Changeset 1654 for branches/3.0-Beta2/components/romio/test/ome/io/nio/utests/DeltaVisionTest.java

Timestamp:

06/20/07 00:46:03 (18 months ago)

Author:

david

Message:

added serial plane MD5 checks

Files:

• branches/3.0-Beta2/components/romio/test/ome/io/nio/utests/DeltaVisionTest.java (modified) (3 diffs)

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

@@ -1 +1 @@
 package ome.io.nio.utests;
 
+import java.io.DataOutputStream;
 import java.io.File;
+import java.io.FileOutputStream;
 import java.net.URL;
+import java.nio.ByteBuffer;
+import java.nio.MappedByteBuffer;
+import java.security.MessageDigest;
+import java.security.NoSuchAlgorithmException;
 
 import junit.framework.TestCase;
 import ome.io.nio.DeltaVision;
 import ome.io.nio.DeltaVisionHeader;
+import ome.io.nio.DimensionsOutOfBoundsException;
 import ome.model.core.OriginalFile;
 import ome.conditions.ResourceError;
@@ -15 +22 @@
 import org.testng.annotations.Configuration;
 import org.testng.annotations.Test;
-
 
 /**
@@ -31 +37 @@
 public class DeltaVisionTest extends TestCase {
 
-        private OriginalFile originalFile;
-
-        private DeltaVision deltaVision;
-
-        private static int setupCount = 0;
-        
-        private static Log log = LogFactory.getLog(DeltaVisionTest.class);
-
-        public final static String FILENAME = "tinyTest.d3d.dv";
-        
-        @Configuration(beforeTestMethod = true)
-        protected void setUp() {
-
-                setupCount++;
-
-                // run this once only
-                if (setupCount == 1) {
-
-                        // create an OriginalFile object and DeltaVision for testing
-                        originalFile = new OriginalFile();
-                        //URL url = getClass().getResource("tinyTest.d3d.dv");
-                        try {
-                                File file = ResourceUtils.getFile("classpath:"+FILENAME);
-
-                                //File file = new File(url.toURI());
-                                originalFile.setPath(file.getCanonicalPath());
-                                //originalFile.setPath("OMERO/tinyTest.d3d.dv");
-                                deltaVision = new DeltaVision(originalFile, true);
-                                
-                        } catch (Exception ex) {
-                log.error("Exception caught, throwing ResourceError", ex.getCause());
-                throw new ResourceError(
-                        ex.getMessage() + " Please check server log.");
-                        }
-                        
-                        log.info("Size X = " + deltaVision.getHeader().getSizeX());
-                        log.info("Size Y = " + deltaVision.getHeader().getSizeY());
-                        log.info("Size Z = " + deltaVision.getHeader().getSizeZ());
-                        log.info("Size C = " + deltaVision.getHeader().getSizeC());
-                        log.info("Size T = " + deltaVision.getHeader().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("Timepoint size = " + deltaVision.getTimepointSize());
-                        log.info("Total size = " + deltaVision.getTotalSize().toString());
-                        
-                        log.info("ImageSequence = (should be 0=ZTC) " + deltaVision.getHeader().getSequence());
-
-                }
-        }
-
-        @Configuration(afterTestMethod = true)
-        protected void tearDown() {
-                if (setupCount == 12) {
-                        originalFile = null;
-                        deltaVision = null;
-                }
-        }
-        
-        @Test
-        public void testGetSizeX() throws Exception {
-                int result = deltaVision.getSizeX();
-                assertTrue(result == 20);
-        }
-        
-        @Test
-        public void testGetSizeY() throws Exception {
-                int result = deltaVision.getSizeY();
-                assertTrue(result == 20);
-        }
-        
-        @Test
-        public void testGetSizeZ() throws Exception {
-                int result = deltaVision.getSizeZ();
-                assertTrue(result == 5);
-        }
-        
-        @Test
-        public void testGetSizeC() throws Exception {
-                int result = deltaVision.getSizeC();
-                assertTrue(result == 1);
-        }
-        
-        @Test
-        public void testGetSizeT() throws Exception {
-                int result = deltaVision.getSizeT();
-                assertTrue(result == 6);
-        }
-        
-        @Test
-        public void testTotalSize() throws Exception {
-                String result = deltaVision.getTotalSize().toString();
-                assertTrue(result.equals("24000"));
-        }
-        
-        @Test
-        public void testTimepointSize() throws Exception {
-                Integer result = deltaVision.getTimepointSize();
