correctly reorient and center coordinates from MRC

- fix #76
- add tests

CHANGELOG

@@ -22,6 +22,11 @@ The rules for this file:
   * use mrcfile library to parse MRC files (including CCP4) using the
     new mrc.MRC class (issue #83)
 
+  Fixes
+
+  * The new mrc module correctly reorients the coordinate system based
+    on mapc, mapr, maps and correctly calculates the origin (issue #76)
+
   Deprecations
 
   * The CCP4 module (replaced by mrc) will be removed in 0.8.0.

gridData/mrc.py

@@ -113,11 +113,18 @@ def read(self, filename):
             # 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])
+            #
+            # All other "xyz" quantitities are also reordered.
+            axes_order = np.hstack([h.mapc, h.mapr, h.maps])
             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.delta = np.diag(
+                np.array([mrc.voxel_size.x, mrc.voxel_size.y, mrc.voxel_size.z])[axes_c_order])
+            # the grid is shifted to the CCP4 origin by offset
+            # (assume orthorhombic)
+            offsets = np.hstack([h.nxstart, h.nystart, h.nzstart])[axes_c_order] * np.diag(self.delta)
+            # GridData origin is centre of cell at x=col=0, y=row=0 z=seg=0
+            self.origin = np.hstack([h.origin.x, h.origin.y, h.origin.z])[axes_c_order] + offsets
             self.rank = 3
 
     @property
@@ -127,7 +134,7 @@ def shape(self):
 
     @property
     def edges(self):
-        """Edges of the grid cells, origin at centre of 0,0,..,0 grid cell.
+        """Edges of the grid cells, origin at centre of 0,0,0 grid cell.
 
         Only works for regular, orthonormal grids.
         """

gridData/tests/test_mrc.py

@@ -94,7 +94,20 @@ 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))
+    assert_equal(ccp4data.shape, (76, 96, 70))
+
+def test_delta(ccp4data):
+    assert_almost_equal(ccp4data.delta, np.array(
+        [[0.5452381, 0.       , 0.       ],
+         [0.       , 0.5452381, 0.       ],
+         [0.       , 0.       , 0.5603125]], dtype=np.float32))
+
+def test_origin(ccp4data):
+    # shift with nxstart, nystart, nzstart and delta
+    #
+    # (visual comparison of CCP4 and DX file in ChimeraX at same
+    # level shows full agreement)
+    assert_almost_equal(ccp4data.origin, [-12.5404758,  -2.1809523,  57.151876 ])
 
 def test_triclinic_ValueError():
     with pytest.raises(ValueError,