waveorder 2.1.0__tar.gz → 2.2.0__tar.gz

{waveorder-2.1.0 → waveorder-2.2.0}/.github/workflows/pytests.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10']
+        python-version: ['3.10', '3.11', '3.12']
 
     steps:
     - name: Checkout repo

{waveorder-2.1.0 → waveorder-2.2.0}/.gitignore

@@ -150,3 +150,4 @@ recOrder/_version.py
 *.npz
 *.png
 *.tif[f]
+*.pdf

{waveorder-2.1.0 → waveorder-2.2.0}/CITATION.cff

@@ -4,30 +4,32 @@
 cff-version: 1.2.0
 title: waveorder
 message: >-
-  A generalist library of wave optical models and inverse
-  algorithms for label-free imaging of density &
-  orientation.
+  Wave optical models and inverse algorithms for label-agnostic imaging of density & orientation.
 type: software
 authors:
-  - given-names: Li-Hao
-    family-names: Yeh
-    affiliation: CZ Biohub
-    orcid: 'https://orcid.org/0000-0003-2803-5996'
   - given-names: Talon
     family-names: Chandler
-    affiliation: CZ Biohub
+    affiliation: Chan Zuckerberg Biohub San Francisco
     orcid: 'https://orcid.org/0000-0002-3033-674X'
+  - given-names: Li-Hao
+    family-names: Yeh
+    affiliation: Chan Zuckerberg Biohub San Francisco
+    orcid: 'https://orcid.org/0000-0003-2803-5996'
   - given-names: Ivan
     family-names: Ivanov
-    affiliation: CZ Biohub
+    affiliation: Chan Zuckerberg Biohub San Francisco
     orcid: 'https://orcid.org/0000-0002-4675-5287'
   - given-names: Cameron
     family-names: Foltz
-    affiliation: CZ Biohub
+    affiliation: Chan Zuckerberg Biohub San Francisco
     orcid: 'https://orcid.org/0000-0001-8933-2172'
+  - given-names: Ziwen
+    family-names: Liu
+    affiliation: Chan Zuckerberg Biohub San Francisco
+    orcid: 'https://orcid.org/0000-0001-7482-1299'
   - given-names: Shalin
     family-names: Mehta
-    affiliation: CZ Biohub
+    affiliation: Chan Zuckerberg Biohub San Francisco
     orcid: 'https://orcid.org/0000-0002-2542-3582'
 identifiers:
   - type: doi
@@ -67,6 +69,7 @@ keywords:
   - qlipp
   - mipolscope
   - simulation
+  - reconstruction
 license: BSD-3-Clause
-version: 1.0.0rc1
-date-released: '2023-02-22'
+version: 2.1.0
+date-released: '2024-03-12'

