Remove wrapper functions to make util.clem import cleaner (#300)

Author: d-j-hatton

src/murfey/cli/lif_to_tiff.py

@@ -1,7 +1,7 @@
 import argparse
 from pathlib import Path
 
-from murfey.util.clem import convert_lif_to_tiff
+from murfey.util.clem.lif import convert_lif_to_tiff
 
 
 def run():

src/murfey/cli/tiff_to_stack.py

@@ -1,7 +1,7 @@
 import argparse
 from pathlib import Path
 
-from murfey.util.clem import convert_tiff_to_stack
+from murfey.util.clem.tiff import convert_tiff_to_stack
 
 
 def run():

src/murfey/server/clem/api.py

@@ -5,7 +5,8 @@
 from fastapi import APIRouter
 
 from murfey.server import _transport_object
-from murfey.util.clem import convert_lif_to_tiff, convert_tiff_to_stack
+from murfey.util.clem.lif import convert_lif_to_tiff
+from murfey.util.clem.tiff import convert_tiff_to_stack
 from murfey.util.models import LifFileInfo, TiffSeriesInfo
 
 # Create APIRouter class object

src/murfey/util/clem/__init__.py

@@ -1,51 +0,0 @@
-"""
-Functions to call for processing LIF and TIFF files generated as part of the cryo-CLEM
-workflow.
-"""
-
-import logging
-from pathlib import Path
-from typing import List, Optional
-
-from murfey.util.clem import lif, tiff
-
-# Create logger object to output messages with
-logger = logging.getLogger("murfey.util.clem")
-
-
-def convert_lif_to_tiff(
-    file: Path,
-    root_folder: str,  # Name of the folder to treat as the root folder for LIF files
-    number_of_processes: int = 1,  # Number of processing threads to run
-):
-    """
-    Wrapper for the actual function in lif.py
-    """
-    result = lif.convert_lif_to_tiff(
-        file,
-        root_folder,
-        number_of_processes,
-    )
-    if result:
-        return True
-    else:
-        return False
-
-
-def convert_tiff_to_stack(
-    tiff_list: List[Path],  # List of TIFFs from a single series
-    root_folder: str,  # Name of the folder to treat as the root folder for TIFF files
-    metadata_file: Optional[Path] = None,  # Option to manually provide metadata file
-):
-    """
-    Wrapper for the actual function in tiff.py
-    """
-    result = tiff.convert_tiff_to_stack(
-        tiff_list,
-        root_folder,
-        metadata_file,
-    )
-    if result:
-        return True
-    else:
-        return False

src/murfey/util/clem/lif.py

@@ -26,7 +26,7 @@ def process_lif_file(
     scene_num: int,
     metadata: ET.Element,
     save_dir: Path,
-):
+) -> bool:
     """
     Takes the LIF file and its corresponding metadata and loads the relevant sub-stack,
     with each channel as its own array. Rescales their intensity values to utilise the
@@ -141,7 +141,7 @@ def convert_lif_to_tiff(
     file: Path,
     root_folder: str,  # Name of the folder to treat as the root folder for LIF files
     number_of_processes: int = 1,  # Number of processing threads to run
-):
+) -> bool:
     """
     Takes a LIF file, extracts its metadata as an XML tree, then parses through the
     sub-images stored inside it, saving each channel in the sub-image as a separate
@@ -198,7 +198,7 @@ def convert_lif_to_tiff(
             f"Subpath {sanitise(root_folder)} was not found in image path "
             f"{sanitise(str(file))}"
         )
-        return None
+        return False
 
     # Create folders if not already present
     processed_dir = Path("/".join(path_parts)).parent / file_name  # Processed images
@@ -255,6 +255,5 @@ def convert_lif_to_tiff(
         result = pool.starmap(process_lif_file, pool_args)
 
     if result:
-        return True
-    else:
-        return None
+        return all(result)
+    return False

src/murfey/util/clem/tiff.py

@@ -26,7 +26,7 @@ def process_tiff_files(
     tiff_list: List[Path],
     metadata_file: Path,
     save_dir: Path,
-):
+) -> bool:
     """
     Opens the TIFF files as NumPy arrays and stacks them.
     """
@@ -225,7 +225,7 @@ def convert_tiff_to_stack(
             f"Subpath {sanitise(root_folder)} was not found in file path "
             f"{sanitise(str(parent_dir))}"
         )
-        return None
+        return False
     # Make directory for processed files
     processed_dir = Path("/".join(path_parts))  # Images
     if not processed_dir.exists():
@@ -241,13 +241,8 @@ def convert_tiff_to_stack(
             logger.info(f"Metadata file found at {xml_file}")
         else:
             logger.error(f"No metadata file found at {xml_file}")
-            return None
+            return False
     else:
         xml_file = metadata_file
 
-    result = process_tiff_files(tiff_list, xml_file, processed_dir)
-
-    if result:
-        return True
-    else:
-        return None
+    return process_tiff_files(tiff_list, xml_file, processed_dir)