Closed r0f1 closed 3 years ago
eric-czech
commented
3 years ago That looks likely. You could check under /lab/data/.cytokit/cache to see if an empty h5 file was downloaded. I don't know why that happens sometimes but it does, e.g. https://github.com/hammerlab/cytokit/issues/21.
If you delete the file or all of cache and run it again, that usually does it.
r0f1
commented
3 years ago Unfortunately, it is still not working. I copied the following code in the Jupyter cell above:
def _save_response_content(response, destination):
chunk_size = 32768
with open(destination, "wb") as f:
for chunk in response.iter_content(chunk_size):
if chunk: # filter out keep-alive new chunks
f.write(chunk)
def _get_confirm_token(response):
for key, value in response.cookies.items():
if key.startswith('download_warning'):
return value
return None
import requests
path = "./test.h5"
url = "https://docs.google.com/uc?export=download"
session = requests.Session()
response = session.get(url, params={'id': "1I9j4oABbcV8EnvO_ufACXP9e4KyfHMtE"}, stream=True)
token = _get_confirm_token(response)
if token:
params = {'id': "1I9j4oABbcV8EnvO_ufACXP9e4KyfHMtE", 'confirm': token}
response = session.get(url, params=params, stream=True)
_save_response_content(response, path)And then calculated the checksum and the filesize:
!md5sum ./*.h5
!ls -halt ./*.h5
b6cd7e93bc7a96c2dc33f819aa3ac651 ./test.h5
-rw-r--r-- 1 root root 141 Apr 20 13:52 ./test.h5These match exactly with the file located at /lab/data/.cytokit/cache/cytometry/model/unet_v2_weights.h5.
However, I have the suspicion that both .h5 files are corrupted or empty. 141 bytes for all the weights of the unet seems a little too small. Could it be that the original file in Google Drive is no longer available?
eric-czech
commented
3 years ago Could it be that the original file in Google Drive is no longer available?
Hmm looks like that's the case. Sadly I think the only way to get them back would be to submit an issue to CellProfiler-plugins. That code to get the weights is roughly from https://github.com/CellProfiler/CellProfiler-plugins/blob/0a63e2dc71dc6a99b6112c3be70f8c2dc9301d2a/CellProfiler4_AutoConvert/classifypixelsunet.py#L149-L151. They could probably tell you where it was moved to.
r0f1
commented
3 years ago Thanks, I raised an issue over there. They are working on it. Therefore I am closing this issue :)
eric-czech
commented
3 years ago Nice, I subscribed to https://github.com/CellProfiler/CellProfiler-plugins/issues/121 and will try to update it here depending on the solution.
I started the docker image, and I am trying to execute the example notebook
marker_profiling_example.ipynb. I get an error in the 8th cell. My guess is that the h5 file is not correctly downloaded in the back.Error message:
Any ideas to solve that?