mirror of
https://github.com/PAMGuard/PAMGuard.git
synced 2024-11-22 07:02:29 +00:00
Updates to imorting
This commit is contained in:
Jamie Mac
parent
66fb82743b
commit
45b0788c0d
@ -3,6 +3,8 @@ package cpod;
|
||||
import java.io.File;
|
||||
import java.util.ArrayList;
|
||||
import java.util.Calendar;
|
||||
import java.util.Collections;
|
||||
import java.util.Comparator;
|
||||
import java.util.Date;
|
||||
import java.util.HashMap;
|
||||
import java.util.List;
|
||||
@ -21,6 +23,7 @@ import binaryFileStorage.BinaryObjectData;
|
||||
import binaryFileStorage.BinaryOutputStream;
|
||||
import binaryFileStorage.BinaryStore;
|
||||
import cpod.CPODUtils.CPODFileType;
|
||||
import cpod.FPODReader.FPODHeader;
|
||||
import cpod.FPODReader.FPODdata;
|
||||
import javafx.application.Platform;
|
||||
import javafx.concurrent.Task;
|
||||
@ -62,7 +65,7 @@ public class CPODImporter {
|
||||
return t ;
|
||||
});
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
public CPODImporter(CPODControl2 cpodControl) {
|
||||
@ -81,8 +84,8 @@ public class CPODImporter {
|
||||
// dataBlock = cpodControl.getCP3DataBlock();
|
||||
//
|
||||
// }
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
/**
|
||||
* Import the CPOD file.
|
||||
@ -94,18 +97,18 @@ public class CPODImporter {
|
||||
*/
|
||||
private int importCPODFile(File cpFile2, CPODClickDataBlock dataBlock, CPODClickTrainDataBlock clickTrainDataBlock, int from, int maxNum) {
|
||||
ArrayList<CPODClick> cpodData = null;
|
||||
|
||||
|
||||
try {
|
||||
cpodData = CPODReader.importCPODFile(cpFile, from, maxNum);
|
||||
} catch (Exception e) {
|
||||
e.printStackTrace();
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
// fileStart + nMinutes * 60000L;
|
||||
|
||||
|
||||
|
||||
|
||||
// fileStart + nMinutes * 60000L;
|
||||
|
||||
|
||||
int nClicks = 0;
|
||||
for (int i=0; i<cpodData.size(); i++) {
|
||||
//System.out.println("Create a new CPOD click: ");
|
||||
@ -113,31 +116,31 @@ public class CPODImporter {
|
||||
dataBlock.addPamData(cpodClick);
|
||||
nClicks++;
|
||||
}
|
||||
|
||||
|
||||
cpodData=null; //trigger garbage collector if needed
|
||||
|
||||
|
||||
return nClicks;
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Process a CPOD click.
|
||||
* @param FPODData - an FPOD data object
|
||||
* @return an CPODClick data unit.
|
||||
*/
|
||||
private CPODClick processCPODClick(CPODClick cpodClick) {
|
||||
|
||||
|
||||
// now a bit of time stretching. Need to get the start time and see how
|
||||
// different this is, then it's a linear stretch.
|
||||
long tMillis = cpodControl.stretchClicktime(cpodClick.getTimeMilliseconds());
|
||||
|
||||
|
||||
cpodClick.setTimeMilliseconds(tMillis);
|
||||
|
||||
return cpodClick;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
/**
|
||||
* Process the click.
|
||||
@ -145,54 +148,15 @@ public class CPODImporter {
|
||||
* @return an CPODClick data unit.
|
||||
*/
|
||||
private CPODClick processFPODClick(FPODdata fpoDdata) {
|
||||
|
||||
|
||||
|
||||
//how many samples are we into the clicks
|
||||
|
||||
|
||||
long fileSamples = (long) (((fpoDdata.minute*60) + (fpoDdata.FiveMusec*5/1000000.))*CPODClickDataBlock.CPOD_SR);
|
||||
|
||||
|
||||
|
||||
// now a bit of time stretching. Need to get the start time and see how
|
||||
// different this is, then it's a linear stretch.
