Got 4 images converted, corrected, and converted back with JCUDA! (72b6bdce) · Commits · Elphel / imagej-elphel

src/main/java/Eyesis_Correction.java

+56 −1

Original line number	Diff line number	Diff line
		@@ -640,6 +640,7 @@ private Panel panel1,
		panelClt_GPU.setLayout(new GridLayout(1, 0, 5, 5)); // rows, columns, vgap, hgap
		addButton("JCUDA TEST", panelClt_GPU);
		addButton("TF TEST", panelClt_GPU);
		addButton("GPU files", panelClt_GPU, color_conf_process);
		addButton("Rig8 gpu", panelClt_GPU, color_conf_process);
		addButton("ShowGPU", panelClt_GPU, color_conf_process);
		add(panelClt_GPU);
		@@ -4579,12 +4580,19 @@ private Panel panel1,
		EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
		getPairImages2();
		return;
		/* ======================================================================== */
		} else if (label.equals("GPU files")) {
		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
		EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
		generateGPUDebugFiles();
		return;
		/* ======================================================================== */
		} else if (label.equals("Rig8 gpu")) {
		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
		EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
		getPairImages2Gpu();
		return;

		/* ======================================================================== */
		} else if (label.equals("ShowGPU")) {
		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
		@@ -5143,6 +5151,52 @@ private Panel panel1,
		return true;
		}

		public boolean generateGPUDebugFiles() {
		if (!prepareRigImages()) return false;
		String configPath=getSaveCongigPath();
		if (configPath.equals("ABORT")) return false;

		if (DEBUG_LEVEL > -2){
		System.out.println("++++++++++++++ Calculating combined correlations ++++++++++++++");
		}
		// reset if ran after 3d model to save memory
		if (QUAD_CLT.tp != null) {
		QUAD_CLT.tp.clt_3d_passes = null; // resetCLTPasses();
		}
		if (QUAD_CLT_AUX.tp != null) {
		QUAD_CLT_AUX.tp.clt_3d_passes = null; // resetCLTPasses();
		}

		try {
		TWO_QUAD_CLT.prepareFilesForGPUDebug(
		QUAD_CLT, // QuadCLT quadCLT_main,
		QUAD_CLT_AUX, // QuadCLT quadCLT_aux,
		CLT_PARAMETERS, // EyesisCorrectionParameters.DCTParameters dct_parameters,
		DEBAYER_PARAMETERS, //EyesisCorrectionParameters.DebayerParameters debayerParameters,
		COLOR_PROC_PARAMETERS, //EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
		// CHANNEL_GAINS_PARAMETERS, //CorrectionColorProc.ColorGainsParameters channelGainParameters,
		// CHANNEL_GAINS_PARAMETERS_AUX, //CorrectionColorProc.ColorGainsParameters channelGainParameters_aux,
		RGB_PARAMETERS, //EyesisCorrectionParameters.RGBParameters rgbParameters,
		THREADS_MAX, //final int threadsMax, // maximal number of threads to launch
		UPDATE_STATUS, //final boolean updateStatus,
		DEBUG_LEVEL);
		} catch (Exception e) {
		// TODO Auto-generated catch block
		e.printStackTrace();
		} //final int debugLevel);
		QUAD_CLT.tp.clt_3d_passes = null; // resetCLTPasses(); // so running "Ground truth" after would be OK
		QUAD_CLT_AUX.tp.clt_3d_passes = null; //.resetCLTPasses();

		if (configPath!=null) {
		saveTimestampedProperties( // save config again
		configPath, // full path or null
		null, // use as default directory if path==null
		true,
		PROPERTIES);
		}
		return true;
		}

		public boolean getPairImages2Gpu() {
		if (!prepareRigImages()) return false;
		String configPath=getSaveCongigPath();
		@@ -5165,6 +5219,7 @@ private Panel panel1,
		System.out.println("Failed to initialize GPU class");
		// TODO Auto-generated catch block
		e.printStackTrace();
		return false;
		} //final int debugLevel);

