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Updates for GE HBCD Sequence #147

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merged 8 commits into from
Sep 23, 2024
Merged

Updates for GE HBCD Sequence #147

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24197be
Updates for GE HBCD Sequence
agudmundson Sep 10, 2024
21fbc4b
Fixed linting errors for GE updates
agudmundson Sep 12, 2024
26ff5f3
More linting errors for GE updates
agudmundson Sep 12, 2024
fb89169
Numpy Versioning/Deprecation Error - Updates for GE HBCD
agudmundson Sep 12, 2024
e3df106
Updates for GE HBCD
agudmundson Sep 12, 2024
2e5eaaf
Updates for GE HBCD_
agudmundson Sep 12, 2024
3f65719
Updates for GE HBCD - data dimensions
agudmundson Sep 13, 2024
4484c89
Updates for GE HBCD - data dimensions - fixed
agudmundson Sep 13, 2024
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28 changes: 20 additions & 8 deletions spec2nii/GE/ge_pfile.py
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Original file line number Diff line number Diff line change
Expand Up @@ -90,24 +90,30 @@ def _process_svs_pfile(pfile):
:return: List of file name suffixes
"""
psd = pfile.hdr.rhi_psdname.decode('utf-8').lower()
proto = pfile.hdr.rhs_se_desc.decode('utf-8').lower()
if psd == 'hbcd' and "press" in proto:
print('\nPSD was: ', psd)
print('Proto is: ', proto)
psd = pfile.hdr.rhs_se_desc.decode('utf-8').lower()
print('PSD updated to: ', psd)

# MM: Some 'gaba' psd strings contain full path names, so truncate to the end of the path
if psd.endswith('gaba'):
psd = 'gaba'

numecho = pfile.hdr.rhi_numecho

if psd in ('probe-p', 'probe-s', 'probe-p_ach'):
if psd in ('mrs-press', 'probe-p', 'probe-s', 'probe-p_ach'):
data, meta, dwelltime, fname_suffix = _process_probe_p(pfile)
elif psd in ('oslaser', 'slaser_cni') and numecho == 1: # MM: If non-edited data, use _process_oslaser
data, meta, dwelltime, fname_suffix = _process_oslaser(pfile)
elif psd == 'oslaser' and numecho > 1: # MM: If edited data, use _process_gaba
data, meta, dwelltime, fname_suffix = _process_gaba(pfile)
elif psd == 'slaser':
data, meta, dwelltime, fname_suffix = _process_slaser(pfile)
elif psd in ('jpress', 'jpress_ac', 'gaba', 'probe-p-mega_rml', 'repress7'):
elif psd in ('hbcd', 'jpress', 'jpress_ac', 'gaba', 'probe-p-mega_rml', 'repress7'):
data, meta, dwelltime, fname_suffix = _process_gaba(pfile)
elif psd in ('hbcd', 'hbcd1', 'hbcd2'): # ATG
elif psd in ('hbcd2'): # ATG
data, meta, dwelltime, fname_suffix = _process_hbcd(pfile) # ATG
else:
raise UnsupportedPulseSequenceError(f'Unrecognised sequence {psd}.')
Expand Down Expand Up @@ -224,7 +230,7 @@ def _add_editing_info(pfile, meta, data):
edit_rf_freq_off1 = pfile.hdr.rhi_user20
edit_rf_freq_off2 = pfile.hdr.rhi_user21
edit_rf_ppm_off1 = edit_rf_freq_off1 / float(pfile.hdr.rhr_rh_ps_mps_freq * 1E-7)
edit_rf_ppm_off2 = edit_rf_freq_off2 / float(pfile.hdr.rhr_rh_ps_mps_freq * 1E-7)
edit_rf_ppm_off2 = edit_rf_freq_off2 / float(pfile.hdr.rhr_rh_ps_mps_freq * 1E-7)
edit_rf_dur = pfile.hdr.rhi_user22
# check for default value (-1) of pulse length
if edit_rf_dur <= 0:
Expand Down Expand Up @@ -351,10 +357,16 @@ def _process_hbcd(pfile):
notestring = f'{notestring} {old_num_avgs} --> {new_num_avgs}' # Note Incomplete Data
print(f'{notestring} \t Corrected**') # Note Incomplete Data

bef_shape = list(lTE_metab.shape) # Remove Averages Dim
bef_shape[4] = bef_shape[4] // 4 # Closest multiple of 4
bef_shape.append(edit_cases) # Include Subscans
lTE_metab = lTE_metab.reshape(bef_shape) # With Subscan Dim
new_shape = list(lTE_metab.shape) # Remove Averages Dim
new_shape[4] = new_shape[4] // 4 # Closest multiple of 4
new_shape.append(edit_cases) # Include Subscans

lTE_metab_ = np.zeros(new_shape, dtype=np.complex128) # New lTE Metab Array
lTE_metab_[:, :, :, :, :, :, 0] = lTE_metab[:, :, :, :, 0::4, :] # Subscan 1
lTE_metab_[:, :, :, :, :, :, 1] = lTE_metab[:, :, :, :, 1::4, :] # Subscan 2
lTE_metab_[:, :, :, :, :, :, 2] = lTE_metab[:, :, :, :, 2::4, :] # Subscan 3
lTE_metab_[:, :, :, :, :, :, 3] = lTE_metab[:, :, :, :, 3::4, :] # Subscan 4
lTE_metab = lTE_metab_ # With Subscan Dim

lTE_metab_meta = _populate_metadata(pfile, water_suppressed=True) # Acquisition Information
lTE_metab_meta.set_standard_def('EchoTime', 0.080) # TE
Expand Down
4 changes: 4 additions & 0 deletions spec2nii/GE/ge_read_pfile.py
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Original file line number Diff line number Diff line change
Expand Up @@ -177,6 +177,9 @@ def get_mapper(self):
return None

psd = self.hdr.rhi_psdname.decode('utf-8').lower()
proto = self.hdr.rhs_se_desc.decode('utf-8').lower()
if psd == 'hbcd' and "press" in proto:
psd = self.hdr.rhs_se_desc.decode('utf-8').lower()

# MM: Some 'gaba' psd strings contain full path names, so truncate to the end of the path
if psd.endswith('gaba'):
Expand All @@ -195,6 +198,7 @@ def get_mapper(self):
'presscsi_nfl', # bjs - added for Govind's SVS data off v25
'epsi_3d_24', # bjs - added for soher check of MIDAS Browndyke data
'fidall' # WTC - added for JG's Hyperpolarised 13C data
'mrs-press' # ATG - Added for GE ShortTE in hbcd
):
mapper = PfileMapper
elif psd in ('oslaser', 'slaser_cni', 'slaser') and numecho == 1:
Expand Down
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