Examples with UnsignedByteType net.imglib2.type.numeric.integer.UnsignedByteType used on opensource projects

Example 6 with UnsignedByteType

use of net.imglib2.type.numeric.integer.UnsignedByteType in project vcell by virtualcell.

the class ProjectService method load.

public Task<Project, String> load(File root) {
    final Task<Project, String> task = new Task<Project, String>() {

        @Override
        protected Project doInBackground() throws Exception {
            Project project = new Project(root.getName());
            String rootPath = root.getAbsolutePath();
            File[] dataFiles = Paths.get(rootPath, "data").toFile().listFiles();
            File[] geometryFiles = Paths.get(rootPath, "geometry").toFile().listFiles();
            File[] modelDirectories = Paths.get(rootPath, "models").toFile().listFiles();
            File[] resultsFiles = Paths.get(rootPath, "results").toFile().listFiles();
            int numFiles = dataFiles.length + geometryFiles.length + modelDirectories.length + resultsFiles.length;
            int numLoaded = 0;
            if (dataFiles != null) {
                for (File dataFile : dataFiles) {
                    try {
                        setSubtask(dataFile.getName());
                        Dataset data = datasetIOService.open(dataFile.getAbsolutePath());
                        project.getData().add(data);
                        numLoaded++;
                        setProgress(numLoaded * 100 / numFiles);
                    } catch (IOException e) {
                        e.printStackTrace();
                    }
                }
            }
            if (geometryFiles != null) {
                for (File geometryFile : geometryFiles) {
                    try {
                        setSubtask(geometryFile.getName());
                        Dataset geometry = datasetIOService.open(geometryFile.getAbsolutePath());
                        // Geometry datasets are saved as 8-bit images so we must convert back to 1-bit
                        if (geometry.firstElement() instanceof UnsignedByteType) {
                            @SuppressWarnings("unchecked") Img<UnsignedByteType> img = (Img<UnsignedByteType>) geometry.getImgPlus().getImg();
                            Img<BitType> converted = opService.convert().bit(img);
                            ImgPlus<BitType> convertedImgPlus = new ImgPlus<>(converted, geometry.getName());
                            geometry.setImgPlus(convertedImgPlus);
                        }
                        project.getGeometry().add(geometry);
                        numLoaded++;
                        setProgress(numLoaded * 100 / numFiles);
                    } catch (IOException e) {
                        e.printStackTrace();
                    }
                }
            }
            if (modelDirectories != null) {
                for (File modelDirectory : modelDirectories) {
                    setSubtask(modelDirectory.getName());
                    SBMLDocument sbmlDocument = null;
                    BufferedImage image = null;
                    File[] modelFiles = modelDirectory.listFiles();
                    System.out.println(modelFiles.length);
                    // Invalid model directory
                    if (modelFiles.length > 2)
                        continue;
                    for (File modelFile : modelFiles) {
                        System.out.println(modelFile.getName());
                        if (FilenameUtils.getExtension(modelFile.getName()).equals("xml")) {
                            sbmlDocument = new SBMLReader().readSBML(modelFile);
                            System.out.println("Loaded sbml");
                        } else if (FilenameUtils.getExtension(modelFile.getName()).equals("png")) {
                            image = ImageIO.read(modelFile);
                            System.out.println("Loaded image");
                        }
                    }
                    if (sbmlDocument != null) {
                        VCellModel vCellModel = new VCellModel(modelDirectory.getName(), null, sbmlDocument);
                        vCellModel.setImage(image);
                        project.getModels().add(vCellModel);
                        System.out.println("Added model");
                    }
                    numLoaded++;
                    setProgress(numLoaded * 100 / numFiles);
                }
            }
            if (resultsFiles != null) {
                for (File resultsFile : resultsFiles) {
                    try {
                        setSubtask(resultsFile.getName());
                        Dataset results = datasetIOService.open(resultsFile.getAbsolutePath());
                        // Loading 1-dimensional tif images adds a dimension
                        // so must crop out empty dimensions
                        @SuppressWarnings("unchecked") ImgPlus<T> imgPlus = (ImgPlus<T>) results.getImgPlus();
                        int numDimensions = imgPlus.numDimensions();
                        long[] dimensions = new long[2 * imgPlus.numDimensions()];
                        for (int i = 0; i < numDimensions; i++) {
                            dimensions[i] = 0;
                            dimensions[i + numDimensions] = imgPlus.dimension(i) - 1;
                        }
                        FinalInterval interval = Intervals.createMinMax(dimensions);
                        ImgPlus<T> cropped = opService.transform().crop(imgPlus, interval, true);
                        results.setImgPlus(cropped);
                        project.getResults().add(results);
                        numLoaded++;
                        setProgress(numLoaded * 100 / numFiles);
                    } catch (IOException e) {
                        e.printStackTrace();
                    }
                }
            }
            currentProjectRoot = root;
            return project;
        }
    };
    return task;
}

