Processing functions on RawAcquisitionData

[aTrotier]

I will create a PR that add the following function acting on RawAcquisitionData object :

Subset of profiles

A function that return subset of profile according to flag. For example if I want to create a raw object only with the [ACQ_IS_PARALLEL_CALIBRATION,ACQ_IS_PARALLEL_CALIBRATION_AND_IMAGING] : raw_subset(raw,ACQ_IS_PARALLEL_CALIBRATION+ACQ_IS_PARALLEL_CALIBRATION_AND_IMAGING) or raw_subset(raw,["ACQ_IS_PARALLEL_CALIBRATION","ACQ_IS_PARALLEL_CALIBRATION_AND_IMAGING"])

Remove readout oversampling

function remove_oversampling!(raw)
ratioFOV = raw.params["encodedFOV"][1] / raw.params["reconFOV"][1]

# Assuming all profiles have the same size
sdim = size(raw.profiles[1].data)
sdim_out = Int(sdim[1] / ratioFOV)
start = Int((sdim[1] - sdim_out) ÷ 2)

Threads.@threads for profile in raw.profiles
    tmp = profile.data
    tmp = ifftshift(ifft(ifftshift(tmp, 1), 1), 1)
    @views tmp = tmp[start:start+sdim_out, :]
    tmp = fftshift(fft(fftshift(tmp, 1), 1), 1)
    
    profile.data = tmp
    profile.head.number_of_samples = sdim_out
    profile.head.center_sample = UInt16(profile.head.center_sample / ratioFOV)
    profile.head.discard_pre = UInt16(profile.head.discard_pre / ratioFOV)
    profile.head.discard_post = UInt16(profile.head.discard_post / ratioFOV)
end
raw.params["encodedSize"][1] = raw.params["encodedSize"][1] ÷ ratioFOV
return raw

end

Coil compression on RawAcquisitionData

SVD calculation will be done on calibration profiles ?

Any other idea about function that acts on RawAcquisitionData ?

[aTrotier]

Ongoing implementation : #232

[aTrotier]

Hmm,
I am now able to filter the acquisition by FLAGS but I think we also need a function to create an "IMAGING" datasets. Any idea how to do that ?

Something like :

function remove_raw_by_flags(rawData::RawAcquisitionData, flags= [ACQ_IS_NOISE_MEASUREMENT,
       ACQ_IS_PARALLEL_CALIBRATION,
       ACQ_IS_NAVIGATION_DATA,
       ACQ_IS_PHASECORR_DATA],
       ACQ_IS_DUMMYSCAN_DATA,     
      ACQ_IS_PHASE_STABILIZATION_REFERENCE,
       ACQ_IS_PHASE_STABILIZATION) 

# return profiles that are not flags
end

I am not sure about the default flags we should remove

       ACQ_IS_NOISE_MEASUREMENT,
       ACQ_IS_PARALLEL_CALIBRATION,
       ACQ_IS_PARALLEL_CALIBRATION_AND_IMAGING, #we should keep it
       ACQ_IS_REVERSE, # we should keep it
       ACQ_IS_NAVIGATION_DATA,
       ACQ_IS_PHASECORR_DATA,
       ACQ_IS_HPFEEDBACK_DATA,
       ACQ_IS_DUMMYSCAN_DATA,
       ACQ_IS_RTFEEDBACK_DATA,
       ACQ_IS_SURFACECOILCORRECTIONSCAN_DATA, #we should keep it
       ACQ_IS_PHASE_STABILIZATION_REFERENCE,
       ACQ_IS_PHASE_STABILIZATION,

@mrikasper Do you have an opinion about it ?