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nph5class module #2

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nph5class module #2

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55 changes: 55 additions & 0 deletions nph_5class/Dockerfile
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# FROM python:3.6.15-buster
# FROM nvidia/cuda:11.7.1-base-ubuntu20.04
FROM python:3.8.13-buster

ENV DEBIAN_FRONTEND noninteractive

RUN apt-get -y update && \
apt-get -y upgrade && \
apt-get -y install python3
RUN apt-get -y install python3-pip

RUN apt install -y vim
RUN apt install -y wget

# ===================Module Dependencies============================

RUN pip install torch torchvision numpy nibabel matplotlib scipy scikit-image SimpleITK
# RUN wget -q http://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py && \
# chmod 775 fslinstaller.py && \
# python3 /fslinstaller.py -d /usr/local/fsl -V 6.0.4 -q && \
# rm -f /fslinstaller.py

# RUN mv /usr/local/fsl /usr/local/bin/fsl


# ===================Copy Source Code===============================

RUN mkdir /module
WORKDIR /module

COPY src /module/src
# RUN chmod +x /module/src/skull_strip.sh

# ===============bqapi for python3 Dependencies=====================
# pip install in this exact order
RUN pip3 install six
RUN pip3 install lxml
RUN pip3 install requests==2.18.4
RUN pip3 install requests-toolbelt
RUN pip3 install tables

# =====================Build Directory Structure====================

EXPOSE 8080
EXPOSE 5000
COPY PythonScriptWrapper.py /module/
COPY bqapi/ /module/bqapi

# Replace the following line with your {ModuleName}.xml
COPY NPHSegmentation.xml /module/NPHSegmentation.xml

ENV PATH /module:$PATH:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
#:/usr/local/fsl/bin
ENV PYTHONPATH $PYTHONPATH:/module/src
# ENV FSLOUTPUTTYPE NIFTI_GZ
71 changes: 71 additions & 0 deletions nph_5class/NPHSegmentation.xml
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<?xml version="1.0" encoding="utf-8"?>
<module name="NPHSegmentation" type="runtime">

<tag name="inputs">

<tag name="Input Image" type="resource">
<template>
<tag name="label" value="Input Image"/>
<tag name="accepted_type" value="image"/>
<tag name="prohibit_upload" value="True"/>
</template>
</tag>
<tag name="mex_url" type="system-input_resource"/>
<tag name="bisque_token" type="system-input_resource"/>
</tag>

<tag name="outputs">

<tag name="NonImage">

<template>

<tag name="label" value="Outputs"/>

</template>

</tag>

<tag name="Segmented Image" type="image">
<template>
<tag name="label" value="Segmented Image"/>
</template>
</tag>
</tag>

<tag name="execute_options">

<tag name="iterable" value="image_url" type="dataset"/>

</tag>

<tag name="module_options">

<tag name="version" value="1"/>

</tag>

<tag name="display_options">

<tag name="group" value="Metadata"/>

</tag>

<tag name="interface">

<tag name="javascript" type="file" value="webapp.js"/>

<tag name="css" type="file" value="webapp.css"/>

</tag>

<tag name="help" type="file" value="public/help.html"/>

<tag name="thumbnail" type="file" value="public/thumbnail.jpg"/>

<tag name="title" type="string" value="NPHSegmentation"/>

<tag name="authors" type="string" value="VB"/>

<tag name="description" type="string" value="New NPH segmentation module"/>
</module>
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