Changeset 7883 for trunk/projects

Timestamp:

02/03/12 11:58:45 (8 years ago)

Author:

curtis

Message:

Add initial version of Prairie OME injection logic

Code is still in progress, not yet tested or working.

File:

• trunk/projects/prairie-ome-tiff/src/main/java/loci/apps/prairie/PrairieInjector.java (modified) (2 diffs)

trunk/projects/prairie-ome-tiff/src/main/java/loci/apps/prairie/PrairieInjector.java

@@ -35 +35 @@
 package loci.apps.prairie;
 
+import java.util.HashMap;
+import java.util.Map;
+import java.util.UUID;
+
+import loci.common.RandomAccessInputStream;
+import loci.common.services.ServiceFactory;
+import loci.common.xml.XMLTools;
+import loci.formats.ImageReader;
+import loci.formats.meta.IMetadata;
+import loci.formats.services.OMEXMLService;
+import loci.formats.tiff.TiffSaver;
+import ome.xml.model.primitives.NonNegativeInteger;
+
 /**
  * Command line tool to inject OME-XML into Prairie TIFF files.
@@ -47 +60 @@
 public class PrairieInjector {
 
-  public static void main(String[] args) {
-    System.out.println("Hello world!");
+  public static void main(String[] args) throws Exception {
+//    System.setProperty("plugins.dir", "C:\\Program Files (x86)\\ImageJ\\plugins");
+//    new ImageJ();
+//    System.out.println("Instance = " + IJ.getInstance());
+
+//    String infile;
+//    String outfile;
+
+//    BufferedReader reader;
+//    reader = new BufferedReader(new InputStreamReader(System.in));
+//
+//    System.out.println("What is name of input file? ");
+//    infile = reader.readLine();
+//
+//    System.out.println("What is name of output file? ");
+//    outfile = reader.readLine();
+
+        //String[] myArgs = {infile, outfile};
+//      "C:\\users\\Kristin\\Documents\\Dropbox\\LOCI\\DataFromJoe\\TIFF-001\\TIFF-001_Cycle001_CurrentSettings_Ch1_000001.tif",
+//      "C:\\users\\Kristin\\Documents\\Dropbox\\LOCI\\DataFromJoe\\TIFF-001\\TestConvert.ome.tif"};
+//    ImageInfo.main(myArgs);
+
+
+    // LAUNCH PROGRAM WITH:
+    // java -cp loci_tools.jar;prairie-injector.jar loci.apps.prairie.Injector myPrairieData.xml
+
+//    JFileChooser chooser = new JFileChooser();
+    ImageReader reader = new ImageReader();
+
+    ServiceFactory serviceFactory = new ServiceFactory();
+    OMEXMLService omexmlService = serviceFactory.getInstance(OMEXMLService.class);
+
+    // create a metadata store, where info is placed
+    IMetadata meta = omexmlService.createOMEXMLMetadata();
+
+    // associate that store with the reader
+    reader.setMetadataStore(meta);
+
+    // parse the Prairie dataset, populating the metadata store
+    // does not read actual image planes
+    String pathToPrairieXMLFile = args[0];
+    reader.setId(pathToPrairieXMLFile);
+
+    String[] files = reader.getUsedFiles();
+
+    // free resources and close any open files
+    // does not wipe out the metadata store
+    reader.close();
+
+    // set the TiffData elements to describe the planar ordering
+    int tiffDataIndex = 0;
+    Map<String, String> uuids = new HashMap<String, String>();
+    for (String file : files) {
+      if (!isTiff(file)) continue;
+
+      // TODO: populate these values from the current filename
+      int c = 0, z = 0, t = 0;
+
+      meta.setTiffDataFirstC(new NonNegativeInteger(c), 0, tiffDataIndex);
+      meta.setTiffDataFirstZ(new NonNegativeInteger(z), 0, tiffDataIndex);
+      meta.setTiffDataFirstT(new NonNegativeInteger(t), 0, tiffDataIndex);
+      meta.setUUIDFileName(file, 0, tiffDataIndex);
+      String uuid = UUID.randomUUID().toString();
+      meta.setUUIDValue(uuid, 0, tiffDataIndex);
+      uuids.put(file, uuid);
+      tiffDataIndex++;
+    }
+
+    for (String file : files) {
+      if (!isTiff(file)) continue;
+
+      // set this TIFF file's UUID to the correct one
+      meta.setUUID(uuids.get(file));
+
+      // write out the XML to the TIFF
+      String xml = omexmlService.getOMEXML(meta);
+      XMLTools.validateXML(xml); // TEMPORARY to make sure it is correct
+      RandomAccessInputStream in = new RandomAccessInputStream(file);
+      TiffSaver tiffSaver = new TiffSaver(file);
+      tiffSaver.overwriteComment(in, xml);
+      in.close();
+    }
+
+
+//    JFileChooser chooser = GUITools.buildFileChooser(reader, true);
+//    int returnVal = chooser.showOpenDialog(null);
+
+//    ImageConverter.main(myArgs);
+
+//    PrairieReader r = new PrairieReader();
+//    r.setId(myFile);
+  }
+
+  private static boolean isTiff(String file) {
+    return file.toLowerCase().endsWith(".tif") ||
+      file.toLowerCase().endsWith(".tiff");
   }
 
 }
+