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Add noiseEstimate function #157

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Add noiseEstimate function #157

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53846e6
add function to calculate noise estimate
jusack Dec 17, 2025
7ea0d0f
write noise estimate to file on calib post processing
jusack Dec 17, 2025
0c5f715
Merge branch 'JA/positions+interpolation' into JA/noise-estimate
jusack Dec 17, 2025
2e57f43
only try to read from MDF files
jusack Dec 17, 2025
d0d2cfa
Merge remote-tracking branch 'origin/master' into JA/noise-estimate
jusack Dec 19, 2025
b20336e
fix keywords
jusack Jan 13, 2026
05c67bd
add fast path for system matrices
jusack Feb 26, 2026
62cf069
Merge remote-tracking branch 'origin/master' into JA/noise-estimate
jusack Jun 25, 2026
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2 changes: 2 additions & 0 deletions src/Conversion.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -243,6 +243,7 @@ function calibPostProcessing(f, params=Dict{Symbol,Any}(); frames=1:acqNumFrames
@info "calculate SNR"
snr = calculateSystemMatrixSNR(f, data, numPeriodAverages=numPeriodAverages, numPeriodGrouping=numPeriodGrouping)
end
setparam!(params, :noiseEstimate, noiseEstimate(f)) # TODO, check if it is worth it to integrate into calculateSystemMatrixSNR to save time
setparam!(params, :calibSNR, snr)

# apply frame selection
Expand Down Expand Up @@ -1007,4 +1008,5 @@ function saveasMDF(file::HDF5.File, params::Dict{Symbol,Any})
end

writeIfAvailable(file, "/custom/auxiliaryData", params, :auxiliaryData)
writeIfAvailable(file, "/custom/noiseEstimate", params, :noiseEstimate)
end
26 changes: 25 additions & 1 deletion src/Derived.jl
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Expand Up @@ -2,7 +2,7 @@ export acqNumFGFrames, acqNumBGFrames, acqOffsetFieldShift, acqFramePeriod,
acqNumPeriods, acqNumPatches, acqNumPeriodsPerPatch, acqFov,
acqGradientDiag,
rxNumFrequencies, rxFrequencies, rxTimePoints,
measFGFrameIdx, measBGFrameIdx, measBGFrameBlockLengths
measFGFrameIdx, measBGFrameIdx, measBGFrameBlockLengths, noiseEstimate

rxNumFrequencies(f::MPIFile, numPeriodGrouping=1) = length(rfftfreq(rxNumSamplingPoints(f)*numPeriodGrouping))

Expand Down Expand Up @@ -133,4 +133,28 @@ function measDataFD(f, frames=1:acqNumFrames(f), periods=1:acqNumPeriodsPerFrame
end

return dataFD
end

function noiseEstimate(f::MPIFile; frequencies=nothing, numPeriodGrouping=1, numPeriodAverages=1, kwargs...)
if hasfield(typeof(f), :file) && haskey(f.file, "/custom/noiseEstimate") && numPeriodGrouping==1 && numPeriodAverages==1
if !isnothing(frequencies)
return f["/custom/noiseEstimate"][frequencies]
else
return f["/custom/noiseEstimate"]
end
else
# Efficient shortcut useful for noise whitening during reconstruction
if measIsCalibProcessed(f) && numPeriodGrouping==1 && numPeriodAverages==1
data_ = measDataRaw(f)
if !measIsFastFrameAxis(f)
data_ = permutedims(data_, [4, 1, 2, 3])
end
if !isnothing(frequencies)
return std(data_[measBGFrameIdx(f), frequencies, :],dims=1)[1,:,]
else
return std(data_[measBGFrameIdx(f), :, :, :],dims=1)[1,:,:,]
end
end
return std(getMeasurementsFD(f, false, frequencies=frequencies, frames=measBGFrameIdx(f), numPeriodAverages=numPeriodAverages, numPeriodGrouping=numPeriodGrouping, bgCorrection = false; kwargs...),dims=(3,4))[:,:,1,1]
end
end
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