vb/nph segmentation pipeline

.gitignore

@@ -129,3 +129,12 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+*/*/reference.dream3d
+
+QRBSA/src/DREAM3D-6.5.141-Linux-x86_64/*
+*.pt
+*.npy
+SpeciesTrackerAndCounter/src/runs/train/*
+*.hdf5
+
+*.tar

3DMaterialGAN/3DMaterialGAN.xml

@@ -0,0 +1,65 @@
+<?xml version="1.0" encoding="utf-8"?>
+<module name="3DMaterialGAN" type="runtime">
+
+     <tag name="inputs">
+
+          <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"/>
+
+                    <tag name="Output Zip" type="file"/>
+               </template>
+
+          </tag>
+
+          <tag name="Output Tiff" type="image">
+               <template>
+                    <tag name="label" value="Output Tiff"/>
+               </template>
+          </tag>
+     </tag>
+
+     <tag name="execute_options">
+
+          <tag name="iterable" type="dataset" value="image_url"/>
+
+     </tag>
+
+     <tag name="module_options">
+
+          <tag name="version" value="1"/>
+
+     </tag>
+
+     <tag name="display_options">
+
+          <tag name="group" value="Materials Science"/>
+
+     </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="3DMaterialGAN"/>
+
+     <tag name="authors" type="string" value="BisQue Team"/>
+
+     <tag name="description" type="string" value="This module generates 3D Grain Data"/>
+</module>

3DMaterialGAN/Dockerfile

@@ -0,0 +1,44 @@
+FROM ubuntu:bionic
+ENV DEBIAN_FRONTEND noninteractive
+
+RUN apt-get update && \
+        apt-get install -y software-properties-common && \
+        add-apt-repository ppa:deadsnakes/ppa && \
+        apt-get update -y
+RUN apt-get install -y build-essential
+RUN apt-get install -y python3.6 python3.6-dev python3-pip && \
+        apt-get install -y git  && \
+        # update pip
+        python3.6 -m pip install pip --upgrade && \
+        python3.6 -m pip install wheel
+
+RUN apt-get -y install python-pip liblapack3 libblas-dev liblapack-dev gfortran
+RUN apt-get update
+RUN pip install torch==1.2.0
+RUN pip install numpy==1.14.5
+RUN pip install tensorflow-gpu==1.13.1
+RUN pip install tensorboardX==2.0
+RUN pip install QtPy==1.9.0
+RUN pip install lxml
+#RUN pip install --user --install-option="--prefix=" -U scikit-learn==0.19.1
+RUN pip install -i https://biodev.ece.ucsb.edu/py/bisque/prod/+simple bisque-api==0.5.9
+
+WORKDIR /module
+COPY src  /module/src
+
+# ===============bqapi for python3 Dependencies=====================
+# pip install in this exact order
+RUN pip install six
+RUN pip install pyyaml scipy tiffile
+RUN pip install requests==2.18.4
+RUN pip install requests-toolbelt
+# =====================Build Directory Structure====================
+RUN alias python='python3.6'
+COPY PythonScriptWrapper.py /module/
+COPY bqapi/ /module/bqapi
+RUN apt-get install zip -y
+# Replace the following line with your {ModuleName}.xml
+COPY 3DMaterialGAN.xml /module/3DMaterialGAN.xml
+
+ENV PATH /module:$PATH:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ENV PYTHONPATH $PYTHONPATH:/module/src