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ENH: mrs_tools vis subtraction #31

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Oct 23, 2024
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ENH: mrs_tools vis subtraction #31

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ee99db1
Subtract metcycle, edit and isis dims when visualising
wtclarke Oct 23, 2024
239fd7f
changelog
wtclarke Oct 23, 2024
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4 changes: 4 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -1,5 +1,9 @@
This document contains the nifti_mrs_tools release history in reverse chronological order.

1.3.2 (Wednesday 23rd October 2024)
-----------------------------------
- Better visualisation using `mrs_tools vis` for data containing ISIS, metabolite cycling or editing.

1.3.1 (Monday 21st October 2024)
--------------------------------
- Drop support for python 3.8. Testing extended to python 3.12 and 3.13.
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16 changes: 10 additions & 6 deletions src/nifti_mrs/vis.py
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Expand Up @@ -28,12 +28,16 @@ def vis_nifti_mrs(data, display_dim=None, ppmlim=None, plot_avg=False, mask=None
print('Performing coil combination')
data = nifti_mrs_proc.coilcombine(data)

def average_dim_if_multiple(dd, dim):
"""Averages a dimension if non-singleton"""
def handle_dim_if_multiple(dd, dim):
"""Handles a dimension if non-singleton"""
if dim is None:
# Protect against loss of dimension during process.
return dd
if dd.shape[dd.dim_position(dim)] > 1:
if dd.shape[dd.dim_position(dim)] > 1\
and dim in ('DIM_EDIT', 'DIM_METCYCLE', 'DIM_ISIS'):
print(f'Subtracting {dim}')
return nifti_mrs_proc.subtract(dd, dim=dim)
elif dd.shape[dd.dim_position(dim)] > 1:
print(f'Averaging {dim}')
return nifti_mrs_proc.average(dd, dim)
else:
Expand All @@ -46,7 +50,7 @@ def average_dim_if_multiple(dd, dim):
if dim is None:
continue
if dim != display_dim:
data = average_dim_if_multiple(data, dim)
data = handle_dim_if_multiple(data, dim)
mrs = []
for fid, _ in data.iterate_over_dims():
mrs.append(
Expand All @@ -59,7 +63,7 @@ def average_dim_if_multiple(dd, dim):

else:
for dim in data.dim_tags:
data = average_dim_if_multiple(data, dim)
data = handle_dim_if_multiple(data, dim)
mrs = MRS(
data[:].squeeze(),
bw=data.bandwidth,
Expand All @@ -71,7 +75,7 @@ def average_dim_if_multiple(dd, dim):

else:
for dim in data.dim_tags:
data = average_dim_if_multiple(data, dim)
data = handle_dim_if_multiple(data, dim)

mrsi = MRSI(
data[:],
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