public void testSkeletonize2() {
ImagePlus t = IJ.openImage(WORM1);
SkeletonizeWrapper sw = new SkeletonizeWrapper();
sw.skeletonize(t);
IJ.save(sw.getLspImage(), WORM1OUT);
IJ.save(sw.getSkeletonImage(), SKELOUT2);
}
@Test
public final void testDilationHilbertCurveC26() {
String fileName = getClass().getResource("/files/hilbert3d.tif").getFile();
ImagePlus imagePlus = IJ.openImage(fileName);
assertNotNull(imagePlus);
assertTrue(imagePlus.getStackSize() > 0);
ImageStack mask = imagePlus.getStack();
int width = mask.getWidth();
int height = mask.getHeight();
int depth = mask.getSize();
int bitDepth = mask.getBitDepth();
ImageStack marker = ImageStack.create(width, height, depth, bitDepth);
marker.setVoxel(3, 0, 0, 255);
GeodesicReconstruction3DHybrid0Gray8 algo = new GeodesicReconstruction3DHybrid0Gray8();
algo.setConnectivity(26);
algo.verbose = false;
ImageStack result = algo.applyTo(marker, mask);
for (int z = 0; z < depth; z++) {
for (int y = 0; y < height; y++) {
for (int x = 0; x < width; x++) {
assertEquals(result.getVoxel(x, y, z), mask.getVoxel(x, y, z), .01);
}
}
}
}
@Test
public final void testDilationCochleaVolumeC6() {
String fileName = getClass().getResource("/files/bat-cochlea-volume.tif").getFile();
ImagePlus imagePlus = IJ.openImage(fileName);
assertNotNull(imagePlus);
assertTrue(imagePlus.getStackSize() > 0);
ImageStack mask = imagePlus.getStack();
// Ensure regularity of the mask
mask = Morphology.opening(mask, CubeStrel.fromRadius(1));
int width = mask.getWidth();
int height = mask.getHeight();
int depth = mask.getSize();
int bitDepth = mask.getBitDepth();
ImageStack marker = ImageStack.create(width, height, depth, bitDepth);
marker.setVoxel(20, 80, 50, 255);
GeodesicReconstruction3DHybrid0Gray8 algo = new GeodesicReconstruction3DHybrid0Gray8();
algo.setConnectivity(6);
algo.verbose = false;
ImageStack result = algo.applyTo(marker, mask);
for (int z = 0; z < depth; z++) {
for (int y = 0; y < height; y++) {
for (int x = 0; x < width; x++) {
assertEquals(result.getVoxel(x, y, z), mask.getVoxel(x, y, z), .01);
}
}
}
}
@Test
public final void testApplyTo() {
GeodesicReconstructionByDilation3DGray8 algo = new GeodesicReconstructionByDilation3DGray8();
String fileName = getClass().getResource("/files/bat-cochlea-volume.tif").getFile();
ImagePlus imagePlus = IJ.openImage(fileName);
assertNotNull(imagePlus);
assertTrue(imagePlus.getStackSize() > 0);
ImageStack mask = imagePlus.getStack();
int width = mask.getWidth();
int height = mask.getHeight();
int depth = mask.getSize();
int bitDepth = mask.getBitDepth();
ImageStack marker = ImageStack.create(width, height, depth, bitDepth);
marker.setVoxel(20, 80, 50, 255);
ImageStack result = algo.applyTo(marker, mask);
for (int z = 0; z < depth; z++) {
for (int y = 0; y < height; y++) {
for (int x = 0; x < width; x++) {
assertEquals(result.getVoxel(x, y, z), mask.getVoxel(x, y, z), .01);
}
}
}
}
/** Test of skeletonize method, of class SkeletonizeWrapper. */
public void testSkeletonize() {
System.out.println("skeletonize");
ImagePlus threshold = IJ.openImage(THRESHOLD);
threshold.getProcessor().invert();
ArrayList<Roi> rois = null;
SkeletonizeWrapper instance = new SkeletonizeWrapper();
instance.skeletonize(threshold);
IJ.save(threshold, SKELOUT);
// TODO review the generated test code and remove the default call to fail.
