Example 11 with VCPixelClass
use of cbit.image.VCPixelClass 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.");
}
final String IMPORT_SOURCE_NAME = "IMPORT_SOURCE_NAME";
// Get image from file
AsynchClientTask selectImageFileTask = new AsynchClientTask("select image file", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {
@Override
public void run(Hashtable<String, Object> hashTable) throws Exception {
File imageFile = DatabaseWindowManager.showFileChooserDialog(requester, null, getUserPreferences(), JFileChooser.FILES_AND_DIRECTORIES);
hashTable.put("imageFile", imageFile);
hashTable.put(IMPORT_SOURCE_NAME, "File: " + imageFile.getName());
}
};
final String FDFOS = "FDFOS";
final String INITIAL_ANNOTATION = "INITIAL_ANNOTATION";
final String ORIG_IMAGE_SIZE_INFO = "ORIG_IMAGE_SIZE_INFO";
final String NEW_IMAGE_SIZE_INFO = "NEW_IMAGE_SIZE_INFO";
final String DIR_FILES = "DIR_FILES";
final String FD_MESH = "FD_MESH";
final String FD_MESHISIZE = "FD_MESHISIZE";
final String FD_TIMEPOINTS = "FD_TIMEPOINTS";
AsynchClientTask parseImageTask = new AsynchClientTask("read and parse image file", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {
@Override
public void run(final Hashtable<String, Object> hashTable) throws Exception {
final Component guiParent = (Component) hashTable.get(ClientRequestManager.GUI_PARENT);
try {
FieldDataFileOperationSpec fdfos = null;
if (documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_FIJI_IMAGEJ) {
hashTable.put("imageFile", ImageJHelper.vcellWantImage(getClientTaskStatusSupport(), "Image for new VCell geometry"));
}
if (documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_BLENDER) {
hashTable.put("imageFile", ImageJHelper.vcellWantSurface(getClientTaskStatusSupport(), "Image for new VCell geometry"));
}
if (documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_FILE || documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_FIJI_IMAGEJ || documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_BLENDER) {
File imageFile = (File) hashTable.get("imageFile");
if (imageFile == null) {
throw new Exception("No file selected");
}
if (ExtensionFilter.isMatchingExtension(imageFile, ".nrrd")) {
DataInputStream dis = null;
try {
dis = new DataInputStream(new BufferedInputStream(new FileInputStream(imageFile)));
int xsize = 1;
int ysize = 1;
int zsize = 1;
double xspace = 1.0;
double yspace = 1.0;
double zspace = 1.0;
NRRDTYPE type = null;
NRRDENCODING encoding = null;
int dimension = -1;
// read header lines
while (true) {
@SuppressWarnings("deprecation") String line = dis.readLine();
if (line == null || line.length() == 0) {
break;
}
StringTokenizer stringTokenizer = new StringTokenizer(line, ": ");
String headerParam = stringTokenizer.nextToken();
// System.out.println(headerParam);
if (headerParam.equals("sizes")) {
if (dimension != -1) {
xsize = Integer.parseInt(stringTokenizer.nextToken());
if (dimension >= 2) {
ysize = Integer.parseInt(stringTokenizer.nextToken());
}
if (dimension >= 3) {
zsize = Integer.parseInt(stringTokenizer.nextToken());
}
for (int i = 4; i < dimension; i++) {
if (Integer.parseInt(stringTokenizer.nextToken()) != 1) {
throw new Exception("Dimensions > 3 not supported");
}
}
} else {
throw new Exception("dimension expected to be set before reading sizes");
}
} else if (headerParam.equals("spacings")) {
if (dimension != -1) {
xspace = Double.parseDouble(stringTokenizer.nextToken());
if (dimension >= 2) {
yspace = Double.parseDouble(stringTokenizer.nextToken());
}
if (dimension >= 3) {
zspace = Double.parseDouble(stringTokenizer.nextToken());
}
// ignore other dimension spacings
} else {
