue mechanical stresses](https://www.biorxiv.org/content/10.1101/2021.03.26.437148v1) 
+This plugin provides tools for the analysis of surfaces in Napari, such as utilities to determine and refine the surface-representation of objects using a ray-casting approach and calculate the curvature of surfaces.
+It re-implements code in Napari that was written for [Gross et al. (2021): STRESS, an automated geometrical characterization of deformable particles for in vivo measurements of cell and tissue mechanical stresses](https://www.biorxiv.org/content/10.1101/2021.03.26.437148v1)
 and has been made open source in [this repository](https://github.com/campaslab/STRESS).
 
 ![](https://github.com/campaslab/napari-stress/raw/main/docs/imgs/function_gifs/spherical_harmonics.gif)
@@ -23,7 +23,7 @@ For documentation on how to use napari-stress both interactively from the napari
 
 ## Installation
 
-Create a new conda environment with the following command. 
+Create a new conda environment with the following command.
 If you have never used conda before, please [read this guide first](https://campaslab.github.io/blog/johannes_mueller/anaconda_getting_started/).
 
 ```

deploy.bat

@@ -5,7 +5,3 @@ python setup.py sdist bdist_wheel
 python -m pip install --user --upgrade twine
 
 python -m twine upload --repository pypi dist/*
-
-
-
-

docs/01_code_usage/01_toolboxes/Readme.md

@@ -1,3 +1,3 @@
 (topic:01_code_usage:toolboxes)=
 
-# Toolboxes
+# Toolboxes

docs/01_code_usage/01_toolboxes/demo_analyze_everything.ipynb

@@ -322,7 +322,7 @@
     "_ = stress_backend.lbdv_info(Max_SPH_Deg=measurement_parameters['max_degree'],\n",
     "                             Num_Quad_Pts=measurement_parameters['n_quadrature_points'])\n",
     "\n",
-    "results_stress_analysis = measurements.comprehensive_analysis(results_reconstruction[3][0], **measurement_parameters,\n",
+    "results_stress_analysis = measurements.comprehensive_analysis(results_reconstruction[2][0], **measurement_parameters,\n",
     "                                                              verbose=verbose, use_dask=parallelize)"
    ]
   },

docs/01_code_usage/02_example_workflows/Readme.md

@@ -1,3 +1,3 @@
 # 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. 
+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.

docs/01_code_usage/code_usage.md

@@ -2,4 +2,4 @@
 
 # From code
 
-This section demonstrates how to use the package from a script.
+This section demonstrates how to use the package from a script.

docs/02_interactive_usage/01_toolboxes/Readme.md

@@ -1,2 +1,2 @@
 (topic:interactive_usage:toolboxes)=
-# Toolboxes
+# Toolboxes

docs/02_interactive_usage/01_toolboxes/demo_stress_toolbox_interactive.md

@@ -16,12 +16,12 @@ The settings require the following input:
 
 * `Input pointcloud`: Layer of a reconstructed droplet. Can be 3D or 4D.
 * `Degree`: Degree of the spherical harmonics expansion fitted to the pointcloud. The higher the degree, the better the fit. For mor details, see [glossary](spherical_harmonics:mathematical_basics:degree).
-* `Number of quadrature points`: Number of points on which curvature will be evaluated. 
+* `Number of quadrature points`: Number of points on which curvature will be evaluated.
 
     *Note 1*: High values (>1000) can lead to signiicant computational expense on first time run.
-    
+
     *Note 2*: Using high-order spherical harmonics requires a specific minimal number of quadrature points. The number of quadrature points can be higher than this number, but not lower.
-    
+
 * `Interfacial surface tension [mN/m]`: Surface tension in mN/m of the evaluated droplet.
 
 

docs/02_interactive_usage/02_example_workflows/Readme.md

@@ -1,3 +1,3 @@
 # Other example workflows
 
-Test  123
+Test  123

docs/02_interactive_usage/02_example_workflows/demo_fit_ellipsoid_interactive.md

@@ -28,7 +28,7 @@ If you want to retrieve a pointcloud on the surface of the fitted ellipsoid, you