Example 7 with UnsignedByteType

use of net.imglib2.type.numeric.integer.UnsignedByteType in project vcell by virtualcell.

the class TestJettyService method exerciseService.

public static void exerciseService() {
    try {
        // HttpClient httpClient = new HttpClient();
        // HostConfiguration hostConfiguration = new HostConfiguration();
        // hostConfiguration.setHost("localhost",8080);
        // HttpMethod method = new GetMethod("/list?type=biom");
        // int var = httpClient.executeMethod(hostConfiguration, method);
        // System.out.println("result="+var);
        // 
        // method = new GetMethod("/");
        // var = httpClient.executeMethod(hostConfiguration, method);
        // System.out.println("result="+var);
        // search for port that vcell is providing IJ related services on
        int lastVCellApiPort = VCellHelper.findVCellApiServerPort();
        // get rest api
        System.out.println(VCellHelper.getApiInfo() + "\n");
        URL[] testUrls = new URL[] { new URL("http://localhost:" + lastVCellApiPort + "/" + "getinfo" + "?" + "open=true" + "&" + "type" + "=" + "quick") // new URL("http://localhost:"+lastVCellApiPort+"/"+"getinfo"+"?"+"open=true"+"&"+"type"+"="+"bm"),
        // new URL("http://localhost:"+lastVCellApiPort+"/"+"getinfo"+"?"+"open=true"+"&"+"type"+"="+"mm"),
        // new URL("http://localhost:"+lastVCellApiPort+"/"+"getinfo"+"?"+"open=false"+"&"+"type"+"="+"quick"),
        // new URL("http://localhost:"+lastVCellApiPort+"/"+"getinfo"+"?"+"open=false"+"&"+"type"+"="+"bm"),
        // new URL("http://localhost:"+lastVCellApiPort+"/"+"getinfo"+"?"+"open=false"+"&"+"type"+"="+"mm")
        };
        for (int i = 0; i < testUrls.length; i++) {
            System.out.println("----------Test " + i + ": " + testUrls[i].toString());
            // System.out.println(VCellHelper.getRawContent(testUrls[i]));
            Document doc = VCellHelper.getDocument(testUrls[i]);
            printDocument(doc, System.out);
            Node simNode = doc.getElementsByTagName("simInfo").item(0);
            String cachekey = simNode.getAttributes().getNamedItem("cacheKey").getNodeValue();
            URL varInfoUrl = new URL("http://localhost:" + lastVCellApiPort + "/" + "getdata" + "?" + "cachekey" + "=" + cachekey);
            System.out.println("  --varInfo=" + varInfoUrl.toString());
            System.out.println(VCellHelper.getRawContent(varInfoUrl));
            doc = VCellHelper.getDocument(varInfoUrl);
            ArrayList<Double> times = new ArrayList<>();
            Node timeNode = doc.getElementsByTagName("times").item(0);
            StringTokenizer st = new StringTokenizer(timeNode.getTextContent(), ",");
            while (st.hasMoreTokens()) {
                StringTokenizer timepointT = new StringTokenizer(st.nextToken(), "='");
                timepointT.nextToken();
                times.add(Double.parseDouble(timepointT.nextToken()));
            }
            String varName = null;
            NodeList varNodes = doc.getElementsByTagName("ijVarInfo");
            for (int j = 0; j < varNodes.getLength(); j++) {
                if (varNodes.item(j).getAttributes().getNamedItem("variableType").getNodeValue().equals("Volume")) {