throw new Exception("dimension expected to be set before reading spacings");
}
} else if (headerParam.equals("type")) {
String nextToken = stringTokenizer.nextToken();
if (nextToken.equalsIgnoreCase("double")) {
type = NRRDTYPE.DOUBLE;
} else if (nextToken.equalsIgnoreCase("float")) {
type = NRRDTYPE.FLOAT;
} else if (nextToken.equalsIgnoreCase("unsigned")) {
nextToken = stringTokenizer.nextToken();
if (nextToken.equalsIgnoreCase("char")) {
type = NRRDTYPE.UNSIGNEDCHAR;
} else {
throw new Exception("Unknown nrrd data type=" + nextToken);
}
} else {
throw new Exception("Unknown nrrd data type=" + nextToken);
}
} else if (headerParam.equals("dimension")) {
dimension = Integer.parseInt(stringTokenizer.nextToken());
if (dimension < 1) {
throw new Exception("unexpected dimension=" + dimension);
}
} else if (headerParam.equals("encoding")) {
encoding = NRRDENCODING.valueOf(stringTokenizer.nextToken().toUpperCase());
}
}
BufferedInputStream bis = null;
if (encoding == NRRDENCODING.GZIP) {
dis.close();
bis = new BufferedInputStream(new FileInputStream(imageFile));
boolean bnewLine = false;
while (true) {
int currentChar = bis.read();
if (currentChar == '\n') {
if (bnewLine) {
// 2 newlines end header
break;
}
bnewLine = true;
} else {
bnewLine = false;
}
}
GZIPInputStream gzipInputStream = new GZIPInputStream(bis);
dis = new DataInputStream(gzipInputStream);
}
double[] data = new double[xsize * ysize * zsize];
double minValue = Double.POSITIVE_INFINITY;
double maxValue = Double.NEGATIVE_INFINITY;
for (int i = 0; i < data.length; i++) {
if (i % 262144 == 0) {
if (getClientTaskStatusSupport() != null) {
getClientTaskStatusSupport().setMessage("Reading " + encoding + " " + type + " NRRD data " + (((long) i * (long) 100) / (long) data.length) + " % done.");
}
}
if (type == NRRDTYPE.DOUBLE) {
data[i] = dis.readDouble();
} else if (type == NRRDTYPE.FLOAT) {
data[i] = dis.readFloat();
} else if (type == NRRDTYPE.UNSIGNEDCHAR) {
data[i] = dis.readUnsignedByte();
} else {
throw new Exception("Unexpected data type=" + type.toString());
}
minValue = Math.min(minValue, data[i]);
maxValue = Math.max(maxValue, data[i]);
}
dis.close();
if (getClientTaskStatusSupport() != null) {
getClientTaskStatusSupport().setMessage("Scaling " + encoding + " " + type + " NRRD data.");
}
short[] dataToSegment = new short[data.length];
double scaleShort = Math.pow(2, Short.SIZE) - 1;
for (int i = 0; i < data.length; i++) {
dataToSegment[i] |= (int) ((data[i] - minValue) / (maxValue - minValue) * scaleShort);
}
fdfos = new FieldDataFileOperationSpec();
fdfos.origin = new Origin(0, 0, 0);
fdfos.extent = new Extent((xsize == 1 ? .5 : (xsize) * xspace), (ysize == 1 ? .5 : (ysize) * yspace), (zsize == 1 ? .5 : (zsize) * zspace));
fdfos.isize = new ISize(xsize, ysize, zsize);
fdfos.shortSpecData = new short[][][] { { dataToSegment } };
} finally {
if (dis != null) {
try {
dis.close();
} catch (Exception e) {
e.printStackTrace();
}
}
}
} else if ((fdfos = createFDOSFromSurfaceFile(imageFile)) != null) {
// try surface file formats
// work already done at this point
} else {
File[] dirFiles = null;
ImageSizeInfo origImageSizeInfo = null;
if (imageFile.isDirectory()) {
dirFiles = imageFile.listFiles(new java.io.FileFilter() {
public boolean accept(File pathname) {
// exclude windows Thumbs.db
return pathname.isFile() && !pathname.isHidden();
}
});
if (dirFiles.length == 0) {
throw new Exception("No valid files in selected directory");
}
String fileExt0 = null;
for (int i = 0; i < dirFiles.length; i++) {
int lastDot = dirFiles[i].getName().lastIndexOf('.');
String fileExt = (lastDot != -1 ? dirFiles[i].getName().substring(lastDot) : null);
if (dirFiles[i].isDirectory()) {
