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script to compare absolute time domain signal of CPMG and echoes #100

Closed guinneak198 closed 4 months ago

jmfranck commented 4 months ago

what this shows for the CPMG is very confusing -- the first step to diagnose would be to see how much signal is in all the pathways:

# do this after squashing t2 and echoes:
s_cohsize = abs(s).mean_all_but(['t2']+[j for j in s.dimlabels if j.startswith('ph')])

and also select out just the two pathways and see what they look like:

s['ph_overall',-1]['ph2',2]['ph1',r_[1,-1]].reorder('nEchoes',first=False) # put echoes on the inside so they show up along x

note that I fixed the above last night 7/2 -- I'm still asking the question below, though

Did you really run with only 4 echoes? That's all that was allowed b/c of the phase cycling?

jmfranck commented 4 months ago

note that I deliberately didn't run black on the whole file -- leading to these flake errors. That was to keep the diffs minimal so you could see what I'm doing.

Obviously, you'll want to run black when getting it ready to merge