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

Example 66 with ISize

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

the class ClientRequestManager method getISizeFromUser.

public static ISize getISizeFromUser(Component guiParent, ISize initISize, String textMessage) throws UserCancelException {
    Integer imageDimension = (initISize == null ? null : (initISize.getX() != 1 ? 1 : 0) + (initISize.getY() != 1 ? 1 : 0) + (initISize.getZ() != 1 ? 1 : 0));
    if (imageDimension != null && (imageDimension < 1 || imageDimension > 3)) {
        throw new IllegalArgumentException("Dimension must be 1, 2 or 3.");
    }
    try {
        int xsize = (imageDimension == null ? -1 : initISize.getX());
        int ysize = (imageDimension == null ? -1 : initISize.getY());
        int zsize = (imageDimension == null ? -1 : initISize.getZ());
        do {
            String result = (imageDimension == null ? "256,256,8" : xsize + "," + ysize + "," + zsize);
            result = DialogUtils.showInputDialog0(guiParent, textMessage, result);
            String tempResult = result;
            try {
                if (result == null || result.length() == 0) {
                    result = "";
                    throw new Exception("No size values entered.");
                }
                xsize = Integer.parseInt(tempResult.substring(0, tempResult.indexOf(",")));
                tempResult = tempResult.substring(tempResult.indexOf(",") + 1, tempResult.length());
                ysize = Integer.parseInt(tempResult.substring(0, tempResult.indexOf(",")));
                tempResult = tempResult.substring(tempResult.indexOf(",") + 1, tempResult.length());
                zsize = Integer.parseInt(tempResult);
                if (imageDimension != null) {
                    if (imageDimension == 2 && zsize != 1) {
                        throw new Exception("Dimension " + imageDimension + " must have z = 1.");
                    } else if (imageDimension == 1 && zsize != 1 && ysize != 1) {
                        throw new Exception("Dimension " + imageDimension + " must have z = 1 and y = 1.");
                    }
                }
                ISize isize = new ISize(xsize, ysize, zsize);
                if (isize.getXYZ() <= 0) {
                    throw new Exception("Total pixels (" + xsize + "*" + ysize + "*" + zsize + ") cannot be <=0.");
                }
                return isize;
            } catch (Exception e) {
                DialogUtils.showErrorDialog(guiParent, "Error entering starting sizes\n" + e.getMessage(), e);
            }
        } while (true);
    } catch (UtilCancelException e2) {
        throw UserCancelException.CANCEL_GENERIC;
    }
}

Example 67 with ISize

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

the class TopLevelWindowManager method addWorkspaceGeomSizeSelection.

