Examples with ExternalDataIdentifier org.vcell.util.document.ExternalDataIdentifier used on opensource projects

Example 31 with ExternalDataIdentifier

use of org.vcell.util.document.ExternalDataIdentifier 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 32 with ExternalDataIdentifier

use of org.vcell.util.document.ExternalDataIdentifier in project vcell by virtualcell.

the class FieldDataGUIPanel method addNewExternalData.

public static AsynchClientTask[] addNewExternalData(final Component requester, final FieldDataGUIPanel fieldDataGUIPanel, final boolean isFromSimulation) {
    final RequestManager clientRequestManager = fieldDataGUIPanel.fieldDataWindowManager.getLocalRequestManager();
    AsynchClientTask task1 = new AsynchClientTask("creating field data", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            FieldDataFileOperationSpec fdos = (FieldDataFileOperationSpec) hashTable.get("fdos");
            String initialExtDataName = (String) hashTable.get("initFDName");
            fdos.specEDI = null;
            FieldDataInfoPanel fdip = new FieldDataInfoPanel();
            fdip.setSimulationMode(isFromSimulation);
            fdip.initISize(fdos.isize);
            fdip.initIOrigin(fdos.origin);
            fdip.initIExtent(fdos.extent);
            fdip.initTimes(fdos.times);
            fdip.initNames(TokenMangler.fixTokenStrict(initialExtDataName), fdos.varNames);
            fdip.setAnnotation(fdos.annotation);
            FieldDataFileOperationSpec userDefinedFDOS = new FieldDataFileOperationSpec();
            while (true) {
                int choice = PopupGenerator.showComponentOKCancelDialog(requester, fdip, "Create new field data");
                if (choice == JOptionPane.OK_OPTION) {
                    // Check values
                    try {
                        userDefinedFDOS.extent = fdip.getExtent();
                    } catch (Exception e) {
                        PopupGenerator.showErrorDialog(requester, "Problem with Extent values. Please re-enter.\n" + e.getMessage() + "\nTry Again.", e);
                        continue;
                    }
                    try {
                        userDefinedFDOS.origin = fdip.getOrigin();
                    } catch (Exception e) {
                        PopupGenerator.showErrorDialog(requester, "Problem with Origin values. Please re-enter.\n" + e.getMessage() + "\nTry Again.", e);
                        continue;
                    }
                    try {
                        userDefinedFDOS.varNames = fdip.getVariableNames();
                    } catch (Exception e) {
                        PopupGenerator.showErrorDialog(requester, "Problem with Variable names. Please re-enter.\n" + e.getMessage() + "\nTry Again.", e);
                        continue;
                    }
                    userDefinedFDOS.annotation = fdip.getAnnotation();
                    userDefinedFDOS.times = fdip.getTimes();
                    try {
                        if (fdip.getFieldName() == null || fdip.getFieldName().length() == 0 || !fdip.getFieldName().equals(TokenMangler.fixTokenStrict(fdip.getFieldName()))) {
                            throw new Exception("Field Data names can contain only letters,digits and underscores");
                        }
                        // Check to see if this name is already used
                        DefaultMutableTreeNode rootNode = (DefaultMutableTreeNode) fieldDataGUIPanel.getJTree1().getModel().getRoot();
                        for (int i = 0; i < rootNode.getChildCount(); i += 1) {
                            ExternalDataIdentifier extDataID = ((FieldDataMainList) ((DefaultMutableTreeNode) rootNode.getChildAt(i)).getUserObject()).externalDataIdentifier;
                            if (fdip.getFieldName().equals(extDataID.getName())) {
                                throw new Exception("New Field Data name " + fdip.getFieldName() + " already used.");
                            }
                        }
                    } catch (Exception e) {
                        PopupGenerator.showErrorDialog(requester, "Error saving Field Data Name to Database. Try again.\n" + e.getMessage(), e);
