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

Example 41 with Origin

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

the class GeometrySizeDialog method Ok.

/**
 * Comment
 */
private void Ok() throws PropertyVetoException {
    final double worldExtentX = Double.valueOf(getSizeXTextField().getText()).doubleValue();
    final double worldExtentY = Double.valueOf(getSizeYTextField().getText()).doubleValue();
    final double worldExtentZ = Double.valueOf(getSizeZTextField().getText()).doubleValue();
    final double worldOriginX = Double.valueOf(getOriginXTextField().getText()).doubleValue();
    final double worldOriginY = Double.valueOf(getOriginYTextField().getText()).doubleValue();
    final double worldOriginZ = Double.valueOf(getOriginZTextField().getText()).doubleValue();
    final GeometrySpec geometrySpec = getGeometry().getGeometrySpec();
    AsynchClientTask extentOriginTask = new AsynchClientTask("Changing domain", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            geometrySpec.setExtent(new Extent(worldExtentX, worldExtentY, worldExtentZ));
            geometrySpec.setOrigin(new Origin(worldOriginX, worldOriginY, worldOriginZ));
            getGeometry().precomputeAll(new GeometryThumbnailImageFactoryAWT());
        }
    };
    ClientTaskDispatcher.dispatch(this.getParent(), new Hashtable<String, Object>(), new AsynchClientTask[] { extentOriginTask }, false);
}

Example 42 with Origin

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

the class FieldDataGUIPanel method copyMethod.

private void copyMethod(int copyMode) {
    String delimiter = "";
    if (copyMode == COPY_NL) {
        delimiter = "\n";
    } else if (copyMode == COPY_CRNL) {
        delimiter = "\r\n";
    } else if (copyMode == COPY_CSV) {
        delimiter = ",";
    } else if (copyMode == COPY_SPACE) {
        delimiter = " ";
    }
    String copyString = "";
    javax.swing.tree.TreePath selPath = getJTree1().getSelectionPath();
    if (selPath != null) {
        javax.swing.tree.DefaultMutableTreeNode lastPathComponent = (javax.swing.tree.DefaultMutableTreeNode) selPath.getLastPathComponent();
        if (lastPathComponent.equals(getJTree1().getModel().getRoot())) {
            int childCount = lastPathComponent.getChildCount();
            for (int i = 0; i < childCount; i += 1) {
                if (i != 0) {
                    copyString += delimiter;
                }
                copyString += ((FieldDataMainList) ((DefaultMutableTreeNode) lastPathComponent.getChildAt(i)).getUserObject()).externalDataIdentifier.getName();
            }
        } else if (lastPathComponent.getUserObject() instanceof FieldDataOriginList) {
            Origin origin = ((FieldDataOriginList) lastPathComponent.getUserObject()).origin;
            copyString = origin.getX() + delimiter + origin.getY() + delimiter + origin.getZ();
        } else if (lastPathComponent.getUserObject() instanceof FieldDataExtentList) {
            Extent extent = ((FieldDataExtentList) lastPathComponent.getUserObject()).extent;
            copyString = extent.getX() + delimiter + extent.getY() + delimiter + extent.getZ();
        } else if (lastPathComponent.getUserObject() instanceof FieldDataISizeList) {
            ISize isize = ((FieldDataISizeList) lastPathComponent.getUserObject()).isize;
            copyString = isize.getX() + delimiter + isize.getY() + delimiter + isize.getZ();
        } else if (lastPathComponent.getUserObject() instanceof FieldDataTimeList) {
            double[] times = ((FieldDataTimeList) lastPathComponent.getUserObject()).times;
            for (int i = 0; i < times.length; i += 1) {
                if (i != 0) {
                    copyString += delimiter;
                }
                copyString += times[i] + "";
            }
        } else if (lastPathComponent.getUserObject() instanceof FieldDataMainList) {
            ExternalDataIdentifier extDataID = ((FieldDataMainList) lastPathComponent.getUserObject()).externalDataIdentifier;
            copyString = extDataID.getName();
        } else if (lastPathComponent.getUserObject() instanceof FieldDataVarList) {
            DataIdentifier dataIdentifier = ((FieldDataVarList) lastPathComponent.getUserObject()).dataIdentifier;
            copyString = dataIdentifier.getName();
        } else if (lastPathComponent.getUserObject() instanceof FieldDataVarMainList) {
            int childCount = lastPathComponent.getChildCount();
            for (int i = 0; i < childCount; i += 1) {
                if (i != 0) {
                    copyString += delimiter;
                }
                copyString += ((FieldDataVarList) ((DefaultMutableTreeNode) lastPathComponent.getChildAt(i)).getUserObject()).dataIdentifier.getName();
            }
        }
        if (copyString.length() > 0) {
            VCellTransferable.sendToClipboard(copyString);
        }
    }
}

