[aaronkanzer]

CrystalMap.get_map_data() and slicing assume the map's x and y coordinates start at 0. If they start anywhere else, columns or rows are silently dropped, or the result is an empty array. This happens with an .ang file exported for a region of interest that keeps its original coordinates, or with a map built from stage coordinates.

import numpy as np
from orix.crystal_map import CrystalMap
from orix.quaternion import Rotation

y, x = np.indices((3, 4))
xmap = CrystalMap(Rotation.identity(12), x=x.ravel() + 1.0, y=y.ravel())
print(xmap.shape)
print(xmap.get_map_data("x"))

Observed on 0.15.0 and develop:

(3, 4)
[[2. 3. 4.]
 [2. 3. 4.]
 [2. 3. 4.]]

Expected: a (3, 4) array whose rows are all [1. 2. 3. 4.].

With an x origin of 10 and a step of 0.5, get_map_data() returns shape (3, 0). Slicing (xmap[:2]) raises ValueError: could not broadcast input array from shape (3,4) into shape (3,0). The same happens after orix.io.load() of an .ang file whose x column starts at 10.

Cause: CrystalMap._data_slices_from_coordinates() turns coordinates into array indices with round(c / step). Those indices are then used on arrays of the original map shape, so they are only correct when the smallest coordinate is 0.

Fix: make the slices relative to the first point of the full map. Maps that start at 0 are unchanged. A regression test covers get_map_data() and slicing on a map with an offset origin.