|
||||
long tMillis = cpodControl.stretchClicktime(fpoDdata.getTimeMillis());
|
||||
|
||||
|
||||
CPODClick cpodClick = CPODClick.makeFPODClick(tMillis, fileSamples, fpoDdata);
|
||||
|
||||
// short[] data = new short[9];
|
||||
//
|
||||
// short nCyc = (short) fpoDdata.Ncyc;
|
||||
// short bw = (short) fpoDdata.BW;
|
||||
// short kHz = (short) FPODReader.IPItoKhz(fpoDdata.IPIatMax);
|
||||
// short endF = (short) FPODReader.IPItoKhz(fpoDdata.EndIPI);
|
||||
// short spl = (short) fpoDdata.MaxPkExtnd;
|
||||
// short slope = 0;
|
||||
//
|
||||
// data[3]=nCyc;
|
||||
// data[4]=bw;
|
||||
// data[5]=kHz;
|
||||
// data[6]=endF;
|
||||
// data[7]=spl;
|
||||
// data[8]=slope;
|
||||
//
|
||||
// //these are the basic data
|
||||
// CPODClick cpodClick = new CPODClick(fpoDdata.getTimeMillis(),
|
||||
// fileSamples, nCyc, bw,
|
||||
// kHz, endF, spl, slope, data);
|
||||
|
||||
// if (fpoDdata.HasWave) {
|
||||
// int[] waveform = FPODReader.makeResampledWaveform(fpoDdata);
|
||||
// System.out.println("FPOD click waveform: " + kHz);
|
||||
// PamArrayUtils.printArray(waveform);
|
||||
// }
|
||||
|
||||
// cpodClick.setDurationInMilliseconds((fpoDdata.duration*5.)/1000.);
|
||||
|
||||
//does the click have a waveform?
|
||||
//TODO
|
||||
|
||||
|
||||
|
||||
return cpodClick;
|
||||
}
|
||||
|
||||
@ -204,22 +168,22 @@ public class CPODImporter {
|
||||
return fileStart;
|
||||
}
|
||||
|
||||
// /**
|
||||
// * Get the data
|
||||
// * @param type
|
||||
// * @return
|
||||
// */
|
||||
// public CPODClickDataBlock getDataBlock(CPODFileType type) {
|
||||
// switch (type) {
|
||||
// case CP1:
|
||||
// case FP1:
|
||||
// return this.cpodControl.getCP1DataBlock();
|
||||
// case CP3:
|
||||
// case FP3:
|
||||
// return this.cpodControl.getCP3DataBlock();
|
||||
// }
|
||||
// return null;
|
||||
// }
|
||||
// /**
|
||||
// * Get the data
|
||||
// * @param type
|
||||
// * @return
|
||||
// */
|
||||
// public CPODClickDataBlock getDataBlock(CPODFileType type) {
|
||||
// switch (type) {
|
||||
// case CP1:
|
||||
// case FP1:
|
||||
// return this.cpodControl.getCP1DataBlock();
|
||||
// case CP3:
|
||||
// case FP3:
|
||||
// return this.cpodControl.getCP3DataBlock();
|
||||
// }
|
||||
// return null;
|
||||
// }
|
||||
|
||||
/**
|
||||
* Run the import task.
|
||||
@ -264,7 +228,7 @@ public class CPODImporter {
|
||||
* @return a list of tasks whihc imports each file type.
|
||||
*/
|
||||
public List<Task<Integer>> importCPODData(List<File> files) {
|
||||
|
||||
|
||||
List<Task<Integer>> tasks = new ArrayList<Task<Integer>>();
|
||||
|
||||
for (int i=0; i<CPODFileType.values().length; i++) {
|
||||
@ -324,7 +288,9 @@ public class CPODImporter {
|
||||
/**
|
||||
* Reference to the CPOD click train datablock.
