Merge pull request #34 from angelolab/fix_bugs

Added approximate option for naming convention

src/nimbus_inference/nimbus.py

@@ -18,19 +18,30 @@
 import re
 
 
-def prep_naming_convention(deepcell_output_dir):
+def prep_naming_convention(deepcell_output_dir, approx=False):
     """Prepares the naming convention for the segmentation data produced with the DeepCell library.
 
     Args:
         deepcell_output_dir (str): path to directory where segmentation data is saved
+        approx (bool): whether to use an approximate naming convention
     Returns:
         function: function that returns the path to the
             segmentation data for a given fov
     """
-
     def segmentation_naming_convention(fov_path):
         """Prepares the path to the segmentation data for a given fov
 
+        Args:
+            fov_path (str): path to fov
+        Returns:
+            str: paths to segmentation fovs
+        """
+        fov_name = os.path.basename(fov_path).replace(".ome.tiff", "")
+        return os.path.join(deepcell_output_dir, fov_name + "_whole_cell.tiff")
+
+    def segmentation_naming_convention_approx(fov_path):
+        """Prepares the path to the segmentation data for a given fov
+
         Args:
             fov_path (str): path to fov
         Returns:
@@ -48,7 +59,11 @@ def segmentation_naming_convention(fov_path):
         if len(fnames) > 1:
             raise ValueError(f"Multiple segmentation data found for fov {fov_name}")
         return fnames[0]
-    return segmentation_naming_convention
+
+    if approx:
+        return segmentation_naming_convention_approx
+    else:
+        return segmentation_naming_convention
 
 
 class Nimbus(nn.Module):