Examples with ISize org.vcell.util.ISize used on opensource projects

Example 96 with ISize

use of org.vcell.util.ISize in project vcell by virtualcell.

the class ROIMultiPaintManager method loadFD.

private void loadFD(Hashtable<String, Object> hashTable) throws Exception {
    final Exception[] excHolder = new Exception[] { null };
    final JDialog jDialog = new JDialog(JOptionPane.getFrameForComponent(this.overlayEditorPanelJAI));
    jDialog.setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE);
    jDialog.setTitle("Import Type");
    jDialog.setModal(true);
    final JPanel okCancelJPanel = new JPanel(new FlowLayout());
    JButton okJButton = new JButton("from File...");
    okJButton.addActionListener(new ActionListener() {

        @Override
        public void actionPerformed(ActionEvent e) {
            try {
                fdDelta = new double[] { 0, 0, 0 };
                fdDeltaLast = new double[] { 0, 0, 0 };
                currScale = 1.0;
                currScaleLast = 1.0;
                VCDocument.DocumentCreationInfo documentCreationInfo = new VCDocument.DocumentCreationInfo(VCDocumentType.GEOMETRY_DOC, VCDocument.GEOM_OPTION_FILE);
                final AsynchClientTask selectImageFile = ClientRequestManager.getSelectImageFileTask(overlayEditorPanelJAI, null);
                final AsynchClientTask parseImageTask = ClientRequestManager.getParseImageTask(overlayEditorPanelJAI, documentCreationInfo, null);
                final AsynchClientTask importFileImage = ClientRequestManager.getImportFileImageTask(documentCreationInfo);
                // final AsynchClientTask resizeImageTask = ClientRequestManager.getResizeImageTask(documentCreationInfo);
                hashTable.put(ClientRequestManager.GUI_PARENT, ROIMultiPaintManager.this.overlayEditorPanelJAI);
                selectImageFile.run(hashTable);
                parseImageTask.run(hashTable);
                hashTable.put(ClientRequestManager.NEW_IMAGE_SIZE_INFO, hashTable.get(ClientRequestManager.ORIG_IMAGE_SIZE_INFO));
                importFileImage.run(hashTable);
                // resizeImageTask.run(hashTable);
                saveFDUnderlay(hashTable);
            } catch (Exception e1) {
                excHolder[0] = e1;
            // e1.printStackTrace();
            // DialogUtils.showErrorDialog(ROIMultiPaintManager.this.overlayEditorPanelJAI, e1.getMessage());
            } finally {
                jDialog.dispose();
            }
        }
    });
    JButton fdJButton = new JButton("from FieldData...");
    fdJButton.addActionListener(new ActionListener() {

        @Override
        public void actionPerformed(ActionEvent e) {
            try {
                ArrayList<Object[]> allRows = new ArrayList<Object[]>();
                ArrayList<ISize> iSizes = new ArrayList<ISize>();
                ArrayList<CartesianMesh> meshes = new ArrayList<CartesianMesh>();
                // DocumentManager documentManager = documentManager.getSessionManager()..getRequestManager().getDocumentManager();
                FieldDataDBOperationSpec fdos = FieldDataDBOperationSpec.createGetExtDataIDsSpec(documentManager.getUser());
                FieldDataDBOperationResults fieldDataDBOperationResults = documentManager.fieldDataDBOperation(fdos);
                ExternalDataIdentifier[] externalDataIdentifierArr = fieldDataDBOperationResults.extDataIDArr;
                Arrays.sort(externalDataIdentifierArr, new Comparator<ExternalDataIdentifier>() {

