fedshyvana
commented
1 year ago If your patching complete successfully, there should be an attribute "patch_level" stored in the .h5 to indicate the level at which it's patched (see here) whereas here i'm not sure its telling you you can't find that attribute.
can you perhaps manually open a few of the .h5 files you have and verify that if one or more of them are missing the attributes?
Great pipeline to work on WSI data. I am trying to run the data using CLAM pipeline.
I started with .tif files and created patches and stiches using following command
_python create_patches_fp.py --source example_data_AB --save_dir example_data_AB_patches1 --patchsize 256 --seg --patch --stitch
Next, with Cuda enabled conda environment, I used following command to get features from each side.
DIR_TO_COORDS = example_data_AB_patches1
CUDA_VISIBLE_DEVICES=0 python extract_features_fp.py --data_h5_dir example_data_AB_patches1 --data_slide_dir example_data_AB --csv_path example_data_AB_patches1/process_list_autogen.csv --feat_dir example_data_AB_features1 --batch_size 512 --slide_ext .tif
warn(f"Failed to load image Python extension: {e}") initializing dataset loading model checkpoint
progress: 0/5 normal_002 Traceback (most recent call last): File "/work_beegfs/usr/usr/Images_DATA/CODES/clam/CLAM/extract_features_fp.py", line 113, in
output_file_path = compute_w_loader(h5_file_path, output_path, wsi,
File "/work_beegfs/usr/usr/Images_DATA/CODES/clam/CLAM/extract_features_fp.py", line 34, in compute_w_loader
dataset = Whole_Slide_Bag_FP(file_path=file_path, wsi=wsi, pretrained=pretrained,
File "/work_beegfs/usr/usr/Images_DATA/CODES/clam/CLAM/datasets/dataset_h5.py", line 123, in init
self.patch_level = f['coords'].attrs['patch_level']
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "/home/usr/.conda/envs/clam4/lib/python3.10/site-packages/h5py/_hl/attrs.py", line 56, in getitem
attr = h5a.open(self._id, self._e(name))
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "h5py/h5a.pyx", line 80, in h5py.h5a.open
KeyError: "Can't open attribute (can't locate attribute: 'patch_level')"
DIR_TO_COORDS = example_data_AB_patches1/patches
warn(f"Failed to load image Python extension: {e}") initializing dataset loading model checkpoint
progress: 0/5 normal_002 Traceback (most recent call last): File "/work_beegfs/usr/usr/Images_DATA/CODES/clam/CLAM/extract_features_fp.py", line 113, in
output_file_path = compute_w_loader(h5_file_path, output_path, wsi,
File "/work_beegfs/usr/usr/Images_DATA/CODES/clam/CLAM/extract_features_fp.py", line 34, in compute_w_loader
dataset = Whole_Slide_Bag_FP(file_path=file_path, wsi=wsi, pretrained=pretrained,
File "/work_beegfs/usr/usr/Images_DATA/CODES/clam/CLAM/datasets/dataset_h5.py", line 121, in init
with h5py.File(self.file_path, "r") as f:
File "/home/usr/.conda/envs/clam4/lib/python3.10/site-packages/h5py/_hl/files.py", line 567, in init
fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr)
File "/home/usr/.conda/envs/clam4/lib/python3.10/site-packages/h5py/_hl/files.py", line 231, in make_fid
fid = h5f.open(name, flags, fapl=fapl)
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "h5py/h5f.pyx", line 106, in h5py.h5f.open
FileNotFoundError: [Errno 2] Unable to open file (unable to open file: name = 'example_data_AB_patches1/patches/patches/normal_002.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)
I am getting error while reading h5 files. It would appreciate all the suggestion.
Thanks in advance