Changeset 1597 for branches/3.0-Beta2

Timestamp:

06/05/07 22:57:10 (17 months ago)

Author:

david

Message:

testNG tests run in Eclipse but not using terminal, will remove if this commit does not work, strange behavior

Location:

branches/3.0-Beta2/components

Files:

• romio/src/ome/io/nio/DeltaVision.java (modified) (4 diffs)
• romio/src/ome/io/nio/DeltaVisionHeader.java (modified) (1 diff)
• romio/test/ome/io/nio/utests/DeltaVisionTest.java (modified) (6 diffs)
• server/test/ome/tools (added)
• server/test/ome/tools/utests (added)
• server/test/ome/tools/utests/RepositoryTaskTest.java (added)

branches/3.0-Beta2/components/romio/src/ome/io/nio/DeltaVision.java

@@ -246 +246 @@
                 return getRegion(size, offset);
         }
+        
+        /**
+         * Privately returns the row number (specific).  Starts with 1
+         * 
+         * @param y
+         * @param z
+         * @param c
+         * @param t
+         * @return
+         */
+        private int getAbsoluteRowOffset(Integer y, Integer z, Integer c, Integer t) {
+
+                int result = 0;
+
+                switch (getHeader().getSequence()) {
+
+                case 0: // (Y)ZTC
+                        result = ((y * getRowSize()) + (c * getSizeT() * getSizeZ()) + (t * getSizeZ()) + z);
+                        break;
+
+                case 1: // (Y)CZT
+                        result = ((y * getRowSize()) + (t * getSizeC() * getSizeZ()) + (z * getSizeC()) + c);
+                        break;
+
+                case 2: // (Y)ZCT
+                        result = ((y * getRowSize()) + (t * getSizeC() * getSizeZ()) + (c * getSizeZ()) + z);
+                        break;
+
+                default:
+                        result = -1;
+                }
+
+                return result;
+        }
 
         /*
@@ -255 +289 @@
         public Long getRowOffset(Integer y, Integer z, Integer c, Integer t)
                         throws DimensionsOutOfBoundsException {
-                // TODO - affected by stack and timepoint
+
                 checkBounds(y, z, c, t);
-
+                int rowNumber = getAbsoluteRowOffset(y, z, c, t);
+                
                 Integer rowSize = getRowSize();
-                Integer timepointSize = getTimepointSize();
-                Integer stackSize = getStackSize();
-                Integer planeSize = getPlaneSize();
-
-                return (long) rowSize * y + (long) timepointSize * t + (long) stackSize
-                                * c + (long) planeSize * z;
+                
+                return (long) rowNumber * rowSize;
         }
 
@@ -334 +365 @@
         public MappedByteBuffer getStack(Integer c, Integer t) throws IOException,
                         DimensionsOutOfBoundsException {
-                // TODO - affected by ZCT ordering
+
                 Long offset = getStackOffset(c, t);
                 Integer size = getStackSize();
@@ -384 +415 @@
 
                 int stackNo = getAbsoluteStackOffset(c, t);
-                return (long) stackNo * stackSize;
+                return (long) stackNo * getStackSize();
                 
         }

branches/3.0-Beta2/components/romio/src/ome/io/nio/DeltaVisionHeader.java

@@ -2 +2 @@
 
 import java.nio.ByteOrder;
-import java.nio.CharBuffer;
 import java.nio.MappedByteBuffer;
 
-import ome.io.nio.utests.DeltaVisionTest;
 
 import org.apache.commons.logging.Log;

branches/3.0-Beta2/components/romio/test/ome/io/nio/utests/DeltaVisionTest.java

@@ -32 +32 @@
 public class DeltaVisionTest extends TestCase {
 
-        OriginalFile originalFile;
+        private OriginalFile originalFile;
 
-        DeltaVision deltaVision;
+        private DeltaVision deltaVision;
 
         private static int setupCount = 0;
-        private transient static Log log = LogFactory.getLog(DeltaVisionTest.class);
-
+        //private transient static Log log = LogFactory.getLog(DeltaVisionTest.class);
+        
         @Configuration(beforeTestMethod = true)
-        protected void setUp() throws Exception {
+        protected void setUp() {
 
                 setupCount++;
@@ -50 +50 @@
                         originalFile = new OriginalFile();
                         URL url = getClass().getResource("tinyTest.d3d.dv");
+                        try {
+                                File file = new File(url.toURI());
+                                originalFile.setPath(file.getAbsolutePath());
+                                deltaVision = new DeltaVision(originalFile, true);
+                        } catch (Exception ex) {
+                                ex.printStackTrace();
+                        }
                         
