Add RL/RLGC deconvolution for 3D fluorescence

docs/examples/cli/configs/fluorescence_2d.yml

@@ -15,7 +15,8 @@ fluorescence:
     wavelength_emission: 0.532              # emission wavelength in micrometers
     confocal_pinhole_diameter: null         # confocal pinhole diameter (null = widefield)
   apply_inverse:
-    reconstruction_algorithm: Tikhonov      # 'Tikhonov' or 'TV' regularization
+    reconstruction_algorithm: Tikhonov      # 'Tikhonov'/'TV' filters or 'RL'/'RLGC' iterative deconvolution
     regularization_strength: 0.01           # strength of regularization
     TV_rho_strength: 0.001                  # ADMM rho parameter for TV regularization
     TV_iterations: 1                        # ADMM iterations for TV regularization
+    rl: null                                # Richardson-Lucy knobs; only valid with reconstruction_algorithm 'RL'/'RLGC', and filled with defaults if omitted there

docs/examples/cli/configs/fluorescence_3d.yml

@@ -15,7 +15,8 @@ fluorescence:
     wavelength_emission: 0.532              # emission wavelength in micrometers
     confocal_pinhole_diameter: null         # confocal pinhole diameter (null = widefield)
   apply_inverse:
-    reconstruction_algorithm: Tikhonov      # 'Tikhonov' or 'TV' regularization
+    reconstruction_algorithm: Tikhonov      # 'Tikhonov'/'TV' filters or 'RL'/'RLGC' iterative deconvolution
     regularization_strength: 0.001          # strength of regularization
     TV_rho_strength: 0.001                  # ADMM rho parameter for TV regularization
     TV_iterations: 1                        # ADMM iterations for TV regularization
+    rl: null                                # Richardson-Lucy knobs; only valid with reconstruction_algorithm 'RL'/'RLGC', and filled with defaults if omitted there

tests/models/test_isotropic_fluorescent_thick_3d.py

@@ -1,11 +1,44 @@
 import numpy as np
+import pytest
 import torch
 
 from waveorder import util
 from waveorder._pixel_size import YXPixelSize
 from waveorder.models import isotropic_fluorescent_thick_3d
 
 
+@pytest.mark.parametrize(
+    "yx_pixel_size, na, confocal_pinhole_diameter",
+    [
+        (0.1, 1.2, None),
+        (0.325, 0.8, None),
+        (0.65, 0.45, None),
+        (0.65, 1.2, None),
+        (1.3, 1.2, None),
+        (0.325, 0.8, 0.5),  # confocal
+    ],
+)
+def test_transfer_function_psf_nonnegative(yx_pixel_size, na, confocal_pinhole_diameter):
+    """The incoherent PSF must be nonnegative.
+
+    Upsampling to Nyquist and then cropping the OTF in Fourier space rings the
+    PSF below zero (worst near sub-Nyquist sampling). This is unphysical and
+    breaks Richardson-Lucy, so ``calculate_transfer_function`` clips it away.
+    """
+    otf = isotropic_fluorescent_thick_3d.calculate_transfer_function(
+        zyx_shape=(24, 64, 64),
+        yx_pixel_size=yx_pixel_size,
+        z_pixel_size=0.5,
+        wavelength_emission=0.515,
+        z_padding=0,
+        index_of_refraction_media=1.4,
+        numerical_aperture_detection=na,
+        confocal_pinhole_diameter=confocal_pinhole_diameter,
+    )
+    psf = torch.real(torch.fft.ifftn(otf, dim=(-3, -2, -1)))
+    assert psf.min() >= -1e-6 * psf.max()
+
+
 def test_pinhole_aperture_otf_small_diameter():
     """Test that pinhole OTF is broader for smaller diameter."""
     yx_shape = (128, 128)