Rel/0.6.9 (#79)

* Messy fixes for new nifti-mrs-tools version. Adds handling of GE sequences.

* Prepare for release.

* new pymapvbvd not yet available

CHANGELOG.md

@@ -1,5 +1,12 @@
 This document contains the Spec2nii release history in reverse chronological order.
 
+0.6.9 (Friday 7th July 2023)
+----------------------------
+- Add handling for the `fidall` sequence in GE.
+- Add handling for the `slaser` sequence in GE.
+- Update to nifti-mrs-tools 1.0.0 API.
+- Minor code fixes contributed by the community.
+
 0.6.8 (Wednesday 22nd March 2023)
 ---------------------------------
 - Added handling for the GE jpress sequence (for JH HURCULES sequence)

requirements.yml

@@ -6,4 +6,4 @@ dependencies:
  - scipy
  - brukerapi>=0.1.8
  - pandas
- - nifti-mrs>=0.1.3
+ - nifti-mrs>=1.0.0

setup.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-from setuptools import setup
+from setuptools import setup, find_packages
 import versioneer
 import yaml
 
@@ -23,12 +23,7 @@
       url='https://github.com/wtclarke/spec2nii',
       long_description=long_description,
       long_description_content_type="text/markdown",
-      packages=['spec2nii',
-                'spec2nii.Siemens',
-                'spec2nii.GSL',
-                'spec2nii.dcm2niiOrientation',
-                'spec2nii.Philips',
-                'spec2nii.GE'],
+      packages=find_packages(),
       install_requires=install_requires,
       classifiers=[
           "Programming Language :: Python :: 3",

spec2nii/GE/ge_pfile.py

@@ -95,6 +95,8 @@ def _process_svs_pfile(pfile):
         data, meta, dwelltime, fname_suffix = _process_probe_p(pfile)
     elif psd in ('oslaser', 'slaser_cni'):
         data, meta, dwelltime, fname_suffix = _process_oslaser(pfile)
+    elif psd in ('slaser'):
+        data, meta, dwelltime, fname_suffix = _process_slaser(pfile)
     elif psd == 'gaba':
         data, meta, dwelltime, fname_suffix = _process_gaba(pfile)
     elif 'jpress_ac' in psd:  # Bergen patch
@@ -132,6 +134,12 @@ def _process_probe_p(pfile):
     meta = _populate_metadata(pfile, water_suppressed=True)
     meta_ref = _populate_metadata(pfile, water_suppressed=False)
 
+    meta.set_dim_info(0, 'DIM_COIL')
+    meta.set_dim_info(1, 'DIM_DYN')
+
+    meta_ref.set_dim_info(0, 'DIM_COIL')
+    meta_ref.set_dim_info(1, 'DIM_DYN')
+
     return [metab, water], [meta, meta_ref], dwelltime, ['', '_ref']
 
 
@@ -154,23 +162,46 @@ def _process_oslaser(pfile):
     data = []
     meta = []
     fname_suffix = []
-
     data.append(water[:, :, :, :, :, [0, 1, 4, 5]])
-    meta.append(_populate_metadata(pfile, water_suppressed=False))
+    meta.append(_populate_metadata(pfile, water_suppressed=False, data_dimensions=data[0].ndim))
     fname_suffix.append('_quant')
     data.append(water[:, :, :, :, :, [2, 3, 6, 7]])
-    meta.append(_populate_metadata(pfile, water_suppressed=False))
+    meta.append(_populate_metadata(pfile, water_suppressed=False, data_dimensions=data[1].ndim))
     fname_suffix.append('_ecc')
 
     data.append(metab)
-    meta.append(_populate_metadata(pfile, water_suppressed=True))
+    meta.append(_populate_metadata(pfile, water_suppressed=True, data_dimensions=metab.ndim))
     fname_suffix.append('')
 
     dwelltime = 1 / pfile.hdr.rhr_spectral_width
 
     return data, meta, dwelltime, fname_suffix
 
 
+def _process_slaser(pfile):
+    '''Extract metabolite and reference data from a slaser format pfile
+
+    This seems to be like a standard probe-p. Maybe slaser is the canonical vendor implementation.
+
+    :param Pfile pfile: Pfile object
+    :return: List numpy data arrays
+    :return: List of file name suffixes
+    '''
+
+    metab = pfile.map.raw_suppressed                    # typically (1,1,1,navg,ncoil,npts)
+    metab = np.transpose(metab, [0, 1, 2, 5, 4, 3])     # swap to (1,1,1,npts,ncoil,navg)
+
+    water = pfile.map.raw_unsuppressed                  # typically (1,1,1,navg,ncoil,npts)
+    water = np.transpose(water, [0, 1, 2, 5, 4, 3])     # swap to (1,1,1,npts,ncoil,navg)
+
+    dwelltime = 1 / pfile.hdr.rhr_spectral_width
+
+    meta = _populate_metadata(pfile, water_suppressed=True, data_dimensions=metab.ndim)
+    meta_ref = _populate_metadata(pfile, water_suppressed=False, data_dimensions=water.ndim)
+
+    return [metab, water], [meta, meta_ref], dwelltime, ['', '_ref']
+
+
 def _process_gaba(pfile):
     '''Extract metabolite and reference data from a gaba (MPRESS) format pfile
 
