Automatic conversion first pass. (#64)

CHANGELOG.md

@@ -1,5 +1,9 @@
 This document contains the Spec2nii release history in reverse chronological order.
 
+0.6.4 (Tuesday 7th February 2023)
+---------------------------------
+- Added first pass at new `spec2nii auto` feature with automatic conversion for some formats.
+
 0.6.3 (Monday 6th February 2023)
 --------------------------------
 - Added handling for GE presscsi and probe-s sequences.

README.md

@@ -68,6 +68,9 @@ By default, spec2nii generates NIfTI files using the NIfTI-2 header format. Use
 
 Manual overrides can be provided for incorrectly interpreted required header fields, namely SpectrometerFrequency, ResonantNucleus and dwell-time, by using the `--override_frequency`, `--override_nucleus`, and `--override_dwelltime` command line options.
 
+### Automatic detection
+`spec2nii auto FILE` will attempt an automatic conversion of the following formats: Twix, RDA, SPAR/SDAT, GE p-file, DICOM. Note that many features of the individual converters are not implemented in this automatic pathway. This feature should be regarded as somewhat experimental. For finer-grained control see the specific subcommands listed below.
+
 ### Twix
 Call `spec2nii twix -v FILE` to view a list of contained MDH flags. -m can be used to specify which multi-raid file to convert if used on VE data.
 

spec2nii/spec2nii.py

@@ -1,20 +1,5 @@
 """ spec2nii - tool for conversion of various MRS data formats to NIFTI format.
 
-spec2nii converts the following formats to NIFTI files.
-Supporting SVS:
-    Siemens "Twix" .dat format
-    Siemens DICOM
-    Philips SPAR/SDAT files
-    GE p-files
-    UIH DICOM
-    LCModel RAW
-    jMRUI text
-    Plain text
-
-Supporting CSI/MRSI:
-    Siemens DICOM
-    UIH DICOM
-
 This module contains the main class to be called as a script (through the main function).
 
 Author: William Clarke <[email protected]>
@@ -65,6 +50,12 @@ def add_common_parameters(subparser):
             subparser.add_argument('--verbose', action='store_true')
             return subparser
 
+        # Auto subcommand - heuristic ID of file type
+        parser_auto = subparsers.add_parser('auto', help='Attempt automatic identification and conversion.')
+        parser_auto.add_argument('file', help='file to convert', type=Path)
+        parser_auto = add_common_parameters(parser_auto)
+        parser_auto.set_defaults(func=self.auto)
+
         # Handle twix subcommand
         parser_twix = subparsers.add_parser('twix', help='Convert from Siemens .dat twix format.')
         parser_twix.add_argument('file', help='file to convert', type=Path)
@@ -91,10 +82,10 @@ def add_common_parameters(subparser):
         parser_dicom.set_defaults(func=self.dicom)
 
         # Handle rda subcommand
-        parser_dicom = subparsers.add_parser('rda', help='Convert from Siemens spectroscopy .rda format.')
-        parser_dicom.add_argument('file', help='file to convert', type=Path)
-        parser_dicom = add_common_parameters(parser_dicom)
-        parser_dicom.set_defaults(func=self.rda)
+        parser_rda = subparsers.add_parser('rda', help='Convert from Siemens spectroscopy .rda format.')
+        parser_rda.add_argument('file', help='file to convert', type=Path)
+        parser_rda = add_common_parameters(parser_rda)
+        parser_rda.set_defaults(func=self.rda)
 
         # Handle UIH DICOM subcommand
         parser_uih_dicom = subparsers.add_parser('uih', help='Convert from UIH DICOM format.')
@@ -376,6 +367,94 @@ def validate_write(self, verbose):
             else:
                 raise self.NIfTIMRSWriteError(f'Output {out.name} in {out.parent} not found!')
 