                        continue;
                    }
                    hashTable.put("userDefinedFDOS", userDefinedFDOS);
                    hashTable.put("fieldName", fdip.getFieldName());
                    break;
                } else {
                    throw UserCancelException.CANCEL_GENERIC;
                }
            }
        }
    };
    AsynchClientTask task2 = new AsynchClientTask("saving field data", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            // Add to Server Disk
            // save Database
            FieldDataFileOperationSpec tempFDOS = (FieldDataFileOperationSpec) hashTable.get("userDefinedFDOS");
            String fieldName = (String) hashTable.get("fieldName");
            FieldDataFileOperationSpec fdos = (FieldDataFileOperationSpec) hashTable.get("fdos");
            DocumentManager documentManager = clientRequestManager.getDocumentManager();
            FieldDataDBOperationSpec newExtDataIDSpec = FieldDataDBOperationSpec.createSaveNewExtDataIDSpec(documentManager.getUser(), fieldName, tempFDOS.annotation);
            tempFDOS.specEDI = documentManager.fieldDataDBOperation(newExtDataIDSpec).extDataID;
            fdos.specEDI = tempFDOS.specEDI;
            fdos.annotation = tempFDOS.annotation;
            try {
                if (!isFromSimulation) {
                    fdos.extent = tempFDOS.extent;
                    fdos.origin = tempFDOS.origin;
                    fdos.varNames = tempFDOS.varNames;
                    fdos.times = tempFDOS.times;
                    // 
                    // Subvolumes and Regions NOT implemented now
                    // 
                    fdos.cartesianMesh = CartesianMesh.createSimpleCartesianMesh(fdos.origin, fdos.extent, fdos.isize, new RegionImage(new // empty regions
                    VCImageUncompressed(// empty regions
                    null, // empty regions
                    new byte[fdos.isize.getXYZ()], fdos.extent, fdos.isize.getX(), fdos.isize.getY(), fdos.isize.getZ()), 0, null, null, RegionImage.NO_SMOOTHING));
                }
                // Add to Server Disk
                documentManager.fieldDataFileOperation(fdos);
            } catch (Exception e) {
                try {
                    // try to cleanup new ExtDataID
                    documentManager.fieldDataDBOperation(FieldDataDBOperationSpec.createDeleteExtDataIDSpec(fdos.specEDI));
                } catch (Exception e2) {
                // ignore
                }
                fdos.specEDI = null;
                throw e;
            }
        }
    };
    AsynchClientTask task3 = new AsynchClientTask("refreshing field data", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            FieldDataFileOperationSpec fdos = (FieldDataFileOperationSpec) hashTable.get("fdos");
            DefaultMutableTreeNode root = ((DefaultMutableTreeNode) fieldDataGUIPanel.getJTree1().getModel().getRoot());
            if (root.getChildCount() == 0) {
                fieldDataGUIPanel.updateJTree(clientRequestManager);
            } else {
                int alphabeticalIndex = -1;
                for (int i = 0; i < root.getChildCount(); i += 1) {
                    if ((((FieldDataMainList) ((DefaultMutableTreeNode) root.getChildAt(i)).getUserObject())).externalDataIdentifier.getName().compareToIgnoreCase(fdos.specEDI.getName()) > 0) {
                        alphabeticalIndex = i;
                        break;
                    }
                }
                if (alphabeticalIndex == -1) {
                    alphabeticalIndex = root.getChildCount();
                }
                DefaultMutableTreeNode mainNode = new DefaultMutableTreeNode(new FieldDataMainList(fdos.specEDI, fdos.annotation));
                mainNode.add(new DefaultMutableTreeNode(new FieldDataVarMainList()));
                ((DefaultTreeModel) fieldDataGUIPanel.getJTree1().getModel()).insertNodeInto(mainNode, root, alphabeticalIndex);
            }
        }
    };
    return new AsynchClientTask[] { task1, task2, task3 };
}

Example 33 with ExternalDataIdentifier

use of org.vcell.util.document.ExternalDataIdentifier in project vcell by virtualcell.

the class FieldDataGUIPanel method updateJTree.

