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RFC: keep hdf5 file open #318

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RFC: keep hdf5 file open #318

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19 changes: 10 additions & 9 deletions dataset_modules/dataset_h5.py
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Original file line number Diff line number Diff line change
Expand Up @@ -60,34 +60,35 @@ def __init__(self,

self.file_path = file_path

with h5py.File(self.file_path, "r") as f:
dset = f['coords']
self.patch_level = f['coords'].attrs['patch_level']
self.patch_size = f['coords'].attrs['patch_size']
self.length = len(dset)
self.hdf5_file = h5py.File(self.file_path, "r")
dset = self.hdf5_file['coords']
self.patch_level = self.hdf5_file['coords'].attrs['patch_level']
self.patch_size = self.hdf5_file['coords'].attrs['patch_size']
self.length = len(dset)

self.summary()

def __len__(self):
return self.length

def summary(self):
hdf5_file = h5py.File(self.file_path, "r")
dset = hdf5_file['coords']
dset = self.hdf5_file['coords']
for name, value in dset.attrs.items():
print(name, value)

print('\nfeature extraction settings')
print('transformations: ', self.roi_transforms)

def __getitem__(self, idx):
with h5py.File(self.file_path,'r') as hdf5_file:
coord = hdf5_file['coords'][idx]
coord = self.hdf5_file['coords'][idx]
img = self.wsi.read_region(coord, self.patch_level, (self.patch_size, self.patch_size)).convert('RGB')

img = self.roi_transforms(img)
return {'img': img, 'coord': coord}

def __del__(self):
self.hdf5_file.close()

class Dataset_All_Bags(Dataset):

def __init__(self, csv_path):
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