waveorder-2.2.0/PKG-INFO

@@ -0,0 +1,186 @@
+Metadata-Version: 2.1
+Name: waveorder
+Version: 2.2.0
+Summary: Wave-optical simulations and deconvolution of optical properties
+Author-email: CZ Biohub SF <compmicro@czbiohub.org>
+Maintainer-email: Talon Chandler <talon.chandler@czbiohub.org>, Shalin Mehta <shalin.mehta@czbiohub.org>
+License: BSD 3-Clause License
+        
+        Copyright (c) 2019, Chan Zuckerberg Biohub
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions are met:
+        
+        1. Redistributions of source code must retain the above copyright notice, this
+           list of conditions and the following disclaimer.
+        
+        2. Redistributions in binary form must reproduce the above copyright notice,
+           this list of conditions and the following disclaimer in the documentation
+           and/or other materials provided with the distribution.
+        
+        3. Neither the name of the copyright holder nor the names of its
+           contributors may be used to endorse or promote products derived from
+           this software without specific prior written permission.
+        
+        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+        
+Project-URL: Homepage, https://github.com/mehta-lab/waveorder
+Project-URL: Repository, https://github.com/mehta-lab/waveorder
+Project-URL: Issues, https://github.com/mehta-lab/waveorder/issues
+Keywords: simulation,optics,phase,scattering,polarization,label-free,permittivity,reconstruction-algorithm,qlipp,mipolscope,permittivity-tensor-imaging
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Operating System :: MacOS
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.24
+Requires-Dist: matplotlib>=3.1.1
+Requires-Dist: scipy>=1.3.0
+Requires-Dist: pywavelets>=1.1.1
+Requires-Dist: ipywidgets>=7.5.1
+Requires-Dist: torch>=2.4.1
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Provides-Extra: examples
+Requires-Dist: napari[all]; extra == "examples"
+Requires-Dist: jupyter; extra == "examples"
+
+# waveorder
+
+[![Python package index](https://img.shields.io/pypi/v/waveorder.svg)](https://pypi.org/project/waveorder)
+[![PyPI monthly downloads](https://img.shields.io/pypi/dm/waveorder.svg)](https://pypistats.org/packages/waveorder)
+[![Total downloads](https://pepy.tech/badge/waveorder)](https://pepy.tech/project/waveorder)
+[![GitHub contributors](https://img.shields.io/github/contributors-anon/mehta-lab/waveorder)](https://github.com/mehta-lab/waveorder/graphs/contributors)
+![GitHub Repo stars](https://img.shields.io/github/stars/mehta-lab/waveorder)
+![GitHub forks](https://img.shields.io/github/forks/mehta-lab/waveorder)
+![PyPI - Python Version](https://img.shields.io/pypi/pyversions/waveorder)
+
+
+This computational imaging library enables wave-optical simulation and reconstruction of optical properties that report microscopic architectural order.
+
+## Computational label-agnostic imaging
+
+https://github.com/user-attachments/assets/4f9969e5-94ce-4e08-9f30-68314a905db6
+
+`waveorder` enables simulations and reconstructions of label-agnostic microscopy data as described in the following [preprint](https://arxiv.org/abs/2412.09775)
+<details>	
+<summary> Chandler et al. 2024 </summary>
+<pre><code>
+@article{chandler_2024,
+    author = {Chandler, Talon and Hirata-Miyasaki, Eduardo and Ivanov, Ivan E. and Liu, Ziwen and Sundarraman, Deepika and Ryan, Allyson Quinn and Jacobo, Adrian and Balla, Keir and Mehta, Shalin B.},
+	title = {waveOrder: generalist framework for label-agnostic computational microscopy},
+	journal = {arXiv},
+	year = {2024},
+	month = dec,
+	eprint = {2412.09775},
+	doi = {10.48550/arXiv.2412.09775}
+}
+</code></pre>
+</details>
+
+Specifically, `waveorder` enables simulation and reconstruction of 2D or 3D:
+
+1. __phase, projected retardance, and in-plane orientation__ from a polarization-diverse volumetric brightfield acquisition ([QLIPP](https://elifesciences.org/articles/55502)),
+
+2. __phase__ from a volumetric brightfield acquisition ([2D phase](https://www.osapublishing.org/ao/abstract.cfm?uri=ao-54-28-8566)/[3D phase](https://www.osapublishing.org/ao/abstract.cfm?uri=ao-57-1-a205)),
