Merge branch 'main' into scaled-reconstruction

mehta-lab · Feb 20, 2025 · 46a4e81 · 46a4e81
2 parents 9028e16 + 1f84072
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diff --git a/.github/workflows/pr.yml b/.github/workflows/pr.yml
@@ -0,0 +1,101 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: lint, style, and tests
+
+on:
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  style:
+    name: Style Check
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: ["3.10"]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install black==25.1.0
+      - name: Check code styling with Black
+        run: |
+          black --diff -S -t py310 waveorder
+          black --check -S -t py310 waveorder
+
+  # lint:
+  #   name: Lint Check
+  #   runs-on: ubuntu-latest
+
+  #   strategy:
+  #     matrix:
+  #       python-version: ["3.10"]
+
+  #   steps:
+  #     - uses: actions/checkout@v3
+  #     - name: Set up Python
+  #       uses: actions/setup-python@v4
+  #       with:
+  #         python-version: ${{ matrix.python-version }}
+  #     - name: Install dependencies
+  #       run: |
+  #         python -m pip install --upgrade pip
+  #         pip install flake8
+  #     - name: Check code with Flake8
+  #       # E203 conflicts with black
+  #       run: |
+  #         flake8 waveorder --extend-ignore=E203
+
+  isort:
+    name: isort Check
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: ["3.10"]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install isort
+      - name: Check code with isort
+        run: |
+          isort --check waveorder
+
+  tests:
+    needs: [style, isort] # lint
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install ".[dev]"
+
+      - name: Test with pytest
+        run: |
+          pytest -v --cov=./ --cov-report=xml
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,34 @@
+
+repos:
+# basic pre-commit
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-added-large-files
+      - id: check-yaml
+      - id: check-toml
+      - id: detect-private-key
+# sorting imports
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+# syntax linting and formatting
+  - repo: https://github.com/myint/autoflake
+    rev: v2.1.1
+    hooks:
+      - id: autoflake
+        args: [--in-place, --remove-all-unused-imports,
+               --ignore-init-module-imports]
+  # - repo: https://github.com/PyCQA/flake8
+  #   rev: 6.0.0
+  #   hooks:
+  #     - id: flake8
+  #       args: [--ignore, "E203,W503", --min-python-version, '3.10']
+  #       additional_dependencies: [flake8-typing-imports==1.12.0]
+  - repo: https://github.com/psf/black
+    rev: 25.1.0
+    hooks:
+      - id: black
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -0,0 +1,62 @@
+# Contributing guide
+
+Thanks for your interest in contributing to `waveorder`!
+
+Please see the following steps for our workflow.
+
+## Getting started
+
+Please read the [README](./README.md) for an overview of the project,
+and how you can install and use the package.
+
+## Issues
+
+We use [issues](https://github.com/mehta-lab/waveorder/issues) to track
+bug reports, feature requests, and provide user support.
+
+Before opening a new issue, please first search existing issues (including closed ones),
+to see if there is an existing discussion about it.
+
+### Setting up development environment
+
+For local development, first install [Git](https://git-scm.com/)
+and Python with an environment management tool
+(e.g. [miniforge](https://github.com/conda-forge/miniforge), a minimal community distribution of Conda).
+
+If you use Conda, set up an environment with:
+
+```sh
+conda create -n waveorder-dev python=3.10
+conda activate waveorder-dev
+```
+
+If you have push permission to the repository,
+clone the repository (the code blocks below are shell commands):
+
+```sh
+cd # to the directory you want to work in
+git clone https://github.com/mehta-lab/waveorder.git
+```
+
+Otherwise, you can follow [these instructions](https://docs.github.com/en/get-started/quickstart/fork-a-repo)
+to [fork](https://github.com/mehta-lab/waveorder/fork) the repository.
+
+Then install the package in editable mode with the development dependencies:
+
+```sh
+cd waveorder/ # or the renamed project root directory
+pip install -e ".[dev]"
+```
+
+Then make the changes and [track them with Git](https://docs.github.com/en/get-started/using-git/about-git#example-contribute-to-an-existing-repository).
+
+
+### Code style
+
+We use [pre-commit](https://pre-commit.com/) to sort imports with [isort](https://github.com/PyCQA/isort) and format code with [black](https://black.readthedocs.io/en/stable/) automatically prior to each commit. To minimize test errors when submitting pull requests, please install pre-commit in your environment as follows:
+
+```bash
+pre-commit install
+```
+
+When these packages are executed within the project root directory, they should automatically use the [project settings](./pyproject.toml).
diff --git a/examples/documentation/PTI_experiment/PTI_Experiment_Recon3D_anisotropic_target_small.py b/examples/documentation/PTI_experiment/PTI_Experiment_Recon3D_anisotropic_target_small.py
@@ -1,16 +1,16 @@
 # %%
 # This notebook-style script requires a ~500 MB download from https://www.ebi.ac.uk/biostudies/files/S-BIAD1063/PTI-BIA/Anisotropic_target_small.zip
 
-import numpy as np
+from pathlib import Path
+
 import matplotlib.pyplot as plt
+import numpy as np
+import zarr
+from iohub import open_ome_zarr
 from numpy.fft import fftshift
 
 import waveorder as wo
-from waveorder import optics, waveorder_reconstructor, util
-
-import zarr
-from pathlib import Path
-from iohub import open_ome_zarr
+from waveorder import optics, util, waveorder_reconstructor
 from waveorder.visuals import jupyter_visuals
 
