updates to PAMGuard command line options and UDP control (#25)

* Fix network sender since it was hopelessly out of date and did not send
data in the correct format. OK now, though only tested on NARW.

* Mods to support command line and Network control of PAMGuard and to
retrieve summary information from some modules.

src/Acquisition/AcquisitionControl.java

@@ -70,6 +70,7 @@ import PamController.PamSettings;
 import PamModel.PamModel;
 import PamModel.SMRUEnable;
 import PamUtils.FrequencyFormat;
+import PamUtils.PamCalendar;
 import PamUtils.PlatformInfo;
 import PamUtils.PlatformInfo.OSType;
 import PamView.MenuItemEnabler;
@@ -776,9 +777,11 @@ public class AcquisitionControl extends PamControlledUnit implements PamSettings
 		return null;
 	}
 	
-	
-	@Override
-	public String getModuleSummary() {
+	/**
+	 * Get a summary of the daq settings for the QA module. 
+	 * @return summary of DAQ settings. 
+	 */
+	public String getDaqSummary() {
 		DaqSystem daqSys = findDaqSystem(null);
 		if (daqSys == null) {
 			return String.format("%s - currently unavailable", acquisitionParameters.daqSystemType);
@@ -794,9 +797,41 @@ public class AcquisitionControl extends PamControlledUnit implements PamSettings
 		return str;
 	}
 	
+	@Override
+	public String tellModule(String command) {
+		/**
+		 * Get timing summary and return as a string. 
+		 */
+		switch (command) {
+		case "gettimeinfo":
+			return getTimeInfoString();
+		}
+		return super.tellModule(command);
+	}
+	
+	
+	/**
+	 * Get a summary of time information as to what's going on in the DAQ
+	 * @return time summary
+	 */
+	private String getTimeInfoString() {
+		/*
+		 * 
+		sprintf(returned,"%s:%lld,%lld,%ld,%lld",getModuleName(),calendar->getRawStartTime(),
+				calendar->getMillisecondTime(),(int)daqProcess->getSampleRate(),acquiredSamples);
+		 */
+		return String.format("%s:%d,%d,%d,%d", getUnitName(), PamCalendar.getSessionStartTime(), PamCalendar.getTimeInMillis(), 
+				(int) acquisitionProcess.getSampleRate(), acquisitionProcess.getTotalSamples(0));
+	}
+	
 	@Override
 	public void pamHasStopped() {
 		acquisitionProcess.pamHasStopped();
 	}
+	
+	@Override
+	public String getModuleSummary(boolean clear) {
+		return getDaqProcess().getRawDataBlock().getSummaryString(clear);
+	}
 
 }

src/PamController/PamControlledUnit.java

@@ -697,11 +697,33 @@ public abstract class PamControlledUnit implements SettingsNameProvider {
 	}
 
 	/**
-	 * Get a module summary text string for shorthand output to 
-	 * summary QC systems. 
+	 * Get a module summary text string for shorthand output to anyting wanting a 
+	 * short summary of data state / numbers of detections. <br> You should not 
+	 * override this version of the function, but instead override getModuleSummary(boolean clear)
+	 * which allows for optional clearing of summary data. 
 	 * @return module summary string - goings on since the last call to this function
 	 */
 	public String getModuleSummary() {
+		return getModuleSummary(true);
+	}
+
+	/**
+	 * Get a module summary text string for shorthand output to anyting wanting a 
+	 * short summary of data state / numbers of detections. 
+	 * @param clear clear data after generating string, so that counts of detections, etc. start again from 0. 
+	 * @return module summary string - goings on since the last call to this function
+	 */
+	public String getModuleSummary(boolean clear) {
+		return null;
+	}
+	
+	/**
+	 * Handle a module specific command sent by the 
+	 * tellmodule command. 
+	 * @param command command line (stripped of the command and the module type and name)
+	 * @return response to command
+	 */
+	public String tellModule(String command) {
 		return null;
 	}
 

