correct orientation of axes from MRC file

- mrcfile only reshapes the data to nz,ny,nx but does not take
  the mapc, mapr, maps into account. For gridData we need to
  do the coordinate system reorientation after transposing the
  mrcfile.data to nx, ny, nz.
- add test (using CCP4_1JZV from the test data which contains
  mapc, mapr, maps = 2, 1, 3
- manually checked 1cbs.ccp4 from issue #76 (also a 2, 1, 3)
  and orientation is now correct but there is still an offset error
  that needs to be fixed

gridData/mrc.py

@@ -107,12 +107,15 @@ def read(self, filename):
                                  "alpha={0}, beta={1}, gamma={2}".format(
                                      h.cellb.alpha, h.cellb.beta, h.cellb.gamma))
             # mrc.data[z, y, x] indexed: convert to x,y,z as used in GridDataFormats
-            # mapc, mapr, maps = 1, 2, 3 for Fortran-ordering and 3, 2, 1 for C-ordering. 
-            # Other combinations are possible. We reorder the data for the general case 
-            # by sorting mapc, mapr, maps in descending order.
+            # together with the axes orientation information in mapc/mapr/maps.
+            # mapc, mapr, maps = 1, 2, 3 for Fortran-ordering and 3, 2, 1 for C-ordering.
+            # Other combinations are possible. We reorder the data for the general case
+            # by sorting mapc, mapr, maps in ascending order, i.e., to obtain x,y,z.
+            # mrcfile provides the data in zyx shape (without regard to map*) so we first
+            # transpose it to xyz and then reorient with axes_c_order.
             axes_order = np.hstack([mrc.header.mapc, mrc.header.mapr, mrc.header.maps])
-            axes_c_order = np.argsort(axes_order)[::-1]
-            self.array = np.transpose(mrc.data, axes = axes_c_order)
+            axes_c_order = np.argsort(axes_order)
+            self.array = np.transpose(np.transpose(mrc.data), axes=axes_c_order)
             self.delta = np.diag([mrc.voxel_size.x, mrc.voxel_size.y, mrc.voxel_size.z])
             self.origin = np.array([h.origin.x, h.origin.y, h.origin.z])
             self.rank = 3

gridData/tests/test_mrc.py

@@ -90,8 +90,15 @@ def test_ccp4_read_header(ccp4data, name, value):
     else:
         assert_equal(ccp4data.header[name], value)
 
+def test_axes_orientation(ccp4data):
+    # correctly interpret mapc, mapr, maps = 2, 1, 3
+    # for nx, ny, nz = 96, 76, 70.
+    # see also #76
+    assert_equal(ccp4data.array.shape, (76, 96, 70))
+
 def test_triclinic_ValueError():
     with pytest.raises(ValueError,
                        match="Only orthorhombic unitcells are currently "
                        "supported, not"):
         Grid(datafiles.MRC_EMD3001, file_format="MRC")
+