use of cbit.vcell.VirtualMicroscopy.ImageDataset in project vcell by virtualcell.
the class PointSpreadFunctionManagement method importPointSpreadFunction.
public void importPointSpreadFunction() {
AsynchClientTask[] taskArray = new AsynchClientTask[3];
// select the desired PSF file
taskArray[0] = new AsynchClientTask("Select a file", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {
public void run(Hashtable<String, Object> hashTable) throws Exception {
ChoosePSFFile(hashTable);
}
};
// create and save the field data object
taskArray[1] = new AsynchClientTask("Import objects", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {
public void run(Hashtable<String, Object> hashTable) throws Exception {
Component requesterComponent = parentWindow;
DocumentWindow documentWindow = (DocumentWindow) BeanUtils.findTypeParentOfComponent(requesterComponent, DocumentWindow.class);
DocumentManager documentManager = documentWindow.getTopLevelWindowManager().getRequestManager().getDocumentManager();
if (documentManager == null) {
throw new RuntimeException("Not connected to server.");
}
// the following line of code may modify initialFieldDataName
// normal file name
checkNameAvailability(hashTable, false, documentManager, requesterComponent);
File filePSF = (File) hashTable.get("filePSF");
String initialFieldDataName = (String) hashTable.get("initialFieldDataName");
ImageDataset imageDataset = ImageDatasetReaderService.getInstance().getImageDatasetReader().readImageDataset(filePSF.getAbsolutePath(), null);
Extent extent = imageDataset.getExtent();
ISize isize = imageDataset.getISize();
Origin origin = new Origin(0, 0, 0);
CartesianMesh cartesianMesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, isize, new RegionImage(new VCImageUncompressed(null, new byte[isize.getXYZ()], extent, isize.getX(), isize.getY(), isize.getZ()), 0, null, null, RegionImage.NO_SMOOTHING));
// save field data
int NumTimePoints = imageDataset.getImageTimeStamps().length;
int NumChannels = 1;
double[][][] pixData = new double[NumTimePoints][NumChannels][];
for (int i = 0; i < NumTimePoints; i++) {
// images according to zIndex at specific time points(tIndex)
short[] originalData = imageDataset.getPixelsZ(0, i);
double[] doubleData = new double[originalData.length];
for (int j = 0; j < originalData.length; j++) {
doubleData[j] = 0x0000ffff & originalData[j];
}
pixData[i][NumChannels - 1] = doubleData;
}
FieldDataFileOperationSpec fdos = new FieldDataFileOperationSpec();
// try {
// fdos = ClientRequestManager.createFDOSFromImageFile(filePSF, false, null);
// } catch (DataFormatException ex) {
// throw new Exception("Cannot read image " + filePSF.getAbsolutePath()+"\n"+ex.getMessage());
// }
fdos.owner = documentManager.getUser();
fdos.opType = FieldDataFileOperationSpec.FDOS_ADD;
fdos.cartesianMesh = cartesianMesh;
fdos.doubleSpecData = pixData;
fdos.specEDI = null;
fdos.varNames = new String[] { SimulationContext.FLUOR_DATA_NAME };
fdos.times = imageDataset.getImageTimeStamps();
fdos.variableTypes = new VariableType[] { VariableType.VOLUME };
fdos.origin = origin;
fdos.extent = extent;
fdos.isize = isize;
ExternalDataIdentifier pSFImageEDI = documentManager.saveFieldData(fdos, initialFieldDataName);
hashTable.put("pSFImageEDI", pSFImageEDI);
}
};
// create a data symbol for the PSF image saved above as field data
taskArray[2] = new AsynchClientTask("Display Data Symbols", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {
public void run(Hashtable<String, Object> hashTable) throws Exception {
// --- create the data symbols associated with the time series
String initialFieldDataName = (String) hashTable.get("initialFieldDataName");
ExternalDataIdentifier pSFImageEDI = (ExternalDataIdentifier) hashTable.get("pSFImageEDI");
String fluorName = "psf_" + initialFieldDataName;
DataSymbol fluorDataSymbol = new FieldDataSymbol(fluorName, DataSymbolType.POINT_SPREAD_FUNCTION, simulationContext.getDataContext(), simulationContext.getModel().getUnitSystem().getInstance_TBD(), pSFImageEDI, SimulationContext.FLUOR_DATA_NAME, VariableType.VOLUME.getTypeName(), 0D);
simulationContext.getDataContext().addDataSymbol(fluorDataSymbol);
}
};
Hashtable<String, Object> hash = new Hashtable<String, Object>();
ClientTaskDispatcher.dispatch(parentWindow, hash, taskArray, false, true, null);
}
use of cbit.vcell.VirtualMicroscopy.ImageDataset in project vcell by virtualcell.
