change the tiffslide to openslide

Dockerfile-CPU

@@ -23,8 +23,11 @@ RUN python3.9 -m pip install -e .
 # Entrypoint forces all commands given via "docker run" to go through python, CMD forces the default entrypoint script argument to be gandlf run
 # If a user calls "docker run gandlf:[tag] anonymize", it will resolve to running "gandlf anonymize" instead.
 # CMD is inherently overridden by args to "docker run", entrypoint is constant.
+ENV LD_LIBRARY_PATH="/usr/local/lib/python3.9/dist-packages/openslide_bin:$LD_LIBRARY_PATH"
+
 ENTRYPOINT gandlf
 CMD run
+#CMD /bin/bash
 
 # The below force the container commands to run as a nonroot user with UID > 10000.
 # This greatly reduces UID collision probability between container and host, helping prevent privilege escalation attacks.

GANDLF/compute/inference_loop.py

@@ -15,7 +15,7 @@
 from skimage.io import imsave
 from tqdm import tqdm
 from torch.cuda.amp import autocast
-import tiffslide as openslide
+import openslide
 from GANDLF.data import get_testing_loader
 from GANDLF.utils import (
     best_model_path_end,

GANDLF/data/inference_dataloader_histopath.py

@@ -1,7 +1,7 @@
 import os
 from typing import Optional
 import numpy as np
-import tiffslide
+import openslide
 from GANDLF.data.patch_miner.opm.utils import get_patch_size_in_microns, tissue_mask
 from skimage.transform import resize
 from torch.utils.data.dataset import Dataset

GANDLF/data/patch_miner/opm/patch_manager.py

@@ -7,8 +7,7 @@
 from tqdm import tqdm
 from pathlib import Path
 import pandas as pd
-import openslide as tiffslide
-
+import openslide
 
 class PatchManager:
     def __init__(self, filename, output_dir):
@@ -41,7 +40,7 @@ def set_subjectID(self, subjectID):
     def set_slide_path(self, filename):
         self.img_path = filename
         self.img_path = convert_to_tiff(self.img_path, self.output_dir, "img")
-        self.slide_object = tiffslide.open_slide(self.img_path)
+        self.slide_object = openslide.open_slide(self.img_path)
         self.slide_dims = self.slide_object.dimensions
 
     def set_label_map(self, path):
@@ -50,7 +49,7 @@ def set_label_map(self, path):
         @param path: path to label map.
         """
         self.label_map = convert_to_tiff(path, self.output_dir, "mask")
-        self.label_map_object = tiffslide.open_slide(self.label_map)
+        self.label_map_object = openslide.open_slide(self.label_map)
 
         assert all(
             x == y for x, y in zip(self.label_map_object.dimensions, self.slide_dims)

GANDLF/data/patch_miner/opm/utils.py

@@ -17,7 +17,7 @@
 
 # import matplotlib.pyplot as plt
 import yaml
-import openslide as tiffslide
+import openslide
 
 # RGB Masking (pen) constants
 RGB_RED_CHANNEL = 0
@@ -428,7 +428,7 @@ def generate_initial_mask(slide_path: str, scale: int) -> Tuple[np.ndarray, tupl
         Tuple[np.ndarray, tuple]: The valid mask and the real scale.
     """
     # Open slide and get properties
-    slide = tiffslide.open_slide(slide_path)
+    slide = openslide.open_slide(slide_path)
     slide_dims = slide.dimensions
 
     # Call thumbnail for effiency, calculate scale relative to whole slide

setup.py

@@ -52,7 +52,6 @@
     "setuptools",
     "seaborn",
     "pyyaml==6.0.1",
-    "tiffslide",
     "matplotlib",
     "gdown==5.1.0",
     "pytest",