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

Example 11 with UserCancelException

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

the class FieldDataGUIPanel method jButtonFDFromSim_ActionPerformed.

private void jButtonFDFromSim_ActionPerformed(java.awt.event.ActionEvent actionEvent) {
    try {
        final RequestManager clientRequestManager = fieldDataWindowManager.getLocalRequestManager();
        final FieldDataWindowManager.OpenModelInfoHolder simInfoHolder = FieldDataWindowManager.selectOpenModelsFromDesktop(this, fieldDataWindowManager.getRequestManager(), true, "Select Simulation for Field Data", true);
        if (simInfoHolder == null) {
            PopupGenerator.showErrorDialog(this, "Please open a Bio or Math model containing the spatial (non-compartmental) simulation you wish to use to create a new Field Data");
            return;
        }
        // Check that the sim is in a state that can be copied
        final SimulationInfo simInfo = simInfoHolder.getSimInfo();
        if (simInfo == null) {
            throw new Exception("Selected sim '" + simInfoHolder.getSimName() + "' has no simInfo (save your model and retry).");
        }
        SimulationStatus simStatus = clientRequestManager.getServerSimulationStatus(simInfo);
        if (simStatus != null && (simStatus.isRunning() || simStatus.isStartRequested())) {
            throw new Exception("Can't copy 'running' simulation data from sim '" + simInfo.getName() + "'");
        }
        final FieldDataFileOperationSpec fdos = FieldDataFileOperationSpec.createCopySimFieldDataFileOperationSpec(null, (simInfo.getParentSimulationReference() != null ? simInfo.getParentSimulationReference() : simInfo.getSimulationVersion().getVersionKey()), simInfo.getOwner(), simInfoHolder.getJobIndex(), clientRequestManager.getDocumentManager().getUser());
        AsynchClientTask[] addTasks = addNewExternalData(this, this, true);
        AsynchClientTask[] taskArray = new AsynchClientTask[1 + addTasks.length];
        // add to the end
        System.arraycopy(addTasks, 0, taskArray, 1, addTasks.length);
        taskArray[0] = new AsynchClientTask("Create Field Data from Simulation", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

            public void run(Hashtable<String, Object> hashTable) throws Exception {
                FieldDataFileOperationResults fdor = clientRequestManager.getDocumentManager().fieldDataFileOperation(FieldDataFileOperationSpec.createInfoFieldDataFileOperationSpec((simInfo.getParentSimulationReference() != null ? simInfo.getParentSimulationReference() : simInfo.getSimulationVersion().getVersionKey()), simInfo.getOwner(), simInfoHolder.getJobIndex()));
                // Create (non-editable) info for display
                fdos.origin = fdor.origin;
                fdos.extent = fdor.extent;
                fdos.isize = fdor.iSize;
                fdos.times = fdor.times;
                fdos.varNames = new String[fdor.dataIdentifierArr.length];
                for (int i = 0; i < fdor.dataIdentifierArr.length; i += 1) {
                    fdos.varNames[i] = (fdor.dataIdentifierArr[i].getVariableType().equals(VariableType.VOLUME) ? "(vol) " : "") + (fdor.dataIdentifierArr[i].getVariableType().equals(VariableType.MEMBRANE) ? "(mbr) " : "") + fdor.dataIdentifierArr[i].getName();
                }
                hashTable.put("fdos", fdos);
                hashTable.put("initFDName", simInfo.getName());
            // addNewExternalData(clientRequestManager, fdos, simInfoHolder.simInfo.getName(), true);
            }
        };
        Hashtable<String, Object> hash = new Hashtable<String, Object>();
        ClientTaskDispatcher.dispatch(this, hash, taskArray, false);
    } catch (UserCancelException e) {
        return;
    } catch (Exception e) {
        PopupGenerator.showErrorDialog(this, "Error creating Field Data from simulation\n" + e.getMessage(), e);
    }
}

Example 12 with UserCancelException

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

the class FieldDataGUIPanel method jButtonFDCopyRef_ActionPerformed.

private void jButtonFDCopyRef_ActionPerformed(java.awt.event.ActionEvent actionEvent) {
    if (actionEvent.getSource() == getJButtonCreateGeom()) {
        DocumentWindow.showGeometryCreationWarning(FieldDataGUIPanel.this);
        return;
    }
    TreePath selPath = getJTree1().getSelectionPath();
    final DefaultMutableTreeNode varNode = (DefaultMutableTreeNode) selPath.getLastPathComponent();
    final DefaultMutableTreeNode mainNode = (DefaultMutableTreeNode) varNode.getParent().getParent();
    SelectedTimes selectedTimes = null;
    try {
        selectedTimes = selectTimeFromNode(mainNode);
    } catch (UserCancelException e) {
        return;
    }
    double selectedTime = selectedTimes.getTimes()[selectedTimes.getSelectedIndex()];
    if (actionEvent.getSource() == getJButtonFDCopyRef()) {
        String fieldFunctionReference = SimulationData.createCanonicalFieldFunctionSyntax(((FieldDataMainList) mainNode.getUserObject()).externalDataIdentifier.getName(), ((FieldDataVarList) varNode.getUserObject()).dataIdentifier.getName(), selectedTime, ((FieldDataVarList) varNode.getUserObject()).dataIdentifier.getVariableType().getTypeName());
        VCellTransferable.sendToClipboard(fieldFunctionReference);
    } else if (actionEvent.getSource() == dsDataSymbolButton && dataSymbolCallBack != null) {
        dataSymbolCallBack.createDataSymbol(((FieldDataMainList) mainNode.getUserObject()).externalDataIdentifier, ((FieldDataVarList) varNode.getUserObject()).dataIdentifier.getName(), ((FieldDataVarList) varNode.getUserObject()).dataIdentifier.getVariableType(), selectedTime);
    }
}