src/PamController/PamController.java

@@ -911,6 +911,29 @@ public class PamController implements PamControllerInterface, PamSettings {
 
 		return l;
 	}
+	/**
+	 * Get a list of PamControlledUnit units of a given type and name, allowing for nulls. 
+	 * @param unitType Controlled unit type, can be null for all units of name
+	 * @param unitName Controlled unit name, can be null for all units of type
+	 * @return list of units. 
+	 */
+	public ArrayList<PamControlledUnit> findControlledUnits(String unitType, String unitName) {
+		ArrayList<PamControlledUnit> l = new ArrayList<PamControlledUnit>();
+		int n = getNumControlledUnits();
+		PamControlledUnit pcu;
+		for (int i = 0; i < n; i++) {
+			pcu = getControlledUnit(i);
+			if (unitType != null && !unitType.equals(pcu.getUnitType())) {
+				continue;
+			}
+			if (unitName != null && !unitName.equals(pcu.getUnitName())) {
+				continue;
+			}
+			l.add(pcu);
+		}
+
+		return l;
+	}
 
 	@Override
 	public PamControlledUnit findControlledUnit(String unitType, String unitName) {

src/PamController/command/CommandManager.java

@@ -32,6 +32,8 @@ public abstract class CommandManager extends PamControlledUnit {
 		commandsList.add(new PingCommand());
 		commandsList.add(new StatusCommand());
 		commandsList.add(new SummaryCommand());
+		commandsList.add(new SummaryPeekCommand());
+		commandsList.add(new TellModuleCommand());
 		commandsList.add(new ExitCommand());
 		commandsList.add(new KillCommand());
 		commandsList.add(new HelpCommand(this));
@@ -120,6 +122,34 @@ public abstract class CommandManager extends PamControlledUnit {
 		}
 		return sbits;
 	}
+	
+	/**
+	 * Get the command string left from the given index. This can be used to get 
+	 * everything left in the string that follows the command name, module type and module name
+	 * fields for example. 
+	 * @param command full command string
+	 * @param index how many items to skip
+	 * @return remainder of the string, warts n all. 
+	 */
+	public static String getCommandFromIndex(String command, int index) {
+		if (command == null) {
+			return null;
+		}
+		int startCharIndex = 0;
+		int foundBits = 0;
+		Matcher m = Pattern.compile("([^\"]\\S*|\".+?\")\\s*").matcher(command);
+		List<String> bits = new ArrayList<>();
+		while (m.find() && foundBits++ < index) {
+			String bit = m.group(1);
+			startCharIndex = command.indexOf(bit, startCharIndex) + bit.length();
+			if (startCharIndex >= command.length()) {
+				return null;
+			}
+		}
+		String wanted = command.substring(startCharIndex+1).trim();
+		return wanted;
+	}
+	
 
 	/**
 	 * Reply to data called from InterpredData

src/PamController/command/ExtCommand.java

@@ -1,9 +1,13 @@
 package PamController.command;
 
 import java.awt.event.ActionListener;
+import java.util.ArrayList;
 
 import javax.swing.SwingUtilities;
 
+import PamController.PamControlledUnit;
+import PamController.PamController;
+
 public abstract class ExtCommand {
 
 	private String name;
@@ -121,4 +125,21 @@ public abstract class ExtCommand {
 	public String getHint() {
 		return null;
 	};
+	
+	/**
+	 * Find a set of controlled units, allowing for wild cards or nulls. 
+	 * @param unitType unit type, can be null or * for wildcards
+	 * @param unitName unit name, can be null or * for wildcards
+	 * @return
+	 */
+	public ArrayList<PamControlledUnit> findControlledUnits(String unitType, String unitName) {
+		if (unitType != null && unitType.equals("*")) {
+			unitType = null;
+		}
+		if (unitName != null && unitName.equals("*")) {
+			unitName = null;
+		}
+		PamController pc = PamController.getInstance();
+		return pc.findControlledUnits(unitType, unitName);
+	}
 }

src/PamController/command/NetworkController.java

@@ -43,6 +43,8 @@ public class NetworkController extends CommandManager {
 	private byte[] byteBuffer = new byte[MAX_COMMAND_LENGTH];
 	
 	private NetworkRecorderTrigger[] recorderTriggers;
+
+	private static NetworkController singleInstance;
 	
 	private static String unitName = "Network Controller";
 