@@ -231,6 +262,8 @@ def fft_and_shift(x, axis):
 
     dwelltime = 1 / pfile.hdr.rhr_spectral_width
     meta = _populate_metadata(pfile)
+    meta.set_dim_info(0, 'DIM_COIL')
+
     orientation = NIFTIOrient(_calculate_affine_mrsi(pfile))
 
     return [gen_nifti_mrs_hdr_ext(data, dwelltime, meta, orientation.Q44, no_conj=True), ], ['', ]
@@ -277,8 +310,22 @@ def _calculate_affine(pfile):
     return affine
 
 
-def _populate_metadata(pfile, water_suppressed=True):
-    ''' Populate a nifti-mrs header extension with the requisite information'''
+def _populate_metadata(pfile, water_suppressed=True, data_dimensions=None):
+    """Populate a nifti-mrs header extension with metadata from the pfile
+
+    If (up to 7) data_dimensions are specified then default dimension tags
+    (coil, dyn, indirect) will be included. Otherwise manually specify
+    outside this function.
+
+    :param pfile: pfile object
+    :type pfile: pfile map object
+    :param water_suppressed: Set water suppression header field, defaults to True
+    :type water_suppressed: bool, optional
+    :param data_dimensions: If set to 5,6, or 7 will inlcude default dim tags for those diemnsions, defaults to None
+    :type data_dimensions: int, optional
+    :return: Header extension object
+    :rtype: nifti_mrs.hdr_ext
+    """
     hdr = pfile.hdr
     spec_frequency = float(pfile.hdr.rhr_rh_ps_mps_freq) / 1e7
 
@@ -304,7 +351,8 @@ def _populate_metadata(pfile, water_suppressed=True):
 
     meta = Hdr_Ext(
         spec_frequency,
-        nucleus)
+        nucleus,
+        dimensions=data_dimensions)
 
     # Standard defined metadata
     # # 5.1 MRS specific Tags

spec2nii/GE/ge_read_pfile.py

@@ -180,7 +180,7 @@ def get_mapper(self):
 
         if psd in ('probe-p', 'probe-s'):
             mapper = PfileMapper
-        elif psd in ('oslaser', 'slaser_cni'):
+        elif psd in ('oslaser', 'slaser_cni', 'slaser'):
             mapper = PfileMapperSlaser
         elif psd == 'presscsi':
             mapper = PfileMapper
@@ -208,6 +208,9 @@ def get_mapper(self):
         elif psd == 'jpress':
             # wtc - Added for HURCULES data.
             mapper = PfileMapperGaba
+        elif psd == 'fidall':
+            # WTC - added for JG's Hyperpolarised 13C data
+            mapper = PfileMapper
         else:
             raise UnknownPfile("No Pfile mapper for pulse sequence = %s" % psd)
 

spec2nii/Philips/philips_data_list.py

@@ -95,7 +95,7 @@ def read_data_list_pair(data_file, list_file, aux_file, special_case=None):
         if data_type == 'STD_0'\
                 and (special_case == 'hyper' or 'hyper' in meta['ProtocolName'].lower()):
             out_hyper, meta_hyper = _special_case_hyper(out_data, meta)
-            # Handle the main acqusition of the HYPER (short TE + editing) sequence
+            # Handle the main acquisition of the HYPER (short TE + editing) sequence
 
             # Insert spatial dimensions
             out_shortte = out_hyper[0].reshape((1, 1, 1) + out_hyper[0].shape)
@@ -119,6 +119,10 @@ def read_data_list_pair(data_file, list_file, aux_file, special_case=None):
                 and (special_case == 'hyper' or 'hyper' in meta['ProtocolName'].lower()):
             # Handle the water ref acqusition of the HYPER sequence
 
+            meta.set_dim_info(
+                0,
+                'DIM_COIL')
+
             meta.set_dim_info(
                 1,
                 'DIM_USER_0',
@@ -285,6 +289,13 @@ def _special_case_hyper(data, meta):
     meta_short_te = meta.copy()
     meta_edited = meta.copy()
 
+    meta_short_te.set_dim_info(
+        0,
+        'DIM_COIL')
+    meta_short_te.set_dim_info(
+        1,
+        'DIM_DYN')
+
     edit_pulse_1   = 1.9
     edit_pulse_2   = 4.58
     edit_pulse_off = 4.18
@@ -296,6 +307,10 @@ def _special_case_hyper(data, meta):
         "C": {"PulseOffset": edit_pulse_1, "PulseDuration": 0.02},
         "D": {"PulseOffset": edit_pulse_off, "PulseDuration": 0.02}}
 
+    meta_edited.set_dim_info(
+        0,
+        'DIM_COIL')
+
     meta_edited.set_dim_info(
         1,
         'DIM_EDIT',

spec2nii/other.py

@@ -68,7 +68,7 @@ def insert_hdr_ext(args):
         from nifti_mrs.hdr_ext import Hdr_Ext
 
         nimg = Image(args.file)
-        hdr_ext = Hdr_Ext.from_header_ext(new_hdr, dimensions=nimg.ndim)
+        hdr_ext = Hdr_Ext.from_header_ext(new_hdr)
         nifti_mrs_img = gen_nifti_mrs_hdr_ext(
             nimg[:],
             nimg.header['pixdim'][4],