Reprocessing

Ironed out a few bugs in restarting processing.

src/Acquisition/FileInputSystem.java

@@ -558,7 +558,10 @@ public class FileInputSystem  extends DaqSystem implements ActionListener, PamSe
 		//		if (fileInputParameters.recentFiles == null) return false;
 		//		if (fileInputParameters.recentFiles.size() < 1) return false;
 		//		String fileName = fileInputParameters.recentFiles.get(0);
-		return runFileAnalysis();
+		if (runFileAnalysis() == false) {
+			return false;
+		}
+		return true;
 	}
 
 	public File getCurrentFile() {
@@ -737,6 +740,8 @@ public class FileInputSystem  extends DaqSystem implements ActionListener, PamSe
 	@Override
 	public boolean startSystem(AcquisitionControl daqControl) {
 
+
+		
 		if (audioStream == null) return false;
 
 		dontStop = true;

src/Acquisition/FolderInputSystem.java

@@ -141,6 +141,7 @@ public class FolderInputSystem extends FileInputSystem implements PamSettings, D
 		String[] selList = {globalFolder};
 		folderInputParameters.setSelectedFiles(selList);
 		// need to immediately make the allfiles list since it's about to get used by the reprocess manager
+		// need to worry about how to wait for this since it's starting in a different thread. 
 		makeSelFileList();
 	}
 
@@ -868,6 +869,8 @@ public class FolderInputSystem extends FileInputSystem implements PamSettings, D
 			long fileStart = getFileStartTime(allFiles.get(i).getAbsoluteFile());
 			if (fileStart >= startTime) {
 				currentFile = i;
+				PamCalendar.setSoundFile(true);
+				PamCalendar.setSessionStartTime(startTime);
 				System.out.printf("Sound Acquisition start processing at file %s time %s\n", allFiles.get(i).getName(),
 						PamCalendar.formatDBDateTime(fileStart));
 				return true;

src/PamController/PamController.java

@@ -1212,6 +1212,8 @@ public class PamController implements PamControllerInterface, PamSettings {
 		}
 
 		/*
+		 * 
+		 * This needs to be called after prepareproces. 
 		 * Now we do some extra checks on the stores to see if we want to overwite data, 
 		 * carry on from where we left off, etc. 
 		 */
@@ -1221,14 +1223,15 @@ public class PamController implements PamControllerInterface, PamSettings {
 			if (goonthen == false) {
 				System.out.println("Data processing will not start since you've chosen not to overwrite existing output data");
 				pamStop();
+				setPamStatus(PAM_IDLE);
 				return false;
 			}
-
-			if (saveSettings) {
-				saveSettings(PamCalendar.getSessionStartTime());
-			}
 		}
-		
+
+		if (saveSettings) {
+			saveSettings(PamCalendar.getSessionStartTime());
+		}
+
 		StorageOptions.getInstance().setBlockOptions();
 
 		t1 = System.currentTimeMillis();

src/PamController/fileprocessing/ReprocessManager.java

@@ -48,6 +48,10 @@ public class ReprocessManager {
 			return true;
 		}
 		
+		if (choiceSummary.getInputStoreInfo() == null) {
+			return true;
+		}
+		
 		// need to decide what to do based on the list of possible choices. 
 		ReprocessStoreChoice choice = chosePartStoreAction(choiceSummary);
 		

src/RightWhaleEdgeDetector/RWEProcess.java

@@ -177,6 +177,7 @@ public class RWEProcess extends PamProcess {
 			minSoundType = rweControl.rweParameters.minSoundType;
 			classifier.setSoundData(getSampleRate(), sourceDataBlock.getFftLength(),
 					sourceDataBlock.getFftHop());
+			System.out.println("Create right whale channel process " + iChannel);
 		}
 		
 		

src/binaryFileStorage/BinaryOutputStream.java

@@ -117,6 +117,8 @@ public class BinaryOutputStream {
 		File outputFile = new File(mainFileName);
 
 		boolean open = openPGDFFile(outputFile);
+		
+//		System.out.println("Open outout file " + outputFile.getAbsolutePath());
 
 		if (open) {
 			addToDataMap(outputFile);
@@ -260,6 +262,7 @@ public class BinaryOutputStream {
 
 	public synchronized boolean closeFile() {
 		boolean ok = true;
+//		System.out.println("Close output file " + mainFileName);
 		if (dataOutputStream != null) {
 			if (currentDataMapPoint != null) {
 				currentDataMapPoint.setBinaryFooter(footer);

src/binaryFileStorage/BinaryStore.java

@@ -2404,6 +2404,7 @@ PamSettingsSource, DataOutputStore {
 		}
 		else {
 			reportError("No valid header in file " + file.getAbsolutePath());
+			inputStream.closeFile();
 			return null;
 		}
 

