Updates to integrate new OPM APIs

gandlf_patchMiner

@@ -12,41 +12,23 @@ import argparse
 import pandas as pd
 import openslide
 import numpy as np
-import yaml
 
 from PIL import Image
 from GANDLF.OPM.opm.patch_manager import PatchManager
-from GANDLF.OPM.opm.utils import tissue_mask, alpha_channel_check, patch_size_check, parse_config
+from GANDLF.OPM.opm.utils import (
+    tissue_mask,
+    alpha_channel_check,
+    patch_size_check,
+    parse_config,
+    generate_initial_mask,
+)
 from functools import partial
 from pathlib import Path
 
 Image.MAX_IMAGE_PIXELS = None
 warnings.simplefilter("ignore")
 
 
-def generate_initial_mask(slide_path, scale):
-    """
-    Helper method to generate random coordinates within a slide
-    :param slide_path: Path to slide (str)
-    :param num_patches: Number of patches you want to generate
-    :return: list of n (x,y) coordinates
-    """
-    # Open slide and get properties
-    slide = openslide.open_slide(slide_path)
-    slide_dims = slide.dimensions
-
-    # Call thumbnail for effiency, calculate scale relative to whole slide
-    slide_thumbnail = np.asarray(
-        slide.get_thumbnail((slide_dims[0] // scale, slide_dims[1] // scale))
-    )
-    real_scale = (
-        slide_dims[0] / slide_thumbnail.shape[1],
-        slide_dims[1] / slide_thumbnail.shape[0],
-    )
-
-    return tissue_mask(slide_thumbnail), real_scale
-
-
 def parse_gandlf_csv(fpath):
     df = pd.read_csv(fpath, dtype=str)
     df = df.drop_duplicates()
@@ -80,13 +62,18 @@ if __name__ == "__main__":
         "--config",
         type=str,
         dest="config",
-        help="config.yml for running OPM. ",
-        required=True,
+        help="config (in YAML) for running OPM. Needs 'scale' and 'patch_size' to be defined, otherwise defaults to 16 and (256, 256), respectively.",
+        required=False,
     )
 
     args = parser.parse_args()
 
-    cfg = parse_config(args.config)
+    if args.config is not None:
+        cfg = parse_config(args.config)
+    else:
+        cfg = {}
+        cfg["scale"] = 16
+        cfg["patch_size"] = (256, 256)
 
     if not os.path.exists(args.output_path):
         Path(args.output_path).mkdir(parents=True, exist_ok=True)
@@ -102,6 +89,8 @@ if __name__ == "__main__":
         manager = PatchManager(slide, args.output_path)
         manager.set_label_map(label)
         manager.set_subjectID(sid)
+        manager.set_image_header("Channel_0")
+        manager.set_mask_header("Label")
 
         # Generate an initial validity mask
         mask, scale = generate_initial_mask(slide, cfg["scale"])
@@ -119,3 +108,5 @@ if __name__ == "__main__":
         # Save patches releases saves all patches stored in manager, dumps to specified output file
         manager.mine_patches(output_csv=out_csv_path, config=cfg)
         print("Total time: {}".format(time.time() - start))
+
+    print("Finished.")

setup.py

@@ -44,6 +44,7 @@
     "psutil",
     "medcam",
     "torchmetrics",
+    "OpenPatchMiner==0.1.6",
 ]
 
 setup(