the class DataSymbolsPanel method addVFrapOriginalImages.
private void addVFrapOriginalImages() {
// add dataset (normal images) from vFrap
AsynchClientTask[] taskArray = new AsynchClientTask[5];
// select the desired vfrap file
taskArray[0] = ChooseVFrapFile();
taskArray[1] = new AsynchClientTask("Import objects", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {
public void run(Hashtable<String, Object> hashTable) throws Exception {
File vFrapFile = (File) hashTable.get("vFrapFile");
Component requesterComponent = DataSymbolsPanel.this;
DocumentWindow documentWindow = (DocumentWindow) BeanUtils.findTypeParentOfComponent(requesterComponent, DocumentWindow.class);
DocumentManager documentManager = documentWindow.getTopLevelWindowManager().getRequestManager().getDocumentManager();
if (documentManager == null) {
throw new RuntimeException("Not connected to server.");
}
// ex ccc8.vfrap
String vFrapFileNameExtended = vFrapFile.getName();
{
// we want to make sure to reload these strings from the hash later on
String initialFieldDataName = vFrapFileNameExtended.substring(0, vFrapFileNameExtended.indexOf(".vfrap"));
// we'll save here the "special" vFrap images (prebleach_avg, ...)
String mixedFieldDataName = initialFieldDataName + "Mx";
hashTable.put("initialFieldDataName", initialFieldDataName);
hashTable.put("mixedFieldDataName", mixedFieldDataName);
}
if (vFrapFileNameExtended.indexOf(".vfrap") <= -1) {
throw new RuntimeException("File extension must be .vfrap");
}
// normal images
checkNameAvailability(hashTable, false, documentManager, requesterComponent);
// ----- read needed info from Virtual FRAP xml file
System.out.println("Loading " + vFrapFileNameExtended + " ...");
String xmlString = XmlUtil.getXMLString(vFrapFile.getAbsolutePath());
MicroscopyXmlReader xmlReader = new MicroscopyXmlReader(true);
Element vFrapRoot = XmlUtil.stringToXML(xmlString, null).getRootElement();
// loading frap images
AnnotatedImageDataset annotatedImages = xmlReader.getAnnotatedImageDataset(vFrapRoot, null);
hashTable.put("annotatedImages", annotatedImages);
// loading ROIs for display purposes only (see next task)
ROI[] rois = xmlReader.getPrimaryROIs(XmlUtil.stringToXML(xmlString, null).getRootElement(), null);
LoadVFrapDisplayRoi(hashTable, annotatedImages, rois);
// Calendar cal = Calendar.getInstance();
// SimpleDateFormat sdf = new SimpleDateFormat("yyyyMMdd_hhmmss");
// DocumentWindow documentWindow = (DocumentWindow)BeanUtils.findTypeParentOfComponent(DataSymbolsPanel.this, DocumentWindow.class);
// DocumentManager documentManager = documentWindow.getTopLevelWindowManager().getRequestManager().getDocumentManager();
// VFrapXmlHelper vFrapXmlHelper = new VFrapXmlHelper();
// if(vFrapXmlHelper.isAlreadyImported(vFrapFileName, documentManager)) {
// throw new RuntimeException("FieldData name already in use.");
// }
// // bioModel.setName(vFrapFileName + "-" + sdf.format(cal.getTime()));
// bioModel.setName(vFrapFileName);
// BioModel feedbackModel = documentManager.save(bioModel, null);
// BioModelChildSummary childSummary = BioModelChildSummary.fromDatabaseSerialization(xmlString);
// BioModelInfo biomodelInfo = new BioModelInfo(feedbackModel.getVersion(), feedbackModel.getVersion().getVersionKey(), childSummary );
// documentWindow.getTopLevelWindowManager().getRequestManager().openDocument(biomodelInfo, documentWindow.getTopLevelWindowManager(), true);
