Added NPHSegmentationPipeline module (pull to main)

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

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="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="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>