StackOrientation features

- Move more functionality onto enum to make it more interoperable with
string
- CoordinateTransformer, ProjectStack use StackOrientation internally

catpy/client.py

@@ -34,15 +34,40 @@ def __str__(self):
 
 
 class StackOrientation(IntEnum):
+    """Can be iterated over or indexed like the lower-case string representation of the orientation"""
     XY = 0
     XZ = 1
     ZY = 2
 
     def __str__(self):
         return self.name.lower()
 
+    @classmethod
+    def from_str(cls, s):
+        return {o.name: o for o in StackOrientation}[s.upper()]
+
+    @classmethod
+    def from_value(cls, value, default='xy'):
+        """Convert an int, str or StackOrientation into a StackOrientation.
+        A NoneType ``value`` will use the default orientation."""
+        if value is None:
+            value = default
+
+        if isinstance(value, string_types):
+            return cls.from_str(value)
+        elif isinstance(value, int):
+            return cls(value)
+        else:
+            raise TypeError("Cannot create a StackOrientation from {}".format(type(value).__name__))
 
-orientation_strs = {o: str(o) for o in StackOrientation}
+    def __iter__(self):
+        return iter(str(self))
+
+    def __getitem__(self, item):
+        return str(self)[item]
+
+    def __contains__(self, item):
+        return item in str(self)
 
 
 def make_url(base_url, *args):
@@ -401,7 +426,7 @@ def __init__(self, resolution=None, translation=None, orientation=StackOrientati
                 StackOrientation
                 int corresponding to StackOrientation
                 'xy', 'xz', or 'zy'
-                None (reverts to default)
+                None (reverts to default 'xy')
             Default StackOrientation.XY
         scale_z : bool
             Whether or not to scale z coordinates when using stack_to_scaled* methods. Default False is recommended, but
@@ -416,7 +441,7 @@ def __init__(self, resolution=None, translation=None, orientation=StackOrientati
         self.translation = {dim: translation.get(dim, 0) for dim in 'zyx'}
         self.scale_z = scale_z
 
-        self.orientation = self._validate_orientation(orientation)
+        self.orientation = StackOrientation.from_value(orientation)
         self.depth_dim = [dim for dim in 'zyx' if dim not in self.orientation][0]
 
         # mapping of project dimension to stack dimension, based on orientation
@@ -428,16 +453,6 @@ def __init__(self, resolution=None, translation=None, orientation=StackOrientati
         # mapping of stack dimension to project dimension, based on orientation
         self._p2s = {value: key for key, value in self._s2p.items()}
 
-    def _validate_orientation(self, orientation):
-        if orientation is None:
-            orientation = StackOrientation.XY
-        orientation = orientation_strs.get(orientation, orientation)
-        lower = orientation.lower()
-        if lower not in orientation_strs.values():
-            raise ValueError("orientation must be a StackOrientation, 'xy', 'xz', or 'zy'")
-
-        return lower
-
     @classmethod
     def from_catmaid(cls, catmaid_client, stack_id):
         """

catpy/image.py

@@ -23,7 +23,7 @@
 from requests_futures.sessions import FuturesSession
 
 from catpy import CoordinateTransformer
-
+from catpy.client import StackOrientation
 
 logger = logging.getLogger()
 
@@ -438,7 +438,7 @@ def __init__(self, dimension, translation, resolution, orientation, broken_slice
         super(ProjectStack, self).__init__(dimension, broken_slices, canary_location)
         self.translation = translation
         self.resolution = resolution
-        self.orientation = orientation
+        self.orientation = StackOrientation.from_value(orientation)
 
     @classmethod
     def from_stack_info(cls, stack_info):
@@ -455,7 +455,7 @@ def from_stack_info(cls, stack_info):
         """
         stack = cls(
             stack_info['dimension'], stack_info['translation'], stack_info['resolution'],
-            cls.orientation_choices[stack_info['orientation']], stack_info['broken_slices'],
+            stack_info['orientation'], stack_info['broken_slices'],
             stack_info['canary_location']
         )
         mirrors = [StackMirror.from_dict(d) for d in stack_info['mirrors']]
@@ -882,7 +882,7 @@ def roi_to_scaled(self, roi, roi_mode, zoom_level):
         if roi_mode == ROIMode.PROJECT:
             if not isinstance(self.stack, ProjectStack):
                 raise ValueError("ImageFetcher's stack is not related to a project, cannot use ROIMode.PROJECT")
-            if self.stack.orientation.lower() != 'xy':
+            if self.stack.orientation != StackOrientation.XY:
                 warn("Stack orientation differs from project: returned array's orientation will reflect"
                      "stack orientation, not project orientation")
             roi_tgt = self.coord_trans.project_to_stack_array(roi_tgt, dims=self.target_orientation)

tests/test_utils/test_coordinate_transformer.py

@@ -225,14 +225,14 @@ def test_stack_to_scaled_array(coordinate_generator, default_coord_transformer,
 ])
 def test_can_validate_orientation_valid(orientation):
     trans = CoordinateTransformer(orientation=orientation)
-    assert trans.orientation == 'xy'
+    assert trans.orientation == StackOrientation.XY
     assert trans.depth_dim == 'z'
 
 
 @pytest.mark.parametrize('orientation,expected_exception', [
-    [3, AttributeError],
-    ['xyz', ValueError],
-    ['xc', ValueError]
+    [3, ValueError],
+    ['xyz', KeyError],
+    ['xc', KeyError]
 ])
 def test_can_validate_orientation_invalid(orientation, expected_exception):
     with pytest.raises(expected_exception):