@@ -53,6 +55,8 @@ public class NetworkController extends CommandManager {
 		listenerThread = new ListenerThread();
 		Thread aThread = new Thread(listenerThread);
 		aThread.start();
+		
+		singleInstance = this;
 	}
 	
 	class ListenerThread implements Runnable {

src/PamController/command/SummaryCommand.java

@@ -21,10 +21,20 @@ public class SummaryCommand extends ExtCommand {
 
 	@Override
 	public String execute(String command) {
-		return getReturnString();
+//		String[] cmdBits = CommandManager.splitCommandLine(command);
+//		boolean clear = true;
+//		// first word is the command, we want one after that. 
+//		if (cmdBits.length >= 2 && cmdBits[1] != null) {
+//			String bit = cmdBits[1].trim().toLowerCase();
+//			if (bit.equals("0") || bit.equals("false")) {
+//				clear = false;
+//			}
+//			
+//		}
+		return getModulesSummary(true);
 	}
-
-	public String getReturnString() {
+	
+	public String getModulesSummary(boolean clear) {
 		PamController pamController = PamController.getInstance();
 		int nMod = pamController.getNumControlledUnits();
 		PamControlledUnit aModule;
@@ -38,7 +48,7 @@ public class SummaryCommand extends ExtCommand {
 		int usedModules = 0;
 		for (int i = 0; i < nMod; i++) {
 			aModule = pamController.getControlledUnit(i);
-			aString = aModule.getModuleSummary();
+			aString = aModule.getModuleSummary(clear);
 			if (aString == null) {
 				continue;
 			}

src/PamController/command/SummaryPeekCommand.java

@@ -0,0 +1,19 @@
+package PamController.command;
+
+public class SummaryPeekCommand extends SummaryCommand {
+
+	public SummaryPeekCommand() {
+		super();
+		setName("summarypeek");
+	}
+
+	@Override
+	public String execute(String command) {
+		return getModulesSummary(false);
+	}
+
+	@Override
+	public String getHint() {
+		return "Get summary information about each running process, don't clear data";
+	}
+}

src/PamController/command/TellModuleCommand.java

@@ -0,0 +1,46 @@
+package PamController.command;
+
+import java.util.ArrayList;
+
+import PamController.PamControlledUnit;
+import PamController.PamSettingManager;
+
+public class TellModuleCommand extends ExtCommand {
+
+	public TellModuleCommand() {
+		super("tellmodule", true);
+		// TODO Auto-generated constructor stub
+	}
+
+	@Override
+	public String execute(String command) {		
+		String[] commandWords = CommandManager.splitCommandLine(command);
+		if (commandWords.length < 3) {
+			return "Unspecified modules for tellmodule. Command must be followed by module name and type";
+		}
+		PamSettingManager settingsManager = PamSettingManager.getInstance();
+		String unitType = commandWords[1];
+		String unitName = commandWords[2];
+		ArrayList<PamControlledUnit> pamControlledUnits = findControlledUnits(unitType, unitName);
+		if (pamControlledUnits.size() == 0) {
+			return "tellmodule: no modules found for command " + command;
+		}
+		String commandPart = CommandManager.getCommandFromIndex(command, 3);
+		if (commandPart == null) {
+			return "tellmodule: No command. Must have a module type, module name and the thing to send to modules";
+		}
+		String retStr = "";
+		for (int i = 0; i < pamControlledUnits.size(); i++) {
+			if (i > 0) {
+				retStr += ";";
+			}
+			retStr += pamControlledUnits.get(i).tellModule(commandPart);
+		}
+		return retStr;
+	}
+
+	@Override
+	public String getHint() {
+		return "Send a command to a module.";
+	}
+}

src/PamView/PamDetectionOverlayGraphics.java

@@ -700,8 +700,11 @@ public class PamDetectionOverlayGraphics extends PanelOverlayDraw {
 				pamDetection.getSampleDuration() * 1000./parentDataBlock.getSampleRate(),
 				frequency[0], 0);
 				