+
+3. __phase__ from an illumination-diverse volumetric acquisition ([2D](https://www.osapublishing.org/oe/fulltext.cfm?uri=oe-23-9-11394&id=315599)/[3D](https://www.osapublishing.org/boe/fulltext.cfm?uri=boe-7-10-3940&id=349951) differential phase contrast),
+
+4. __fluorescence density__ from a widefield volumetric fluorescence acquisition (fluorescence deconvolution).  
+
+The [examples](https://github.com/mehta-lab/waveorder/tree/main/examples) demonstrate simulations and reconstruction for 2D QLIPP, 3D PODT, 3D fluorescence deconvolution, and 2D/3D PTI methods.
+
+If you are interested in deploying QLIPP, phase from brightfield, or fluorescence deconvolution for label-agnostic imaging at scale, checkout our [napari plugin](https://www.napari-hub.org/plugins/recOrder-napari),  [`recOrder-napari`](https://github.com/mehta-lab/recOrder).
+
+## Permittivity tensor imaging 
+
+Additionally, `waveorder` enabled the development of a new label-free imaging method, __permittivity tensor imaging (PTI)__, that measures density and  3D orientation of biomolecules with diffraction-limited resolution. These measurements are reconstructed from polarization-resolved images acquired with a sequence of oblique illuminations.
+
+The acquisition, calibration, background correction, reconstruction, and applications of PTI are described in the following [paper](https://doi.org/10.1101/2020.12.15.422951) published in Nature Methods:
+
+<details>
+<summary> Yeh et al. 2024 </summary>
+<pre><code>
+@article{yeh_2024,
+	author = {Yeh, Li-Hao and Ivanov, Ivan E. and Chandler, Talon and Byrum, Janie R. and Chhun, Bryant B. and Guo, Syuan-Ming and Foltz, Cameron and Hashemi, Ezzat and Perez-Bermejo, Juan A. and Wang, Huijun and Yu, Yanhao and Kazansky, Peter G. and Conklin, Bruce R. and Han, May H. and Mehta, Shalin B.},
+	title = {Permittivity tensor imaging: modular label-free imaging of 3D dry mass and 3D orientation at high resolution},
+	journal = {Nature Methods},
+	volume = {21},
+	number = {7},
+	pages = {1257--1274},
+	year = {2024},
+	month = jul,
+	issn = {1548-7105},
+	publisher = {Nature Publishing Group},
+	doi = {10.1038/s41592-024-02291-w}
+}
+</code></pre>
+</details>
+
+PTI provides volumetric reconstructions of mean permittivity ($\propto$ material density), differential permittivity ($\propto$ material anisotropy), 3D orientation, and optic sign. The following figure summarizes PTI acquisition and reconstruction with a small optical section of the mouse brain tissue:
+
+![Data_flow](https://github.com/mehta-lab/waveorder/blob/main/readme.png?raw=true)
+
+## Examples
+The [examples](https://github.com/mehta-lab/waveorder/tree/main/examples) illustrate simulations and reconstruction for 2D QLIPP, 3D phase from brightfield, and 2D/3D PTI methods.
+
+If you are interested in deploying QLIPP or phase from brightbrield, or fluorescence deconvolution for label-agnostic imaging at scale, checkout our [napari plugin](https://www.napari-hub.org/plugins/recOrder-napari),  [`recOrder-napari`](https://github.com/mehta-lab/recOrder).
+
+## Citation
+
+Please cite this repository, along with the relevant preprint or paper, if you use or adapt this code. The citation information can be found by clicking "Cite this repository" button in the About section in the right sidebar.
+
+## Installation
+
+Create a virtual environment:
+
+```sh
+conda create -y -n waveorder python=3.10
+conda activate waveorder
+```
+
+Install `waveorder` from PyPI:
+
+```sh
+pip install waveorder
+```
+
+Use `waveorder` in your scripts:
+
+```sh
+python
+>>> import waveorder
+```
+
+(Optional) Install example dependencies, clone the repository, and run an example script:
+```sh
+pip install waveorder[examples]
+git clone https://github.com/mehta-lab/waveorder.git
+python waveorder/examples/models/phase_thick_3d.py
+```
+
+(M1 users) `pytorch` has [incomplete GPU support](https://github.com/pytorch/pytorch/issues/77764),
+so please use `export PYTORCH_ENABLE_MPS_FALLBACK=1`
+to allow some operators to fallback to CPU
+if you plan to use GPU acceleration for polarization reconstruction. 

