1.0.0 (#1)

* 1.0.0: Initial commit

* ENH: Update manifest.

* DOC: minor manifest formatting

* FIX: manifest typo

* FIX: typo

* ENH: Generate PNG montage from each map

* add suite key + doc/ignore cleanup

.dockerignore

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+output
+testdata
+.git

.gitignore

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+output

Dockerfile

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+# Create Docker container that can run dtiError analysis.
+
+# Start with the Matlab runtime container
+FROM flywheel/matlab-mcr:v92.1
+
+MAINTAINER Michael Perry <[email protected]>
+
+# ADD the Matlab Stand-Alone (MSA) into the container
+COPY src/bin/*dtiinitDiffusionMaps* /usr/local/bin/
+
+# Ensure that the executable files are executable
+RUN chmod +x /usr/local/bin/*dtiinitDiffusionMaps*
+
+# Copy and configure run script and metadata code
+COPY manifest.json ${FLYWHEEL}/manifest.json
+
+# Configure entrypoint
+ENTRYPOINT ["/usr/local/bin/run_dtiinitDiffusionMaps.sh"]

README.md

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-# fw-gear-dtiinit-diffusion-maps
+# vistalab/fw-gear-dtiinit-diffusion-maps
+
+Generate diffusion maps (in NIfTI format), including Fractional Anisotropy (FA), Axial Diffusivity (AD), Mean Diffusivity (MD), and Radial Diffusivity (RD). The input to this Gear is a dtiInit archive, generated from either [dtiInit](https://github.com/scitran-apps/dtiinit), or as part of the [AFQ](https://github.com/scitran-apps/afq-pipeline) processing pipeline.
+
+## Inputs
+The input to this Gear is a dtiInit archive, containing a 'dt6.mat' file. This archive is generated from either [dtiInit](https://github.com/scitran-apps/dtiinit), or as part of the [AFQ](https://github.com/scitran-apps/afq-pipeline) processing pipeline.
+
+```bash
+dtiInit_29-Aug-2018_17-34-24.zip
+```
+
+## Outputs
+Diffusion maps (in NIfTI format), including Fractional Anisotropy (FA), Axial Diffusivity (AD), Mean Diffusivity (MD), and Radial Diffusivity (RD).
+
+```bash
+fa.nii.gz
+md.nii.gz
+ad.nii.gz
+rd.nii.gz
+```
+
+## Example Usage/Testing
+
+To run/test this Gear you will need to:
+1. Download the Flywheel CLI and login to your Flywheel Instance 
+2. Build the Docker image 
+3. Execute the Gear using the Flywheel CLI
+
+
+#### 1. Download the Flywheel CLI and login
+Visit: Flywheel for instruction on dowloading the CLIhttps://docs.flywheel.io/hc/en-us/articles/360008162214-Installing-the-Command-Line-Interface-CLI-
+
+Once you have that, you can login:
+```bash
+fw login <your_flywheel_api_key>
+```
+
+#### 2. Build the image with Docker
+```#bash
+git clone https://github.com/vistalab/fw-gear-dtiinit-diffusion-maps
+docker build -t vistalab/dtiinit-diffusion-maps:1.0.0
+```
+_Important note: The version (`1.0.0` in the example above) should be read from the `version` key within [manifest.json](manifest.json) file.
+
+#### 3. Run the Gear locally with the test data
+```bash
+fw gear local --dtiinit_archive ./testdata/dtiInit_29-Aug-2018_17-34-24.zip
+```
+Example output:
+
+```
+lmperry@warrior:/Users/lmperry/dtiinit-diffusion-maps:$ fw gear local --dtiinit_archive ./testdata/dtiInit_29-Aug-2018_17-34-24.zip
+
+Checking if vistalab/dtiinit-diffusion-maps:1.0.0 is available locally...
+        Found tag locally.
+Creating container from vistalab/dtiinit-diffusion-maps:1.0.0 ...
+        Created de36f2efba27
+Attaching to logs...
+
+------------------------------------------
+Setting up environment variables
+---
+LD_LIBRARY_PATH is .:/opt/mcr/v92/runtime/glnxa64:/opt/mcr/v92/bin/glnxa64:/opt/mcr/v92/sys/os/glnxa64:/opt/mcr/v92/sys/opengl/lib/glnxa64
+
+archive_path =
+
+    '/flywheel/v0/input/dtiinit_archive/dtiInit_29-Aug-2018_17-34-24.zip'
+
+Unpacking archive...
+Locating dt6.mat file from archive...
+Found /tmp/dtiInit_29-Aug-2018_17-34-24/dti90trilin/dt6.mat!
+Generating diffusion maps...
+Generating fa map ... Writing /flywheel/v0/output/fa.nii.gz...Done.
+Generating md map ... Writing /flywheel/v0/output/md.nii.gz...Done.
+Generating ad map ... Writing /flywheel/v0/output/ad.nii.gz...Done.
+Generating rd map ... Writing /flywheel/v0/output/rd.nii.gz...Done.
+Complete!
+
+Removing container de36f2efba27 ...
+        Removed container
+
+```
+
+### Developer's Corner: Compiling the Matlab Executable
+This Gear runs a Matlab Executable via the Matlab Compiler Runtime, which is build in the base image. __Note that the image uses MCR v92 (Matlabr2017a)__ - this MCR versions used to maintain Docker image compatibility with the other tools generating the dtiInit_Archives.
+
+If you find that need to make changes to the [source code](src/dtiinitDiffusionMaps_build.m) you will need to recompile the [executable](src/bin/run_dtiinitDiffusionMaps) and re-build the Docker image. 
+
+In order to recompile the Matlab executable you can use the provided [`.m`](src/dtiinitDiffusionMaps_build.m) file (you need to use Matlabr2017a for the binary to be compatible with the [Docker image](Dockerfile) we generate here). 
+
+The [`dtiinitDiffusionMaps_build.m`](src/dtiinitDiffusionMaps_build.m) file contains all the required instruction to compile the binary, including downloading the source code and setting required paths. 
+
+You can run the code from the command line like so:
+```bash
+/<path_to_your_matlabr2017a_binary> -nodesktop -r 'dtiinitDiffusionMaps_build.m'
+```
+
+If you already have your Matlab 2017a terminal open, you can simply run [the code](src/dtiinitDiffusionMaps_build.m):
+```Matlab
+dtiinitDiffusionMaps_build
+```
+