+		boolean isWrapped = false;
 		if (botRight.x < topLeft.x){
-			botRight.x = g.getClipBounds().width;
+			// this means it's wrapped.
+			isWrapped = true;
+			botRight.x += g.getClipBounds().width;
 		}
 		if (generalProjector.isViewer()) {
 			Coordinate3d middle = new Coordinate3d();
@@ -723,8 +726,13 @@ public class PamDetectionOverlayGraphics extends PanelOverlayDraw {
 			// Not actually drawing on a spectrogramProjector, so don't have any info on the background color
 		}
 
+		if (isWrapped) {
+			g.drawRect((int) topLeft.x-g.getClipBounds().width, (int) topLeft.y, 
+					(int) botRight.x - (int) topLeft.x, (int) botRight.y - (int) topLeft.y);
+		}
 		g.drawRect((int) topLeft.x, (int) topLeft.y, 
 				(int) botRight.x - (int) topLeft.x, (int) botRight.y - (int) topLeft.y);
+		
 		return new Rectangle((int) topLeft.x, (int) topLeft.y, 
 				(int) botRight.x - (int) topLeft.x, (int) botRight.y - (int) topLeft.y);
 	}

src/PamguardMVC/PamRawDataBlock.java

@@ -50,6 +50,11 @@ public class PamRawDataBlock extends AcousticDataBlock<RawDataUnit> {
 	
 	private long desiredSample = -1;
 	private long[] prevChannelSample = new long[PamConstants.MAX_CHANNELS];
+	
+	private double[] summaryTotals = new double[PamConstants.MAX_CHANNELS];
+	private double[] summaryTotals2 = new double[PamConstants.MAX_CHANNELS];
+	private double[] summaryMaxVal = new double[PamConstants.MAX_CHANNELS];
+	private int[] summaryCount = new int[PamConstants.MAX_CHANNELS];
 
 	/**
 	 * Keep a record of the last sample added. 
@@ -167,10 +172,12 @@ public class PamRawDataBlock extends AcousticDataBlock<RawDataUnit> {
 		prevChannelSample[thisChannel] = pamDataUnit.getStartSample();
 //		System.out.println(String.format("Sample %d channel %d in %s is in  synch - expected sample %d",
 //				pamDataUnit.getStartSample(), thisChannel, getDataName(), desiredSample));
+		addSummaryData(thisChannel, pamDataUnit);
 		
 		super.addPamData(pamDataUnit);
 	}
 	
+
 	/**
 	 * Get available data from the raw data block. Similar to the functionality of 
 	 * getSamplesforMillis, but this will not throw an exception if not all of the samples
@@ -517,6 +524,66 @@ public class PamRawDataBlock extends AcousticDataBlock<RawDataUnit> {
 		super.addObserver(o, reThread);
 	}
 