waveorder-2.2.0/README.md

@@ -0,0 +1,118 @@
+# waveorder
+
+[![Python package index](https://img.shields.io/pypi/v/waveorder.svg)](https://pypi.org/project/waveorder)
+[![PyPI monthly downloads](https://img.shields.io/pypi/dm/waveorder.svg)](https://pypistats.org/packages/waveorder)
+[![Total downloads](https://pepy.tech/badge/waveorder)](https://pepy.tech/project/waveorder)
+[![GitHub contributors](https://img.shields.io/github/contributors-anon/mehta-lab/waveorder)](https://github.com/mehta-lab/waveorder/graphs/contributors)
+![GitHub Repo stars](https://img.shields.io/github/stars/mehta-lab/waveorder)
+![GitHub forks](https://img.shields.io/github/forks/mehta-lab/waveorder)
+![PyPI - Python Version](https://img.shields.io/pypi/pyversions/waveorder)
+
+
+This computational imaging library enables wave-optical simulation and reconstruction of optical properties that report microscopic architectural order.
+
+## Computational label-agnostic imaging
+
+https://github.com/user-attachments/assets/4f9969e5-94ce-4e08-9f30-68314a905db6
+
+`waveorder` enables simulations and reconstructions of label-agnostic microscopy data as described in the following [preprint](https://arxiv.org/abs/2412.09775)
+<details>	
+<summary> Chandler et al. 2024 </summary>
+<pre><code>
+@article{chandler_2024,
+    author = {Chandler, Talon and Hirata-Miyasaki, Eduardo and Ivanov, Ivan E. and Liu, Ziwen and Sundarraman, Deepika and Ryan, Allyson Quinn and Jacobo, Adrian and Balla, Keir and Mehta, Shalin B.},
+	title = {waveOrder: generalist framework for label-agnostic computational microscopy},
+	journal = {arXiv},
+	year = {2024},
+	month = dec,
+	eprint = {2412.09775},
+	doi = {10.48550/arXiv.2412.09775}
+}
+</code></pre>
+</details>
+
+Specifically, `waveorder` enables simulation and reconstruction of 2D or 3D:
+
+1. __phase, projected retardance, and in-plane orientation__ from a polarization-diverse volumetric brightfield acquisition ([QLIPP](https://elifesciences.org/articles/55502)),
+
+2. __phase__ from a volumetric brightfield acquisition ([2D phase](https://www.osapublishing.org/ao/abstract.cfm?uri=ao-54-28-8566)/[3D phase](https://www.osapublishing.org/ao/abstract.cfm?uri=ao-57-1-a205)),
+
+3. __phase__ from an illumination-diverse volumetric acquisition ([2D](https://www.osapublishing.org/oe/fulltext.cfm?uri=oe-23-9-11394&id=315599)/[3D](https://www.osapublishing.org/boe/fulltext.cfm?uri=boe-7-10-3940&id=349951) differential phase contrast),
+
+4. __fluorescence density__ from a widefield volumetric fluorescence acquisition (fluorescence deconvolution).  
+
+The [examples](https://github.com/mehta-lab/waveorder/tree/main/examples) demonstrate simulations and reconstruction for 2D QLIPP, 3D PODT, 3D fluorescence deconvolution, and 2D/3D PTI methods.
+
+If you are interested in deploying QLIPP, phase from brightfield, or fluorescence deconvolution for label-agnostic imaging at scale, checkout our [napari plugin](https://www.napari-hub.org/plugins/recOrder-napari),  [`recOrder-napari`](https://github.com/mehta-lab/recOrder).
+
+## Permittivity tensor imaging 
+