manifest.json

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+{
+  "name": "dtiinit-diffusion-maps",
+  "label": "dtiInit: Diffusion Map Generation",
+  "description": "Generate diffusion maps, including Fractional Anisotropy (FA), Axial Diffusivity (AD), Mean Diffusivity (MD), and Radial Diffusivity (RD). The input to this Gear is a dtiInit archive, containing a 'dt6.mat' file. This archive is generated from either the dtiInit Flywheel Gear, or from the Flywheel Gear which executes the AFQ processing pipeline. Outputs are fa, md, rd, and ad files (in gzipped NIfTI format).",
+  "maintainer": "Michael Perry <[email protected]>",
+  "author": "Stanford VISTA Lab (vistalab.stanford.edu)",
+  "url": "https://github.com/vistalab/vistasoft/wiki",
+  "source": "https://github.com/vistalab/fw-gear-dtiinit-diffusion-maps",
+  "license": "GPL-2.0",
+  "flywheel": "0",
+  "version": "1.0.0",
+  "custom": {
+    "flywheel": {
+      "suite": "VISTA Lab"
+    },
+    "gear-builder": {
+      "image": "vistalab/dtiinit-diffusion-maps:1.0.0",
+      "category": "analysis"
+    }
+  },
+  "inputs": {
+    "dtiinit_archive": {
+      "base": "file",
+      "description": "Output archive (.zip) from dtiinit gear run, or AFQ.",
+      "type": {
+        "enum": [
+          "archive"
+        ]
+      }
+    }
+  },
+  "config": {},
+  "environment": {
+    "LD_LIBRARY_PATH": "/opt/mcr/v92/runtime/glnxa64:/opt/mcr/v92/bin/glnxa64:/opt/mcr/v92/sys/os/glnxa64",
+    "XAPPLRESDIR": "XAPPLRESDIR"
+  },
+  "command": "/usr/local/bin/run_dtiinitDiffusionMaps.sh /opt/mcr/v92 /flywheel/v0/config.json"
+}

