Examples with ImageException cbit.image.ImageException used on opensource projects

Example 11 with ImageException

use of cbit.image.ImageException in project vcell by virtualcell.

the class DisplayTimeSeriesOp method displayImageTimeSeries.

public void displayImageTimeSeries(final ImageTimeSeries<? extends Image> imageTimeSeries, final String title, final WindowListener windowListener) throws ImageException, IOException {
    try {
        System.out.println("starting to prepare data for time series viewing");
        final PDEDataViewer pdeDataViewer = new PDEDataViewer();
        DataSetControllerProvider dataSetControllerProvider;
        try {
            dataSetControllerProvider = getDataSetControllerProvider(imageTimeSeries, pdeDataViewer);
        } catch (ImageException | IOException e1) {
            e1.printStackTrace();
            throw new RuntimeException(e1.getMessage(), e1);
        }
        VCDataManager vcDataManager = new VCDataManager(dataSetControllerProvider);
        OutputContext outputContext = new OutputContext(new AnnotatedFunction[0]);
        final VCDataIdentifier vcDataIdentifier = new VCDataIdentifier() {

            public User getOwner() {
                return new User("nouser", null);
            }

            public KeyValue getDataKey() {
                return null;
            }

            public String getID() {
                return "mydata";
            }
        };
        PDEDataManager pdeDataManager = new PDEDataManager(outputContext, vcDataManager, vcDataIdentifier);
        final ClientPDEDataContext myPdeDataContext = new ClientPDEDataContext(pdeDataManager);
        final RequestManager requestManager = new RequestManagerAdapter() {
        };
        final DataViewerManager dataViewerManager = new DataViewerManager() {

            public void dataJobMessage(DataJobEvent event) {
            }

            public void exportMessage(ExportEvent event) {
            }

            public void addDataListener(DataListener newListener) {
            }

            public UserPreferences getUserPreferences() {
                // getRequestManager().getUserPreferences();
                return null;
            }

            public void removeDataListener(DataListener newListener) {
            }

            public void startExport(Component requester, OutputContext outputContext, ExportSpecs exportSpecs) {
            // getLocalRequestManager().startExport(outputContext, FieldDataWindowManager.this, exportSpecs);
            }

            public void simStatusChanged(SimStatusEvent simStatusEvent) {
            }

            public User getUser() {
                return new User("dummy", new KeyValue("123"));
            // return getRequestManager().getDocumentManager().getUser();
            }

            public RequestManager getRequestManager() {
                return requestManager;
            }
        };
        System.out.println("ready to display time series");
        SwingUtilities.invokeAndWait(new Runnable() {

            @Override
            public void run() {
                JFrame jframe = new TopLevelFrame();
                jframe.setTitle(title);
                jframe.getContentPane().add(pdeDataViewer);
                jframe.setSize(1000, 600);
                jframe.setVisible(true);
                if (windowListener != null) {
                    jframe.addWindowListener(windowListener);
                }
                try {
                    pdeDataViewer.setDataViewerManager(dataViewerManager);
                } catch (PropertyVetoException e) {
                    e.printStackTrace();
                }
                pdeDataViewer.setPdeDataContext(myPdeDataContext);
            }
        });
    } catch (InvocationTargetException | InterruptedException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
}

Example 12 with ImageException

use of cbit.image.ImageException in project vcell by virtualcell.

the class WorkflowObjectsPanel method displayData.

private void displayData(TaskContext taskContext, WorkflowObject workflowObject) {
    if (workflowObject instanceof DataInput || workflowObject instanceof DataOutput) {
        String title = parametersFunctionsTableModel.getName(workflowObject);
        WindowListener listener = new WindowAdapter() {
        };
        Object data = null;
        if (workflowObject instanceof WorkflowDataSource) {
            WorkflowDataSource dataHolder = (WorkflowDataSource) workflowObject;
            data = taskContext.getRepository().getData(dataHolder);
        } else if (workflowObject instanceof DataInput) {
            DataInput dataInput = (DataInput) workflowObject;
            data = taskContext.getData(dataInput);
        }
        if (data instanceof RowColumnResultSet) {
            RowColumnResultSet rc = (RowColumnResultSet) data;
            try {
                new DisplayPlotOp().displayPlot(rc, title, listener);
            } catch (ExpressionException e) {
                e.printStackTrace();
            }
        } else if (data instanceof ROI) {
            ROI roi = (ROI) data;
            Image image = roi.getRoiImages()[0];
            new DisplayImageOp().displayImage(image, title, listener);
        } else if (data instanceof ProfileData[]) {
            ProfileData[] profileData = (ProfileData[]) data;
            new DisplayProfileLikelihoodPlotsOp().displayProfileLikelihoodPlots(profileData, title, listener);
        } else if (data instanceof Image) {
            Image image = (Image) data;
            new DisplayImageOp().displayImage(image, title, listener);
        } else if (data instanceof ImageTimeSeries) {
            ImageTimeSeries imageTimeSeries = (ImageTimeSeries) data;
            try {
                DisplayTimeSeries.displayImageTimeSeries(imageTimeSeries, title, listener);
            } catch (ImageException | IOException e) {
                e.printStackTrace();
            }
        }
    }
}

Example 13 with ImageException

use of cbit.image.ImageException in project vcell by virtualcell.

the class MicroscopyXmlReader method getUShortImage.

