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

Example 16 with ExternalDataIdentifier

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

the class MicroscopyXmlReader method getExternalDataIdentifier.

/**
 * Method getExternalDataIdentifier.
 * @param externalDataIDElement Element
 * @return ExternalDataIdentifier
 */
private static ExternalDataIdentifier getExternalDataIdentifier(Element externalDataIDElement) {
    String name = externalDataIDElement.getAttributeValue(XMLTags.NameAttrTag);
    String keyValueStr = externalDataIDElement.getAttributeValue(XMLTags.KeyValueAttrTag);
    String ownerName = externalDataIDElement.getAttributeValue(MicroscopyXMLTags.OwnerNameAttrTag);
    String ownerKey = externalDataIDElement.getAttributeValue(XMLTags.OwnerKeyAttrTag);
    return new ExternalDataIdentifier(new KeyValue(keyValueStr), new User(ownerName, new KeyValue(ownerKey)), name);
}

Example 17 with ExternalDataIdentifier

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

the class VFrapXmlHelper method LoadVFrapSpecialImages.

// // load and compute prebleach average and first postbleach images
// public void LoadVFrapSpecialImages(AnnotatedImageDataset annotatedImages, int startingIndexRecovery)
// {
// // unnormalized prebleach average
// prebleachAvg = new double[annotatedImages.getImageDataset().getImage(0, 0, startingIndexRecovery).getNumXYZ()];
// for(int j = 0; j < prebleachAvg.length; j++)
// {
// double pixelTotal = 0;
// for(int i = 0 ; i < startingIndexRecovery; i++)
// {
// pixelTotal = pixelTotal + (annotatedImages.getImageDataset().getImage(0, 0, i).getPixels()[j] & 0x0000FFFF);
// }
// prebleachAvg[j] = pixelTotal/startingIndexRecovery;
// }
// 
// // unnormalized first post bleach
// firstPostBleach = new double[annotatedImages.getImageDataset().getImage(0, 0, startingIndexRecovery).getNumXYZ()];
// short[] pixels = annotatedImages.getImageDataset().getImage(0, 0, startingIndexRecovery).getPixels();
// for(int i = 0; i< pixels.length; i++)
// {
// firstPostBleach[i] = pixels[i] & 0x0000FFFF;
// }
// }
// 
// Locate the special images within the vFrap files and load them in memory
// 
public static boolean LoadVFrapSpecialImages(Hashtable<String, Object> hashTable, Element vFrapRoot) throws IOException, DataAccessException, MathException, ImageException {
    // ------ parse the vfrap file and the log/zip files referred within -----
    // many channels of 1 timepoint each
    int NumTimePoints = 1;
    // the channels: prebleach, postbleach, roi1, roi2 ... roiN
    int NumChannels = tokenNames.length;
    String[] channelNames = new String[NumChannels];
    VariableType[] channelTypes = new VariableType[NumChannels];
    DataSymbolType[] channelVFrapImageType = new DataSymbolType[NumChannels];
    double[][][] pixData = new double[NumTimePoints][NumChannels][];
    // get the path of the file tagged with "ROIExternalDataInfoTag" and open it
    Element roiExternalDataInfoElement = vFrapRoot.getChild(MicroscopyXMLTags.ROIExternalDataInfoTag);
    if (roiExternalDataInfoElement == null) {
        // can't load FieldData for some reason, fall back to importing the biomodel only
        return false;
    }
    // <ROIExternalDataInfo Filename="c:\vFrap\VirtualMicroscopy\SimulationData\SimID_1282941232246_0_.log">
    // <ExternalDataIdentifier Name="timeData" KeyValue="1282941232246" OwnerName="SimulationData" OwnerKey="0" />
    // </ImageDatasetExternalDataInfo>
    // c:\VirtualMicroscopy\SimulationData\SimID_1284149203811_0_.log
    String filename = (roiExternalDataInfoElement).getAttributeValue("Filename");
    Element childElement = (roiExternalDataInfoElement).getChild("ExternalDataIdentifier");
    if (childElement == null) {
        // can't load FieldData for some reason, fall back to importing the biomodel only
        return false;
    }
    StringTokenizer tokens = new StringTokenizer(filename, "/\\.");
    final ArrayList<String> tokenArray = new ArrayList<String>();
    while (tokens.hasMoreElements()) {
        tokenArray.add(tokens.nextToken());
    }
    final String dataID = tokenArray.get(tokenArray.size() - 2);
    final String userName = tokenArray.get(tokenArray.size() - 3);
    VCDataIdentifier vcDataIdentifier = new VCDataIdentifier() {