		}
		@@ -5186,6 +5241,7 @@ private Panel panel1,
		} catch (Exception e) {
		// TODO Auto-generated catch block
		e.printStackTrace();
		return false;
		} //final int debugLevel);
		QUAD_CLT.tp.clt_3d_passes = null; // resetCLTPasses(); // so running "Ground truth" after would be OK
		QUAD_CLT_AUX.tp.clt_3d_passes = null; //.resetCLTPasses();
		@@ -5203,7 +5259,6 @@ private Panel panel1,




		public boolean rigPlanes() {
		if ((QUAD_CLT == null) \|\| (QUAD_CLT.tp == null) \|\| (QUAD_CLT.tp.clt_3d_passes == null) \|\| (QUAD_CLT.tp.clt_3d_passes.size() == 0)) {
		String msg = "DSI data is not available. Please run \"CLT 3D\" first";

src/main/java/GPUTileProcessor.java

+829 −43

File changed.

Preview size limit exceeded, changes collapsed.

src/main/java/QuadCLT.java

+102 −9

Original line number	Diff line number	Diff line
		@@ -4489,6 +4489,56 @@ public class QuadCLT {
		return rslt;
		}

		// float
		public ImagePlus linearStackToColor(
		EyesisCorrectionParameters.CLTParameters clt_parameters,
		EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
		EyesisCorrectionParameters.RGBParameters rgbParameters,
		String name,
		String suffix, // such as disparity=...
		boolean toRGB,
		boolean bpp16, // 16-bit per channel color mode for result
		boolean saveShowIntermediate, // save/show if set globally
		boolean saveShowFinal, // save/show result (color image?)
		float [][] iclt_data,
		int width, // int tilesX,
		int height, // int tilesY,
		double scaleExposure,
		int debugLevel
		)
		{
		showDoubleFloatArrays sdfa_instance = new showDoubleFloatArrays(); // just for debugging?
		// convert to ImageStack of 3 slices
		String [] sliceNames = {"red", "blue", "green"};
		float [] alpha = null; // (0..1.0)
		float [][] rgb_in = {iclt_data[0],iclt_data[1],iclt_data[2]};
		if (iclt_data.length > 3) alpha = iclt_data[3];
		ImageStack stack = sdfa_instance.makeStack(
		rgb_in, // iclt_data,
		width, // (tilesX + 0) * clt_parameters.transform_size,
		height, // (tilesY + 0) * clt_parameters.transform_size,
		sliceNames, // or use null to get chn-nn slice names
		true); // replace NaN with 0.0
		return linearStackToColor(
		clt_parameters, // EyesisCorrectionParameters.CLTParameters clt_parameters,
		colorProcParameters, // EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
		rgbParameters, // EyesisCorrectionParameters.RGBParameters rgbParameters,
		name, // String name,
		suffix, // String suffix, // such as disparity=...
		toRGB, // boolean toRGB,
		bpp16, // boolean bpp16, // 16-bit per channel color mode for result
		saveShowIntermediate, // boolean saveShowIntermediate, // save/show if set globally
		saveShowFinal, // boolean saveShowFinal, // save/show result (color image?)
		stack, // ImageStack stack,
		alpha, // float [] alpha_pixels,
		width, // int width, // int tilesX,
		height, // int height, // int tilesY,
		scaleExposure, // double scaleExposure,
		debugLevel); //int debugLevel


		}
		// double data
		public ImagePlus linearStackToColor(
		EyesisCorrectionParameters.CLTParameters clt_parameters,
		EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
		@@ -4511,19 +4561,64 @@ public class QuadCLT {
		String [] sliceNames = {"red", "blue", "green"};
		double [] alpha = null; // (0..1.0)
		double [][] rgb_in = {iclt_data[0],iclt_data[1],iclt_data[2]};
		if (iclt_data.length > 3) alpha = iclt_data[3];
		float [] alpha_pixels = null;
		if (iclt_data.length > 3) {
		alpha = iclt_data[3];
		if (alpha != null){
		alpha_pixels = new float [alpha.length];
		for (int i = 0; i <alpha.length; i++){
		alpha_pixels[i] = (float) alpha[i];
		}
		}
		}
		ImageStack stack = sdfa_instance.makeStack(
		rgb_in, // iclt_data,
		width, // (tilesX + 0) * clt_parameters.transform_size,
		height, // (tilesY + 0) * clt_parameters.transform_size,
		sliceNames, // or use null to get chn-nn slice names
		true); // replace NaN with 0.0

