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imagej-elphel
Commit 40db267c authored by Andrey Filippov's avatar Andrey Filippov
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making work with cuda-11.2.0 and eclipse-21-06

parent 0246d531
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Showing with 53 additions and 28951 deletions
pom.xml
View file @ 40db267c
...@@ -35,8 +35,9 @@ ...@@ -35,8 +35,9 @@
<dependency> <dependency>
<groupId>org.jcuda</groupId> <groupId>org.jcuda</groupId>
<artifactId>jcuda</artifactId> <artifactId>jcuda</artifactId>
<version>10.1.0</version> <version>11.2.0</version>
</dependency> </dependency>
<!-- <version>10.1.0</version> -->
<!-- <!--
As of 2018/09/11 TF for GPU on Maven supports CUDA 9.0 (vs latest 9.2) As of 2018/09/11 TF for GPU on Maven supports CUDA 9.0 (vs latest 9.2)
Workaround: Workaround:
...@@ -164,11 +165,29 @@ ...@@ -164,11 +165,29 @@
</testResources> </testResources>
<pluginManagement> <pluginManagement>
<plugins> <plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-plugin-plugin</artifactId>
<!-- https://stackoverflow.com/questions/35511860/how-do-i-get-my-eclipse-maven-project-to-automatically-update-its-classpath-when-->
<!-- -below version fixed "mvn clean install -U -X" -->
<version>3.5.1</version>
<!--
<goals>
<goal>descriptor</goal>
</goals> -->
<!-- Caused by: org.apache.maven.plugin.MojoExecutionException: Error extracting plugin descriptor: 'No mojo definitions were found for plugin: com.elphel:imagej-elphel.'
-->
<configuration><skipErrorNoDescriptorsFound>true</skipErrorNoDescriptorsFound></configuration>
</plugin>
<plugin> <plugin>
<groupId>org.eclipse.m2e</groupId> <groupId>org.eclipse.m2e</groupId>
<artifactId>lifecycle-mapping</artifactId> <artifactId>lifecycle-mapping</artifactId>
<version>1.0.0</version> <version>1.0.0</version>
<configuration> <configuration>
<!-- <skipErrorNoDescriptorsFound>true</skipErrorNoDescriptorsFound> -->
<lifecycleMappingMetadata> <lifecycleMappingMetadata>
<pluginExecutions> <pluginExecutions>
<pluginExecution> <pluginExecution>
...@@ -193,10 +212,19 @@ ...@@ -193,10 +212,19 @@
<artifactId> <artifactId>
maven-plugin-plugin maven-plugin-plugin
</artifactId> </artifactId>
<versionRange>[3.3,)</versionRange> <!-- <versionRange>[3.3,)</versionRange> -->
<version>3.4</version>
<!-- <configuration>
<skipErrorNoDescriptorsFound>true</skipErrorNoDescriptorsFound>
</configuration> -->
<goals> <goals>
<goal>descriptor</goal> <goal>descriptor</goal>
</goals> </goals>
<!-- <extractors>
<extractor/>
</extractors> -->
</pluginExecutionFilter> </pluginExecutionFilter>
<action> <action>
<ignore></ignore> <ignore></ignore>
...@@ -245,6 +273,15 @@ ...@@ -245,6 +273,15 @@
<!-- <item>foxel-MRHM7AP</item> --> <!-- <item>foxel-MRHM7AP</item> -->
</items> </items>
</configuration> </configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.1</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin> </plugin>
</plugins> </plugins>
</pluginManagement> </pluginManagement>
...@@ -281,8 +318,13 @@ ...@@ -281,8 +318,13 @@
<id>other</id> <id>other</id>
<url>http://mirror.elphel.com/maven-dependencies</url> <url>http://mirror.elphel.com/maven-dependencies</url>
</repository> </repository>
<!--
<repository>
<id>mvnrepository</id>
<url>https://mvnrepository.com/artifact</url>
</repository>
-->
</repositories> </repositories>
<scm> <scm>
<connection>scm:git:git://git.elphel.com/Elphel/imagej-elphel</connection> <connection>scm:git:git://git.elphel.com/Elphel/imagej-elphel</connection>
<developerConnection>scm:git:https://git.elphel.com/Elphel/imagej-elphel</developerConnection> <developerConnection>scm:git:https://git.elphel.com/Elphel/imagej-elphel</developerConnection>
......