        public String getID() {
            return dataID;
        }

        public KeyValue getDataKey() {
            return null;
        }

        public User getOwner() {
            return new User(userName, new KeyValue("123345432334"));
        }
    };
    // ------- recover simulation data for this user name, load the images in memory ------------
    // ex  c:\\VirtualMicroscopy\\SimulationData
    String userDirName = filename.substring(0, filename.indexOf(dataID) - 1);
    File userDir = new File(userDirName);
    SimulationData.SimDataAmplistorInfo simDataAmplistorInfo = AmplistorUtils.getSimDataAmplistorInfoFromPropertyLoader();
    SimulationData simData = new SimulationData(vcDataIdentifier, userDir, null, simDataAmplistorInfo);
    // build a valid mesh in 2 steps, what we have in simData is incomplete
    CartesianMesh incompleteMesh = simData.getMesh();
    Extent extent = incompleteMesh.getExtent();
    ISize isize = new ISize(incompleteMesh.getSizeX(), incompleteMesh.getSizeY(), incompleteMesh.getSizeZ());
    Origin origin = new Origin(0, 0, 0);
    CartesianMesh mesh = 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));
    DataIdentifier[] dataIdentifiers = simData.getVarAndFunctionDataIdentifiers(null);
    double[] times = simData.getDataTimes();
    for (int i = 0; i < dataIdentifiers.length; i++) {
        // ex: prebleach_avg, postbleach_first, postbleach_last, bleached_mask, cell_mask, ring1_mask,... ring8_mask
        System.out.println(dataIdentifiers[i].getName());
        for (double time : times) {
            // this loops only once, we have just 1 timepoint for each "special" image
            SimDataBlock simDataBlock = simData.getSimDataBlock(null, dataIdentifiers[i].getName(), time);
            channelNames[i] = dataIdentifiers[i].getName();
            channelTypes[i] = VariableType.VOLUME;
            channelVFrapImageType[i] = SymbolEquivalence.typeFromToken(dataIdentifiers[i].getName());
            pixData[0][i] = simDataBlock.getData();
            // var = prebleach_avg, time = 0.0, data = { 1.0832530361887216 1.0832530361887216 1.0832530361887216 1.0 .... }
            System.out.print("var = " + dataIdentifiers[i].getName() + ", time = " + time + ", data = { ");
            // show a few
            for (int j = 0; j < 5; j++) {
                System.out.print(pixData[0][i][j] + " ");
            }
            // show a few
            ;
            // show a few
            System.out.println(" ... ");
        }
    }
    hashTable.put("mesh", mesh);
    hashTable.put("pixData", pixData);
    hashTable.put("channelNames", channelNames);
    hashTable.put("channelTypes", channelTypes);
    hashTable.put("channelVFrapImageType", channelVFrapImageType);
    return true;
}

Example 18 with ExternalDataIdentifier

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

the class VFrapXmlHelper method SaveVFrapSpecialImagesAsFieldData.

