use of java.util.zip.DataFormatException in project vcell by virtualcell.
the class MediaMethods method makeTrackAtom.
/**
* This method was created in VisualAge.
* @return TrackAtom
* @param movie Movie
* @param track Track
*/
private static final TrackAtom makeTrackAtom(MediaMovie movie, int trackIndex) throws DataFormatException {
if ((0 <= trackIndex) && (trackIndex < movie.getTracks().length)) {
MediaTrack track = movie.getTracks()[trackIndex];
MediaInformation minf = MediaMethods.makeMediaInformation(track);
int componentSubtype = 0;
if (track.getMediaType().equals(AtomConstants.MEDIA_TYPE_VIDEO))
componentSubtype = AtomConstants.COMPONENT_SUBTYPE_VIDEO;
if (track.getMediaType().equals(AtomConstants.MEDIA_TYPE_OBJECT))
componentSubtype = AtomConstants.COMPONENT_SUBTYPE_OBJECT;
if (track.getMediaType().equals(AtomConstants.MEDIA_TYPE_QTVR))
componentSubtype = AtomConstants.COMPONENT_SUBTYPE_QTVR;
HandlerReference mhlr = new HandlerReference("mhlr", componentSubtype);
MediaHeader mdhd = new MediaHeader(movie.getTimeScale(), track.getDuration());
MediaAtom mdia = new MediaAtom(mdhd, mhlr, minf);
TrackHeader tkhd = new TrackHeader(trackIndex + 1, track.getDuration(), track.getWidth(), track.getHeight());
Edit[] edits;
if (track.getEdits() == null)
edits = new Edit[] { new Edit(track.getDuration()) };
else
edits = track.getEdits();
EditList elst = new EditList(edits);
EditAtom edts = new EditAtom(elst);
TrackAtom trak = null;
if (movie instanceof VRMediaMovie) {
TrackReference trakRef = ((VRMediaMovie) movie).getTrackReference(trackIndex);
trak = new TrackAtom(tkhd, null, null, edts, trakRef, null, null, mdia, null);
} else {
trak = new TrackAtom(tkhd, edts, mdia);
}
return trak;
} else
throw new DataFormatException("Track index out of bounds !");
}
use of java.util.zip.DataFormatException in project vcell by virtualcell.
the class IMGExporter method writeQTVRWorker.
public static void writeQTVRWorker(DataOutputStream dataOutputStream, VideoMediaChunk[] videoMediaChunks, int numTimePoints, int numslices, int width, int height) throws java.io.IOException, java.util.zip.DataFormatException {
/* make the single node VR World and required chunks */
if (numTimePoints * numslices != videoMediaChunks.length) {
throw new DataFormatException("NumTimePoints x Numslices != VideoMediaChunk length.");
}
VRWorld singleObjVRWorld = VRWorld.createSingleObjectVRWorld(videoMediaChunks[0].getDuration(), numTimePoints, numslices, (float) (width / 2), (float) (height / 2));
// reverse pan controls (set bit 3)
singleObjVRWorld.getVRObjectSampleAtom(0).setControlSettings(singleObjVRWorld.getVRObjectSampleAtom(0).getControlSettings() | (Integer.parseInt("00001000", 2)));
VRMediaChunk vrChunk = new VRMediaChunk(singleObjVRWorld);
ObjectMediaChunk objChunk = new ObjectMediaChunk(singleObjVRWorld);
/* assemble tracks and write the rest of the file */
MediaTrack qtvrTrack = new MediaTrack(vrChunk);
MediaTrack objectTrack = new MediaTrack(objChunk);
MediaTrack imageTrack = new MediaTrack(videoMediaChunks);
qtvrTrack.setWidth(imageTrack.getWidth());
qtvrTrack.setHeight(imageTrack.getHeight());
objectTrack.setWidth(imageTrack.getWidth());
objectTrack.setHeight(imageTrack.getHeight());
VRMediaMovie vrMovie = VRMediaMovie.createVRMediaMovie(qtvrTrack, objectTrack, imageTrack, null, imageTrack.getDuration(), videoMediaChunks[0].getDuration());
MediaMethods.writeMovie(dataOutputStream, vrMovie);
}
use of java.util.zip.DataFormatException 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]);
}
use of java.util.zip.DataFormatException in project leopard by tanhaichao.
the class tls_sigature method CheckTLSSignatureEx.