fileExt = "dir";
}
if (i == 0) {
fileExt0 = fileExt;
} else if (!Compare.isEqualOrNull(fileExt, fileExt0)) {
String result = DialogUtils.showWarningDialog(requester.getComponent(), "Files in '" + imageFile.getAbsolutePath() + "' have different name extensions, continue?", new String[] { "OK", "Cancel" }, "Cancel");
if (!"OK".equals(result)) {
throw UserCancelException.CANCEL_FILE_SELECTION;
}
break;
}
}
hashTable.put(IMPORT_SOURCE_NAME, "Directory: " + imageFile.getAbsolutePath());
origImageSizeInfo = ImageDatasetReaderService.getInstance().getImageDatasetReader().getImageSizeInfoForceZ(dirFiles[0].getAbsolutePath(), dirFiles.length);
if (dirFiles.length > 1) {
final String importZ = "Import Z-Sections";
final String cancelOption = "Cancel";
String result = DialogUtils.showWarningDialog(guiParent, "Import all files in directory '" + imageFile.getAbsolutePath() + "' as Z-Sections", new String[] { importZ, cancelOption }, importZ);
if (result.equals(cancelOption)) {
throw UserCancelException.CANCEL_GENERIC;
}
}
hashTable.put(DIR_FILES, dirFiles);
} else {
origImageSizeInfo = ImageDatasetReaderService.getInstance().getImageDatasetReader().getImageSizeInfo(imageFile.getAbsolutePath());
hashTable.put(IMPORT_SOURCE_NAME, "File: " + imageFile.getAbsolutePath());
}
hashTable.put(ORIG_IMAGE_SIZE_INFO, origImageSizeInfo);
return;
}
} else if (documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_FIELDDATA) {
getClientTaskStatusSupport().setMessage("Reading data from VCell server.");
VCDocument.GeomFromFieldDataCreationInfo docInfo = (VCDocument.GeomFromFieldDataCreationInfo) documentCreationInfo;
PDEDataContext pdeDataContext = getMdiManager().getFieldDataWindowManager().getPDEDataContext(docInfo.getExternalDataID(), null);
ImageSizeInfo newImageSizeInfo = (ImageSizeInfo) hashTable.get(NEW_IMAGE_SIZE_INFO);
pdeDataContext.setVariableNameAndTime(docInfo.getVarName(), newImageSizeInfo.getTimePoints()[newImageSizeInfo.getSelectedTimeIndex()]);
double[] data = pdeDataContext.getDataValues();
hashTable.put(INITIAL_ANNOTATION, hashTable.get(IMPORT_SOURCE_NAME));
CartesianMesh mesh = (CartesianMesh) hashTable.get(FD_MESH);
ISize meshISize = (ISize) hashTable.get(FD_MESHISIZE);
double minValue = Double.POSITIVE_INFINITY;
double maxValue = Double.NEGATIVE_INFINITY;
for (int i = 0; i < data.length; i++) {
minValue = Math.min(minValue, data[i]);
maxValue = Math.max(maxValue, data[i]);
}
short[] dataToSegment = new short[data.length];
double scaleShort = Math.pow(2, Short.SIZE) - 1;
for (int i = 0; i < data.length; i++) {
dataToSegment[i] |= (int) ((data[i] - minValue) / (maxValue - minValue) * scaleShort);
}
fdfos = new FieldDataFileOperationSpec();
fdfos.origin = mesh.getOrigin();
fdfos.extent = mesh.getExtent();
fdfos.isize = meshISize;
fdfos.shortSpecData = new short[][][] { { dataToSegment } };
} else if (documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_FROM_SCRATCH) {
ISize isize = getISizeFromUser(guiParent, new ISize(256, 256, 8), "Enter # of pixels for x,y,z (e.g. 3D{256,256,8}, 2D{256,256,1}, 1D{256,1,1})");
fdfos = new FieldDataFileOperationSpec();
fdfos.origin = new Origin(0, 0, 0);
fdfos.extent = new Extent(1, 1, 1);
fdfos.isize = isize;
hashTable.put(IMPORT_SOURCE_NAME, "Scratch: New Geometry");
// final int SCRATCH_SIZE_LIMIT = 512*512*20;
// if(isize.getXYZ() > (SCRATCH_SIZE_LIMIT)){
// throw new Exception("Total pixels (x*y*z) cannot be >"+SCRATCH_SIZE_LIMIT+".");
// }
} else if (documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_FROM_WORKSPACE_ANALYTIC) {
if (hashTable.get(ClientRequestManager.GEOM_FROM_WORKSPACE) != null) {