// fail("The test case is a prototype.");
}
private ImagePlus openCachedImage(String url) {
if (url == null || !url.contains("ij/images")) return null;
String ijDir = IJ.getDirectory("imagej");
if (ijDir == null) return null;
int slash = url.lastIndexOf('/');
File file = new File(ijDir + "samples", url.substring(slash + 1));
if (!file.exists()) return null;
if (url.endsWith(".gif")) // ij.plugin.GIF_Reader does not correctly handle inverting LUTs
return openJpegOrGif(file.getParent() + File.separator, file.getName());
return IJ.openImage(file.getPath());
}
public static void main(final String... args) throws FileNotFoundException {
AAP_wStimulus aap = new AAP_wStimulus();
String path;
try {
path = "D:\\# Projects (Noam)\\# SLITE\\# DATA\\AAP 1.1.0\\"; // LAB
ImagePlus imp_test = IJ.openImage(path + "TEXT_20msON_10Hz_SLITE_2.tif");
if (imp_test == null) {
throw new FileNotFoundException("Your not in Lab....");
}
} catch (FileNotFoundException error) {
path =
"C:\\Users\\noambox\\Dropbox\\# Graduate studies M.Sc\\# SLITE\\ij - plugin data\\"; // HOME
}
aap.imp_r = IJ.openImage(path + "TEXT_20msON_10Hz_SLITE_2.tif"); // DEBUG
aap.imp_s = AVI_Reader.open(path + "OLEDstim_ON0.02_OFF9.98_FlashingText 21.avi", true);
aap.imp_r.show();
aap.imp_s.show();
String argv = "";
aap.run(argv);
}
public DataImporter(final String resultsFilePath, final boolean readWeights) {
super();
final ImageStack file = IJ.openImage(resultsFilePath).getImageStack();
slices = file.getSize();
for (int i = 1; i <= file.getSize(); i++) {
for (int y = 0; y < file.getHeight(); y++) {
final float[] point = new float[14];
for (int x = 0; x < file.getWidth(); x++) {
point[x] = file.getProcessor(i).getf(x, y);
}
this.add(point);
}
}
}
/**
* Main method for debugging.
*
* <p>For debugging, it is convenient to have a method that starts ImageJ, loads an image and
* calls the plugin, e.g. after setting breakpoints.
*
* @param args unused
*/
public static void main(String[] args) {
// set the plugins.dir property to make the plugin appear in the Plugins menu
Class<?> clazz = Panorama_View.class;
String url = clazz.getResource("/" + clazz.getName().replace('.', '/') + ".class").toString();
String pluginsDir = url.substring(5, url.length() - clazz.getName().length() - 6);
System.setProperty("plugins.dir", pluginsDir);
// start ImageJ
new ImageJ();
// open the Clown sample
ImagePlus image =
IJ.openImage(
"http://fly.mpi-cbg.de/~saalfeld/Projects/download/panorama/theaterplatz_3400.jpg");
image.show();
// run the plugin
IJ.runPlugIn(clazz.getName(), "");
}
public int[] extractBytes(String ImageName) {
// open image
int n = 0;
int chardata[] = new int[35];
ImagePlus I3 = IJ.openImage(ImageName);
ImageProcessor ip1 = I3.getProcessor();
for (int j = 0; j < 7; j++) {
for (int k = 0; k < 5; k++) {
int temp = ip1.getPixel(k, j);
if (temp == 255) {
chardata[n] = 1;
} else {
chardata[n] = 0;
}
// System.out.println("getpixel = "+temp);
n++;
}
}
return chardata;
}
@Test
public final void testErosionCochleaVolumeC26() {
String fileName = getClass().getResource("/files/bat-cochlea-volume.tif").getFile();
ImagePlus imagePlus = IJ.openImage(fileName);
assertNotNull(imagePlus);
assertTrue(imagePlus.getStackSize() > 0);
ImageStack mask = imagePlus.getStack();
// Ensure regularity of the mask
mask = Morphology.opening(mask, CubeStrel.fromRadius(1));
invertGray8Stack(mask);
int width = mask.getWidth();
int height = mask.getHeight();
int depth = mask.getSize();
int bitDepth = mask.getBitDepth();
ImageStack marker = ImageStack.create(width, height, depth, bitDepth);
marker.setVoxel(20, 80, 50, 255);
invertGray8Stack(marker);
GeodesicReconstruction3DHybrid0Gray8 algo =
