@Override public void close() throws IOException { close(false); }
@Override public void close() throws IOException { close(false); }
@Override public void close(boolean fileOnly) throws IOException { super.close(fileOnly); if (!fileOnly) { if (helperReader != null) { helperReader.close(); } helperReader = null; } }
@Override public void close(boolean fileOnly) throws IOException { super.close(fileOnly); if (!fileOnly) { if (helperReader != null) { helperReader.close(); } helperReader = null; } }
public static void time(String id) throws IOException, FormatException { System.out.print("Timing " + new File(id).getName() + ": "); long t1 = System.currentTimeMillis(); boolean result = reader.isThisType(id); long t2 = System.currentTimeMillis(); System.out.print((t2 - t1) + " ms to check type (" + result + "); "); long t3 = System.currentTimeMillis(); reader.setId(id); long t4 = System.currentTimeMillis(); System.out.println((t4 - t3) + " ms to initialize"); reader.close(); }
@Override public void close(boolean fileOnly) throws IOException { super.close(fileOnly); if (helper != null) helper.close(fileOnly); if (!fileOnly) { helper = null; dataFile = encoding = null; offset = 0; pixelSizes = null; initializeHelper = false; if (gzip != null) { gzip.close(); } gzip = null; lastPlane = -1; } }
@Override public void close(boolean fileOnly) throws IOException { super.close(fileOnly); if (helper != null) helper.close(fileOnly); if (!fileOnly) { helper = null; dataFile = encoding = null; offset = 0; pixelSizes = null; initializeHelper = false; if (gzip != null) { gzip.close(); } gzip = null; lastPlane = -1; } }
@Override public void close(boolean fileOnly) throws IOException { super.close(fileOnly); if (reader != null) reader.close(fileOnly); if (!fileOnly) reader = null; for (String name : mappedFiles) { IRandomAccess handle = Location.getMappedFile(name); Location.mapFile(name, null); if (handle != null) { handle.close(); } } mappedFiles.clear(); entryName = null; }
@Override public void close(boolean fileOnly) throws IOException { super.close(fileOnly); if (reader != null) reader.close(fileOnly); if (!fileOnly) reader = null; for (String name : mappedFiles) { IRandomAccess handle = Location.getMappedFile(name); Location.mapFile(name, null); if (handle != null) { handle.close(); } } mappedFiles.clear(); entryName = null; }
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(); } }
@Test public void testLosslessPixels() throws Exception { int failureCount = 0; for (int i=0; i<files.size(); i++) { ImageReader reader = new ImageReader(); reader.setId(files.get(i)); byte[] plane = reader.openBytes(0); if (plane[0] != pixels[i][0]) { LOGGER.debug("FAILED on {}", pixels[i][0]); failureCount++; } reader.close(); } assertEquals(failureCount, 0); }
private void parseROIs(MetadataStore store) throws FormatException, IOException { String roiID = MetadataTools.createLSID("ROI", 0, 0); String maskID = MetadataTools.createLSID("Shape", 0, 0); store.setROIID(roiID, 0); store.setMaskID(maskID, 0, 0); String positionData = DataTools.readFile(roiDrawFile); String[] coordinates = positionData.split("[ ,]"); double x1 = Double.parseDouble(coordinates[1]); double y1 = Double.parseDouble(coordinates[2]); double x2 = Double.parseDouble(coordinates[3]); double y2 = Double.parseDouble(coordinates[5]); store.setMaskX(x1, 0, 0); store.setMaskY(y1, 0, 0); store.setMaskWidth(x2 - x1, 0, 0); store.setMaskHeight(y2 - y1, 0, 0); store.setImageROIRef(roiID, 0, 0); ImageReader roiReader = new ImageReader(); roiReader.setId(roiFile); byte[] roiPixels = roiReader.openBytes(0); roiReader.close(); BitWriter bits = new BitWriter(roiPixels.length / 8); for (int i=0; i<roiPixels.length; i++) { bits.write(roiPixels[i] == 0 ? 0 : 1, 1); } store.setMaskBinData(bits.toByteArray(), 0, 0); }