public void updateJTree(final RequestManager clientRequestManager) {
    if (clientRequestManager == null) {
        DefaultMutableTreeNode emptyNode = new DefaultMutableTreeNode("No Info Available");
        getJTree1().setModel(new DefaultTreeModel(emptyNode));
    } else {
        DefaultMutableTreeNode startupNode = new DefaultMutableTreeNode("Gathering Field Data Information... (Please wait)");
        getJTree1().setModel(new DefaultTreeModel(startupNode));
        AsynchClientTask gatherInfo = new AsynchClientTask("gatherInfo", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                try {
                    DocumentManager documentManager = clientRequestManager.getDocumentManager();
                    FieldDataDBOperationSpec fdos = FieldDataDBOperationSpec.createGetExtDataIDsSpec(documentManager.getUser());
                    FieldDataDBOperationResults fieldDataDBOperationResults = documentManager.fieldDataDBOperation(fdos);
                    ExternalDataIdentifier[] externalDataIdentifierArr = fieldDataDBOperationResults.extDataIDArr;
                    String[] extDataAnnotArr = fieldDataDBOperationResults.extDataAnnotArr;
                    TreeMap<ExternalDataIdentifier, String> sortedExtDataIDTreeMap = new TreeMap<ExternalDataIdentifier, String>(new Comparator<ExternalDataIdentifier>() {

                        public int compare(ExternalDataIdentifier o1, ExternalDataIdentifier o2) {
                            return o1.getName().compareToIgnoreCase(o2.getName());
                        }
                    });
                    for (int i = 0; i < externalDataIdentifierArr.length; i += 1) {
                        sortedExtDataIDTreeMap.put(externalDataIdentifierArr[i], extDataAnnotArr[i]);
                    }
                    DefaultMutableTreeNode rootNode = new DefaultMutableTreeNode(new InitializedRootNode("Field Data Info" + (externalDataIdentifierArr.length == 0 ? " (None Defined)" : "")));
                    Iterator<Entry<ExternalDataIdentifier, String>> sortIter = sortedExtDataIDTreeMap.entrySet().iterator();
                    while (sortIter.hasNext()) {
                        Entry<ExternalDataIdentifier, String> entry = sortIter.next();
                        DefaultMutableTreeNode mainNode = new DefaultMutableTreeNode(new FieldDataMainList(entry.getKey(), entry.getValue()));
                        mainNode.add(new DefaultMutableTreeNode(new FieldDataVarMainList()));
                        rootNode.add(mainNode);
                    }
                    hashTable.put("rootNode", rootNode);
                } catch (Exception e) {
                    DefaultMutableTreeNode errorNode = new DefaultMutableTreeNode("Error Getting Field Data Information");
                    hashTable.put("rootNode", errorNode);
                    throw e;
                }
            }
        };
        AsynchClientTask updateTree = new AsynchClientTask("updateTree", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                DefaultMutableTreeNode rootNode = (DefaultMutableTreeNode) hashTable.get("rootNode");
                getJTree1().setModel(new DefaultTreeModel(rootNode));
            }
        };
        ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { gatherInfo, updateTree });
    }
}

Example 34 with ExternalDataIdentifier

use of org.vcell.util.document.ExternalDataIdentifier in project vcell by virtualcell.

the class VFrapXmlHelper method VFRAPToBioModel.

