Java tutorial
/* * org.openmicroscopy.is.HttpImageServer * *------------------------------------------------------------------------------ * * Copyright (C) 2003 Open Microscopy Environment * Massachusetts Institute of Technology, * National Institutes of Health, * University of Dundee * * * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Lesser General Public * License as published by the Free Software Foundation; either * version 2.1 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public * License along with this library; if not, write to the Free Software * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA * *------------------------------------------------------------------------------ */ /*------------------------------------------------------------------------------ * * Written by: Douglas Creager <dcreager@alum.mit.edu> * *------------------------------------------------------------------------------ */ package org.openmicroscopy.is; //AF - import for tmp hack, to be removed. import java.io.InputStream; import java.io.File; import java.io.IOException; import java.io.FileNotFoundException; import java.io.ByteArrayInputStream; import java.util.StringTokenizer; import java.awt.image.BufferedImage; import javax.imageio.ImageIO; import org.apache.commons.httpclient.HttpClient; import org.apache.commons.httpclient.HttpStatus; import org.apache.commons.httpclient.MultiThreadedHttpConnectionManager; import org.apache.commons.httpclient.methods.MultipartPostMethod; import org.apache.commons.httpclient.methods.multipart.FilePart; import org.apache.commons.httpclient.methods.multipart.ByteArrayPartSource; /** * <p>A concrete subclass of {@link ImageServer} which provides an * HTTP connection to an OMEIS instance. There is no public * constructor for this class; instead, instances should be created * with the {@link ImageServer#getDefaultImageServer} and {@link * ImageServer#getHTTPImageServer} methods. * * @author Douglas Creager (dcreager@alum.mit.edu) * @version 2.2 <i>(Internal: $Revision$ $Date$)</i> * @since OME2.2 */ public class HttpImageServer extends ImageServer { /** * The URL of the image server that this instance is connected to. */ private String url; /** * The session key to use for authentication with the image * server. */ private String sessionKey; /** * The HTTP client object used to connect to the image server. */ private HttpClient client; /** * <b>Non-public method:</b> Creates a new instance connected to * an image server at the specified URL. */ HttpImageServer(String url, String sessionKey) { super(); setURL(url); this.sessionKey = sessionKey; } /** * Sets the URL for this instance, and creates the instance's * {@link HttpClient} object. */ private void setURL(String url) { this.url = url; this.client = createHttpClient(); } /** * Creates the {@link HttpClient} object for this instance to use. * Can be overridden if a class other than the default should be * used. */ protected HttpClient createHttpClient() { MultiThreadedHttpConnectionManager cm = new MultiThreadedHttpConnectionManager(); HttpClient client = new HttpClient(cm); client.setConnectionTimeout(10000); return client; } /** * Creates the HTTP method object for this instance to use. Can * be overridden if a class other than the default should be used. */ protected MultipartPostMethod createPostMethod() { MultipartPostMethod post = new MultipartPostMethod(url); post.setUseExpectHeader(false); return post; } private MultipartPostMethod startCall() { return createPostMethod(); } private void executeCall(MultipartPostMethod post) throws ImageServerException { int status = 0; try { post.addParameter("SessionKey", sessionKey); status = client.executeMethod(post); } catch (IOException e) { e.printStackTrace(); throw new ImageServerException(e.getMessage()); } if (status != HttpStatus.SC_OK) { throw new