}
};
// show the images from the vfrap file in an OverlayEditorPanelJAI dialog
taskArray[2] = new AsynchClientTask("Display images", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {
public void run(Hashtable<String, Object> hashTable) throws Exception {
String initialFieldDataName = (String) hashTable.get("initialFieldDataName");
if (initialFieldDataName.equals("")) {
JOptionPane.showMessageDialog(DataSymbolsPanel.this, "Field Data name " + initialFieldDataName + " already in use.");
// prevents the rest of tasks below from running
throw UserCancelException.CANCEL_GENERIC;
}
AnnotatedImageDataset annotatedImages = (AnnotatedImageDataset) hashTable.get("annotatedImages");
BufferedImage[] displayROI = (BufferedImage[]) hashTable.get("displayROI");
if (annotatedImages == null || displayROI == null) {
return;
}
// display the images
OverlayEditorPanelJAI overlayPanel = new OverlayEditorPanelJAI();
overlayPanel.setAllowAddROI(false);
ImageDataset imageDataset = annotatedImages.getImageDataset();
overlayPanel.setImages(imageDataset, 1, 0, new OverlayEditorPanelJAI.AllPixelValuesRange(1, 200));
overlayPanel.setAllROICompositeImage(displayROI, OverlayEditorPanelJAI.FRAP_DATA_INIT_PROPERTY);
int choice = DialogUtils.showComponentOKCancelDialog(DataSymbolsPanel.this, overlayPanel, "vFrap Field Data");
if (choice != JOptionPane.OK_OPTION) {
throw UserCancelException.CANCEL_GENERIC;
}
}
};
// save the timepoints from memory to the database as field data
taskArray[3] = new AsynchClientTask("Saving time series data", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {
public void run(Hashtable<String, Object> hashTable) throws Exception {
AnnotatedImageDataset annotatedImages = (AnnotatedImageDataset) hashTable.get("annotatedImages");
String initialFieldDataName = (String) hashTable.get("initialFieldDataName");
DocumentWindow documentWindow = (DocumentWindow) BeanUtils.findTypeParentOfComponent(DataSymbolsPanel.this, DocumentWindow.class);
DocumentManager dm = documentWindow.getTopLevelWindowManager().getRequestManager().getDocumentManager();
if (dm == null) {
throw new RuntimeException("Not connected to server.");
}
User owner = null;
Version version = simulationContext.getVersion();
if (version == null) {
// new document, so the owner is the user
owner = dm.getUser();
} else {
owner = simulationContext.getVersion().getOwner();
}
// mesh
ImageDataset imageDataset = annotatedImages.getImageDataset();
Extent extent = imageDataset.getExtent();
ISize isize = imageDataset.getISize();
Origin origin = new Origin(0, 0, 0);
CartesianMesh cartesianMesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, isize, new RegionImage(new VCImageUncompressed(null, new byte[isize.getXYZ()], extent, isize.getX(), isize.getY(), isize.getZ()), 0, null, null, RegionImage.NO_SMOOTHING));
// save field data
int NumTimePoints = imageDataset.getImageTimeStamps().length;
int NumChannels = 1;
double[][][] pixData = new double[NumTimePoints][NumChannels][];
for (int i = 0; i < NumTimePoints; i++) {
// images according to zIndex at specific time points(tIndex)
short[] originalData = imageDataset.getPixelsZ(0, i);
double[] doubleData = new double[originalData.length];
for (int j = 0; j < originalData.length; j++) {
doubleData[j] = 0x0000ffff & originalData[j];
}
pixData[i][NumChannels - 1] = doubleData;
}
