String objectiveID = "Objective:" + value; store.setObjectiveID(objectiveID, 0, 0); for (int series=0; series<getSeriesCount(); series++) { store.setObjectiveSettingsID(objectiveID, series); Length sizeX = FormatTools.getPhysicalSizeX(size); if (sizeX != null) { for (int series=0; series<getSeriesCount(); series++) { store.setPixelsPhysicalSizeX(sizeX, series); Length sizeY = FormatTools.getPhysicalSizeY(size); if (sizeY != null) { for (int series=0; series<getSeriesCount(); series++) { store.setPixelsPhysicalSizeY(sizeY, series); Length sizeZ = FormatTools.getPhysicalSizeZ(size); if (sizeZ != null) { for (int series=0; series<getSeriesCount(); series++) { store.setPixelsPhysicalSizeZ(sizeZ, series); String detectorID = MetadataTools.createLSID("Detector", 0, 0); store.setDetectorID(detectorID, 0, 0); for (int series=0; series<getSeriesCount(); series++) { for (int c=0; c<getSizeC(); c++) { store.setDetectorSettingsBinning( String detectorID = MetadataTools.createLSID("Detector", 0, 0); store.setDetectorID(detectorID, 0, 0); for (int series=0; series<getSeriesCount(); series++) {
String objectiveID = "Objective:" + value; store.setObjectiveID(objectiveID, 0, 0); for (int series=0; series<getSeriesCount(); series++) { store.setObjectiveSettingsID(objectiveID, series); Length sizeX = FormatTools.getPhysicalSizeX(size); if (sizeX != null) { for (int series=0; series<getSeriesCount(); series++) { store.setPixelsPhysicalSizeX(sizeX, series); Length sizeY = FormatTools.getPhysicalSizeY(size); if (sizeY != null) { for (int series=0; series<getSeriesCount(); series++) { store.setPixelsPhysicalSizeY(sizeY, series); Length sizeZ = FormatTools.getPhysicalSizeZ(size); if (sizeZ != null) { for (int series=0; series<getSeriesCount(); series++) { store.setPixelsPhysicalSizeZ(sizeZ, series); String detectorID = MetadataTools.createLSID("Detector", 0, 0); store.setDetectorID(detectorID, 0, 0); for (int series=0; series<getSeriesCount(); series++) { for (int c=0; c<getSizeC(); c++) { store.setDetectorSettingsBinning( String detectorID = MetadataTools.createLSID("Detector", 0, 0); store.setDetectorID(detectorID, 0, 0); for (int series=0; series<getSeriesCount(); series++) {
break; case 'T': lengths[lengthIndex++] = getSeriesCount(); lengths[lengthIndex++] = getSizeT(); break; addGlobalMeta("Number of focal planes", sizeZ); for (int series=0; series<getSeriesCount(); series++) { setSeries(series); for (int plane=0; plane<getImageCount(); plane++) { int[] coords = getZCTCoords(plane); int tIndex = getSeriesCount() * coords[2] + series; DVExtHdrFields hdr = extHdrFields[coords[0]][coords[1]][tIndex]; store.setInstrumentID(instrumentID, 0); for (int i=0; i<getSeriesCount(); i++) { store.setImageInstrumentRef(instrumentID, i);
break; case 'T': lengths[lengthIndex++] = getSeriesCount(); lengths[lengthIndex++] = getSizeT(); break; addGlobalMeta("Number of focal planes", sizeZ); for (int series=0; series<getSeriesCount(); series++) { setSeries(series); for (int plane=0; plane<getImageCount(); plane++) { int[] coords = getZCTCoords(plane); int tIndex = getSeriesCount() * coords[2] + series; DVExtHdrFields hdr = extHdrFields[coords[0]][coords[1]][tIndex]; store.setInstrumentID(instrumentID, 0); for (int i=0; i<getSeriesCount(); i++) { store.setImageInstrumentRef(instrumentID, i);
@Test(dependsOnMethods={"testSetId"}) public void testPlaneData() throws FormatException, IOException { for (int i = 0; i < pixelsOnly.getSeriesCount(); i++) { pixelsOnly.setSeries(i); all.setSeries(i); assertEquals(all.getImageCount(), pixelsOnly.getImageCount()); for (int j = 0; j < pixelsOnly.getImageCount(); j++) { byte[] pixelsOnlyPlane = pixelsOnly.openBytes(j); String sha1PixelsOnlyPlane = sha1(pixelsOnlyPlane); byte[] allPlane = all.openBytes(j); String sha1AllPlane = sha1(allPlane); if (!sha1PixelsOnlyPlane.equals(sha1AllPlane)) { fail(String.format( "MISMATCH: Series:%d Image:%d PixelsOnly:%s All:%s", i, j, sha1PixelsOnlyPlane, sha1AllPlane)); } } } }
@Test(dependsOnMethods={"testSetId"}) public void testDimensions() { assertEquals(all.getSeriesCount(), pixelsOnly.getSeriesCount()); assertEquals(all.getSizeX(), pixelsOnly.getSizeX()); assertEquals(all.getSizeY(), pixelsOnly.getSizeY()); assertEquals(all.getSizeZ(), pixelsOnly.getSizeZ()); assertEquals(all.getSizeC(), pixelsOnly.getSizeC()); assertEquals(all.getSizeT(), pixelsOnly.getSizeT()); assertEquals(all.getPixelType(), pixelsOnly.getPixelType()); }
for (int series=0; series<getSeriesCount(); series++) { if (store instanceof IMinMaxStore) { IMinMaxStore minMaxStore = (IMinMaxStore) store; if (getSeriesCount() == 1) { xTiles = 1; yTiles = 1; for (int series=0; series<getSeriesCount(); series++) { int seriesIndex = series; if (backwardsStage) { int[] coords = getZCTCoords(i); int tIndex = getSeriesCount() * coords[2] + seriesIndex; DVExtHdrFields hdr = extHdrFields[coords[0]][coords[1]][tIndex]; if (!logFound || getSeriesCount() > 1) { store.setPlanePositionX(hdr.stageXCoord, series, i); store.setPlanePositionY(hdr.stageYCoord, series, i);
for (int series=0; series<getSeriesCount(); series++) { if (store instanceof IMinMaxStore) { IMinMaxStore minMaxStore = (IMinMaxStore) store; if (getSeriesCount() == 1) { xTiles = 1; yTiles = 1; for (int series=0; series<getSeriesCount(); series++) { int seriesIndex = series; if (backwardsStage) { int[] coords = getZCTCoords(i); int tIndex = getSeriesCount() * coords[2] + seriesIndex; DVExtHdrFields hdr = extHdrFields[coords[0]][coords[1]][tIndex]; if (!logFound || getSeriesCount() > 1) { store.setPlanePositionX(hdr.stageXCoord, series, i); store.setPlanePositionY(hdr.stageYCoord, series, i);
for (int series=0; series<getSeriesCount(); series++) { store.setObjectiveSettingsID(objectiveID, series);
for (int series=0; series<getSeriesCount(); series++) { store.setObjectiveSettingsID(objectiveID, series);