Example 13 with UserCancelException

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

the class FieldDataInfoPanel method getJButtonVarNameEdit.

/**
 * This method initializes jButtonVarNameEdit
 *
 * @return javax.swing.JButton
 */
private JButton getJButtonVarNameEdit() {
    if (jButtonVarNameEdit == null) {
        jButtonVarNameEdit = new JButton();
        jButtonVarNameEdit.setText("Edit Var...");
        jButtonVarNameEdit.addActionListener(new java.awt.event.ActionListener() {

            public void actionPerformed(java.awt.event.ActionEvent e) {
                try {
                    String newVarName = inputStrictName(jComboBoxVarNames.getSelectedItem().toString(), "Edit Variable Name");
                    int selIndex = jComboBoxVarNames.getSelectedIndex();
                    ((DefaultComboBoxModel) jComboBoxVarNames.getModel()).removeElementAt(selIndex);
                    ((DefaultComboBoxModel) jComboBoxVarNames.getModel()).insertElementAt(newVarName, selIndex);
                    jComboBoxVarNames.setSelectedIndex(selIndex);
                } catch (UserCancelException e2) {
                // ignore
                }
            }
        });
    }
    return jButtonVarNameEdit;
}

Example 14 with UserCancelException

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

the class ROIMultiPaintManager method askInitialize.

private void askInitialize(boolean bForceAddDistinct) {
    final TreeSet<Integer> sortedPixVal = new TreeSet<Integer>();
    BitSet uniquePixelBS = new BitSet((int) Math.pow(2, Short.SIZE));
    for (int i = 0; i < getImageDataSetChannel().getAllImages().length; i++) {
        short[] dataToSegment = getImageDataSetChannel().getAllImages()[i].getPixels();
        for (int j = 0; j < dataToSegment.length; j++) {
            if ((int) (dataToSegment[j] & 0x0000FFFF) != 0) {
                if (!uniquePixelBS.get((int) (dataToSegment[j] & 0x0000FFFF))) {
                    sortedPixVal.add((int) (dataToSegment[j] & 0x0000FFFF));
                }
                uniquePixelBS.set((int) (dataToSegment[j] & 0x0000FFFF));
            }
        }
    }
    boolean bNotAddDomains = uniquePixelBS.cardinality() >= 256 || /*too many to add*/
    !bHasOriginalData || /*no import*/
    uniquePixelBS.cardinality() == 0;
    final String addROIManual = "1. Add empty Domain";
    final String addAllDistinct = "2. Assume Pre-Segmented";
    final String cancel = "Cancel";
    String result = null;
    String distinctDescr = "The current image contains " + uniquePixelBS.cardinality() + " distinct non-zero pixel values.";
    if (!bForceAddDistinct) {
        result = DialogUtils.showWarningDialog(overlayEditorPanelJAI, "Image Editor", distinctDescr + "  Segmenting an image begins with defining Domain(s) manually or automatically." + "  Editing tools are used to create/edit more Domains.  Choose an action:\n" + "1. Add an 'empty' Domain to begin segmenting manually." + (bNotAddDomains ? "" : "\n2. Pre-Segmented (add Domains for every distinct pixel value)."), (bNotAddDomains ? new String[] { addROIManual, cancel } : new String[] { addROIManual, addAllDistinct, cancel }), cancel);
        if (result.equals(cancel)) {
            // throw UserCancelException.CANCEL_GENERIC;
            return;
        }
    } else {
        if (uniquePixelBS.cardinality() == 0) {
            DialogUtils.showWarningDialog(overlayEditorPanelJAI, "Underlay contains no non-zero pixel values available for Domain assignment.");
            return;
        }
        boolean bHasExistingROIs = overlayEditorPanelJAI.getAllCompositeROINamesAndColors() != null && overlayEditorPanelJAI.getAllCompositeROINamesAndColors().length > 0;
        result = DialogUtils.showWarningDialog(overlayEditorPanelJAI, (bHasExistingROIs ? "Warning: Existing Domains may be overwritten.  " : "") + distinctDescr, new String[] { addAllDistinct, cancel }, addAllDistinct);
        if (result.equals(cancel)) {
            // throw UserCancelException.CANCEL_GENERIC;
            return;
        }
    }
    try {
        if (result.equals(addAllDistinct)) {
            // try add all distinct, fail if too many regions
            final String LOOKUP_KEY = "LOOKUP_KEY";
            AsynchClientTask createDistinctROI = new AsynchClientTask("Create distinct ROI...", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