FieldDataFileOperationSpec timeSeriesFieldDataOpSpec = new FieldDataFileOperationSpec();
timeSeriesFieldDataOpSpec.opType = FieldDataFileOperationSpec.FDOS_ADD;
timeSeriesFieldDataOpSpec.cartesianMesh = cartesianMesh;
timeSeriesFieldDataOpSpec.doubleSpecData = pixData;
timeSeriesFieldDataOpSpec.specEDI = null;
timeSeriesFieldDataOpSpec.varNames = new String[] { SimulationContext.FLUOR_DATA_NAME };
timeSeriesFieldDataOpSpec.owner = owner;
timeSeriesFieldDataOpSpec.times = imageDataset.getImageTimeStamps();
timeSeriesFieldDataOpSpec.variableTypes = new VariableType[] { VariableType.VOLUME };
timeSeriesFieldDataOpSpec.origin = origin;
timeSeriesFieldDataOpSpec.extent = extent;
timeSeriesFieldDataOpSpec.isize = isize;
// realignment for the case when first timepoint is not zero
if (timeSeriesFieldDataOpSpec.times[0] != 0) {
double shift = timeSeriesFieldDataOpSpec.times[0];
for (int i = 0; i < NumTimePoints; i++) {
timeSeriesFieldDataOpSpec.times[i] -= shift;
}
}
Calendar cal = Calendar.getInstance();
SimpleDateFormat sdf = new SimpleDateFormat("yyMMMdd_hhmmss");
String formattedDate = sdf.format(cal.getTime());
hashTable.put("formattedDate", formattedDate);
// ExternalDataIdentifier timeSeriesEDI = dm.saveFieldData(timeSeriesFieldDataOpSpec,
// initialFieldDataName + "_" + formattedDate);
ExternalDataIdentifier timeSeriesEDI = dm.saveFieldData(timeSeriesFieldDataOpSpec, initialFieldDataName);
hashTable.put("imageDataset", imageDataset);
hashTable.put("timeSeriesEDI", timeSeriesEDI);
}
};
// create the data symbols for the images saved above and display them in the tree/table
taskArray[4] = new AsynchClientTask("Display Data Symbols", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {
public void run(Hashtable<String, Object> hashTable) throws Exception {
// --- create the data symbols associated with the time series
String initialFieldDataName = (String) hashTable.get("initialFieldDataName");
ImageDataset imageDataset = (ImageDataset) hashTable.get("imageDataset");
ExternalDataIdentifier timeSeriesEDI = (ExternalDataIdentifier) hashTable.get("timeSeriesEDI");
for (double time : imageDataset.getImageTimeStamps()) {
// String fluorName = TokenMangler.fixTokenStrict("fluor_"+time+"_");
// while (simulationContext.getDataContext().getDataSymbol(fluorName)!=null){
// fluorName = TokenMangler.getNextEnumeratedToken(fluorName);
// }
// max time interval we can display is about 11 days
DecimalFormat df = new DecimalFormat("###000.00");
// String fluorName = "fluor_" + df.format(time) + "_" + formattedDate;
String fluorName = "fluor_" + df.format(time).substring(0, df.format(time).indexOf(".")) + "s" + df.format(time).substring(1 + df.format(time).indexOf(".")) + "_" + initialFieldDataName;
// FieldFunctionArguments fluorFFArgs = new FieldFunctionArguments(timeSeriesEDI.getName(), fluorName, new Expression(time), VariableType.VOLUME);
DataSymbol fluorDataSymbol = new FieldDataSymbol(fluorName, DataSymbolType.VFRAP_TIMEPOINT, simulationContext.getDataContext(), simulationContext.getModel().getUnitSystem().getInstance_TBD(), timeSeriesEDI, SimulationContext.FLUOR_DATA_NAME, VariableType.VOLUME.getTypeName(), time);
simulationContext.getDataContext().addDataSymbol(fluorDataSymbol);
}
}
};
Hashtable<String, Object> hash = new Hashtable<String, Object>();
ClientTaskDispatcher.dispatch(this, hash, taskArray, false, true, null);
// String name = null;
// try {