+	private void addSummaryData(int channel, RawDataUnit pamDataUnit) {
+		double[] data = pamDataUnit.getRawData();
+		synchronized(summaryTotals) {
+			double tot = 0, tot2 = 0, mx = 0;
+			for (int i = 0; i < data.length; i++) {
+				double dat = data[i];
+				tot += dat;
+				tot2 += dat*dat;
+				mx = Math.max(mx, dat);
+			}
+			summaryTotals[channel] += tot/data.length;
+			summaryTotals2[channel] += tot2/data.length;
+			summaryMaxVal[channel] = Math.max(summaryMaxVal[channel], mx);
+			summaryCount[channel] ++;
+		}
+		
+	}
+	
+	public String getSummaryString(boolean clear) {
+		/*
+		 * 
+	sumString[0] = 0;
+	float rms, max, mean;
+	for (int i = 0; i < ringBufferChannels; i++) {
+		//		rms = sqrt(summaryTotals[i]/summaryCount);
+		rms = sqrt(summaryTotals2[i]/summaryCount) + 0.01;
+		max = (double)summaryMaxVal[i] + 0.01;
+		mean = summaryTotals[i]/summaryCount;
+		//		sprintf(sumString+strlen(sumString), "ch%d,%3.1f,%3.1f,", i, 20.*log10((double)summaryMaxVal[i]/32768.),
+		//				20*log10(rms/32768.));
+		sprintf(sumString+strlen(sumString), "ch%d,%3.1f,%3.1f,%3.1f,", i, mean, 20.*log10(max/32768.),
+				20.*log10(rms/32768.));
+	}
+		 */
+		String str = "";
+		int nChan = PamUtils.getNumChannels(getChannelMap());
+		synchronized(summaryTotals) {
+			for (int i = 0; i < nChan; i++) {
+				double rms = Math.sqrt(summaryTotals2[i]/summaryCount[i])+1e-6;
+				double max = summaryMaxVal[i]+1e-6;
+				double mean = summaryTotals[i]/summaryCount[i];
+				str += String.format("ch%d,%3.1f,%3.1f,%3.1f,", i, mean, 20.*Math.log10(max),
+						20.*Math.log10(rms));
+			}
+		}
+		if (clear) {
+			clearSummaryData();
+		}
+		return str;
+	}
+	
+	public void clearSummaryData() {
+		synchronized(summaryTotals) {
+			for (int i = 0; i < summaryTotals.length; i++) {
+				summaryTotals[i] = summaryTotals2[i] = summaryMaxVal[i] = 0;
+				summaryCount[i] = 0;
+			}
+		}
+	}
+
 //	@Override
 //	protected void findParentSource() {
 //		super.findParentSource();

src/RightWhaleEdgeDetector/RWEControl.java

@@ -147,4 +147,10 @@ public class RWEControl extends PamControlledUnit implements PamSettings {
 		return rweParameters;
 	}
 
+
+	@Override
+	public String getModuleSummary(boolean clear) {
+		return rweProcess.getModuleSummary(clear);
+	}
+
 }

src/RightWhaleEdgeDetector/RWEProcess.java

@@ -154,6 +154,8 @@ public class RWEProcess extends PamProcess {
 		private int minSoundType;
 		private RWClassifier classifier = new RWStandardClassifier();
 		
+		private int[] soundCounts = new int[RWStandardClassifier.MAXSOUNDTYPE+1];
+		
 		public RWEChannelProcess(RWEProcess rweProcess, int iChannel) {
 			this.rweProcess = rweProcess;
 			this.iChannel = iChannel;
@@ -216,11 +218,19 @@ public class RWEProcess extends PamProcess {
 					f[1] = aSound.maxFreq * getSampleRate()/sourceDataBlock.getFftLength();
 					rweDataUnit.setFrequency(f);
 					rweDataBlock.addPamData(rweDataUnit);
+					soundCounts[rweDataUnit.rweSound.soundType]++;
 //					System.out.printf("RW %d at %s\n", rweDataUnit.rweSound.soundType, PamCalendar.formatTime(rweDataUnit.getTimeMilliseconds()));
 				}
 			}
 		}
 		
+		/**
+		 * Clear sound counts
+		 */
+		private void clearSoundCounts() {
+			Arrays.fill(soundCounts, 0);
+		}
+		
 		private RWEDetectionPeak[] findPeaks(ComplexArray complexArray) {
 			RWEDetectionPeak[] detectedPeaks = null;
 			int nPeaks = 0;
@@ -481,6 +491,24 @@ public class RWEProcess extends PamProcess {
 //		}
 	}
 
