Merge pull request #493 from rdvincent/rdv-minc-reader-fixes

MRG: Miscellaneous MINC reader fixes

This PR is a potpourri of small fixes for the MINC1 and MINC2 readers.

Author: matthew-brett

nibabel/externals/netcdf.py

@@ -210,6 +210,14 @@ def __init__(self, filename, mode='r', mmap=None, version=1):
             self.fp = open(self.filename, '%sb' % mode)
             if mmap is None:
                 mmap = True
+        try:
+            self.fp.seek(0, 2)
+        except ValueError:
+            self.file_bytes = -1 # Unknown file length (gzip).
+        else:
+            self.file_bytes = self.fp.tell()
+            self.fp.seek(0)
+
         self.use_mmap = mmap
         self.version_byte = version
 
@@ -599,14 +607,22 @@ def _read_var_array(self):
             else:  # not a record variable
                 # Calculate size to avoid problems with vsize (above)
                 a_size = reduce(mul, shape, 1) * size
-                if self.use_mmap:
+                if self.file_bytes >= 0 and begin_ + a_size > self.file_bytes:
+                    data = fromstring(b'\x00'*a_size, dtype=dtype_)
+                elif self.use_mmap:
                     mm = mmap(self.fp.fileno(), begin_+a_size, access=ACCESS_READ)
                     data = ndarray.__new__(ndarray, shape, dtype=dtype_,
                             buffer=mm, offset=begin_, order=0)
                 else:
                     pos = self.fp.tell()
                     self.fp.seek(begin_)
-                    data = fromstring(self.fp.read(a_size), dtype=dtype_)
+                    # Try to read file, which may fail because the data is
+                    # at or past the end of file. In that case, we treat
+                    # this data as zeros.
+                    buf = self.fp.read(a_size)
+                    if len(buf) < a_size:
+                        buf = b'\x00'*a_size
+                    data = fromstring(buf, dtype=dtype_)
                     data.shape = shape
                     self.fp.seek(pos)
 

nibabel/minc1.py

@@ -95,8 +95,8 @@ def get_data_shape(self):
     def get_zooms(self):
         """ Get real-world sizes of voxels """
         # zooms must be positive; but steps in MINC can be negative
-        return tuple(
-            [abs(float(dim.step)) for dim in self._dims])
+        return tuple([abs(float(dim.step)) if hasattr(dim, 'step') else 1.0
+                      for dim in self._dims])
 
     def get_affine(self):
         nspatial = len(self._spatial_dims)
@@ -106,13 +106,11 @@ def get_affine(self):
         dim_names = list(self._dim_names)  # for indexing in loop
         for i, name in enumerate(self._spatial_dims):
             dim = self._dims[dim_names.index(name)]
-            try:
-                dir_cos = dim.direction_cosines
-            except AttributeError:
-                dir_cos = _default_dir_cos[name]
-            rot_mat[:, i] = dir_cos
-            steps[i] = dim.step
-            starts[i] = dim.start
+            rot_mat[:, i] = (dim.direction_cosines
+                             if hasattr(dim, 'direction_cosines')
+                             else _default_dir_cos[name])
+            steps[i] = dim.step if hasattr(dim, 'step') else 1.0
+            starts[i] = dim.start if hasattr(dim, 'start') else 0.0
         origin = np.dot(rot_mat, starts)
         aff = np.eye(nspatial + 1)
         aff[:nspatial, :nspatial] = rot_mat * steps

nibabel/minc2.py

@@ -77,7 +77,10 @@ def _get_dimensions(self, var):
             dimorder = var.attrs['dimorder'].decode()
         except KeyError:  # No specified dimensions
             return []
-        return dimorder.split(',')
+        # The dimension name list must contain only as many entries
+        # as the variable has dimensions. This reduces errors when an
+        # unnecessary dimorder attribute is left behind.
+        return dimorder.split(',')[:len(var.shape)]
 
     def get_data_dtype(self):
         return self._image.dtype
@@ -95,7 +98,7 @@ def _get_valid_range(self):
         info = np.iinfo(ddt.type)
         try:
             valid_range = self._image.attrs['valid_range']
-        except AttributeError:
+        except (AttributeError, KeyError):
             valid_range = [info.min, info.max]
         else:
             if valid_range[0] < info.min or valid_range[1] > info.max:

nibabel/tests/data/minc1-no-att.mnc

@@ -83,6 +83,21 @@
             max=1.498039216,
             mean=0.9090422837),
         is_proxy=True),
+    dict(
+        fname=pjoin(data_path, 'minc1-no-att.mnc'),
+        shape=(10, 20, 20),
+        dtype=np.uint8,
+        affine=np.array([[0, 0, 1.0, 0],
+                         [0, 1.0, 0, 0],
+                         [1.0, 0, 0, 0],
+                         [0, 0, 0, 1]]),
+        zooms=(1., 1., 1.),
+        # These values from SPM2/mincstats
+        data_summary=dict(
+            min=0.20784314,
+            max=0.74901961,
+            mean=0.6061103),
+        is_proxy=True),
 ]
 
 

nibabel/tests/data/minc2-4d-d.mnc

@@ -72,7 +72,37 @@
             min=0.2078431373,
             max=1.498039216,
             mean=0.9090422837),
-        is_proxy=True)
+        is_proxy=True),
+    dict(
+        fname=pjoin(data_path, 'minc2-no-att.mnc'),
+        shape=(10, 20, 20),
+        dtype=np.uint8,
+        affine=np.array([[0, 0, 1.0, 0],
+                         [0, 1.0, 0, 0],
+                         [1.0, 0, 0, 0],
+                         [0, 0, 0, 1]]),
+        zooms=(1., 1., 1.),
+        # These values from SPM2/mincstats
+        data_summary=dict(
+            min=0.20784314,
+            max=0.74901961,
+            mean=0.6061103),
+        is_proxy=True),
+    dict(
+        fname=pjoin(data_path, 'minc2-4d-d.mnc'),
+        shape=(5, 16, 16, 16),
+        dtype=np.float64,
+        affine=np.array([[1., 0., 0.,  -6.96 ],
+                         [0., 1., 0., -12.453],
+                         [0., 0., 1.,  -9.48 ],
+                         [0., 0., 0., 1.]]),
+        zooms=(1., 1., 1., 1.),
+        # These values from mincstats
+        data_summary=dict(
+            min=0.0,
+            max=5.0,
+            mean=2.00078125),
+        is_proxy=True),
 ]
 
 if have_h5py: