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

Example 71 with Extent

use of org.vcell.util.Extent 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 72 with Extent

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

the class ROIMultiPaintManager method showGUI.

public Geometry showGUI(final String okButtonText, final String sourceDataName, final Component parentComponent, String initalAnnotation, final VCPixelClass[] vcPixelClasses, UserPreferences userPreferences, boolean bFieldData) {
    originalAnnotation = initalAnnotation;
    final Geometry[] finalGeometryHolder = new Geometry[1];
    if (overlayEditorPanelJAI == null) {
        overlayEditorPanelJAI = new OverlayEditorPanelJAI();
        overlayEditorPanelJAI.setCalcCoords(new CalcCoords());
        overlayEditorPanelJAI.setUserPreferences(userPreferences);
        overlayEditorPanelJAI.setMinimumSize(new Dimension(700, 600));
        overlayEditorPanelJAI.setPreferredSize(new Dimension(700, 600));
        overlayEditorPanelJAI.addPropertyChangeListener(ROIMultiPaintManager.this);
    }
    // delete all names
    overlayEditorPanelJAI.deleteROIName(null);
    // when user selects image "from DB" or "from current geometry"
    applyPixelClasses(vcPixelClasses, parentComponent);
    if (getImageDataset().length > 1) {
        String[] channelNames = new String[getImageDataset().length];
        for (int i = 0; i < channelNames.length; i++) {
            channelNames[i] = "channel " + i;
        }
        overlayEditorPanelJAI.setChannelNames(channelNames);
    } else {
        overlayEditorPanelJAI.setChannelNames(null);
    }
    updateUnderlayHistogramDisplay();
    overlayEditorPanelJAI.setContrastToMinMax();
    overlayEditorPanelJAI.setAllROICompositeImage(roiComposite, OverlayEditorPanelJAI.FRAP_DATA_INIT_PROPERTY);
    final JDialog jDialog = new JDialog(JOptionPane.getFrameForComponent(parentComponent));
    jDialog.setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE);
    jDialog.setTitle("Geometry Editor (" + sourceDataName + ")");
    jDialog.setModal(true);
    final JButton cancelJButton = new JButton("Cancel");
    cancelJButton.addActionListener(new ActionListener() {

        public void actionPerformed(ActionEvent e) {
            final String QUIT_ANSWER = "Quit Geometry Editor";
            String result = DialogUtils.showWarningDialog(jDialog, "Confirm cancel", "Quit geometry editor and lose all changes?", new String[] { QUIT_ANSWER, "back" }, QUIT_ANSWER);
            if (result != null && result.equals(QUIT_ANSWER)) {
                jDialog.dispose();
            }
        }
    });
    jDialog.addWindowListener(new WindowAdapter() {

        @Override
        public void windowOpened(WindowEvent e) {
            super.windowOpened(e);
            if (bHasOriginalData) {
                calculateHistogram();
            }
            updateUndoAfter(false);
            if (vcPixelClasses == null) {
                askInitialize(false);
            }
        }

        @Override
        public void windowClosing(WindowEvent e) {
            // TODO Auto-generated method stub
            super.windowClosing(e);
            cancelJButton.doClick();
        }
    });
    final JPanel okCancelJPanel = new JPanel(new FlowLayout());
    JButton okJButton = new JButton(okButtonText);
    okJButton.addActionListener(new ActionListener() {

        public void actionPerformed(ActionEvent e) {
            try {
                VCImage finalImage = checkAll();
                finalImage.setDescription((editedGeometryAttributes != null ? editedGeometryAttributes.annotation : originalAnnotation));
                finalGeometryHolder[0] = new Geometry((String) null, finalImage);
                finalGeometryHolder[0].getGeometrySpec().setOrigin((editedGeometryAttributes != null ? editedGeometryAttributes.origin : originalOrigin));
                finalGeometryHolder[0].getGeometrySpec().setExtent((editedGeometryAttributes != null ? editedGeometryAttributes.extent : originalExtent));
                finalGeometryHolder[0].setDescription((editedGeometryAttributes != null ? editedGeometryAttributes.annotation : originalAnnotation));
                jDialog.dispose();
            } catch (UserCancelException uce) {
            } catch (Exception exc) {
                DialogUtils.showErrorDialog(overlayEditorPanelJAI, "Error validating compartments.\n" + exc.getMessage(), exc);
            }
        }
    });
    JButton attributesJButton = new JButton("Attributes...");
    attributesJButton.addActionListener(new ActionListener() {

        public void actionPerformed(ActionEvent e) {
            try {
                editedGeometryAttributes = showEditGeometryAttributes(jDialog, editedGeometryAttributes);
            } catch (UserCancelException uce) {
            // ignore
            }
        }
    });
    // JButton surfaceButton = new JButton("View Surfaces...");
    // surfaceButton.addActionListener(new ActionListener() {
    // public void actionPerformed(ActionEvent e) {
    // showDataValueSurfaceViewer(geomAttr);
    // }
    // });
    JButton fieldDataJButton = null;
    if (bFieldData) {
        fieldDataJButton = new JButton("FieldData...");
        fieldDataJButton.addActionListener(new ActionListener() {

