Examples with UniformRandomProvider org.apache.commons.rng.UniformRandomProvider used on opensource projects

Example 86 with UniformRandomProvider

use of org.apache.commons.rng.UniformRandomProvider in project GDSC-SMLM by aherbert.

the class PeakResultStoreTest method canStoreResults.

@SuppressWarnings("null")
private static void canStoreResults(RandomSeed seed, PeakResultStore store) {
    final boolean isList = store instanceof PeakResultStoreList;
    final PeakResultStoreList storeList = (isList) ? (PeakResultStoreList) store : null;
    PeakResult result;
    final UniformRandomProvider r = RngUtils.create(seed.getSeed());
    PeakResult[] list = new PeakResult[20];
    int size = 0;
    Assertions.assertEquals(size, store.size(), "Not empty on construction");
    Assertions.assertEquals(size, store.toArray().length, "Not empty list");
    // Can store data in order
    for (int i = 0; i < 10; i++) {
        result = create(r);
        list[size++] = result;
        store.add(result);
    }
    assertEquals(list, size, store);
    // Can sort
    if (isList) {
        Arrays.sort(list, 0, size, FrameIdPeakResultComparator.INSTANCE);
        storeList.sort();
        for (int i = 0; i < size; i++) {
            Assertions.assertTrue(list[i] == storeList.get(i), "List entry not same reference");
        }
        final Comparator<PeakResult> c = new Comparator<PeakResult>() {

            @Override
            public int compare(PeakResult o1, PeakResult o2) {
                return o1.getOrigX() - o2.getOrigX();
            }
        };
        Arrays.sort(list, 0, size, c);
        storeList.sort(c);
        for (int i = 0; i < size; i++) {
            Assertions.assertTrue(list[i] == storeList.get(i), "List entry not same reference after sort");
        }
    }
    // Can trim to size
    store.trimToSize();
    assertEquals(list, size, store);
    // Can remove null results
    store.add(null);
    result = create(r);
    list[size++] = result;
    store.add(result);
    store.add(null);
    for (int i = 0; i < 3; i++) {
        result = create(r);
        list[size++] = result;
        store.add(result);
    }
    Assertions.assertTrue(size != store.size(), "Same size after adding null results");
    store.removeIf(Objects::isNull);
    assertEquals(list, size, store);
    // Can clear
    size = 0;
    store.clear();
    assertEquals(list, size, store);
    // Can add collection
    for (int i = 0; i < 10; i++) {
        result = create(r);
        list[size++] = result;
    }
    store.addCollection(Arrays.asList(Arrays.copyOf(list, size)));
    assertEquals(list, size, store);
    // Can add array
    size = 0;
    store.clear();
    for (int i = 0; i < 10; i++) {
        result = create(r);
        list[size++] = result;
    }
    store.addArray(Arrays.copyOf(list, size));
    assertEquals(list, size, store);
    // Can add store
    size = 0;
    store.clear();
    for (int i = 0; i < 10; i++) {
        result = create(r);
        list[size++] = result;
    }
    final PeakResultStore store2 = store.copy();
    store2.addArray(Arrays.copyOf(list, size));
    // Ensure the store is not at full capacity
    store2.remove(list[--size]);
    store.addStore(store2);
    assertEquals(list, size, store);
    // Can copy
    final PeakResultStore copy = store.copy();
    // Assertions.assertNotEquals(copy, store);
    Assertions.assertTrue(copy != store, "Copy is the same reference");
    assertEquals(list, size, store);
    // Can remove single
    for (int j = 0; j < 5; j++) {
        size = 0;
        store.clear();
        PeakResult toRemove = null;
        for (int i = 0; i < 5; i++) {
            result = create(r);
            if (j != i) {
                list[size++] = result;
            } else {
                toRemove = result;
            }
            store.add(result);
        }
        Assertions.assertTrue(size != store.size(), "Same size after adding extra single result");
        store.remove(toRemove);
        assertEquals(list, size, store);
    }
    // Can remove collection
    for (int j = 0; j < 5; j++) {
        size = 0;
        store.clear();
        for (int i = 0; i < 20; i++) {
            result = create(r);
            list[size++] = result;
            store.add(result);
        }
        final int[] indices = RandomUtils.sample(3, size, r);
        Arrays.sort(indices);
        final PeakResult[] list1 = new PeakResult[size - indices.length];
        final PeakResult[] toRemove = new PeakResult[indices.length];
        for (int i = 0; i < indices.length; i++) {
            toRemove[i] = list[indices[i]];
        }
        for (int i = 0, k = 0; i < size; i++) {
            if (Arrays.binarySearch(indices, i) < 0) {
                list1[k++] = list[i];
            }
        }
        store.removeCollection(Arrays.asList(toRemove));
        assertEquals(list1, list1.length, store);
    }
    // Can remove range
    if (!isList) {
        return;
    }
    size = 0;
    store.clear();
    for (int i = 0; i < 20; i++) {
        result = create(r);
        list[size++] = result;
        store.add(result);
    }
    // From the end
    storeList.remove(size - 1, size - 1);
    assertEquals(list, --size, store);
    storeList.remove(size - 2, size - 1);
    size -= 2;
    assertEquals(list, size, store);
    // From the start
    storeList.remove(0, 0);
    list = Arrays.copyOfRange(list, 1, size);
    size = list.length;
    assertEquals(list, size, store);
    storeList.remove(0, 1);
    list = Arrays.copyOfRange(list, 2, size);
    size = list.length;
    assertEquals(list, size, store);
    // From the middle
    storeList.remove(3, 3);
    System.arraycopy(list, 4, list, 3, size - 4);
    size--;
    assertEquals(list, size, store);
    storeList.remove(3, 4);
    System.arraycopy(list, 5, list, 3, size - 5);
    size -= 2;
    assertEquals(list, size, store);
}