                    varName = varNodes.item(j).getAttributes().getNamedItem("name").getNodeValue();
                    break;
                }
            }
            URL dataUrl = new URL("http://localhost:" + lastVCellApiPort + "/" + "getdata" + "?" + "cachekey" + "=" + cachekey + "&" + "varname" + "=" + varName + "&" + "timepoint" + "=" + times.get(times.size() / 2) + "&" + "jobid=0");
            System.out.println("  --data=" + dataUrl.toString());
            doc = VCellHelper.getDocument(dataUrl);
            BasicStackDimensions basicStackDimensions = VCellHelper.getVCStackDims(doc);
            double[] data = VCellHelper.getData(doc);
            System.out.println(basicStackDimensions.getTotalSize());
            System.out.println(data.length);
        }
        if (true) {
            return;
        }
        int cachekey = 4;
        // get rest api
        System.out.println(VCellHelper.getApiInfo());
        // System.out.println(VCellHelper.getRawContent(new URL("http://localhost:"+lastVCellApiPort+"/"+"getinfo"+"?"+"open=true"+"&"+"type"+"="+"bm")));//generate cachekeys user can reference to get data
        // get variable names
        System.out.println(VCellHelper.getRawContent(new URL("http://localhost:" + lastVCellApiPort + "/" + "getdata" + "?" + /*+"open=true"+"&"*/
        "cachekey" + "=" + cachekey)));
        // get data
        Document doc = VCellHelper.getDocument(new URL("http://localhost:" + lastVCellApiPort + "/" + "getdata" + "?" + "cachekey" + "=" + cachekey + "&" + "varname" + "=" + "C_cyt" + "&" + "timepoint" + "=5.55394648006857" + "&" + "jobid=0"));
        BasicStackDimensions basicStackDimensions = VCellHelper.getVCStackDims(doc);
        double[] data = VCellHelper.getData(doc);
        System.out.println(basicStackDimensions.getTotalSize());
        System.out.println(data.length);
        long[] dims = new long[basicStackDimensions.numDimensions()];
        basicStackDimensions.dimensions(dims);
        ArrayImg<DoubleType, DoubleArray> img = ArrayImgs.doubles(data, dims);
        // ArrayImg<DoubleType, DoubleArray> img = (ArrayImg<DoubleType, DoubleArray>)new ArrayImgFactory< DoubleType >().create( basicStackDimensions, new DoubleType() );
        // ArrayCursor<DoubleType> cursor = img.cursor();
        // while(cursor.hasNext()) {
        // cursor.next().set
        // }
        // Img< UnsignedByteType > img = new ArrayImgFactory< UnsignedByteType >().create( new long[] { 400, 320 }, new UnsignedByteType() );
        ImageJFunctions.show(img);
        DialogUtils.showInfoDialog(JOptionPane.getRootFrame(), "blah");
    // JAXBContext jaxbContext = JAXBContext.newInstance(IJData.class);
    // Unmarshaller jaxbUnmarshaller = jaxbContext.createUnmarshaller();
    // IJData ijData = (IJData) jaxbUnmarshaller.unmarshal(new URL("http://localhost:8080/"+ApiEnum.getdata.name()+"?"/*+"open=true"+"&"*/+IJGetDataParams.cachekey.name()+"=0"));
    // System.out.println(ijData);
    // URLConnection con = url.openConnection();
    // InputStream in = con.getInputStream();
    // String encoding = con.getContentEncoding();
    // encoding = encoding == null ? "UTF-8" : encoding;
    // String body = IOUtils.toString(in, encoding);
    // System.out.println(body);
    } catch (Exception e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
}