 ![](imgs/demo_fit_ellipsoid6.png)
 
 **Vedo**
-This section describes the implementation taken from the [vedo repository](https://vedo.embl.es/). It uses a [pca-algorithm](https://en.wikipedia.org/wiki/Principal_component_analysis) to calculate the minor/major axes. Use it via `Tools > Points > Points > Fit ellipsoid to pointcloud (vedo, n-STRESS)`. As an additional parameter, it requires you to set which percentage of the input points should be contained by the surface of the fitted ellipse, which is controlled by the `inside fraction` parameter. 
+This section describes the implementation taken from the [vedo repository](https://vedo.embl.es/). It uses a [pca-algorithm](https://en.wikipedia.org/wiki/Principal_component_analysis) to calculate the minor/major axes. Use it via `Tools > Points > Points > Fit ellipsoid to pointcloud (vedo, n-STRESS)`. As an additional parameter, it requires you to set which percentage of the input points should be contained by the surface of the fitted ellipse, which is controlled by the `inside fraction` parameter.
 
 ![](imgs/demo_fit_ellipsoid1.png)
 
@@ -56,4 +56,4 @@ You can calculate how well the ellipsoid approximates the pointcloud by calculat
 
 ![](imgs/demo_fit_ellipsoid8.png)
 
-Measureing the lengths of these vectors will soon be possible.
+Measureing the lengths of these vectors will soon be possible.

docs/02_interactive_usage/02_example_workflows/demo_measure_curvature.md

@@ -19,4 +19,4 @@ The results are then stored in the `layer.features`. In case the curvature value
 
 ![](imgs/demo_measure_curvature3.png)
 
-Type  to retrieve specifically the curvature values.
+Type  to retrieve specifically the curvature values.

docs/02_interactive_usage/02_example_workflows/demo_surface_reconstruction_interactive.md

@@ -29,7 +29,3 @@ Such surfaces typically consist of a large ammount of vertices. This behaviour c
 ![](../../imgs/viewer_screenshots/reconstruct_surface4.png)
 
 If you are interested in doing this from code, check out this [example notebook](glossary:surface_reconstruction:code)=
-
-
-
-

docs/02_interactive_usage/02_example_workflows/visualize_measurements_in_viewer.md

@@ -9,4 +9,4 @@ In order to use it, check out the documentation on the [napari-matplotlib page](
 
 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)
+![](./imgs/demo_visualize_featureHistogram2.png)

docs/02_interactive_usage/interactive_usage.md

@@ -1,4 +1,4 @@
 (topic:interactive_usage)=
 # Interactive usage
 
-This section demonstrates how to use napari-stress interactively from the napari viewer.
+This section demonstrates how to use napari-stress interactively from the napari viewer.

docs/03_glossary/01_spherical_harmonics/01_spherical_harmonics.md

@@ -6,7 +6,7 @@ In this notebook you will learn about [spherical harmonics](https://en.wikipedia
 
 ## Polar coordinates
 
-Generally speaking, spherical harmonics provide a mathematical framework to tackle problems that are best described in polar coordinates. When we use polar coordinates, we describe the location of a point in space in terms of 
+Generally speaking, spherical harmonics provide a mathematical framework to tackle problems that are best described in polar coordinates. When we use polar coordinates, we describe the location of a point in space in terms of
 
 * latitude $\theta$
 * longitude $\phi$
@@ -42,7 +42,7 @@ $f(\theta, \phi) = \sum_{l=0}^{\inf} \sum_{m=-l}^{l} f_l^m Y_l^m(\theta, \phi)$
 
 where $f_l^m$ are the coefficients that determine how much each degree and order of the spherical harmonics functions $Y_l^m(\theta, \phi)$ contribute to the sum. In other words, you can use this superposition to approximate the value of any function that depends on latitude and longitude as inputs. It is important to understand that this definition is assuming spheres of radius $r=1$ - the result of $f(\theta, \phi)$ can represent any property on the surface of this sphere. The Wikipedia page features a nice [visualization](https://en.wikipedia.org/wiki/Spherical_harmonics#/media/File:Rotating_spherical_harmonics.gif) for the contributions of spherical harmonics of specific degree and order on the surface of a sphere.
 