|
||||
*/
|
||||
private CPODClickTrainDataBlock clickTrainDataBlock;
|
||||
private CPODClickTrainDataBlock clickTrainDataBlock;
|
||||
|
||||
private ArrayList<CPODClick> cpodTrainList;
|
||||
|
||||
/**
|
||||
*
|
||||
@ -343,6 +309,9 @@ public class CPODImporter {
|
||||
protected Integer call() throws Exception {
|
||||
try {
|
||||
|
||||
System.out.println(("HELLO IMPORT THREAD: " ));
|
||||
|
||||
|
||||
BinaryDataSource binarySource = cpodDataBlock.getBinaryDataSource();
|
||||
binaryStore = (BinaryStore) PamController.getInstance().findControlledUnit(BinaryStore.defUnitType);
|
||||
if (binaryStore == null) {
|
||||
@ -370,27 +339,32 @@ public class CPODImporter {
|
||||
int importedClicks = -1;
|
||||
|
||||
this.updateProgress(-1, 1);
|
||||
|
||||
|
||||
CPODClickDataBlock tempCPODDataBlock = new CPODClickDataBlock("Temp CPOD Detections",
|
||||
null, 0);
|
||||
|
||||
long[] fileStartEnd = getFileStartEnd(cpxFile.get(i));
|
||||
|
||||
while (importedClicks>0 || importedClicks==-1) {
|
||||
|
||||
|
||||
|
||||
CPODFileType fileType = CPODUtils.getFileType(cpxFile.get(i));
|
||||
|
||||
this.updateMessage(("Importing from " + fileType + " " + i + " of " + cpxFile.size()));
|
||||
|
||||
System.out.println(("Importing from " + fileType + " " + i + " of " + cpxFile.size() + " from detection " + nClicks));
|
||||
|
||||
this.updateMessage(("Importing from " + fileType + " " + i + " of " + cpxFile.size() + " from detection " + nClicks));
|
||||
|
||||
//import the CPOD or FPOD data
|
||||
this.updateProgress(-1, 1);
|
||||
importedClicks = importFile(cpxFile.get(i), tempCPODDataBlock, clickTrainDataBlock, nClicks, MAX_SAVE);
|
||||
|
||||
|
||||
System.out.println("Number of CPOD data units in the data block: " + tempCPODDataBlock.getUnitsCount() + " progress: " + (i+1) + " " + cpxFile.size() );
|
||||
|
||||
|
||||
ListIterator<CPODClick> iterator = tempCPODDataBlock.getListIterator(0);
|
||||
|
||||
|
||||
//save the click trains to the database
|
||||
clickTrainDataBlock.saveViewerData();
|
||||
|
||||
|
||||
//save the raw clicks to the binary file.s
|
||||
CPODClick click;
|
||||
double day = -1;
|
||||
@ -400,48 +374,67 @@ public class CPODImporter {
|
||||
while (iterator.hasNext()) {
|
||||
if (this.isCancelled()) return -1;
|
||||
click = iterator.next();
|
||||
count++;
|
||||
|
||||
//System.out.println("Saving click: " + click.getUID());
|
||||
System.out.println("Saving click: " + click.getUID());
|
||||
|
||||
//new binary file every daya;
|
||||
cal.setTimeInMillis(click.getTimeMilliseconds());
|
||||
int dayYear = cal.get(Calendar.DAY_OF_YEAR);
|
||||
|
||||
if (day!=dayYear) {
|
||||
this.updateProgress(i+(count/(double) importedClicks), cpxFile.size());
|
||||
|
||||
if (day!=dayYear) {
|
||||
|
||||
//set the progress
|
||||
double progress=(((double) click.getTimeMilliseconds()-fileStartEnd[0]))/(fileStartEnd[1]-fileStartEnd[0]);
|
||||
this.updateProgress(i+(progress), cpxFile.size());
|
||||
|
||||
|
||||
if (day>-1) {
|
||||
|
||||
//save left over CP1 data
|
||||
if (cpodTrainList!=null) {
|
||||
//all duplicate clicks will have been removed. Save the data now
|
||||
for (int j=0; j<cpodTrainList.size(); j++) {
|
||||
data = cpodDataBlock.getBinaryDataSource().getPackedData(cpodTrainList.get(j));
|
||||
this.binaryStream.storeData(data.getObjectType(), click.getBasicData(), data);
|
||||
}
|
||||
System.out.println("HAVE REMOVED " + count + " CP1 detections: " + cpodTrainList.size());
|
||||
count = 0;
|
||||
}
|
||||
|
||||
//close current file
|
||||
binaryStream.writeModuleFooter();
|
||||
binaryStream.writeFooter(click.getTimeMilliseconds(), System.currentTimeMillis(), BinaryFooter.END_UNKNOWN);
|
||||
binaryStream.closeFile();
|
||||
binaryStream.createIndexFile();
|
||||
|
||||
|
||||
}
|
||||
|
||||
System.out.println("Open new binary file: " + PamCalendar.formatDBDateTime(click.getTimeMilliseconds()));
|
||||
|
||||
|
||||
//send an update message
|
||||
final String timeMillisStr = PamCalendar.formatDBDateTime(click.getTimeMilliseconds());
|
||||
Platform.runLater(()->{
|
||||
this.updateMessage(("Saving file: " + timeMillisStr));
|
||||
});
|
||||
|
||||
|
||||
//get a list of the currently loaded click data if this is CP3 data
|
||||
if (fileType.equals(CPODFileType.CP3) || fileType.equals(CPODFileType.FP3)) {
|
||||
|
||||
cpodDataBlock.clearAll();
|
||||
|
||||
//load the view from the data block for that day.
|
||||
long millisDayStart = roundToDay(click.getTimeMilliseconds());
|
||||
cpodDataBlock.loadViewerData(millisDayStart, millisDayStart+24*60*60*1000L-1, null);
|
||||
|
||||
|
||||
cpodDataBlock.clearAll();
|
||||
|
||||
//load the view from the data block for that day.
|
||||
long millisDayStart = roundToDay(click.getTimeMilliseconds());
|
||||
cpodDataBlock.loadViewerData(millisDayStart, millisDayStart+24*60*60*1000L-1, null);
|
||||
|
||||
//now the tricky bit - if we are loading viewer files we want to save the data from the CP3 on top of the
|
||||
//CP1 file but we DO NOT want to add in duplicate clicks.
|
||||
if (cpodDataBlock.getUnitsCount()>0) {
|
||||
System.out.println("There are already data units from CP1 or FP1 files " + cpodDataBlock.getUnitsCount());
|
||||
//TODO
|
||||
cpodTrainList = cpodDataBlock.getDataCopy();
|
||||
Collections.sort(cpodTrainList, new CPODClickOmparator());
|
||||
cpodDataBlock.clearAll(); //just incase
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
//write the module head
|
||||
@ -452,31 +445,70 @@ public class CPODImporter {
|
||||
day=dayYear;
|
||||
}
|
||||
|
||||
if (cpodTrainList!=null && cpodTrainList.size()>0) {
|
||||
// index of the target
|
||||
int index = Collections.binarySearch(
|
||||
cpodTrainList, click, new CPODClickOmparator());
|
||||
|
||||
if (index>-1) {
|
||||
//the click in the cp3 file is present in the CP1 file. Save this click as it has a super detection. DO NOT save the
|
||||
//CP1 click;
|
||||
cpodTrainList.remove(index);
|
||||
count++;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
data = cpodDataBlock.getBinaryDataSource().getPackedData(click);
|
||||
this.binaryStream.storeData(data.getObjectType(), click.getBasicData(), data);
|
||||
}
|
||||
|
||||
|
||||
cpodDataBlock.clearAll();
|
||||
tempCPODDataBlock.clearAll();
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
//update number of clicks.
