Remove deconvolution debugging code

ctrueden · ctrueden · commit d40aa7b2988b · 2019-11-18T13:47:58.000-06:00
diff --git a/src/main/java/net/imagej/ops/deconvolve/NonCirculantFirstGuess.java b/src/main/java/net/imagej/ops/deconvolve/NonCirculantFirstGuess.java
@@ -87,8 +87,6 @@ public RandomAccessibleInterval<O> apply(RandomAccessibleInterval<I> in, final O
 
 		final Img<O> firstGuess = create.apply(in, outType);
 
-		RichardsonLucyC.dump(firstGuess, "firstGuess-initial");
-
 		// set first guess to be a constant = to the average value
 
 		// so first compute the sum...
@@ -110,7 +108,6 @@ public RandomAccessibleInterval<O> apply(RandomAccessibleInterval<I> in, final O
 			type.setReal(average);
 		}
 
-		RichardsonLucyC.dump(firstGuess, "firstGuess-result");
 		return firstGuess;
 	}
 }
diff --git a/src/main/java/net/imagej/ops/deconvolve/NonCirculantNormalizationFactor.java b/src/main/java/net/imagej/ops/deconvolve/NonCirculantNormalizationFactor.java
@@ -216,15 +216,11 @@ protected void createNormalizationImageSemiNonCirculant(Interval fastFFTInterval
 
 		final Img<O> tempImg = create.apply(fd, type);
 
-		RichardsonLucyC.dump(normalization, "normalization-preCorrelate");
-
 		// 3. correlate psf with the output of step 2.
 		correlater.compute(normalization, null, fftInput, fftKernel, true, false, es, tempImg);
 
 		normalization = tempImg;
 
-		RichardsonLucyC.dump(normalization, "normalization-postCorrelate");
-
 		final Cursor<O> cursorN = normalization.cursor();
 
 		while (cursorN.hasNext()) {
@@ -235,7 +231,5 @@ protected void createNormalizationImageSemiNonCirculant(Interval fastFFTInterval
 
 			}
 		}
-
-		RichardsonLucyC.dump(normalization, "normalization-final");
 	}
 }
diff --git a/src/main/java/net/imagej/ops/deconvolve/RichardsonLucyC.java b/src/main/java/net/imagej/ops/deconvolve/RichardsonLucyC.java
@@ -29,7 +29,6 @@
 
 package net.imagej.ops.deconvolve;
 
-import java.util.Arrays;
 import java.util.List;
 import java.util.concurrent.ExecutorService;
 import java.util.function.BiFunction;
@@ -160,69 +159,50 @@ public void compute(RandomAccessibleInterval<I> in, RandomAccessibleInterval<K>
 		// setFFTKernel(getCreateOp().calculate(in));
 		// }
 
-		dump(Views.flatIterable(in), "initial");
-
 		// if a starting point for the estimate was not passed in then create
 		// estimate Img and use the input as the starting point
 		if (raiExtendedEstimate == null) {
 
 			raiExtendedEstimate = createOp.apply(in, Util.getTypeFromInterval(out));
 
 			copyOp.compute(in, raiExtendedEstimate);
-
-			dump(Views.flatIterable(raiExtendedEstimate), "postCopy");
 		}
-		dump(Views.flatIterable(raiExtendedEstimate), "initialEE");
 
 		// create image for the reblurred
 		RandomAccessibleInterval<O> raiExtendedReblurred = createOp.apply(in, Util.getTypeFromInterval(out));
 
 		// perform fft of psf
 		fftKernelOp.compute(kernel, es, fftKernel);
 
-		dump(Views.flatIterable(fftKernel), "fftKernel");
-
 		// -- perform iterations --
 
 		for (int i = 0; i < maxIterations; i++) {
 
-			dump(Views.flatIterable(raiExtendedEstimate), i + "-preConvolve");
-
 			// create reblurred by convolving kernel with estimate
 			// NOTE: the FFT of the PSF of the kernel has been passed in as a
 			// parameter. when the op was set up, and computed above, so we can use
 			// compute
 			convolverOp.compute(raiExtendedEstimate, null, fftInput, fftKernel, true, false, es,
 				raiExtendedReblurred);
 
-			dump(Views.flatIterable(raiExtendedReblurred), i + "-preCorrection");
-
 			// compute correction factor
 			rlCorrectionOp.compute(in, raiExtendedReblurred, fftInput, fftKernel, es, raiExtendedReblurred);
 
-			dump(Views.flatIterable(raiExtendedReblurred), i + "-preUpdate");
-
 			// perform update to calculate new estimate
 			updateOp.compute(raiExtendedReblurred, raiExtendedEstimate);
 