-                assertTrue(result.equals(new Integer(4000)));
-        }
-
-        @Test
-        public void testRowSize() throws Exception {
-                Integer result = deltaVision.getRowSize();
-                assertTrue(result.equals(new Integer(40)));
-                
-        }
-        
-        @Test
-        public void testStackSize() throws Exception {
-                Integer result = deltaVision.getStackSize();
-                assertTrue(result.equals(new Integer(4000)));
-        }
-        
-        @Test
-        public void testPlaneSize() throws Exception {
-                Integer result = deltaVision.getPlaneSize();
-                assertTrue(result.equals(new Integer(800)));
-                
-        }
-        
-        @Test
-        public void testGetPlaneIndex() throws Exception {
-                Long result = deltaVision.getPlaneOffset(2, 0, 3); // (2,0,3) plane 17 ?
-                //log.info("Plane offset = " + result.intValue());
-                // should be 17 * planeSize=800 = 13600
-                assertTrue(result.equals(new Long(13600)));
-        }
-        
-        @Test
-        public void testGetStackIndex() throws Exception {
-                Long result = deltaVision.getStackOffset(0, 2);
-                //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)));
-//              
-//      }
+    private OriginalFile originalFile;
+
+    private DeltaVision deltaVision;
+
+    private static int setupCount = 0;
+
+    private static Log log = LogFactory.getLog(DeltaVisionTest.class);
+
+    public final static String FILENAME = "tinyTest.d3d.dv";
+
+    @Configuration(beforeTestMethod = true)
+    protected void setUp() {
+
+        setupCount++;
+
+        // run this once only
+        if (setupCount == 1) {
+
+            // create an OriginalFile object and DeltaVision for testing
+            originalFile = new OriginalFile();
+            // URL url = getClass().getResource("tinyTest.d3d.dv");
+            try {
+                File file = ResourceUtils.getFile("classpath:" + FILENAME);
+
+                // File file = new File(url.toURI());
+                originalFile.setPath(file.getCanonicalPath());
+                // originalFile.setPath("OMERO/tinyTest.d3d.dv");
+                deltaVision = new DeltaVision(originalFile, true);
+
+            } catch (Exception ex) {
+                log.error("Exception caught, throwing ResourceError", ex
+                        .getCause());
+                throw new ResourceError(ex.getMessage()
+                        + " Please check server log.");
+            }
+
+            log.info("Size X = " + deltaVision.getHeader().getSizeX());
+            log.info("Size Y = " + deltaVision.getHeader().getSizeY());
+            log.info("Size Z = " + deltaVision.getHeader().getSizeZ());
+            log.info("Size C = " + deltaVision.getHeader().getSizeC());
+            log.info("Size T = " + deltaVision.getHeader().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("Timepoint size = " + deltaVision.getTimepointSize());
+            log.info("Total size = " + deltaVision.getTotalSize().toString());
+
+            log.info("ImageSequence = (should be 0=ZTC) "
+                    + deltaVision.getHeader().getSequence());
+
+        }
+    }
+
+    @Configuration(afterTestMethod = true)
+    protected void tearDown() {
+        if (setupCount == 13) {
+            originalFile = null;
+            deltaVision = null;
+        }
+    }
+
+    @Test
+    public void testGetSizeX() throws Exception {
+        int result = deltaVision.getSizeX();
+        assertTrue(result == 20);
+    }
+
+    @Test
+    public void testGetSizeY() throws Exception {
+        int result = deltaVision.getSizeY();
+        assertTrue(result == 20);
+    }
+
+    @Test
+    public void testGetSizeZ() throws Exception {
+        int result = deltaVision.getSizeZ();
+        assertTrue(result == 5);
+    }
+
+    @Test
+    public void testGetSizeC() throws Exception {
+        int result = deltaVision.getSizeC();
+        assertTrue(result == 1);
+    }
+
+    @Test
+    public void testGetSizeT() throws Exception {
+        int result = deltaVision.getSizeT();
+        assertTrue(result == 6);
+    }
+
+    @Test
+    public void testTotalSize() throws Exception {
+        String result = deltaVision.getTotalSize().toString();
+        assertTrue(result.equals("24000"));
+    }
+
+    @Test
+    public void testTimepointSize() throws Exception {
+        Integer result = deltaVision.getTimepointSize();
+        assertTrue(result.equals(new Integer(4000)));
+    }
+
+    @Test
+    public void testRowSize() throws Exception {
+        Integer result = deltaVision.getRowSize();
+        assertTrue(result.equals(new Integer(40)));
+
+    }
+
+    @Test
+    public void testStackSize() throws Exception {