                    @Override
                    public int compare(ExternalDataIdentifier o1, ExternalDataIdentifier o2) {
                        // TODO Auto-generated method stub
                        return o1.getName().compareToIgnoreCase(o2.getName());
                    }
                });
                ArrayList<ExternalDataIdentifier> okEDI = new ArrayList<ExternalDataIdentifier>();
                for (int i = 0; externalDataIdentifierArr != null && i < externalDataIdentifierArr.length; i++) {
                    try {
                        FieldDataFileOperationSpec fieldDataFileOperationSpec = FieldDataFileOperationSpec.createInfoFieldDataFileOperationSpec(externalDataIdentifierArr[i].getSimulationKey(), externalDataIdentifierArr[i].getOwner(), externalDataIdentifierArr[i].getJobIndex());
                        FieldDataFileOperationResults fieldDataFileOperationResults = documentManager.fieldDataFileOperation(fieldDataFileOperationSpec);
                        // System.out.println(externalDataIdentifierArr[i].getName()+" "+fieldDataFileOperationResults.iSize);
                        ISize iSize = fieldDataFileOperationResults.iSize;
                        iSizes.add(iSize);
                        // isizes.add(iSize);
                        okEDI.add(externalDataIdentifierArr[i]);
                        allRows.add(new Object[] { iSize.getX(), iSize.getY(), iSize.getZ(), "FieldData='" + externalDataIdentifierArr[i].getName() + "'" });
                        VCImageUncompressed vcImageUnc = new VCImageUncompressed(null, new byte[iSize.getXYZ()], fieldDataFileOperationResults.extent, iSize.getX(), iSize.getY(), iSize.getZ());
                        int dimension = 1 + (iSize.getY() > 1 ? 1 : 0) + (iSize.getZ() > 1 ? 1 : 0);
                        CartesianMesh simpleMesh = CartesianMesh.createSimpleCartesianMesh(fieldDataFileOperationResults.origin, fieldDataFileOperationResults.extent, iSize, new RegionImage(vcImageUnc, dimension, fieldDataFileOperationResults.extent, fieldDataFileOperationResults.origin, RegionImage.NO_SMOOTHING));
                        meshes.add(simpleMesh);
                    } catch (Exception e2) {
                        e2.printStackTrace();
                    }
                }
                if (allRows.size() > 0) {
                    Object[][] rowData = allRows.toArray(new Object[0][]);
                    int[] selections = DialogUtils.showComponentOKCancelTableList(ROIMultiPaintManager.this.overlayEditorPanelJAI, "Select Simulation for Geom Size", new String[] { "X", "Y", "Z", "Name" }, rowData, ListSelectionModel.SINGLE_SELECTION);
                    if (selections != null && selections.length == 1) {
                        FieldDataFileOperationResults fdfor = documentManager.fieldDataFileOperation(FieldDataFileOperationSpec.createInfoFieldDataFileOperationSpec(okEDI.get(selections[0]).getSimulationKey(), okEDI.get(selections[0]).getOwner(), okEDI.get(selections[0]).getJobIndex()));
                        SimDataBlock simDataBlock = VCellClientTest.getVCellClient().getClientServerManager().getDataSetController().getSimDataBlock(null, okEDI.get(selections[0]), fdfor.dataIdentifierArr[0].getName(), 0.0);
                        FieldDataFileOperationSpec fieldDataFileOperationSpec = new FieldDataFileOperationSpec();
                        fieldDataFileOperationSpec.isize = meshes.get(selections[0]).getISize();
                        fieldDataFileOperationSpec.shortSpecData = new short[][][] { { new short[fieldDataFileOperationSpec.isize.getXYZ()] } };
                        for (int i = 0; i < simDataBlock.getData().length; i++) {
                            fieldDataFileOperationSpec.shortSpecData[0][0][i] = (short) simDataBlock.getData()[i];
                        // if(simDataBlock.getData()[i] != 0) {
                        // System.out.println(simDataBlock.getData()[i]);
                        // }
                        }
                        hashTable.put(ClientRequestManager.FDFOS, fieldDataFileOperationSpec);
                        hashTable.put(ClientRequestManager.IMPORT_SOURCE_NAME, "FieldData=" + okEDI.get(selections[0]).getName());
                        saveFDUnderlay(hashTable);
                    // ROIMultiPaintManager.this.fdShort = (FieldDataFileOperationSpec)hashTable.get(ClientRequestManager.FDFOS);
                    // ROIMultiPaintManager.this.importSourceName = (String)hashTable.get(ClientRequestManager.IMPORT_SOURCE_NAME);
                    // (outMax-outMin)(inVal - inMin)
                    // ------------------------------ + outMin
                    // inMax - inMin
                    // externalDataIdentifierArr[selections[0]].
                    // //						ImageSizeInfo imagesizeInfo = new ImageSizeInfo("internal",meshes.get(selections[0]).getISize(),1,new double[] {0},0);
                    // ImageSizeInfo imagesizeInfo = new ImageSizeInfo("internal",iSizes.get(selections[0]),1,new double[] {0},0);
                    // hashTable.put(ClientRequestManager.NEW_IMAGE_SIZE_INFO, imagesizeInfo);
                    // 
                    // VCImage image = sourceGeom.getGeometrySpec().getImage();
                    // ISize samplingSize = new ISize(image.getNumX(),image.getNumY(),image.getNumZ());//
                    // VCImageUncompressed vcImageUnc = new VCImageUncompressed(null, new byte[samplingSize.getXYZ()], sourceGeom.getExtent(), samplingSize.getX(), samplingSize.getY(), samplingSize.getZ());
                    // CartesianMesh sourceMesh = CartesianMesh.createSimpleCartesianMesh(
                    // sourceGeom.getOrigin(),
                    // sourceGeom.getExtent(),
                    // samplingSize,
                    // new RegionImage(vcImageUnc, sourceGeom.getDimension(), sourceGeom.getExtent(), sourceGeom.getOrigin(), RegionImage.NO_SMOOTHING));
                    // 
                    // hashTable.put("newMesh", meshes.get(selections[0]));
                    // hashTable.put("sourceMesh", sourceMesh);
                    }
                }
            } catch (Exception e1) {
                excHolder[0] = e1;
            // e1.printStackTrace();
            // DialogUtils.showErrorDialog(ROIMultiPaintManager.this.overlayEditorPanelJAI, e1.getMessage());
            } finally {
                jDialog.dispose();
            }
        }
    });
    JButton clipbboardJButton = new JButton("from Clipboard");
    clipbboardJButton.addActionListener(new ActionListener() {

