Giter Club home page Giter Club logo

cafi's People

Contributors

mpriessner avatar

Stargazers

 avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar

Watchers

 avatar  avatar  avatar

cafi's Issues

Error: No module named 'download_from_gdrive'

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)

Running CAFI locally

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!

Running ZoomingSlowMo Colab tensorflow 2.x

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 :)

RuntimeError: cuda runtime error (77)

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

ModuleNotFoundError: No module named 'conda'

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.

CondaHTTPError and ModuleNotFoundError: No module named 'filterinterpolation_cuda'

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.

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    ๐Ÿ–– Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. ๐Ÿ“Š๐Ÿ“ˆ๐ŸŽ‰

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google โค๏ธ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.