Reference Code - Githubissues

I managed to identify and fix the bug mentioned in issue #34. I uploaded the current code to the reference branch in the reference directory. There seemed to be two problems in the singlePhotonDetector.h file:

for some reason it crashed when allocating the variable double var[ny][nx] on the stack. The current workaround is to allocate this matrix on the heap like this (lines 336-338):
```
double **val = new double *[ny];
for (int i = 0; i < ny; ++i)
val[i] = new double[nx];
```
and free this at the end (lines 460 - 462) like this:
```
for (int i = 0; i < ny; ++i)
delete[] val[i];
delete[] val;
```
The loops beginning in line 362 iterated over the full detector. In addition to this some inner loops iterate from -(clusterSizeY / 2) to (clusterSizeY / 2) + 1 and are added onto the main index resulting into indices which are outside of the frame by (clusterSizeY / 2). This was fixed by taking these cluster sizes into account in the outer loops like this (lines 362, 363):
```
for (int iy = ymin + (clusterSizeY / 2); iy < ymax - ((clusterSizeY / 2) + 1); iy++) {
for (int ix = xmin + (clusterSizeY / 2); ix < xmax - ((clusterSizeY / 2) + 1); ix++) {
// ...
}
}
```

Additionally, it seems that no frame numbers were stored which was fixed by changing lines 555 to 560 to:

for (int i = 0; i < nph; i++) {
  // save the frame number
  (cl + i)->iframe = fn + i;
  (cl + i)->write(f);
}

To adapt the program to take pedestal input, we also modified moench03ClusterFinder.cpp (see all parts annotated with //NOTE: modified).

Now the program compiles and runs. But generates a very large cluster file with your ordered data set. It was executed like this: ./moenchClusterFinderReordered ../../../ordered outdir e17050_1_00018_00000_image 1 2 ../../../../moench_data/1000_frames_pede_e17050_1_00018_00000.dat

Could you verify that this program still works as intended and if it doesn't give some hints on what went wrong?

Cheers, Jonas

ComputationalRadiationPhysics / jungfrau-photoncounter

Reference Code #54