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-rw-r--r--fly-tools/FlyTrackingMain.cpp110
-rwxr-xr-xprocess-video-beta3
2 files changed, 63 insertions, 50 deletions
diff --git a/fly-tools/FlyTrackingMain.cpp b/fly-tools/FlyTrackingMain.cpp
index 4114a08..2e963a8 100644
--- a/fly-tools/FlyTrackingMain.cpp
+++ b/fly-tools/FlyTrackingMain.cpp
@@ -1976,7 +1976,7 @@ void processASequence(int startOfATrackSequence, int endOfATrackSequence) {
vector<FlyObject > fOVector = currentFI.getFOVector();
FlyObject cFFirstFO = fOVector[0];
FlyObject cFSecondFO = fOVector[1];
-
+
sequenceFirstAverage += cFFirstFO.getArea();
sequenceSecondAverage += cFSecondFO.getArea();
@@ -2021,22 +2021,55 @@ ofstream foutSt;
ofstream foutDebugCen;
ofstream foutDebugSpeed;
-int main(int argc, char* argv[])
+int main(int argc, char **argv)
{
- if (argc < 5)
- {
- cerr << "Usage: executablename <inputFile.txt> <originalImagePath> <finalOutputPath> <maskImagePath> <outputFilePrefix>" << endl; // input file contains name of the
- // input image files
- return -1;
- }
-
- MagickCore::SetMagickResourceLimit(MagickCore::MemoryResource, 1536);
- MagickCore::SetMagickResourceLimit(MagickCore::MapResource, 4092);
-
- string ifns(argv[1]);
- inputFileName = ifns;
-// cout << "input file name is "<<inputFileName<<endl;
-
+ int c;
+ int writeFinalImages;
+ string usage = "Usage: FlyTracking -i <inputFile.txt> -o <originalImagePath> -f <finalOutputPath> -m <maskImagePath> -O <outputFilePrefix>";
+ string origImagePath;
+ string finalOutputPath;
+ string outputFilePrefix;
+ string maskImagePath;
+ string inputFileName;
+ opterr = 0;
+
+ while ((c = getopt (argc, argv, "i:f:m:p:o:hx")) != -1)
+ switch (c)
+ {
+ case 'i':
+ inputFileName = optarg;
+ break;
+ case 'o':
+ origImagePath = optarg;
+ break;
+ case 'f':
+ finalOutputPath = optarg;
+ break;
+ case 'm':
+ maskImagePath = optarg;
+ break;
+ case 'p':
+ outputFilePrefix = optarg;
+ break;
+ case 'h':
+ cout << usage << endl;
+ exit(1);
+ break;
+ case 'x':
+ writeFinalImages;
+ break;
+ default:
+ break;
+ }
+
+ //MagickCore::SetMagickResourceLimit(MagickCore::MemoryResource, 1536);
+ //MagickCore::SetMagickResourceLimit(MagickCore::MapResource, 4092);
+
+ i
+ if( inputFileName.empty() || origImagePath.empty() || finalOutputPath.empty() || maskImagePath.empty() || outputFilePrefix.empty() ) {
+ cerr << usage << endl;
+ exit(1);
+ }
string fileName;
ifstream inputFile(inputFileName.c_str());
// save the input file name
@@ -2045,25 +2078,8 @@ int main(int argc, char* argv[])
cout << "cannot open the input file that contains name of the input images\n";
exit(1);
}
-
- //cout<<"come here ------------------------- 1"<<endl;
- // set the global paths
- string tempOIP(argv[2]);
- origImagePath = tempOIP;
-
- //cout<<"come here ------------------------- 2"<<endl;
-
- string tempFOP(argv[3]);
- finalOutputPath = tempFOP;
- //cout<<"come here ------------------------- 3"<<endl;
-
- string tempOFP(argv[5]);
- outputFilePrefix = tempOFP;
-
- //cout<<"come here ------------------------- 4"<<endl;
-
- string statFileName = tempFOP + outputFilePrefix + "_statFile.txt";
+ string statFileName = finalOutputPath + outputFilePrefix + "_statFile.txt";
//cout << "Statfilename is "<<statFileName<<endl;
foutSt.open(statFileName.c_str());
if (foutSt.fail()) {
@@ -2072,7 +2088,7 @@ int main(int argc, char* argv[])
}
// debug file
- string foutDebugCenFN = tempFOP + outputFilePrefix + "_statFileDebug.txt";
+ string foutDebugCenFN = finalOutputPath + outputFilePrefix + "_statFileDebug.txt";