ImageServerException(HttpStatus.getStatusText(status)); } } private void finishCall(MultipartPostMethod post) { post.releaseConnection(); } /** * Helper method -- adds all of the parameters specified by the * given {@link CompositingSettings} to the parameters of the * given HTTP post. */ private void addCompositingSettings(MultipartPostMethod post, CompositingSettings settings) { post.addParameter("theZ", Integer.toString(settings.getTheZ())); post.addParameter("theT", Integer.toString(settings.getTheT())); post.addParameter("LevelBasis", settings.getLevelBasisSpec()); if (settings.isResized()) post.addParameter("Size", settings.getSizeSpec()); if (settings.isGrayChannelOn()) post.addParameter("GrayChannel", settings.getGrayChannelSpec()); if (settings.isRedChannelOn()) post.addParameter("RedChannel", settings.getRedChannelSpec()); if (settings.isGreenChannelOn()) post.addParameter("GreenChannel", settings.getGreenChannelSpec()); if (settings.isBlueChannelOn()) post.addParameter("BlueChannel", settings.getBlueChannelSpec()); } /** * Helper method -- ensures that the next token from the specified * {@link StringTokenizer} has the desired value. * * @throws ImageServerException if the next value from the * tokenizer does not match the <code>correctValue</code> * parameter */ private void checkToken(StringTokenizer token, String correctValue) throws ImageServerException { String realValue = token.nextToken(); if (realValue == null || !realValue.equals(correctValue)) throw new ImageServerException("Invalid response: expected " + correctValue + ", got " + realValue); } /** * Helper method -- ensures that the next token from the specified * {@link StringTokenizer} has the desired value. Simultaneously * sets a new list of delimeters for the tokenizer. * * @throws ImageServerException if the next value from the * tokenizer does not match the <code>correctValue</code> * parameter */ private void checkToken(StringTokenizer token, String correctValue, String newDelim) throws ImageServerException { String realValue = token.nextToken(newDelim); if (realValue == null || !realValue.equals(correctValue)) throw new ImageServerException("Invalid response: expected " + correctValue + ", got " + realValue); } /** * Returns the next token from the tokenizer as an <code>int</code>. * * @throws ImageServerException if the conversion fails */ private int getIntToken(StringTokenizer token) throws ImageServerException { String value = token.nextToken(); try { int intValue = Integer.parseInt(value); return intValue; } catch (NumberFormatException e) { throw new ImageServerException("Invalid response: expected number, got " + value); } } /** * Returns the next token from the tokenizer as a <code>long</code>. * * @throws ImageServerException if the conversion fails */ private long getLongToken(StringTokenizer token) throws ImageServerException { String value = token.nextToken(); try { long longValue = Long.parseLong(value); return longValue; } catch (NumberFormatException e) { throw new ImageServerException("Invalid response: expected number, got " + value); } } /** * Returns the next token from the tokenizer as a <code>double</code>. * * @throws ImageServerException if the conversion fails */ private double getDoubleToken(StringTokenizer token) throws ImageServerException { String value = token.nextToken(); if (value.equalsIgnoreCase("nan")) return Double.NaN; try { double doubleValue = Double.parseDouble(value); return doubleValue; } catch (NumberFormatException e) { throw new ImageServerException("Invalid response: expected number, got " + value); } } /** * Returns whether two image servers refer to the same image * server installation. */ public boolean equals(HttpImageServer is) { return url.equals(is.url) && sessionKey.equals(is.sessionKey); } // JAVADOC NOTICE: // All of these public methods inherit their javadoc documentation // from