/**
 * This method returns a VCIMage object from a XML representation.
 * Creation date: (3/16/2001 3:41:24 PM)
 * @param param org.jdom.Element
 * @return VCImage
 * @throws XmlParseException
 */
private UShortImage getUShortImage(Element param) throws XmlParseException {
    // get the attributes
    Element tempelement = param.getChild(XMLTags.ImageDataTag);
    int aNumX = Integer.parseInt(tempelement.getAttributeValue(XMLTags.XAttrTag));
    int aNumY = Integer.parseInt(tempelement.getAttributeValue(XMLTags.YAttrTag));
    int aNumZ = Integer.parseInt(tempelement.getAttributeValue(XMLTags.ZAttrTag));
    int compressSize = Integer.parseInt(tempelement.getAttributeValue(XMLTags.CompressedSizeTag));
    final int BYTES_PER_SHORT = 2;
    int UNCOMPRESSED_SIZE_BYTES = aNumX * aNumY * aNumZ * BYTES_PER_SHORT;
    // getpixels
    String hexEncodedBytes = tempelement.getText();
    byte[] rawBytes = org.vcell.util.Hex.toBytes(hexEncodedBytes);
    ByteArrayInputStream rawByteArrayInputStream = new ByteArrayInputStream(rawBytes);
    InputStream rawInputStream = rawByteArrayInputStream;
    if (compressSize != UNCOMPRESSED_SIZE_BYTES) {
        rawInputStream = new InflaterInputStream(rawByteArrayInputStream);
    }
    byte[] shortsAsBytes = new byte[UNCOMPRESSED_SIZE_BYTES];
    int readCount = 0;
    try {
        while ((readCount += rawInputStream.read(shortsAsBytes, readCount, shortsAsBytes.length - readCount)) != shortsAsBytes.length) {
        }
    } catch (Exception e) {
        e.printStackTrace();
        throw new XmlParseException("error reading image pixels: ", e);
    } finally {
        if (rawInputStream != null) {
            try {
                rawInputStream.close();
            } catch (Exception e2) {
                e2.printStackTrace();
            }
        }
    }
    ByteBuffer byteBuffer = ByteBuffer.wrap(shortsAsBytes);
    short[] shortPixels = new short[aNumX * aNumY * aNumZ];
    for (int i = 0; i < shortPixels.length; i++) {
        shortPixels[i] = byteBuffer.getShort();
    }
    Element extentElement = param.getChild(XMLTags.ExtentTag);
    Extent extent = null;
    if (extentElement != null) {
        extent = vcellXMLReader.getExtent(extentElement);
    }
    Element originElement = param.getChild(XMLTags.OriginTag);
    Origin origin = null;
    if (originElement != null) {
        origin = vcellXMLReader.getOrigin(originElement);
    }
    // //set attributes
    // String name = this.unMangle( param.getAttributeValue(XMLTags.NameAttrTag) );
    // String annotation = param.getChildText(XMLTags.AnnotationTag);
    UShortImage newimage;
    try {
        newimage = new UShortImage(shortPixels, origin, extent, aNumX, aNumY, aNumZ);
    } catch (ImageException e) {
        e.printStackTrace();
        throw new XmlParseException("error reading image: ", e);
    }
    return newimage;
}

Example 14 with ImageException

use of cbit.image.ImageException in project vcell by virtualcell.

the class GeomDbDriver method insertBrowseImageDataSQL.

