* bfconvert and showinf now exit if an unknown flag or argument is sp…

…ecified.

* bfconvert now prompts the user if the specified output file already exists.

Closes #524.

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

@@ -24,6 +24,8 @@
 package loci.formats.tools;
 
 import java.awt.image.IndexColorModel;
+import java.io.BufferedReader;
+import java.io.InputStreamReader;
 import java.io.IOException;
 
 import loci.common.DebugTools;
@@ -101,12 +103,20 @@ else if (args[i].equals("-series")) {
             }
             catch (NumberFormatException exc) { }
           }
-          else LOGGER.warn("Ignoring unknown command flag: {}", args[i]);
+          else {
+            LOGGER.error("Found unknown command flag: {}; exiting.", args[i]);
+            return false;
+          }
         }
         else {
           if (in == null) in = args[i];
           else if (out == null) out = args[i];
-          else LOGGER.warn("Ignoring unknown argument: {}", args[i]);
+          else {
+            LOGGER.error("Found unknown argument: {}; exiting.", args[i]);
+            LOGGER.error("You should specify exactly one input file and " +
+              "exactly one output file.");
+            return false;
+          }
         }
       }
     }
@@ -161,6 +171,19 @@ else if (args[i].equals("-series")) {
       return false;
     }
 
+    if (new Location(out).exists()) {
+      LOGGER.warn("Output file {} exists.", out);
+      LOGGER.warn("Do you want to overwrite it? ([y]/n)");
+      BufferedReader r = new BufferedReader(new InputStreamReader(System.in));
+      String choice = r.readLine().trim().toLowerCase();
+      boolean overwrite = !choice.startsWith("n");
+      if (!overwrite) {
+        LOGGER.warn("Exiting; next time, please specify an output file that " +
+          "does not exist.");
+        return false;
+      }
+    }
+
     if (map != null) Location.mapId(in, map);
 
     long start = System.currentTimeMillis();

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

@@ -122,7 +122,7 @@ public class ImageInfo {
 
   // -- ImageInfo methods --
 
-  public void parseArgs(String[] args) {
+  public boolean parseArgs(String[] args) {
     id = null;
     printVersion = false;
     pixels = true;
@@ -152,7 +152,7 @@ public void parseArgs(String[] args) {
     swapOrder = null;
     shuffleOrder = null;
     map = null;
-    if (args == null) return;
+    if (args == null) return false;
     for (int i=0; i<args.length; i++) {
       if (args[i].startsWith("-")) {
         if (args[i].equals("-nopix")) pixels = false;
@@ -205,13 +205,20 @@ else if (args[i].equals("-shuffle")) {
         }
         else if (args[i].equals("-map")) map = args[++i];
         else if (args[i].equals("-format")) format = args[++i];
-        else LOGGER.warn("Ignoring unknown command flag: {}", args[i]);
+        else {
+          LOGGER.error("Found unknown command flag: {}; exiting.", args[i]);
+          return false;
+        }
       }
       else {
         if (id == null) id = args[i];
-        else LOGGER.warn("Ignoring unknown argument: {}", args[i]);
+        else {
+          LOGGER.error("Found unknown argument: {}; exiting.", args[i]);
+          return false;
+        }
       }
     }
+    return true;
   }
 
   public void printUsage() {
@@ -879,7 +886,8 @@ public boolean testRead(String[] args)
     throws FormatException, ServiceException, IOException
   {
     DebugTools.enableLogging("INFO");
-    parseArgs(args);
+    boolean validArgs = parseArgs(args);
+    if (!validArgs) return false;
     if (printVersion) {
       LOGGER.info("Version: {}", FormatTools.VERSION);
       LOGGER.info("SVN revision: {}", FormatTools.SVN_REVISION);