-Using this framework has several desirable characteristics: 
+Using this framework has several desirable characteristics:
 
 - Any real function on the surface of a sphere can be approximated with a spherical harmonics expansion
 - An obtained spherical harmonics expansion can be described entirely by the coefficients $f_l^m$
@@ -101,4 +101,4 @@ where the coefficients $f_x$, $f_y$, $f_z$ refer to the spherical harmonics coef
 
 ### iii ) Calculate other coordinates as a function of latitude and longitude
 
-In principle, the previously described coordinate parametrizations can be expanded to any set of coordinate parametrization. Other coordinate formulations that can be used for this sort of coordinate parametrization are [cylindrical coordinates ](https://en.wikipedia.org/wiki/Cylindrical_coordinate_system) or [ellipsoidal coordinates](https://en.wikipedia.org/wiki/Ellipsoidal_coordinates).
+In principle, the previously described coordinate parametrizations can be expanded to any set of coordinate parametrization. Other coordinate formulations that can be used for this sort of coordinate parametrization are [cylindrical coordinates ](https://en.wikipedia.org/wiki/Cylindrical_coordinate_system) or [ellipsoidal coordinates](https://en.wikipedia.org/wiki/Ellipsoidal_coordinates).

docs/03_glossary/01_spherical_harmonics/02_analyzing_spherical_harmonics.md

@@ -29,7 +29,7 @@ An interesting parameter that can be obtained from a spherical harmonics expansi
 
 * The surface integrated curvature $H_{0, surf~int}$: This is the ratio of the area of the obtained expansion and the surface of a unit sphere $H_{0, surf~int} = \frac{A_{manifold}}{A_{Sphere}}$
 
-The [stress paper](https://www.biorxiv.org/content/10.1101/2021.03.26.437148v1.abstract) uses the second definition ($H_{0, surf~int}$) for the description of curvatures oon the surface. 
+The [stress paper](https://www.biorxiv.org/content/10.1101/2021.03.26.437148v1.abstract) uses the second definition ($H_{0, surf~int}$) for the description of curvatures oon the surface.
 
 (spherical_harmonics:measurements:gauss_bonnet)=
 ## Gauss-Bonnet test
@@ -42,4 +42,4 @@ In other words, the Gauss-Bonnet test gives you the possibility to measure wheth
 
 $\Delta_{Gauss-Bonnet, rel} = \frac{\Delta_{Gauss-Bonnet, abs}}{4\pi}$
 
-To differentiate between a "good" and a "bad" surface expansion, the [stress paper](https://www.biorxiv.org/content/10.1101/2021.03.26.437148v1.full) suggests a threshold value of $1\cdot10^{-2}$ for the relative error.
+To differentiate between a "good" and a "bad" surface expansion, the [stress paper](https://www.biorxiv.org/content/10.1101/2021.03.26.437148v1.full) suggests a threshold value of $1\cdot10^{-2}$ for the relative error.

docs/03_glossary/01_spherical_harmonics/Readme.md

@@ -7,4 +7,4 @@ Topics:
 * [Mathematical basics I](glossary:spherical_harmonics:mathematical_basics)
 * [Mathematical basics II](glossary:spherical_harmonics:mathematical_basics2)
 * [Usage from code](glossary:spherical_harmonics:code)
-* [Interactive usage](glossary:spherical_harmonics:interactive)
+* [Interactive usage](glossary:spherical_harmonics:interactive)

docs/04_FAQ/Acknowledgement_and_citation.md

@@ -34,4 +34,4 @@ If you use napari-stress in your research, please cite the following paper:
         order Gauss-Markov quadrature formulae invariant under the
         octahedron group with inversion'
        Computational Mathematics and Mathematical Physics, Vol. 15,
-       1975, pp. 44-51.
+       1975, pp. 44-51.

docs/04_FAQ/Installation.md

@@ -50,4 +50,4 @@ ERROR: Could not install packages due to an OSError: [WinError 5] Access is deni
 Consider using the `--user` option or check the permissions.
 ```
 