foutDebugCen.open(foutDebugCenFN.c_str());
if (foutDebugCen.fail()) {
cout << "cannot open the statDebug file"<<endl;
@@ -2081,15 +2097,14 @@ int main(int argc, char* argv[])
// debug file speed distribution
- string foutDebugSpeedFN = tempFOP + outputFilePrefix + "_speedDebug.txt";
+ string foutDebugSpeedFN = finalOutputPath + outputFilePrefix + "_speedDebug.txt";
foutDebugSpeed.open(foutDebugSpeedFN.c_str());
if (foutDebugSpeed.fail()) {
cout << "cannot open the speedDebug file"<<endl;
exit(1);
}
- string tempMIP(argv[4]);
- maskImagePath = tempMIP;
+
// open the file for statistics
string lPSFileName("LongestPositive.txt");
@@ -2114,10 +2129,10 @@ int main(int argc, char* argv[])
bool currentlyCalculatingHead = true;
-
+
while (inputFile>>fileName) {
-// Image* img = new Image(argv[1]);// = new Image(argv[1]);
+ // Image* img = new Image(argv[1]);// = new Image(argv[1]);
int fi = fileName.find("_");
// current sequence numbers spans from 0 - 18019, so 5 digits are needed
@@ -2136,7 +2151,7 @@ int main(int argc, char* argv[])
cout << "Reading file "<<fileName<<endl;
Image* img = new Image(fileName.c_str());
int width = img->columns(),height = img->rows();
- diagLength= static_cast<int> ( sqrt( (height*height) + (width*width) ) );
+ diagLength= static_cast<int> ( sqrt( (height*height) + (width*width) ) );
//cout << "Diagonal length is "<<diagLength<<endl;
// Image* imgWithInfo;
// imgWithInfo = new Image(fileName.c_str());
@@ -2184,13 +2199,12 @@ int main(int argc, char* argv[])
}
}
-
+
delete img;
-
delete residual;
-// cout<<"Sorting the objects according to size"<<endl;
-// bubbleSort(tempFOV);
+ // cout<<"Sorting the objects according to size"<<endl;
+ // bubbleSort(tempFOV);
fOVector.clear();
@@ -2793,8 +2807,8 @@ void drawTheFlyObject(FrameInfo currentFI, string fileName, int isFirst, bool si
bool eVDirection = currentFO.getHeadIsInDirectionMAEV();
// debug:
- cout<<"Calling the findTheStartPoint() function"<<endl;
- cout<<"Female size "<<femaleSize<<" maleSize "<<maleSize<<" MaleCentroid = "<<centroid.first<<", "<<centroid.second<<endl;
+ //cout<<"Calling the findTheStartPoint() function"<<endl;
+ //cout<<"Female size "<<femaleSize<<" maleSize "<<maleSize<<" MaleCentroid = "<<centroid.first<<", "<<centroid.second<<endl;
// initialize the flag with false for the next found of findTheStartPoint()
isFoundStartPoint = false;
@@ -2837,7 +2851,7 @@ void drawTheFlyObject(FrameInfo currentFI, string fileName, int isFirst, bool si
bool eVDirection = currentFO.getHeadIsInDirectionMAEV();
- double ev_x, ev_y;
+ //double ev_x, ev_y;
// draw the female when tracked by the male fly
if (isHitting == 1) {
diff --git a/process-video-beta b/process-video-beta
index e37980e..97aeffa 100755
--- a/process-video-beta
+++ b/process-video-beta
@@ -202,7 +202,7 @@ while read crop; do
cd $output_dir
#parallel -i FlyTrackingIterativeFilter {} 15 $output_dir/Masks/$setname/Masks/ $output_dir/Filtered/$setname/ -- $( ls $output_dir/Masks/$setname/Masks/ )
- ls $output_dir/Masks/$setname/Masks/ | parallel -v -j +0 -S $server_list /site/kuiper/jcm357/FlyTrackingIterativeFilter {} 15 $output_dir/Masks/$setname/Masks/ $output_dir/Filtered/$setname/
+ ls $output_dir/Masks/$setname/Masks/ | parallel -v -j +0 -S $server_list /site/kuiper/jcm357/FilterFlyMask {} 15 $output_dir/Masks/$setname/Masks/ $output_dir/Filtered/$setname/
i=$(( $i + 1 ))
done < $crop_file
@@ -227,4 +227,3 @@ done < $crop_file
wait
fi
-echo "Finished"
generated by cgit v1.2.3 (git 2.39.1) at 2025-02-23 13:24:31 +0000