the ImageServer superclass. public boolean equals(ImageServer is) { if (is instanceof HttpImageServer) return equals((HttpImageServer) is); else return (is == this); } public long newPixels(int sizeX, int sizeY, int sizeZ, int sizeC, int sizeT, int bytesPerPixel, boolean isSigned, boolean isFloat) throws ImageServerException { String dims = sizeX + "," + sizeY + "," + sizeZ + "," + sizeC + "," + sizeT + "," + bytesPerPixel; MultipartPostMethod post = startCall(); try { post.addParameter("Method", "NewPixels"); post.addParameter("Dims", dims); post.addParameter("IsSigned", isSigned ? "1" : "0"); post.addParameter("IsFloat", isFloat ? "1" : "0"); executeCall(post); return Long.parseLong(post.getResponseBodyAsString().trim()); } catch (NumberFormatException e) { throw new ImageServerException("Illegal response: Invalid pixels ID"); } finally { finishCall(post); } } public PixelsFileFormat getPixelsInfo(long pixelsID) throws ImageServerException { MultipartPostMethod post = startCall(); try { post.addParameter("Method", "PixelsInfo"); post.addParameter("PixelsID", Long.toString(pixelsID)); executeCall(post); String result = post.getResponseBodyAsString(); StringTokenizer token = new StringTokenizer(result, "\r\n=,"); checkToken(token, "Dims"); int sizeX = getIntToken(token); int sizeY = getIntToken(token); int sizeZ = getIntToken(token); int sizeC = getIntToken(token); int sizeT = getIntToken(token); int bytesPerPixel = getIntToken(token); checkToken(token, "Finished"); getIntToken(token); checkToken(token, "Signed"); int isSigned = getIntToken(token); checkToken(token, "Float"); int isFloat = getIntToken(token); return new PixelsFileFormat(sizeX, sizeY, sizeZ, sizeC, sizeT, bytesPerPixel, isSigned == 1, isFloat == 1); } finally { finishCall(post); } } public String getPixelsSHA1(long pixelsID) throws ImageServerException { MultipartPostMethod post = startCall(); try { post.addParameter("Method", "PixelsSHA1"); post.addParameter("PixelsID", Long.toString(pixelsID)); executeCall(post); return post.getResponseBodyAsString().trim(); } finally { finishCall(post); } } public String getPixelsServerPath(long pixelsID) throws ImageServerException { MultipartPostMethod post = startCall(); try { post.addParameter("Method", "GetLocalPath"); post.addParameter("PixelsID", Long.toString(pixelsID)); executeCall(post); return post.getResponseBodyAsString().trim(); } finally { finishCall(post); } } public boolean isPixelsFinished(long pixelsID) throws ImageServerException { MultipartPostMethod post = startCall(); try { post.addParameter("Method", "PixelsInfo"); post.addParameter("PixelsID", Long.toString(pixelsID)); executeCall(post); String result = post.getResponseBodyAsString(); StringTokenizer token = new StringTokenizer(result, "\r\n=,"); checkToken(token, "Dims"); getIntToken(token); getIntToken(token); getIntToken(token); getIntToken(token); getIntToken(token); getIntToken(token); checkToken(token, "Finished"); int isFinished = getIntToken(token); checkToken(token, "Signed"); getIntToken(token); checkToken(token, "Float"); getIntToken(token); return (isFinished == 1); } finally { finishCall(post); } } public byte[] getPixels(long pixelsID, boolean bigEndian) throws ImageServerException { MultipartPostMethod post = startCall(); try { post.addParameter("Method", "GetPixels"); post.addParameter("PixelsID", Long.toString(pixelsID)); post.addParameter("BigEndian", bigEndian ? "1" : "0"); executeCall(post); return post.getResponseBody(); } finally { finishCall(post); } } public byte[] getStack(long pixelsID, int theC, int theT, boolean bigEndian) throws ImageServerException { MultipartPostMethod post = startCall(); try { post.addParameter("Method", "GetStack"); post.addParameter("PixelsID", Long.toString(pixelsID)); post.addParameter("theC", Integer.toString(theC)); post.addParameter("theT", Integer.toString(theT)); post.addParameter("BigEndian", bigEndian ? "1" : "0"); executeCall(post); return post.getResponseBody(); } finally { finishCall(post); } } //AF - tmp hacked version, *don't* code against it! public InputStream getStackStream(long pixelsID, int theC, int theT, boolean bigEndian) throws ImageServerException { MultipartPostMethod post = startCall(); try { post.addParameter("Method", "GetStack"); post.addParameter("PixelsID", Long.toString(pixelsID)); post.addParameter("theC", Integer.toString(theC)); post.addParameter("theT", Integer.toString(theT)); post.addParameter("BigEndian", bigEndian ? "1" : "0"); executeCall(post); return post.getResponseBodyAsStream(); } catch (IOException ioe) { throw new ImageServerException("IO Exception: " + ioe); } //The caller will have to close the stream explicitely, this should //release the connection as well b/c of the auto-close mechanism used //in HttpMethodBase.readResponseBody(HttpConnection) line 2103. //REQUIRES FURTHER INVESTIGATION. } public byte[] getPlane(long pixelsID, int theZ, int theC, int theT, boolean bigEndian) throws ImageServerException { MultipartPostMethod post = startCall(); try { post.addParameter("Method", "GetPlane"); post.addParameter("PixelsID", Long.toString(pixelsID)); post.addParameter("theZ", Integer.toString(theZ)); post.addParameter("theC", Integer.toString(theC)); post.addParameter("theT", Integer.toString(theT)); post.addParameter("BigEndian", bigEndian ? "1" : "0"); executeCall(post); return post.getResponseBody(); } finally { finishCall(post); } } public byte[] getROI(long pixelsID, int x0, int y0, int z0, int c0, int t0, int x1, int y1, int z1, int c1, int t1, boolean bigEndian) throws ImageServerException { String roi = x0 + "," + y0 + "," + z0 + "," + c0 + "," + t0 + "," + x1 + "," + y1 + "," + z1 + "," + c1 + "," + t1; MultipartPostMethod post = startCall(); try { post.addParameter("Method", "GetROI"); post.addParameter("PixelsID", Long.toString(pixelsID)); post.addParameter("ROI", roi); post.addParameter("BigEndian", bigEndian ? "1" : "0"); executeCall(post); return post.getResponseBody(); } finally { finishCall(post); } } public void setPixels(long pixelsID, byte[] buf, boolean bigEndian) throws ImageServerException { MultipartPostMethod post = startCall(); try { post.addParameter("Method", "SetPixels"); post.addParameter("PixelsID", Long.toString(pixelsID)); post.addParameter("UploadSize", Long.toString(buf.length)); post.addParameter("BigEndian", bigEndian ? "1" : "0"); post.addPart(new FilePart("Pixels", new ByteArrayPartSource("pixels", buf))); executeCall(post); return; } finally { finishCall(post); } } public void setPixels(long pixelsID, File file, boolean bigEndian) throws ImageServerException, FileNotFoundException { MultipartPostMethod post = startCall(); try { post.addParameter("Method", "SetPixels"); post.addParameter("PixelsID", Long.toString(pixelsID)); post.addParameter("BigEndian", bigEndian ? "1" : "0"); post.addParameter("Pixels", file); executeCall(post); return; } finally { finishCall(post); } } public void setStack(long pixelsID, int theC, int theT, byte[] buf, boolean bigEndian) throws ImageServerException { MultipartPostMethod post = startCall(); try { post.addParameter("Method", "SetStack"); post.addParameter("PixelsID", Long.toString(pixelsID)); post.addParameter("theC", Integer.toString(theC)); post.addParameter("theT", Integer.toString(theT)); post.addParameter("UploadSize", Long.toString(buf.length)); post.addParameter("BigEndian", bigEndian ? "1" : "0"); post.addPart(new FilePart("Pixels", new ByteArrayPartSource("pixels", buf))); executeCall(post); return; } finally { finishCall(post); } } public void setStack(long pixelsID, int theC, int theT, File file, boolean bigEndian) throws ImageServerException, FileNotFoundException { MultipartPostMethod post = startCall(); try { post.addParameter("Method", "SetStack"); post.addParameter("PixelsID", Long.toString(pixelsID)); post.addParameter("theC", Integer.toString(theC)); post.addParameter("theT", Integer.toString(theT)); post.addParameter("BigEndian", bigEndian ? "1" : "0"); post.addParameter("Pixels", file); executeCall(post); return; } finally { finishCall(post); } } public void setPlane(long pixelsID, int theZ, int theC, int theT, byte[] buf, boolean bigEndian) throws ImageServerException { MultipartPostMethod post = startCall(); try { post.addParameter("Method", "SetPlane"); post.addParameter("PixelsID", Long.toString(pixelsID)); post.addParameter("theZ", Integer.toString(theZ)); post.addParameter("theC", Integer.toString(theC)); post.addParameter("theT", Integer.toString(theT)); post.addParameter("UploadSize", Long.toString(buf.length)); post.addParameter("BigEndian", bigEndian ? "1" : "0"); post.addPart(new FilePart("Pixels", new ByteArrayPartSource("pixels", buf))); executeCall(post); return; } finally { finishCall(post); } } public void setPlane(long pixelsID, int theZ, int theC, int theT, File file, boolean bigEndian) throws ImageServerException, FileNotFoundException { MultipartPostMethod post = startCall(); try { post.addParameter("Method", "SetPlane"); post.addParameter("PixelsID", Long.toString(pixelsID)); post.addParameter("theZ", Integer.toString(theZ)); post.addParameter("theC", Integer.toString(theC)); post.addParameter("theT", Integer.toString(theT)); post.addParameter("BigEndian", bigEndian ? "1" : "0"); post.addParameter("Pixels", file); executeCall(post); return; } finally { finishCall(post); } } public void setROI(long pixelsID, int x0, int y0, int z0, int c0, int t0, int x1, int y1, int z1, int c1, int t1, byte[] buf, boolean bigEndian) throws ImageServerException { String roi = x0 + "," + y0 + "," + z0 + "," + c0 + "," + t0 + "," + x1 + "," + y1 + "," + z1 + "," + c1 + "," + t1; MultipartPostMethod post = startCall(); try { post.addParameter("Method", "SetROI"); post.addParameter("PixelsID", Long.toString(pixelsID)); post.addParameter("ROI", roi); post.addParameter("UploadSize", Long.toString(buf.length)); post.addParameter("BigEndian", bigEndian ? "1" : "0"); post.addPart(new FilePart("Pixels", new ByteArrayPartSource("pixels", buf))); executeCall(post); return; } finally { finishCall(post); } } public void setROI(long pixelsID, int x0, int y0, int z0, int c0, int t0, int x1, int y1, int z1, int c1, int t1, File file, boolean bigEndian) throws ImageServerException, FileNotFoundException { String roi = x0 + "," + y0 + "," + z0 + "," + c0 + "," + t0 + "," + x1 + "," + y1 + "," + z1 + "," + c1 + "," + t1; MultipartPostMethod post = startCall(); try { post.addParameter("Method", "SetROI"); post.addParameter("PixelsID", Long.toString(pixelsID)); post.addParameter("ROI", roi); post.addParameter("BigEndian", bigEndian ? "1" : "0"); post.addParameter("Pixels", file); executeCall(post); return; } finally { finishCall(post); } } public long finishPixels(long pixelsID) throws ImageServerException { MultipartPostMethod post = startCall(); try { post.addParameter("Method", "FinishPixels"); post.addParameter("PixelsID", Long.toString(pixelsID)); executeCall(post); return Long.parseLong(post.getResponseBodyAsString().trim()); } finally { finishCall(post); } } public BufferedImage getComposite(long pixelsID, CompositingSettings settings) throws ImageServerException { MultipartPostMethod post = startCall(); try { post.addParameter("Method", "Composite"); post.addParameter("PixelsID", Long.toString(pixelsID)); post.addParameter("Format", "JPEG"); addCompositingSettings(post, settings); executeCall(post); byte[] imageBuf = post.getResponseBody(); ByteArrayInputStream is = new ByteArrayInputStream(imageBuf); try { return ImageIO.read(is); } catch (IOException e) { throw new ImageServerException("Cannot read byte array stream?"); } } finally { finishCall(post); } } public void setThumbnail(long pixelsID, CompositingSettings settings) throws ImageServerException { MultipartPostMethod post = startCall(); try { post.addParameter("Method", "Composite"); post.addParameter("PixelsID", Long.toString(pixelsID)); post.addParameter("SetThumb", "1"); addCompositingSettings(post, settings); executeCall(post); return; } finally { finishCall(post); } } public BufferedImage getThumbnail(long pixelsID) throws ImageServerException { MultipartPostMethod post = startCall(); try { post.addParameter("Method", "GetThumb"); post.addParameter("PixelsID", Long.toString(pixelsID)); executeCall(post); byte[] imageBuf = post.getResponseBody(); ByteArrayInputStream is = new ByteArrayInputStream(imageBuf); try { return ImageIO.read(is); } catch (IOException e) { throw new ImageServerException("Cannot read byte array stream?"); } } finally { finishCall(post); } } public BufferedImage getThumbnail(long pixelsID, int sizeX, int sizeY) throws ImageServerException { MultipartPostMethod post = startCall(); try { post.addParameter("Method", "GetThumb"); post.addParameter("PixelsID", Long.toString(pixelsID)); String size = Integer.toString(sizeX) + "," + Integer.toString(sizeY); post.addParameter("Size", size); executeCall(post); byte[] imageBuf = post.getResponseBody(); ByteArrayInputStream is = new ByteArrayInputStream(imageBuf); try { return ImageIO.read(is); } catch (IOException e) { throw new ImageServerException("Cannot read byte array stream?"); } } finally { finishCall(post); } } public long uploadFile(File file) throws ImageServerException, FileNotFoundException { MultipartPostMethod post = startCall(); try { post.addParameter("Method", "UploadFile"); post.addParameter("File", file); executeCall(post); return Long.parseLong(post.getResponseBodyAsString().trim()); } catch (NumberFormatException e) { throw new ImageServerException("Illegal response: Invalid file ID"); } finally { finishCall(post); } } public FileInfo getFileInfo(long fileID) throws ImageServerException { MultipartPostMethod post = startCall(); try { post.addParameter("Method", "FileInfo"); post.addParameter("FileID", Long.toString(fileID)); executeCall(post); String result = post.getResponseBodyAsString(); StringTokenizer token = new StringTokenizer(result, "\r\n=,"); checkToken(token, "Name"); // Just for the filename token, ignore "=" and "," as // delimeters. Also, there will be a leading "=" that we // need to remove. String name = token.nextToken("\r\n").substring(1); // Set the delimeters back checkToken(token, "Length", "\r\n=,"); long length = getLongToken(token); return new FileInfo(name, length); } finally { finishCall(post); } } public String getFileSHA1(long fileID) throws ImageServerException { MultipartPostMethod post = startCall(); try { post.addParameter("Method", "FileSHA1"); post.addParameter("FileID", Long.toString(fileID)); executeCall(post); return post.getResponseBodyAsString().trim(); } finally { finishCall(post); } } public String getFileServerPath(long fileID) throws ImageServerException { MultipartPostMethod post = startCall(); try { post.addParameter("Method", "GetLocalPath"); post.addParameter("FileID", Long.toString(fileID)); executeCall(post); return post.getResponseBodyAsString().trim(); } finally { finishCall(post); } } public byte[] readFileWithoutCaching(final long fileID, final long offset, final int length) throws ImageServerException { MultipartPostMethod post = startCall(); try { post.addParameter("Method", "ReadFile"); post.addParameter("FileID", Long.toString(fileID)); post.addParameter("Offset", Long.toString(offset)); post.addParameter("Length", Integer.toString(length)); executeCall(post); return post.getResponseBody(); } finally { finishCall(post); } } public long convertStack(final long pixelsID, final int theC, final int theT, final long fileID, final long offset, final