+Additionally, `waveorder` enabled the development of a new label-free imaging method, __permittivity tensor imaging (PTI)__, that measures density and  3D orientation of biomolecules with diffraction-limited resolution. These measurements are reconstructed from polarization-resolved images acquired with a sequence of oblique illuminations.
+
+The acquisition, calibration, background correction, reconstruction, and applications of PTI are described in the following [paper](https://doi.org/10.1101/2020.12.15.422951) published in Nature Methods:
+
+<details>
+<summary> Yeh et al. 2024 </summary>
+<pre><code>
+@article{yeh_2024,
+	author = {Yeh, Li-Hao and Ivanov, Ivan E. and Chandler, Talon and Byrum, Janie R. and Chhun, Bryant B. and Guo, Syuan-Ming and Foltz, Cameron and Hashemi, Ezzat and Perez-Bermejo, Juan A. and Wang, Huijun and Yu, Yanhao and Kazansky, Peter G. and Conklin, Bruce R. and Han, May H. and Mehta, Shalin B.},
+	title = {Permittivity tensor imaging: modular label-free imaging of 3D dry mass and 3D orientation at high resolution},
+	journal = {Nature Methods},
+	volume = {21},
+	number = {7},
+	pages = {1257--1274},
+	year = {2024},
+	month = jul,
+	issn = {1548-7105},
+	publisher = {Nature Publishing Group},
+	doi = {10.1038/s41592-024-02291-w}
+}
+</code></pre>
+</details>
+
+PTI provides volumetric reconstructions of mean permittivity ($\propto$ material density), differential permittivity ($\propto$ material anisotropy), 3D orientation, and optic sign. The following figure summarizes PTI acquisition and reconstruction with a small optical section of the mouse brain tissue:
+
+![Data_flow](https://github.com/mehta-lab/waveorder/blob/main/readme.png?raw=true)
+
+## Examples
+The [examples](https://github.com/mehta-lab/waveorder/tree/main/examples) illustrate simulations and reconstruction for 2D QLIPP, 3D phase from brightfield, and 2D/3D PTI methods.
+
+If you are interested in deploying QLIPP or phase from brightbrield, or fluorescence deconvolution for label-agnostic imaging at scale, checkout our [napari plugin](https://www.napari-hub.org/plugins/recOrder-napari),  [`recOrder-napari`](https://github.com/mehta-lab/recOrder).
+
+## Citation
+
+Please cite this repository, along with the relevant preprint or paper, if you use or adapt this code. The citation information can be found by clicking "Cite this repository" button in the About section in the right sidebar.
+
+## Installation
+
+Create a virtual environment:
+
+```sh
+conda create -y -n waveorder python=3.10
+conda activate waveorder
+```
+
+Install `waveorder` from PyPI:
+
+```sh
+pip install waveorder
+```
+
+Use `waveorder` in your scripts:
+
+```sh
+python
+>>> import waveorder
+```
+
+(Optional) Install example dependencies, clone the repository, and run an example script:
+```sh
+pip install waveorder[examples]
+git clone https://github.com/mehta-lab/waveorder.git
+python waveorder/examples/models/phase_thick_3d.py
+```
+
+(M1 users) `pytorch` has [incomplete GPU support](https://github.com/pytorch/pytorch/issues/77764),
+so please use `export PYTORCH_ENABLE_MPS_FALLBACK=1`
+to allow some operators to fallback to CPU
+if you plan to use GPU acceleration for polarization reconstruction. 