Example 43 with Origin

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

the class ClientRequestManager method createFDOSFromVCImage.

private static FieldDataFileOperationSpec createFDOSFromVCImage(VCImage dbImage) throws ImageException {
    int[] temp = new int[256];
    short[] templateShorts = new short[dbImage.getNumXYZ()];
    for (int i = 0; i < dbImage.getPixels().length; i++) {
        templateShorts[i] = (short) (0x00FF & dbImage.getPixels()[i]);
        temp[templateShorts[i]]++;
    }
    for (int j = 0; j < dbImage.getPixelClasses().length; j++) {
        short tempshort = (short) (0x00FF & dbImage.getPixelClasses()[j].getPixel());
    }
    FieldDataFileOperationSpec fdfos = null;
    fdfos = new FieldDataFileOperationSpec();
    fdfos.origin = new Origin(0, 0, 0);
    fdfos.extent = dbImage.getExtent();
    fdfos.isize = new ISize(dbImage.getNumX(), dbImage.getNumY(), dbImage.getNumZ());
    fdfos.shortSpecData = new short[][][] { { templateShorts } };
    return fdfos;
}

Example 44 with Origin

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

the class FRAPStudy method getPSFFieldData.

public static FieldDataIdentifierSpec getPSFFieldData(LocalWorkspace localWorkspace) {
    // create ROI image
    short[] psfFieldData = null;
    psfFieldData = new short[9];
    psfFieldData[4] = (short) 1;
    // create field data
    int NumTimePoints = 1;
    // 8 rois integrated into 1 image
    int NumChannels = 1;
    short[][][] pixData = new short[NumTimePoints][NumChannels][1];
    pixData[0][0] = psfFieldData;
    // get extental data id
    ExternalDataIdentifier newPsfExtDataID = FRAPStudy.createNewExternalDataInfo(localWorkspace, FRAPStudy.PSF_DATA_NAME).getExternalDataIdentifier();
    CartesianMesh cartesianMesh;
    try {
        Origin origin = new Origin(0, 0, 0);
        Extent ext = new Extent(1, 1, 1);
        ISize isize = new ISize(3, 3, 1);
        cartesianMesh = CartesianMesh.createSimpleCartesianMesh(origin, ext, isize, new RegionImage(new VCImageUncompressed(null, new byte[isize.getXYZ()], ext, isize.getX(), isize.getY(), isize.getZ()), 0, null, null, RegionImage.NO_SMOOTHING));
        FieldDataFileOperationSpec fdos = new FieldDataFileOperationSpec();
        fdos.opType = FieldDataFileOperationSpec.FDOS_ADD;
        fdos.cartesianMesh = cartesianMesh;
        fdos.shortSpecData = pixData;
        fdos.specEDI = newPsfExtDataID;
        fdos.varNames = new String[] { "psfVar" };
        fdos.owner = LocalWorkspace.getDefaultOwner();
        fdos.times = new double[] { 0.0 };
        fdos.variableTypes = new VariableType[] { VariableType.VOLUME };
        fdos.origin = origin;
        fdos.extent = ext;
        fdos.isize = isize;
        localWorkspace.getDataSetControllerImpl().fieldDataFileOperation(fdos);
        FieldFunctionArguments psfFieldFunc = new FieldFunctionArguments(PSF_DATA_NAME, "psfVar", new Expression(0.0), VariableType.VOLUME);
        FieldDataIdentifierSpec fdis = new FieldDataIdentifierSpec(psfFieldFunc, newPsfExtDataID);
        return fdis;
    } catch (Exception e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
        return null;
    }
}

Example 45 with Origin

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

the class FRAPStudy method getCartesianMesh.

public CartesianMesh getCartesianMesh() throws Exception {
    CartesianMesh cartesianMesh = null;
    ImageDataset imgDataSet = getFrapData().getImageDataset();
    Extent extent = imgDataSet.getExtent();
    ISize isize = imgDataSet.getISize();
    Origin origin = new Origin(0, 0, 0);
    if (getBioModel() == null) {
        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));
    } else {
        RegionImage regionImage = getBioModel().getSimulationContexts()[0].getGeometry().getGeometrySurfaceDescription().getRegionImage();
        if (regionImage == null) {
            getBioModel().getSimulationContexts()[0].getGeometry().getGeometrySurfaceDescription().updateAll();
            regionImage = getBioModel().getSimulationContexts()[0].getGeometry().getGeometrySurfaceDescription().getRegionImage();
        }
        cartesianMesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, isize, regionImage);
    }
    return cartesianMesh;
}