Example 87 with UniformRandomProvider

use of org.apache.commons.rng.UniformRandomProvider in project GDSC-SMLM by aherbert.

the class PeakResultsReaderTest method canReadIntoPreferredUnits.

private static void canReadIntoPreferredUnits(RandomSeed seed, ResultsFileFormat fileFormat) {
    final UniformRandomProvider rg = RngUtils.create(seed.getSeed());
    final MemoryPeakResults out = createResults(rg, 200, false, false, false, false, false);
    // Output in nm and count
    final CalibrationWriter cal = new CalibrationWriter(out.getCalibration());
    cal.setDistanceUnit(DistanceUnit.NM);
    cal.setIntensityUnit(IntensityUnit.COUNT);
    if (fileFormat == ResultsFileFormat.TSF) {
        // For now just support using the native float TSF value
        cal.setNmPerPixel((float) cal.getNmPerPixel());
    }
    out.setCalibration(cal.getCalibration());
    final String filename = createFile();
    writeFile(false, fileFormat, false, false, false, false, false, false, out, filename);
    final MemoryPeakResults in = readFile(filename, false, false);
    // Change to preferred units
    out.convertToUnits(MemoryPeakResults.PREFERRED_DISTANCE_UNIT, MemoryPeakResults.PREFERRED_INTENSITY_UNIT, MemoryPeakResults.PREFERRED_ANGLE_UNIT);
    checkEqual(fileFormat, false, false, false, false, false, false, out, in);
}

Example 88 with UniformRandomProvider

use of org.apache.commons.rng.UniformRandomProvider in project GDSC-SMLM by aherbert.

the class PeakResultsReaderTest method writeMatchesRead.

// -=-=-=-=-
private static void writeMatchesRead(RandomSeed seed, boolean sequential, ResultsFileFormat fileFormat, boolean showDeviations, boolean showEndFrame, boolean showId, boolean showPrecision, boolean showCategory, boolean sort) {
    final UniformRandomProvider rg = RngUtils.create(seed.getSeed());
    final MemoryPeakResults out = createResults(rg, 200, showDeviations, showEndFrame, showId, showPrecision, showCategory);
    if (fileFormat == ResultsFileFormat.MALK) {
        final CalibrationWriter cal = new CalibrationWriter(out.getCalibration());
        cal.setDistanceUnit(DistanceUnit.NM);
        cal.setIntensityUnit(IntensityUnit.PHOTON);
        out.setCalibration(cal.getCalibration());
        out.setPsf(PsfHelper.create(PSFType.CUSTOM));
    }
    if (fileFormat == ResultsFileFormat.TSF) {
        final CalibrationWriter cal = new CalibrationWriter(out.getCalibration());
        // For now just support using the native float TSF datatype
        cal.setNmPerPixel((float) cal.getNmPerPixel());
        out.setCalibration(cal.getCalibration());
        // TSF converts the width parameters so make sure they are not zero
        out.forEach(new PeakResultProcedure() {