public static BioModel VFRAPToBioModel(Hashtable<String, Object> hashTable, XMLSource xmlSource, DocumentManager documentManager, final TopLevelWindowManager requester) throws XmlParseException, IOException, DataAccessException, MathException, DivideByZeroException, ExpressionException, ImageException, UtilCancelException {
    Component requesterComponent = requester.getComponent();
    File vFrapFile = xmlSource.getXmlFile();
    // ---
    // ex  ccc8.vfrap
    String vFrapFileNameExtended = vFrapFile.getName();
    {
        // we want to make sure to reload these strings from the hash later on
        String initialFieldDataName = vFrapFileNameExtended.substring(0, vFrapFileNameExtended.indexOf(".vfrap"));
        // we'll save here the "special" vFrap images (prebleach_avg, ...)
        String mixedFieldDataName = initialFieldDataName + "Mx";
        hashTable.put("mixedFieldDataName", mixedFieldDataName);
        hashTable.put("initialFieldDataName", initialFieldDataName);
    }
    if (vFrapFileNameExtended.indexOf(".vfrap") < 0) {
        throw new RuntimeException("File extension must be .vfrap");
    }
    // VFrapXmlHelper vFrapXmlHelper = new VFrapXmlHelper();
    checkNameAvailability(hashTable, true, documentManager, requesterComponent);
    System.out.println("Loading " + vFrapFileNameExtended + " ...");
    String xmlString = XmlUtil.getXMLString(vFrapFile.getAbsolutePath());
    MicroscopyXmlReader xmlReader = new MicroscopyXmlReader(true);
    Element vFrapRoot = XmlUtil.stringToXML(xmlString, null).getRootElement();
    // ----- read the biomodel from Virtual FRAP xml file ----------
    BioModel bioModel = null;
    XmlReader vcellXMLReader = new XmlReader(true);
    Element bioModelElement = vFrapRoot.getChild(XMLTags.BioModelTag);
    if (bioModelElement == null) {
        throw new RuntimeException("Unable to load biomodel.");
    }
    String docSoftwareVersion = vFrapRoot.getAttributeValue(XMLTags.SoftwareVersionAttrTag);
    bioModel = vcellXMLReader.getBioModel(bioModelElement, (docSoftwareVersion == null ? null : VCellSoftwareVersion.fromString(docSoftwareVersion)));
    // ------ locate the special images within the vFrap files and load them in memory
    if (!LoadVFrapSpecialImages(hashTable, vFrapRoot)) {
        // just return the biomodel if image loading fails for some reason
        return bioModel;
    }
    // ------- save the special images in the database as field data ------------
    ExternalDataIdentifier vfrapMisc = SaveVFrapSpecialImagesAsFieldData(hashTable, documentManager);
    // ------- create and save data symbols for the vFrap "special" images -----------
    CreateSaveVFrapDataSymbols(hashTable, bioModel, vfrapMisc);
    // -------- replace vFrap default names in field function arguments with data symbol names -----
    ReplaceVFrapNamesWithSymbolNames(bioModel);
    return bioModel;
}

Example 35 with ExternalDataIdentifier

use of org.vcell.util.document.ExternalDataIdentifier in project vcell by virtualcell.

the class VFrapXmlHelper method isAlreadyImported.

// double[] firstPostBleach = null;
// double[] prebleachAvg = null;
// BufferedImage[] roiComposite = null;
// 
// public double[] getFirstPostBleach() {
// if(firstPostBleach == null) {
// throw new RuntimeException("Missing vFrap FirstPostbleach Image");
// } else {
// return firstPostBleach;
// }
// }
// public double[] getPrebleachAvg() {
// if(prebleachAvg == null) {
// throw new RuntimeException("Missing vFrap PrebleachAverage Image");
// } else {
// return prebleachAvg;
// }
// }
// public BufferedImage[] getRoiComposite() {
// if(roiComposite == null) {
// throw new RuntimeException("Missing vFrap RoiComposite Image");
// } else {
// return roiComposite;
// }
// }
public static boolean isAlreadyImported(String candidateName, DocumentManager documentManager) throws DataAccessException {
    FieldDataDBOperationSpec fdos = FieldDataDBOperationSpec.createGetExtDataIDsSpec(documentManager.getUser());
    FieldDataDBOperationResults fieldDataDBOperationResults = documentManager.fieldDataDBOperation(fdos);
    ExternalDataIdentifier[] externalDataIdentifierArr = fieldDataDBOperationResults.extDataIDArr;
    for (ExternalDataIdentifier edi : externalDataIdentifierArr) {
        if (candidateName.equals(edi.getName())) {
            return true;
        }
    }
    return false;
}