Optimised conditionals and updated comments for CLEM functions (#301)

Author: tieneupin

src/murfey/client/contexts/clem.py

@@ -27,7 +27,7 @@ def _file_transferred_to(
     environment: MurfeyInstanceEnvironment, source: Path, file_path: Path
 ) -> Optional[Path]:
     """
-    Returns the Path of the transferred file on the DLS file system
+    Returns the Path of the transferred file on the DLS file system.
     """
     machine_config = get_machine_config(
         str(environment.url.geturl()), demo=environment.demo
@@ -45,7 +45,7 @@ def _get_source(
     file_path: Path, environment: MurfeyInstanceEnvironment
 ) -> Optional[Path]:
     """
-    Returns the Path of the file on the client PC
+    Returns the Path of the file on the client PC.
     """
     for s in environment.sources:
         if file_path.is_relative_to(s):
@@ -54,7 +54,6 @@ def _get_source(
 
 
 # WORK IN PROGRESS
-# Will need to add context for TIFF files associated with CLEM
 class CLEMContext(Context):
     def __init__(self, acquisition_software: str, basepath: Path):
         super().__init__("CLEM", acquisition_software)
@@ -107,13 +106,13 @@ def post_transfer(
                 return False
 
             # Process TIF/TIFF files
-            if any(transferred_file.suffix == s for s in [".tif", ".tiff"]):
+            if transferred_file.suffix in (".tif", ".tiff"):
                 # Files should be named "PositionX--ZXX--CXX.tif" by default
                 if not len(transferred_file.stem.split("--")) == 3:
                     logger.warning(
                         "This TIFF file is likely not part of the CLEM workflow"
                     )
-                    return False  # Not sure if None, False, or True is most appropriate
+                    return False
 
                 # Get series name from file name
                 series_name = "/".join(

src/murfey/util/clem/images.py

@@ -66,7 +66,7 @@ def rescale_across_channel(
     """
 
     # Check that bit depth is valid before processing even begins
-    if not any(bit_depth == b for b in [8, 16, 32, 64]):
+    if bit_depth not in (8, 16, 32, 64):
         raise_BitDepthError(bit_depth)
 
     # Use shorter variable names
@@ -114,7 +114,7 @@ def rescale_to_bit_depth(
     bit_final = target_bit_depth
 
     # Check that target bit depth is allowed
-    if not any(bit_final == b for b in [8, 16, 32, 64]):
+    if bit_final not in (8, 16, 32, 64):
         raise_BitDepthError(bit_final)
 
     # Rescale (DIVIDE BEFORE MULTIPLY)
@@ -142,7 +142,7 @@ def process_img_stk(
     bdi = initial_bit_depth
     bdt = target_bit_depth
 
-    if not any(bdi == b for b in [8, 16, 32, 64]):
+    if bdi not in (8, 16, 32, 64):
         logger.info(f"{bdi}-bit is not supported by NumPy; converting to 16-bit")
         arr = (
             rescale_to_bit_depth(array=arr, initial_bit_depth=bdi, target_bit_depth=16)
@@ -201,6 +201,10 @@ def write_to_tiff(
     axes: str,
     image_labels: List[str],
 ):
+    """
+    Writes the NumPy array as a calibrated greyscale TIFF image stack.
+    """
+
     # Use shorter aliases and calculate what is needed
     arr = array
     z_size = (1 / z_res) if z_res > 0 else float(0)
@@ -212,7 +216,7 @@ def write_to_tiff(
         save_name,
         arr,
         imagej=True,  # ImageJ compatible
-        photometric="minisblack",  # Grayscale image
+        photometric="minisblack",  # Greyscale image
         shape=np.shape(arr),
         dtype=arr.dtype,
         resolution=(x_res * 10**6 / 10**6, y_res * 10**6 / 10**6),

src/murfey/util/clem/lif.py

@@ -45,7 +45,7 @@ def process_lif_file(
     # Create save dirs for TIFF files and their metadata
     img_dir = save_dir / img_name
     img_xml_dir = img_dir / "metadata"
-    for folder in [img_dir, img_xml_dir]:
+    for folder in (img_dir, img_xml_dir):
         if not folder.exists():
             folder.mkdir(parents=True)
             logger.info(f"Created {folder}")
@@ -203,7 +203,7 @@ def convert_lif_to_tiff(
     # Create folders if not already present
     processed_dir = Path("/".join(path_parts)).parent / file_name  # Processed images
     raw_xml_dir = file.parent / "metadata"  # Raw metadata
-    for folder in [processed_dir, raw_xml_dir]:
+    for folder in (processed_dir, raw_xml_dir):
         if not folder.exists():
             folder.mkdir(parents=True)
             logger.info(f"Created {sanitise(str(folder))}")

src/murfey/util/clem/xml.py

@@ -25,8 +25,8 @@ def get_lif_xml_metadata(
     save_xml: Optional[Path] = None,
 ) -> ET.Element:
     """
-    Extracts and returns the file metadata as a formatted XML Element. Provides option
-    to save it as an XML file to the specified file path
+    Extracts and returns the metadata from the LIF file as a formatted XML Element.
+    It can be optionally saved as an XML file to the specified file path.
     """
 
     # Use readlif function to get XML metadata