Geometry workspaceGeom = (Geometry) hashTable.get(ClientRequestManager.GEOM_FROM_WORKSPACE);
ISize defaultISize = workspaceGeom.getGeometrySpec().getDefaultSampledImageSize();
ISize isize = getISizeFromUser(guiParent, defaultISize, "Warning: converting analytic expression geometry into an image based geometry\nwill remove analytic expressions after new image is created.\n\n" + "Enter size (x,y,z) for new geometry image (e.g. " + defaultISize.getX() + "," + defaultISize.getY() + "," + defaultISize.getZ() + ")");
hashTable.put(IMPORT_SOURCE_NAME, "Workspace from Analytic Geometry");
VCImage img = workspaceGeom.getGeometrySpec().createSampledImage(isize);
Enumeration<SubVolume> enumSubvolume = workspaceGeom.getGeometrySpec().getAnalyticOrCSGSubVolumes();
ArrayList<VCPixelClass> vcPixelClassArrList = new ArrayList<VCPixelClass>();
while (enumSubvolume.hasMoreElements()) {
SubVolume subVolume = enumSubvolume.nextElement();
vcPixelClassArrList.add(new VCPixelClass(null, subVolume.getName(), subVolume.getHandle()));
}
if (vcPixelClassArrList.size() > img.getPixelClasses().length) {
String result = DialogUtils.showOKCancelWarningDialog(requester.getComponent(), null, "Warning: sampling size is too small to include all subvolumes.");
if (result == null || !result.equals(SimpleUserMessage.OPTION_OK)) {
throw UserCancelException.CANCEL_GENERIC;
}
}
hashTable.put(VCPIXELCLASSES, vcPixelClassArrList.toArray(new VCPixelClass[0]));
fdfos = createFDOSFromVCImage(img);
} else {
throw new Exception("Expecting image source for GEOM_OPTION_FROM_WORKSPACE_ANALYTIC");
}
} else if (documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_FROM_WORKSPACE_IMAGE) {
if (hashTable.get(ClientRequestManager.GEOM_FROM_WORKSPACE) != null) {
Geometry workspaceGeom = (Geometry) hashTable.get(ClientRequestManager.GEOM_FROM_WORKSPACE);
hashTable.put(IMPORT_SOURCE_NAME, "Workspace Image");
fdfos = createFDOSFromVCImage(workspaceGeom.getGeometrySpec().getImage());
if (workspaceGeom.getGeometrySpec().getImage().getDescription() != null) {
hashTable.put(INITIAL_ANNOTATION, workspaceGeom.getGeometrySpec().getImage().getDescription());
}
hashTable.put(VCPIXELCLASSES, workspaceGeom.getGeometrySpec().getImage().getPixelClasses());
} else {
throw new Exception("Expecting image source for GEOM_OPTION_FROM_WORKSPACE");
}
}
hashTable.put(FDFOS, fdfos);
} catch (DataFormatException ex) {
throw new Exception("Cannot read image file.\n" + ex.getMessage());
}
}
};
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 = new AsynchClientTask("Importing Image from File...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {
@Override
public void run(Hashtable<String, Object> hashTable) throws Exception {
if (documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_FILE && hashTable.get(FDFOS) == null) {
ImageSizeInfo origImageSizeInfo = (ImageSizeInfo) hashTable.get(ORIG_IMAGE_SIZE_INFO);
ImageSizeInfo newImageSizeInfo = (ImageSizeInfo) hashTable.get(NEW_IMAGE_SIZE_INFO);
File[] dirFiles = (File[]) hashTable.get(DIR_FILES);
File imageFile = (File) hashTable.get("imageFile");
FieldDataFileOperationSpec fdfos = null;
boolean bMergeChannels = origImageSizeInfo.getNumChannels() != newImageSizeInfo.getNumChannels();
ISize resize = (origImageSizeInfo.getiSize().compareEqual(newImageSizeInfo.getiSize()) ? null : newImageSizeInfo.getiSize());
if (dirFiles != null) {
Arrays.sort(dirFiles, new Comparator<File>() {
public int compare(File o1, File o2) {
return o1.getName().compareToIgnoreCase(o2.getName());
}
});
hashTable.put(INITIAL_ANNOTATION, dirFiles[0].getAbsolutePath() + "\n.\n.\n.\n" + dirFiles[dirFiles.length - 1].getAbsolutePath());
short[][] dataToSegment = null;