// 
// save the special images in the database as field data
// 
public static ExternalDataIdentifier SaveVFrapSpecialImagesAsFieldData(Hashtable<String, Object> hashTable, DocumentManager documentManager) throws DataAccessException {
    CartesianMesh mesh = (CartesianMesh) hashTable.get("mesh");
    double[][][] pixData = (double[][][]) hashTable.get("pixData");
    String[] channelNames = (String[]) hashTable.get("channelNames");
    VariableType[] channelTypes = (VariableType[]) hashTable.get("channelTypes");
    // DataSymbolType[] channelVFrapImageType = (DataSymbolType[])hashTable.get("channelVFrapImageType");
    String mixedFieldDataName = (String) hashTable.get("mixedFieldDataName");
    FieldDataFileOperationSpec vfrapMiscFieldDataOpSpec = new FieldDataFileOperationSpec();
    vfrapMiscFieldDataOpSpec.opType = FieldDataFileOperationSpec.FDOS_ADD;
    vfrapMiscFieldDataOpSpec.cartesianMesh = mesh;
    vfrapMiscFieldDataOpSpec.doubleSpecData = pixData;
    vfrapMiscFieldDataOpSpec.specEDI = null;
    // item name as it comes from vFrap
    vfrapMiscFieldDataOpSpec.varNames = channelNames;
    vfrapMiscFieldDataOpSpec.owner = documentManager.getUser();
    vfrapMiscFieldDataOpSpec.times = new double[] { 0.0 };
    vfrapMiscFieldDataOpSpec.variableTypes = channelTypes;
    vfrapMiscFieldDataOpSpec.origin = new Origin(0, 0, 0);
    vfrapMiscFieldDataOpSpec.extent = mesh.getExtent();
    vfrapMiscFieldDataOpSpec.isize = new ISize(mesh.getSizeX(), mesh.getSizeY(), mesh.getSizeZ());
    ExternalDataIdentifier vfrapMisc = documentManager.saveFieldData(vfrapMiscFieldDataOpSpec, mixedFieldDataName);
    return vfrapMisc;
}

Example 19 with ExternalDataIdentifier

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

the class PointSpreadFunctionManagement method importPointSpreadFunction.

