How do I turn off debug output? When I read the image, it produces a lot of output #171

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1. CDPDisk commented on Nov 28, 2024

   

   CDPDisk

   on Nov 28, 2024

   Last edited by CDPDisk

   Author

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   And this is code, referenced this code: @tand826/wsiprocess#49 (comment)

   
   import os
   import contextlib
   # install openslide-bin when use openslide-python > 1.4.1
   # with os.add_dll_directory('C:/Program Files/openslide-win64-20220811/bin'):
   #     from openslide import OpenSlide
   # import openslide
   # from openslide import OpenSlide
   import javabridge
   import bioformats
   import torch
   from torch.utils.data import Dataset, DataLoader
   from torchvision import transforms
   import numpy as np
   import time
   import multiprocessing
   
   class DatasetWithBioformats(Dataset):
   
       def __init__(self, wsi, tile_size):
           self.wsi = wsi
           self.tile_size = tile_size
           self.transform = transforms.Resize((self.tile_size, self.tile_size))
   
       def lazy_load(self):
           javabridge.start_vm(class_path=bioformats.JARS, run_headless=True)
           self.reader = bioformats.ImageReader(self.wsi)
           self.set_params()
   
       def __del__(self):
           if hasattr(self, "reader"):
               self.reader.close()
           javabridge.kill_vm()
   
       def __len__(self):
           return len(self.coords)
   
       def __getitem__(self, idx):
           if not hasattr(self, "reader"):
               self.lazy_load()
           x, y = np.random.randint(0, self.width-self.tile_size), np.random.randint(0, self.height-self.tile_size)
           w = min(self.tile_size, self.width - x)
           h = min(self.tile_size, self.height - y)
           w, h = min(self.tile_size, self.width - x), min(self.tile_size, self.height - y)
           tile = self.reader.read(c=0, rescale=False, XYWH=(x, y, w, h))
           tensor = torch.tensor(tile, dtype=torch.uint8).reshape(h, w, 3).permute(2, 0, 1)
           return self.transform(tensor)
   
       def set_params(self):
           ImageReader = javabridge.JClassWrapper("loci.formats.ImageReader")
           reader = ImageReader()
           reader.setId(self.wsi)
           self.width = reader.getSizeX()
           self.height = reader.getSizeY()
           reader.close()
   
   try:
       tile_size = 256*40
       wsi = '../../data/FUSCC2/vlm/batch1/NeoPlatform/2022-34841.svs'
       dataset = DatasetWithBioformats(wsi, tile_size)
       start_time = time.time()
       print('start')
       for i in range(1):
           dataset.__getitem__(i)
       print(f"Time elapsed: {time.time()-start_time:.2f} s")
       print('Done')
   finally:
       javabridge.kill_vm()
   
2. CDPDisk commented on Nov 28, 2024

   

   CDPDisk

   on Nov 28, 2024

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   By the way, I'm getting the following error when I close ImageReader, but I have no idea:

   Exception ignored in: <function DatasetWithBioformats.__del__ at 0x2aaca72745e0>
   Traceback (most recent call last):
     File "test_multiprocess_java2.py", line 31, in __del__
     File "/data/aim_nuist/aim_chendp/.conda/envs/envtest/lib/python3.8/site-packages/bioformats/formatreader.py", line 712, in close
     File "/data/aim_nuist/aim_chendp/.conda/envs/envtest/lib/python3.8/site-packages/javabridge/jutil.py", line 961, in method
     File "/data/aim_nuist/aim_chendp/.conda/envs/envtest/lib/python3.8/site-packages/javabridge/jutil.py", line 888, in call
     File "/data/aim_nuist/aim_chendp/.conda/envs/envtest/lib/python3.8/site-packages/javabridge/jutil.py", line 842, in make_call
   AttributeError: 'NoneType' object has no attribute 'get_object_class'