Merge pull request #262 from matt-sd-watson/dev

Update readimc to 0.7.0 + lenient parsing option

.gitignore

@@ -1,5 +1,6 @@
 /data/
 /steinbock/_version.py
+images.csv
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

requirements.txt

@@ -3,17 +3,18 @@ anndata==0.8.0
 # cellpose  # not included in default Docker containers (see Dockerfile for version)
 click==8.1.3
 click-log==0.4.0
-deepcell==0.12.4
+deepcell==0.12.6
 fcswrite==0.6.2
 h5py==3.8.0
 imageio==2.25.0
-napari[all]==0.4.17
+lxml_html_clean==0.1.1
+napari[all]==0.4.19
 networkx==3.0
 numpy==1.23.5  # deepcell 0.12.4 requires <1.24
 opencv-python-headless==4.7.0.68
 pandas==1.5.3
 pyyaml==6.0
-readimc==0.6.2
+readimc==0.7.0
 scikit-image==0.19.3
 scipy==1.10.0
 tifffile==2023.1.23.1

steinbock/preprocessing/_cli/imc.py

@@ -191,9 +191,19 @@ def panel_cmd(
     show_default=True,
     help="Path to the image information output file",
 )
+@click.option(
+    "--strict",
+    "strict",
+    default=True,
+    show_default=True,
+    type=bool,
+    help="Use strict parsing (skip and throw errors on corrupted ROIs)",
+)
 @click_log.simple_verbosity_option(logger=steinbock_logger)
 @catch_exception(handle=SteinbockException)
-def images_cmd(mcd_dir, txt_dir, unzip, panel_file, hpf, img_dir, image_info_file):
+def images_cmd(
+    mcd_dir, txt_dir, unzip, panel_file, hpf, img_dir, image_info_file, strict
+):
     channel_names = None
     if Path(panel_file).is_file():
         panel = io.read_panel(panel_file)
@@ -212,7 +222,12 @@ def images_cmd(mcd_dir, txt_dir, unzip, panel_file, hpf, img_dir, image_info_fil
         recovery_txt_file,
         recovered,
     ) in imc.try_preprocess_images_from_disk(
-        mcd_files, txt_files, channel_names=channel_names, hpf=hpf, unzip=unzip
+        mcd_files,
+        txt_files,
+        channel_names=channel_names,
+        hpf=hpf,
+        unzip=unzip,
+        strict=strict,
     ):
         img_file_stem = Path(mcd_or_txt_file).stem
         if acquisition is not None:

steinbock/preprocessing/imc.py

@@ -334,6 +334,7 @@ def _try_preprocess_mcd_images_from_disk(
     channel_names: Optional[Sequence[str]] = None,
     hpf: Optional[float] = None,
     unzip: bool = False,
+    strict: bool = False,
 ) -> Generator[Tuple[Acquisition, np.ndarray, Optional[Path], bool], None, None]:
     try:
         with MCDFile(mcd_file) as f_mcd:
@@ -355,7 +356,7 @@ def _try_preprocess_mcd_images_from_disk(
                             )
                             continue
                     try:
-                        img = f_mcd.read_acquisition(acquisition)
+                        img = f_mcd.read_acquisition(acquisition, strict=strict)
                         if channel_ind is not None:
                             img = img[channel_ind, :, :]
                         img = preprocess_image(img, hpf=hpf)
@@ -415,6 +416,7 @@ def try_preprocess_images_from_disk(
     channel_names: Optional[Sequence[str]] = None,
     hpf: Optional[float] = None,
     unzip: bool = False,
+    strict: bool = False,
 ) -> Generator[
     Tuple[Path, Optional["Acquisition"], np.ndarray, Optional[Path], bool],
     None,
@@ -439,6 +441,7 @@ def try_preprocess_images_from_disk(
                 channel_names=channel_names,
                 hpf=hpf,
                 unzip=unzip,
+                strict=strict,
             ):
                 yield Path(mcd_file), acquisition, img, recovery_txt_file, recovered
                 del img
@@ -458,6 +461,7 @@ def try_preprocess_images_from_disk(
                         channel_names=channel_names,
                         hpf=hpf,
                         unzip=unzip,
+                        strict=strict,
                     ):
                         yield (
                             Path(mcd_file),