waveorder 2.2.0__tar.gz → 2.2.1b0__tar.gz

waveorder-2.2.1b0/.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

waveorder-2.2.1b0/.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

waveorder-2.2.1b0/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).

{waveorder-2.2.0 → waveorder-2.2.1b0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: waveorder
-Version: 2.2.0
+Version: 2.2.1b0
 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>
@@ -62,6 +62,7 @@ Requires-Dist: torch>=2.4.1
 Provides-Extra: dev
 Requires-Dist: pytest; extra == "dev"
 Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: black==25.1.0; extra == "dev"
 Provides-Extra: examples
 Requires-Dist: napari[all]; extra == "examples"
 Requires-Dist: jupyter; extra == "examples"

{waveorder-2.2.0 → waveorder-2.2.1b0}/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 @@ PTI_file = zarr.open(PTI_file_name, mode="r")
 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 @@ jupyter_visuals.parallel_4D_viewer(
 # "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 @@ differential_permittivity_PT = np.array(
     [
         ((-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 @@ mat_map = PTI_array[7:]
 
 # 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 @@ differential_permittivity_PT = np.array(
     [
         ((-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)
     ]

{waveorder-2.2.0 → waveorder-2.2.1b0}/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
 
 #####################################################################

{waveorder-2.2.0 → waveorder-2.2.1b0}/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 @@ plt.show()
 # in-plane orientation
 from matplotlib.colors import hsv_to_rgb
 
-
 ret_min_color = 0
 ret_max_color = 1.5
 

{waveorder-2.2.0 → waveorder-2.2.1b0}/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

{waveorder-2.2.0 → waveorder-2.2.1b0}/examples/maintenance/QLIPP_simulation/2D_QLIPP_forward.py

@@ -10,14 +10,11 @@
 #####################################################################################################
 
 
-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
 
 # Key parameters

{waveorder-2.2.0 → waveorder-2.2.1b0}/examples/maintenance/QLIPP_simulation/2D_QLIPP_recon.py

@@ -10,13 +10,11 @@
 #  eLife 9:e55502 (2020).```                                                                        #
 #####################################################################################################
 
-import numpy as np
 import matplotlib.pyplot as plt
-from waveorder import (
-    waveorder_reconstructor,
-)
-from waveorder.visuals import jupyter_visuals
+import numpy as np
 
+from waveorder import waveorder_reconstructor
+from waveorder.visuals import jupyter_visuals
 
 # ### Load simulated data
 # Load simulations

{waveorder-2.2.0 → waveorder-2.2.1b0}/examples/models/inplane_oriented_thick_pol3d_vector.py

@@ -1,9 +1,7 @@
-import torch
 import napari
+import torch
 
-from waveorder.models import (
-    inplane_oriented_thick_pol3d_vector,
-)
+from waveorder.models import inplane_oriented_thick_pol3d_vector
 
 # Parameters
 # all lengths must use consistent units e.g. um
@@ -25,20 +23,22 @@ fzyx_object = inplane_oriented_thick_pol3d_vector.generate_test_phantom(
 )
 
 # Calculate transfer function
-sfZYX_transfer_function, intensity_to_stokes_matrix, singular_system = (
-    inplane_oriented_thick_pol3d_vector.calculate_transfer_function(
-        swing,
-        scheme,
-        zyx_shape,
-        yx_pixel_size,
-        z_pixel_size,
-        wavelength_illumination,
-        z_padding,
-        index_of_refraction_media,
-        numerical_aperture_illumination,
-        numerical_aperture_detection,
-        fourier_oversample_factor=fourier_oversample_factor,
-    )
+(
+    sfZYX_transfer_function,
+    intensity_to_stokes_matrix,
+    singular_system,
+) = inplane_oriented_thick_pol3d_vector.calculate_transfer_function(
+    swing,
+    scheme,
+    zyx_shape,
+    yx_pixel_size,
+    z_pixel_size,
+    wavelength_illumination,
+    z_padding,
+    index_of_refraction_media,
+    numerical_aperture_illumination,
+    numerical_aperture_detection,
+    fourier_oversample_factor=fourier_oversample_factor,
 )
 
 # Display transfer function

{waveorder-2.2.0 → waveorder-2.2.1b0}/examples/models/isotropic_thin_3d.py

@@ -5,7 +5,7 @@
 
 import napari
 import numpy as np
-from waveorder import util
+
 from waveorder.models import isotropic_thin_3d
 
 # Parameters

{waveorder-2.2.0 → waveorder-2.2.1b0}/examples/models/phase_thick_3d.py

@@ -5,7 +5,7 @@
 
 import napari
 import numpy as np
-from waveorder import util
+
 from waveorder.models import phase_thick_3d
 
 # Parameters

{waveorder-2.2.0 → waveorder-2.2.1b0}/examples/visuals/plot_greens_tensor.py

@@ -1,17 +1,19 @@
-from skimage import measure
+import os
+
 import napari
-from napari.experimental import link_layers
 import numpy as np
 import torch
-import os
-from waveorder import util, optics
+from napari.experimental import link_layers
 from scipy.ndimage import gaussian_filter
+from skimage import measure
+
+from waveorder import optics, util
 
 # Parameters
 # all lengths must use consistent units e.g. um
 output_dirpath = "./greens_plots"
 os.makedirs(output_dirpath, exist_ok=True)
-grid_size = 100 # 300 for publication
+grid_size = 100  # 300 for publication
 blur_width = grid_size // 35  # blurring to smooth sharp corners
 zyx_shape = 3 * (grid_size,)
 yx_pixel_size = 6.5 / 63

