fix: remove bfio and use tifffile for docker integration.

PolusAI · May 22, 2024 · 9ba335b · 9ba335b
1 parent bf32f5c
commit 9ba335b
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Showing 3 changed files with 16 additions and 15 deletions.
diff --git a/segmentation/rt-cetsa-plate-extraction-tool/pyproject.toml b/segmentation/rt-cetsa-plate-extraction-tool/pyproject.toml
@@ -16,7 +16,7 @@ typer = "^0.7.0"
 filepattern = "^2.0.5"
 numpy = "^1.26.4"
 scikit-image = "0.22.0"
-bfio = "^2.3.6"
+bfio = "2.3.6"
 
 [tool.poetry.group.dev.dependencies]
 bump2version = "^1.0.1"

diff --git a/...plate-extraction-tool/src/polus/images/segmentation/rt_cetsa_plate_extraction/__init__.py b/...plate-extraction-tool/src/polus/images/segmentation/rt_cetsa_plate_extraction/__init__.py
@@ -7,6 +7,7 @@
 
 import bfio
 import filepattern
+import tifffile
 from polus.images.segmentation.rt_cetsa_plate_extraction.core import PlateParams
 from polus.images.segmentation.rt_cetsa_plate_extraction.core import create_mask
 from polus.images.segmentation.rt_cetsa_plate_extraction.core import crop_and_rotate
@@ -43,8 +44,8 @@ def extract_plates(inp_dir, pattern, out_dir) -> PlateParams:
 
     # extract plate params from first image
     first_image_path = inp_files[0]
-    with bfio.BioReader(first_image_path) as reader:
-        first_image = reader[:]
+
+    first_image = tifffile.imread(first_image_path)
 
     params: PlateParams = get_plate_params(first_image)
 
@@ -54,24 +55,24 @@ def extract_plates(inp_dir, pattern, out_dir) -> PlateParams:
     num_images = len(inp_files)
     for index, f in enumerate(inp_files):
         logger.info(f"Processing Image {index+1}/{num_images}: {f}")
-        with bfio.BioReader(f) as reader:
-            image = reader[:]
-            cropped_and_rotated = crop_and_rotate(image, params)
+        image = tifffile.imread(f)
+        cropped_and_rotated = crop_and_rotate(image, params)
 
-            if index == 1:
-                first_image = cropped_and_rotated
+        if index == 1:
+            first_image = cropped_and_rotated
 
-            out_path = out_dir / "images" / (f.stem + POLUS_IMG_EXT)
-            with bfio.BioWriter(out_path) as writer:
-                writer.dtype = cropped_and_rotated.dtype
-                writer.shape = cropped_and_rotated.shape
-                writer[:] = cropped_and_rotated
+        out_path = out_dir / "images" / (f.stem + POLUS_IMG_EXT)
+        with bfio.BioWriter(out_path) as writer:
+            writer.dtype = cropped_and_rotated.dtype
+            writer.shape = cropped_and_rotated.shape
+            writer[:] = cropped_and_rotated
 
     # save plate parameters for the first processed image
     processed_params = get_plate_params(first_image)
-    plate_path = out_dir / "params" / "plate.csv"
+    plate_path = out_dir / "params" / "plate.json"
     with plate_path.open("w") as f:
         f.write(processed_params.model_dump_json())  # type: ignore
+        logger.info(f"Plate params saved: {plate_path}")
 
     # save the corresponding mask for reference
     mask = create_mask(processed_params)

diff --git a/...plate-extraction-tool/src/polus/images/segmentation/rt_cetsa_plate_extraction/__main__.py b/...plate-extraction-tool/src/polus/images/segmentation/rt_cetsa_plate_extraction/__main__.py
@@ -75,7 +75,7 @@ def main(
             "masks": [
                 (Path("masks") / f"{inp_files[0].stem}{POLUS_IMG_EXT}").as_posix(),
             ],
-            "params": [Path("params") / "plate.csv"],
+            "params": [Path("params") / "plate.json"],
         }
 
         with (out_dir / "preview.json").open("w") as f: