Changeset 6996

Timestamp:

09/28/10 10:59:32 (9 years ago)

Author:

melissa

Message:

Merged changes to common component and logging into 4.2: r6696, r6722, r6723, r6737, and r6793.

Location:

branches/4.2

Files:

• . (modified) (1 prop)
• components/bio-formats/src/loci/formats/in (modified) (1 prop)
• components/bio-formats/src/loci/formats/tiff (modified) (1 prop)
• components/bio-formats/src/loci/formats/tools/ImageConverter.java (modified) (3 diffs)
• components/bio-formats/src/loci/formats/tools/ImageInfo.java (modified) (3 diffs)
• components/common/src/loci/common/DataTools.java (modified) (4 diffs)
• components/common/src/loci/common/DebugTools.java (modified) (2 diffs)
• components/common/src/loci/common/StatusEvent.java (modified) (1 diff)
• components/common/src/loci/common/services/ServiceFactory.java (modified) (1 diff)
• components/loci-plugins (modified) (1 prop)
• components/loci-plugins/src/loci/plugins (modified) (1 prop)
• components/loci-plugins/src/loci/plugins/in/Calibrator.java (modified) (1 prop)
• components/ome-xml (modified) (1 prop)

branches/4.2/components/bio-formats/src/loci/formats/tools/ImageConverter.java

@@ -27 +27 @@
 import java.io.IOException;
 
+import loci.common.DebugTools;
 import loci.common.Location;
 import loci.common.services.DependencyException;
@@ -75 +76 @@
     throws FormatException, IOException
   {
+    DebugTools.enableLogging("INFO");
     String in = null, out = null;
     String map = null;
@@ -85 +87 @@
         if (args[i].startsWith("-") && args.length > 1) {
           if (args[i].equals("-debug")) {
-            LOGGER.warn("To enable debugging, edit the log4j.properties file,");
-            LOGGER.warn("changing log4j.rootCategory from INFO to DEBUG");
-            LOGGER.warn("(or TRACE for extreme verbosity).");
+            DebugTools.enableLogging("DEBUG");
           }
           else if (args[i].equals("-stitch")) stitch = true;

branches/4.2/components/bio-formats/src/loci/formats/tools/ImageInfo.java

@@ -31 +31 @@
 import loci.common.ByteArrayHandle;
 import loci.common.DataTools;
+import loci.common.DebugTools;
 import loci.common.Location;
 import loci.common.RandomAccessInputStream;
@@ -173 +174 @@
         else if (args[i].equals("-autoscale")) autoscale = true;
         else if (args[i].equals("-debug")) {
-          LOGGER.warn("");
-          LOGGER.warn("To enable debugging, edit the log4j.properties file,");
-          LOGGER.warn("changing log4j.rootCategory from INFO to DEBUG");
-          LOGGER.warn("(or TRACE for extreme verbosity).");
+          DebugTools.enableLogging("DEBUG");
         }
         else if (args[i].equals("-preload")) preload = true;
@@ -864 +862 @@
    */
   public boolean testRead(String[] args)
-    throws FormatException, ServiceException, IOException {
+    throws FormatException, ServiceException, IOException
+  {
+    DebugTools.enableLogging("INFO");
     parseArgs(args);
     if (printVersion) {

branches/4.2/components/common/src/loci/common/DataTools.java

@@ -487 +487 @@
 
   /** @deprecated Use {@link #unpackBytes(long, byte[], int, int, boolean) */
+  @Deprecated
   public static void unpackShort(short value, byte[] buf, int ndx,
     boolean little)
@@ -520 +521 @@
 
   /**
-   * Convert a byte array to the appropriate primitive type array.
+   * Convert a byte array to the appropriate 1D primitive type array.
+   *
    * @param b Byte array to convert.
    * @param bpp Denotes the number of bytes in the returned primitive type
@@ -527 +529 @@
    * @param little Whether byte array is in little-endian order.
    */
-  public static Object makeDataArray(byte[] b, int bpp, boolean fp,
-    boolean little)
+  public static Object makeDataArray(byte[] b,
+    int bpp, boolean fp, boolean little)
   {
     if (bpp == 1) {
@@ -576 +578 @@
    *   regardless of signedness.
    */
+  @Deprecated
   public static Object makeDataArray(byte[] b,
     int bpp, boolean fp, boolean little, boolean signed)
   {
     return makeDataArray(b, bpp, fp, little);
+  }
+
+  /**
+   * Convert a byte array to the appropriate 2D primitive type array.
+   *
+   * @param b Byte array to convert.
+   * @param bpp Denotes the number of bytes in the returned primitive type
+   *   (e.g. if bpp == 2, we should return an array of type short).
+   * @param fp If set and bpp == 4 or bpp == 8, then return floats or doubles.
+   * @param little Whether byte array is in little-endian order.
+   * @param height The height of the output primitive array (2nd dim length).
+   *
+   * @return a 2D primitive array of appropriate type,
+   *   dimensioned [height][b.length / (bpp * height)]
+   *
+   * @throws IllegalArgumentException if input byte array does not divide
+   *   evenly into height pieces
+   */
+  public static Object makeDataArray2D(byte[] b,
+    int bpp, boolean fp, boolean little, int height)
+  {
+    if (b.length % (bpp * height) != 0) {
+      throw new IllegalArgumentException("Array length mismatch: " +
+        "b.length=" + b.length + "; bpp=" + bpp + "; height=" + height);
+    }
+    final int width = b.length / (bpp * height);
+    if (bpp == 1) {
+      byte[][] b2 = new byte[height][width];
+      for (int y=0; y<height; y++) {
+        int index = width*y;
+        System.arraycopy(b, index, b2[y], 0, width);
+      }
+      return b2;
+    }
+    else if (bpp == 2) {
+      short[][] s = new short[height][width];
+      for (int y=0; y<height; y++) {
+        for (int x=0; x<width; x++) {
+          int index = 2*(width*y + x);
+          s[y][x] = bytesToShort(b, index, 2, little);
+        }
+      }
+      return s;
+    }
+    else if (bpp == 4 && fp) {
+      float[][] f = new float[height][width];
+      for (int y=0; y<height; y++) {
+        for (int x=0; x<width; x++) {
+          int index = 4*(width*y + x);
+          f[y][x] = bytesToFloat(b, index, 4, little);
+        }
+      }
+      return f;
+    }
+    else if (bpp == 4) {
+      int[][] i = new int[height][width];
+      for (int y=0; y<height; y++) {
+        for (int x=0; x<width; x++) {
+          int index = 4*(width*y + x);
+          i[y][x] = bytesToInt(b, index, 4, little);
+        }
+      }
+      return i;
+    }
+    else if (bpp == 8 && fp) {
+      double[][] d = new double[height][width];
+      for (int y=0; y<height; y++) {
+        for (int x=0; x<width; x++) {
+          int index = 8*(width*y + x);
+          d[y][x] = bytesToDouble(b, index, 8, little);
+        }
+      }
+      return d;
+    }
+    else if (bpp == 8) {
+      long[][] l = new long[height][width];
+      for (int y=0; y<height; y++) {
+        for (int x=0; x<width; x++) {
+          int index = 8*(width*y + x);
+          l[y][x] = bytesToLong(b, index, 8, little);
+        }
+      }
+      return l;
+    }
+    return null;
   }
 

branches/4.2/components/common/src/loci/common/DebugTools.java

@@ -26 +26 @@
 import java.io.ByteArrayOutputStream;
 import java.io.PrintStream;
+import java.util.Enumeration;
 
 /**
@@ -51 +52 @@
   }
 
+  /**
+   * Attempts to enable SLF4J logging via log4j
+   * without an external configuration file.
+   *
+   * @param level A string indicating the desired level
+   *   (i.e.: ALL, DEBUG, ERROR, FATAL, INFO, OFF, TRACE, WARN).
+   * @return true iff logging was successfully enabled
+   */
+  public static synchronized boolean enableLogging(String level) {
+    ReflectedUniverse r = new ReflectedUniverse();
+    try {
+      r.exec("import org.apache.log4j.Level");
+      r.exec("import org.apache.log4j.Logger");
+      r.exec("root = Logger.getRootLogger()");
+      r.exec("root.setLevel(Level." + level + ")");
+      Enumeration en = (Enumeration) r.exec("root.getAllAppenders()");
+      if (!en.hasMoreElements()) {
+        // no appenders yet; attach a simple console appender
+        r.exec("import org.apache.log4j.ConsoleAppender");
+        r.exec("import org.apache.log4j.PatternLayout");
+        r.setVar("pattern", "%m%n");
+        r.exec("layout = new PatternLayout(pattern)");
+        r.exec("appender = new ConsoleAppender(layout)");
+        r.exec("root.addAppender(appender)");
+      }
+    }
+    catch (ReflectException exc) {
+      return false;
+    }
+    return true;
+  }
+
 }

branches/4.2/components/common/src/loci/common/StatusEvent.java

@@ -86 +86 @@
   public boolean isWarning() { return warning; }
 
+  // -- Object API methods --
+
+  @Override
+  public String toString() {
+    StringBuilder sb = new StringBuilder();
+    sb.append("Status");
+    sb.append(": progress=" + progress);
+    sb.append(", maximum=" + maximum);
+    sb.append(", warning=" + warning);
+    sb.append(", status='" + status + "'");
+    return sb.toString();
+  }
+
 }

branches/4.2/components/common/src/loci/common/services/ServiceFactory.java

@@ -108 +108 @@
       }
       catch (Throwable t) {
-        LOGGER.warn("CLASSPATH missing interface: {}", interfaceName, t);
+        LOGGER.debug("CLASSPATH missing interface: {}", interfaceName, t);
         continue;
       }