use of org.vcell.util.ISize in project vcell by virtualcell.
the class BioformatsImageDatasetReader method getImageSizeInfoForceZ.
@Override
public ImageSizeInfo getImageSizeInfoForceZ(String fileName, int forceZSize) throws Exception {
try (TTransport transport = new TSocket("localhost", port)) {
transport.open();
TProtocol protocol = new TBinaryProtocol(transport);
ImageDatasetService.Client client = new ImageDatasetService.Client(protocol);
org.vcell.imagedataset.ImageSizeInfo t_imageSizeInfo = client.getImageSizeInfoForceZ(fileName, forceZSize);
org.vcell.imagedataset.ISize t_size = t_imageSizeInfo.getISize();
double[] timePoints = new double[t_imageSizeInfo.getTimePoints().size()];
for (int i = 0; i < t_imageSizeInfo.getTimePointsSize(); i++) {
timePoints[i] = t_imageSizeInfo.getTimePoints().get(i);
}
ImageSizeInfo imageSizeInfo = new ImageSizeInfo(t_imageSizeInfo.imagePath, new ISize(t_size.getX(), t_size.getY(), t_size.getZ()), t_imageSizeInfo.numChannels, timePoints, t_imageSizeInfo.selectedTimeIndex);
return imageSizeInfo;
}
}
use of org.vcell.util.ISize in project vcell by virtualcell.
the class RunRefSimulationFastOp method saveExternalData.
private void saveExternalData(Image image, String varName, ExternalDataIdentifier newROIExtDataID, LocalWorkspace localWorkspace) throws ObjectNotFoundException, ImageException, IOException {
Extent extent = image.getExtent();
Origin origin = image.getOrigin();
ISize isize = image.getISize();
VCImage vcImage = new VCImageUncompressed(null, new byte[isize.getXYZ()], extent, isize.getX(), isize.getY(), isize.getZ());
RegionImage regionImage = new RegionImage(vcImage, 0, null, null, RegionImage.NO_SMOOTHING);
CartesianMesh simpleCartesianMesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, isize, regionImage);
int NumTimePoints = 1;
int NumChannels = 1;
// dimensions: time points, channels, whole image ordered by z slices.
double[][][] pixData = new double[NumTimePoints][NumChannels][];
pixData[0][0] = image.getDoublePixels();
FieldDataFileOperationSpec fdos = new FieldDataFileOperationSpec();
fdos.opType = FieldDataFileOperationSpec.FDOS_ADD;
fdos.cartesianMesh = simpleCartesianMesh;
fdos.doubleSpecData = pixData;
fdos.specEDI = newROIExtDataID;
fdos.varNames = new String[] { varName };
fdos.owner = LocalWorkspace.getDefaultOwner();
fdos.times = new double[] { 0.0 };
fdos.variableTypes = new VariableType[] { VariableType.VOLUME };
fdos.origin = origin;
fdos.extent = extent;
fdos.isize = isize;
localWorkspace.getDataSetControllerImpl().fieldDataFileOperation(fdos);
}
use of org.vcell.util.ISize in project vcell by virtualcell.
the class ClientRequestManager method createFDOSFromSurfaceFile.
public static FieldDataFileOperationSpec createFDOSFromSurfaceFile(File surfaceFile) throws Exception {
SurfaceCollection surfaceCollection = createSurfaceCollectionFromSurfaceFile(surfaceFile);
if (surfaceCollection != null) {
Geometry geometry = RayCaster.createGeometryFromSTL(new GeometryThumbnailImageFactoryAWT(), surfaceCollection, 1000000);
FieldDataFileOperationSpec fdfos = new FieldDataFileOperationSpec();
fdfos.origin = geometry.getOrigin();
fdfos.extent = geometry.getExtent();
VCImage image = geometry.getGeometrySpec().getImage();
if (image.getNumPixelClasses() == 1) {
throw new Exception("STL import failed during processing, pixelclass count=1");
}
fdfos.isize = new ISize(image.getNumX(), image.getNumY(), image.getNumZ());
byte[] pixels = image.getPixels();
short[] dataToSegment = new short[image.getNumXYZ()];
for (int i = 0; i < pixels.length; i++) {
dataToSegment[i] = pixels[i];
}
fdfos.shortSpecData = new short[][][] { { dataToSegment } };
return fdfos;
}
return null;
}
use of org.vcell.util.ISize in project vcell by virtualcell.
