Update decon script to use IJ ops RLTV

- Add a citation
- Add parameter descriptions
- Use RLTV

Author: elevans

src/main/resources/script_templates/Deconvolution/DeconWithTheoreticalPSF.py

@@ -1,45 +1,76 @@
 #@ OpService ops
 #@ UIService ui
-#@ ImgPlus img
-#@ Integer numIterations(value=30)
-#@ Float numericalAperture(value=1.4)
-#@ Float wavelength(value=550)
-#@ Float riImmersion(value=1.5)
-#@ Float riSample(value=1.4)
-#@ Float xySpacing(value=62.9)
-#@ Float zSpacing(value=160)
-#@OUTPUT ImgPlus psf
-#@OUTPUT ImgPlus deconvolved
+#@ Img (label = "Input image:", autofill = false) img
+#@ Integer (label="Iterations", value=15) iterations
+#@ Float (label="Numerical Aperture", style="format:0.00", min=0.00, value=1.45) numerical_aperture
+#@ Integer (label="Emission Wavelength (nm)", value=457) wavelength
+#@ Float (label="Refractive Index (immersion)", style="format:0.00", min=0.00, value=1.5) ri_immersion
+#@ Float (label="Refractive Index (sample)", style="format:0.00", min=0.00, value=1.4) ri_sample
+#@ Float (label="Lateral spacing (μm/pixel)", style="format:0.0000", min=0.0000, value=0.065) lateral_spacing
+#@ Float (label="Axial spacing (μm/pixel)", style="format:0.0000", min=0.0000, value=0.1) axial_spacing
+#@ Float (label="Particle/sample Position (μm)", style="format:0.0000", min=0.0000, value=0) p_z
+#@ Float (label="Regularization factor", style="format:0.00000", min=0.00000, value=0.002) reg_factor
+#@ Boolean (label = "Show PSF:", value = false) show_psf
+#@output Img result
 
-from net.imglib2 import FinalDimensions
-from net.imglib2.type.numeric.real import FloatType;
-
-# convert to float (TODO: make sure deconvolution op works on other types)
-imgF=ops.convert().float32(img)
+# Richardson-Lucy Total Variation deconvolution with a simulated point spread function.
+#
+# This script utilizes an ImageJ Ops implementation of Richardson-Lucy Total Variation (RLTV)
+# deconvolution as described by Dey et al. 2006 and a simulated point spread function (PSF)
+# using the Gibson-Lanni model.
+#
+# Arguments
+#    * `img`: A 3-dimensional image with known lateral (x and y) and axial (z) spacing.
+#    * `iterations`: The number of iterations to perform (default = 15).
+#    * `numerical_aperture`: The numerical aperature (NA) of the objective used.
+#    * `wavelength`: The emission wavelength in nanometers (nm) of the image.
+#    * `ri_immersion`: The refractive index of immersion medium (air, oil, etc...).
+#    * `ri_sample`: The refractive index of the sample, a measured value (default = 1.4)
+#    * `lateral_spacing`: The X and Y pixel spacing in μm/pixel of the image.
+#    * `axial_spacing`: The Z spacing in μm/pixel of the image.
+#    * `p_z`: The position of the sample from the coverslip.
+#    * `reg_factor`: The regularization factor.
+#    * `show_psf`: Optionally display the simulated PSF.
+#
+# Returns
+#    * `result`: The deconvolved data.
+#    * `PSF`: The simulated PSF (optional).
+#
+# Reference
+#
+# https://doi.org/10.1002/jemt.20294
 
-# make psf same size as image
-psfSize=FinalDimensions([img.dimension(0), img.dimension(1), img.dimension(2)]);
+from net.imglib2 import FinalDimensions
+from net.imglib2.type.numeric.real import FloatType
 
-# add border in z direction
-borderSize=[0,0,psfSize.dimension(2)/2];
+# convert input image to float
+img = ops.convert().float32(img)
 
-wavelength=wavelength*1E-9
-xySpacing=xySpacing*1E-9
-zSpacing=zSpacing*1E-9
+# use image dimensions for PSF size
+psf_size = FinalDimensions(img.dimensionsAsLongArray())
 
-# currently there is a bug when generating a PSF with wavelength < 545 nm
-# (this has been fixed, but the fix has not yet been distributed)
-if wavelength<545E-09:
-	wavelength = 545E-09;
+# convert the input parameters to meters (m)
+wavelength = float(wavelength) * 1E-9
+lateral_spacing *= 1E-6
+axial_spacing *= 1E-6
+p_z *= 1E-6
 
-riImmersion = 1.5;
-riSample = 1.4;
-xySpacing = 62.9E-9;
-zSpacing = 160E-9;
-depth = 0;
+# create the synthetic PSF
+psf = ops.create().kernelDiffraction(
+    psf_size,
+    numerical_aperture,
+    wavelength,
+    ri_sample,
+    ri_immersion,
+    lateral_spacing,
+    axial_spacing,
+    p_z,
+    FloatType()
+    )
 
-psf = ops.create().kernelDiffraction(psfSize, numericalAperture, wavelength,
-				riSample, riImmersion, xySpacing, zSpacing, depth, FloatType());
+# deconvolve image
+result = ops.deconvolve().richardsonLucyTV(img, psf, iterations, reg_factor)
 
-deconvolved = ops.deconvolve().richardsonLucy(imgF, psf, borderSize, None,
-					None, None, None, numIterations, True, True);
+# optionally show the PSF
+if show_psf:
+    ui.show("PSF", psf)