Enhance support for GE data

.gitignore

@@ -8,3 +8,4 @@ __pycache__
 .DS_Store
 *.png
 prototyping
+.idea/

CHANGELOG.md

@@ -1,5 +1,9 @@
 This document contains the Spec2nii release history in reverse chronological order.
 
+0.7.4 (WIP)
+---------------------------------
+- Refinements and improvements to the GE SVS pipeline from Mark Mikkelsen
+
 0.7.3 (Tuesday 12th March 2024)
 -------------------------------
 - Siemens .rda format now had corrected and validated orientations (tested on VE11 baseline).

spec2nii/GE/ge_hdr_fields.py

@@ -1,4 +1,4 @@
-'''List of GE p-file offsets.
+"""List of GE p-file offsets.
 
 This code is taken from the VESPA project https://scion.duhs.duke.edu/vespa/project.
 I therefore include their BSD statement here.
@@ -60,7 +60,7 @@
     ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
     (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
     SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-'''
+"""
 
 import ctypes as ct
 import numpy as np
@@ -754,10 +754,16 @@ def get_pfile_hdr_fields(version):
         plist.append(('rhr_rh_npasses',           ct.c_short))
         plist.append(('pad_xx',                   ct.c_char * 2))
         plist.append(('rhr_rh_nslices',           ct.c_short))
-        plist.append(('pad_xx',                   ct.c_char * 10))
+        plist.append(('rhr_rh_nechoes',           ct.c_short))
+        plist.append(('rhr_rh_navs',              ct.c_short))
+        plist.append(('rhr_rh_nframes',           ct.c_short))
+        plist.append(('pad_xx',                   ct.c_char * 4))
         plist.append(('rhr_rh_frame_size',        ct.c_ushort))
         plist.append(('rhr_rh_point_size',        ct.c_short))
-        plist.append(('pad_xx',                   ct.c_char * 32))
+        plist.append(('pad_xx',                   ct.c_char * 18))
+        plist.append(('rhr_rh_da_xres',           ct.c_short))
+        plist.append(('rhr_rh_da_yres',           ct.c_short))
+        plist.append(('pad_xx',                   ct.c_char * 10))
         plist.append(('rhr_rh_raw_pass_size',     ct.c_uint))
         plist.append(('pad_xx',                   ct.c_char * 80))
         plist.append(('rhr_rh_dab[0]_start_rcv',  ct.c_short))
@@ -978,10 +984,16 @@ def get_pfile_hdr_fields(version):
         plist.append(('rhr_rh_npasses',           ct.c_short))
         plist.append(('pad_xx',                   ct.c_char * 2))
         plist.append(('rhr_rh_nslices',           ct.c_short))
-        plist.append(('pad_xx',                   ct.c_char * 10))
+        plist.append(('rhr_rh_nechoes',           ct.c_short))
+        plist.append(('rhr_rh_navs',              ct.c_short))
+        plist.append(('rhr_rh_nframes',           ct.c_short))
+        plist.append(('pad_xx',                   ct.c_char * 4))
         plist.append(('rhr_rh_frame_size',        ct.c_ushort))
         plist.append(('rhr_rh_point_size',        ct.c_short))
-        plist.append(('pad_xx',                   ct.c_char * 32))
+        plist.append(('pad_xx',                   ct.c_char * 18))
+        plist.append(('rhr_rh_da_xres',           ct.c_short))
+        plist.append(('rhr_rh_da_yres',           ct.c_short))
+        plist.append(('pad_xx',                   ct.c_char * 10))
         plist.append(('rhr_rh_raw_pass_size',     ct.c_uint))
         plist.append(('pad_xx',                   ct.c_char * 80))
         plist.append(('rhr_rh_dab[0]_start_rcv',  ct.c_short))
@@ -1202,10 +1214,16 @@ def get_pfile_hdr_fields(version):
         plist.append(('rhr_rh_npasses',           ct.c_short))
         plist.append(('pad_xx',                   ct.c_char * 2))
         plist.append(('rhr_rh_nslices',           ct.c_short))
-        plist.append(('pad_xx',                   ct.c_char * 10))
+        plist.append(('rhr_rh_nechoes',           ct.c_short))
+        plist.append(('rhr_rh_navs',              ct.c_short))
+        plist.append(('rhr_rh_nframes',           ct.c_short))
+        plist.append(('pad_xx',                   ct.c_char * 4))
         plist.append(('rhr_rh_frame_size',        ct.c_ushort))
         plist.append(('rhr_rh_point_size',        ct.c_short))
-        plist.append(('pad_xx',                   ct.c_char * 32))
+        plist.append(('pad_xx',                   ct.c_char * 18))
+        plist.append(('rhr_rh_da_xres',           ct.c_short))
+        plist.append(('rhr_rh_da_yres',           ct.c_short))
+        plist.append(('pad_xx',                   ct.c_char * 10))
         plist.append(('rhr_rh_raw_pass_size',     ct.c_uint))
         plist.append(('pad_xx',                   ct.c_char * 80))
         plist.append(('rhr_rh_dab[0]_start_rcv',  ct.c_short))

spec2nii/GE/ge_pfile.py

@@ -1,4 +1,4 @@
-'''spec2nii module containing functions specific to interpreting the GE pfile format
+"""spec2nii module containing functions specific to interpreting the GE pfile format
 
