Merge branch 'fixup/cellIds' into 'master'

Fixup/cell ids

See merge request !1

AGIPD/correct_agipd_batch.py

@@ -179,10 +179,10 @@ def correct_module(cells, inp):
         infile = h5py.File(filename, "r", driver="core")
         im = np.array(infile["/INSTRUMENT/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/data".format(channel)])
 
-        cellid = np.array(infile["/INSTRUMENT/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/cellId".format(channel)][::2])
-        pulses = np.array(infile["/INSTRUMENT/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/pulseId".format(channel)][::2])
-        trains = np.array(infile["/INSTRUMENT/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/trainId".format(channel)][::2])
-        statii = np.array(infile["/INSTRUMENT/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/status".format(channel)][::2])
+        cellid = np.array(infile["/INSTRUMENT/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/cellId".format(channel)])
+        pulses = np.array(infile["/INSTRUMENT/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/pulseId".format(channel)])
+        trains = np.array(infile["/INSTRUMENT/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/trainId".format(channel)])
+        statii = np.array(infile["/INSTRUMENT/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/status".format(channel)])
 
 
         dont_copy = ["data", "pulseId", "cellId", "trainId", "status"]
@@ -202,11 +202,20 @@ def correct_module(cells, inp):
         infile.visititems(visitor)
         outfile.flush()
 
-        outfile["/INSTRUMENT/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/cellId".format(channel)] = cellid
-        outfile["/INSTRUMENT/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/pulseId".format(channel)] = pulses
-        outfile["/INSTRUMENT/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/trainId".format(channel)] = trains
-        outfile["/INSTRUMENT/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/status".format(channel)] = statii
-
+        fixedCellIds = np.zeros(im.shape[2], cellid.dtype)
+        fixedPulseIds = np.zeros(im.shape[2], pulses.dtype)
+        fixedTrainIds = np.zeros(im.shape[2], trains.dtype)
+        fixedStatii = np.zeros(im.shape[2], statii.dtype)
+        for c in range(im.shape[2]//cells):
+            fixedCellIds[c*cells:(c+1)*cells] = np.squeeze(cellid[c*2*cells:(c+1)*2*cells-cells])
+            fixedPulseIds[c*cells:(c+1)*cells] = np.squeeze(pulses[c*2*cells:(c+1)*2*cells-cells])
+            fixedTrainIds[c*cells:(c+1)*cells] = np.squeeze(trains[c*2*cells:(c+1)*2*cells-cells])
+            fixedStatii[c*cells:(c+1)*cells] = np.squeeze(statii[c*2*cells:(c+1)*2*cells-cells])
+
+        outfile["/INSTRUMENT/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/cellId".format(channel)] = fixedCellIds
+        outfile["/INSTRUMENT/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/pulseId".format(channel)] = fixedPulseIds
+        outfile["/INSTRUMENT/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/trainId".format(channel)] = fixedTrainIds
+        outfile["/INSTRUMENT/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/status".format(channel)] = fixedStatii
         outfile.flush()
         infile.close()