Example 8 with UnsignedByteType

use of net.imglib2.type.numeric.integer.UnsignedByteType in project vcell by virtualcell.

the class SmallCR method openExample.

public static ExampleDatasets openExample(ImageJ ij, File exampleDataDir) throws Exception {
    final String[] exampleFiles = new String[] { "Experimental.zip", "Seg Geom_3d.zip", "PreBleach.zip", "Analysis ROI.zip" };
    // final String[] exampleFiles = new String[] {"testDiff_1_2.zip","Seg Geom_3d.zip","testPreBleach.zip","Analysis ROI.zip"};// for test
    // List<Display<?>> displays0 = ij.display().getDisplays();
    // for (Display<?> display : displays0) {
    // System.out.println("----------disp "+display.getName()+" "+display.getIdentifier());
    // }
    List<ImageDisplay> knownImageDisplays = ij.imageDisplay().getImageDisplays();
    // for (ImageDisplay imageDisplay : imageDisplays0) {
    // System.out.println("----------imgdisp "+imageDisplay.getName()+" "+imageDisplay.getIdentifier());
    // }
    // 2D
    ImgPlus<? extends RealType<?>> experimentalData = null;
    // 2D or 3D (if 3D will be z-project for analysis withg 2D experimental data)
    ImgPlus<UnsignedByteType> segmentedGeom = null;
    // 2D
    ImgPlus<? extends RealType<?>> preBleachImage = null;
    // 2D
    ImgPlus<UnsignedByteType> analysisROI = null;
    // Open example images if they are not already open
    for (int exampleFilesIndex = 0; exampleFilesIndex < exampleFiles.length; exampleFilesIndex++) {
        DefaultDataset exampleFileDataset = null;
        for (ImageDisplay imageDisplay : knownImageDisplays) {
            if (imageDisplay.getName().equals(exampleFiles[exampleFilesIndex])) {
                exampleFileDataset = (DefaultDataset) imageDisplay.getActiveView().getData();
                break;
            }
        }
        if (exampleFileDataset == null) {
            exampleFileDataset = (DefaultDataset) ij.io().open(new File(exampleDataDir, exampleFiles[exampleFilesIndex]).getAbsolutePath());
            // ij.ui().show(exampleFileDataset);
            showAndZoom(ij, exampleFiles[exampleFilesIndex], exampleFileDataset, 4);
        }
        // Print names of axes (x,y,z,time,channel,unknown,...)
        System.out.print(exampleFileDataset.getName() + ": ");
        for (int dimensionIndex = 0; dimensionIndex < exampleFileDataset.numDimensions(); dimensionIndex++) {
            System.out.print((exampleFileDataset.axis(dimensionIndex) != null ? exampleFileDataset.axis(dimensionIndex).type().toString() + " " : "null "));
        }
        System.out.println();
        // Assign variables (defaultDataset corresponds to open 'exampleFiles' element
        switch(exampleFilesIndex) {
            case 0:
                experimentalData = exampleFileDataset.getImgPlus();
                break;
            case 1:
                segmentedGeom = (ImgPlus<UnsignedByteType>) exampleFileDataset.getImgPlus();
                break;
            case 2:
                preBleachImage = exampleFileDataset.getImgPlus();
                break;
            case 3:
                analysisROI = (ImgPlus<UnsignedByteType>) exampleFileDataset.getImgPlus();
                break;
        }
    }
    return new ExampleDatasets(experimentalData, preBleachImage, segmentedGeom, analysisROI);
}

Example 9 with UnsignedByteType

use of net.imglib2.type.numeric.integer.UnsignedByteType in project vcell by virtualcell.

the class SmallCR method createGeometry.

public static IJGeom createGeometry(ImgPlus<UnsignedByteType> nonZProjectedSegmentedGeom, int xIndex, int yIndex, int assumedZIndex, int xsize, int ysize, int zsize, HashMap<Integer, String> segmentedGeomValuesMapSubvolumeName) throws Exception {
    // Create byte array that defines vcell subvolumes ids (handles)
    byte[] vcellSubvolumeHandles = new byte[(int) Intervals.numElements(nonZProjectedSegmentedGeom)];
    Cursor<UnsignedByteType> nonZProjectedSegmentedGeomCursor = nonZProjectedSegmentedGeom.localizingCursor();
    while (nonZProjectedSegmentedGeomCursor.hasNext()) {
        UnsignedByteType segmentedGeomValue = (UnsignedByteType) nonZProjectedSegmentedGeomCursor.next();
        int currentZ = (assumedZIndex == -1 ? 0 : nonZProjectedSegmentedGeomCursor.getIntPosition(assumedZIndex));
        int currXYPixelIndex = nonZProjectedSegmentedGeomCursor.getIntPosition(yIndex) * xsize + nonZProjectedSegmentedGeomCursor.getIntPosition(xIndex);
        int currXYZPixelIndex = currXYPixelIndex + (assumedZIndex == -1 ? 0 : currentZ * (xsize * ysize));
        vcellSubvolumeHandles[currXYZPixelIndex] = (byte) segmentedGeomValue.get();
    }
    // Define new Geometry with domain equal to xyz pixel size for ease of use
    String[] subvolumeNames = segmentedGeomValuesMapSubvolumeName.values().toArray(new String[0]);
    Integer[] subvolumePixelValues = segmentedGeomValuesMapSubvolumeName.keySet().toArray(new Integer[0]);
    double[] origin = new double[] { 0, 0, 0 };
    double[] extent = new double[] { xsize, ysize, zsize };
    IJGeom ijGeom = new IJGeom(subvolumeNames, subvolumePixelValues, xsize, ysize, zsize, origin, extent, vcellSubvolumeHandles);
    return ijGeom;
}

Example 10 with UnsignedByteType

use of net.imglib2.type.numeric.integer.UnsignedByteType in project imagej-ops by imagej.

the class TubenessTest method testTubeness.

@Test
public void testTubeness() {
    Img<UnsignedByteType> input = openUnsignedByteType(Ops.class, "TubesInput.png");
    Img<DoubleType> expected = openDoubleImg("tube.tif");
    final double scale = 5;
    final double sigma = scale / Math.sqrt(2);
    Img<DoubleType> actual = ops.create().img(input, new DoubleType());
    ops.filter().tubeness(actual, input, sigma);
    assertIterationsEqual(expected, actual);
}