ISize isize = null;
Origin origin = null;
Extent extent = null;
int sizeXY = 0;
ISize firstImageISize = null;
for (int i = 0; i < dirFiles.length; i++) {
ImageDataset[] imageDatasets = ImageDatasetReaderService.getInstance().getImageDatasetReader().readImageDatasetChannels(dirFiles[i].getAbsolutePath(), null, bMergeChannels, null, resize);
for (int c = 0; c < imageDatasets.length; c++) {
if (imageDatasets[c].getSizeZ() != 1 || imageDatasets[c].getSizeT() != 1) {
throwImportWholeDirectoryException(imageFile, dirFiles[i].getAbsolutePath() + " has Z=" + imageDatasets[c].getSizeZ() + " T=" + imageDatasets[c].getSizeT());
}
if (isize == null) {
firstImageISize = imageDatasets[c].getISize();
sizeXY = imageDatasets[c].getISize().getX() * imageDatasets[c].getISize().getY();
dataToSegment = new short[imageDatasets.length][sizeXY * dirFiles.length];
isize = new ISize(imageDatasets[c].getISize().getX(), imageDatasets[c].getISize().getY(), dirFiles.length);
origin = imageDatasets[c].getAllImages()[0].getOrigin();
extent = imageDatasets[c].getExtent();
}
if (!firstImageISize.compareEqual(imageDatasets[c].getISize())) {
throwImportWholeDirectoryException(imageFile, dirFiles[0].getAbsolutePath() + " " + firstImageISize + " does not equal " + dirFiles[i].getAbsolutePath() + " " + imageDatasets[c].getISize());
}
System.arraycopy(imageDatasets[c].getImage(0, 0, 0).getPixels(), 0, dataToSegment[c], sizeXY * i, sizeXY);
}
}
fdfos = new FieldDataFileOperationSpec();
fdfos.origin = origin;
fdfos.extent = extent;
fdfos.isize = isize;
fdfos.shortSpecData = new short[][][] { dataToSegment };
} else {
hashTable.put(INITIAL_ANNOTATION, imageFile.getAbsolutePath());
Integer userPreferredTimeIndex = null;
if (origImageSizeInfo.getTimePoints().length > 1) {
userPreferredTimeIndex = newImageSizeInfo.getSelectedTimeIndex();
}
getClientTaskStatusSupport().setMessage("Reading file...");
ImageDataset[] imageDatasets = ImageDatasetReaderService.getInstance().getImageDatasetReader().readImageDatasetChannels(imageFile.getAbsolutePath(), null, bMergeChannels, userPreferredTimeIndex, resize);
fdfos = ClientRequestManager.createFDOSWithChannels(imageDatasets, null);
}
hashTable.put(FDFOS, fdfos);
hashTable.remove(NEW_IMAGE_SIZE_INFO);
hashTable.remove(ORIG_IMAGE_SIZE_INFO);
hashTable.remove(DIR_FILES);
}
}
};
AsynchClientTask resizeImageTask = new AsynchClientTask("Resizing Image...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {
@Override
public void run(Hashtable<String, Object> hashTable) throws Exception {
ImageSizeInfo newImageSizeInfo = (ImageSizeInfo) hashTable.get(NEW_IMAGE_SIZE_INFO);
FieldDataFileOperationSpec fdfos = (FieldDataFileOperationSpec) hashTable.get(FDFOS);
if (newImageSizeInfo != null && fdfos != null && !fdfos.isize.compareEqual(newImageSizeInfo.getiSize())) {
resizeImage((FieldDataFileOperationSpec) hashTable.get(FDFOS), newImageSizeInfo.getiSize(), documentCreationInfo.getOption());
}
}
};
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.initROIData((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());
}
};
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, 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_FIJI_IMAGEJ || documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_BLENDER) {
tasksV.addAll(Arrays.asList(new AsynchClientTask[] { 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]);
}
Also used :
BngUnitOrigin(org.vcell.model.bngl.BngUnitSystem.BngUnitOrigin)
Origin(org.vcell.util.Origin)
VCPixelClass(cbit.image.VCPixelClass)
FieldDataFileOperationSpec(cbit.vcell.field.io.FieldDataFileOperationSpec)
ArrayList(java.util.ArrayList)
BufferedInputStream(java.io.BufferedInputStream)