// getNewDataSymbolPanel().setSymbolName("");
// getNewDataSymbolPanel().setSymbolExpression("vcField(dataset1,var1,0.0,Volume)");
// int newSettings = org.vcell.util.gui.DialogUtils.showComponentOKCancelDialog(this, getNewDataSymbolPanel(), "New DataSymbol");
// if (newSettings == JOptionPane.OK_OPTION) {
// name = getNewDataSymbolPanel().getSymbolName();
// String expression = getNewDataSymbolPanel().getSymbolExpression();
// Expression exp = new Expression(expression);
// FunctionInvocation[] functionInvocations = exp.getFunctionInvocations(null);
// // DataSymbol ds = new FieldDataSymbol(DataSymbolType.GENERIC_SYMBOL, name, "",
// // simulationContext.getDataContext(), VCUnitDefinition.UNIT_TBD,
// // new FieldFunctionArguments(functionInvocations[0]));
// DataSymbol ds = new FieldDataSymbol(name, DataSymbolType.GENERIC_SYMBOL,
// simulationContext.getDataContext(), VCUnitDefinition.UNIT_TBD);
// simulationContext.getDataContext().addDataSymbol(ds);
// }
// } catch (java.lang.Throwable ivjExc) {
// DialogUtils.showErrorDialog(this, "Data symbol " + name + " already exists");
// }
}
use of cbit.vcell.VirtualMicroscopy.ImageDataset in project vcell by virtualcell.
the class ROIMultiPaintManager method smoothImageDataset.
private ImageDataset[] smoothImageDataset(ImageDataset[] origImageDatasetChannels, int enhanceImageAmount, ClientTaskStatusSupport clientTaskStatusSupport) throws Exception {
if (enhanceImageAmount == ROIMultiPaintManager.ENHANCE_NONE) {
return null;
}
ImageDataset[] smoothedImageDatasetChannels = new ImageDataset[origImageDatasetChannels.length];
int allCount = origImageDatasetChannels.length * origImageDatasetChannels[0].getSizeZ();
int progress = 0;
for (int c = 0; c < origImageDatasetChannels.length; c++) {
UShortImage[] smoothedZSections = new UShortImage[origImageDatasetChannels[c].getISize().getZ()];
// *2+1;
int radius = enhanceImageAmount;
// int[] divideTable = BoxBlurFilter.createDivideTable(radius);
short[] intermediateArr = new short[origImageDatasetChannels[c].getAllImages()[0].getPixels().length];
for (int z = 0; z < origImageDatasetChannels[c].getAllImages().length; z++) {
smoothedZSections[z] = new UShortImage(new short[origImageDatasetChannels[c].getISize().getX() * origImageDatasetChannels[c].getISize().getY()], ROIMultiPaintManager.DEFAULT_ORIGIN, ROIMultiPaintManager.DEFAULT_EXTENT, origImageDatasetChannels[c].getISize().getX(), origImageDatasetChannels[c].getISize().getY(), 1);
short[] enhancedData = smoothedZSections[z].getPixels();
short[] roiSourceData = origImageDatasetChannels[c].getAllImages()[z].getPixels();
BoxBlurFilter.blur(roiSourceData, intermediateArr, origImageDatasetChannels[c].getISize().getX(), origImageDatasetChannels[c].getISize().getY(), radius);
BoxBlurFilter.blur(intermediateArr, enhancedData, origImageDatasetChannels[c].getISize().getY(), origImageDatasetChannels[c].getISize().getX(), radius);
if (clientTaskStatusSupport != null) {
if (clientTaskStatusSupport.isInterrupted()) {
return null;
}
progress++;
clientTaskStatusSupport.setProgress(progress * 100 / allCount);
}
}
ImageDataset smoothedImageDataset = new ImageDataset(smoothedZSections, new double[] { 0 }, origImageDatasetChannels[c].getISize().getZ());
smoothedImageDatasetChannels[c] = smoothedImageDataset;
}
return smoothedImageDatasetChannels;
}
use of cbit.vcell.VirtualMicroscopy.ImageDataset in project vcell by virtualcell.