		return linearStackToColor(
		clt_parameters, // EyesisCorrectionParameters.CLTParameters clt_parameters,
		colorProcParameters, // EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
		rgbParameters, // EyesisCorrectionParameters.RGBParameters rgbParameters,
		name, // String name,
		suffix, // String suffix, // such as disparity=...
		toRGB, // boolean toRGB,
		bpp16, // boolean bpp16, // 16-bit per channel color mode for result
		saveShowIntermediate, // boolean saveShowIntermediate, // save/show if set globally
		saveShowFinal, // boolean saveShowFinal, // save/show result (color image?)
		stack, // ImageStack stack,
		alpha_pixels, // float [] alpha_pixels,
		width, // int width, // int tilesX,
		height, // int height, // int tilesY,
		scaleExposure, // double scaleExposure,
		debugLevel); //int debugLevel
		}


		public ImagePlus linearStackToColor(
		EyesisCorrectionParameters.CLTParameters clt_parameters,
		EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
		EyesisCorrectionParameters.RGBParameters rgbParameters,
		String name,
		String suffix, // such as disparity=...
		boolean toRGB,
		boolean bpp16, // 16-bit per channel color mode for result
		boolean saveShowIntermediate, // save/show if set globally
		boolean saveShowFinal, // save/show result (color image?)
		ImageStack stack,
		float [] alpha_pixels,
		int width, // int tilesX,
		int height, // int tilesY,
		double scaleExposure,
		int debugLevel
		)
		{
		// showDoubleFloatArrays sdfa_instance = new showDoubleFloatArrays(); // just for debugging?
		if (debugLevel > -1) { // 0){
		double [] chn_avg = {0.0,0.0,0.0};
		float [] pixels;
		// int width = stack.getWidth();
		// int height = stack.getHeight();

		for (int c = 0; c <3; c++){
		pixels = (float[]) stack.getPixels(c+1);
		for (int i = 0; i<pixels.length; i++){
		@@ -4610,11 +4705,7 @@ public class QuadCLT {
		titleFull=name+"-YPrPb"+suffix;
		if (debugLevel > 1) System.out.println("Using full stack, including YPbPr");
		}
		if (alpha != null){
		float [] alpha_pixels = new float [alpha.length];
		for (int i = 0; i <alpha.length; i++){
		alpha_pixels[i] = (float) alpha[i];
		}
		if (alpha_pixels != null){
		stack.addSlice("alpha",alpha_pixels);
		}

		@@ -4674,6 +4765,8 @@ public class QuadCLT {

		}



		public void apply_fine_corr(
		double [][][] corr,
		int debugLevel)

src/main/java/TwoQuadCLT.java

+290 −3

File changed.

Preview size limit exceeded, changes collapsed.

src/main/java/showDoubleFloatArrays.java

+24 −0

Original line number	Diff line number	Diff line
		@@ -213,6 +213,30 @@ import ij.process.ImageProcessor;
		return array_stack;
		}

		public ImageStack makeStack(float[][] pixels, int width, int height, String [] titles, boolean noNaN) {
		float [] fpixels;
		ImageStack array_stack=new ImageStack(width,height);
		for (int i=0;i<pixels.length;i++) if (pixels[i]!=null) {
		if (pixels[i].length!=(width*height)){
		System.out.println("showArrays(): pixels["+i+"].length="+pixels[i].length+" != width (+"+width+") * height("+height+")="+(width*height));
		return null;
		}
		if (noNaN){
		fpixels=new float[pixels[i].length];
		for (int j=0;j<fpixels.length;j++) fpixels[j]= Float.isNaN(pixels[i][j])? 0.0F: ((float)pixels[i][j]);
		} else {
		fpixels=pixels[i];
		}
		if (titles!=null){
		array_stack.addSlice(titles[i], fpixels);
		} else {
		array_stack.addSlice("chn-"+i, fpixels);
		}
		}
		return array_stack;
		}


		public ImagePlus [] makeArrays(double[][] pixels, int width, int height, String title) {
		int i,j;
		float [] fpixels;

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