the class ClientRequestManager method createFDOSFromVCImage.
private static FieldDataFileOperationSpec createFDOSFromVCImage(VCImage dbImage) throws ImageException {
int[] temp = new int[256];
short[] templateShorts = new short[dbImage.getNumXYZ()];
for (int i = 0; i < dbImage.getPixels().length; i++) {
templateShorts[i] = (short) (0x00FF & dbImage.getPixels()[i]);
temp[templateShorts[i]]++;
}
for (int j = 0; j < dbImage.getPixelClasses().length; j++) {
short tempshort = (short) (0x00FF & dbImage.getPixelClasses()[j].getPixel());
}
FieldDataFileOperationSpec fdfos = null;
fdfos = new FieldDataFileOperationSpec();
fdfos.origin = new Origin(0, 0, 0);
fdfos.extent = dbImage.getExtent();
fdfos.isize = new ISize(dbImage.getNumX(), dbImage.getNumY(), dbImage.getNumZ());
fdfos.shortSpecData = new short[][][] { { templateShorts } };
return fdfos;
}
use of org.vcell.util.ISize in project vcell by virtualcell.
the class ClientRequestManager method createNewGeometryTasks.
public AsynchClientTask[] createNewGeometryTasks(final TopLevelWindowManager requester, final VCDocument.DocumentCreationInfo documentCreationInfo, final AsynchClientTask[] afterTasks, final String okButtonText) {
if (!isImportGeometryType(documentCreationInfo)) {
throw new IllegalArgumentException("Analytic geometry not implemented.");
}
AsynchClientTask selectImageFileTask = getSelectImageFileTask(requester.getComponent(), getUserPreferences());
final String INITIAL_ANNOTATION = "INITIAL_ANNOTATION";
final String NEW_IMAGE_SIZE_INFO = "NEW_IMAGE_SIZE_INFO";
final String FD_TIMEPOINTS = "FD_TIMEPOINTS";
AsynchClientTask parseImageTask = getParseImageTask(requester.getComponent(), documentCreationInfo, getMdiManager());
AsynchClientTask getFieldDataImageParams = new AsynchClientTask("Getting DB Image parameters...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {
@Override
public void run(Hashtable<String, Object> hashTable) throws Exception {
VCDocument.GeomFromFieldDataCreationInfo docInfo = (VCDocument.GeomFromFieldDataCreationInfo) documentCreationInfo;
PDEDataContext pdeDataContext = getMdiManager().getFieldDataWindowManager().getPDEDataContext(docInfo.getExternalDataID(), null);
CartesianMesh mesh = pdeDataContext.getCartesianMesh();
ISize meshISize = new ISize(mesh.getSizeX(), mesh.getSizeY(), mesh.getSizeZ());
double[] timePoints = pdeDataContext.getTimePoints();
hashTable.put(FD_MESH, mesh);
hashTable.put(FD_MESHISIZE, meshISize);
hashTable.put(FD_TIMEPOINTS, timePoints);
}
};
AsynchClientTask queryImageResizeTask = new AsynchClientTask("Query File Image Resize...", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {
@Override
public void run(Hashtable<String, Object> hashTable) throws Exception {
String importSourceName = (String) hashTable.get(IMPORT_SOURCE_NAME);
if ((ImageSizeInfo) hashTable.get(ORIG_IMAGE_SIZE_INFO) != null) {
// from file
ImageSizeInfo newImagesiSizeInfo = queryImageResize(requester.getComponent(), (ImageSizeInfo) hashTable.get(ORIG_IMAGE_SIZE_INFO), true);
hashTable.put(NEW_IMAGE_SIZE_INFO, newImagesiSizeInfo);
} else if (documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_FIELDDATA) {
// from fielddata
VCDocument.GeomFromFieldDataCreationInfo docInfo = (VCDocument.GeomFromFieldDataCreationInfo) documentCreationInfo;
double[] fieldDataTimes = (double[]) hashTable.get(FD_TIMEPOINTS);
hashTable.remove(FD_TIMEPOINTS);
ISize fieldDataISize = (ISize) hashTable.get(FD_MESHISIZE);
ImageSizeInfo origImageSizeInfo = new ImageSizeInfo(importSourceName, fieldDataISize, 1, fieldDataTimes, null);
ImageSizeInfo newImagesiSizeInfo = queryImageResize(requester.getComponent(), origImageSizeInfo, true);
hashTable.put(NEW_IMAGE_SIZE_INFO, newImagesiSizeInfo);