+    # Attempt automatic file type identification
+    def auto(self, args):
+        """Attempt automatic file type identification and conversion
+
+        Currently handles: Twix, RDA, SPAR/SDAT, GE pfile, DICOM
+        """
+        from warnings import warn
+        warn('Automatic conversion is an experimental feature. Please verify the output carefully.')
+
+        # Twix format - ID by extension
+        if args.file.suffix.lower() == '.dat':
+            print("Attempting conversion as Siemens Twix (.dat), evalinfo = 'image'")
+            setattr(args, 'evalinfo', 'image')
+            setattr(args, 'quiet', False)
+            setattr(args, 'view', False)
+            for idx in range(5, 8):
+                setattr(args, f'dim{idx}', None)
+                setattr(args, f'tag{idx}', None)
+            setattr(args, 'remove_os', False)
+            self.twix(args)
+
+        # Siemens RDA format - ID by extension
+        elif args.file.suffix.lower() == '.rda':
+            print('Attempting conversion as Siemens RDA (.rda)')
+            self.rda(args)
+
+        # Philips SPAR/SDAT format - ID by extension(s)
+        elif args.file.suffix.lower() in ('.spar', '.sdat'):
+            print('Attempting conversion as Philips SPAR/SDAT pair')
+            if args.file.with_suffix('.SPAR').is_file()\
+                    and args.file.with_suffix('.SDAT').is_file():
+                setattr(args, 'spar', args.file.with_suffix('.SPAR'))
+                setattr(args, 'sdat', args.file.with_suffix('.SDAT'))
+            else:
+                raise Spec2niiError(
+                    'Unable to find both files in SPAR/SDAT pair.'
+                    'Please use manual selection of subcomands. '
+                    'e.g. spec2nii philips ...')
+            setattr(args, 'tags', ["DIM_DYN", None, None])
+            setattr(args, 'shape', None)
+            setattr(args, 'special', None)
+            self.philips(args)
+
+        # Philips DATA/LIST - Reject bcause of unknown aux file format.
+        elif args.file.suffix.lower() in ('.data', '.list'):
+            raise Spec2niiError(
+                'Automatic conversion not setup for data/list conversion. '
+                'Please use manual selection of subcomand. '
+                'e.g. spec2nii philips_dl ...')
+
+        # GE pfile (.7) format - ID by extension
+        elif args.file.suffix.lower() == '.7':
+            self.ge(args)
+
+        # If no matches assume DICOM - ID by loading file
+        else:
+            import pydicom as pdcm
+            try:
+                if args.file.is_dir():
+                    files_in = \
+                        sorted(args.file.rglob('*.IMA')) + \
+                        sorted(args.file.rglob('*.ima')) + \
+                        sorted(args.file.rglob('*.dcm'))
+                    file = pdcm.read_file(files_in[0])
+                else:
+                    file = pdcm.read_file(args.file)
+
+                manufacturer = file.Manufacturer
+                setattr(args, 'tag', None)
+                if manufacturer.lower() == 'siemens':
+                    print('Attempting conversion as Siemens DICOM.')
+                    setattr(args, 'voi', False)
+                    self.dicom(args)
+                elif manufacturer.lower() == 'uih':
+                    print('Attempting conversion as UIH DICOM.')
+                    self.uih_dicom(args)
+                elif manufacturer.lower() == 'philips medical systems':
+                    print('Attempting conversion as Philips DICOM.')
+                    self.philips_dicom(args)
+                else:
+                    raise Spec2niiError(f'Unknown DICOM manufacturer {manufacturer}.')
+            # No sucessful ID as DICOM - fail at automatic load.
+            except pdcm.errors.InvalidDicomError:
+                raise Spec2niiError(
+                    'Unable to automatically identify file type. '
+                    'Please use manual selection of subcomands. '
+                    'e.g. spec2nii twix ..., spec2nii philips ...')
+
     # Start of the specific format handling functions.
     # Siemens twix (.dat) format
     def twix(self, args):

