public void getPixelsPhysicalSizeX(Double[] sizeX) { int imageIndex = r.getSeries(); MetadataRetrieve retrieve = (MetadataRetrieve) r.getMetadataStore(); Length x = retrieve.getPixelsPhysicalSizeX(imageIndex); if (x != null) { sizeX[0] = x.value(UNITS.MICROMETER).doubleValue(); } if (sizeX[0] == null) sizeX[0] = new Double(Double.NaN); }
public void getPixelsPhysicalSizeX(Double[] sizeX) { int imageIndex = r.getSeries(); MetadataRetrieve retrieve = (MetadataRetrieve) r.getMetadataStore(); Length x = retrieve.getPixelsPhysicalSizeX(imageIndex); if (x != null) { sizeX[0] = x.value(UNITS.MICROMETER).doubleValue(); } if (sizeX[0] == null) sizeX[0] = new Double(Double.NaN); }
@Test(dataProvider = "physical sizes") public void testPhysicalSizeXIni(String value, Length length) throws Exception { mkIni("foo.fake.ini", "physicalSizeX = " + value); reader.setId(wd.resolve("foo.fake").toString()); m = service.asRetrieve(reader.getMetadataStore()); assertTrue(service.validateOMEXML(service.getOMEXML(m))); assertEquals(m.getPixelsPhysicalSizeX(0), length); reader.close(); testDefaultValues(); }
@Test(dataProvider = "physical sizes") public void testPhysicalSizeX(String value, Length length) throws Exception { reader.setId("foo&physicalSizeX=" + value + ".fake"); m = service.asRetrieve(reader.getMetadataStore()); assertTrue(service.validateOMEXML(service.getOMEXML(m))); assertEquals(m.getPixelsPhysicalSizeX(0), length); reader.close(); testDefaultValues(); }
Length f = retrieve.getPixelsPhysicalSizeX( 0 ); if ( f != null ) cal = f.value().floatValue();
double vY = 1.0; double vZ = 1.0; if(meta.getPixelsPhysicalSizeX(0) != null) { vX = meta.getPixelsPhysicalSizeX(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); }
double vY = 1.0; double vZ = 1.0; if(meta.getPixelsPhysicalSizeX(0) != null) { vX = meta.getPixelsPhysicalSizeX(0).value(UNITS.MICROMETER).doubleValue();
pszX = meta.getPixelsPhysicalSizeX( i );
Length f = retrieve.getPixelsPhysicalSizeX( 0 ); if ( f != null ) cal = f.value().floatValue();
Number value = 1.0; if (dim == 'X') { if (meta.getPixelsPhysicalSizeX(0) != null) { value = meta.getPixelsPhysicalSizeX(0).value(UNITS.MICROMETER).doubleValue();
Number value = 1.0; if (dim == 'X') { if (meta.getPixelsPhysicalSizeX(0) != null) { value = meta.getPixelsPhysicalSizeX(0).value(UNITS.MICROMETER).doubleValue();
cal = retrieve.getPixelsPhysicalSizeX( 0 ); if ( posX >= 0 && cal != null && cal.value().doubleValue() != 0 ) calX = cal.value().doubleValue();
final Length sizex = retrieve.getPixelsPhysicalSizeX(0); final Length sizey = retrieve.getPixelsPhysicalSizeY(0); final Length sizez = retrieve.getPixelsPhysicalSizeZ(0);
cal = retrieve.getPixelsPhysicalSizeX( series ); if ( posX >= 0 && cal != null && cal.value().doubleValue() != 0 ) calX = cal.value().doubleValue();
float cal = retrieve.getPixelsPhysicalSizeX( 0 ).value().floatValue(); if ( cal == 0 )
ifd.put(new Integer(IFD.IMAGE_LENGTH), new Long(height)); Length px = retrieve.getPixelsPhysicalSizeX(series); Double physicalSizeX = px == null || px.value(UNITS.MICROMETER) == null ? null : px.value(UNITS.MICROMETER).doubleValue(); if (physicalSizeX == null || physicalSizeX.doubleValue() == 0) {
int sizeC = retrieve.getPixelsSizeC(imageIndex).getValue(); final int sizeT = retrieve.getPixelsSizeT(imageIndex).getValue(); final Length physX = retrieve.getPixelsPhysicalSizeX(imageIndex); final Length physY = retrieve.getPixelsPhysicalSizeY(imageIndex); final Length physZ = retrieve.getPixelsPhysicalSizeZ(imageIndex);
ifd.put(new Integer(IFD.IMAGE_LENGTH), new Long(height)); Length px = retrieve.getPixelsPhysicalSizeX(series); Double physicalSizeX = px == null || px.value(UNITS.MICROMETER) == null ? null : px.value(UNITS.MICROMETER).doubleValue(); if (physicalSizeX == null || physicalSizeX.doubleValue() == 0) {