/**
* Extract the plane at the different positions and concatenate the Dataset
*
* @param newValue
* @return
*/
private CallbackTask<Void, Void> createSampleImage(File newValue) {
return new CallbackTask<Void, Void>()
.run(
() -> {
try {
File fileTarget = workflowModel.getMapImages().get(newValue);
Dataset datasetTarget = (Dataset) iOService.open(fileTarget.getAbsolutePath());
ImageDisplay imageDisplayTarget = new SilentImageDisplay();
context.inject(imageDisplayTarget);
imageDisplayTarget.display(datasetTarget);
selectPosition(
imageDisplayTarget,
workflowModel.getPositionLeft(),
workflowModel.getPositionRight(),
imageDisplayPaneRight);
Dataset datasetSource = (Dataset) iOService.open(newValue.getAbsolutePath());
ImageDisplay imageDisplaySource = new SilentImageDisplay();
context.inject(imageDisplaySource);
imageDisplaySource.display(datasetSource);
selectPosition(
imageDisplaySource,
workflowModel.getPositionLeft(),
workflowModel.getPositionRight(),
imageDisplayPaneLeft);
} catch (IOException ex) {
Logger.getLogger(ProcessWorkflow.class.getName()).log(Level.SEVERE, null, ex);
}
})
.submit(loadingScreenService);
}
@Test
public void testReadmesExample() throws Exception {
// extract the example script
final File readme = new File("README.md");
final String contents = new String(FileUtils.readFile(readme), "UTF-8");
final String telltale = String.format("```python%n");
final int begin = contents.indexOf(telltale) + telltale.length();
assertTrue(begin > telltale.length());
assertTrue(contents.indexOf(telltale, begin) < 0);
final int end = contents.indexOf(String.format("```%n"), begin);
assertTrue(end > 0);
final String snippet = contents.substring(begin, end);
assertTrue(snippet.startsWith("# @ImageJ ij"));
final Context context = new Context();
final ScriptService script = context.getService(ScriptService.class);
// create mock ImageJ gateway
script.addAlias("ImageJ", Mock.class);
final ScriptModule module = script.run("op-example.py", snippet, true).get();
assertNotNull(module);
module.run();
final Mock ij = context.getService(Mock.class);
assertEquals(3, ij.images.size());
assertEquals(11.906, ij.getPixel("sinusoid", 50, 50), 1e-3);
assertEquals(100, ij.getPixel("gradient", 50, 50), 1e-3);
assertEquals(111.906, ij.getPixel("composite", 50, 50), 1e-3);
}
@Test
public void testRot13() throws Exception {
final Context context = new Context(ScriptService.class);
final ScriptService scriptService = context.getService(ScriptService.class);
final ScriptLanguage hello = scriptService.getLanguageByName("Hello");
assertNotNull(hello);
final ScriptLanguage rot13 = scriptService.getLanguageByName("Rot13");
assertEquals(hello, rot13);
assertEquals("Svool", rot13.getScriptEngine().eval("Hello"));
}
@Test
public void testScriptModuleValue() throws Exception {
final Context context = new Context(ScriptService.class);
final ScriptService scriptService = context.getService(ScriptService.class);
final ScriptModule module =
scriptService
.run("test.rot13", ScriptModule.class.getName(), false, (Map<String, Object>) null)
.get();
final ScriptModule scriptModule = Rot13Engine.latestModule;
assertEquals(module, scriptModule);
assertNotNull(scriptModule);
final ScriptInfo info = scriptModule.getInfo();
assertEquals(context, info.context());
}
public static void main(final String... args) throws Exception {
// make a SciJava application context
final Context context = new Context();
// create the script interpreter
final ScriptREPL scriptCLI = new ScriptREPL(context);
// start the REPL
scriptCLI.loop();
// clean up
context.dispose();
System.exit(0);
}
/** Populates the bindings with the context + services + gateways. */
private void populateBindings(final Bindings bindings) {