        @Override
        public void actionPerformed(ActionEvent e) {
            Transferable contents = Toolkit.getDefaultToolkit().getSystemClipboard().getContents(null);
            try {
                Object transferData = contents.getTransferData(DataFlavor.stringFlavor);
                if (transferData instanceof String) {
                    StringTokenizer st = new StringTokenizer(((String) transferData).toString(), ",");
                    String varName = st.nextToken();
                    String vcDataIdentifer = st.nextToken();
                    double timePoint = Double.parseDouble(st.nextToken());
                    ISize isize = new ISize(Integer.parseInt(st.nextToken()), Integer.parseInt(st.nextToken()), Integer.parseInt(st.nextToken()));
                    Range inRange = new Range(Double.parseDouble(st.nextToken()), Double.parseDouble(st.nextToken()));
                    String simDataFile = st.nextToken();
                    DataInputStream dis = new DataInputStream(new FileInputStream(simDataFile));
                    FieldDataFileOperationSpec fieldDataFileOperationSpec = new FieldDataFileOperationSpec();
                    fieldDataFileOperationSpec.isize = isize;
                    fieldDataFileOperationSpec.shortSpecData = new short[][][] { { new short[fieldDataFileOperationSpec.isize.getXYZ()] } };
                    double outMax = 65535;
                    double outMin = 0;
                    double scale = (outMax - outMin) / (inRange.getMax() - inRange.getMin());
                    for (int i = 0; i < isize.getXYZ(); i++) {
                        double val = dis.readDouble();
                        fieldDataFileOperationSpec.shortSpecData[0][0][i] = (short) (scale * (val - inRange.getMin()) + outMin);
                    }
                    hashTable.put(ClientRequestManager.FDFOS, fieldDataFileOperationSpec);
                    hashTable.put(ClientRequestManager.IMPORT_SOURCE_NAME, "SimData=" + vcDataIdentifer + " varName=" + varName + " time=" + timePoint);
                    saveFDUnderlay(hashTable);
                    ROIMultiPaintManager.this.overlayEditorPanelJAI.setFDScale(new double[] { scale, inRange.getMin(), outMin });
                }
            } catch (Exception e1) {
                excHolder[0] = e1;
            // e1.printStackTrace();
            // DialogUtils.showErrorDialog(ROIMultiPaintManager.this.overlayEditorPanelJAI, e1.getMessage());
            } finally {
                jDialog.dispose();
            }
        }
    });
    final boolean[] bCanelHolder = new boolean[] { false };
    JButton cancelJButton = new JButton("Cancel");
    cancelJButton.addActionListener(new ActionListener() {

        @Override
        public void actionPerformed(ActionEvent e) {
            jDialog.dispose();
            bCanelHolder[0] = true;
        }
    });
    okCancelJPanel.add(okJButton);
    okCancelJPanel.add(fdJButton);
    okCancelJPanel.add(clipbboardJButton);
    okCancelJPanel.add(cancelJButton);
    jDialog.getContentPane().add(okCancelJPanel, BorderLayout.SOUTH);
    jDialog.pack();
    // jDialog.setSize(300,250);
    DialogUtils.showModalJDialogOnTop(jDialog, overlayEditorPanelJAI);
    if (bCanelHolder[0]) {
        throw UserCancelException.CANCEL_GENERIC;
    }
    if (excHolder[0] != null) {
        throw excHolder[0];
    }
}

Example 97 with ISize

use of org.vcell.util.ISize 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);
}

Example 98 with ISize

use of org.vcell.util.ISize in project vcell by virtualcell.

the class ROIMultiPaintManager method cropROIData.

