RF: Better support for nifti1/2 + FSLOUTPUTTYPE

fsl/data/image.py

@@ -39,7 +39,6 @@ import                      json
 import                      string
 import                      logging
 import                      tempfile
-import                      warnings
 
 import                      six
 import numpy             as np
@@ -1099,11 +1098,12 @@ class Image(Nifti):
                 if header is not None: xform = header.get_best_affine()
                 else:                  xform = np.identity(4)
 
-            # We default to NIFTI1 and not
-            # NIFTI2, because the rest of
-            # FSL is not yet NIFTI2 compatible.
+            # default to NIFTI1 if FSLOUTPUTTYPE
+            # is not set, just to be safe.
             if header is None:
-                ctr = nib.nifti1.Nifti1Image
+                outputType = os.environ.get('FSLOUTPUTTYPE', 'NIFTI_GZ')
+                if 'NIFTI2' in outputType: ctr = nib.Nifti2Image
+                else:                      ctr = nib.Nifti1Image
 
             # make sure that the data type is correct,
             # in case this header was passed in from
@@ -1648,9 +1648,14 @@ def defaultExt():
 
     # TODO: Add analyze support.
     options = {
-        'NIFTI'      : '.nii',
-        'NIFTI_PAIR' : '.img',
-        'NIFTI_GZ'   : '.nii.gz',
+        'NIFTI'          : '.nii',
+        'NIFTI2'         : '.nii',
+        'NIFTI_GZ'       : '.nii.gz',
+        'NIFTI2_GZ'      : '.nii.gz',
+        'NIFTI_PAIR'     : '.img',
+        'NIFTI2_PAIR'    : '.img',
+        'NIFTI_PAIR_GZ'  : '.img.gz',
+        'NIFTI2_PAIR_GZ' : '.img.gz',
     }
 
     outputType = os.environ.get('FSLOUTPUTTYPE', 'NIFTI_GZ')

tests/test_image.py

@@ -246,6 +246,11 @@ def _test_Image_atts(imgtype):
 
     allowedExts = fslimage.ALLOWED_EXTENSIONS
     fileGroups  = fslimage.FILE_GROUPS
+    typeMap     = {np.uint8   : constants.NIFTI_DT_UINT8,
+                   np.int16   : constants.NIFTI_DT_INT16,
+                   np.int32   : constants.NIFTI_DT_INT32,
+                   np.float32 : constants.NIFTI_DT_FLOAT32,
+                   np.float64 : constants.NIFTI_DT_FLOAT64}
 
     # (file, dims, pixdims, dtype)
     dtypes = [np.uint8, np.int16, np.int32, np.float32, np.double]
@@ -307,14 +312,15 @@ def _test_Image_atts(imgtype):
             assert tuple(i.nibImage.shape)              == tuple(dims)
             assert tuple(i.nibImage.header.get_zooms()) == tuple(pixdims)
 
-            assert i.nvals      == 1
-            assert i.ndim       == expndims
-            assert i.dtype      == dtype
-            assert i.name       == op.basename(path)
-            assert i.dataSource == fslpath.addExt(path,
-                                                  allowedExts=allowedExts,
-                                                  mustExist=True,
-                                                  fileGroups=fileGroups)
+            assert i.nvals         == 1
+            assert i.ndim          == expndims
+            assert i.dtype         == dtype
+            assert i.niftiDataType == typeMap[dtype]
+            assert i.name          == op.basename(path)
+            assert i.dataSource    == fslpath.addExt(path,
+                                                     allowedExts=allowedExts,
+                                                     mustExist=True,
+                                                     fileGroups=fileGroups)
             i = None