refactor deepcell transform to pixelwise (#56)

* refactor deepcell transform to pixelwise * leave 'deepcell' as a lookup for postprocessing functions for backwards compat
vanvalenlab · Aug 23, 2019 · 791293e · 791293e
1 parent 239094e
commit 791293e
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Showing 3 changed files with 9 additions and 8 deletions.
diff --git a/redis_consumer/processing.py b/redis_consumer/processing.py
@@ -57,7 +57,7 @@ def mibi(prediction, edge_threshold=.25, interior_threshold=.25):
     boundary is reached.
 
     Args:
-        prediction: output from a deepcell transform (edge, interior, bg)
+        prediction: output from a pixelwise transform (edge, interior, bg)
         edge_threshold: confidence threshold to determine edge pixels
         interior_threshold: confidence threshold to determine interior pixels
 
@@ -158,12 +158,12 @@ def watershed(image, min_distance=10, threshold_abs=0.05):
     return results
 
 
-def deepcell(prediction, threshold=.8):
-    """Post-processing for deepcell transform predictions.
+def pixelwise(prediction, threshold=.8):
+    """Post-processing for pixelwise transform predictions.
     Uses the interior predictions to uniquely label every instance.
 
     Args:
-        prediction: deepcell transform prediction
+        prediction: pixelwise transform prediction
         threshold: confidence threshold for interior predictions
 
     Returns:

diff --git a/redis_consumer/processing_test.py b/redis_consumer/processing_test.py
@@ -101,11 +101,11 @@ def test_mibi():
     np.testing.assert_equal(mibi_img.shape, (300, 300, 1))
 
 
-def test_deepcell():
+def test_pixelwise():
     channels = 4
     img = np.random.rand(300, 300, channels)
-    deepcell_img = processing.deepcell(img)
-    np.testing.assert_equal(deepcell_img.shape, (300, 300, 1))
+    pixelwise_img = processing.pixelwise(img)
+    np.testing.assert_equal(pixelwise_img.shape, (300, 300, 1))
 
 
 def test_watershed():

diff --git a/redis_consumer/settings.py b/redis_consumer/settings.py
@@ -121,7 +121,8 @@ def _strip(x):
         'normalize': processing.noramlize,
     },
     'post': {
-        'deepcell': processing.deepcell,
+        'deepcell': processing.pixelwise,  # TODO: this is deprecated.
+        'pixelwise': processing.pixelwise,
         'mibi': processing.mibi,
         'watershed': processing.watershed,
         'retinanet': processing.retinanet_to_label_image,