private void cropROIData(final Crop3D cropRectangle3D) /*,boolean bThread*/
{
    final AsynchClientTask cropTask = new AsynchClientTask("Cropping...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            ISize origISize = getImageDataSetChannel().getISize();
            CoordinateIndex cropLow = new CoordinateIndex(-cropRectangle3D.low.x, -cropRectangle3D.low.y, -cropRectangle3D.low.z);
            CoordinateIndex cropHigh = new CoordinateIndex(cropRectangle3D.low.x + cropRectangle3D.width - origISize.getX(), cropRectangle3D.low.y + cropRectangle3D.height - origISize.getY(), cropRectangle3D.low.z + cropRectangle3D.depth - origISize.getZ());
            resizeImpl(ResizeInfo.createPadCropResizeInfo(origISize, cropLow, cropHigh), getClientTaskStatusSupport());
            updateAuxiliaryInfo(origISize, getClientTaskStatusSupport());
        }
    };
    final AsynchClientTask updatePanelTask = getUpdateDisplayAfterCropTask();
    final Hashtable<String, Object> taskHash = new Hashtable<String, Object>();
    ClientTaskDispatcher.dispatch(overlayEditorPanelJAI, taskHash, new AsynchClientTask[] { cropTask, updatePanelTask }, false, false, null, true);
// if(bThread){
// ClientTaskDispatcher.dispatch(overlayEditorPanelJAI,taskHash,
// new AsynchClientTask[] {cropTask,updatePanelTask},false,false,null,true);
// }else{
// new Thread(new Runnable() {
// public void run(){
// try{
// cropTask.run(taskHash);
// SwingUtilities.invokeAndWait(new Runnable() {
// public void run() {
// try {
// updatePanelTask.run(taskHash);
// } catch (Exception e) {
// e.printStackTrace();
// throw new RuntimeException(e);
// }
// }
// });
// }catch(Exception e){
// e.printStackTrace();
// DialogUtils.showErrorDialog(overlayEditorPanelJAI, "Crop failed:\n"+e.getMessage()+
// (e.getCause()!= null?"\n"+e.getCause().getMessage():""), e);
// }
// }
// }).run();
// }
}

Example 99 with ISize

use of org.vcell.util.ISize 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);
}

Example 100 with ISize

use of org.vcell.util.ISize in project vcell by virtualcell.

the class ROIMultiPaintManager method checkBorders.

private VCImage checkBorders(VCImage checkThisVCImage) throws Exception {
    boolean bAddBorder = false;
    BorderInfo borderInfo = checkBorderInfo(checkThisVCImage);
    if (borderInfo.bXYTouch || borderInfo.bZTouch) {
        boolean b3DTouch = borderInfo.bXYTouch && borderInfo.bZTouch;
        String edgeDescrFrag = "on the " + (b3DTouch ? "XY and Z" : (borderInfo.bXYTouch ? "XY" : "Z")) + " border.";
        final String addBorder = "Add empty border";
        final String keep = "Keep as is";
        final String cancel = "Cancel";
        String result = DialogUtils.showWarningDialog(overlayEditorPanelJAI, "One or more Domain Regions touches the outer boundary " + edgeDescrFrag + "\n" + "Choose an option:\n" + "1. Keep as is, do not change.\n" + "2. Add empty 'background' border around outer boundary so no Domain Region touches an outer edge.", new String[] { keep, addBorder, cancel }, keep);
        if (result.equals(cancel)) {
            throw UserCancelException.CANCEL_GENERIC;
        } else if (result.equals(addBorder)) {
            bAddBorder = true;
            ;
        }
    }
    if (!bAddBorder) {
        return null;
    }
    ISize checkThisVCImageISize = new ISize(checkThisVCImage.getNumX(), checkThisVCImage.getNumY(), checkThisVCImage.getNumZ());
    boolean bxy = borderInfo.bXYTouch;
    boolean bz = borderInfo.bZTouch;
    ROIMultiPaintManager.PaddedInfo paddedInfo = copyToPadded(checkThisVCImage.getPixels(), checkThisVCImageISize, null, checkThisVCImage.getExtent(), new ISize((bxy ? 1 : 0), (bxy ? 1 : 0), (bz ? 1 : 0)), new ISize((bxy ? 1 : 0), (bxy ? 1 : 0), (bz ? 1 : 0)));
    VCImage newVCImage = new VCImageUncompressed(null, (byte[]) paddedInfo.paddedArray, DEFAULT_EXTENT, /*paddedInfo.paddedExtent*/
    paddedInfo.paddedISize.getX(), paddedInfo.paddedISize.getY(), paddedInfo.paddedISize.getZ());
    return newVCImage;
}