extraction/examples/pos_example.py → examples/extraction/pos_example.py

-from extraction.core.parameters import Parameters
 from extraction.core.extractor import Extractor
-import numpy as np
+from extraction.core.parameters import Parameters
 
 params = Parameters(
     tree={
@@ -15,6 +14,4 @@ params = Parameters(
 
 
 ext = Extractor(params, omero_id=19310)
-# ext.extract_exp(tile_size=117)
-d=ext.extract_tp(tp=1,tile_size=117)
-
+d = ext.extract_tp(tp=1, tile_size=117)

extraction/core/__init__.py

-#!/usr/bin/env python
-

extraction/core/functions/distributors.py

-import numpy as np
-
-
-def trap_apply(cell_fun, cell_masks, trap_image, **kwargs):
-    """
-    Apply a cell_function to a mask, trap_image pair
-
-    :param cell_fun: function to apply to a cell (from extraction/cell.py)
-    :param cell_masks: (numpy 3d array) cells' segmentation mask
-    :param trap_image: the image for the trap in which the cell is (all
-    channels)
-    :**kwargs: parameters to pass if needed for custom functions
-    """
-
-    cells_iter = (*range(cell_masks.shape[2]),)
-    return [cell_fun(cell_masks[..., i], trap_image, **kwargs) for i in cells_iter]
-
-
-def reduce_z(trap_image, fun):
-    # Optimise the reduction function if possible
-    if isinstance(fun, np.ufunc):
-        return fun.reduce(trap_image, axis=2)
-    else:
-        return np.apply_along_axis(fun, 2, trap_image)