+	public String getModuleSummary(boolean clear) {
+		String str = String.format("%d", RWStandardClassifier.MAXSOUNDTYPE+1);
+		for (int c = 0; c < rweChannelProcesses.length; c++) {
+			if (rweChannelProcesses[c] == null) {
+				continue;
+			}
+			str += String.format("ch%d", c);
+			int[] counts = rweChannelProcesses[c].soundCounts;
+			for (int i = 0; i < counts.length; i++) {
+				str += String.format(",%d", counts[i]);
+			}
+			if (clear) {
+				rweChannelProcesses[c].clearSoundCounts();
+			}
+		}
+		return str;
+	}
+
 //	private void recalculateAllAngles() {
 //		synchronized(rweDataBlock.getSynchLock()) {
 //			ListIterator<RWEDataUnit> it = rweDataBlock.getListIterator(0);

src/SoundRecorder/RecorderControl.java

@@ -3,6 +3,7 @@ package SoundRecorder;
 import java.awt.Frame;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.io.File;
 import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.Calendar;
@@ -22,6 +23,7 @@ import PamController.PamController;
 import PamController.PamControllerInterface;
 import PamController.PamSettingManager;
 import PamController.PamSettings;
+import PamController.command.CommandManager;
 import PamUtils.PamCalendar;
 import PamUtils.PamUtils;
 import PamView.MenuItemEnabler;
@@ -563,4 +565,71 @@ public class RecorderControl extends PamControlledUnit implements PamSettings {
 		return backupInformation;
 	}
 
+	@Override
+	public String tellModule(String command) {
+		String[] parts = command.split(" ");
+		if (parts.length < 1) {
+			return "Unknown command to sound recorder: " + command;
+		}
+		switch(parts[0]) {
+		case "start":
+			buttonCommand(RecorderView.BUTTON_START);
+			break;
+		case "startbuffered":
+			buttonCommand(RecorderView.BUTTON_START_BUFFERED);
+			break;
+		case "stop":
+			buttonCommand(RecorderView.BUTTON_OFF);
+			break;
+		case "cycle":
+			buttonCommand(RecorderView.BUTTON_AUTO);
+			break;
+		case "outputfolder":
+			return setOutputFolder(command);
+		default:
+			return "Unknown command to sound recorder: " + command;
+		}
+		return getUnitName() + " executed " + command;
+	}
+
+	/**
+	 * set output folder. Trim off the command first. 
+	 * @param command
+	 * @return 
+	 */
+	private String setOutputFolder(String command) {
+		String[] parts = CommandManager.splitCommandLine(command);
+		if (parts.length < 2) {
+			return "Unspecified output folder for sound recorder";
+		}
+		File path = new File(parts[1].trim());
+		if (path.exists() == false) {
+			path.mkdirs();
+		}
+		if (path.isDirectory()) {
+			recorderSettings.outputFolder = path.getAbsolutePath();
+			return getUnitName() + "storing recordings in " + path.getAbsolutePath();
+		}
+		else {
+			return getUnitName() + "unable to switch to storage folder " + path.getAbsolutePath();
+		}
+	}
+
+	@Override
+	public String getModuleSummary(boolean clear) {
+		File path = new File(recorderSettings.outputFolder);
+		long space = -1;
+		double freeSpace = -1;
+		try {
+			space = path.getFreeSpace();
+			freeSpace = (double) space / 1048576.;
+		}
+		catch (SecurityException e) {
+			freeSpace = -9999;
+		}
+		int currButton = pressedButton;
+		int currState = recorderStatus;
+		return String.format("%d,%d,%3.1f", currButton, currState, freeSpace);
+	}
+
 }

src/qa/analyser/QASystemReport.java

@@ -47,7 +47,7 @@ public class QASystemReport {
 			section.addSectionText("Configuration error: No acqusition system found");
 		}
 		else {
-			section.addSectionText("Acquisition System: " + daqControl.getModuleSummary());
+			section.addSectionText("Acquisition System: " + daqControl.getDaqSummary());
 		}
 		report.addSection(section);
 		report.addSection(makeArraySection(ArrayManager.getArrayManager().getCurrentArray(), daqControl));