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Added NPHSegmentationPipeline module (pull to main) #11

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Added NPHSegmentationPipeline module (pull to main) #11

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1ee5e5b
Added NPHSegmentationPipeline module
Electrum9 May 7, 2023
86ce46b
Replaced value with segmentation
Electrum9 May 9, 2023
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38 changes: 38 additions & 0 deletions NPHSegmentationPipeline/Dockerfile
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FROM fsl_flirt:v1.0.3

ENV DEBIAN_FRONTEND noninteractive

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

RUN pip3 install nibabel numpy onnx onnxruntime scikit-image scipy

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

RUN mkdir /module
WORKDIR /module

COPY src /module/src

####################################################################
######################## Append From Here Down #####################
####################################################################

# ===============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====================

COPY PythonScriptWrapper.py /module/
COPY bqapi/ /module/bqapi

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

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

<tag name="inputs">

<tag name="Input Scans" type="resource">
<template>
<tag name="label" value="Input Scans"/>
<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="Output Scan" type="image">
<template>
<tag name="label" value="Output Scan"/>
</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="Segmentation"/>

</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="NPHSegmentationPipeline"/>

<tag name="authors" type="string" value="Krithika, Shailja, Sanjay, Vikram"/>

<tag name="description" type="string" value="Performs segmentation of CT scans, using ResNet patch based method."/>
</module>
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