            @Override
            public void actionPerformed(ActionEvent e) {
                try {
                    Component c = overlayEditorPanelJAI;
                    do {
                        System.out.println(c.getClass().getName());
                        if (c instanceof DocumentWindow) {
                            // BeanUtils.printComponentInfo((Container)c);
                            ArrayList<Component> comps = new ArrayList<Component>();
                            BeanUtils.findComponent((Container) c, InitialConditionsPanel.class, comps);
                            InitialConditionsPanel initialConditionsPanel = (InitialConditionsPanel) comps.get(0);
                            SpeciesContextSpec[] speciesContextSpecs = initialConditionsPanel.getInitConditionVars();
                            Object[][] objs = new Object[speciesContextSpecs.length][1];
                            for (int i = 0; i < speciesContextSpecs.length; i++) {
                                if (speciesContextSpecs[i].getSimulationContext() == initialConditionsPanel.getSimulationContext()) {
                                    objs[i][0] = speciesContextSpecs[i].getSpeciesContext().getName();
                                }
                            }
                            int[] select = DialogUtils.showComponentOKCancelTableList(overlayEditorPanelJAI, "Select species to add InitialCondition Field Data, App:'" + initialConditionsPanel.getSimulationContext().getName() + "'", new String[] { "speciesContext" }, objs, ListSelectionModel.SINGLE_SELECTION);
                            if (select != null && select.length > 0) {
                                // try {
                                String scName = speciesContextSpecs[select[0]].getSpeciesContext().getName();
                                Origin orig = (editedGeometryAttributes != null ? editedGeometryAttributes.origin : originalOrigin);
                                Extent extent = (editedGeometryAttributes != null ? editedGeometryAttributes.extent : originalExtent);
                                String fieldDataName = null;
                                boolean bDone = false;
                                do {
                                    try {
                                        fieldDataName = DialogUtils.showInputDialog0(ROIMultiPaintManager.this.overlayEditorPanelJAI, "Enter FieldData name", (fieldDataName == null ? ROIMultiPaintManager.this.importSourceName : fieldDataName));
                                        createFD(false, fieldDataName, ROIMultiPaintManager.this.importSourceName, extent, orig, new String[] { scName }, new double[] { 0.0 }, initImageDataSetChannels[0].getISize());
                                        bDone = true;
                                    } catch (UtilCancelException uce) {
                                        return;
                                    } catch (Exception e1) {
                                        e1.printStackTrace();
                                        if (e1.getMessage().toUpperCase().contains("ORA-00001")) {
                                            DialogUtils.showWarningDialog(ROIMultiPaintManager.this.overlayEditorPanelJAI, fieldDataName + " already used, enter a different name");
                                            continue;
                                        }
                                        throw e1;
                                    }
                                } while (!bDone);
                                initialConditionsPanel.setGeneratedFieldData(scName, "vcField('" + fieldDataName + "','" + scName + "',0.0,'Volume')");
                            // if(true) {
                            // return;
                            // }
                            // ISize iSize = initImageDataSetChannels[0].getISize();
                            // Extent extent = initImageDataSetChannels[0].getExtent();
                            // Origin orig = (editedGeometryAttributes!=null?editedGeometryAttributes.origin:originalOrigin);
                            // Extent extent = (editedGeometryAttributes!=null?editedGeometryAttributes.extent:originalExtent);
                            // createFD(false, fieldDataName, ROIMultiPaintManager.this.importSourceName, extent, orig, new String[] {scName}, new double[] {0.0},initImageDataSetChannels[0].getISize());
                            // export();
                            // ORA-00001
                            // } catch (Exception e1) {
                            // if(e1 instanceof UserCancelException) {
                            // return;
                            // }
                            // e1.printStackTrace();
                            // DialogUtils.showErrorDialog(overlayEditorPanelJAI, e1.getMessage());
                            // }
                            }
                        }
                    } while ((c = c.getParent()) != null);
                } catch (Exception e2) {
                    e2.printStackTrace();
                    if (e2 instanceof UserCancelException || e2 instanceof UtilCancelException) {
                        return;
                    }
                    DialogUtils.showErrorDialog(ROIMultiPaintManager.this.overlayEditorPanelJAI, e2.getMessage());
                }
            }
        });
    }
    JButton exportJButton = new JButton("Export...");
    exportJButton.addActionListener(new ActionListener() {