@Test public void testEquivalentPixels16Bit() throws Exception { ImageReader reader = new ImageReader(); reader.setId(FILE_16); byte[] plane = reader.openBytes(0); assertEquals(plane.length, PIXELS_16.length); for (int q=0; q<plane.length; q++) { assertEquals(plane[q], PIXELS_16[q]); } reader.close(); }
@Test public void testEquivalentPixels8Bit() throws Exception { ImageReader reader = new ImageReader(); reader.setId(FILE_8); byte[] plane = reader.openBytes(0); assertEquals(plane.length, PIXELS_8.length); for (int q=0; q<plane.length; q++) { assertEquals(plane[q], PIXELS_8[q]); } reader.close(); }
private void parseROIs(MetadataStore store) throws FormatException, IOException { String roiID = MetadataTools.createLSID("ROI", 0, 0); String maskID = MetadataTools.createLSID("Shape", 0, 0); store.setROIID(roiID, 0); store.setMaskID(maskID, 0, 0); String positionData = DataTools.readFile(roiDrawFile); String[] coordinates = positionData.split("[ ,]"); double x1 = Double.parseDouble(coordinates[1]); double y1 = Double.parseDouble(coordinates[2]); double x2 = Double.parseDouble(coordinates[3]); double y2 = Double.parseDouble(coordinates[5]); store.setMaskX(x1, 0, 0); store.setMaskY(y1, 0, 0); store.setMaskWidth(x2 - x1, 0, 0); store.setMaskHeight(y2 - y1, 0, 0); store.setImageROIRef(roiID, 0, 0); ImageReader roiReader = new ImageReader(); roiReader.setId(roiFile); byte[] roiPixels = roiReader.openBytes(0); roiReader.close(); BitWriter bits = new BitWriter(roiPixels.length / 8); for (int i=0; i<roiPixels.length; i++) { bits.write(roiPixels[i] == 0 ? 0 : 1, 1); } store.setMaskBinData(bits.toByteArray(), 0, 0); }
@Test public void testOptionsExplicit() throws Exception { DynamicMetadataOptions opt = new DynamicMetadataOptions(); opt.set(KEY, VALUE); ImageReader reader = new ImageReader(); reader.setMetadataOptions(opt); reader.setId("test.fake"); MetadataOptions rOpt = reader.getReader().getMetadataOptions(); assertTrue(rOpt instanceof DynamicMetadataOptions); String v = ((DynamicMetadataOptions) rOpt).get(KEY); assertNotNull(v); assertEquals(v, VALUE); reader.close(); }
@Test(dataProvider = "levels") public void testOptionsImplicit(MetadataLevel level) throws Exception { ImageReader reader = new ImageReader(); reader.getMetadataOptions().setMetadataLevel(level); reader.setId("test.fake"); MetadataLevel rLevel = reader.getReader().getMetadataOptions().getMetadataLevel(); assertEquals(rLevel, level); reader.close(); }
public static void main(String[] args) throws Exception { OriginalMetadataRequestI omr = new OriginalMetadataRequestI(null); ImageReader reader = new ImageReader(); for (String file : args) { reader.setId(file); final Hashtable<String, Object> bfglobal = reader.getGlobalMetadata(); final Hashtable<String, Object> bfseries = reader.getSeriesMetadata(); Map<String, RType> global = omr.wrap(bfglobal); Map<String, RType> series = omr.wrap(bfseries); printMap("[GlobalMetadata]", global); printMap("[SeriesMetadata]", series); } reader.close(); }
@Test public void testImageWidthWrittenCorrectly() throws Exception { OMETiffWriter writer = new OMETiffWriter(); writer.setMetadataRetrieve(ms); writer.setId(target.getAbsolutePath()); writer.saveBytes(0, buf, 0, 0, buf.length, 1); writer.close(); ImageReader reader = new ImageReader(); reader.setId(target.getAbsolutePath()); assertEquals(reader.getFormat(), "OME-TIFF"); reader.close(); } }
reader.close();