boolean bigEndian) throws ImageServerException { MultipartPostMethod post = startCall(); try { post.addParameter("Method", "ConvertStack"); post.addParameter("PixelsID", Long.toString(pixelsID)); post.addParameter("theC", Integer.toString(theC)); post.addParameter("theT", Integer.toString(theT)); post.addParameter("FileID", Long.toString(fileID)); post.addParameter("Offset", Long.toString(offset)); post.addParameter("BigEndian", bigEndian ? "1" : "0"); executeCall(post); return Long.parseLong(post.getResponseBodyAsString().trim()); } finally { finishCall(post); } } public long convertPlane(final long pixelsID, final int theZ, final int theC, final int theT, final long fileID, final long offset, final boolean bigEndian) throws ImageServerException { MultipartPostMethod post = startCall(); try { post.addParameter("Method", "ConvertPlane"); post.addParameter("PixelsID", Long.toString(pixelsID)); post.addParameter("theZ", Integer.toString(theZ)); post.addParameter("theC", Integer.toString(theC)); post.addParameter("theT", Integer.toString(theT)); post.addParameter("FileID", Long.toString(fileID)); post.addParameter("Offset", Long.toString(offset)); post.addParameter("BigEndian", bigEndian ? "1" : "0"); executeCall(post); return Long.parseLong(post.getResponseBodyAsString().trim()); } finally { finishCall(post); } } public long convertPlaneFromTIFF(final long pixelsID, final int theZ, final int theC, final int theT, final long fileID) throws ImageServerException { MultipartPostMethod post = startCall(); try { post.addParameter("Method", "ConvertTIFF"); post.addParameter("PixelsID", Long.toString(pixelsID)); post.addParameter("theZ", Integer.toString(theZ)); post.addParameter("theC", Integer.toString(theC)); post.addParameter("theT", Integer.toString(theT)); post.addParameter("FileID", Long.toString(fileID)); executeCall(post); return Long.parseLong(post.getResponseBodyAsString().trim()); } finally { finishCall(post); } } public long convertPlaneFromTIFF(final long pixelsID, final int theZ, final int theC, final int theT, final long fileID, final int directory) throws ImageServerException { MultipartPostMethod post = startCall(); try { post.addParameter("Method", "ConvertTIFF"); post.addParameter("PixelsID", Long.toString(pixelsID)); post.addParameter("theZ", Integer.toString(theZ)); post.addParameter("theC", Integer.toString(theC)); post.addParameter("theT", Integer.toString(theT)); post.addParameter("FileID", Long.toString(fileID)); post.addParameter("TIFFDirIndex", Integer.toString(directory)); executeCall(post); return Long.parseLong(post.getResponseBodyAsString().trim()); } finally { finishCall(post); } } public long convertRows(final long pixelsID, final int theY, final int numRows, final int theZ, final int theC, final int theT, final long fileID, final long offset, final boolean bigEndian) throws ImageServerException { MultipartPostMethod post = startCall(); try { post.addParameter("Method", "ConvertRows"); post.addParameter("PixelsID", Long.toString(pixelsID)); post.addParameter("theY", Integer.toString(theY)); post.addParameter("nRows", Integer.toString(numRows)); post.addParameter("theZ", Integer.toString(theZ)); post.addParameter("theC", Integer.toString(theC)); post.addParameter("theT", Integer.toString(theT)); post.addParameter("FileID", Long.toString(fileID)); post.addParameter("Offset", Long.toString(offset)); post.addParameter("BigEndian", bigEndian ? "1" : "0"); executeCall(post); return Long.parseLong(post.getResponseBodyAsString().trim()); } finally { finishCall(post); } } public PlaneStatistics getPlaneStatistics(long pixelsID) throws ImageServerException { PixelsFileFormat pff = getPixelsInfo(pixelsID); int sizeZ = pff.getSizeZ(); int sizeC = pff.getSizeC(); int sizeT = pff.getSizeT(); MultipartPostMethod post = startCall(); try { post.addParameter("Method", "GetPlaneStats"); post.addParameter("PixelsID", Long.toString(pixelsID)); executeCall(post); double[][][] minimum = new double[sizeZ][sizeC][sizeT], maximum = new double[sizeZ][sizeC][sizeT], mean = new double[sizeZ][sizeC][sizeT], sigma = new double[sizeZ][sizeC][sizeT], geomean = new double[sizeZ][sizeC][sizeT], geosigma = new double[sizeZ][sizeC][sizeT], centroidX = new double[sizeZ][sizeC][sizeT], centroidY = new double[sizeZ][sizeC][sizeT], sumI = new double[sizeZ][sizeC][sizeT], sumI2 = new double[sizeZ][sizeC][sizeT], sumLogI = new double[sizeZ][sizeC][sizeT], sumXI = new double[sizeZ][sizeC][sizeT], sumYI = new double[sizeZ][sizeC][sizeT], sumZI = new double[sizeZ][sizeC][sizeT]; String result = post.getResponseBodyAsString(); StringTokenizer rtoken = new StringTokenizer(result, "\r\n"); while (rtoken.hasMoreTokens()) { String line = rtoken.nextToken(); StringTokenizer ltoken = new StringTokenizer(line, "\t"); int theC = getIntToken(ltoken); int theT = getIntToken(ltoken); int theZ = getIntToken(ltoken); minimum[theZ][theC][theT] = getDoubleToken(ltoken); maximum[theZ][theC][theT] = getDoubleToken(ltoken); mean[theZ][theC][theT] = getDoubleToken(ltoken); geomean[theZ][theC][theT] = getDoubleToken(ltoken); geosigma[theZ][theC][theT] = getDoubleToken(ltoken); centroidX[theZ][theC][theT] = getDoubleToken(ltoken); centroidY[theZ][theC][theT] = getDoubleToken(ltoken); sumI[theZ][theC][theT] = getDoubleToken(ltoken); sumI2[theZ][theC][theT] = getDoubleToken(ltoken); sumLogI[theZ][theC][theT] = getDoubleToken(ltoken); sumXI[theZ][theC][theT] = getDoubleToken(ltoken); sumYI[theZ][theC][theT] = getDoubleToken(ltoken); sumZI[theZ][theC][theT] = getDoubleToken(ltoken); } return new PlaneStatistics(minimum, maximum, mean, sigma, geomean, geosigma, centroidX, centroidY, sumI, sumI2, sumLogI, sumXI, sumYI, sumZI); } finally { finishCall(post); } } public StackStatistics getStackStatistics(long pixelsID) throws ImageServerException { PixelsFileFormat pff = getPixelsInfo(pixelsID); int sizeC = pff.getSizeC(); int sizeT = pff.getSizeT(); MultipartPostMethod post = startCall(); try { post.addParameter("Method", "GetStackStats"); post.addParameter("PixelsID", Long.toString(pixelsID)); executeCall(post); double[][] minimum = new double[sizeC][sizeT], maximum = new double[sizeC][sizeT], mean = new double[sizeC][sizeT], sigma = new double[sizeC][sizeT], geomean = new double[sizeC][sizeT], geosigma = new double[sizeC][sizeT], centroidX = new double[sizeC][sizeT], centroidY = new double[sizeC][sizeT], centroidZ = new double[sizeC][sizeT], sumI = new double[sizeC][sizeT], sumI2 = new double[sizeC][sizeT], sumLogI = new double[sizeC][sizeT], sumXI = new double[sizeC][sizeT], sumYI = new double[sizeC][sizeT], sumZI = new double[sizeC][sizeT]; String result = post.getResponseBodyAsString(); StringTokenizer rtoken = new StringTokenizer(result, "\r\n"); while (rtoken.hasMoreTokens()) { String line = rtoken.nextToken(); StringTokenizer ltoken = new StringTokenizer(line, "\t"); int theC = getIntToken(ltoken); int theT = getIntToken(ltoken); minimum[theC][theT] = getDoubleToken(ltoken); maximum[theC][theT] = getDoubleToken(ltoken); mean[theC][theT] = getDoubleToken(ltoken); geomean[theC][theT] = getDoubleToken(ltoken); geosigma[theC][theT] = getDoubleToken(ltoken); centroidX[theC][theT] = getDoubleToken(ltoken); centroidY[theC][theT] = getDoubleToken(ltoken); centroidZ[theC][theT] = getDoubleToken(ltoken); sumI[theC][theT] = getDoubleToken(ltoken); sumI2[theC][theT] = getDoubleToken(ltoken); sumLogI[theC][theT] = getDoubleToken(ltoken); sumXI[theC][theT] = getDoubleToken(ltoken); sumYI[theC][theT] = getDoubleToken(ltoken); sumZI[theC][theT] = getDoubleToken(ltoken); } return new StackStatistics(minimum, maximum, mean, sigma, geomean, geosigma, centroidX, centroidY, centroidZ, sumI, sumI2, sumLogI, sumXI, sumYI, sumZI); } finally { finishCall(post); } } }