        public void actionPerformed(ActionEvent e) {
            export();
        }
    });
    JButton importJButton = new JButton("Import stl...");
    importJButton.addActionListener(new ActionListener() {

        public void actionPerformed(ActionEvent e) {
            JFileChooser importJFC = new JFileChooser(ClientRequestManager.getPreferredPath(UserPreferences.getLastUserPreferences()));
            importJFC.setDialogTitle("Choose .stl file(s) to import");
            importJFC.setMultiSelectionEnabled(true);
            int result = importJFC.showOpenDialog(overlayEditorPanelJAI);
            if (result == JFileChooser.APPROVE_OPTION) {
                File[] selectedFiles = importJFC.getSelectedFiles();
                if (selectedFiles != null && selectedFiles.length > 0) {
                    ClientRequestManager.setPreferredPath(UserPreferences.getLastUserPreferences(), selectedFiles[0]);
                    Vect3d sampleSize = new Vect3d(getImageDataset()[0].getISize().getX(), getImageDataset()[0].getISize().getY(), getImageDataset()[0].getISize().getZ());
                    ArrayList<AsynchClientTask> stlImportTasks = getImportSTLtasks(selectedFiles, sampleSize, new Vect3d(0, 0, 0));
                    ClientTaskDispatcher.dispatch(overlayEditorPanelJAI, new Hashtable<>(), stlImportTasks.toArray(new AsynchClientTask[0]));
                } else {
                    DialogUtils.showErrorDialog(overlayEditorPanelJAI, "Select at least 1 .stl file for import.");
                }
            }
        }
    });
    okCancelJPanel.add(okJButton);
    okCancelJPanel.add(attributesJButton);
    okCancelJPanel.add(exportJButton);
    okCancelJPanel.add(importJButton);
    // okCancelJPanel.add(surfaceButton);
    if (bFieldData) {
        okCancelJPanel.add(fieldDataJButton);
    }
    this.overlayEditorPanelJAI.translateToolButton.setVisible(bFieldData);
    this.overlayEditorPanelJAI.scaleToolButton.setVisible(bFieldData);
    okCancelJPanel.add(cancelJButton);
    jDialog.getContentPane().add(overlayEditorPanelJAI, BorderLayout.CENTER);
    jDialog.getContentPane().add(okCancelJPanel, BorderLayout.SOUTH);
    jDialog.setSize(700, 600);
    DialogUtils.showModalJDialogOnTop(jDialog, parentComponent);
    if (finalGeometryHolder[0] == null) {
        throw UserCancelException.CANCEL_GENERIC;
    }
    return finalGeometryHolder[0];
}

Example 73 with Extent

use of org.vcell.util.Extent 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 74 with Extent

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

the class ROIAssistPanel method calculateRegionInfos.

private RegionInfo[] calculateRegionInfos(short[] validatePixels) throws Exception {
    byte[] roiBytes = new byte[validatePixels.length];
    for (int i = 0; i < roiBytes.length; i++) {
        roiBytes[i] = (byte) (validatePixels[i] == 0 ? 0 : 1);
    }
    VCImageUncompressed roiVCImage = new VCImageUncompressed(null, roiBytes, new Extent(1, 1, 1), originalROI.getISize().getX(), originalROI.getISize().getY(), originalROI.getISize().getZ());
    RegionImage roiRegionImage = new RegionImage(roiVCImage, 0, null, null, RegionImage.NO_SMOOTHING);
    return roiRegionImage.getRegionInfos();
}

Example 75 with Extent

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

the class VFrap_ROIAssistPanel method calculateRegionInfos.

private RegionInfo[] calculateRegionInfos(short[] validatePixels) throws Exception {
    byte[] roiBytes = new byte[validatePixels.length];
    for (int i = 0; i < roiBytes.length; i++) {
        roiBytes[i] = (byte) (validatePixels[i] == 0 ? 0 : 1);
    }
    VCImageUncompressed roiVCImage = new VCImageUncompressed(null, roiBytes, new Extent(1, 1, 1), originalROI.getISize().getX(), originalROI.getISize().getY(), originalROI.getISize().getZ());
    RegionImage roiRegionImage = new RegionImage(roiVCImage, 0, null, null, RegionImage.NO_SMOOTHING);
    return roiRegionImage.getRegionInfos();
}