waveorder-2.2.0/examples/README.md

@@ -0,0 +1,10 @@
+`waveorder` is undergoing a significant refactor, and this `examples/` folder serves as a good place to understand the current state of the repository.
+
+Some examples require `pip install waveorder[examples]` for `napari` and `jupyter`. Visit the [napari installation guide](https://napari.org/dev/tutorials/fundamentals/installation.html) if napari installation fails.
+
+| Folder      | Requires                   | Description                                                                                           |
+|------------------|----------------------------|-------------------------------------------------------------------------------------------------------|
+| `models/`        | `pip install waveorder[examples]`      | Demonstrates the latest functionality of `waveorder` through simulations and reconstructions using various models. |
+| `maintenance/`   | `pip install waveorder`                | Examples of computational imaging methods enabled by functionality of waveorder; scripts are maintained with automated tests.               |
+| `visuals/`       | `pip install waveorder[examples]`      | Visualizations of transfer functions and Green's tensors.                                    |
+| `documentation/` | `pip install waveorder`, complete datasets | Provides examples of real-data reconstructions; serves as documentation and is not actively maintained. |

{waveorder-2.1.0 → waveorder-2.2.0}/examples/documentation/PTI_experiment/PTI_Experiment_Recon3D_anisotropic_target_small.py

@@ -6,11 +6,12 @@ import matplotlib.pyplot as plt
 from numpy.fft import fftshift
 
 import waveorder as wo
-from waveorder import optics, waveorder_reconstructor, util, visual
+from waveorder import optics, waveorder_reconstructor, util
 
 import zarr
 from pathlib import Path
 from iohub import open_ome_zarr
+from waveorder.visuals import jupyter_visuals
 
 # %%
 # Initialization
@@ -110,7 +111,7 @@ for i in range(len(Source)):
     Source_PolState[i, 1] = E_in[1]
 
 
-visual.plot_multicolumn(
+jupyter_visuals.plot_multicolumn(
     fftshift(Source, axes=(1, 2)), origin="lower", num_col=5
 )
 
@@ -162,7 +163,7 @@ S_image_tm[2] = (
 
 # %%
 # browse raw intensity stacks (stack_idx_1: z index, stack_idx2: pattern index)
-visual.parallel_5D_viewer(
+jupyter_visuals.parallel_5D_viewer(
     np.transpose(I_meas[:, :, :, :, ::-1], (4, 1, 0, 2, 3)),
     num_col=4,
     size=10,
@@ -171,7 +172,7 @@ visual.parallel_5D_viewer(
 
 # %%
 # browse uncorrected Stokes parameters (stack_idx_1: z index, stack_idx2: pattern index)
-visual.parallel_5D_viewer(
+jupyter_visuals.parallel_5D_viewer(
     np.transpose(S_image_recon, (4, 1, 0, 2, 3)),
     num_col=3,
     size=8,
@@ -182,7 +183,7 @@ visual.parallel_5D_viewer(
 
 # %%
 # browse corrected Stokes parameters (stack_idx_1: z index, stack_idx2: pattern index)
-visual.parallel_5D_viewer(
+jupyter_visuals.parallel_5D_viewer(
     np.transpose(S_image_tm, (4, 1, 0, 2, 3)),
     num_col=3,
     size=8,
@@ -213,7 +214,7 @@ f_tensor = setup.scattering_potential_tensor_recon_3D_vec(
 
 # %%
 # browse the z-stack of components of scattering potential tensor
-visual.parallel_4D_viewer(
+jupyter_visuals.parallel_4D_viewer(
     np.transpose(f_tensor, (3, 0, 1, 2)),
     num_col=4,
     origin="lower",
@@ -278,7 +279,7 @@ differential_permittivity_PT = np.array(
 
 # %%
 # browse the reconstructed physical properties
-visual.parallel_4D_viewer(
+jupyter_visuals.parallel_4D_viewer(
     np.transpose(
         np.stack(
             [
@@ -546,7 +547,7 @@ ax[5, 1].set_title("inclination (+) (xz)")
 
 # %%
 # browse XY planes of the phase and differential permittivity
-visual.parallel_4D_viewer(
+jupyter_visuals.parallel_4D_viewer(
     np.transpose(
         [
             np.clip(phase_PT, phase_min, phase_max),
@@ -585,7 +586,7 @@ orientation_3D_image = np.transpose(
     ),
     (3, 1, 2, 0),
 )
-orientation_3D_image_RGB = visual.orientation_3D_to_rgb(
+orientation_3D_image_RGB = jupyter_visuals.orientation_3D_to_rgb(
     orientation_3D_image, interp_belt=20 / 180 * np.pi, sat_factor=1
 )
 
@@ -600,7 +601,7 @@ plt.imshow(
 
 # plot the top view of 3D orientation colorsphere
 plt.figure(figsize=(3, 3))
-visual.orientation_3D_colorwheel(
+jupyter_visuals.orientation_3D_colorwheel(
     wheelsize=256, circ_size=50, interp_belt=20 / 180 * np.pi, sat_factor=1
 )
 