new GeodesicReconstruction3DHybrid0Gray8(GeodesicReconstructionType.BY_EROSION);
algo.setConnectivity(26);
ImageStack result = algo.applyTo(marker, mask);
for (int z = 0; z < depth; z++) {
for (int y = 0; y < height; y++) {
for (int x = 0; x < width; x++) {
if (Math.abs(result.getVoxel(x, y, z) - mask.getVoxel(x, y, z)) > .1) {
System.out.println("x=" + x + " y=" + y + " z=" + z);
System.out.println(" mask = " + (int) mask.getVoxel(x, y, z));
System.out.println(" res = " + (int) result.getVoxel(x, y, z));
assertTrue(false);
}
}
}
}
}
@Test
public final void testRegionalMaxima_BatCochlea() {
String fileName = getClass().getResource("/files/bat-cochlea-volume.tif").getFile();
ImagePlus imagePlus = IJ.openImage(fileName);
assertNotNull(imagePlus);
assertTrue(imagePlus.getStackSize() > 0);
// load the reference image, and get its size
ImageStack image = imagePlus.getStack();
int sizeX = image.getWidth();
int sizeY = image.getHeight();
int sizeZ = image.getSize();
// create test image:
// use cochlea volume, but add a band with value 127 in the middle
int zMid = sizeZ / 2;
for (int y = 0; y < sizeY; y++) {
for (int x = 0; x < sizeX; x++) {
double val = image.getVoxel(x, y, zMid);
if (val == 255) image.setVoxel(x, y, zMid, 127);
}
}
ImageStack maxima = MinimaAndMaxima3D.regionalMaxima(image);
for (int z = 0; z < sizeZ; z++) {
for (int y = 0; y < sizeY; y++) {
for (int x = 0; x < sizeX; x++) {
int v0 = (int) image.getVoxel(x, y, z);
int v = (int) maxima.getVoxel(x, y, z);
if (v0 == 255) assertEquals(255, v);
else assertEquals(0, v);
}
}
}
}
public void set(String name) {
Im = IJ.openImage(name);
run("");
}
/**
* This main method is used for testing. It starts ImageJ, loads a test image and starts the
* plugin.
*
* <p>User interaction is necessary, as the plugin uses a GUI.
*
* <p><a href=
* "https://github.com/imagej/minimal-ij1-plugin/blob/master/src/main/java/Process_Pixels.java"
* >see minimal-ij1-plugin on GitHub</a>
*
* @param args
*/
public static void main(final String[] args) {
EFTEMj_Debug.setDebugLevel(EFTEMj_Debug.DEBUG_FULL);
/*
* start ImageJ
*/
new ImageJ();
String baseFolder = "C:/Temp/";
final String os = System.getProperty("os.name").toLowerCase();
if (os.indexOf("nix") >= 0 || os.indexOf("nux") >= 0 || os.indexOf("aix") > 0) {
final String userHome = System.getProperty("user.home");
baseFolder = userHome + "/Downloads/";
}
/*
* Check if the test image is available. Otherwise prompt a message with
* the download link.
*/
final File testImage =
new File(baseFolder + "20140106 SM125 -20%/20140106_SR-EELS_TestImage_small.tif");
if (!testImage.exists()) {
final String url = "http://eftemj.entrup.com.de/SR-EELS_TestImage.zip";
/*
* IJ.showMessage("Test image not found", "<html>" +
* "Please download the file" + "<br />" + "<a href='" + url +
* "'>SR-EELS_TestImage.zip</a> from" + "<br/>" + url + "<br />" +
* "and extract it to 'C:\\temp\\'." + "</html>");
*/
final GenericDialog gd = new GenericDialog("Test image not found");
gd.addMessage(
"Please download the file 'SR-EELS_TestImage.zip' and extract it to '"
+ baseFolder
+ "'.");
gd.addMessage("Copy the following link, or click Ok to open it with your default browser.");
gd.addStringField("", url, url.length());
gd.showDialog();
if (gd.wasOKed()) {
try {
final URI link = new URI(url);
final Desktop desktop = Desktop.getDesktop();
desktop.browse(link);
} catch (final Exception exc) {
IJ.showMessage("An Exception occured", exc.getMessage());
return;
}
}
return;
}
/*
* open the test image
*/
final ImagePlus image =
IJ.openImage(baseFolder + "20140106 SM125 -20%/20140106_SR-EELS_TestImage_small.tif");
image.show();
/*
* run the plugin
*/
final Class<?> clazz = SR_EELS_CorrectionPlugin.class;
IJ.runPlugIn(clazz.getName(), "");
}