|
||||
nClicks=nClicks+MAX_SAVE+1;
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
}
|
||||
catch (Exception e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
|
||||
this.updateMessage("Finished saving data units: ");
|
||||
|
||||
this.updateMessage("Finished saving detections");
|
||||
System.out.println("CPOD import thread finished: " + this);
|
||||
|
||||
return 1;
|
||||
}
|
||||
|
||||
|
||||
private long[] getFileStartEnd(File file) {
|
||||
CPODFileType fileType = CPODUtils.getFileType(file);
|
||||
|
||||
long[] timelims = null;
|
||||
switch (fileType){
|
||||
case CP1:
|
||||
case CP3:
|
||||
//TODO
|
||||
break;
|
||||
case FP1:
|
||||
case FP3:
|
||||
FPODHeader header =FPODReader.readHeader(file);
|
||||
if (header==null) return null;
|
||||
timelims=new long[] {CPODUtils.podTimeToMillis(header.FirstLoggedMin), CPODUtils.podTimeToMillis(header.LastLoggedMin)};
|
||||
break;
|
||||
default:
|
||||
break;
|
||||
|
||||
}
|
||||
|
||||
return timelims;
|
||||
}
|
||||
|
||||
|
||||
|
||||
/**
|
||||
* Rounds millis to start of da=y
|
||||
* @param millis
|
||||
@ -484,16 +516,16 @@ public class CPODImporter {
|
||||
*/
|
||||
long roundToDay(long millis) {
|
||||
Date date = new Date(millis);
|
||||
Calendar calendar = Calendar.getInstance();
|
||||
calendar.setTime(date);
|
||||
calendar.set(Calendar.HOUR_OF_DAY, 0);
|
||||
calendar.set(Calendar.MINUTE, 0);
|
||||
calendar.set(Calendar.SECOND, 0);
|
||||
calendar.set(Calendar.MILLISECOND, 0);
|
||||
return calendar.getTimeInMillis();
|
||||
Calendar calendar = Calendar.getInstance();
|
||||
calendar.setTime(date);
|
||||
calendar.set(Calendar.HOUR_OF_DAY, 0);
|
||||
calendar.set(Calendar.MINUTE, 0);
|
||||
calendar.set(Calendar.SECOND, 0);
|
||||
calendar.set(Calendar.MILLISECOND, 0);
|
||||
return calendar.getTimeInMillis();
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
/**
|
||||
* Import a FPOD file.
|
||||
* @param cpFile - the FP1 or FP3 file.
|
||||
@ -502,65 +534,65 @@ public class CPODImporter {
|
||||
* @return the total number of clicks in the file.
|
||||
*/
|
||||
protected int importFPODFile(File cpFile, CPODClickDataBlock dataBlock, CPODClickTrainDataBlock clickTrainDataBlock, int from, int maxNum) {
|
||||
|
||||
|
||||
ArrayList<FPODdata> fpodData = new ArrayList<FPODdata>();
|
||||
|
||||
|
||||
try {
|
||||
FPODReader.importFile(cpFile, fpodData, from, maxNum);
|
||||
|
||||
// fileStart + nMinutes * 60000L;
|
||||
|
||||
HashMap<Integer, CPODClickTrainDataUnit> cpodClickTrains = new HashMap<Integer, CPODClickTrainDataUnit>();
|
||||
|
||||
int nClicks = 0;
|
||||
for (int i=0; i<fpodData.size(); i++) {
|
||||
if (i%40000 ==0) {
|
||||
System.out.println("Create a new CPOD click: " + i + " of " + fpodData.size() + PamCalendar.formatDateTime(fpodData.get(i).getTimeMillis()));
|
||||
}
|
||||
CPODClick cpodClick = processFPODClick(fpodData.get(i));
|
||||
dataBlock.addPamData(cpodClick);
|
||||
|
||||
if (fpodData.get(i).getClassification()!=null) {
|
||||
CPODClickTrainDataUnit clickTrain = cpodClickTrains.get(fpodData.get(i).getClassification().clicktrainID);
|
||||
if (clickTrain==null) {
|
||||
clickTrain= new CPODClickTrainDataUnit(cpodClick.getTimeMilliseconds(), null, fpodData.get(i).getClassification());
|
||||
cpodClickTrains.put(fpodData.get(i).getClassification().clicktrainID, clickTrain);
|
||||
|
||||
// fileStart + nMinutes * 60000L;
|
||||
|
||||
HashMap<Integer, CPODClickTrainDataUnit> cpodClickTrains = new HashMap<Integer, CPODClickTrainDataUnit>();
|
||||
|
||||
int nClicks = 0;
|
||||
for (int i=0; i<fpodData.size(); i++) {
|
||||
if (i%40000 ==0) {
|
||||
System.out.println("Create a new CPOD click: " + i + " of " + fpodData.size() + PamCalendar.formatDateTime(fpodData.get(i).getTimeMillis()));
|
||||
}
|
||||
clickTrain.addSubDetection(cpodClick);
|
||||
CPODClick cpodClick = processFPODClick(fpodData.get(i));
|
||||
dataBlock.addPamData(cpodClick);
|
||||
|
||||
if (fpodData.get(i).getClassification()!=null) {
|
||||
CPODClickTrainDataUnit clickTrain = cpodClickTrains.get(fpodData.get(i).getClassification().clicktrainID);
|
||||
if (clickTrain==null) {
|
||||
clickTrain= new CPODClickTrainDataUnit(cpodClick.getTimeMilliseconds(), null, fpodData.get(i).getClassification());
|
||||
cpodClickTrains.put(fpodData.get(i).getClassification().clicktrainID, clickTrain);
|
||||
}
|
||||
clickTrain.addSubDetection(cpodClick);
|
||||
}
|
||||
nClicks++;
|
||||
}
|
||||
nClicks++;
|
||||
}
|
||||
|
||||
System.out.println("Add click train to datablock: ");
|
||||
|
||||
//add all the click trains with sub detections ot the datablock.
|
||||
int count =0;
|
||||
for (Integer key: cpodClickTrains.keySet()) {
|
||||
|
||||
if (count%100 == 0) {
|
||||
this.updateMessage(("Add click train data to datablock: " + count + " of " + cpodClickTrains.keySet().size()));
|
||||
this.updateProgress(count, cpodClickTrains.keySet().size());
|
||||
// System.out.println("Add click train data to datablock: " + count + " " + cpodClickTrains.keySet().size());
|
||||
System.out.println("Add click train to datablock: ");
|
||||
|
||||
//add all the click trains with sub detections ot the datablock.
|
||||
int count =0;
|
||||
for (Integer key: cpodClickTrains.keySet()) {
|
||||
|
||||
if (count%100 ==0) {
|
||||
this.updateMessage(("Add click train data to datablock: " + count + " of " + cpodClickTrains.keySet().size()));
|
||||
this.updateProgress(count, cpodClickTrains.keySet().size());
|
||||
|
||||
// System.out.println("Add click train data to datablock: " + count + " " + cpodClickTrains.keySet().size());
|
||||
}
|
||||
|
||||
clickTrainDataBlock.addPamData(cpodClickTrains.get(key));
|
||||
count++;
|
||||
}
|
||||
|
||||
|
||||
clickTrainDataBlock.addPamData(cpodClickTrains.get(key));
|
||||
count++;
|
||||
}
|
||||
|
||||
System.out.println("Finished adding click train to datablock: ");
|
||||
System.out.println("Finished adding click train to datablock: ");
|
||||
|
||||
|
||||
fpodData=null; //trigger garbage collector if needed
|
||||
|
||||
return nClicks;
|
||||
|
||||
fpodData=null; //trigger garbage collector if needed
|
||||
|
||||
return nClicks;
|
||||
|
||||
} catch (Exception e) {
|
||||
e.printStackTrace();
|
||||
return 0;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Import a CPOD or FPOD file.
|
||||
* @param cpFile - the CP1/FP1 or CP3/FP3 file.
