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PeterJackNaylor / DRFNS

This repository contains the code necessary in order to reproduce the work contained in the submitted paper: "Segmentation of Nuclei in Histopathology Images by deep regression of the distance map".
MIT License
47 stars 13 forks source link

Data downloading through download_data.sh is incomplete #11

Closed lucas-sancere closed 2 years ago

lucas-sancere commented 2 years ago

Hi,

Thank you for your work which is very promising. I faced an issue trying to download the data needed to run nextflow run realdataset.nf --epoch 80 -c nextflow.config -resume. To this aim, I ran download_data.sh and it looks like it is impossible to access some of the data as you can see at the end of the output:


(DRFNS) lsancere@LAPTOP-D9SH18G5:~/anaconda3/envs/DRFNS/lib/python2.7/site-packages/DRFNS/datafolder$ bash download_data.sh

--2021-11-19 09:57:23--  https://zenodo.org/record/1175282/files/TNBC_NucleiSegmentation.zip
Resolving zenodo.org (zenodo.org)... 137.138.76.77
Connecting to zenodo.org (zenodo.org)|137.138.76.77|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 25279869 (24M) [application/octet-stream]
Saving to: ‘TNBC_NucleiSegmentation.zip’

TNBC_NucleiSegmentation.zip                                 100%[========================================================================================================================================>]  24.11M  8.14MB/s    in 3.0s

2021-11-19 09:57:27 (8.14 MB/s) - ‘TNBC_NucleiSegmentation.zip’ saved [25279869/25279869]

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--2021-11-19 09:57:28--  http://members.cbio.mines-paristech.fr/~pnaylor/Downloads/pretrained.zip
Resolving members.cbio.mines-paristech.fr (members.cbio.mines-paristech.fr)... 77.158.180.100
Connecting to members.cbio.mines-paristech.fr (members.cbio.mines-paristech.fr)|77.158.180.100|:80... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: https://members.cbio.mines-paristech.fr/~pnaylor/Downloads/pretrained.zip [following]
--2021-11-19 09:57:28--  https://members.cbio.mines-paristech.fr/~pnaylor/Downloads/pretrained.zip
Connecting to members.cbio.mines-paristech.fr (members.cbio.mines-paristech.fr)|77.158.180.100|:443... connected.
ERROR: cannot verify members.cbio.mines-paristech.fr's certificate, issued by ‘CN=GEANT OV RSA CA 4,O=GEANT Vereniging,C=NL’:
  Unable to locally verify the issuer's authority.
To connect to members.cbio.mines-paristech.fr insecurely, use `--no-check-certificate'.
--2021-11-19 09:57:28--  http://members.cbio.mines-paristech.fr/~pnaylor/Downloads/ForDataGenTrainTestVal.zip
Resolving members.cbio.mines-paristech.fr (members.cbio.mines-paristech.fr)... 77.158.180.100
Connecting to members.cbio.mines-paristech.fr (members.cbio.mines-paristech.fr)|77.158.180.100|:80... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: https://members.cbio.mines-paristech.fr/~pnaylor/Downloads/ForDataGenTrainTestVal.zip [following]
--2021-11-19 09:57:28--  https://members.cbio.mines-paristech.fr/~pnaylor/Downloads/ForDataGenTrainTestVal.zip
Connecting to members.cbio.mines-paristech.fr (members.cbio.mines-paristech.fr)|77.158.180.100|:443... connected.
ERROR: cannot verify members.cbio.mines-paristech.fr's certificate, issued by ‘CN=GEANT OV RSA CA 4,O=GEANT Vereniging,C=NL’:
  Unable to locally verify the issuer's authority.
To connect to members.cbio.mines-paristech.fr insecurely, use `--no-check-certificate'

I don't have access to the data stored in mines-paristech website. Just to validate I went inside download_data.sh and checked the following:


[...]

wget http://members.cbio.mines-paristech.fr/~pnaylor/Downloads/pretrained.zip && \
unzip pretrained.zip -d pretrained && \
rm pretrained.zip

wget http://members.cbio.mines-paristech.fr/~pnaylor/Downloads/ForDataGenTrainTestVal.zip && \
unzip ForDataGenTrainTestVal.zip -d ForDataGenTrainTestVal && \
rm ForDataGenTrainTestVal.zip
~

The access to these website paths is forbidden. Can you help with this? Can the data be available somewhere else?

I really want to test your well designed network,

Thank you for your support!

PeterJackNaylor commented 2 years ago

Hi,

Thank you for your interest in our work and sorry for the flaky data download, I need to change the host as the data from cbio will one day be unreachable but they are still reachable at the moment. Sorry for the trouble, I succeeded in downloading them by adding '--no-check-certificate' to the wget.

I hope this fixes your issue. Don't hesitate for further help.

lucas-sancere commented 2 years ago

Hi Peter,

As it was stated to connect insecurely I didn't try.... But thank you very much, your solution is working!

Thank you for your support