@@ -639,7 +640,7 @@ plt.imshow(
     in_plane_orientation[:, y_layer], origin="lower", aspect=z_step / ps
 )
 plt.figure(figsize=(3, 3))
-visual.orientation_2D_colorwheel()
+jupyter_visuals.orientation_2D_colorwheel()
 
 # %%
 # out-of-plane tilt
@@ -686,7 +687,7 @@ z_layer = 44
 
 fig, ax = plt.subplots(1, 1, figsize=(15, 15))
 
-visual.plot3DVectorField(
+jupyter_visuals.plot3DVectorField(
     np.abs(differential_permittivity_PT[1, :, :, z_layer]),
     azimuth[1, :, :, z_layer],
     theta[1, :, :, z_layer],
@@ -722,7 +723,7 @@ plt.imshow(
 # %%
 # Angular histogram of 3D orientation
 
-visual.orientation_3D_hist(
+jupyter_visuals.orientation_3D_hist(
     azimuth[1].flatten(),
     theta[1].flatten(),
     ret_mask.flatten(),

{waveorder-2.1.0 → waveorder-2.2.0}/examples/maintenance/PTI_simulation/PTI_Simulation_Forward_2D3D.py

@@ -15,9 +15,9 @@ from numpy.fft import fftshift
 from waveorder import (
     optics,
     waveorder_simulator,
-    visual,
     util,
 )
+from waveorder.visuals import jupyter_visuals
 
 #####################################################################
 # Initialization - imaging system and sample                        #
@@ -145,7 +145,7 @@ biref_map = ne_map_copy - no_map_copy
 ### Visualize sample properties
 
 #### XY sections
-visual.plot_multicolumn(
+jupyter_visuals.plot_multicolumn(
     [
         target[:, :, z_layer],
         azimuth[:, :, z_layer] % (2 * np.pi),
@@ -158,7 +158,7 @@ visual.plot_multicolumn(
     set_title=True,
 )
 #### XZ sections
-visual.plot_multicolumn(
+jupyter_visuals.plot_multicolumn(
     [
         np.transpose(target[y_layer, :, :]),
         np.transpose(azimuth[y_layer, :, :]) % (2 * np.pi),
@@ -197,7 +197,7 @@ orientation_3D_image = np.transpose(
     ),
     (3, 1, 2, 0),
 )
-orientation_3D_image_RGB = visual.orientation_3D_to_rgb(
+orientation_3D_image_RGB = jupyter_visuals.orientation_3D_to_rgb(
     orientation_3D_image, interp_belt=20 / 180 * np.pi, sat_factor=1
 )
 
@@ -206,7 +206,7 @@ plt.imshow(orientation_3D_image_RGB[z_layer], origin="lower")
 plt.figure(figsize=(10, 10))
 plt.imshow(orientation_3D_image_RGB[:, y_layer], origin="lower")
 plt.figure(figsize=(3, 3))
-visual.orientation_3D_colorwheel(
+jupyter_visuals.orientation_3D_colorwheel(
     wheelsize=128,
     circ_size=50,
     interp_belt=20 / 180 * np.pi,
@@ -216,7 +216,7 @@ visual.orientation_3D_colorwheel(
 plt.show()
 
 #### Angular histogram of 3D orientation
-visual.orientation_3D_hist(
+jupyter_visuals.orientation_3D_hist(
     azimuth.flatten(),
     inclination.flatten(),
     np.abs(target).flatten(),
@@ -258,7 +258,7 @@ epsilon_tensor[2, 1] = epsilon_del * np.sin(2 * inclination) * np.sin(azimuth)
 epsilon_tensor[2, 2] = epsilon_mean + epsilon_del * np.cos(2 * inclination)
 
 
-visual.plot_multicolumn(
+jupyter_visuals.plot_multicolumn(
     [
         epsilon_tensor[0, 0, :, :, z_layer],
         epsilon_tensor[0, 1, :, :, z_layer],
@@ -334,7 +334,7 @@ del_f_component[6] = (
 )
 
