Optimisations to TIFF image stack creation in CLEM workflow (#314)

* Overhauled functions used for array manipulation during image stack creation
* Added more parameters for more comprehensive metadata transfer during image stack creation

Author: tieneupin

src/murfey/cli/tiff_to_stack.py

@@ -35,7 +35,7 @@ def run():
     # Convert to correct object types
     tiff_file = Path(args.tiff_path)
     # Generate list from the single file provided
-    tiff_list = [
+    tiff_list: list[Path] = [
         f.resolve()
         for f in tiff_file.parent.glob("./*")
         if f.suffix in {".tif", ".tiff"}

src/murfey/server/clem/api.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-import importlib.metadata
+import sys
 
 from fastapi import APIRouter
 
@@ -9,6 +9,12 @@
 from murfey.util.clem.tiff import convert_tiff_to_stack
 from murfey.util.models import LifFileInfo, TiffSeriesInfo
 
+# Use backport from importlib_metadata for Python <3.10
+if sys.version_info.major == 3 and sys.version_info.minor < 10:
+    from importlib_metadata import entry_points
+else:
+    from importlib.metadata import entry_points
+
 # Create APIRouter class object
 router = APIRouter()
 
@@ -18,16 +24,20 @@ def lif_to_tiff(
     session_id: int,  # Used by the decorator
     lif_info: LifFileInfo,
 ):
-    murfey_workflows = importlib.metadata.entry_points().select(
+    # Get command line entry point
+    murfey_workflows = entry_points().select(
         group="murfey.workflows", name="lif_to_tiff"
     )
+
+    # Use entry point if found
     if murfey_workflows:
         murfey_workflows[0].load()(
             # Match the arguments found in murfey.workflows.lif_to_tiff
             file=lif_info.name,
             root_folder="images",
             messenger=_transport_object,
         )
+    # Call function directly otherwise
     else:
         convert_lif_to_tiff(
             file=lif_info.name,
@@ -40,9 +50,12 @@ def tiff_to_stack(
     session_id: int,  # Used by the decorator
     tiff_info: TiffSeriesInfo,
 ):
-    murfey_workflows = importlib.metadata.entry_points().select(
-        group="murfey.workflows", name="tiff_to_stack"
+    # Get command line entry point
+    murfey_workflows = entry_points().select(
+        group="murfey.workflows", name="lif_to_tiff"
     )
+
+    # Use entry point if found
     if murfey_workflows:
         murfey_workflows[0].load()(
             # Match the arguments found in murfey.workflows.tiff_to_stack
@@ -51,6 +64,7 @@ def tiff_to_stack(
             metadata=tiff_info.series_metadata,
             messenger=_transport_object,
         )
+    # Call function directly otherwise
     else:
         convert_tiff_to_stack(
             tiff_list=tiff_info.tiff_files,