SubVolume(cbit.vcell.geometry.SubVolume)
AnalyticSubVolume(cbit.vcell.geometry.AnalyticSubVolume)
Vector(java.util.Vector)
VCDocument(org.vcell.util.document.VCDocument)
ROIMultiPaintManager(cbit.vcell.geometry.gui.ROIMultiPaintManager)
FileInputStream(java.io.FileInputStream)
ImageSizeInfo(cbit.image.ImageSizeInfo)
CartesianMesh(cbit.vcell.solvers.CartesianMesh)
ChooseFile(cbit.vcell.client.task.ChooseFile)
File(java.io.File)
PDEDataContext(cbit.vcell.simdata.PDEDataContext)
AsynchClientTask(cbit.vcell.client.task.AsynchClientTask)
ImageDataset(cbit.vcell.VirtualMicroscopy.ImageDataset)
Extent(org.vcell.util.Extent)
ISize(org.vcell.util.ISize)
VCImage(cbit.image.VCImage)
GZIPInputStream(java.util.zip.GZIPInputStream)
GeometryThumbnailImageFactoryAWT(cbit.vcell.geometry.GeometryThumbnailImageFactoryAWT)
Component(java.awt.Component)
Enumeration(java.util.Enumeration)
Hashtable(java.util.Hashtable)
DataInputStream(java.io.DataInputStream)
ProgrammingException(org.vcell.util.ProgrammingException)
GeometryException(cbit.vcell.geometry.GeometryException)
IOException(java.io.IOException)
DataAccessException(org.vcell.util.DataAccessException)
PropertyVetoException(java.beans.PropertyVetoException)
ImageException(cbit.image.ImageException)
UtilCancelException(org.vcell.util.UtilCancelException)
DataFormatException(java.util.zip.DataFormatException)
UserCancelException(org.vcell.util.UserCancelException)
Geometry(cbit.vcell.geometry.Geometry)
StringTokenizer(java.util.StringTokenizer)
CommentStringTokenizer(org.vcell.util.CommentStringTokenizer)
DataFormatException(java.util.zip.DataFormatException)
Example 12 with VCPixelClass
use of cbit.image.VCPixelClass in project vcell by virtualcell.
the class XmlReader method getVCImage.
/**
* This method returns a VCIMage object from a XML representation.
* Creation date: (3/16/2001 3:41:24 PM)
* @return VCImage
* @param param org.jdom.Element
*/
VCImage getVCImage(Element param, Extent extent) throws XmlParseException {
// try to get metadata(version)
Version version = getVersion(param.getChild(XMLTags.VersionTag, vcNamespace));
// get the attributes
Element tempelement = param.getChild(XMLTags.ImageDataTag, vcNamespace);
int aNumX = Integer.parseInt(tempelement.getAttributeValue(XMLTags.XAttrTag));
int aNumY = Integer.parseInt(tempelement.getAttributeValue(XMLTags.YAttrTag));
int aNumZ = Integer.parseInt(tempelement.getAttributeValue(XMLTags.ZAttrTag));
// getpixels
String temp = tempelement.getText();
// decode
byte[] data = Hex.toBytes(temp);
// create the VCImage object
VCImageCompressed newimage = null;
try {
newimage = new VCImageCompressed(version, data, extent, aNumX, aNumY, aNumZ);
} catch (ImageException e) {
e.printStackTrace();
throw new XmlParseException("An imageException occurred while trying to create a VCImage!", e);
}
// set attributes
String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
try {
newimage.setName(name);
// String annotation = param.getAttributeValue(XMLTags.AnnotationAttrTag);
// if (annotation!=null) {
// newimage.setDescription(unMangle(annotation));
// }
// read the annotation
String annotation = param.getChildText(XMLTags.AnnotationTag, vcNamespace);
if (annotation != null && annotation.length() > 0) {
newimage.setDescription(unMangle(annotation));
}
} catch (java.beans.PropertyVetoException e) {
e.printStackTrace(System.out);
throw new XmlParseException(e);
}
// get PixelClasses
List<Element> pixelClassList = param.getChildren(XMLTags.PixelClassTag, vcNamespace);
if (pixelClassList.size() != 0) {
VCPixelClass[] pixelClassArray = new VCPixelClass[pixelClassList.size()];
int pixelClassCounter = 0;
