public void getPixelsPhysicalSizeZ(Double[] sizeZ) { int imageIndex = r.getSeries(); MetadataRetrieve retrieve = (MetadataRetrieve) r.getMetadataStore(); Length z = retrieve.getPixelsPhysicalSizeZ(imageIndex); if (z != null) { sizeZ[0] = z.value(UNITS.MICROMETER).doubleValue(); } if (sizeZ[0] == null) sizeZ[0] = new Double(Double.NaN); }
public void getPixelsPhysicalSizeZ(Double[] sizeZ) { int imageIndex = r.getSeries(); MetadataRetrieve retrieve = (MetadataRetrieve) r.getMetadataStore(); Length z = retrieve.getPixelsPhysicalSizeZ(imageIndex); if (z != null) { sizeZ[0] = z.value(UNITS.MICROMETER).doubleValue(); } if (sizeZ[0] == null) sizeZ[0] = new Double(Double.NaN); }
@Test(dataProvider = "physical sizes") public void testPhysicalSizeZIni(String value, Length length) throws Exception { mkIni("foo.fake.ini", "physicalSizeZ = " + value); reader.setId(wd.resolve("foo.fake").toString()); m = service.asRetrieve(reader.getMetadataStore()); assertTrue(service.validateOMEXML(service.getOMEXML(m))); assertEquals(m.getPixelsPhysicalSizeZ(0), length); reader.close(); testDefaultValues(); }
f = retrieve.getPixelsPhysicalSizeZ( 0 ); if ( f != null ) cal = f.value().floatValue();
@Test(dataProvider = "physical sizes") public void testPhysicalSizeZ(String value, Length length) throws Exception { reader.setId("foo&physicalSizeZ=" + value + ".fake"); m = service.asRetrieve(reader.getMetadataStore()); assertTrue(service.validateOMEXML(service.getOMEXML(m))); assertEquals(m.getPixelsPhysicalSizeZ(0), length); reader.close(); testDefaultValues(); }
vY = meta.getPixelsPhysicalSizeY(0).value(UNITS.MICROMETER).doubleValue(); if(meta.getPixelsPhysicalSizeZ(0) != null) { vZ = meta.getPixelsPhysicalSizeZ(0).value(UNITS.MICROMETER).doubleValue();
@Test public void testDefaultValues() throws Exception { reader.setId("default.fake"); m = service.asRetrieve(reader.getMetadataStore()); assertTrue(service.validateOMEXML(service.getOMEXML(m))); assertEquals(reader.getSizeX(), FakeReader.DEFAULT_SIZE_X); assertEquals(reader.getSizeY(), FakeReader.DEFAULT_SIZE_Y); assertEquals(reader.getSizeZ(), FakeReader.DEFAULT_SIZE_Z); assertEquals(reader.getSizeC(), FakeReader.DEFAULT_SIZE_C); assertEquals(reader.getSizeT(), FakeReader.DEFAULT_SIZE_T); assertEquals(reader.getPixelType(), FakeReader.DEFAULT_PIXEL_TYPE); assertEquals(reader.getRGBChannelCount(), FakeReader.DEFAULT_RGB_CHANNEL_COUNT); assertEquals(reader.getDimensionOrder(), FakeReader.DEFAULT_DIMENSION_ORDER); assertEquals(m.getImageAcquisitionDate(0), null); assertEquals(m.getPixelsPhysicalSizeX(0), null); assertEquals(m.getPixelsPhysicalSizeY(0), null); assertEquals(m.getPixelsPhysicalSizeZ(0), null); assertEquals(m.getROICount(), 0); assertEquals(m.getExperimentCount(), 0); }
vY = meta.getPixelsPhysicalSizeY(0).value(UNITS.MICROMETER).doubleValue(); if(meta.getPixelsPhysicalSizeZ(0) != null) { vZ = meta.getPixelsPhysicalSizeZ(0).value(UNITS.MICROMETER).doubleValue();
pszZ = meta.getPixelsPhysicalSizeZ( i );
f = retrieve.getPixelsPhysicalSizeZ( 0 ); if ( f != null ) cal = f.value().floatValue();
if (meta.getPixelsPhysicalSizeZ(0) != null) { value = meta.getPixelsPhysicalSizeZ(0).value(UNITS.MICROMETER).doubleValue();
if (meta.getPixelsPhysicalSizeZ(0) != null) { value = meta.getPixelsPhysicalSizeZ(0).value(UNITS.MICROMETER).doubleValue();
cal = retrieve.getPixelsPhysicalSizeZ( 0 ); if ( posZ >= 0 && cal != null && cal.value().doubleValue() != 0 ) calZ = cal.value().doubleValue();
final Length sizex = retrieve.getPixelsPhysicalSizeX(0); final Length sizey = retrieve.getPixelsPhysicalSizeY(0); final Length sizez = retrieve.getPixelsPhysicalSizeZ(0); final Time sizet = retrieve.getPixelsTimeIncrement(0);
cal = retrieve.getPixelsPhysicalSizeZ( series ); if ( posZ >= 0 && cal != null && cal.value().doubleValue() != 0 ) calZ = cal.value().doubleValue();
cal = retrieve.getPixelsPhysicalSizeZ( 0 ).value().floatValue(); if ( cal == 0 )
final Length physX = retrieve.getPixelsPhysicalSizeX(imageIndex); final Length physY = retrieve.getPixelsPhysicalSizeY(imageIndex); final Length physZ = retrieve.getPixelsPhysicalSizeZ(imageIndex); final Time physT = retrieve.getPixelsTimeIncrement(imageIndex); final double calX = physX == null ? 1.0 : physX.value().doubleValue();