nifti-mrs package depndency + hyper handling (Philips) (#59)

* Initial move to nifti-mrs package.

* Fix conjugation added with nifti_mrs package.

* Add hyper handling to spar/sdat pathway.

* Fix twix issues identified by CJD.

* First pass at data/list HYPER handling.

* Add commandline special case parameter.

* Add version info

* Add hyper handling to data list, add hyper tests on philips.

* Renable bruker conversion pathway and tests.

* Typo in requirements.

* Reduce restrictions in dependency.

* Touch up bruker tests.

* Touch up bruker tests.

CHANGELOG.md

@@ -1,5 +1,17 @@
 This document contains the Spec2nii release history in reverse chronological order.
 
+0.6.1 (Wednesday 18 January 2023)
+---------------------------------
+- Fixed conjugation issue introduced by new nifti-mrs package dependency
+- SPAR/SDAT pipeline now handles HYPER special case.
+- Data/list pipeline now handles HYPER special case.
+- Fixed issue with XA Twix PatientSex and TxOffset attributes.
+- Reenable Bruker conversion. 
+
+0.6.0 (Wednesday 11th January 2023)
+-----------------------------------
+- NIfTI-MRS creation/handling/verification now performed by nifti-mrs package.
+
 0.5.0 (Friday 2nd December 2022)
 --------------------------------
 - NIfTI-MRS version 0.6

requirements.yml

@@ -4,5 +4,6 @@ dependencies:
  - pydicom
  - pyMapVBVD>=0.5.2
  - scipy
- - brukerapi>=0.1.4.0
+ - brukerapi>=0.1.8
  - pandas
+ - nifti-mrs>=0.1.3

setup.py

@@ -27,7 +27,6 @@
                 'spec2nii.Siemens',
                 'spec2nii.GSL',
                 'spec2nii.dcm2niiOrientation',
-                'spec2nii.nifti_mrs',
                 'spec2nii.Philips',
                 'spec2nii.GE'],
       install_requires=install_requires,

spec2nii/GE/ge_pfile.py

@@ -43,9 +43,11 @@
 # 3rd party modules
 import numpy as np
 
+from nifti_mrs.create_nmrs import gen_nifti_mrs_hdr_ext
+from nifti_mrs.hdr_ext import Hdr_Ext
+
 # Our modules
 from spec2nii.GE.ge_read_pfile import Pfile
-from spec2nii import nifti_mrs
 from spec2nii.nifti_orientation import NIFTIOrient
 from spec2nii import __version__ as spec2nii_ver
 
@@ -104,7 +106,7 @@ def _process_svs_pfile(pfile):
 
     out_nmrs = []
     for dd, mm in zip(data, meta):
-        out_nmrs.append(nifti_mrs.NIfTI_MRS(dd, orientation.Q44, dwelltime, mm))
+        out_nmrs.append(gen_nifti_mrs_hdr_ext(dd, dwelltime, mm, orientation.Q44, no_conj=True))
 
     return out_nmrs, fname_suffix
 
@@ -228,7 +230,7 @@ def fft_and_shift(x, axis):
     meta = _populate_metadata(pfile)
     orientation = NIFTIOrient(_calculate_affine_mrsi(pfile))
 
-    return [nifti_mrs.NIfTI_MRS(data, orientation.Q44, dwelltime, meta), ], ['', ]
+    return [gen_nifti_mrs_hdr_ext(data, dwelltime, meta, orientation.Q44, no_conj=True), ], ['', ]
 
 
 def _calculate_affine_mrsi(pfile):
@@ -297,8 +299,9 @@ def _populate_metadata(pfile, water_suppressed=True):
               'Use the --override_nucleus option to specify a different nuclide.')
         nucleus = "1H"
 
-    meta = nifti_mrs.hdr_ext(spec_frequency,
-                             nucleus)
+    meta = Hdr_Ext(
+        spec_frequency,
+        nucleus)
 
     # Standard defined metadata
     # # 5.1 MRS specific Tags

spec2nii/Philips/philips.py

@@ -6,27 +6,32 @@
 from ast import literal_eval
 
 import numpy as np
+from nifti_mrs.create_nmrs import gen_nifti_mrs_hdr_ext
+from nifti_mrs.hdr_ext import Hdr_Ext
 
 from spec2nii.nifti_orientation import NIFTIOrient, calc_affine
-from spec2nii import nifti_mrs
 from spec2nii import __version__ as spec2nii_ver
 
