Fixing coordinate issues with max_proj

starfish/core/imagestack/imagestack.py

@@ -1152,7 +1152,7 @@ def max_proj(self, *dims: Axes) -> "ImageStack":
         max_projection = self._data.max([dim.value for dim in dims])
         max_projection = max_projection.expand_dims(tuple(dim.value for dim in dims))
         max_projection = max_projection.transpose(*self.xarray.dims)
-        max_proj_stack = self.from_numpy(max_projection.values)
+        max_proj_stack = self.from_numpy(max_projection.values, coordinates=self.xarray.coords)
         return max_proj_stack
 
     def _squeezed_numpy(self, *dims: Axes):

starfish/core/imagestack/parser/numpy/__init__.py

@@ -122,12 +122,6 @@ def get_tile(self, r: int, ch: int, z: int) -> TileData:
         pos_ch = self.index_labels[Axes.CH].index(ch)
         pos_z = self.index_labels[Axes.ZPLANE].index(z)
 
-        selectors: Mapping[str, Any] = {
-            Axes.ROUND.value: r,
-            Axes.CH.value: ch,
-            Axes.ZPLANE.value: z,
-        }
-
         coordinates: MutableMapping[Coordinates, Tuple[Number, Number]] = dict()
 
         if self.coordinates is not None:
@@ -136,14 +130,9 @@ def get_tile(self, r: int, ch: int, z: int) -> TileData:
                     (Coordinates.Y, PhysicalCoordinateTypes.Y_MIN, PhysicalCoordinateTypes.Y_MAX),
                     (Coordinates.Z, PhysicalCoordinateTypes.Z_MIN, PhysicalCoordinateTypes.Z_MAX),
             ):
-                min_selectors = dict(selectors)
-                min_selectors[PHYSICAL_COORDINATE_DIMENSION] = min_selector_value.value
-                max_selectors = dict(selectors)
-                max_selectors[PHYSICAL_COORDINATE_DIMENSION] = max_selector_value.value
-
                 coordinates[coordinate_type] = (
-                    self.coordinates.loc[min_selectors].item(),
-                    self.coordinates.loc[max_selectors].item())
+                    float(self.coordinates[coordinate_type][0]),
+                    float(self.coordinates[coordinate_type][-1]))
         else:
             # fake coordinates!
             coordinates[Coordinates.X] = (0.0, 0.001)

starfish/core/imagestack/test/test_max_proj.py

@@ -1,5 +1,6 @@
 import numpy as np
 
+from starfish import data
 from starfish.core.types import Axes
 from ..imagestack import ImageStack
 
@@ -11,3 +12,12 @@ def test_max_projection_preserves_dtype():
 
     max_projection = image.max_proj(Axes.CH, Axes.ROUND, Axes.ZPLANE)
     assert max_projection.xarray.dtype == original_dtype
+
+
+def test_max_projection_preserves_coordinates():
+    e = data.ISS(use_test_data=True)
+    nuclei = e.fov().get_image('nuclei')
+    nuclei_proj = nuclei.max_proj(Axes.ROUND, Axes.CH, Axes.ZPLANE)
+    # Since this data already has only 1 round, 1 ch, 1 zplane
+    # let's just assert that the max_proj operation didn't change anything
+    assert nuclei.xarray.equals(nuclei_proj.xarray)