From 9684fb6422293323ce71ff74fbd9bedf0dc33998 Mon Sep 17 00:00:00 2001 From: Kevin Mader Date: Wed, 9 May 2018 16:36:46 +0200 Subject: [PATCH 1/9] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index ee758a8..1f23ad7 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@ # Digits Docker in Binder using a Dockerfile -A simple repository to get [NVIDIA DIGITS](https://github.com/NVIDIA/DIGITS) running inside of Binder for easier experimentation and exploration. +A simple repository to get [NVIDIA DIGITS](https://github.com/NVIDIA/DIGITS) running inside of Binder for easier experimentation and exploration. Here we try the latest DIGITS image [![Binder](http://mybinder.org/badge.svg)](http://mybinder.org/v2/gh/4Quant/digits-docker-binder/master?urlpath=digits) From 76fa233568c4e93598d16b0dab9ace1f0958852a Mon Sep 17 00:00:00 2001 From: Kevin Mader Date: Wed, 9 May 2018 17:06:43 +0200 Subject: [PATCH 2/9] Update Dockerfile adding tensorflow to image --- Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/Dockerfile b/Dockerfile index a2533b1..9e41b42 100644 --- a/Dockerfile +++ b/Dockerfile @@ -41,6 +41,7 @@ RUN mv ${HOME}/4q.ico ${HOME}/digits/digits/static/images/nvidia.ico # move the layout with fixed links RUN mv ${HOME}/layout.html ${HOME}/digits/digits/templates/layout.html WORKDIR ${HOME}/digits +RUN pip install https://storage.googleapis.com/tensorflow/linux/cpu/tensorflow-1.2.1-cp27-none-linux_x86_64.whl --upgrade RUN python setup.py install # install two plugins From 045f6e6808a61ec00cfed10fbdf9937dce1f0299 Mon Sep 17 00:00:00 2001 From: Kevin Mader Date: Wed, 9 May 2018 17:08:02 +0200 Subject: [PATCH 3/9] Update layout.html fixing layout.html --- layout.html | 3 +++ 1 file changed, 3 insertions(+) diff --git a/layout.html b/layout.html index 8fd8da2..1694e2b 100644 --- a/layout.html +++ b/layout.html @@ -12,6 +12,9 @@ {% block title %}DIGITS{% endblock %} + From d4ad5f3bd0d10b00af2fc036feb648e6d468fb9c Mon Sep 17 00:00:00 2001 From: Kevin Mader Date: Wed, 9 May 2018 17:14:24 +0200 Subject: [PATCH 4/9] Update Dockerfile let pip choose the right TF wheel --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 9e41b42..ad9ac8b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -41,7 +41,7 @@ RUN mv ${HOME}/4q.ico ${HOME}/digits/digits/static/images/nvidia.ico # move the layout with fixed links RUN mv ${HOME}/layout.html ${HOME}/digits/digits/templates/layout.html WORKDIR ${HOME}/digits -RUN pip install https://storage.googleapis.com/tensorflow/linux/cpu/tensorflow-1.2.1-cp27-none-linux_x86_64.whl --upgrade +RUN pip install tensorflow==1.2.1 --upgrade RUN python setup.py install # install two plugins From 3563548d8f7a32c50dc603368c082d34e6fdd9e7 Mon Sep 17 00:00:00 2001 From: Kevin Mader Date: Wed, 9 May 2018 17:38:40 +0200 Subject: [PATCH 5/9] Update Dockerfile changing pip for tf to pip2 --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index ad9ac8b..c4a4604 100644 --- a/Dockerfile +++ b/Dockerfile @@ -41,7 +41,7 @@ RUN mv ${HOME}/4q.ico ${HOME}/digits/digits/static/images/nvidia.ico # move the layout with fixed links RUN mv ${HOME}/layout.html ${HOME}/digits/digits/templates/layout.html WORKDIR ${HOME}/digits -RUN pip install tensorflow==1.2.1 --upgrade +RUN pip2 install tensorflow==1.2.1 --upgrade RUN python setup.py install # install two plugins From 6d21ed0dc45a1ae9368ac8a2cd2fbe0b6e6e7787 Mon Sep 17 00:00:00 2001 From: Kevin Mader Date: Wed, 9 May 2018 21:02:22 +0200 Subject: [PATCH 6/9] Update Dockerfile removing --upgrade from pip --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index c4a4604..0ac4b1f 100644 --- a/Dockerfile +++ b/Dockerfile @@ -41,7 +41,7 @@ RUN mv ${HOME}/4q.ico ${HOME}/digits/digits/static/images/nvidia.ico # move the layout with fixed links RUN mv ${HOME}/layout.html ${HOME}/digits/digits/templates/layout.html WORKDIR ${HOME}/digits -RUN pip2 install tensorflow==1.2.1 --upgrade +RUN pip2 install tensorflow==1.2.1 RUN python setup.py install # install two plugins From c67ef82470c4db5df10282230a52caf64b67d32f Mon Sep 17 00:00:00 2001 From: Kevin Mader Date: Wed, 9 May 2018 23:49:37 +0200 Subject: [PATCH 7/9] Update Dockerfile adding opencv install for the sunnybrook segmentation plugin, download data --- Dockerfile | 16 ++++++++++++++-- 1 file changed, 14 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 0ac4b1f..233b529 100644 --- a/Dockerfile +++ b/Dockerfile @@ -41,6 +41,7 @@ RUN mv ${HOME}/4q.ico ${HOME}/digits/digits/static/images/nvidia.ico # move the layout with fixed links RUN mv ${HOME}/layout.html ${HOME}/digits/digits/templates/layout.html WORKDIR ${HOME}/digits +RUN pip2 install opencv-python RUN pip2 install tensorflow==1.2.1 RUN python setup.py install @@ -55,12 +56,23 @@ WORKDIR ${HOME} RUN python -m digits.download_data cifar10 ~/cifar10 RUN chown -R ${NB_USER} ${HOME} -WORKDIR ${HOME} USER ${NB_USER} - +WORKDIR ${HOME} +# download sunnybrook data +RUN mkdir ${HOME}/sunnybrook +WORKDIR ${HOME}/sunnybrook +RUN curl 'http://www.cardiacatlas.org/share/download.php?id=3&token=WgD8N1RrY2QvAL245wTPMCAeSAcRTjJG&download' -o dicoms.zip +RUN unzip dicoms.zip +RUN rm dicoms.zip +RUN curl 'http://www.cardiacatlas.org/share/download.php?id=2&token=IlxjOeV7ZviYLTqP627LmqqVHtyUuuK3&download' -o contours.zip +RUN unzip contours.zip +RUN rm contours.zip +WORKDIR ${HOME} +# setup environment ENV DIGITS_JOBS_DIR=${HOME}/jobs ENV DIGITS_LOGFILE_FILENAME=${HOME}/digits.log ENV PYTHONPATH=/usr/local/python + ENTRYPOINT [""] CMD ["jupyter", "notebook", "--ip", "0.0.0.0"] From 6b8a93fce94b1fcc462de610bf921dfaf6c3a887 Mon Sep 17 00:00:00 2001 From: Kevin Mader Date: Thu, 10 May 2018 00:01:53 +0200 Subject: [PATCH 8/9] Update Dockerfile fixing permissions and user --- Dockerfile | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index 233b529..390a077 100644 --- a/Dockerfile +++ b/Dockerfile @@ -54,10 +54,7 @@ RUN python setup.py install WORKDIR ${HOME} # get some test data to play with RUN python -m digits.download_data cifar10 ~/cifar10 -RUN chown -R ${NB_USER} ${HOME} -USER ${NB_USER} -WORKDIR ${HOME} # download sunnybrook data RUN mkdir ${HOME}/sunnybrook WORKDIR ${HOME}/sunnybrook @@ -67,6 +64,9 @@ RUN rm dicoms.zip RUN curl 'http://www.cardiacatlas.org/share/download.php?id=2&token=IlxjOeV7ZviYLTqP627LmqqVHtyUuuK3&download' -o contours.zip RUN unzip contours.zip RUN rm contours.zip +# fix permissions and change user +RUN chown -R ${NB_USER} ${HOME} +USER ${NB_USER} WORKDIR ${HOME} # setup environment ENV DIGITS_JOBS_DIR=${HOME}/jobs From 69aa57c993330cce9762f5ac9ec90a83c50c8467 Mon Sep 17 00:00:00 2001 From: Kevin Mader Date: Thu, 10 May 2018 00:22:51 +0200 Subject: [PATCH 9/9] Update Dockerfile silencing unzip and combining steps --- Dockerfile | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/Dockerfile b/Dockerfile index 390a077..666b27e 100644 --- a/Dockerfile +++ b/Dockerfile @@ -58,12 +58,10 @@ RUN python -m digits.download_data cifar10 ~/cifar10 # download sunnybrook data RUN mkdir ${HOME}/sunnybrook WORKDIR ${HOME}/sunnybrook -RUN curl 'http://www.cardiacatlas.org/share/download.php?id=3&token=WgD8N1RrY2QvAL245wTPMCAeSAcRTjJG&download' -o dicoms.zip -RUN unzip dicoms.zip -RUN rm dicoms.zip -RUN curl 'http://www.cardiacatlas.org/share/download.php?id=2&token=IlxjOeV7ZviYLTqP627LmqqVHtyUuuK3&download' -o contours.zip -RUN unzip contours.zip -RUN rm contours.zip +RUN curl 'http://www.cardiacatlas.org/share/download.php?id=3&token=WgD8N1RrY2QvAL245wTPMCAeSAcRTjJG&download' -o dicoms.zip &&\ + unzip -q dicoms.zip && rm dicoms.zip +RUN curl 'http://www.cardiacatlas.org/share/download.php?id=2&token=IlxjOeV7ZviYLTqP627LmqqVHtyUuuK3&download' -o contours.zip &&\ + unzip -q contours.zip && rm contours.zip # fix permissions and change user RUN chown -R ${NB_USER} ${HOME} USER ${NB_USER}