tests/test_auto.py

@@ -0,0 +1,113 @@
+'''Tests automatic conversion routines.
+
+Copyright William Clarke, University of Oxford 2023
+Subject to the BSD 3-Clause License.
+'''
+
+import subprocess
+from pathlib import Path
+
+test_base = Path(__file__).parent / 'spec2nii_test_data'
+testdata = {
+    'twix': test_base / 'Siemens' / 'VEData' / 'Twix' / 'meas_MID00242_FID62747_svs_se_iso_tra_sat.dat',
+    'rda': test_base / 'Siemens' / 'XAData' / 'XA20' / 'rda' / 'spct_002.MR.MRI-LAB Test_Dir.5.1.114540.rda',
+    'spar': test_base / 'philips' / 'P1' / 'SV_PRESS_sh_6_2_raw_act.SPAR',
+    'data_list': test_base / 'philips' / 'hyper' / 'raw_226.list',
+    'ge_p': test_base / 'ge' / 'pFiles' / 'svMRS' / 'P03072.7',
+    'dicom_siemens': test_base / 'Siemens' / 'XAData' / 'XA20' / 'DICOM' / '26516628.dcm',
+    'dicom_uih': test_base / 'UIH' / 'mrs_data' / 'dicom' / 'svs_press_te144_SVS_801' / '00000001.dcm',
+    'dicom_philips': test_base / 'philips' / 'DICOM' / 'SV_phantom_center' / 'IM-0018-0002-0001.dcm'}
+
+
+def test_auto_twix(tmp_path):
+    subprocess.run([
+        'spec2nii', 'auto',
+        testdata['twix'],
+        '-o', tmp_path,
+        '-f', 'test_file'])
+
+    assert (tmp_path / 'test_file.nii.gz').is_file()
+
+
+def test_auto_rda(tmp_path):
+    subprocess.run([
+        'spec2nii', 'auto',
+        testdata['rda'],
+        '-o', tmp_path,
+        '-f', 'test_file'])
+
+    assert (tmp_path / 'test_file.nii.gz').is_file()
+
+
+def test_auto_sdat_spar(tmp_path):
+    subprocess.run([
+        'spec2nii', 'auto',
+        testdata['spar'],
+        '-o', tmp_path,
+        '-f', 'test_file'])
+
+    assert (tmp_path / 'test_file.nii.gz').is_file()
+
+
+def test_auto_ge(tmp_path):
+    subprocess.run([
+        'spec2nii', 'auto',
+        testdata['ge_p'],
+        '-o', tmp_path,
+        '-f', 'test_file'])
+
+    assert (tmp_path / 'test_file.nii.gz').is_file()
+
+
+def test_auto_siemens_dicom(tmp_path):
+    subprocess.run([
+        'spec2nii', 'auto',
+        testdata['dicom_siemens'],
+        '-o', tmp_path,
+        '-f', 'test_file'])
+
+    assert (tmp_path / 'test_file.nii.gz').is_file()
+
+    subprocess.run([
+        'spec2nii', 'auto',
+        testdata['dicom_siemens'].parent,
+        '-o', tmp_path,
+        '-f', 'test_dir'])
+
+    assert (tmp_path / 'test_dir.nii.gz').is_file()
+
+
+def test_auto_uih_dicom(tmp_path):
+    subprocess.run([
+        'spec2nii', 'auto',
+        testdata['dicom_uih'],
+        '-o', tmp_path,
+        '-f', 'test_file'])
+
+    assert (tmp_path / 'test_file.nii.gz').is_file()
+
+    subprocess.run([
+        'spec2nii', 'auto',
+        testdata['dicom_uih'].parent,
+        '-o', tmp_path,
+        '-f', 'test_dir'])
+
+    assert (tmp_path / 'test_dir.nii.gz').is_file()
+
+
+def test_auto_philips_dicom(tmp_path):
+    subprocess.run([
+        'spec2nii', 'auto',
+        testdata['dicom_philips'],
+        '-o', tmp_path,
+        '-f', 'test_file'])
+
+    assert (tmp_path / 'test_file.nii.gz').is_file()
+
+    subprocess.run([
+        'spec2nii', 'auto',
+        testdata['dicom_philips'].parent,
+        '-o', tmp_path,
+        '-f', 'test_dir'])
+
+    assert (tmp_path / 'test_dir.nii.gz').is_file()