|
||||
@ -570,7 +602,7 @@ public class CPODImporter {
|
||||
*/
|
||||
protected int importFile(File cpFile, CPODClickDataBlock dataBlock, CPODClickTrainDataBlock clickTrainDataBlock, int from, int maxNum) {
|
||||
CPODFileType fileType = CPODUtils.getFileType( cpFile);
|
||||
|
||||
|
||||
switch (fileType) {
|
||||
case CP1:
|
||||
case CP3:
|
||||
@ -579,11 +611,11 @@ public class CPODImporter {
|
||||
case FP3:
|
||||
return importFPODFile(cpFile, dataBlock, clickTrainDataBlock, from, maxNum);
|
||||
}
|
||||
|
||||
|
||||
return 0;
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Import a file.
|
||||
* @param cpFile - the CP1 file.
|
||||
@ -593,9 +625,29 @@ public class CPODImporter {
|
||||
return importFile( cpFile, dataBlock, clickTrainDataBlock, -1, Integer.MAX_VALUE);
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
||||
// Comparator to sort a list
|
||||
class CPODClickOmparator implements Comparator<CPODClick> {
|
||||
@Override public int compare(CPODClick s1, CPODClick s2)
|
||||
{
|
||||
if (s1.getTimeMilliseconds() > s2.getTimeMilliseconds()) {
|
||||
return 1;
|
||||
}
|
||||
else if (s1.getTimeMilliseconds() < s2.getTimeMilliseconds()) {
|
||||
return -1;
|
||||
}
|
||||
else if (s1.getTimeMilliseconds() == s2.getTimeMilliseconds()) {
|
||||
|
||||
if (s1.getStartSample()>s2.getStartSample()) return 1;
|
||||
else if (s1.getStartSample()<s2.getStartSample()) return -1;
|
||||
else return 0;
|
||||
}
|
||||
return -1;
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
@ -71,6 +71,34 @@ public class FPODReader {
|
||||
|
||||
public static final float FPOD_WAV_SAMPLERATE = 1000000;
|
||||
|
||||
public static FPODHeader readHeader(File cpFile) {
|
||||
|
||||
BufferedInputStream bis = null;
|
||||
int bytesRead;
|
||||
FileInputStream fileInputStream = null;
|
||||
int totalBytes = 0;
|
||||
try {
|
||||
bis = new BufferedInputStream(fileInputStream = new FileInputStream(cpFile));
|
||||
} catch (FileNotFoundException e) {
|
||||
e.printStackTrace();
|
||||
return null;
|
||||
}
|
||||
|
||||
FPODHeader header = new FPODHeader();
|
||||
try {
|
||||
if (readHeader(bis, header) != FPOD_HEADER) {
|
||||
return null;
|
||||
}
|
||||
bis.close();
|
||||
} catch (IOException e) {
|
||||
// TODO Auto-generated catch block
|
||||
e.printStackTrace();
|
||||
}
|
||||
|
||||
return header;
|
||||
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Import an FPOD file.
|
||||
@ -110,13 +138,13 @@ public class FPODReader {
|
||||
|
||||
//keep track of wav data
|
||||
FPODWavData wavData = null;
|
||||
|
||||
|
||||
//holds a map of the click train detections.
|
||||
HashMap<Integer, CPODClassification> clickTrains = new HashMap<Integer, CPODClassification>();
|
||||
|
||||
|
||||
//the click train of the current data unit.
|
||||
CPODClassification cpodClassification = null;
|
||||
|
||||
|
||||
int wavbufpos = 0;
|
||||
try {
|
||||
while (true) {
|
||||
@ -299,7 +327,7 @@ public class FPODReader {
|
||||
wavData = null;
|
||||
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Set the classification (if FP3 file)
|
||||
*/
|
||||
@ -324,7 +352,7 @@ public class FPODReader {
|
||||
|
||||
}
|
||||
else if (toUnsigned(bufPosN[0])==250) {
|
||||
|
||||
|
||||
//wav data preceedes the next click
|
||||
|
||||
if (wavData==null) {
|
||||
@ -357,49 +385,49 @@ public class FPODReader {
|
||||
//wav data
|
||||
nWavClicks++;
|
||||
}
|
||||
|
||||
|
||||
else if(toUnsigned(bufPosN[0])==249) {
|
||||
//click train data - this is not included - for now
|
||||
//click train data precedes the next click
|
||||
|
||||
|
||||
//the train ID is unique to the minute,
|
||||
short trainID = toUnsigned(bufPosN[15]);
|
||||
|
||||
|
||||
//1 is NBHF
|
||||
//2 is dolphin
|
||||
//3 is uncalssified
|
||||
//4 is sonar?