                @Override
                public void run(Hashtable<String, Object> hashTable) throws Exception {
                    Integer[] uniquePivValArr = sortedPixVal.toArray(new Integer[0]);
                    int[] lookup = new int[uniquePivValArr[uniquePivValArr.length - 1] + 1];
                    Arrays.fill(lookup, -1);
                    for (int i = 0; i < uniquePivValArr.length; i++) {
                        lookup[uniquePivValArr[i]] = i + 1;
                        overlayEditorPanelJAI.addROIName("roi_" + uniquePivValArr[i], false, "roi_" + uniquePivValArr[0], true, i + 1);
                    }
                    hashTable.put(LOOKUP_KEY, lookup);
                }
            };
            AsynchClientTask applyDistinctROI = new AsynchClientTask("Apply distinct ROI...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

                @Override
                public void run(Hashtable<String, Object> hashTable) throws Exception {
                    int[] lookup = (int[]) hashTable.get(LOOKUP_KEY);
                    for (int i = 0; i < getImageDataSetChannel().getAllImages().length; i++) {
                        short[] dataToSegment = getImageDataSetChannel().getAllImages()[i].getPixels();
                        byte[] roiBytes = ((DataBufferByte) roiComposite[i].getRaster().getDataBuffer()).getData();
                        for (int j = 0; j < dataToSegment.length; j++) {
                            if ((int) (dataToSegment[j] & 0x0000FFFF) != 0) {
                                roiBytes[j] = (byte) lookup[(int) (dataToSegment[j] & 0x0000FFFF)];
                            }
                        }
                    }
                }
            };
            AsynchClientTask failTask = new AsynchClientTask("Check fail...", AsynchClientTask.TASKTYPE_SWING_BLOCKING, false, false, true) {

                @Override
                public void run(Hashtable<String, Object> hashTable) throws Exception {
                    Throwable throwable = (Throwable) hashTable.get(ClientTaskDispatcher.TASK_ABORTED_BY_ERROR);
                    if (throwable != null) {
                        // cleanup
                        ComboboxROIName[] comboboxROINames = overlayEditorPanelJAI.getAllCompositeROINamesAndColors();
                        for (int i = 0; i < comboboxROINames.length; i++) {
                            overlayEditorPanelJAI.deleteROIName(comboboxROINames[i]);
                        }
                        for (int i = 0; i < roiComposite.length; i++) {
                            byte[] roiBytes = ((DataBufferByte) roiComposite[i].getRaster().getDataBuffer()).getData();
                            Arrays.fill(roiBytes, (byte) 0);
                        }
                    }
                }
            };
            AsynchClientTask clearHighlightsTask = new AsynchClientTask("Apply distinct ROI...", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

                @Override
                public void run(Hashtable<String, Object> hashTable) throws Exception {
                    overlayEditorPanelJAI.setHighliteInfo(null, OverlayEditorPanelJAI.FRAP_DATA_INIT_PROPERTY);
                }
            };
            ClientTaskDispatcher.dispatch(overlayEditorPanelJAI, new Hashtable<String, Object>(), new AsynchClientTask[] { createDistinctROI, applyDistinctROI, createRegionImageTask, failTask, clearHighlightsTask, saveSortRegionImageTask, updateList }, false, false, null, true);
        } else {
            try {
                addNewROI(overlayEditorPanelJAI.getAllCompositeROINamesAndColors(), null);
            } catch (Exception e) {
                e.printStackTrace();
                DialogUtils.showErrorDialog(overlayEditorPanelJAI, e.getMessage());
            }
        }
    } catch (UserCancelException e) {
    // do nothing
    }
}

Example 15 with UserCancelException

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

the class ROIMultiPaintManager method resizeDataset.

private void resizeDataset() {
    final ISize currentISize = new ISize(roiComposite[0].getWidth(), roiComposite[0].getHeight(), roiComposite.length);
    ImageSizeInfo origImageSizeInfo = new ImageSizeInfo(null, currentISize, 0, new double[] { 0 }, 0);
    ImageSizeInfo newImageSizeInfo = null;
    try {
        newImageSizeInfo = ClientRequestManager.queryImageResize(overlayEditorPanelJAI, origImageSizeInfo, false);
    } catch (UserCancelException e) {
        return;
    }
    final ISize newImageSize = newImageSizeInfo.getiSize();
    AsynchClientTask resizeTask = new AsynchClientTask("Resizing...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            resizeImpl(ResizeInfo.createScaleResizeInfo(currentISize, newImageSize), getClientTaskStatusSupport());
        }
    };
    final AsynchClientTask updatePanelTask = getUpdateDisplayAfterCropTask();
    ClientTaskDispatcher.dispatch(overlayEditorPanelJAI, new Hashtable<String, Object>(), new AsynchClientTask[] { resizeTask, updatePanelTask }, false, false, null, true);
}