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imagej-elphel
Commit 885f44ef authored by Oleg Dzhimiev's avatar Oleg Dzhimiev
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+new files

parent 2ea5f0f4
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Showing with 297 additions and 17 deletions
pom.xml
View file @ 885f44ef
......@@ -11,7 +11,7 @@
<version>3.1</version>
<relativePath/>
</parent>
<properties>
<imagej.app.directory>/home/foxel/Desktop/Fiji.app</imagej.app.directory>
</properties>
......@@ -19,7 +19,7 @@
<groupId>com.elphel</groupId>
<artifactId>imagej-elphel</artifactId>
<!-- <artifactId>Aberration_Calibration</artifactId> -->
<version>1.0.0-SNAPSHOT</version>
<name>plugins/imagej_elphel.jar</name>
......@@ -31,22 +31,27 @@
<dependency>
<groupId>net.imagej</groupId>
<artifactId>ij</artifactId>
<version>1.52d</version>
<version>1.52e</version>
<!-- <version>${imagej1.version}</version> -->
</dependency>
<dependency>
<groupId>org.jcuda</groupId>
<artifactId>jcuda</artifactId>
<version>0.9.2</version>
</dependency>
<dependency>
<groupId>commons-configuration</groupId>
<artifactId>commons-configuration</artifactId>
<version>1.7</version>
<version>1.8</version>
</dependency>
<!-- https://mvnrepository.com/artifact/gov.nist.math/jama -->
<dependency>
<groupId>gov.nist.math</groupId>
<artifactId>jama</artifactId>
<version>1.0.3</version>
</dependency>
<!--
<!-- https://mvnrepository.com/artifact/gov.nist.math/jama -->
<dependency>
<groupId>gov.nist.math</groupId>
<artifactId>jama</artifactId>
<version>1.0.3</version>
</dependency>
<!--
<dependency>
<groupId>jama</groupId>
<artifactId>jama</artifactId>
......@@ -126,7 +131,7 @@
</lifecycleMappingMetadata>
</configuration>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>exec-maven-plugin</artifactId>
......@@ -140,8 +145,8 @@
</execution>
</executions>
<configuration>
<!-- <mainClass>Aberration_Calibration</mainClass> -->
<mainClass>Eyesis_Correction</mainClass>
<!-- <mainClass>Aberration_Calibration</mainClass> -->
<mainClass>Eyesis_Correction</mainClass>
</configuration>
</plugin>
<plugin>
......@@ -168,7 +173,7 @@
</plugin>
</plugins>
</pluginManagement>
</build>
<developers>
......
src/main/java/Eyesis_Correction.java
View file @ 885f44ef
......@@ -4721,7 +4721,17 @@ private Panel panel1,
} else if (label.equals("DSI show")) {
showDSI();
return;
/* ======================================================================== */
} else if (label.equals("JCUDA TEST")) {
System.out.println("JCUDA TEST");
JCuda_ImageJ_Example_Plugin jcuda = new JCuda_ImageJ_Example_Plugin();
//jcuda.run();
return;
/* ======================================================================== */
} else if (label.equals("TF TEST")) {
System.out.println("TF TEST");
return;
//JTabbedTest
// End of buttons code
}
......
src/main/java/JCuda_ImageJ_Example_Plugin.java 0 → 100644
View file @ 885f44ef
/**
* 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
src/main/resources/JCudaImageJExampleKernel.cu 0 → 100644
View file @ 885f44ef
extern "C"
__global__ void invert(uchar4* data, int w, int h)
{
int x = threadIdx.x+blockIdx.x*blockDim.x;
int y = threadIdx.y+blockIdx.y*blockDim.y;
if (x < w && y < h)
{
int index = y*w+x;
uchar4 pixel = data[index];
pixel.x = 255 - pixel.x;
pixel.y = 255 - pixel.y;
pixel.z = 255 - pixel.z;
pixel.w = 255 - pixel.w;
data[index] = pixel;
}
}
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