[easy] Modularize segmentation mask

starfish/core/segmentation_mask/__init__.py

@@ -0,0 +1 @@
+from .segmentation_mask import SegmentationMaskCollection

starfish/core/segmentation_mask.py → starfish/core/segmentation_mask/segmentation_mask.py

@@ -7,40 +7,10 @@
 from skimage.measure import regionprops
 
 from starfish.core.types import Axes, Coordinates
+from .util import _get_axes_names
 
 
-AXES = [a.value for a in Axes if a not in (Axes.ROUND, Axes.CH)]
-COORDS = [c.value for c in Coordinates]
-
-
-def _get_axes_names(ndim: int) -> Tuple[List[str], List[str]]:
-    """Get needed axes names given the number of dimensions.
-
-    Parameters
-    ----------
-    ndim : int
-        Number of dimensions.
-
-    Returns
-    -------
-    axes : List[str]
-        Axes names.
-    coords : List[str]
-        Coordinates names.
-    """
-    if ndim == 2:
-        axes = [axis for axis in AXES if axis != Axes.ZPLANE.value]
-        coords = [coord for coord in COORDS if coord != Coordinates.Z.value]
-    elif ndim == 3:
-        axes = AXES
-        coords = COORDS
-    else:
-        raise TypeError('expected 2- or 3-D image')
-
-    return axes, coords
-
-
-def validate_segmentation_mask(arr: xr.DataArray):
+def _validate_segmentation_mask(arr: xr.DataArray):
     """Validate if the given array is a segmentation mask.
 
     Parameters
@@ -108,7 +78,7 @@ def append(self, mask: xr.DataArray):
         arr : xr.DataArray
             Segmentation mask.
         """
-        validate_segmentation_mask(mask)
+        _validate_segmentation_mask(mask)
         self._masks.append(mask)
 
         for axis in Axes:

starfish/core/test/test_segmentation_mask.py → starfish/core/segmentation_mask/test/test_segmentation_mask.py

@@ -4,11 +4,8 @@
 import pytest
 import xarray as xr
 
-from starfish.core.segmentation_mask import (
-    SegmentationMaskCollection,
-    validate_segmentation_mask,
-)
 from starfish.core.types import Axes, Coordinates
+from ..segmentation_mask import _validate_segmentation_mask, SegmentationMaskCollection
 
 
 def test_validate_segmentation_mask():
@@ -19,7 +16,7 @@ def test_validate_segmentation_mask():
                                     y=[0, 1],
                                     xc=('x', [0.5, 1.5, 2.5]),
                                     yc=('y', [0.5, 1.5])))
-    validate_segmentation_mask(good)
+    _validate_segmentation_mask(good)
 
     good = xr.DataArray([[[True], [False], [False]],
                          [[False], [True], [True]]],
@@ -30,7 +27,7 @@ def test_validate_segmentation_mask():
                                     zc=('z', [0.5, 1.5]),
                                     yc=('y', [1.5, 2.5, 3.5]),
                                     xc=('x', [42.5])))
-    validate_segmentation_mask(good)
+    _validate_segmentation_mask(good)
 
     bad = xr.DataArray([[1, 2, 3],
                         [4, 5, 6]],
@@ -40,14 +37,14 @@ def test_validate_segmentation_mask():
                                    xc=('x', [0.5, 1.5, 2.5]),
                                    yc=('y', [0.5, 1.5])))
     with pytest.raises(TypeError):
-        validate_segmentation_mask(bad)
+        _validate_segmentation_mask(bad)
 
     bad = xr.DataArray([True],
                        dims=('x'),
                        coords=dict(x=[0],
                                    xc=('x', [0.5])))
     with pytest.raises(TypeError):
-        validate_segmentation_mask(bad)
+        _validate_segmentation_mask(bad)
 
     bad = xr.DataArray([[True]],
                        dims=('z', 'y'),
@@ -56,12 +53,12 @@ def test_validate_segmentation_mask():
                                    zc=('z', [0.5]),
                                    yc=('y', [0.5])))
     with pytest.raises(TypeError):
-        validate_segmentation_mask(bad)
+        _validate_segmentation_mask(bad)
 
     bad = xr.DataArray([[True]],
                        dims=('x', 'y'))
     with pytest.raises(TypeError):
-        validate_segmentation_mask(bad)
+        _validate_segmentation_mask(bad)
 
 
 def test_from_label_image():

starfish/core/segmentation_mask/util.py

@@ -0,0 +1,34 @@
+from typing import List, Tuple
+
+from starfish.core.types import Axes, Coordinates
+
+
+AXES = [a.value for a in Axes if a not in (Axes.ROUND, Axes.CH)]
+COORDS = [c.value for c in Coordinates]
+
+
+def _get_axes_names(ndim: int) -> Tuple[List[str], List[str]]:
+    """Get needed axes names given the number of dimensions.
+
+    Parameters
+    ----------
+    ndim : int
+        Number of dimensions.
+
+    Returns
+    -------
+    axes : List[str]
+        Axes names.
+    coords : List[str]
+        Coordinates names.
+    """
+    if ndim == 2:
+        axes = [axis for axis in AXES if axis != Axes.ZPLANE.value]
+        coords = [coord for coord in COORDS if coord != Coordinates.Z.value]
+    elif ndim == 3:
+        axes = AXES
+        coords = COORDS
+    else:
+        raise TypeError('expected 2- or 3-D image')
+
+    return axes, coords