-			dump(Views.flatIterable(raiExtendedEstimate), i + "-postUpdate");
-
 			// apply post processing
 			if (iterativePostProcessingOps != null) {
 				for (Inplace<RandomAccessibleInterval<O>> pp : iterativePostProcessingOps) {
 					pp.mutate(raiExtendedEstimate);
 				}
-				dump(Views.flatIterable(raiExtendedEstimate), i + "-postPostProc");
 			}
 
 			// accelerate the algorithm by taking a larger step
 			// TODO: do we need the nullcheck?
 			if (accelerator != null) {
 				accelerator.mutate(raiExtendedEstimate);
-				dump(Views.flatIterable(raiExtendedEstimate), i + "-postAccel");
 			}
-
-			dump(Views.flatIterable(raiExtendedEstimate), i + "-final");
 		}
 
 		// -- copy crop padded back to original size
@@ -237,24 +217,4 @@ public void compute(RandomAccessibleInterval<I> in, RandomAccessibleInterval<K>
 
 		copy2Op.compute(Views.interval(raiExtendedEstimate, new FinalInterval(start, end)), out);
 	}
-
-	public static void dump(Iterable<?> image, String fileName) {
-		java.io.ByteArrayOutputStream baos = new java.io.ByteArrayOutputStream();
-		java.io.PrintWriter pout = new java.io.PrintWriter(baos);
-		int count = 0;
-		for (Object item : image) {
-			count++;
-			pout.println(count + ": " + item);
-		}
-		pout.println("--END--");
-		pout.flush();
-		byte[] sjBytes = baos.toByteArray();
-		try {
-			org.scijava.util.FileUtils.writeFile(new java.io.File("/Users/curtis/sj-" + fileName + ".txt"), sjBytes);
-			final byte[] ijBytes = org.scijava.util.FileUtils.readFile(new java.io.File("/Users/curtis/ij-" + fileName + ".txt"));
-			final boolean same = Arrays.equals(sjBytes, ijBytes);
-			System.out.println(fileName + " WRITTEN" + (same ? "" : " --> DIVERGED"));
-		}
-		catch (java.io.IOException exc) { exc.printStackTrace(); }
-	}
 }

Original file line number	Diff line number	Diff line change
`@@ -87,8 +87,6 @@ public RandomAccessibleInterval<O> apply(RandomAccessibleInterval<I> in, final O`
`87`	`87`
`88`	`88`	`final Img<O> firstGuess = create.apply(in, outType);`
`89`	`89`
`90`		`- RichardsonLucyC.dump(firstGuess, "firstGuess-initial");`
`91`		`-`
`92`	`90`	`// set first guess to be a constant = to the average value`
`93`	`91`
`94`	`92`	`// so first compute the sum...`
`@@ -110,7 +108,6 @@ public RandomAccessibleInterval<O> apply(RandomAccessibleInterval<I> in, final O`
`110`	`108`	`type.setReal(average);`
`111`	`109`	`}`
`112`	`110`
`113`		`- RichardsonLucyC.dump(firstGuess, "firstGuess-result");`
`114`	`111`	`return firstGuess;`
`115`	`112`	`}`
`116`	`113`	`}`
Original file line number	Diff line number	Diff line change
`@@ -216,15 +216,11 @@ protected void createNormalizationImageSemiNonCirculant(Interval fastFFTInterval`
`216`	`216`
`217`	`217`	`final Img<O> tempImg = create.apply(fd, type);`
`218`	`218`
`219`		`- RichardsonLucyC.dump(normalization, "normalization-preCorrelate");`
`220`		`-`
`221`	`219`	`// 3. correlate psf with the output of step 2.`
`222`	`220`	`correlater.compute(normalization, null, fftInput, fftKernel, true, false, es, tempImg);`
`223`	`221`
`224`	`222`	`normalization = tempImg;`
`225`	`223`
`226`		`- RichardsonLucyC.dump(normalization, "normalization-postCorrelate");`
`227`		`-`
`228`	`224`	`final Cursor<O> cursorN = normalization.cursor();`
`229`	`225`
`230`	`226`	`while (cursorN.hasNext()) {`
`@@ -235,7 +231,5 @@ protected void createNormalizationImageSemiNonCirculant(Interval fastFFTInterval`
`235`	`231`
`236`	`232`	`}`
`237`	`233`	`}`
`238`		`-`
`239`		`- RichardsonLucyC.dump(normalization, "normalization-final");`
`240`	`234`	`}`
`241`	`235`	`}`