mpriessner / cafi Goto Github PK
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License: MIT License
Combined Repos from DAIN and Zooming SlowMo
License: MIT License
Hi,
I tried to run the ZoomingSlowMo_4_Microscopy.ipynb notebook with mine own and also provided datasets, however it throwed following error in section 4.3.1 with both datasets:
RuntimeError: cuda runtime error (77) : an illegal memory access was encountered at /pytorch/aten/src/THC/THCCachingHostAllocator.cpp:296
In another case, I was trying to use a 5D dataset (TZXYC). When I give the file in section 3 it gives following result: "The TIF image dimensions are (20, 19, 2, 1024, 1024)". I guess it was supposed to give the image dimensions as (20, 19, 1024, 1024, 2). Probably because of this it couldn't prepare the data for training. Then I splitted channels and reached until section 4.3.1.
Please let me know if you need further information.
I am interested to use the notebook for Airyscan live cell imaging data which are of between 20-50 timepoints, around 20 z-slices and less than 1024x1024 in dimensions.
I appreciate your quick response.
Regards,
Sujan
Hi!
I got the following error while installing DAIN_4_Microscopy.ipynb
notebook:
---------------------------------------------------------------------------
ModuleNotFoundError Traceback (most recent call last)
<ipython-input-3-09fd65144275> in <module>()
52 _ = (sys.path.append("/usr/local/lib/python3.6/site-packages"))
53 sys.path.insert(0,'/content/DAIN/load_functions')
---> 54 from download_from_gdrive import download_file_from_google_drive
55 best_pretrained = "1EYgrdsaffVJuQlcBSK4dGqO2BXBkSlZf"
56 if not os.path.exists("/content/DAIN/model_weights"):
ModuleNotFoundError: No module named 'download_from_gdrive'
Solved it with:
!pip install googledrivedownloader
from google_drive_downloader import GoogleDriveDownloader as gdd
gdd.download_file_from_google_drive(best_pretrained, file_path)
Hi,
I would like to run CAFI using my local resources. Would you mind sharing a requirement text file that includes all the dependencies and packages necessary to run CAFI on a local conda environment? Thanks!
I am trying to follow the DAIN_4_Mic notebook by running it on collab with GPU enabled and after those first lines:
import os
!wget -c https://repo.anaconda.com/miniconda/Miniconda3-4.5.4-Linux-x86_64.sh
!chmod +x Miniconda3-4.5.4-Linux-x86_64.sh
!bash ./Miniconda3-4.5.4-Linux-x86_64.sh -b -f -p /usr/local
I get this error:
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Traceback (most recent call last):
File "/usr/local/bin/conda", line 7, in <module>
from conda.cli import main
ModuleNotFoundError: No module named 'conda'
Traceback (most recent call last):
File "/usr/local/bin/conda", line 7, in <module>
from conda.cli import main
ModuleNotFoundError: No module named 'conda'
Thanks for the help.
Hello and first off, thank you for making your work publicly available !
I have been trying to run the ZoomingSlowMo Colab but Google Colab removed support for Tensorflow 1, and it is not possible to use %tensorflow_version 1.x magic anymore.
I've tried to make it work with Tensorflow 2.x but keep getting during the requirement installation step.
Is there by any chance an up-to-date version of the Colab available ?
Thank you for your answer :)
Hello,
When I run the DAIN_4_Microscopy.ipynb notebook in colab, I got this error when running "Install the requirements" section:
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
`$ /usr/local/bin/conda install pytorch==1.1 cudatoolkit torchvision -c pytorch -y`
environment variables:
CIO_TEST=<not set>
COLAB_DEBUG_ADAPTER_MUX_PATH=/usr/local/bin/dap_multiplexer
COLAB_LANGUAGE_SERVER_PROXY=<set>
CONDA_ROOT=/usr/local
LD_LIBRARY_PATH=/usr/lib64-nvidia
LIBRARY_PATH=/usr/local/cuda/lib64/stubs
PATH=/opt/bin:/usr/local/nvidia/bin:/usr/local/cuda/bin:/usr/local/sbin:/us
r/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/tools/node/bin:/tools/googl
e-cloud-sdk/bin
PYTHONPATH=/env/python
PYTHONWARNINGS=ignore:::pip._internal.cli.base_command
REQUESTS_CA_BUNDLE=<not set>
SSL_CERT_FILE=<not set>
TCLLIBPATH=/usr/share/tcltk/tcllib1.20
active environment : None
user config file : /root/.condarc
populated config files :
conda version : 4.5.4
conda-build version : not installed
python version : 3.6.5.final.0
base environment : /usr/local (writable)
channel URLs : https://conda.anaconda.org/pytorch/linux-64
https://conda.anaconda.org/pytorch/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/free/linux-64
https://repo.anaconda.com/pkgs/free/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
https://repo.anaconda.com/pkgs/pro/linux-64
https://repo.anaconda.com/pkgs/pro/noarch
package cache : /usr/local/pkgs
/root/.conda/pkgs
envs directories : /usr/local/envs
/root/.conda/envs
platform : linux-64
user-agent : conda/4.5.4 requests/2.18.4 CPython/3.6.5 Linux/6.1.85+ ubuntu/22.04 glibc/2.35
UID:GID : 0:0
netrc file : None
offline mode : False
V V V V V V V V V V V V V V V V V V V V V V V V V V V V V V V
CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://repo.anaconda.com/pkgs/pro/linux-64/repodata.json.bz2>
Elapsed: -
An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.
If your current network has https://www.anaconda.com/ blocked, please file
a support request with your network engineering team.
SSLError(MaxRetryError('HTTPSConnectionPool(host=\'repo.anaconda.com\', port=443): Max retries exceeded with url: /pkgs/pro/linux-64/repodata.json.bz2 (Caused by SSLError(SSLError("bad handshake: Error([(\'SSL routines\', \'ssl3_get_server_certificate\', \'certificate verify failed\')],)",),))',),)
A reportable application error has occurred. Conda has prepared the above report.
Upload successful.
Solving environment: failed
It looks like the connection to conda failed. So I install the torch package with pip command pip install torch==1.1.0 torchvision==0.3.0
successfully. But then when I run "Perfome DAIN Frame Interpolation" section (I want to directly use pretrained model for prediction, so I skip the section 3 and 4), I got this error
ModuleNotFoundError: No module named 'filterinterpolation_cuda'
I'm wonderring whether there are any solution for this problem, thanks.
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