 
-visual.plot_multicolumn(
+jupyter_visuals.plot_multicolumn(
     [
         del_f_component[0, :, :, z_layer],
         del_f_component[1, :, :, z_layer],
@@ -425,11 +425,11 @@ for i in range(len(Source)):
 
 #### Circularly polarized illumination patterns
 
-visual.plot_multicolumn(
+jupyter_visuals.plot_multicolumn(
     fftshift(Source_cont, axes=(1, 2)), origin="lower", num_col=5, size=5
 )
 # discretized illumination patterns used in simulation (faster forward model)
-visual.plot_multicolumn(
+jupyter_visuals.plot_multicolumn(
     fftshift(Source, axes=(1, 2)), origin="lower", num_col=5, size=5
 )
 print(Source_PolState)

{waveorder-2.1.0 → waveorder-2.2.0}/examples/maintenance/PTI_simulation/PTI_Simulation_Recon2D.py

@@ -16,8 +16,8 @@ from numpy.fft import fftshift
 from waveorder import (
     optics,
     waveorder_reconstructor,
-    visual,
 )
+from waveorder.visuals import jupyter_visuals
 
 ## Initialization
 ## Load simulated images and parameters
@@ -76,7 +76,7 @@ setup = waveorder_reconstructor.waveorder_microscopy(
 ## Visualize 2  D transfer functions as a function of illumination pattern
 
 # illumination patterns used
-visual.plot_multicolumn(
+jupyter_visuals.plot_multicolumn(
     fftshift(Source_cont, axes=(1, 2)), origin="lower", num_col=5, size=5
 )
 plt.show()
@@ -118,7 +118,7 @@ f_tensor = setup.scattering_potential_tensor_recon_2D_vec(
     S_image_tm, reg_inc=reg_inc, cupy_det=True
 )
 
-visual.plot_multicolumn(
+jupyter_visuals.plot_multicolumn(
     f_tensor,
     num_col=4,
     origin="lower",
@@ -255,14 +255,14 @@ orientation_3D_image = np.transpose(
     ),
     (1, 2, 0),
 )
-orientation_3D_image_RGB = visual.orientation_3D_to_rgb(
+orientation_3D_image_RGB = jupyter_visuals.orientation_3D_to_rgb(
     orientation_3D_image, interp_belt=20 / 180 * np.pi, sat_factor=1
 )
 
 plt.figure(figsize=(5, 5))
 plt.imshow(orientation_3D_image_RGB, origin="lower")
 plt.figure(figsize=(3, 3))
-visual.orientation_3D_colorwheel(
+jupyter_visuals.orientation_3D_colorwheel(
     wheelsize=256, circ_size=50, interp_belt=20 / 180 * np.pi, sat_factor=1
 )
 plt.show()
@@ -297,7 +297,7 @@ in_plane_orientation = hsv_to_rgb(I_hsv.copy())
 plt.figure(figsize=(5, 5))
 plt.imshow(in_plane_orientation, origin="lower")
 plt.figure(figsize=(3, 3))
-visual.orientation_2D_colorwheel()
+jupyter_visuals.orientation_2D_colorwheel()
 plt.show()
 
 # out-of-plane tilt
@@ -339,7 +339,7 @@ spacing = 4
 plt.figure(figsize=(10, 10))
 
 fig, ax = plt.subplots(1, 1, figsize=(20, 10))
-visual.plot3DVectorField(
+jupyter_visuals.plot3DVectorField(
     np.abs(retardance_pr_nm[0]),
     azimuth[0],
     theta[0],
@@ -362,7 +362,7 @@ ret_mask[ret_mask < 0.5] = 0
 
 plt.figure(figsize=(10, 10))
 plt.imshow(ret_mask, cmap="gray", origin="lower")
-visual.orientation_3D_hist(
+jupyter_visuals.orientation_3D_hist(
     azimuth[0].flatten(),
     theta[0].flatten(),
     ret_mask.flatten(),