WIP: adding Philips XML/REC support

bin/xmlrec2nii

@@ -0,0 +1,10 @@
+#!python
+"""XML/REC to NIfTI converter
+"""
+
+# parrec2nii reads XML/REC as well
+from nibabel.cmdline.parrec2nii import main
+
+
+if __name__ == '__main__':
+    main()

nibabel/cmdline/parrec2nii.py

@@ -10,6 +10,7 @@
 import csv
 import nibabel
 import nibabel.parrec as pr
+import nibabel.xmlrec as xr
 from nibabel.parrec import one_line
 from nibabel.mriutils import calculate_dwell_time, MRIError
 import nibabel.nifti1 as nifti1
@@ -147,7 +148,15 @@ def error(msg, exit_code):
 
 def proc_file(infile, opts):
     # figure out the output filename, and see if it exists
-    basefilename = splitext_addext(os.path.basename(infile))[0]
+    basefilename, ext = splitext_addext(os.path.basename(infile))[:2]
+
+    ext = ext.lower()
+    if (ext == '.xml' or
+            (ext == '.rec' and os.path.exists(basefilename + '.xml'))):
+        pr_module = xr
+    else:
+        pr_module = pr
+
     if opts.outdir is not None:
         # set output path
         basefilename = os.path.join(opts.outdir, basefilename)
@@ -165,10 +174,10 @@ def proc_file(infile, opts):
     # load the PAR header and data
     scaling = 'dv' if opts.scaling == 'off' else opts.scaling
     infile = fname_ext_ul_case(infile)
-    pr_img = pr.load(infile,
-                     permit_truncated=opts.permit_truncated,
-                     scaling=scaling,
-                     strict_sort=opts.strict_sort)
+    pr_img = pr_module.load(infile,
+                            permit_truncated=opts.permit_truncated,
+                            scaling=scaling,
+                            strict_sort=opts.strict_sort)
     pr_hdr = pr_img.header
     affine = pr_hdr.get_affine(origin=opts.origin)
     slope, intercept = pr_hdr.get_data_scaling(scaling)

nibabel/imageclasses.py

@@ -18,6 +18,7 @@
 from .nifti1 import Nifti1Pair, Nifti1Image
 from .nifti2 import Nifti2Pair, Nifti2Image
 from .parrec import PARRECImage
+from .xmlrec import XMLRECImage
 from .spm99analyze import Spm99AnalyzeImage
 from .spm2analyze import Spm2AnalyzeImage
 from .volumeutils import Recoder
@@ -32,7 +33,7 @@
                      Cifti2Image, Nifti2Image,  # Cifti2 before Nifti2
                      Spm2AnalyzeImage, Spm99AnalyzeImage, AnalyzeImage,
                      Minc1Image, Minc2Image, MGHImage,
-                     PARRECImage, GiftiImage, AFNIImage]
+                     PARRECImage, XMLRECImage, GiftiImage, AFNIImage]
 
 
 # DEPRECATED: mapping of names to classes and class functionality
@@ -90,6 +91,11 @@ def __getitem__(self, *args, **kwargs):
          'has_affine': True,
          'makeable': False,
          'rw': False},
+    xml={'class': XMLRECImage,
+         'ext': '.xml',
+         'has_affine': True,
+         'makeable': False,
+         'rw': False},
     afni={'class': AFNIImage,
           'ext': '.brik',
           'has_affine': True,
@@ -113,6 +119,7 @@ def __getitem__(self, *args, **kwargs):
     ('mgh', '.mgh'),
     ('mgz', '.mgz'),
     ('par', '.par'),
+    ('xml', '.xml'),
     ('brik', '.brik')
 ))
 
@@ -121,7 +128,7 @@ def __getitem__(self, *args, **kwargs):
 # here.
 KNOWN_SPATIAL_FIRST = (Nifti1Pair, Nifti1Image, Nifti2Pair, Nifti2Image,
                        Spm2AnalyzeImage, Spm99AnalyzeImage, AnalyzeImage,
-                       MGHImage, PARRECImage, AFNIImage)
+                       MGHImage, PARRECImage, XMLRECImage, AFNIImage)
 
 
 def spatial_axes_first(img):

nibabel/loadsave.py

@@ -19,6 +19,7 @@
 from .arrayproxy import is_proxy
 from .py3k import FileNotFoundError
 from .deprecated import deprecate_with_version
+from .parrec import PARRECImage
 
 
 def load(filename, **kwargs):
@@ -46,6 +47,15 @@ def load(filename, **kwargs):
     for image_klass in all_image_classes:
         is_valid, sniff = image_klass.path_maybe_image(filename, sniff)
         if is_valid:
+            if image_klass is PARRECImage and '.REC' in filename:
+                # a .REC file can have either a .PAR of .xml header.
+                # This skip case assumes PARRECImage is beforeXMLRECImage in
+                # all_image_classes.
+                par_exists = os.path.exists(filename.replace('.REC', '.PAR'))
+                xml_exists = os.path.exists(filename.replace('.REC', '.xml'))
+                if not par_exists and xml_exists:
+                    continue  # skip trying .PAR and proceed to .xml
+            print(image_klass)
             img = image_klass.from_filename(filename, **kwargs)
             return img
 

nibabel/parrec.py

@@ -865,7 +865,7 @@ def get_data_offset(self):
     def set_data_offset(self, offset):
         """ PAR header always has 0 data offset (into REC file) """
         if offset != 0:
-            raise PARRECError("PAR header assumes offset 0")
+            raise PARRECError("header assumes offset 0")
 
     def _calc_zooms(self):
         """Compute image zooms from header data.
@@ -894,7 +894,7 @@ def _calc_zooms(self):
         # If 4D dynamic scan, convert time from milliseconds to seconds
         if len(zooms) > 3 and self.general_info['dyn_scan']:
             if len(self.general_info['repetition_time']) > 1:
-                warnings.warn("multiple TRs found in .PAR file")
+                warnings.warn("multiple TRs found in header file")
             zooms[3] = self.general_info['repetition_time'][0] / 1000.
         return zooms