 
-def read_sdat_spar_pair(sdat_file, spar_file, shape=None, tags=None):
-    """_summary_
-
-    _extended_summary_
-
-    :param sdat_file: _description_
-    :type sdat_file: _type_
-    :param spar_file: _description_
-    :type spar_file: _type_
-    :param shape: _description_, defaults to None
-    :type shape: _type_, optional
-    :param tags: _description_, defaults to None
-    :type tags: _type_, optional
-    :return: _description_
-    :rtype: _type_
+def read_sdat_spar_pair(sdat_file, spar_file, shape=None, tags=None, fileout=None, special=None):
+    """Read and convert SPAR/SDAT pairs from Philips scanners
+
+    :param sdat_file: Path to .SDAT file
+    :type sdat_file: pathlib.Path
+    :param spar_file: Path to .SPAR file
+    :type spar_file: pathlib.Path
+    :param shape: List of dimension shapes to reshape array, defaults to None
+    :type shape: list of ints, optional
+    :param tags: List of higher dimension tags, defaults to None
+    :type tags: List of strings, optional
+    :param fileout: File name string passed by user, defaults to None/stem of file
+    :type fileout: str, optional
+    :param special: Identifier for special-cased sequence, defaults to None
+    :type special: str, optional
+    :return: List of NIFTI-MRS objects
+    :rtype: list of nifti_mrs.nifti_mrs.NIFTI_MRS
+    :return: List of file name parts
+    :rtype: list of strings
     """
     spar_params = read_spar(spar_file)
     data = read_sdat(sdat_file,
@@ -62,7 +67,21 @@ def read_sdat_spar_pair(sdat_file, spar_file, shape=None, tags=None):
         affine = np.diag(np.array([10000, 10000, 10000, 1]))
     orientation = NIFTIOrient(affine)
 
-    return [nifti_mrs.NIfTI_MRS(data, orientation.Q44, dwelltime, meta), ]
+    # name of output
+    if fileout is not None:
+        mainStr = fileout
+    else:
+        mainStr = sdat_file.stem
+
+    # Special cases
+    if spar_params['scan_id'].lower() == 'hyper'\
+            or (special is not None and
+                special.lower() == 'hyper'):
+        return _special_case_hyper(data, dwelltime, meta, orientation.Q44, mainStr)
+    else:
+        # Normal case
+        return [gen_nifti_mrs_hdr_ext(data, dwelltime, meta, orientation.Q44, no_conj=True), ],\
+               [mainStr, ]
 
 
 def read_spar(filename):
@@ -143,8 +162,9 @@ def spar_to_nmrs_hdrext(spar_dict):
 
     # Extract required metadata and create hdr_ext object
     cf = float(spar_dict["synthesizer_frequency"]) / 1E6
-    obj = nifti_mrs.hdr_ext(cf,
-                            spar_dict["nucleus"])
+    obj = Hdr_Ext(
+        cf,
+        spar_dict["nucleus"])
 
     def set_standard_def(nifti_mrs_key, location, key, cast=None):
         try:
@@ -266,3 +286,37 @@ def _vax_to_ieee_single_float(data):
             # may want to raise an exception here ...
 
     return f
+
+
+def _special_case_hyper(data, dwelltime, meta, orientation, fout_str):
+    # Reorganise the data. This unfortunately makes hardcoded assumptions about the size of each part.
+    data_short_te = data[:, :, :, :, :32]
+    data_edited = data[:, :, :, :, 32:]
+    data_edited = data_edited.T.reshape((56, 4, data.shape[3], 1, 1, 1)).T
+
+    meta_short_te = meta.copy()
+    meta_edited = meta.copy()
+
+    edit_pulse_1 = 1.9
+    edit_pulse_2 = 4.58
+    edit_pulse_off = 4.18
+    dim_info = "HERCULES j-difference editing, four conditions"
+    dim_header = {"EditCondition": ["A", "B", "C", "D"]}
+    edit_pulse_val = {
+        "A": {"PulseOffset": [edit_pulse_1, edit_pulse_2], "PulseDuration": 0.02},
+        "B": {"PulseOffset": [edit_pulse_off, edit_pulse_2], "PulseDuration": 0.02},
+        "C": {"PulseOffset": edit_pulse_1, "PulseDuration": 0.02},
+        "D": {"PulseOffset": edit_pulse_off, "PulseDuration": 0.02}}
+
+    meta_edited.set_dim_info(
+        0,
+        'DIM_EDIT',
+        dim_info,
+        dim_header)
+
+    meta_edited.set_dim_info(1, 'DIM_DYN')
+    meta_edited.set_standard_def("EditPulse", edit_pulse_val)
+
+    return [gen_nifti_mrs_hdr_ext(data_short_te, dwelltime, meta_short_te, orientation, no_conj=True),
+            gen_nifti_mrs_hdr_ext(data_edited, dwelltime, meta_edited, orientation, no_conj=True)],\
+           [fout_str + '_hyper_short_te', fout_str + '_hyper_edited']