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[FIX] fix for empty scans #28

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[FIX] fix for empty scans #28

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12 changes: 12 additions & 0 deletions src/diapysef/scripts/convertTDFtoMzML.py
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Original file line number Diff line number Diff line change
Expand Up @@ -116,6 +116,10 @@ def store_frame(frame_id, td, conn, exp, verbose=False, compressFrame=True, keep
allmz.append(mz)
allint.append(intens)
allim.append( [drift_time for dr_time in mz] )
if len(mz) == 0 :
allmz.append([0])
allint.append([0])
allim.append( [drift_time for dr_time in [0] ] )

# We have multiple MS2 spectra in each frame, we need to separate
# them based on the information from PasefFrameMsMsInfo which
Expand Down Expand Up @@ -167,6 +171,14 @@ def store_frame(frame_id, td, conn, exp, verbose=False, compressFrame=True, keep
exp.consumeSpectrum(sframe)

def handle_compressed_frame(allmz, allint, allim, mslevel, rtime, center, width):
"""
Store a full frame with N scans as a single MSSpectrum

One spectrum per frame is stored. This puts all peaks into a single
spectrum (while storing the IM data in an extra array). This is more
efficient for storage and allows analysis that is ignorant of the IM
dimension.
"""
mz = np.concatenate(allmz)
intens = np.concatenate(allint)
ims = np.concatenate(allim)
Expand Down