 Author: William Clarke <[email protected]>
 Copyright (C) 2020 University of Oxford
@@ -33,7 +33,7 @@
 
     For portions of this code, copyright and license information differs from
     the above. In these cases, copyright and/or license information is inline.
-'''
+"""
 
 # Python modules
 from datetime import datetime
@@ -83,25 +83,29 @@ def read_pfile(filename, fname_out):
 
 
 def _process_svs_pfile(pfile):
-    '''Handle SVS data
+    """Handle SVS data
 
     :param Pfile pfile: Pfile object
     :return: List of NIFTI MRS data objects
     :return: List of file name suffixes
-    '''
+    """
     psd = pfile.hdr.rhi_psdname.decode('utf-8').lower()
 
-    if psd in ('probe-p', 'probe-s'):
+    # 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'):
         data, meta, dwelltime, fname_suffix = _process_probe_p(pfile)
-    elif psd in ('oslaser', 'slaser_cni'):
+    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 ('gaba', 'hbcd'):
-        data, meta, dwelltime, fname_suffix = _process_gaba(pfile)
-    elif 'jpress_ac' in psd:  # Bergen patch
-        data, meta, dwelltime, fname_suffix = _process_gaba(pfile)
-    elif psd == 'jpress':
+    elif psd in ('jpress', 'jpress_ac', 'gaba', 'hbcd', 'probe-p-mega_rml', 'repress7'):
         data, meta, dwelltime, fname_suffix = _process_gaba(pfile)
     else:
         raise UnsupportedPulseSequenceError(f'Unrecognised sequence {psd}.')
@@ -116,12 +120,12 @@ def _process_svs_pfile(pfile):
 
 
 def _process_probe_p(pfile):
-    '''Extract metabolite and reference data from a prob_p format pfile
+    """Extract metabolite and reference data from a prob_p format pfile
 
     :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)
@@ -144,15 +148,15 @@ def _process_probe_p(pfile):
 
 
 def _process_oslaser(pfile):
-    '''Extract metabolite and reference data from a oslaser format pfile
+    """Extract metabolite and reference data from a oslaser format pfile
 
     I think this is like the CMRR sLASER sequence with 2 ecc and 2 water scaling
     scans at the start and end of each acquisition.
 
     :param Pfile pfile: Pfile object
     :return: List numpy data arrays
     :return: List of file name suffixes
-    '''
+    """
 
     water = pfile.map.raw_unsuppressed                  # typically (1,1,1,navg,ncoil,npts)
     metab = pfile.map.raw_suppressed
@@ -179,14 +183,14 @@ def _process_oslaser(pfile):
 
 
 def _process_slaser(pfile):
-    '''Extract metabolite and reference data from a slaser format 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)
@@ -203,12 +207,12 @@ def _process_slaser(pfile):
 
 
 def _process_gaba(pfile):
-    '''Extract metabolite and reference data from a gaba (MPRESS) format pfile
+    """Extract metabolite and reference data from a gaba (MPRESS) format pfile
 
     :param Pfile pfile: Pfile object
     :return: List numpy data arrays
     :return: List of file name suffixes
-    '''
+    """
 
     # Note that custom mapper sorts dimensions already
     metab = pfile.map.raw_suppressed
@@ -231,12 +235,12 @@ def _process_gaba(pfile):
 
 
 def _process_mrsi_pfile(pfile):
-    '''Handle MRSI data
+    """Handle MRSI data
 
     :param Pfile pfile: Pfile object
     :return: List of NIFTI MRS data objects
     :return: List of file name suffixes
-    '''
+    """
     psd = pfile.hdr.rhi_psdname.decode('utf-8').lower()
 
     known_formats = ('probe-p', 'probe-sl', 'slaser_cni', 'presscsi')
@@ -270,7 +274,7 @@ def fft_and_shift(x, axis):
 
 
 def _calculate_affine_mrsi(pfile):
-    '''Calculate the 4x4 affine matrix for mrsi'''
+    """Calculate the 4x4 affine matrix for mrsi"""
 
     dcos = pfile.map.get_dcos.T
     dcos[dcos == 0.0] = 0.0             # remove -0.0 values
@@ -292,7 +296,7 @@ def _calculate_affine_mrsi(pfile):
 
 
 def _calculate_affine(pfile):
-    '''Calculate the 4x4 affine matrix'''
+    """Calculate the 4x4 affine matrix"""
 
     dcos = pfile.map.get_dcos.T
     dcos[dcos == 0.0] = 0.0             # remove -0.0 values
@@ -321,7 +325,7 @@ def _populate_metadata(pfile, water_suppressed=True, data_dimensions=None):
     :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
+    :param data_dimensions: If set to 5,6, or 7 will include default dim tags for those dimensions, defaults to None
     :type data_dimensions: int, optional
     :return: Header extension object
     :rtype: nifti_mrs.hdr_ext