+        Integer result = deltaVision.getStackSize();
+        assertTrue(result.equals(new Integer(4000)));
+    }
+
+    @Test
+    public void testPlaneSize() throws Exception {
+        Integer result = deltaVision.getPlaneSize();
+        assertTrue(result.equals(new Integer(800)));
+
+    }
+
+    @Test
+    public void testGetPlaneIndex() throws Exception {
+        Long result = deltaVision.getPlaneOffset(2, 0, 3); // (2,0,3) plane 17
+        // ?
+        // log.info("Plane offset = " + result.intValue());
+        // should be 17 * planeSize=800 = 13600
+        assertTrue(result.equals(new Long(13600)));
+    }
+
+    @Test
+    public void testGetStackIndex() throws Exception {
+        Long result = deltaVision.getStackOffset(0, 2);
+        // log.info("Stack offset = " + result.intValue());
+        // should be 2 * stackSize=4000 = 8000
+        assertTrue(result.equals(new Long(8000)));
+    }
+
+    @Test
+    public void testGetDigest() throws Exception {
+        MessageDigest md;
+        String[] controls = {
+                "472b52ffbeb0f6397571c8a8482e2e37", // 0
+                "36afde357e0e89905403cf1563182798", // 1
+                "87b7f3e5653550d550d54377e8aa32c3", // 2
+                "1fd67721b392c746a8c82d63352b3930", // 3
+                "4245d518c4c3ab9cf22211df8b59b9dc", // 4
+                "d71ee5397381961763729e7806ba70e6", // 5
+                "2d8819f668b9bcb3e77297c110fdc2b8", // 6
+                "354f6a7a057bf6e229dce28483b6b666", // 7
+                "44a9db6eb3e665897715561e881947e7", // 8
+                "3e62132a4145f545034313dc3ccb8406", // 9
+                "e67de55f57dcd328e082b1925d828286", // 10
+                "ceaaea38d478de45d32f8c7488f9c003", // 11
+                "d1992745966a8f6eb4e56fc458ad3ea1", // 12
+                "588678a268c0875efd1570d34e39c6ab", // 13
+                "a60f2e0b40a5bf0f41a6a68f8f79bbd4", // 14
+                "8fb13befd7b046766e000daf61cb3029", // 15
+                "1acadc8c7bedc55388fad61bc2a5d81d", // 16
+                "b5ca57b86d799876ada84cf2c36dd726", // 17
+                "0dd76877705ac7e27011c7d9314981c0", // 18
+                "4ff64f897a512516b643870fb416e771", // 19
+                "91b9dace231080254403fdcef181ff8a", // 20
+                "d7683987d3a68d6d1ddbd2a5d9aacad7", // 21
+                "1ff104dba9ac95275be383f6a6c4c04e", // 22
+                "ae7623339f2486efef9178b19bc97ea1", // 23
+                "c162e80f350dc2dbb20fbf8f479ae1e8", // 24
+                "1f4278861506438b5a9e623b0db7b61c", // 25
+                "2071ba00d672e3e73b5cdb771d7234d2", // 26
+                "606ec319d5126ba99636f4b573947315", // 27
+                "47662680c45544f9ba080072eddb7832", // 28
+                "5ba8cc329b663dfdb59d3432b799e1e6"};  // 29           
+
+        
+        try {
+            md = MessageDigest.getInstance("MD5");
+        } catch (NoSuchAlgorithmException e) {
+            throw new RuntimeException(
+                    "Required MD5 message digest algorithm unavailable.");
+        }
+
+        int begin = deltaVision.header.getPixelBeginOffset();
+        int i = 0;
+        int offset = 0;
+
+        while (i < 30) {
+            
+            offset = begin + (800 * i);
+
+            MappedByteBuffer buffer = deltaVision.getRegion(new Integer(800),
+                    new Long(offset)); // plane 0
+
+//            File file = new File("myplane" + i + ".dat");
+//            FileOutputStream out = new FileOutputStream (file);
+//            byte[] planebytes = ByteBuffer.allocate(800).array();
+//            
+//            for (int j=0; j<planebytes.length; j++) {
+//                planebytes[j] = buffer.get(j);
+//            }
+//   
+//            out.write(planebytes);
+
+            md.update(buffer);
+            byte[] bytes = md.digest();
+
+
+            System.out.println("md5 version is " + byteArrayToHexString(bytes));
+            assertTrue(byteArrayToHexString(bytes).equals(controls[i]));
+            
+            i++;
+//            out.close();
+            
+        }
+    }
+
+
+    static String byteArrayToHexString(byte in[]) {
+
+        byte ch = 0x00;
+        int i = 0;
+
+        if (in == null || in.length <= 0)
+            return null;
+
+        String pseudo[] = { "0", "1", "2", "3", "4", "5", "6", "7", "8", "9",
+                "a", "b", "c", "d", "e", "f" };
+
+        StringBuffer out = new StringBuffer(in.length * 2);
+
+        while (i < in.length) {
+
+            ch = (byte) (in[i] & 0xF0);
+            ch = (byte) (ch >>> 4);
+            ch = (byte) (ch & 0x0F);
+            out.append(pseudo[(int) ch]);
+            ch = (byte) (in[i] & 0x0F);
+            out.append(pseudo[(int) ch]);
+            i++;
+
+        }
+
+        String rslt = new String(out);
+        return rslt;
+    }
 }