@Test(dependsOnMethods={"testSetId"}) public void testUsedFiles() throws FormatException, IOException { for (int i=0; i<pixelsOnly.getSeriesCount(); i++) { pixelsOnly.setSeries(i); all.setSeries(i); noOverlays.setSeries(i); String[] pixelsOnlyFiles = pixelsOnly.getSeriesUsedFiles(); String[] allFiles = all.getSeriesUsedFiles(); String[] noOverlaysFiles = noOverlays.getSeriesUsedFiles(); assertEquals(allFiles.length, pixelsOnlyFiles.length); assertEquals(allFiles.length, noOverlaysFiles.length); Arrays.sort(allFiles); Arrays.sort(pixelsOnlyFiles); Arrays.sort(noOverlaysFiles); for (int j=0; j<pixelsOnlyFiles.length; j++) { assertEquals(allFiles[j], pixelsOnlyFiles[j]); assertEquals(allFiles[j], noOverlaysFiles[j]); } } }
@Test(dependsOnMethods={"testSetId"}) public void testPlaneData() throws FormatException, IOException { for (int i=0; i<pixelsOnly.getSeriesCount(); i++) { pixelsOnly.setSeries(i); all.setSeries(i); noOverlays.setSeries(i); assertEquals(all.getImageCount(), pixelsOnly.getImageCount()); assertEquals(all.getImageCount(), noOverlays.getImageCount()); for (int j=0; j<pixelsOnly.getImageCount(); j++) { byte[] pixelsOnlyPlane = pixelsOnly.openBytes(j); String pixelsOnlySHA1 = sha1(pixelsOnlyPlane); byte[] allPlane = all.openBytes(j); String allSHA1 = sha1(allPlane); byte[] noOverlaysPlane = noOverlays.openBytes(j); String noOverlaysSHA1 = sha1(noOverlaysPlane); if (!pixelsOnlySHA1.equals(allSHA1)) { fail(String.format("MISMATCH: Series:%d Image:%d PixelsOnly%s All:%s", i, j, pixelsOnlySHA1, allSHA1)); } if (!noOverlaysSHA1.equals(allSHA1)) { fail(String.format("MISMATCH: Series:%d Image:%d PixelsOnly%s All:%s", i, j, noOverlaysSHA1, allSHA1)); } } } }
public static void main(String[] args) { ImageReader reader = new ImageReader(); reader.setMetadataStore( new OMEXMLMetadataImpl()); try { reader.setId( new OpenDialog("pick file").getPath() ); for (int i = 0; i < reader.getSeriesCount(); i++) { reader.setSeries( i ); Arrays.asList( reader.getSeriesUsedFiles() ).forEach( s -> System.out.println( s ) ); System.out.println( ((OMEXMLMetadataImpl)reader.getMetadataStore()).dumpXML()); } reader.close(); } catch ( FormatException | IOException e ) { // TODO Auto-generated catch block e.printStackTrace(); } }
reader.setSeries( i ); for (String usedFileI : reader.getSeriesUsedFiles()) state.getGroupUsageMap().put( usedFileI , new ValuePair< File, Integer >( currentFile, i ));
reader.setSeries( i ); MetadataRetrieve meta = (MetadataRetrieve)reader.getMetadataStore();
reader.setSeries(s);
@Test(dependsOnMethods={"testSetId"}) public void testDimensions() { assertEquals(all.getSeriesCount(), pixelsOnly.getSeriesCount()); assertEquals(all.getSeriesCount(), noOverlays.getSeriesCount()); for (int i=0; i<pixelsOnly.getSeriesCount(); i++) { all.setSeries(i); pixelsOnly.setSeries(i); noOverlays.setSeries(i); 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()); assertEquals(all.isLittleEndian(), pixelsOnly.isLittleEndian()); assertEquals(all.isIndexed(), pixelsOnly.isIndexed()); assertEquals(all.getSizeX(), noOverlays.getSizeX()); assertEquals(all.getSizeY(), noOverlays.getSizeY()); assertEquals(all.getSizeZ(), noOverlays.getSizeZ()); assertEquals(all.getSizeC(), noOverlays.getSizeC()); assertEquals(all.getSizeT(), noOverlays.getSizeT()); assertEquals(all.getPixelType(), noOverlays.getPixelType()); assertEquals(all.isLittleEndian(), noOverlays.isLittleEndian()); assertEquals(all.isIndexed(), noOverlays.isIndexed()); } }