private void addWorkspaceGeomSizeSelection(final Hashtable<String, Object> hash, Geometry sourceGeom) throws Exception {
    if (TopLevelWindowManager.this instanceof DocumentWindowManager) {
        Simulation[] simulations = null;
        SimulationContext[] simContexts = null;
        SimulationContext selectedSC = null;
        ArrayList<Object[]> allRows = new ArrayList<Object[]>();
        ArrayList<ISize> iSizes = new ArrayList<ISize>();
        if (this instanceof BioModelWindowManager) {
            BioModelWindowManager bmwm = ((BioModelWindowManager) this);
            // System.out.println(bmwm);
            if (bmwm.getDocumentEditor() instanceof cbit.vcell.client.desktop.biomodel.BioModelEditor) {
                cbit.vcell.client.desktop.biomodel.BioModelEditor bme = (cbit.vcell.client.desktop.biomodel.BioModelEditor) bmwm.getDocumentEditor();
                // System.out.println(bme);
                selectedSC = bme.getSelectedSimulationContext();
            // System.out.println(selectedSC);
            }
        }
        if (((DocumentWindowManager) TopLevelWindowManager.this).getVCDocument() instanceof BioModel) {
            simContexts = ((BioModel) ((DocumentWindowManager) TopLevelWindowManager.this).getVCDocument()).getSimulationContexts();
        } else if (((DocumentWindowManager) TopLevelWindowManager.this).getVCDocument() instanceof MathModel) {
            simulations = ((MathModel) ((DocumentWindowManager) TopLevelWindowManager.this).getVCDocument()).getSimulations();
        }
        String[] simColumnNames = null;
        if (simContexts != null) {
            simColumnNames = new String[] { "x", "y", "z", "appName", "simName" };
        } else {
            simColumnNames = new String[] { "x", "y", "z", "simName" };
        }
        ArrayList<Object[]> simRows = new ArrayList<Object[]>();
        ArrayList<CartesianMesh> meshes = new ArrayList<CartesianMesh>();
        for (int j = 0; j < (simContexts == null ? 1 : simContexts.length); j++) {
            Geometry geom = null;
            if (simContexts != null) {
                if (simContexts[j] != selectedSC) {
                    continue;
                }
                simulations = simContexts[j].getSimulations();
                geom = simContexts[j].getGeometry();
            } else {
                geom = ((MathModel) ((DocumentWindowManager) TopLevelWindowManager.this).getVCDocument()).getGeometry();
            }
            // ISize defaultSamplesize = geom.getGeometrySpec().getDefaultSampledImageSize();
            if (simulations != null && simulations.length > 0) {
                for (int i = 0; i < simulations.length; i++) {
                    Object[] row = new Object[simColumnNames.length];
                    // }
                    if (simulations[i].getMeshSpecification() != null && simulations[i].getMeshSpecification() != null) {
                        row = new Object[simColumnNames.length];
                        ISize samplingSize = simulations[i].getMeshSpecification().getSamplingSize();
                        row[0] = samplingSize.getX();
                        row[1] = samplingSize.getY();
                        row[2] = samplingSize.getZ();
                        row[3] = (simContexts != null ? simContexts[j].getName() : simulations[i].getName());
                        if (simContexts != null) {
                            row[4] = simulations[i].getName();
                        }
                        simRows.add(row);
                        VCImageUncompressed vcImageUnc = new VCImageUncompressed(null, new byte[samplingSize.getXYZ()], geom.getExtent(), samplingSize.getX(), samplingSize.getY(), samplingSize.getZ());
                        CartesianMesh simpleMesh = CartesianMesh.createSimpleCartesianMesh(geom.getOrigin(), geom.getExtent(), samplingSize, new RegionImage(vcImageUnc, geom.getDimension(), geom.getExtent(), geom.getOrigin(), RegionImage.NO_SMOOTHING));
                        meshes.add(simpleMesh);
                    }
                }
            }
        }
        for (int i = 0; i < simRows.size(); i++) {
            ISize iSize = meshes.get(i).getISize();
            iSizes.add(iSize);
            allRows.add(new Object[] { iSize.getX(), iSize.getY(), iSize.getZ(), "Simulation=" + (simColumnNames.length == 4 ? simRows.get(i)[3] : simRows.get(i)[3] + ":" + simRows.get(i)[4]) });
        }
        // if(allRows.size() > 0) {
        if (simRows.size() > 0) {
            Object[][] rowData = simRows.toArray(new Object[0][]);
            int[] selections = DialogUtils.showComponentOKCancelTableList(TopLevelWindowManager.this.getComponent(), "Select Simulation for Geom Size", simColumnNames, rowData, ListSelectionModel.SINGLE_SELECTION);
            if (selections != null && selections.length == 1) {
                // 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);
                hash.put(ClientRequestManager.NEW_IMAGE_SIZE_INFO, imagesizeInfo);
                VCImage image = null;
                if (sourceGeom.getGeometrySpec().getImage() == null) {
                    image = sourceGeom.getGeometrySpec().createSampledImage(iSizes.get(selections[0]));
                } else {
                    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));
                hash.put("newMesh", meshes.get(selections[0]));
                hash.put("sourceMesh", sourceMesh);
            }
        }
    }
}

Example 68 with ISize

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

the class ClientRequestManager method continueAfterMathModelGeomChangeWarning.