bindings.put("ctx", context);
for (final Service service : context.getServiceIndex().getAll()) {
final String name = serviceName(service);
bindings.put(name, service);
}
for (final Gateway gateway : gateways()) {
bindings.put(gateway.getShortName(), gateway);
}
}
@Override
public void setItem(WorkflowStep t) {
if (configPane == null) {
configPane = new ModuleConfigPane();
context.inject(configPane);
popover.setContentNode(configPane);
// popover.setAnchorLocation(PopupWindow.AnchorLocation.WINDOW_TOP_RIGHT);
popover.setArrowLocation(PopOver.ArrowLocation.RIGHT_TOP);
}
this.step = t;
configPane.configure(step);
titleLabel.setText(step.getModule().getInfo().getTitle());
}
public OpViewer(final Context context) {
super("Op Viewer");
context.inject(this);
// Load the frame size
loadPreferences();
// Top node of the JTree
final DefaultMutableTreeNode top = new DefaultMutableTreeNode("Available Ops");
createNodes(top);
final JTree tree = new JTree(top);
tree.getSelectionModel().setSelectionMode(TreeSelectionModel.SINGLE_TREE_SELECTION);
setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE);
// Make the JTree scrollable
final JScrollPane pane =
new JScrollPane(
tree,
ScrollPaneConstants.VERTICAL_SCROLLBAR_AS_NEEDED,
ScrollPaneConstants.HORIZONTAL_SCROLLBAR_AS_NEEDED);
setContentPane(pane);
try {
if (SwingUtilities.isEventDispatchThread()) {
pack();
} else {
SwingUtilities.invokeAndWait(
new Runnable() {
@Override
public void run() {
pack();
}
});
}
} catch (final Exception ie) {
/* ignore */
}
setLocationRelativeTo(null); // center on screen
requestFocus();
}
public static Dataset makeDataset(final Context context, final byte[][] data, final String name) {
final int w = data.length;
final int h = data[0].length;
final ArrayImg<ByteType, ByteArray> img =
new ArrayImgFactory<ByteType>().createByteInstance(new long[] {w, h}, 1);
final ByteType t = new ByteType(img);
img.setLinkedType(t);
final RandomAccess<ByteType> ra = img.randomAccess();
for (int i = 0; i < w; i++) {
ra.setPosition(i, 0);
for (int j = 0; j < h; j++) {
ra.setPosition(j, 1);
ra.get().set(data[i][j]);
}
}
final DatasetService datasetService = context.getService(DatasetService.class);
return datasetService.create(new ImgPlus<ByteType>(img, name, new AxisType[] {Axes.X, Axes.Y}));
}
public void dummySegmentation() {
List<Dataset> predictDataset = new ArrayList<>(imgDatasets.size());
INDArray predict = dummyClassification();
int currIdx = 0;
for (int ds = 0; ds < imgDatasets.size(); ds++) {
List<List<int[]>> profilesSet = testData.get(ds).getProfiles();
predictDataset.add(imagePlaneService.createEmptyPlaneDataset(imgDatasets.get(ds)));
Dataset currDataset = predictDataset.get(ds);
RandomAccess<RealType<?>> randomAccess = currDataset.randomAccess();
for (List<int[]> p : profilesSet) {
for (int i = 0; i < p.size(); i++) {
randomAccess.setPosition(p.get(i)[0], 0);
randomAccess.setPosition(p.get(i)[1], 1);
double value = predict.getRow(currIdx).getDouble(i);
if (value != 0) randomAccess.get().setReal(value);
}
}
Overlay[] overlays = BinaryToOverlay.transform(context, currDataset, true);
// List<Overlay> overlayList = Arrays.asList(BinaryToOverlay.transform(context,
// currDataset, true));
overlayStatService.setRandomColor(Arrays.asList(overlays));
ImageDisplay display = new DefaultImageDisplay();
context.inject(display);
display.display(currDataset);
for (Overlay o : overlays) {
display.display(o);
}
uis.show(display);
}
}
public ScriptREPL(final Context context, final OutputStream out) {
context.inject(this);
this.out = out instanceof PrintStream ? (PrintStream) out : new PrintStream(out);
}
@Override
public void setContext(final Context context) {
context.inject(this);
}