public void importPointSpreadFunction() {
    AsynchClientTask[] taskArray = new AsynchClientTask[3];
    // select the desired PSF file
    taskArray[0] = new AsynchClientTask("Select a file", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            ChoosePSFFile(hashTable);
        }
    };
    // create and save the field data object
    taskArray[1] = new AsynchClientTask("Import objects", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            Component requesterComponent = parentWindow;
            DocumentWindow documentWindow = (DocumentWindow) BeanUtils.findTypeParentOfComponent(requesterComponent, DocumentWindow.class);
            DocumentManager documentManager = documentWindow.getTopLevelWindowManager().getRequestManager().getDocumentManager();
            if (documentManager == null) {
                throw new RuntimeException("Not connected to server.");
            }
            // the following line of code may modify initialFieldDataName
            // normal file name
            checkNameAvailability(hashTable, false, documentManager, requesterComponent);
            File filePSF = (File) hashTable.get("filePSF");
            String initialFieldDataName = (String) hashTable.get("initialFieldDataName");
            ImageDataset imageDataset = ImageDatasetReaderService.getInstance().getImageDatasetReader().readImageDataset(filePSF.getAbsolutePath(), null);
            Extent extent = imageDataset.getExtent();
            ISize isize = imageDataset.getISize();
            Origin origin = new Origin(0, 0, 0);
            CartesianMesh 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));
            // save field data
            int NumTimePoints = imageDataset.getImageTimeStamps().length;
            int NumChannels = 1;
            double[][][] pixData = new double[NumTimePoints][NumChannels][];
            for (int i = 0; i < NumTimePoints; i++) {
                // images according to zIndex at specific time points(tIndex)
                short[] originalData = imageDataset.getPixelsZ(0, i);
                double[] doubleData = new double[originalData.length];
                for (int j = 0; j < originalData.length; j++) {
                    doubleData[j] = 0x0000ffff & originalData[j];
                }
                pixData[i][NumChannels - 1] = doubleData;
            }
            FieldDataFileOperationSpec fdos = new FieldDataFileOperationSpec();
            // try {
            // fdos = ClientRequestManager.createFDOSFromImageFile(filePSF, false, null);
            // } catch (DataFormatException ex) {
            // throw new Exception("Cannot read image " + filePSF.getAbsolutePath()+"\n"+ex.getMessage());
            // }
            fdos.owner = documentManager.getUser();
            fdos.opType = FieldDataFileOperationSpec.FDOS_ADD;
            fdos.cartesianMesh = cartesianMesh;
            fdos.doubleSpecData = pixData;
            fdos.specEDI = null;
            fdos.varNames = new String[] { SimulationContext.FLUOR_DATA_NAME };
            fdos.times = imageDataset.getImageTimeStamps();
            fdos.variableTypes = new VariableType[] { VariableType.VOLUME };
            fdos.origin = origin;
            fdos.extent = extent;
            fdos.isize = isize;
            ExternalDataIdentifier pSFImageEDI = documentManager.saveFieldData(fdos, initialFieldDataName);
            hashTable.put("pSFImageEDI", pSFImageEDI);
        }
    };
    // create a data symbol for the PSF image saved above as field data
    taskArray[2] = new AsynchClientTask("Display Data Symbols", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            // --- create the data symbols associated with the time series
            String initialFieldDataName = (String) hashTable.get("initialFieldDataName");
            ExternalDataIdentifier pSFImageEDI = (ExternalDataIdentifier) hashTable.get("pSFImageEDI");
            String fluorName = "psf_" + initialFieldDataName;
            DataSymbol fluorDataSymbol = new FieldDataSymbol(fluorName, DataSymbolType.POINT_SPREAD_FUNCTION, simulationContext.getDataContext(), simulationContext.getModel().getUnitSystem().getInstance_TBD(), pSFImageEDI, SimulationContext.FLUOR_DATA_NAME, VariableType.VOLUME.getTypeName(), 0D);
            simulationContext.getDataContext().addDataSymbol(fluorDataSymbol);
        }
    };
    Hashtable<String, Object> hash = new Hashtable<String, Object>();
    ClientTaskDispatcher.dispatch(parentWindow, hash, taskArray, false, true, null);
}

Example 20 with ExternalDataIdentifier

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

the class DataSymbolsPanel method addAssociate.

private void addAssociate() {
    DocumentWindow documentWindow = (DocumentWindow) BeanUtils.findTypeParentOfComponent(this, DocumentWindow.class);
    documentWindow.getTopLevelWindowManager().getRequestManager().showFieldDataWindow(new FieldDataWindowManager.DataSymbolCallBack() {

        public void createDataSymbol(ExternalDataIdentifier dataSetID, String fieldDataVarName, VariableType fieldDataVarType, double fieldDataVarTime) {
            System.out.println(dataSetID + " " + fieldDataVarName + " " + fieldDataVarType + " " + fieldDataVarTime);
            // ex: incomplete 51780592 danv(26766043)      fluor     Volume_VariableType     23.680419921875
            // max time interval we can display is about 11 days
            DecimalFormat df = new DecimalFormat("###000.00");
            String fluorName = fieldDataVarName + "_" + df.format(fieldDataVarTime).substring(0, df.format(fieldDataVarTime).indexOf(".")) + "s" + df.format(fieldDataVarTime).substring(1 + df.format(fieldDataVarTime).indexOf(".")) + "_" + dataSetID.getName();
            // TODO:  symbol names may not be unique, must check for unicity and prompt the user
            FieldDataSymbol dataSymbol = new FieldDataSymbol(fluorName, DataSymbolType.GENERIC_SYMBOL, simulationContext.getDataContext(), simulationContext.getModel().getUnitSystem().getInstance_TBD(), dataSetID, fieldDataVarName, fieldDataVarType.getTypeName(), fieldDataVarTime);
            simulationContext.getDataContext().addDataSymbol(dataSymbol);
        }
    });
}