src/main/java/com/elphel/imagej/correction/Eyesis_Correction.java
View file @ 40db267c
...@@ -84,7 +84,7 @@ import com.elphel.imagej.common.ShowDoubleFloatArrays; ...@@ -84,7 +84,7 @@ import com.elphel.imagej.common.ShowDoubleFloatArrays;
import com.elphel.imagej.common.WindowTools; import com.elphel.imagej.common.WindowTools;
import com.elphel.imagej.dct.FactorConvKernel; import com.elphel.imagej.dct.FactorConvKernel;
import com.elphel.imagej.gpu.GPUTileProcessor; import com.elphel.imagej.gpu.GPUTileProcessor;
import com.elphel.imagej.gpu.JCuda_ImageJ_Example_Plugin; //import com.elphel.imagej.gpu.JCuda_ImageJ_Example_Plugin;
import com.elphel.imagej.jp4.JP46_Reader_camera; import com.elphel.imagej.jp4.JP46_Reader_camera;
import com.elphel.imagej.lwir.LwirReader; import com.elphel.imagej.lwir.LwirReader;
import com.elphel.imagej.readers.EyesisTiff; import com.elphel.imagej.readers.EyesisTiff;
...@@ -5214,7 +5214,7 @@ private Panel panel1, ...@@ -5214,7 +5214,7 @@ private Panel panel1,
/* ======================================================================== */ /* ======================================================================== */
} else if (label.equals("JCUDA TEST")) { } else if (label.equals("JCUDA TEST")) {
/*
ImagePlus impl = WindowManager.getCurrentImage(); ImagePlus impl = WindowManager.getCurrentImage();
if (impl!=null) { if (impl!=null) {
...@@ -5222,17 +5222,15 @@ private Panel panel1, ...@@ -5222,17 +5222,15 @@ private Panel panel1,
JCuda_ImageJ_Example_Plugin jcuda = new JCuda_ImageJ_Example_Plugin(); JCuda_ImageJ_Example_Plugin jcuda = new JCuda_ImageJ_Example_Plugin();
/* // In a standalone test JCUDA plugin it's unknown where .setup() is called from...
* In a standalone test JCUDA plugin it's unknown where .setup() is called from... // As well as .run(). But it works like this.
* As well as .run(). But it works like this.
*/
jcuda.setup(null,impl); jcuda.setup(null,impl);
jcuda.run(impr); jcuda.run(impr);
}else { }else {
System.out.println("Missing the current image. Open one."); System.out.println("Missing the current image. Open one.");
} }
*/
return; return;
/* ======================================================================== */ /* ======================================================================== */
} else if (label.equals("TF TEST")) { } else if (label.equals("TF TEST")) {
...@@ -11609,7 +11607,7 @@ G= Y +Pr*(- 2*Kr*(1-Kr))/Kg + Pb*(-2*Kb*(1-Kb))/Kg ...@@ -11609,7 +11607,7 @@ G= Y +Pr*(- 2*Kr*(1-Kr))/Kg + Pb*(-2*Kb*(1-Kb))/Kg
stack.addSlice("Pr", fpixels_pr); stack.addSlice("Pr", fpixels_pr);
stack.addSlice("Pb", fpixels_pb); stack.addSlice("Pb", fpixels_pb);
stack.addSlice("Y", fpixels_y); stack.addSlice("Y", fpixels_y);
stack.addSlice("Y0", fpixels_y0); // not filtered by low-pass, preliminary (for comaprison only) stack.addSlice("Y0", fpixels_y0); // not filtered by low-pass, preliminary (for comparison only)
if (DEBUG_LEVEL>2) { if (DEBUG_LEVEL>2) {
stack.addSlice("Yr",fpixels_yR); stack.addSlice("Yr",fpixels_yR);
stack.addSlice("Yg",fpixels_yG); stack.addSlice("Yg",fpixels_yG);
......