for (Element pcElement : pixelClassList) {
pixelClassArray[pixelClassCounter] = getPixelClass(pcElement);
pixelClassCounter++;
}
try {
newimage.setPixelClasses(pixelClassArray);
} catch (java.beans.PropertyVetoException e) {
e.printStackTrace(System.out);
throw new XmlParseException(e);
}
} else {
// Invalid format
System.out.println("Format Error! No <PixelClass> references found inside <Image name=\"" + name + "\">!");
System.out.println("Valid format for images is:");
System.out.println("<Image Name=\"??\">");
System.out.println(" <ImageData Z=\"?\" Y=\"?\" Z=\"?\" CompressedSize=\"?\">");
System.out.println(" ......Image content...");
System.out.println(" </ImageData>");
System.out.println(" <PixelClass Name=\"?\" ImagePixelValue=\"?\"/>");
System.out.println(" ...");
System.out.println(" <PixelClass Name=\"?\" ImagePixelValue=\"?\"/>");
System.out.println(" <Version Name=\"?\"/>");
System.out.println("</Image>");
throw new XmlParseException("Invalid VCML format error!\nNo <PixelClass> references found inside <Image name=\"" + name + "\">!");
}
return newimage;
}
Also used :
VCPixelClass(cbit.image.VCPixelClass)
ImageException(cbit.image.ImageException)
Element(org.jdom.Element)
VCImageCompressed(cbit.image.VCImageCompressed)
PropertyVetoException(java.beans.PropertyVetoException)
Version(org.vcell.util.document.Version)
RedistributionVersion(cbit.vcell.solvers.mb.MovingBoundarySolverOptions.RedistributionVersion)
SimulationVersion(org.vcell.util.document.SimulationVersion)
VCellSoftwareVersion(org.vcell.util.document.VCellSoftwareVersion)
Example 13 with VCPixelClass
use of cbit.image.VCPixelClass in project vcell by virtualcell.
the class Xmlproducer method getXML.
/**
* This methods returns a XML represnetation of a VCImage object.
* Creation date: (3/1/2001 3:02:37 PM)
* @return Element
* @param param cbit.image.VCImage
*/
Element getXML(VCImage param) throws XmlParseException {
Element image = new Element(XMLTags.ImageTag);
// add atributes
image.setAttribute(XMLTags.NameAttrTag, mangle(param.getName()));
// Add annotation
if (param.getDescription() != null && param.getDescription().length() > 0) {
Element annotationElement = new Element(XMLTags.AnnotationTag);
annotationElement.setText(mangle(param.getDescription()));
image.addContent(annotationElement);
}
// Add Imagedata subelement
byte[] compressedPixels = null;
try {
compressedPixels = param.getPixelsCompressed();
} catch (ImageException e) {
e.printStackTrace();
throw new XmlParseException("An ImageParseException occurred when tring to retrieving the compressed Pixels", e);
}
Element imagedata = new Element(XMLTags.ImageDataTag);
// Get imagedata attributes
imagedata.setAttribute(XMLTags.XAttrTag, String.valueOf(param.getNumX()));
imagedata.setAttribute(XMLTags.YAttrTag, String.valueOf(param.getNumY()));
imagedata.setAttribute(XMLTags.ZAttrTag, String.valueOf(param.getNumZ()));
imagedata.setAttribute(XMLTags.CompressedSizeTag, String.valueOf(compressedPixels.length));
// Get imagedata content
// encode
imagedata.addContent(Hex.toString(compressedPixels));
// Add imagedata to VCImage element
image.addContent(imagedata);
// Add PixelClass elements
VCPixelClass[] pixelClasses = param.getPixelClasses();
for (int i = 0; i < pixelClasses.length; i++) {
image.addContent(getXML(pixelClasses[i]));
}
// Add Metadata information
if (param.getVersion() != null) {
image.addContent(getXML(param.getVersion(), param));
}
return image;
}
Also used :
VCPixelClass(cbit.image.VCPixelClass)
ImageException(cbit.image.ImageException)
Element(org.jdom.Element)
Example 14 with VCPixelClass
use of cbit.image.VCPixelClass in project vcell by virtualcell.
