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

Example 1 with UnsignedByteType

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

the class InvertTest method testUnsignedByteTypeInvert.

@Test
public void testUnsignedByteTypeInvert() {
    final Img<UnsignedByteType> inUnsignedByteType = generateUnsignedByteArrayTestImg(true, 5, 5);
    final Img<UnsignedByteType> outUnsignedByteType = inUnsignedByteType.factory().create(inUnsignedByteType, new UnsignedByteType());
    assertDefaultInvert(inUnsignedByteType, outUnsignedByteType);
    assertDefaultInvertMinMaxProvided(inUnsignedByteType, outUnsignedByteType, new UnsignedByteType((byte) 127), new UnsignedByteType((byte) 127));
    assertDefaultInvertMinMaxProvided(inUnsignedByteType, outUnsignedByteType, new UnsignedByteType((byte) -12), new UnsignedByteType((byte) -10));
}

Example 2 with UnsignedByteType

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

the class ImageMomentsTest method createImg.

@BeforeClass
public static void createImg() {
    Img<UnsignedByteType> tmp = ArrayImgs.unsignedBytes(new long[] { 100, 100 });
    Random rand = new Random(1234567890L);
    final Cursor<UnsignedByteType> cursor = tmp.cursor();
    while (cursor.hasNext()) {
        cursor.next().set(rand.nextInt((int) tmp.firstElement().getMaxValue()));
    }
    img = tmp;
}

Example 3 with UnsignedByteType

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

the class CopyArrayImgTest method createData.

@Before
public void createData() {
    input = new ArrayImgFactory<UnsignedByteType>().create(new int[] { 120, 100 }, new UnsignedByteType());
    final Random r = new Random(System.currentTimeMillis());
    final Cursor<UnsignedByteType> inc = input.cursor();
    while (inc.hasNext()) {
        inc.next().setReal(r.nextDouble() * 255);
    }
}

Example 4 with UnsignedByteType

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

the class SmallCR method calcMSE.

