use of cbit.vcell.VirtualMicroscopy.importer.AnnotatedImageDataset 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.importer.AnnotatedImageDataset in project vcell by virtualcell.
the class DataSymbolsPanel method addVFrapDerivedImages.
private void addVFrapDerivedImages() {
// add special (computed) images from vFrap
AsynchClientTask[] taskArray = new AsynchClientTask[5];
// select the desired vfrap file
taskArray[0] = ChooseVFrapFile();
// load the images from the vfrap file, compute derived images, store them all in memory
taskArray[1] = new AsynchClientTask("Import images", 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");
}
// for derived images and ROIs
checkNameAvailability(hashTable, true, 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 and a ROIs subset for display purposes only (see next task)
AnnotatedImageDataset annotatedImages = xmlReader.getAnnotatedImageDataset(vFrapRoot, null);
hashTable.put("annotatedImages", annotatedImages);
ROI[] rois = xmlReader.getPrimaryROIs(XmlUtil.stringToXML(xmlString, null).getRootElement(), null);
LoadVFrapDisplayRoi(hashTable, annotatedImages, rois);
// ------ locate the special images within the vFrap files and load them in memory
if (!LoadVFrapSpecialImages(hashTable, vFrapRoot)) {
throw new RuntimeException("Unable to recover derived images from vFrap.");
}
// int startingIndexRecovery = xmlReader.getStartindIndexForRecovery(XmlUtil.stringToXML(xmlString, null).getRootElement());
// vFrapXmlHelper.LoadVFrapSpecialImages(annotatedImages, startingIndexRecovery); // prebleach average and first postbleach
// vFrapXmlHelper.LoadVFrapRoiCompositeImages(annotatedImages, rois);
}
};
// 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 mixedFieldDataName = (String) hashTable.get("mixedFieldDataName");
if (mixedFieldDataName.equals("")) {
JOptionPane.showMessageDialog(DataSymbolsPanel.this, "Field Data name " + mixedFieldDataName + " 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 ROIs, prebleach average and the first postbleach frame from memory to the database as field data
taskArray[3] = new AsynchClientTask("Saving roi masks, pre-bleach average and first post-bleach", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {
public void run(Hashtable<String, Object> hashTable) throws Exception {
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.");
}
ExternalDataIdentifier derivedEDI = SaveVFrapSpecialImagesAsFieldData(hashTable, documentManager);
hashTable.put("derivedEDI", derivedEDI);
}
};
// 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 {
ExternalDataIdentifier derivedEDI = (ExternalDataIdentifier) hashTable.get("derivedEDI");
BioModel bioModel = simulationContext.getBioModel();
CreateSaveVFrapDataSymbols(hashTable, bioModel, derivedEDI);
}
};
// save the ROIs, prebleach average and the first postbleach frame from memory to the database as field data
// taskArray[4] = new AsynchClientTask("Saving roi masks, pre-bleach average and first post-bleach", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {
// public void run(Hashtable<String, Object> hashTable) throws Exception {
// File vFrapFile = (File)hashTable.get("vFrapFile");
// if(vFrapFile == null) {
// return;
// }
// 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");
// }
//
// // 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));
// double[] firstPostBleach = (double[])hashTable.get("firstPostBleach");
// double[] prebleachAvg = (double[])hashTable.get("prebleachAverage");
// ROI[] rois = (ROI[])hashTable.get("rois");
//
// int NumTimePoints = 1;
// int NumChannels = 2+rois.length; // prebleach, postbleach, roi1, roi2 ... roiN
// String[] channelNames = new String[NumChannels];
// VariableType[] channelTypes = new VariableType[NumChannels];
// DataSymbolType[] channelVFrapImageType = new DataSymbolType[NumChannels];
// double[][][] pixData = new double[NumTimePoints][NumChannels][];
// pixData[0][0] = firstPostBleach;
// channelNames[0] = "firstPostBleach";
// channelTypes[0] = VariableType.VOLUME;
// channelVFrapImageType[0] = DataSymbolType.VFRAP_FIRST_POSTBLEACH;
// pixData[0][1] = prebleachAvg;
// channelNames[1] = "prebleachAverage";
// channelTypes[1] = VariableType.VOLUME;
// channelVFrapImageType[1] = DataSymbolType.VFRAP_PREBLEACH_AVG;
// int index = 0;
// for (ROI roi : rois){
// short[] ushortPixels = roi.getPixelsXYZ();
// double[] doublePixels = new double[ushortPixels.length];
// for (int i = 0; i < ushortPixels.length; i++) {
// doublePixels[i] = ((int)ushortPixels[i])&0xffff;
// }
// pixData[0][index+2] = doublePixels;
// channelNames[index+2] = "roi_"+index;
// channelTypes[index+2] = VariableType.VOLUME;
// channelVFrapImageType[index+2] = DataSymbolType.VFRAP_ROI;
// index++;
// }
// double[] times = new double[] { 0.0 };