src/main/java/com/elphel/imagej/gpu/JCuda_ImageJ_Example_Plugin.java deleted 100644 → 0
View file @ 0246d531
package com.elphel.imagej.gpu;
/**
* ImageJ Plugin using JCuda
*
* Copyright (c) 2013-2018 Marco Hutter - http://www.jcuda.org
*/
import static jcuda.driver.JCudaDriver.cuCtxCreate;
import static jcuda.driver.JCudaDriver.cuCtxSynchronize;
import static jcuda.driver.JCudaDriver.cuDeviceGet;
import static jcuda.driver.JCudaDriver.cuInit;
import static jcuda.driver.JCudaDriver.cuLaunchKernel;
import static jcuda.driver.JCudaDriver.cuMemAlloc;
import static jcuda.driver.JCudaDriver.cuMemFree;
import static jcuda.driver.JCudaDriver.cuMemcpyDtoH;
import static jcuda.driver.JCudaDriver.cuMemcpyHtoD;
import static jcuda.driver.JCudaDriver.cuModuleGetFunction;
import static jcuda.driver.JCudaDriver.cuModuleLoadData;
import static jcuda.nvrtc.JNvrtc.nvrtcCompileProgram;
import static jcuda.nvrtc.JNvrtc.nvrtcCreateProgram;
import static jcuda.nvrtc.JNvrtc.nvrtcDestroyProgram;
import static jcuda.nvrtc.JNvrtc.nvrtcGetPTX;
import static jcuda.nvrtc.JNvrtc.nvrtcGetProgramLog;
import java.io.IOException;
import java.io.InputStream;
import java.util.Scanner;
import ij.IJ;
import ij.ImagePlus;
import ij.plugin.filter.PlugInFilter;
import ij.process.ImageProcessor;
import jcuda.Pointer;
import jcuda.Sizeof;
import jcuda.driver.CUcontext;
import jcuda.driver.CUdevice;
import jcuda.driver.CUdeviceptr;
import jcuda.driver.CUfunction;
import jcuda.driver.CUmodule;
import jcuda.driver.JCudaDriver;
import jcuda.nvrtc.JNvrtc;
import jcuda.nvrtc.nvrtcProgram;
/**
* A simple example for an ImageJ Plugin that uses JCuda.
*/
public class JCuda_ImageJ_Example_Plugin implements PlugInFilter
{
/**
* The current image to operate on
*/
private ImagePlus currentImage = null;
/**
* The kernel function
*/
private CUfunction kernelFunction = null;
@Override
public void run(ImageProcessor imageProcessor)
{
int[] pixels = (int[])imageProcessor.getPixels();
int w = imageProcessor.getWidth();
int h = imageProcessor.getHeight();
execute(pixels, w, h);
currentImage.updateAndDraw();
}
/**
* Will execute the CUDA kernel with the given parameters
*
* @param pixels An array containing the pixels of the
* image as RGB integers
* @param w The width of the image
* @param h The height of the image
*/
void execute(int pixels[], int w, int h)
{
if (kernelFunction == null)
{
IJ.showMessage("Error", "The kernel was not initialized");
return;
}
// Allocate memory on the device, and copy the host data to the device
int size = w * h * Sizeof.INT;
CUdeviceptr pointer = new CUdeviceptr();
cuMemAlloc(pointer, size);
cuMemcpyHtoD(pointer, Pointer.to(pixels), size);
// Set up the kernel parameters: A pointer to an array
// of pointers which point to the actual values.
