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public List<CoreMetadata> getSeriesList() { List<CoreMetadata> l = new ArrayList<>(); for (int i = 0; i < size(); ++i) { l.add(new CoreMetadata(get(i, 0))); } for (CoreMetadata c : l) { c.resolutionCount = 1; } return l; }
public List<CoreMetadata> getSeriesList() { List<CoreMetadata> l = new ArrayList<>(); for (int i = 0; i < size(); ++i) { l.add(new CoreMetadata(get(i, 0))); } for (CoreMetadata c : l) { c.resolutionCount = 1; } return l; }
public List<CoreMetadata> getFlattenedList() { List<CoreMetadata> l = new ArrayList<>(); int[] sizes = sizes(); for (int i = 0; i < sizes.length; ++i) { if (sizes[i] > 0) { get(i, 0).resolutionCount = sizes[i]; } for (int j = 0; j < sizes[i]; ++j) { l.add(new CoreMetadata(get(i,j))); } } return l; }
public List<CoreMetadata> getFlattenedList() { List<CoreMetadata> l = new ArrayList<>(); int[] sizes = sizes(); for (int i = 0; i < sizes.length; ++i) { if (sizes[i] > 0) { get(i, 0).resolutionCount = sizes[i]; } for (int j = 0; j < sizes[i]; ++j) { l.add(new CoreMetadata(get(i,j))); } } return l; }
/** * Initializes the given file (parsing header information, etc.). * Most subclasses should override this method to perform * initialization operations such as parsing metadata. * * @throws FormatException if a parsing error occurs processing the file. * @throws IOException if an I/O error occurs processing the file */ protected void initFile(String id) throws FormatException, IOException { LOGGER.debug("{}.initFile({})", this.getClass().getName(), id); if (currentId != null) { String[] s = getUsedFiles(); for (int i=0; i<s.length; i++) { if (id.equals(s[i])) return; } } coreIndex = 0; series = 0; close(); currentId = id; metadata = new Hashtable<String, Object>(); core = new ArrayList<CoreMetadata>(); CoreMetadata core0 = new CoreMetadata(); core.add(core0); core0.orderCertain = true; // reinitialize the MetadataStore // NB: critical for metadata conversion to work properly! getMetadataStore().createRoot(); }
/** * Initializes the given file (parsing header information, etc.). * Most subclasses should override this method to perform * initialization operations such as parsing metadata. * * @throws FormatException if a parsing error occurs processing the file. * @throws IOException if an I/O error occurs processing the file */ protected void initFile(String id) throws FormatException, IOException { LOGGER.debug("{}.initFile({})", this.getClass().getName(), id); if (currentId != null) { String[] s = getUsedFiles(); for (int i=0; i<s.length; i++) { if (id.equals(s[i])) return; } } coreIndex = 0; series = 0; close(); currentId = id; metadata = new Hashtable<String, Object>(); core = new ArrayList<CoreMetadata>(); CoreMetadata core0 = new CoreMetadata(); core.add(core0); core0.orderCertain = true; // reinitialize the MetadataStore // NB: critical for metadata conversion to work properly! getMetadataStore().createRoot(); }
@Override public void setId(String id) throws FormatException, IOException { super.setId(id); // insert a single sub-resolution core.add(new CoreMetadata(core.get(0))); core.get(0).resolutionCount++; core.get(1).sizeX /= 2; core.get(1).sizeY /= 2; } }
public void populateMetadataStore(String[] jsonData) throws FormatException, IOException { FormatTools.assertId(currentId, false, 1); currentId = "in-memory-json"; core.clear(); positions = new Vector<Position>(); for (int pos=0; pos<jsonData.length; pos++) { core.add(new CoreMetadata()); Position p = new Position(); p.metadataFile = "Position #" + (pos + 1); positions.add(p); setSeries(pos); parsePosition(jsonData[pos], pos); } setSeries(0); populateMetadata(); }
public void populateMetadataStore(String[] jsonData) throws FormatException, IOException { FormatTools.assertId(currentId, false, 1); currentId = "in-memory-json"; core.clear(); positions = new Vector<Position>(); for (int pos=0; pos<jsonData.length; pos++) { core.add(new CoreMetadata()); Position p = new Position(); p.metadataFile = "Position #" + (pos + 1); positions.add(p); setSeries(pos); parsePosition(jsonData[pos], pos); } setSeries(0); populateMetadata(); }
ms = new CoreMetadata(); ms.sizeX = Integer.parseInt(backgroundX); ms.sizeY = Integer.parseInt(backgroundY); ms.moduloT.start = 0; ms.moduloT.end = ms.sizeT - 1; core.add(ms);
ms = new CoreMetadata(); ms.sizeX = Integer.parseInt(backgroundX); ms.sizeY = Integer.parseInt(backgroundY); ms.moduloT.start = 0; ms.moduloT.end = ms.sizeT - 1; core.add(ms);
if (filelist.get(projection) == null) { filelist.put(projection, new String[sizeT][sizeC]); core.add(new CoreMetadata(this, 0));
if (filelist.get(projection) == null) { filelist.put(projection, new String[sizeT][sizeC]); core.add(new CoreMetadata(this, 0));
list1.add(new CoreMetadata()); list2.add(new CoreMetadata()); list2.add(new CoreMetadata()); list2.add(new CoreMetadata()); list2.add(new CoreMetadata()); list3.add(new CoreMetadata()); list3.add(new CoreMetadata()); list3.add(new CoreMetadata()); list3.add(new CoreMetadata()); list3.add(new CoreMetadata()); list3.get(0).resolutionCount = 5; list3.get(0).sizeX = 4096; list4.add(new CoreMetadata());
core.add(new CoreMetadata(this, 0));
core.add(new CoreMetadata(this, 0));
core.add(new CoreMetadata(c)); core.get(core.size() - 1).thumbnail = true; ((Attachment) segment).attachmentData = thumbReader.openBytes(0);
core.add(new CoreMetadata(c)); core.get(core.size() - 1).thumbnail = true; ((Attachment) segment).attachmentData = thumbReader.openBytes(0);
core.clear(); for (int i=0; i<seriesCount; i++) { core.add(new CoreMetadata()); setSeries(i); parsePosition(i);
core.clear(); for (int i=0; i<seriesCount; i++) { core.add(new CoreMetadata()); setSeries(i); parsePosition(i);