hashTable.put(IMPORT_SOURCE_NAME, "FieldData: " + docInfo.getExternalDataID().getName() + " varName=" + docInfo.getVarName() + " timeIndex=" + newImagesiSizeInfo.getTimePoints()[newImagesiSizeInfo.getSelectedTimeIndex()]);
}
}
};
AsynchClientTask importFileImageTask = getImportFileImageTask(documentCreationInfo);
AsynchClientTask resizeImageTask = getResizeImageTask(documentCreationInfo);
AsynchClientTask finishTask = new AsynchClientTask("Finishing...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {
@Override
public void run(final Hashtable<String, Object> hashTable) throws Exception {
getClientTaskStatusSupport().setMessage("Initializing...");
final ROIMultiPaintManager roiMultiPaintManager = new ROIMultiPaintManager();
roiMultiPaintManager.setDocumentManager(ClientRequestManager.this.getDocumentManager());
roiMultiPaintManager.initROIAndUnderlay((FieldDataFileOperationSpec) hashTable.get(FDFOS));
final Geometry[] geomHolder = new Geometry[1];
final VCPixelClass[] postProcessPixelClasses = (VCPixelClass[]) hashTable.get(VCPIXELCLASSES);
AsynchClientTask task1 = new AsynchClientTask("edit geometry", AsynchClientTask.TASKTYPE_SWING_BLOCKING, false) {
@Override
public void run(Hashtable<String, Object> hashTable) throws Exception {
geomHolder[0] = roiMultiPaintManager.showGUI(okButtonText, (String) hashTable.get(IMPORT_SOURCE_NAME), (Component) hashTable.get(GUI_PARENT), (String) hashTable.get(INITIAL_ANNOTATION), postProcessPixelClasses, getUserPreferences(), (hashTable.get(BioModelWindowManager.FIELD_DATA_FLAG) == null ? false : ((Boolean) hashTable.get(BioModelWindowManager.FIELD_DATA_FLAG)).booleanValue()));
}
};
AsynchClientTask task2 = new AsynchClientTask("update geometry", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {
@Override
public void run(Hashtable<String, Object> hashTable) throws Exception {
// Create default name for image
String dateTimeString = BeanUtils.generateDateTimeString();
geomHolder[0].getGeometrySpec().getImage().setName("img_" + dateTimeString);
geomHolder[0].setName("geom_" + dateTimeString);
// cause update in this thread so later swing threads won't be delayed
geomHolder[0].precomputeAll(new GeometryThumbnailImageFactoryAWT());
hashTable.put("doc", geomHolder[0]);
}
};
AsynchClientTask[] finalTasks = afterTasks;
if (finalTasks == null) {
finalTasks = new AsynchClientTask[] { getSaveImageAndGeometryTask() };
}
AsynchClientTask[] tasks = new AsynchClientTask[2 + finalTasks.length];
tasks[0] = task1;
tasks[1] = task2;
System.arraycopy(finalTasks, 0, tasks, 2, finalTasks.length);
ClientTaskDispatcher.dispatch((Component) hashTable.get(GUI_PARENT), hashTable, tasks, false, false, null, true);
}
};
Vector<AsynchClientTask> tasksV = new Vector<AsynchClientTask>();
if (documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_FROM_SCRATCH) {
tasksV.addAll(Arrays.asList(new AsynchClientTask[] { parseImageTask, finishTask }));
} else if (documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_FROM_WORKSPACE_ANALYTIC) {
tasksV.addAll(Arrays.asList(new AsynchClientTask[] { parseImageTask, finishTask }));
} else if (documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_FROM_WORKSPACE_IMAGE) {
tasksV.addAll(Arrays.asList(new AsynchClientTask[] { parseImageTask, resizeImageTask, finishTask }));
} else if (documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_FILE) {
tasksV.addAll(Arrays.asList(new AsynchClientTask[] { selectImageFileTask, parseImageTask, queryImageResizeTask, importFileImageTask, /* resizes */
finishTask }));
} else // }
if (documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_FIELDDATA) {
tasksV.addAll(Arrays.asList(new AsynchClientTask[] { getFieldDataImageParams, queryImageResizeTask, parseImageTask, resizeImageTask, finishTask }));
}
return tasksV.toArray(new AsynchClientTask[0]);
}
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