//
// FieldDataFileOperationSpec vfrapMiscFieldDataOpSpec = new FieldDataFileOperationSpec();
// vfrapMiscFieldDataOpSpec.opType = FieldDataFileOperationSpec.FDOS_ADD;
// vfrapMiscFieldDataOpSpec.cartesianMesh = cartesianMesh;
// vfrapMiscFieldDataOpSpec.doubleSpecData = pixData;
// vfrapMiscFieldDataOpSpec.specEDI = null;
// vfrapMiscFieldDataOpSpec.varNames = channelNames;
// vfrapMiscFieldDataOpSpec.owner = dm.getUser();
// vfrapMiscFieldDataOpSpec.times = times;
// vfrapMiscFieldDataOpSpec.variableTypes = channelTypes;
// vfrapMiscFieldDataOpSpec.origin = origin;
// vfrapMiscFieldDataOpSpec.extent = extent;
// vfrapMiscFieldDataOpSpec.isize = isize;
// // localWorkspace.getDataSetControllerImpl().fieldDataFileOperation(fdos);
//
// // String formattedDate = (String)hashTable.get("formattedDate");
// // String fieldDataName = initialFieldDataName + "_vfrapMisc_" + formattedDate;
// String mixedFieldDataName = (String)hashTable.get("mixedFieldDataName");
// ExternalDataIdentifier vfrapMisc = dm.saveFieldData(vfrapMiscFieldDataOpSpec, mixedFieldDataName);
//
// hashTable.put("channelNames", channelNames);
// hashTable.put("channelVFrapImageType", channelVFrapImageType);
// hashTable.put("vfrapMisc", vfrapMisc);
// }
// };
// create the data symbols for the images saved above and display them in the tree/table
// taskArray[5] = 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");
// String mixedFieldDataName = (String)hashTable.get("mixedFieldDataName");
// String formattedDate = (String)hashTable.get("formattedDate");
// 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);
// // }
// DecimalFormat df = new DecimalFormat("0.##");
// // String fluorName = "fluor_" + df.format(time) + "_" + formattedDate;
// String fluorName = "fluor_" + df.format(time) + "_" + initialFieldDataName;
// // FieldFunctionArguments fluorFFArgs = new FieldFunctionArguments(timeSeriesEDI.getName(), fluorName, new Expression(time), VariableType.VOLUME);
// DataSymbol fluorDataSymbol = new FieldDataSymbol( fluorName, DataSymbolType.VFRAP_TIMEPOINT,
// simulationContext.getDataContext(), VCUnitDefinition.UNIT_TBD,
// timeSeriesEDI, fluorName, VariableType.VOLUME.getTypeName(), time);
// simulationContext.getDataContext().addDataSymbol(fluorDataSymbol);
// }
// // --- create the vFrap-specific symbols (ROIs, first postbleach, prebleach average)
// String[] channelNames = (String[])hashTable.get("channelNames");
// DataSymbolType[] channelVFrapImageType = (DataSymbolType[])hashTable.get("channelVFrapImageType");
// ExternalDataIdentifier vfrapMisc = (ExternalDataIdentifier)hashTable.get("vfrapMisc");
//
// for (int i=0; i<channelNames.length; i++) {
// String dataSymbolID = channelNames[i] + "_" + mixedFieldDataName;
// // while (simulationContext.getDataContext().getDataSymbol(dataSymbolID)!=null){
// // dataSymbolID = TokenMangler.getNextEnumeratedToken(dataSymbolID);
// // }
// // FieldFunctionArguments prebleachFFArgs = new FieldFunctionArguments(vfrapMisc.getName(), channelNames[i], new Expression(0.0), VariableType.VOLUME);
// // DataSymbol dataSymbol = new FieldDataSymbol(channelNames[i], channelVFrapImageType[i],
// // DataSymbol dataSymbol = new FieldDataSymbol(dataSymbolID + "_" + formattedDate, channelVFrapImageType[i],
// DataSymbol dataSymbol = new FieldDataSymbol(dataSymbolID, channelVFrapImageType[i],
// simulationContext.getDataContext(), VCUnitDefinition.UNIT_TBD,
// vfrapMisc, channelNames[i], VariableType.VOLUME.getTypeName(), 0D);
// simulationContext.getDataContext().addDataSymbol(dataSymbol);
// }
// }
// };
Hashtable<String, Object> hash = new Hashtable<String, Object>();
ClientTaskDispatcher.dispatch(this, hash, taskArray, false, true, null);
}
use of cbit.vcell.VirtualMicroscopy.importer.AnnotatedImageDataset in project vcell by virtualcell.
the class ImportRawTimeSeriesFromVFrapOp method importRawTimeSeriesFromVFrap.
public ImageTimeSeries<UShortImage> importRawTimeSeriesFromVFrap(File vfrapFile) throws Exception {
String xmlString = XmlUtil.getXMLString(vfrapFile.getAbsolutePath());
MicroscopyXmlReader xmlReader = new MicroscopyXmlReader(true);
Element vFrapRoot = XmlUtil.stringToXML(xmlString, null).getRootElement();
// loading frap images and a ROIs subset for display purposes only (see next task)
AnnotatedImageDataset annotatedImages = xmlReader.getAnnotatedImageDataset(vFrapRoot, null);
ImageDataset imageDataset = annotatedImages.getImageDataset();
UShortImage[] allImages = imageDataset.getAllImages();
double[] imageTimeStamps = imageDataset.getImageTimeStamps();
ImageTimeSeries<UShortImage> imageTimeSeries = new ImageTimeSeries<UShortImage>(UShortImage.class, allImages, imageTimeStamps, 1);
return imageTimeSeries;
}
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