public static void continueAfterMathModelGeomChangeWarning(MathModelWindowManager mathModelWindowManager, Geometry newGeometry) throws UserCancelException {
    MathModel mathModel = mathModelWindowManager.getMathModel();
    if (mathModel != null && mathModel.getMathDescription() != null) {
        Geometry oldGeometry = mathModel.getMathDescription().getGeometry();
        if (oldGeometry != null && oldGeometry.getDimension() == 0) {
            return;
        }
        boolean bMeshResolutionChange = true;
        if (oldGeometry == null) {
            bMeshResolutionChange = false;
        }
        if (newGeometry != null && oldGeometry != null && oldGeometry.getDimension() == newGeometry.getDimension()) {
            bMeshResolutionChange = false;
        }
        boolean bHasSims = (mathModel.getSimulations() != null) && (mathModel.getSimulations().length > 0);
        StringBuffer meshResolutionChangeSB = new StringBuffer();
        if (bHasSims && bMeshResolutionChange) {
            ISize newGeomISize = MeshSpecification.calulateResetSamplingSize(newGeometry);
            for (int i = 0; i < mathModel.getSimulations().length; i++) {
                if (mathModel.getSimulations()[i].getMeshSpecification() != null) {
                    String simName = mathModel.getSimulations()[i].getName();
                    ISize simMeshSize = mathModel.getSimulations()[i].getMeshSpecification().getSamplingSize();
                    meshResolutionChangeSB.append((i != 0 ? "\n" : "") + "'" + simName + "' Mesh" + simMeshSize + " will be reset to " + newGeomISize + "");
                }
            }
        }
        String result = DialogUtils.showWarningDialog(JOptionPane.getFrameForComponent(mathModelWindowManager.getComponent()), "After changing MathModel geometry please note:\n" + "  1.  Check Geometry subvolume names match MathModel compartment names." + (bHasSims && bMeshResolutionChange ? "\n" + "  2.  All existing simulations mesh sizes will be reset" + " because the new Geometry spatial dimension(" + newGeometry.getDimension() + "D)" + " does not equal the current Geometry spatial dimension(" + oldGeometry.getDimension() + "D)" + "\n" + meshResolutionChangeSB.toString() : ""), new String[] { "Continue", "Cancel" }, "Continue");
        if (result != null && result.equals("Continue")) {
            return;
        }
    } else {
        return;
    }
    throw UserCancelException.CANCEL_GENERIC;
}

Example 69 with ISize

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

the class MeshSpecificationPanel method updateSize.

/**
 * Comment
 */
private void updateSize() {
    String error = null;
    String sx = getXTextField().getText();
    String sy = getYTextField().getText();
    String sz = getZTextField().getText();
    sx = (sx == null || sx.equals("")) ? "1" : sx;
    sy = (sy == null || sy.equals("")) ? "1" : sy;
    sz = (sz == null || sz.equals("")) ? "1" : sz;
    try {
        ISize iSize = new ISize(sx, sy, sz);
        getMeshSpecification().setSamplingSize(iSize);
    } catch (NumberFormatException nexc) {
        error = "NumberFormatException " + nexc.getMessage();
    } catch (java.beans.PropertyVetoException pexc) {
        error = pexc.getMessage();
    }
    if (error != null) {
        DialogUtils.showErrorDialog(this, "Error setting mesh size : " + error);
    }
}

Example 70 with ISize

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

the class MeshSpecificationPanel method updateTotalSizeAndSpatialStep.

private void updateTotalSizeAndSpatialStep() {
    if (getMeshSpecification() == null) {
        return;
    }
    if (getMeshSpecification().getGeometry() == null || getMeshSpecification().getGeometry().getExtent() == null) {
        return;
    }
    ISize samplingSize = getMeshSpecification().getSamplingSize();
    if (samplingSize == null) {
        return;
    }
    try {
        int dim = getMeshSpecification().getGeometry().getDimension();
        String xtext = getXTextField().getText();
        int numX = Integer.parseInt(xtext);
        int numY = 1;
        int numZ = 1;
        String totalSizeText = "";
        long totalSizeValue = numX;
        if (dim > 1) {
            String ytext = getYTextField().getText();
            numY = Integer.parseInt(ytext);
            totalSizeText += numX + " x " + numY;
            totalSizeValue *= numY;
            if (dim > 2) {
                String ztext = getZTextField().getText();
                numZ = Integer.parseInt(ztext);
                totalSizeText += " x " + numZ;
                totalSizeValue *= numZ;
            }
        }
        totalSizeTextField.setText(totalSizeText + (totalSizeText.length() == 0 ? "" : " = ") + totalSizeValue);
        Coordinate h = computeDxDyDz(numX, numY, numZ);
        ivjDxTextField.setText(h.getX() + "");
        ivjDyTextField.setText(h.getY() + "");
        ivjDzTextField.setText(h.getZ() + "");
    } catch (NumberFormatException ex) {
        clearTotalSizeAndSpatialStep();
    }
}