// public static IJSolverStatus runFrapSolver(VCellHelper vh,double diffusionRate,String cacheKey,VCellHelper.IJGeom overrideGeom) throws Exception{
// //Override Model/Simulation parameter values (user must have knowledge of chosen model to know what parameter names to override)
// HashMap<String,String> simulationParameterOverrides = new HashMap<>();
// simulationParameterOverrides.put("rf_diffusionRate", ""+diffusionRate);
// HashMap<String, String> speciesContextInitialConditionsOverrides = new HashMap<>();
// String laserArea = "((x >=  "+43+") && (x <= "+47+") && (y >=  "+22+") && (y <= "+26+"))";
// speciesContextInitialConditionsOverrides.put("Laser", laserArea);
// double newEndTime = 10.0;
// //Start Frap simulation
// IJSolverStatus ijSolverStatus = vh.startVCellSolver(Long.parseLong(cacheKey), overrideGeom, simulationParameterOverrides, speciesContextInitialConditionsOverrides,newEndTime);
// return ijSolverStatus;
// }
// public static String waitForSolverGetCacheForData(VCellHelper vh,IJSolverStatus ijSolverStatus) throws Exception{
// //Wait for solver to finish
// System.out.println(ijSolverStatus.toString());
// String simulationJobId = ijSolverStatus.simJobId;
// while(true) {
// Thread.sleep(5000);
// ijSolverStatus =  vh.getSolverStatus(simulationJobId);
// System.out.println(ijSolverStatus.toString());
// String statusName = ijSolverStatus.statusName.toLowerCase();
// if(statusName.equals("finished") || statusName.equals("stopped") || statusName.equals("aborted")) {
// break;
// }
// }
// return vh.getSimulationDataCacheKey(ijSolverStatus.simJobId);
// }
// public static SCIFIOImgPlus<DoubleType> zProjectNormalizeSimData(VCellHelper vh,
// String newImgPlusName,String simulationDataCachekey,String varToAnalyze,int preBleachTimeIndex,int solverStatus_jobIndex,int ANALYZE_BEGIN_TIMEINDEX,int ANALYZE_END_TIMEINDEX) throws Exception{
// 
// int ANALYZE_COUNT = ANALYZE_END_TIMEINDEX - ANALYZE_BEGIN_TIMEINDEX+1;
// // Get the SIMULATION pre-bleach timepoint data for normalizing
// VCellHelper.TimePointData timePointData = vh.getTimePointData(simulationDataCachekey, varToAnalyze, new int[] {preBleachTimeIndex}, solverStatus_jobIndex);
// int xysize = timePointData.getBasicStackDimensions().xsize*timePointData.getBasicStackDimensions().ysize;
// double[] bleachedTimeStack = new double[ANALYZE_COUNT*xysize];
// //	    checkSizes(timePointData.getBasicStackDimensions(), xsize, xysize, zsize);
// //    	URL dataUrl = new URL("http://localhost:"+vh.findVCellApiServerPort()+"/"+"getdata"+"?"+"cachekey"+"="+cachekey+"&"+"varname"+"="+varToAnalyze+"&"+"timeindex"+"="+(int)(0)+"&"+"jobid="+ijSolverStatus.getJobIndex());
// double[] zProjectedSimNormalizer = getNormalizedZProjected(timePointData,null);
// //showAndZoom(ij, "Sim Data PreBleach", ArrayImgs.doubles(simNormalizer, xsize,ysize), 4);
// 
// // Get the SIMULATION post-bleach data to analyze
// for(int timeIndex = ANALYZE_BEGIN_TIMEINDEX;timeIndex<=ANALYZE_END_TIMEINDEX;timeIndex++){
// timePointData = vh.getTimePointData(simulationDataCachekey, varToAnalyze, new int[] {timeIndex}, solverStatus_jobIndex);
// //	    	checkSizes(timePointData.getBasicStackDimensions(), xsize, xysize, zsize);
// //	    	dataUrl = new URL("http://localhost:"+vh.findVCellApiServerPort()+"/"+"getdata"+"?"+"cachekey"+"="+cachekey+"&"+"varname"+"="+varToAnalyze+"&"+"timeindex"+"="+(int)timeIndex+"&"+"jobid="+ijSolverStatus.getJobIndex());
// double[] data = getNormalizedZProjected(timePointData,zProjectedSimNormalizer);
// System.arraycopy(data, 0, bleachedTimeStack, (timeIndex-ANALYZE_BEGIN_TIMEINDEX)*xysize, data.length);
// }
// 
// //Turn VCell data into iterableinterval
// //    	FinalInterval zProjectedSimDataSize = FinalInterval.createMinSize(new long[] {0,0,0, xsize,ysize,ANALYZE_COUNT});//xyzt:origin and xyzt:size
// ArrayImg<DoubleType, DoubleArray> simImgs = ArrayImgs.doubles(bleachedTimeStack, new long[] {timePointData.getBasicStackDimensions().xsize,timePointData.getBasicStackDimensions().ysize,ANALYZE_COUNT});
// SCIFIOImgPlus<DoubleType> annotatedZProjectedSimPostBleachData = new SCIFIOImgPlus<>(simImgs,newImgPlusName /*"Sim Data "+diffusionRate*/,new AxisType[] {Axes.X,Axes.Y,Axes.TIME});
// //    	RandomAccessibleInterval<DoubleType> simExtracted = ij.op().transform().crop(annotatedSimData, simExtractInterval);
// //showAndZoom(ij, "Sim Data "+diffusionRate, annotatedZProjectedSimPostBleachData, 4);
// return annotatedZProjectedSimPostBleachData;
// }
// public static double[] getNormalizedZProjected(VCellHelper.TimePointData timePointData,double[] normalizer) throws Exception{
// BasicStackDimensions basicStackDimensions = timePointData.getBasicStackDimensions();//VCellHelper.getDimensions(nodes.item(0));
// //Sum pixel values in Z direction to match experimental data (open pinhole confocal, essentially brightfield)
// int xysize = basicStackDimensions.xsize*basicStackDimensions.ysize;
// double[] normalizedData = new double[xysize];
// for (int i = 0; i < timePointData.getTimePointData().length; i++) {
// normalizedData[(i%xysize)]+= timePointData.getTimePointData()[i];
// }
// if(normalizer != null) {
// for (int i = 0; i < normalizedData.length; i++) {
// if(normalizedData[i] != 0) {
// normalizedData[i] = (normalizedData[i]+Double.MIN_VALUE)/(normalizer[i]+Double.MIN_VALUE);