-                        File file = new File(url.toURI());
-                        originalFile.setPath(file.getAbsolutePath());
-                        deltaVision = new DeltaVision(originalFile, true);
-                        DeltaVisionHeader header = deltaVision.getHeader();
-                        
-                        
-                        log.info("Size X = " + header.getSizeX());
-                        log.info("Size Y = " + header.getSizeY());
-                        log.info("Size Z = " + header.getSizeZ());
-                        log.info("Size C = " + header.getSizeC());
-                        log.info("Size T = " + header.getSizeT());
-
-                        
-                        
-                        log.info(deltaVision.getPath());
-                        log.info("Row size = " + new Integer(deltaVision.getRowSize()).intValue());
-                        log.info("Stack size = " + new Integer(deltaVision.getStackSize()).intValue());
-                        log.info("Plane size = " + new Integer(deltaVision.getPlaneSize()).intValue());
-                        
-                        log.info(deltaVision.calculateMessageDigest().toString());
-                        log.info("Timepoint size = " + deltaVision.getTimepointSize());
-                        log.info("Total size = " + deltaVision.getTotalSize().toString());
-                        
-                        log.info("ImageSequence = (should be 0=ZTC) " + deltaVision.getHeader().getSequence());
+//                      log.info("Size X = " + header.getSizeX());
+//                      log.info("Size Y = " + header.getSizeY());
+//                      log.info("Size Z = " + header.getSizeZ());
+//                      log.info("Size C = " + header.getSizeC());
+//                      log.info("Size T = " + header.getSizeT());
+//
+//                      
+//                      
+//                      log.info(deltaVision.getPath());
+//                      log.info("Row size = " + new Integer(deltaVision.getRowSize()).intValue());
+//                      log.info("Stack size = " + new Integer(deltaVision.getStackSize()).intValue());
+//                      log.info("Plane size = " + new Integer(deltaVision.getPlaneSize()).intValue());
+//                      
+//                      log.info(deltaVision.calculateMessageDigest().toString());
+//                      log.info("Timepoint size = " + deltaVision.getTimepointSize());
+//                      log.info("Total size = " + deltaVision.getTotalSize().toString());
+//                      
+//                      log.info("ImageSequence = (should be 0=ZTC) " + deltaVision.getHeader().getSequence());
 
                 }
@@ -80 +81 @@
 
         @Configuration(afterTestMethod = true)
-        protected void tearDown() throws Exception {
+        protected void tearDown() {
                 if (setupCount == 12) {
+                        originalFile = null;
                         deltaVision = null;
-                        originalFile = null;
                 }
         }
-
+        
         @Test
         public void testGetSizeX() throws Exception {
@@ -115 +116 @@
                 int result = deltaVision.getSizeT();
                 assertTrue(result == 6);
-        }
-        
-        public void testGetPath() throws Exception {
-                String path = deltaVision.getPath();
-                assertTrue(path.equals("/OMERO/tinyTest.d3d.dv"));
         }
         
@@ -157 +153 @@
         public void testGetPlaneIndex() throws Exception {
                 Long result = deltaVision.getPlaneOffset(2, 0, 3); // (2,0,3) plane 17 ?
-                log.info("Plane offset = " + result.intValue());
+                //log.info("Plane offset = " + result.intValue());
                 // should be 17 * planeSize=800 = 13600
                 assertTrue(result.equals(new Long(13600)));
@@ -165 +161 @@
         public void testGetStackIndex() throws Exception {
                 Long result = deltaVision.getStackOffset(0, 2);
-                log.info("Stack offset = " + result.intValue());
+                //log.info("Stack offset = " + result.intValue());
                 // should be 2 * stackSize=4000 = 8000
                 assertTrue(result.equals(new Long(8000)));
         }
+        
+        
+//      public void testGetRowIndex() throws Exception {
+//              Long result = deltaVision.getRowOffset(10, 2, 0, 3); // row 170 * rowsize
+//              log.info("Row offset = " + result.intValue());
+//              assertTrue(result.equals(new Long(6800)));
+//              
+//      }
 }