Pointer kernelParameters = Pointer.to(
Pointer.to(pointer),
Pointer.to(new int[] { w }),
Pointer.to(new int[] { h })
);
// Call the kernel function
int blockSize = 16;
int gridSize = (Math.max(w, h) + blockSize - 1) / blockSize;
cuLaunchKernel(kernelFunction,
gridSize, gridSize, 1, // Grid dimension
blockSize, blockSize, 1, // Block dimension
0, null, // Shared memory size and stream
kernelParameters, null // Kernel- and extra parameters
);
cuCtxSynchronize();
// Copy the data from the device back to the host and clean up
cuMemcpyDtoH(Pointer.to(pixels), pointer, size);
cuMemFree(pointer);
}
@Override
public int setup(String arg, ImagePlus imagePlus)
{
if (arg != null && arg.equals("about"))
{
IJ.showMessage(
"About JCuda ImageJ Plugin...",
"An example of an ImageJ plugin using JCuda\n");
return DOES_RGB;
}
currentImage = imagePlus;
// Enable exceptions and omit all subsequent error checks
JCudaDriver.setExceptionsEnabled(true);
JNvrtc.setExceptionsEnabled(true);
// Initialize the driver and create a context for the first device.
cuInit(0);
CUdevice device = new CUdevice();
cuDeviceGet(device, 0);
CUcontext context = new CUcontext();
cuCtxCreate(context, 0, device);
// Obtain the CUDA source code from the CUDA file
String cuFileName = "JCudaImageJExampleKernel.cu";
String sourceCode = readResourceAsString(cuFileName);
if (sourceCode == null)
{
IJ.showMessage("Error",
"Could not read the kernel source code");
return DOES_RGB;
}
// Create the kernel function
this.kernelFunction = createFunction(sourceCode, "invert");
return DOES_RGB;
}
/**
* Create the CUDA function object for the kernel function with the
* given name that is contained in the given source code
*
* @param sourceCode The source code
* @param kernelName The kernel function name
* @return
*/
private static CUfunction createFunction(
String sourceCode, String kernelName)
{
// Use the NVRTC to create a program by compiling the source code
nvrtcProgram program = new nvrtcProgram();
nvrtcCreateProgram(
program, sourceCode, null, 0, null, null);
nvrtcCompileProgram(program, 0, null);
// Obtain the compilation log, and print it if it is not empty
// (for the case there are any warnings)
String programLog[] = new String[1];
nvrtcGetProgramLog(program, programLog);
String log = programLog[0].trim();
if (!log.isEmpty())
{
System.err.println("Program compilation log:\n" + log);
}
// Obtain the PTX ("CUDA Assembler") code of the compiled program
String[] ptx = new String[1];
nvrtcGetPTX(program, ptx);
nvrtcDestroyProgram(program);
// Create a CUDA module from the PTX code
CUmodule module = new CUmodule();
cuModuleLoadData(module, ptx[0]);
// Obtain the function pointer to the kernel function from the module
CUfunction function = new CUfunction();
cuModuleGetFunction(function, module, kernelName);
return function;
}
/**
* Read the resource with the given name, and return its contents as
* a string. Returns <code>null</code> if the resource cannot be found
* or read.
*
* @param name The name of the resource
* @return The contents of the resource
*/
private static String readResourceAsString(String name)
{
InputStream inputStream =
JCuda_ImageJ_Example_Plugin.class.getResourceAsStream(name);
if (inputStream == null)
{
IJ.showMessage("Error",
"Resource was not found:\n" + name);
return null;
}
try
{
return readStreamAsString(inputStream);
}
catch (IOException e)
{
IJ.showMessage("Error",
"Could not read the resource:\n" + e.getMessage());
return null;
}
}
/**
* Read the contents of the given input stream, and return it as a string
*
* @param inputStream The input stream
* @return The string
* @throws IOException If the input cannot be read
*/
private static String readStreamAsString(
InputStream inputStream) throws IOException
{
try(Scanner s = new Scanner(inputStream))
{
Scanner scanner = s.useDelimiter("\\A");
if (scanner.hasNext())
{
return s.next();
}
throw new IOException("Could not read input stream");
}
}
}
\ No newline at end of file
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