// }
// }
// }
// return normalizedData;
// }
// public static void checkSizes(BasicStackDimensions basicStackDimensions,int xsize,int ysize,int zsize) throws Exception{
// if(basicStackDimensions.xsize != xsize || basicStackDimensions.ysize != ysize || basicStackDimensions.zsize != zsize) {
// throw new Exception("One or more sim data xyz dimensions="+basicStackDimensions.xsize+","+basicStackDimensions.ysize+","+basicStackDimensions.zsize+" does not match expected xyz sizes="+xsize+","+ysize+","+zsize);
// }
// }
public static double calcMSE(ImageJ ij, SCIFIOImgPlus<DoubleType> annotatedZProjectedSimPostBleachData, ExampleDatasets exampleDatasets, FinalInterval analyzeOrigInterval) throws Exception {
    // Calculate mean-squared-error as example, normalize experimental data by dividing by a prebleach image
    RandomAccessibleInterval<? extends RealType<?>> zProjectedExperimentalPostBleach = ij.op().transform().crop(exampleDatasets.experimentalData, analyzeOrigInterval);
    Cursor<DoubleType> zProjectedSimPostBleachDataCursor = IterableRandomAccessibleInterval.create(annotatedZProjectedSimPostBleachData).localizingCursor();
    Cursor<? extends RealType<?>> zProjectedExpPostBleachDataCursor = IterableRandomAccessibleInterval.create(zProjectedExperimentalPostBleach).localizingCursor();
    IterableRandomAccessibleInterval<? extends RealType<?>> zProjectedPreBleachInterval = IterableRandomAccessibleInterval.create(exampleDatasets.preBleachImage);
    BigDecimal sumSquaredDiff = new BigDecimal(0);
    int[] analysisPosition = new int[exampleDatasets.analysisROI.numDimensions()];
    int[] preBleachPosition = new int[zProjectedPreBleachInterval.numDimensions()];
    int[] experimentalPosition = new int[zProjectedExperimentalPostBleach.numDimensions()];
    int[] simulationPosition = new int[annotatedZProjectedSimPostBleachData.numDimensions()];
    int numValsInMask = 0;
    while (zProjectedSimPostBleachDataCursor.hasNext()) {
        Cursor<UnsignedByteType> analysisCursor = exampleDatasets.analysisROI.localizingCursor();
        Cursor<? extends RealType<?>> preBleachNormalizingCursor = zProjectedPreBleachInterval.localizingCursor();
        while (analysisCursor.hasNext()) {
            boolean maskBit = !(analysisCursor.next().get() == 0);
            DoubleType simPostBleachVal = zProjectedSimPostBleachDataCursor.next();
            RealType<?> expPostBleachVal = zProjectedExpPostBleachDataCursor.next();
            RealType<?> preBleachNormalizingVal = preBleachNormalizingCursor.next();
            if (!maskBit) {
                // skip areas where analysis mask is 0
                continue;
            }
            // Get the position of all the cursors and check they are in sync
            analysisCursor.localize(analysisPosition);
            preBleachNormalizingCursor.localize(preBleachPosition);
            zProjectedExpPostBleachDataCursor.localize(experimentalPosition);
            zProjectedSimPostBleachDataCursor.localize(simulationPosition);
            // System.out.println("analysis="+Arrays.toString(analysisPosition)+" prebleach="+Arrays.toString(preBleachPosition)+" exp="+Arrays.toString(experimentalPosition)+" sim="+Arrays.toString(simulationPosition));
            if (!Arrays.equals(analysisPosition, preBleachPosition) || !Arrays.equals(experimentalPosition, simulationPosition)) {
                throw new Exception("Cursor positions not equal");
            }
            if (analysisPosition[0] != experimentalPosition[0] || analysisPosition[1] != experimentalPosition[1]) {
                // check xy are same
                throw new Exception("XY Cursor position not equal for analysisROI mask and experimental data");
            }
            double normalizedExpDataVal = 0;
            if (expPostBleachVal.getRealDouble() != 0) {
                normalizedExpDataVal = (expPostBleachVal.getRealDouble()) / (preBleachNormalizingVal.getRealDouble() + Double.MIN_VALUE);
            }
            double diff = simPostBleachVal.get() - (normalizedExpDataVal);
            sumSquaredDiff = sumSquaredDiff.add(new BigDecimal(Math.pow(diff, 2.0)));
            numValsInMask++;
        }
    }
    return sumSquaredDiff.divide(new BigDecimal(numValsInMask), 8, RoundingMode.HALF_UP).doubleValue();
}

Example 5 with UnsignedByteType

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

the class ProjectService method saveDataset.

private void saveDataset(Dataset dataset, Path path) throws IOException {
    Dataset datasetToSave = dataset.duplicate();
    // SCIFIO cannot save 1-bit images so we must convert to 8-bit
    if (datasetToSave.firstElement() instanceof BitType) {
        @SuppressWarnings("unchecked") Img<BitType> img = (Img<BitType>) dataset.getImgPlus().getImg();
        Img<UnsignedByteType> converted = opService.convert().uint8(img);
        ImgPlus<UnsignedByteType> convertedImgPlus = new ImgPlus<>(converted, dataset.getName());
        datasetToSave.setImgPlus(convertedImgPlus);
    }
    String name = dataset.getName();
    if (FilenameUtils.getExtension(name).isEmpty()) {
        // Default save extension
        name += ".tif";
    }
    Path filePath = Paths.get(path.toString(), name);
    datasetIOService.save(datasetToSave, filePath.toString());
}