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LEK SI2Conc edit #130

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LEK SI2Conc edit #130

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c0ab6af
LEK SI2Conc edit
LucyKershaw May 2, 2023
d9f96e4
Merge branch 'develop' into LEK_Contribution_edit_SI2Conc
notZaki Sep 5, 2023
a06ff8e
Update import
notZaki Sep 5, 2023
0b1c6ab
Delete test/SI_to_Conc/test_SI2Conc_LEK_EdinburghUK.py
stadmill Sep 5, 2023
1b18536
Use newer API for LEK SI2Conc
notZaki Sep 5, 2023
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8 changes: 4 additions & 4 deletions src/original/LEK_UoEdinburgh_UK/SignalToConcentration/SI2Conc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,17 +11,17 @@

# Inputs:
# SIcurve numpy array of SI values
# TR TR for FLAHS sequence, in seconds
# TR TR for FLASH sequence, in seconds
# flip Flip angle for FLASH sequence in degrees
# T1base Native T1 corresponding to the baseline signal intensity, in seconds
# baselinepts Number of data points before the arrival of contrast agent
# baselinepts Range of data points to be used for baseline, indexes to start and end at [start,end]
# S0 Equilibrium signal, if known. Default is to calculate it here

# Output:
#H numpy array of curve as delta R1 in s^-1


def SI2Conc(SIcurve,TR,flip,T1base,baselinepts,S0=None):
def SI2Conc(SIcurve,TR,flip,T1base,baselinepts_range,S0=None):

# Convert flip angle to radians
rflip=flip*np.pi/180
Expand All @@ -31,7 +31,7 @@ def SI2Conc(SIcurve,TR,flip,T1base,baselinepts,S0=None):

# If S0 isn't specified, calculate from baseline
if S0 is None:
SIbase=np.mean(SIcurve[1:baselinepts])
SIbase=np.mean(SIcurve[baselinepts_range[0]:baselinepts_range[1]])
S0=CalcM0(SIbase,TR,flip,T1base)

# Now calculate the R1 curve
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2 changes: 1 addition & 1 deletion test/SI_to_Conc/test_SI2Conc_LEK_Edinburgh_UK.py
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Expand Up @@ -32,7 +32,7 @@ def test_LEK_UoEdinburgh_UK_SI2Conc(label, fa, tr, T1base, BLpts, r1, s_array, c

# run test
tic = perf_counter()
conc_curve = SI2Conc.SI2Conc(s_array,tr,fa,T1base,BLpts,S0=None)
conc_curve = SI2Conc.SI2Conc(s_array,tr,fa,T1base,[1,BLpts],S0=None)
exc_time = 1e6 * (perf_counter() - tic)

# log results
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