public static CheckTLSSignatureResult CheckTLSSignatureEx(String urlSig, long sdkAppid, String identifier, String publicKey) throws DataFormatException {
CheckTLSSignatureResult result = new CheckTLSSignatureResult();
Security.addProvider(new BouncyCastleProvider());
// DeBaseUrl64 urlSig to json
Base64 decoder = new Base64();
byte[] compressBytes = base64_url.base64DecodeUrl(urlSig.getBytes(Charset.forName("UTF-8")));
// Decompression
Inflater decompression = new Inflater();
decompression.setInput(compressBytes, 0, compressBytes.length);
byte[] decompressBytes = new byte[1024];
int decompressLength = decompression.inflate(decompressBytes);
decompression.end();
String jsonString = new String(Arrays.copyOfRange(decompressBytes, 0, decompressLength));
// Get TLS.Sig from json
JSONObject jsonObject = new JSONObject(jsonString);
String sigTLS = jsonObject.getString("TLS.sig");
// debase64 TLS.Sig to get serailString
byte[] signatureBytes = decoder.decode(sigTLS.getBytes(Charset.forName("UTF-8")));
try {
String strSdkAppid = jsonObject.getString("TLS.sdk_appid");
String sigTime = jsonObject.getString("TLS.time");
String sigExpire = jsonObject.getString("TLS.expire_after");
if (Integer.parseInt(strSdkAppid) != sdkAppid) {
result.errMessage = new String("sdkappid " + strSdkAppid + " in tls sig not equal sdkappid " + sdkAppid + " in request");
return result;
}
if (System.currentTimeMillis() / 1000 - Long.parseLong(sigTime) > Long.parseLong(sigExpire)) {
result.errMessage = new String("TLS sig is out of date");
return result;
}
// Get Serial String from json
String SerialString = "TLS.appid_at_3rd:" + 0 + "\n" + "TLS.account_type:" + 0 + "\n" + "TLS.identifier:" + identifier + "\n" + "TLS.sdk_appid:" + sdkAppid + "\n" + "TLS.time:" + sigTime + "\n" + "TLS.expire_after:" + sigExpire + "\n";
Reader reader = new CharArrayReader(publicKey.toCharArray());
PEMParser parser = new PEMParser(reader);
JcaPEMKeyConverter converter = new JcaPEMKeyConverter();
Object obj = parser.readObject();
parser.close();
PublicKey pubKeyStruct = converter.getPublicKey((SubjectPublicKeyInfo) obj);
Signature signature = Signature.getInstance("SHA256withECDSA", "BC");
signature.initVerify(pubKeyStruct);
signature.update(SerialString.getBytes(Charset.forName("UTF-8")));
boolean bool = signature.verify(signatureBytes);
result.expireTime = Integer.parseInt(sigExpire);
result.initTime = Integer.parseInt(sigTime);
result.verifyResult = bool;
} catch (Exception e) {
e.printStackTrace();
result.errMessage = "Failed in checking sig";
}
return result;
}
use of java.util.zip.DataFormatException in project vcell by virtualcell.
the class ClientRequestManager method createFDOSFromImageFile.
// public void prepareDocumentToLoad(VCDocument doc) throws Exception {
// Simulation[] simulations = null;
// if (doc instanceof MathModel) {
// Geometry geometry = ((MathModel)doc).getMathDescription().getGeometry();
// geometry.precomputeAll();
// simulations = ((MathModel)doc).getSimulations();
// } else if (doc instanceof Geometry) {
// ((Geometry)doc).precomputeAll();
// } else if (doc instanceof BioModel) {
// BioModel bioModel = (BioModel)doc;
// SimulationContext[] simContexts = bioModel.getSimulationContexts();
// for (SimulationContext simContext : simContexts) {
// simContext.getGeometry().precomputeAll();
// }
// simulations = ((BioModel)doc).getSimulations();
// }
// if (simulations != null) {
// // preload simulation status
// VCSimulationIdentifier simIDs[] = new VCSimulationIdentifier[simulations.length];
// for (int i = 0; i < simulations.length; i++){
// simIDs[i] = simulations[i].getSimulationInfo().getAuthoritativeVCSimulationIdentifier();
// }
// getDocumentManager().preloadSimulationStatus(simIDs);
// }
// }
public static FieldDataFileOperationSpec createFDOSFromImageFile(File imageFile, boolean bCropOutBlack, Integer saveOnlyThisTimePointIndex) throws DataFormatException, ImageException {
try {
ImageDatasetReader imageDatasetReader = ImageDatasetReaderService.getInstance().getImageDatasetReader();
ImageDataset[] imagedataSets = imageDatasetReader.readImageDatasetChannels(imageFile.getAbsolutePath(), null, false, saveOnlyThisTimePointIndex, null);
if (imagedataSets != null && bCropOutBlack) {
for (int i = 0; i < imagedataSets.length; i++) {
Rectangle nonZeroRect = imagedataSets[i].getNonzeroBoundingRectangle();
if (nonZeroRect != null) {
imagedataSets[i] = imagedataSets[i].crop(nonZeroRect);
}
}
}
return createFDOSWithChannels(imagedataSets, null);
} catch (Exception e) {
e.printStackTrace(System.out);
throw new DataFormatException(e.getMessage());
}
}
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