Changeset 2307

Timestamp:

03/21/08 13:53:11 (9 months ago)

Author:

brain

Message:

closing out old tickets. Fixing a few bugs

Location:

branches/3.0-Beta2.3/components/bioformats-omero

Files:

• .classpath (modified) (1 diff)
• src/ome/formats/OMEROMetadataStore.java (modified) (4 diffs)
• src/ome/formats/importer/ImportFixture.java (modified) (1 diff)
• src/ome/formats/importer/ImportHandler.java (modified) (4 diffs)
• src/ome/formats/importer/ImportLibrary.java (modified) (3 diffs)
• src/ome/formats/importer/LoginHandler.java (modified) (1 diff)

branches/3.0-Beta2.3/components/bioformats-omero/.classpath

@@ -4 +4 @@
         <classpathentry kind="src" path="resources"/>
         <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
-        <classpathentry kind="lib" path="lib/TableLayout.jar"/>
+        <classpathentry kind="lib" path="lib/TableLayout.jar">
+                <attributes>
+                        <attribute name="org.eclipse.jdt.launching.CLASSPATH_ATTR_LIBRARY_PATH_ENTRY" value="2.3branch/lib"/>
+                </attributes>
+        </classpathentry>
         <classpathentry kind="lib" path="lib/spring-2.0.6.jar"/>
         <classpathentry kind="lib" path="lib/quaqua-filechooser-only.jar">

branches/3.0-Beta2.3/components/bioformats-omero/src/ome/formats/OMEROMetadataStore.java

@@ -150 +150 @@
             // Instantiate our service factory
             sf = new ServiceFactory(server, login);
-
-            // Now initialize all our services
-            iQuery = sf.getQueryService();
-            iUpdate = sf.getUpdateService();
-            pservice = sf.createRawPixelsStore();
-            rawFileStore = sf.createRawFileStore();
-            iInfo = sf.getRepositoryInfoService();
+            
+            InitializeServices(sf);
             
             exp = iQuery.findByString(Experimenter.class, "omeName", username);
@@ -184 +179 @@
         {
             // Now initialize all our services
-            iQuery = sf.getQueryService();
-            iUpdate = sf.getUpdateService();
-            pservice = sf.createRawPixelsStore();
+            InitializeServices(sf);
+            
         } catch (Throwable t)
         {
             throw new Exception(t);
         }
+    }
+    
+    
+    /**
+     * Private class used by constructor to initialze the services of the service factory.
+     * 
+     * @param factory a non-null, active {@link ServiceFactory}
+     */
+    private void InitializeServices(ServiceFactory sf)
+    {
+        // Now initialize all our services
+        iQuery = sf.getQueryService();
+        iUpdate = sf.getUpdateService();
+        pservice = sf.createRawPixelsStore();
+        rawFileStore = sf.createRawFileStore();
+        iInfo = sf.getRepositoryInfoService();
     }
 
@@ -1256 +1266 @@
                 channels.get(logicalChannelIndex).getLogicalChannel();
             lc.setExcitationWave(exWave);
+            if (lc.getPhotometricInterpretation() == null)
+            {
+                log.debug("Setting Photometric iterpretation to monochrome");
+                PhotometricInterpretation pi = (PhotometricInterpretation) 
+                    getEnumeration(PhotometricInterpretation.class, "Monochrome");
+                lc.setPhotometricInterpretation(pi);
+            }
         }
         }
@@ -1279 +1296 @@
                 channels.get(logicalChannelIndex).getLogicalChannel();
             lc.setEmissionWave(emWave);
+            if (lc.getPhotometricInterpretation() == null)
+            {
+                log.debug("Setting Photometric iterpretation to monochrome");
+                PhotometricInterpretation pi = (PhotometricInterpretation) 
+                    getEnumeration(PhotometricInterpretation.class, "Monochrome");
+                lc.setPhotometricInterpretation(pi);
+            }
         }
         }

branches/3.0-Beta2.3/components/bioformats-omero/src/ome/formats/importer/ImportFixture.java

@@ -90 +90 @@
     public void setUp() throws Exception
     {
-        this.library = new ImportLibrary(store, reader, fadMap(this.fads));
+        this.library = new ImportLibrary(store, reader);
     }
 

branches/3.0-Beta2.3/components/bioformats-omero/src/ome/formats/importer/ImportHandler.java

@@ -43 +43 @@
     private Thread runThread;
     HistoryDB db = null;
+    private ImportContainer[] fads = null;
 
     
@@ -60 +61 @@
             OMEROWrapper reader, ImportContainer[] fads)
     {
+        this.fads = fads;
         db = HistoryDB.getHistoryDB();
         
@@ -73 +75 @@
             this.store = store;
             this.qTable = qTable;
-            this.library = new ImportLibrary(store, reader, fads);
+            this.library = new ImportLibrary(store, reader);
             library.addObserver(qTable);
             library.addObserver(viewer);
@@ -119 +121 @@
         viewer.appendToOutputLn("> Starting import at: " + myDate + "\n");
         viewer.statusBar.setStatusIcon("gfx/import_icon_16.png", "Now importing.");
-        
-        ImportContainer[] fads = library.getFilesAndDatasets();
+
         qTable.importBtn.setText("Cancel");
         qTable.importing = true;

branches/3.0-Beta2.3/components/bioformats-omero/src/ome/formats/importer/ImportLibrary.java

@@ -18 +18 @@
 import java.io.File;
 import java.io.IOException;
-import java.io.PrintWriter;
-import java.io.StringWriter;
 import java.nio.ByteBuffer;
 import java.nio.IntBuffer;
@@ -117 +115 @@
      * @param fads2 not null, length > 0
      */
-    public ImportLibrary(OMEROMetadataStore store, OMEROWrapper reader,
-            ImportContainer[] fads)
+    public ImportLibrary(OMEROMetadataStore store, OMEROWrapper reader)
     {
         this.store = store;
         this.reader = reader;
-        this.fads = fads;
-        
-        if (store == null || reader == null || fads == null
-                || fads.length == 0)
+        
+        if (store == null || reader == null)
         {
             throw new ApiUsageException(
@@ -377 +372 @@
             
             notifyObservers(Actions.DATA_STORED, args);
-
+            
             if (archive == true)
             {

branches/3.0-Beta2.3/components/bioformats-omero/src/ome/formats/importer/LoginHandler.java

@@ -76 +76 @@
 
     private boolean modal;
-    
-
+      
     LoginHandler(Main viewer, boolean modal, boolean center)
     {