/**
 * This method was created in VisualAge.
 * @param vcimage cbit.image.VCImage
 * @param userid java.lang.String
 * @exception java.rmi.RemoteException The exception description.
 */
private void insertBrowseImageDataSQL(Connection con, KeyValue key, KeyValue imageKey, VCImage image) throws SQLException, DataAccessException, ImageException, GifParsingException {
    String sql;
    sql = "INSERT INTO " + browseImageDataTable.getTableName() + " " + browseImageDataTable.getSQLColumnList() + " VALUES " + browseImageDataTable.getSQLValueList(key, imageKey, dbSyntax);
    // System.out.println(sql);
    byte[] gifEncodedImage = null;
    try {
        if (image != null) {
            if (image.getNumZ() > 1) {
                byte[] sliceBytes = new byte[image.getNumX() * image.getNumY()];
                System.arraycopy(image.getPixels(), 0, sliceBytes, 0, sliceBytes.length);
                gifEncodedImage = BrowseImage.makeBrowseGIFImage(new VCImageUncompressed(null, sliceBytes, new Extent(1, 1, 1), image.getNumX(), image.getNumY(), 1)).getGifEncodedData();
            } else {
                gifEncodedImage = BrowseImage.makeBrowseGIFImage(image).getGifEncodedData();
            }
        }
    } catch (Exception e) {
        e.printStackTrace();
    }
    if (gifEncodedImage == null) {
        gifEncodedImage = BrowseImage.makeBrowseGIFImage(new VCImageUncompressed(null, new byte[BrowseImage.BROWSE_XSIZE * BrowseImage.BROWSE_YSIZE], new Extent(1, 1, 1), BrowseImage.BROWSE_XSIZE, BrowseImage.BROWSE_YSIZE, 1)).getGifEncodedData();
    }
    switch(dbSyntax) {
        case ORACLE:
            {
                updateCleanSQL(con, sql);
                updateCleanLOB(con, browseImageDataTable.id.toString(), key, browseImageDataTable.tableName, browseImageDataTable.data, gifEncodedImage, dbSyntax);
                break;
            }
        case POSTGRES:
            {
                updatePreparedCleanSQL(con, sql, gifEncodedImage);
                break;
            }
        default:
            {
                throw new RuntimeException("unexpected DatabaseSyntax " + dbSyntax);
            }
    }
}

Example 15 with ImageException

use of cbit.image.ImageException in project vcell by virtualcell.

the class XmlReader method getVCImage.

/**
 * This method returns a VCIMage object from a XML representation.
 * Creation date: (3/16/2001 3:41:24 PM)
 * @return VCImage
 * @param param org.jdom.Element
 */
VCImage getVCImage(Element param, Extent extent) throws XmlParseException {
    // try to get metadata(version)
    Version version = getVersion(param.getChild(XMLTags.VersionTag, vcNamespace));
    // get the attributes
    Element tempelement = param.getChild(XMLTags.ImageDataTag, vcNamespace);
    int aNumX = Integer.parseInt(tempelement.getAttributeValue(XMLTags.XAttrTag));
    int aNumY = Integer.parseInt(tempelement.getAttributeValue(XMLTags.YAttrTag));
    int aNumZ = Integer.parseInt(tempelement.getAttributeValue(XMLTags.ZAttrTag));
    // getpixels
    String temp = tempelement.getText();
    // decode
    byte[] data = Hex.toBytes(temp);
    // create the VCImage object
    VCImageCompressed newimage = null;
    try {
        newimage = new VCImageCompressed(version, data, extent, aNumX, aNumY, aNumZ);
    } catch (ImageException e) {
        e.printStackTrace();
        throw new XmlParseException("An imageException occurred while trying to create a VCImage!", e);
    }
    // set attributes
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    try {
        newimage.setName(name);
        // String annotation = param.getAttributeValue(XMLTags.AnnotationAttrTag);
        // if (annotation!=null) {
        // newimage.setDescription(unMangle(annotation));
        // }
        // read the annotation
        String annotation = param.getChildText(XMLTags.AnnotationTag, vcNamespace);
        if (annotation != null && annotation.length() > 0) {
            newimage.setDescription(unMangle(annotation));
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace(System.out);
        throw new XmlParseException(e);
    }
    // get PixelClasses
    List<Element> pixelClassList = param.getChildren(XMLTags.PixelClassTag, vcNamespace);
    if (pixelClassList.size() != 0) {
        VCPixelClass[] pixelClassArray = new VCPixelClass[pixelClassList.size()];
        int pixelClassCounter = 0;
        for (Element pcElement : pixelClassList) {
            pixelClassArray[pixelClassCounter] = getPixelClass(pcElement);
            pixelClassCounter++;
        }
        try {
            newimage.setPixelClasses(pixelClassArray);
        } catch (java.beans.PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException(e);
        }
    } else {
        // Invalid format
        System.out.println("Format Error! No <PixelClass> references found inside <Image name=\"" + name + "\">!");
        System.out.println("Valid format for images is:");
        System.out.println("<Image Name=\"??\">");
        System.out.println(" <ImageData Z=\"?\" Y=\"?\" Z=\"?\" CompressedSize=\"?\">");
        System.out.println("     ......Image content...");
        System.out.println(" </ImageData>");
        System.out.println(" <PixelClass Name=\"?\" ImagePixelValue=\"?\"/>");
        System.out.println("  ...");
        System.out.println(" <PixelClass Name=\"?\" ImagePixelValue=\"?\"/>");
        System.out.println(" <Version Name=\"?\"/>");
        System.out.println("</Image>");
        throw new XmlParseException("Invalid VCML format error!\nNo <PixelClass> references found inside <Image name=\"" + name + "\">!");
    }
    return newimage;
}