-If this occurs, close all open Python instances (e.g., anaconda command line prompts, Jupyterlab instances, etc) and try again - this should fix the issue.
+If this occurs, close all open Python instances (e.g., anaconda command line prompts, Jupyterlab instances, etc) and try again - this should fix the issue.

docs/_toc.yml

@@ -12,7 +12,7 @@ parts:
   - caption: Usage
     chapters:
     - file: 01_code_usage/code_usage
-      sections: 
+      sections:
       - file: 01_code_usage/01_toolboxes/Readme
         sections:
         - file: 01_code_usage/01_toolboxes/demo_droplet_reconstruction_toolbox_code

docs/conf.py

@@ -5,37 +5,80 @@
 ###############################################################################
 import os
 import sys
+
 sys.path.insert(0, os.path.abspath("../"))
 
 add_module_names = True
-author = 'Johannes Soltwedel'
+author = "Johannes Soltwedel"
 autosummary_generate = True
-bibtex_bibfiles = ['references.bib']
-comments_config = {'hypothesis': False, 'utterances': False}
-copyright = '2022'
-exclude_patterns = ['**.ipynb_checkpoints', '.DS_Store', 'Thumbs.db', '_build']
-extensions = ['sphinx_togglebutton', 'sphinx_copybutton', 'myst_nb', 'jupyter_book', 'sphinx_thebe', 'sphinx_comments', 'sphinx_external_toc', 'sphinx.ext.intersphinx', 'sphinx_design', 'sphinx_book_theme', 'sphinx.ext.autodoc', 'sphinx.ext.napoleon', 'sphinx.ext.viewcode', 'sphinx.ext.autosummary', 'sphinxcontrib.bibtex', 'sphinx_jupyterbook_latex']
+bibtex_bibfiles = ["references.bib"]
+comments_config = {"hypothesis": False, "utterances": False}
+copyright = "2022"
+exclude_patterns = ["**.ipynb_checkpoints", ".DS_Store", "Thumbs.db", "_build"]
+extensions = [
+    "sphinx_togglebutton",
+    "sphinx_copybutton",
+    "myst_nb",
+    "jupyter_book",
+    "sphinx_thebe",
+    "sphinx_comments",
+    "sphinx_external_toc",
+    "sphinx.ext.intersphinx",
+    "sphinx_design",
+    "sphinx_book_theme",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.autosummary",
+    "sphinxcontrib.bibtex",
+    "sphinx_jupyterbook_latex",
+]
 external_toc_exclude_missing = False
-external_toc_path = '_toc.yml'
-html_baseurl = ''
-html_favicon = ''
-html_logo = 'logo.png'
-html_sourcelink_suffix = ''
-html_theme = 'sphinx_book_theme'
-html_theme_options = {'search_bar_text': 'Search this book...', 'launch_buttons': {'notebook_interface': 'classic', 'binderhub_url': '', 'jupyterhub_url': '', 'thebe': False, 'colab_url': ''}, 'path_to_docs': '', 'repository_url': 'https://github.com/executablebooks/jupyter-book', 'repository_branch': 'master', 'extra_footer': '', 'home_page_in_toc': True, 'announcement': '', 'analytics': {'google_analytics_id': ''}, 'use_repository_button': False, 'use_edit_page_button': False, 'use_issues_button': False}
-html_title = 'Napari-stress documentation'
-latex_engine = 'pdflatex'
-myst_enable_extensions = ['colon_fence', 'dollarmath', 'linkify', 'substitution', 'tasklist']
-myst_url_schemes = ['mailto', 'http', 'https']
+external_toc_path = "_toc.yml"
+html_baseurl = ""
+html_favicon = ""
+html_logo = "logo.png"
+html_sourcelink_suffix = ""
+html_theme = "sphinx_book_theme"
+html_theme_options = {
+    "search_bar_text": "Search this book...",
+    "launch_buttons": {
+        "notebook_interface": "classic",
+        "binderhub_url": "",
+        "jupyterhub_url": "",
+        "thebe": False,
+        "colab_url": "",
+    },
+    "path_to_docs": "",
+    "repository_url": "https://github.com/executablebooks/jupyter-book",
+    "repository_branch": "master",
+    "extra_footer": "",
+    "home_page_in_toc": True,
+    "announcement": "",
+    "analytics": {"google_analytics_id": ""},
+    "use_repository_button": False,
+    "use_edit_page_button": False,
+    "use_issues_button": False,
+}
+html_title = "Napari-stress documentation"
+latex_engine = "pdflatex"
+myst_enable_extensions = [
+    "colon_fence",
+    "dollarmath",
+    "linkify",
+    "substitution",
+    "tasklist",
+]
+myst_url_schemes = ["mailto", "http", "https"]
 nb_execution_allow_errors = False
-nb_execution_cache_path = ''
+nb_execution_cache_path = ""
 nb_execution_excludepatterns = []
 nb_execution_in_temp = False
-nb_execution_mode = 'off'
+nb_execution_mode = "off"
 nb_execution_timeout = 30
-nb_output_stderr = 'show'
+nb_output_stderr = "show"
 numfig = True
-pygments_style = 'sphinx'
-suppress_warnings = ['myst.domains']
+pygments_style = "sphinx"
+suppress_warnings = ["myst.domains"]
 use_jupyterbook_latex = True
 use_multitoc_numbering = True

docs/intro.md

@@ -31,8 +31,8 @@ If you use napari-stress in your research, please check the [acknowledgements an
 
 ## Issues
 
-If you encounter any issues during installation, please 
+If you encounter any issues during installation, please
 
 * browse the [FAQ section](FAQ:installation) for known issues
 * file an [issue on github](https://github.com/BiAPoL/napari-stress/issues)
-* check out the [image.sc forum](https://forum.image.sc/) for help (Please tag @EL_Pollo_Diablo to notify the developers)
+* check out the [image.sc forum](https://forum.image.sc/) for help (Please tag @EL_Pollo_Diablo to notify the developers)

pyproject.toml

@@ -1,5 +1,3 @@
 [build-system]
 requires = ["setuptools", "wheel"]
 build-backend = "setuptools.build_meta"
-
-

setup.py

@@ -1,6 +1,4 @@
 # -*- coding: utf-8 -*-
 from setuptools import setup, find_packages
 
-setup(
-      packages=find_packages()
-      )
+setup(packages=find_packages())