{waveorder-2.2.0 → waveorder-2.2.1b0}/examples/visuals/plot_vector_transfer_function_support.py

@@ -1,7 +1,7 @@
+import os
+
 import napari
 import numpy as np
-import os
-import matplotlib.pyplot as plt
 
 
 def plot_otf_support(
@@ -28,8 +28,14 @@ def plot_otf_support(
     points = np.array(
         [
             [0, 0],
-            [det_na - ill_na, (1 - ill_na**2) ** 0.5 - (1 - det_na**2) ** 0.5],
-            [det_na + ill_na, (1 - ill_na**2) ** 0.5 - (1 - det_na**2) ** 0.5],
+            [
+                det_na - ill_na,
+                (1 - ill_na**2) ** 0.5 - (1 - det_na**2) ** 0.5,
+            ],
+            [
+                det_na + ill_na,
+                (1 - ill_na**2) ** 0.5 - (1 - det_na**2) ** 0.5,
+            ],
             [2 * ill_na, 0],
         ]
     )
@@ -203,7 +209,6 @@ my_colors = [
 ]
 
 for my_color in my_colors:
-
     plot_otf_support(
         ill_na,
         det_na,

{waveorder-2.2.0 → waveorder-2.2.1b0}/pyproject.toml

@@ -55,7 +55,7 @@ dependencies = [
 dynamic = ["version"]
 
 [project.optional-dependencies]
-dev = ["pytest", "pytest-cov"]
+dev = ["pytest", "pytest-cov", "black==25.1.0"]
 examples = ["napari[all]", "jupyter"]
 
 [project.urls]

{waveorder-2.2.0 → waveorder-2.2.1b0}/tests/models/test_isotropic_fluorescent_thick_3d.py

@@ -1,4 +1,3 @@
-import pytest
 import torch
 
 from waveorder.models import isotropic_fluorescent_thick_3d

{waveorder-2.2.0 → waveorder-2.2.1b0}/tests/models/test_phase_thick_3d.py

@@ -1,5 +1,6 @@
-import pytest
 import numpy as np
+import pytest
+
 from waveorder.models import phase_thick_3d
 
 
@@ -27,7 +28,6 @@ def simulate_phase_recon(
     z_pixel_size_um=0.1,
     yx_pixel_size_um=6.5 / 63,
 ):
-
     z_fov_um = 50
     yx_fov_um = 50
 
@@ -98,4 +98,4 @@ def test_phase_invariance():
 
     # test yx pixel size invariance
     recon2 = simulate_phase_recon(yx_pixel_size_um=0.7 * 6.5 / 63)
-    assert np.abs((recon2 - recon) / recon) < 0.02
+    assert np.abs((recon2 - recon) / recon) < 0.02

{waveorder-2.2.0 → waveorder-2.2.1b0}/tests/test_examples.py

@@ -1,8 +1,9 @@
-import subprocess
 import os
-import pytest
+import subprocess
 import sys
 
+import pytest
+
 
 def _run_scripts(scripts):
     for script in scripts:

waveorder-2.2.1b0/tests/test_filter.py

@@ -0,0 +1,57 @@
+import pytest
+import torch
+
+from waveorder import filter
+
+
+def test_apply_transfer_function_filter():
+    input_array = torch.tensor([[[1.0, 2.0], [3.0, 4.0]]])
+    transfer_function_bank = torch.tensor([[[[1, 0], [0, 0]]]])
+    result = filter.apply_filter_bank(transfer_function_bank, input_array)
+    expected = torch.tensor([[[10, 10], [10, 10]]]) / 4
+    assert torch.allclose(result, expected)
+
+    # Test with incompatible shapes
+    input_array = torch.tensor([[[1.0, 2.0], [3.0, 4.0]]])
+    transfer_function_bank = torch.tensor(
+        [[[[0.5, 0.5, 0.5], [0.5, 0.5, 0.5]]]]
+    )
+    with pytest.raises(ValueError):
+        filter.apply_filter_bank(transfer_function_bank, input_array)
+
+
+def test_stretched_multiply():
+    small_array = torch.tensor([[1, 2], [3, 4]])
+    large_array = torch.tensor(
+        [[1, 2, 3, 4], [5, 6, 7, 8], [9, 10, 11, 12], [13, 14, 15, 16]]
+    )
+    result = filter.stretched_multiply(small_array, large_array)
+    expected = torch.tensor(
+        [[1, 2, 6, 8], [5, 6, 14, 16], [27, 30, 44, 48], [39, 42, 60, 64]]
+    )
+    assert torch.all(result == expected)
+    assert torch.all(
+        filter.stretched_multiply(large_array, large_array) == large_array**2
+    )
+
+    # Test that output dims are correct
+    rand_array_3x3x3 = torch.rand((3, 3, 3))
+    rand_array_99x99x99 = torch.rand((99, 99, 99))
+    result = filter.stretched_multiply(rand_array_3x3x3, rand_array_99x99x99)
+    assert result.shape == (99, 99, 99)
+
+
+def test_stretched_multiply_incompatible_dims():
+    # small_array > large_array
+    small_array = torch.tensor([[1, 2, 3], [4, 5, 6], [7, 8, 9]])
+    large_array = torch.tensor([[1, 2], [3, 4]])
+    with pytest.raises(ValueError):
+        filter.stretched_multiply(small_array, large_array)
+
+    # Mismatched dims
+    small_array = torch.tensor([[1, 2], [3, 4]])
+    large_array = torch.tensor(
+        [[[1, 2], [4, 5], [7, 8]], [[10, 11], [13, 14], [16, 17]]]
+    )
+    with pytest.raises(ValueError):
+        filter.stretched_multiply(small_array, large_array)