the class ImageAttributePanel method saveRegionName.
/**
* Comment
*/
private void saveRegionName() {
if (getCurrentPixelClassIndex() != null) {
int currentRegion = getCurrentPixelClassIndex().intValue();
VCPixelClass orig = vcPixelClassArr[currentRegion];
vcPixelClassArr[currentRegion] = new cbit.image.VCPixelClass(orig.getKey(), getRegionNameJTextField().getText(), orig.getPixel());
}
}
Also used :
VCPixelClass(cbit.image.VCPixelClass)
VCPixelClass(cbit.image.VCPixelClass)
Example 15 with VCPixelClass
use of cbit.image.VCPixelClass in project vcell by virtualcell.
the class GeomDbDriver method getPixelClass.
/**
* This method was created in VisualAge.
* @param vcImage cbit.image.VCImage
*/
private VCPixelClass getPixelClass(QueryHashtable dbc, Connection con, KeyValue imageRegionKey) throws SQLException, DataAccessException {
//
// check object cache first
//
VCPixelClass vcPixelClass = (VCPixelClass) dbc.get(imageRegionKey);
if (vcPixelClass != null) {
return vcPixelClass;
}
String sql;
sql = " SELECT *" + " FROM " + imageRegionTable.getTableName() + " WHERE " + imageRegionTable.id + " = " + imageRegionKey;
//
// System.out.println(sql);
//
// Connection con = conFact.getConnection();
Statement stmt = con.createStatement();
try {
ResultSet rset = stmt.executeQuery(sql);
//
if (rset.next()) {
KeyValue vcpcKey = new KeyValue(rset.getBigDecimal(imageRegionTable.id.toString()));
String rName = rset.getString(imageRegionTable.regionName.toString()).trim();
int pixValue = rset.getInt(imageRegionTable.pixelValue.toString());
vcPixelClass = new VCPixelClass(vcpcKey, rName, pixValue);
dbc.put(vcpcKey, vcPixelClass);
} else {
throw new ObjectNotFoundException("ImageRegion(" + imageRegionKey + ") not found");
}
return vcPixelClass;
} finally {
// Release resources include resultset
stmt.close();
}
}
Also used :
VCPixelClass(cbit.image.VCPixelClass)
KeyValue(org.vcell.util.document.KeyValue)
Statement(java.sql.Statement)
ObjectNotFoundException(org.vcell.util.ObjectNotFoundException)
ResultSet(java.sql.ResultSet)
Aggregations
VCPixelClass (cbit.image.VCPixelClass)17
VCImage (cbit.image.VCImage)7
KeyValue (org.vcell.util.document.KeyValue)7
SubVolume (cbit.vcell.geometry.SubVolume)6
PropertyVetoException (java.beans.PropertyVetoException)6
ImageException (cbit.image.ImageException)4
Geometry (cbit.vcell.geometry.Geometry)4
ArrayList (java.util.ArrayList)4
Vector (java.util.Vector)4
DataAccessException (org.vcell.util.DataAccessException)4
VCImageCompressed (cbit.image.VCImageCompressed)3
VCImageUncompressed (cbit.image.VCImageUncompressed)3
AnalyticSubVolume (cbit.vcell.geometry.AnalyticSubVolume)3
GeometryException (cbit.vcell.geometry.GeometryException)3
GeometrySpec (cbit.vcell.geometry.GeometrySpec)3
ImageSubVolume (cbit.vcell.geometry.ImageSubVolume)3
IOException (java.io.IOException)3
Extent (org.vcell.util.Extent)3
ISize (org.vcell.util.ISize)3
Origin (org.vcell.util.Origin)3