|
||||
short species = (short) ((bufPosN[14] >>> 2) & 3);
|
||||
|
||||
|
||||
//quality level for the click train
|
||||
short qualitylevel = (short) ((bufPosN[14]) & 3);
|
||||
|
||||
boolean echo = false;
|
||||
if ((bufPosN[14] & 32) == 32) {
|
||||
echo = true;
|
||||
echo = true;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
//generate a unique train ID within the file
|
||||
int trainUID = Integer.valueOf(String.format("%06d", nMinutes) + String.format("%d", trainID));
|
||||
|
||||
|
||||
//find the click train from the hash map - if it is not there, create a new one.
|
||||
cpodClassification = clickTrains.get(trainUID);
|
||||
|
||||
cpodClassification = clickTrains.get(trainUID);
|
||||
|
||||
if (cpodClassification==null) {
|
||||
cpodClassification = new CPODClassification();
|
||||
cpodClassification.isEcho = echo;
|
||||
cpodClassification.clicktrainID = trainUID;
|
||||
cpodClassification.species = CPODUtils.getSpecies(species);
|
||||
|
||||
|
||||
|
||||
clickTrains.put(trainUID, cpodClassification);
|
||||
|
||||
|
||||
//System.out.println("Click train ID: " + trainUID + " minutes: " + nMinutes + " species: " + species + " quality level: " + qualitylevel);
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
}
|
||||
else if(toUnsigned(bufPosN[0])==254){
|
||||
nMinutes ++;
|
||||
@ -982,7 +1010,7 @@ public class FPODReader {
|
||||
public int minute;
|
||||
|
||||
private FPODWavData wavData;
|
||||
|
||||
|
||||
//******Click Train Info******//
|
||||
|
||||
|
||||
@ -1000,7 +1028,7 @@ public class FPODReader {
|
||||
public void setClassification(CPODClassification cpodClassification) {
|
||||
this.cpodClassification=cpodClassification;
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Get the species classification i.e. which click train the click belongs to.
|
||||
* @return the species classification object.
|
||||
@ -1323,8 +1351,8 @@ public class FPODReader {
|
||||
if (MHzArrPtr < MhzSampledArr.length) {
|
||||
MhzSampledArr[MHzArrPtr] = 0;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
int[] waveform = Arrays.copyOf(MhzSampledArr, MHzArrPtr);
|
||||
//waveform is backwards so flip it.
|
||||
@ -1340,7 +1368,7 @@ public class FPODReader {
|
||||
// String filePath = "/Users/au671271/Library/CloudStorage/GoogleDrive-macster110@gmail.com/My Drive/PAMGuard_dev/CPOD/FPOD_NunBank/0866 NunBankB 2023 06 27 FPOD_6480 file0.FP1";
|
||||
|
||||
String filePath = "D:\\DropBox\\PAMGuard_dev\\CPOD\\FPOD_NunBank\\0866 NunBankB 2023 06 27 FPOD_6480 file0.FP1";
|
||||
// String filePath = "D:\\DropBox\\PAMGuard_dev\\CPOD\\FPOD_NunBank\\0866 NunBankB 2023 06 27 FPOD_6480 file0.FP3";
|
||||
// String filePath = "D:\\DropBox\\PAMGuard_dev\\CPOD\\FPOD_NunBank\\0866 NunBankB 2023 06 27 FPOD_6480 file0.FP3";
|
||||
|
||||
File fpfile = new File(filePath);
|
||||
|
||||
|
||||
Loading…
Reference in New Issue
Block a user