the class ROIMultiPaintManager method resizeImpl.
private void resizeImpl(ResizeInfo resizeInfo, ClientTaskStatusSupport clientTaskStatusSupport) throws Exception {
resizeImpl0(resizeInfo, (bHasOriginalData ? initImageDataSetChannels : null), roiComposite);
ISize newISize = resizeInfo.getNewSize();
ISize oldISize = resizeInfo.getOriginalSize();
Extent resizeExtent = createResizeExtent(originalExtent, oldISize, newISize);
if (bHasOriginalData) {
for (int c = 0; c < initImageDataSetChannels.length; c++) {
UShortImage[] zImageSet = new UShortImage[newISize.getZ()];
for (int z = 0; z < zImageSet.length; z++) {
zImageSet[z] = new UShortImage(resizeInfo.underlayC[c][z], originalOrigin, resizeExtent, newISize.getX(), newISize.getY(), 1);
}
initImageDataSetChannels[c] = new ImageDataset(zImageSet, new double[] { 0.0 }, newISize.getZ());
}
} else {
initImageDataSet(null, newISize);
}
roiComposite = resizeInfo.roiComposite;
updateAuxiliaryInfo(originalISize, clientTaskStatusSupport);
}
use of cbit.vcell.VirtualMicroscopy.ImageDataset in project vcell by virtualcell.
the class ROIMultiPaintManager method duplicateROIData.
private void duplicateROIData(final int newZSize) {
final AsynchClientTask extrudeTask = new AsynchClientTask("Extruding...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {
@Override
public void run(Hashtable<String, Object> hashTable) throws Exception {
ISize origSize = getImageDataSetChannel().getISize();
if (origSize.getZ() != 1 || newZSize < 1) {
throw new IllegalArgumentException("Extrude assumes starting with 2D and new Z size >= 1.");
}
UShortImage[][] newUnderLayImageArr = new UShortImage[initImageDataSetChannels.length][newZSize];
BufferedImage[] newROICompositeArr = new BufferedImage[newZSize];
for (int i = 0; i < newZSize; i++) {
for (int c = 0; c < initImageDataSetChannels.length; c++) {
// short[] zslice = new short[initImageDataSetChannels[c].getAllImages()[0].getPixels().length];
// System.arraycopy(initImageDataSetChannels[c].getAllImages()[0].getPixels(), 0, zslice, 0, zslice.length);
newUnderLayImageArr[c][i] = new UShortImage(// zslice,
initImageDataSetChannels[c].getAllImages()[0].getPixels().clone(), DEFAULT_ORIGIN, DEFAULT_EXTENT, initImageDataSetChannels[c].getAllImages()[0].getNumX(), initImageDataSetChannels[c].getAllImages()[0].getNumY(), 1);
}
newROICompositeArr[i] = new BufferedImage(roiComposite[0].getWidth(), roiComposite[0].getHeight(), BufferedImage.TYPE_BYTE_INDEXED, getContrastIndexColorModel());
System.arraycopy((byte[]) ((DataBufferByte) roiComposite[0].getRaster().getDataBuffer()).getData(), 0, (byte[]) ((DataBufferByte) newROICompositeArr[i].getRaster().getDataBuffer()).getData(), 0, origSize.getX() * origSize.getY());
}
for (int c = 0; c < initImageDataSetChannels.length; c++) {
initImageDataSetChannels[c] = new ImageDataset(newUnderLayImageArr[c], null, newZSize);
}
roiComposite = newROICompositeArr;
if (!(enhanceImageAmount == ROIMultiPaintManager.ENHANCE_NONE)) {
getClientTaskStatusSupport().setMessage("smoothing...");
}
updateAuxiliaryInfo(origSize, getClientTaskStatusSupport());
}
};
final AsynchClientTask updatePanelTask = getUpdateDisplayAfterCropTask();
ClientTaskDispatcher.dispatch(overlayEditorPanelJAI, new Hashtable<String, Object>(), new AsynchClientTask[] { extrudeTask, updatePanelTask }, false, false, null, true);
}
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