add additional log message

src/sparcscore/pipeline/segmentation.py

@@ -657,6 +657,7 @@ def calculate_sharding_plan(self, image_size):
     def cleanup_shards(self, sharding_plan):
         file_identifiers_plots = [".png", ".tif", ".tiff", ".jpg", ".jpeg", ".pdf"]
 
+        self.log("Moving generated plots from shard directory to main directory.")
         for i, window in enumerate(sharding_plan):
             local_shard_directory = os.path.join(self.shard_directory, str(i))
             for file in os.listdir(local_shard_directory):
@@ -945,7 +946,6 @@ def process(self, input_image):
 
     def complete_segmentation(self, input_image):
         self.save_zarr = False
-        self.save_input_image(input_image)
         self.shard_directory = os.path.join(self.directory, self.DEFAULT_SHARD_FOLDER)
 
         # check to make sure that the shard directory exisits, if not exit and return error
@@ -954,6 +954,9 @@ def complete_segmentation(self, input_image):
                 "No Shard Directory found for the given project. Can not complete a segmentation which has not started. Please rerun the segmentation method."
             )
 
+        #save input image to segmentation.h5
+        self.save_input_image(input_image)
+
         # check to see which tiles are incomplete
         tile_directories = os.listdir(self.shard_directory)
         incomplete_indexes = []