Need to add a check for compression level 1, when the data is only zlib compressed. This is usually is not the case if you output a sqMass directly from OpenSwathWorkflow. However, if you output a chrom.mzML and then convert the chrom.mzML to chrom.sqMass, then the compression can be set to 1, zlib only, depending on what flags are set inOpenSwathMzMLFileCacher
Can simply add the following in the _returnDataForChromatogram method
import struct
if compr == 1:
tmp = zlib.decompress(d)
result = struct.unpack("<%sd" % (len(tmp) // 8), tmp)
Note: this assumes the data is 64 bit data. I don't think the sqmass stores what type of data the arrays are stored as, but for 32-bit, we could just do result = struct.unpack("<%sd" % (len(tmp) // 4), tmp)
singjc
commented
7 months ago
Need to add a check for compression level 1, when the data is only zlib compressed. This is usually is not the case if you output a sqMass directly from OpenSwathWorkflow. However, if you output a chrom.mzML and then convert the chrom.mzML to chrom.sqMass, then the compression can be set to 1, zlib only, depending on what flags are set in
OpenSwathMzMLFileCacherCan simply add the following in the
_returnDataForChromatogrammethodNote: this assumes the data is 64 bit data. I don't think the sqmass stores what type of data the arrays are stored as, but for 32-bit, we could just do
result = struct.unpack("<%sd" % (len(tmp) // 4), tmp)