            @Override
            public void execute(PeakResult peakResult) {
                check(peakResult.getParameters());
                if (showDeviations) {
                    check(peakResult.getParameterDeviations());
                }
            }

            private void check(float[] parameters) {
                for (int i = 0; i < parameters.length; i++) {
                    if (parameters[i] == 0) {
                        parameters[i] = 0.1f;
                    }
                }
            }
        });
    }
    // System.out.println(out.getCalibration());
    // System.out.println(out.getPSF().toString());
    // 
    // System.out.println(TextFormat.shortDebugString(out.getCalibration()));
    // 
    // try
    // {
    // Printer printer = JsonFormat.printer()
    // .omittingInsignificantWhitespace()
    // //.includingDefaultValueFields()
    // ;
    // System.out.println(printer.print(out.getCalibration()));
    // System.out.println(printer.print(out.getPSF()));
    // }
    // catch (InvalidProtocolBufferException e)
    // {
    // // This shouldn't happen so throw it
    // }
    final String filename = createFile();
    writeFile(sequential, fileFormat, showDeviations, showEndFrame, showId, showPrecision, showCategory, sort, out, filename);
    final MemoryPeakResults in = readFile(filename, false);
    checkEqual(fileFormat, showDeviations, showEndFrame, showId, showPrecision, showCategory, sort, out, in);
}

Example 89 with UniformRandomProvider

use of org.apache.commons.rng.UniformRandomProvider in project GDSC-SMLM by aherbert.

the class PeakResultsReaderTest method canConvertMalkToNmAndPhotons.

@SeededTest
void canConvertMalkToNmAndPhotons(RandomSeed seed) {
    final UniformRandomProvider rg = RngUtils.create(seed.getSeed());
    final MemoryPeakResults out = createResults(rg, 200, false, false, false, false, false);
    // Output in pixel and count
    final CalibrationWriter cal = new CalibrationWriter(out.getCalibration());
    cal.setDistanceUnit(DistanceUnit.PIXEL);
    cal.setIntensityUnit(IntensityUnit.COUNT);
    out.setCalibration(cal.getCalibration());
    out.setPsf(PsfHelper.create(PSFType.CUSTOM));
    final String filename = createFile();
    writeFile(false, ResultsFileFormat.MALK, false, false, false, false, false, false, out, filename);
    final MemoryPeakResults in = readFile(filename, false);
    // Change to nm and photon for the validation
    out.convertToUnits(DistanceUnit.NM, IntensityUnit.PHOTON, null);
    checkEqual(ResultsFileFormat.MALK, false, false, false, false, false, false, out, in);
}

Example 90 with UniformRandomProvider

use of org.apache.commons.rng.UniformRandomProvider in project GDSC-SMLM by aherbert.

the class PeakResultsReaderTest method checkScannerMatchesNonScanner.

private static void checkScannerMatchesNonScanner(RandomSeed seed, boolean showDeviations, boolean showEndFrame, boolean showId, boolean showPrecision, boolean showCategory, boolean sort) {
    final UniformRandomProvider rg = RngUtils.create(seed.getSeed());
    final MemoryPeakResults out = createResults(rg, 1000, showDeviations, showEndFrame, showId, showPrecision, showCategory);
    final String filename = createFile();
    final ResultsFileFormat fileFormat = ResultsFileFormat.TEXT;
    writeFile(false, fileFormat, showDeviations, showEndFrame, showId, showPrecision, showCategory, sort, out, filename);
    final MemoryPeakResults in = readFile(filename, false);
    final MemoryPeakResults in2 = readFile(filename, true);
    checkEqual(fileFormat, showDeviations, showEndFrame, showId, showPrecision, showCategory, sort, in, in2);
}