src/binaryFileStorage/BinaryStoreDeleter.java

@@ -142,9 +142,10 @@ public class BinaryStoreDeleter {
 		boolean headOk = false;
 		BinaryHeader binaryHead = new BinaryHeader();
 		try {
-			DataInputStream dis = new DataInputStream(new BufferedInputStream(new FileInputStream(indexFile)));
+			FileInputStream fis = new FileInputStream(indexFile);
+			DataInputStream dis = new DataInputStream(new BufferedInputStream(fis));
 			headOk = binaryHead.readHeader(dis);
-			dis.close();
+			fis.close();
 		}
 		catch (IOException e) {
 			headOk = false;
@@ -188,6 +189,7 @@ public class BinaryStoreDeleter {
 	}
 	
 	private boolean partialCopyFile(PamDataBlock aBlock, File dataFile, long timeMillis) {
+		System.out.printf("Partial delete of file %s from %s\n", dataFile.getAbsoluteFile(), PamCalendar.formatDBDateTime(timeMillis));
 		try {
 			BinaryInputStream inputStream = new BinaryInputStream(binaryStore, aBlock);
 			if (inputStream.openFile(dataFile) == false) {
@@ -303,10 +305,11 @@ public class BinaryStoreDeleter {
 	 * @return
 	 */
 	private boolean deleteFileSet(File dataFile) {
+		System.out.printf("Deleting full file set for %s\n", dataFile.getAbsoluteFile());
+		boolean deleteOk = true;
 		try {
 			File indexFile = binaryStore.findIndexFile(dataFile, true);
 			File noiseFile = binaryStore.findNoiseFile(dataFile, true);
-			boolean deleteOk = true;
 			deleteOk &= dataFile.delete();
 			if (indexFile != null) {
 				deleteOk &= indexFile.delete();
@@ -314,11 +317,14 @@ public class BinaryStoreDeleter {
 			if (noiseFile != null) {
 				deleteOk &= noiseFile.delete();
 			}
-			return deleteOk;
 		}
 		catch (Exception e) {
-			return false;
+			deleteOk = false;
 		}
+
+		System.out.printf("Deleting full file set %s for %s\n", deleteOk?"OK":"Error", dataFile.getAbsoluteFile());
+		
+		return deleteOk;
 		
 	}
 

src/binaryFileStorage/BinaryStoreStatusFuncs.java

@@ -136,15 +136,16 @@ public class BinaryStoreStatusFuncs {
 		 *  get the UID and time of the last item in the file. Can return these in the form of
 		 *  a BinaryFooter since it's pretty much the same information needed.  
 		 */
+		BinaryInputStream inputStream = new BinaryInputStream(binaryStore, null);
 		try {
 			// need to work through the file now. 
-			BinaryInputStream inputStream = new BinaryInputStream(binaryStore, null);
 			if (inputStream.openFile(aFile) == false) {
 				return null;
 			};
 			BinaryObjectData binaryObjectData;
 			BinaryHeader bh = inputStream.readHeader();
 			if (bh==null) {
+				inputStream.closeFile();
 				return null; 
 			}
 			int inputFormat = bh.getHeaderFormat();
@@ -159,6 +160,7 @@ public class BinaryStoreStatusFuncs {
 					bf = new BinaryFooter();
 					if (bf.readFooterData(binaryObjectData.getDataInputStream(), inputFormat)) {
 						if (bf.getDataDate() != 0) {
+							inputStream.closeFile();
 							return bf;
 						}
 					}
@@ -184,11 +186,18 @@ public class BinaryStoreStatusFuncs {
 					}
 				}
 			}
-			inputStream.closeFile();
 		}
 		catch (Exception e) {
 			System.out.printf("Corrupt data file %s: %s\n", aFile, e.getMessage());
 //			return null;
+		}
+		try {
+			if (inputStream != null) {
+				inputStream.closeFile();
+			}
+		}
+		catch (Exception e) {
+			
 		}
 		if (lastTime != null && lastUID != null) {
 			BinaryFooter bf = new BinaryFooter();
@@ -211,18 +220,23 @@ public class BinaryStoreStatusFuncs {
 	 */
 	private BinaryHeader findFirstHeader(List<File> binFiles) {
 		BinaryHeader binaryHead = new BinaryHeader();
+		DataInputStream dis = null;
 		for (File aFile : binFiles) {
 			try {
-				DataInputStream dis = new DataInputStream(new BufferedInputStream(new FileInputStream(aFile)));
-				if (binaryHead.readHeader(dis)) {
-					return binaryHead;
-				}
+				dis = new DataInputStream(new BufferedInputStream(new FileInputStream(aFile)));
 			}
 			catch (IOException e) {
+				binaryHead = null;
 				continue;
 			}
+			try {
+				dis.close();
+			}
+			catch (IOException e) {
+				
+			}
 		}
-		return null;
+		return binaryHead;
 	}
 
 	/**