 # %%
@@ -62,10 +62,12 @@
 I_cali_mean = np.array(PTI_file.I_cali_mean)
 
 # source polarization, instrument matrix calibration
-E_in, A_matrix, I_cali_mean = (
-    wo.waveorder_reconstructor.instrument_matrix_and_source_calibration(
-        I_cali_mean, handedness="RCP"
-    )
+(
+    E_in,
+    A_matrix,
+    I_cali_mean,
+) = wo.waveorder_reconstructor.instrument_matrix_and_source_calibration(
+    I_cali_mean, handedness="RCP"
 )
 
 # %%
@@ -238,15 +240,18 @@
 # "negative" -> only solution of negatively uniaxial material
 # "unknown" -> both solutions of positively and negatively uniaxial material + optic sign estimation
 
-differential_permittivity, azimuth, theta, mat_map = (
-    setup.scattering_potential_tensor_to_3D_orientation(
-        f_tensor,
-        S_image_tm,
-        material_type="unknown",
-        reg_ret_pr=reg_differential_permittivity,
-        itr=10,
-        fast_gpu_mode=True,
-    )
+(
+    differential_permittivity,
+    azimuth,
+    theta,
+    mat_map,
+) = setup.scattering_potential_tensor_to_3D_orientation(
+    f_tensor,
+    S_image_tm,
+    material_type="unknown",
+    reg_ret_pr=reg_differential_permittivity,
+    itr=10,
+    fast_gpu_mode=True,
 )
 
 # %%
@@ -264,7 +269,10 @@
     [
         ((-1) ** i)
         * util.wavelet_softThreshold(
-            ((-1) ** i) * differential_permittivity_PT[i], "db8", 0.00303, level=1
+            ((-1) ** i) * differential_permittivity_PT[i],
+            "db8",
+            0.00303,
+            level=1,
         )
         for i in range(2)
     ]
@@ -374,17 +382,27 @@
 
 # compute the physical properties from the scattering potential tensor
 
-differential_permittivity_p, azimuth_p, theta_p = (
-    optics.scattering_potential_tensor_to_3D_orientation_PN(
-        f_tensor, material_type="positive", reg_ret_pr=reg_differential_permittivity
-    )
-)
-differential_permittivity_n, azimuth_n, theta_n = (
-    optics.scattering_potential_tensor_to_3D_orientation_PN(
-        f_tensor, material_type="negative", reg_ret_pr=reg_differential_permittivity
-    )
+(
+    differential_permittivity_p,
+    azimuth_p,
+    theta_p,
+) = optics.scattering_potential_tensor_to_3D_orientation_PN(
+    f_tensor,
+    material_type="positive",
+    reg_ret_pr=reg_differential_permittivity,
+)
+(
+    differential_permittivity_n,
+    azimuth_n,
+    theta_n,
+) = optics.scattering_potential_tensor_to_3D_orientation_PN(
+    f_tensor,
+    material_type="negative",
+    reg_ret_pr=reg_differential_permittivity,
+)
+differential_permittivity = np.array(
+    [differential_permittivity_p, differential_permittivity_n]
 )
-differential_permittivity = np.array([differential_permittivity_p, differential_permittivity_n])
 azimuth = np.array([azimuth_p, azimuth_n])
 theta = np.array([theta_p, theta_n])
 
@@ -402,7 +420,10 @@
     [
         ((-1) ** i)
         * util.wavelet_softThreshold(
-            ((-1) ** i) * differential_permittivity_PT[i], "db8", 0.00303, level=1
+            ((-1) ** i) * differential_permittivity_PT[i],
+            "db8",
+            0.00303,
+            level=1,
         )
         for i in range(2)
     ]

diff --git a/examples/maintenance/PTI_simulation/PTI_Simulation_Forward_2D3D.py b/examples/maintenance/PTI_simulation/PTI_Simulation_Forward_2D3D.py
@@ -9,14 +9,11 @@
 #  density and anisotropy," bioRxiv 2020.12.15.422951 (2020).```   #
 ####################################################################
 
-import numpy as np
 import matplotlib.pyplot as plt
+import numpy as np
 from numpy.fft import fftshift
-from waveorder import (
-    optics,
-    waveorder_simulator,
-    util,
-)
+
+from waveorder import optics, util, waveorder_simulator
 from waveorder.visuals import jupyter_visuals
 
 #####################################################################

diff --git a/examples/maintenance/PTI_simulation/PTI_Simulation_Recon2D.py b/examples/maintenance/PTI_simulation/PTI_Simulation_Recon2D.py
@@ -9,14 +9,11 @@
 #  density and anisotropy," bioRxiv 2020.12.15.422951 (2020).```   #
 ####################################################################
 
-import numpy as np
 import matplotlib.pyplot as plt
+import numpy as np
 from numpy.fft import fftshift
 
-from waveorder import (
-    optics,
-    waveorder_reconstructor,
-)
+from waveorder import optics, waveorder_reconstructor
 from waveorder.visuals import jupyter_visuals
 
 ## Initialization
@@ -271,7 +268,6 @@
 # in-plane orientation
 from matplotlib.colors import hsv_to_rgb
 
-
 ret_min_color = 0
 ret_max_color = 1.5
 

diff --git a/examples/maintenance/PTI_simulation/PTI_Simulation_Recon3D.py b/examples/maintenance/PTI_simulation/PTI_Simulation_Recon3D.py
@@ -8,13 +8,11 @@
 #  "uPTI: uniaxial permittivity tensor imaging of intrinsic        #
 #  density and anisotropy," bioRxiv 2020.12.15.422951 (2020).```   #
 ####################################################################
-import numpy as np
 import matplotlib.pyplot as plt
+import numpy as np
 from numpy.fft import fftshift
-from waveorder import (
-    optics,
-    waveorder_reconstructor,
-)
+
+from waveorder import optics, waveorder_reconstructor
 from waveorder.visuals import jupyter_visuals
 
 ## Initialization