src/bin/mccExcludedFiles.log

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+The List of Excluded Files
+Excluded files	 Exclusion Message ID	 Reason For Exclusion	 Exclusion Rule

src/bin/readme.txt

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+MATLAB Compiler
+
+1. Prerequisites for Deployment 
+
+. Verify the MATLAB Runtime is installed and ensure you    
+  have installed version 9.2 (R2017a).   
+
+. If the MATLAB Runtime is not installed, do the following:
+  (1) enter
+
+      >>mcrinstaller
+
+      at MATLAB prompt. The MCRINSTALLER command displays the 
+      location of the MATLAB Runtime installer.
+
+  (2) run the MATLAB Runtime installer.
+
+Or download the Linux 64-bit version of the MATLAB Runtime for R2017a 
+from the MathWorks Web site by navigating to
+
+   http://www.mathworks.com/products/compiler/mcr/index.html
+
+
+For more information about the MATLAB Runtime and the MATLAB Runtime installer, see 
+Package and Distribute in the MATLAB Compiler documentation  
+in the MathWorks Documentation Center.    
+
+
+2. Files to Deploy and Package
+
+Files to package for Standalone 
+================================
+-dtiinitDiffusionMaps 
+-run_dtiinitDiffusionMaps.sh (shell script for temporarily setting environment variables 
+                              and executing the application)
+   -to run the shell script, type
+
+       ./run_dtiinitDiffusionMaps.sh <mcr_directory> <argument_list>
+
+    at Linux or Mac command prompt. <mcr_directory> is the directory 
+    where version 9.2 of the MATLAB Runtime is installed or the directory where 
+    MATLAB is installed on the machine. <argument_list> is all the 
+    arguments you want to pass to your application. For example, 
+
+    If you have version 9.2 of the MATLAB Runtime installed in 
+    /mathworks/home/application/v92, run the shell script as:
+
+       ./run_dtiinitDiffusionMaps.sh /mathworks/home/application/v92
+
+    If you have MATLAB installed in /mathworks/devel/application/matlab, 
+    run the shell script as:
+
+       ./run_dtiinitDiffusionMaps.sh /mathworks/devel/application/matlab
+-MCRInstaller.zip
+   -if end users are unable to download the MATLAB Runtime using the above  
+    link, include it when building your component by clicking 
+    the "Runtime downloaded from web" link in the Deployment Tool
+-This readme file 
+
+3. Definitions
+
+For information on deployment terminology, go to 
+http://www.mathworks.com/help. Select MATLAB Compiler >   
+Getting Started > About Application Deployment > 
+Deployment Product Terms in the MathWorks Documentation 
+Center.
+
+
+4. Appendix 
+
+A. Linux x86-64 systems:
+In the following directions, replace MCR_ROOT by the directory where the MATLAB Runtime 
+   is installed on the target machine.
+
+(1) Set the environment variable XAPPLRESDIR to this value:
+
+    MCR_ROOT/v92/X11/app-defaults
+
+
+(2) If the environment variable LD_LIBRARY_PATH is undefined, set it to the concatenation 
+   of the following strings:
+
+    MCR_ROOT/v92/runtime/glnxa64:
+    MCR_ROOT/v92/bin/glnxa64:
+    MCR_ROOT/v92/sys/os/glnxa64:
+    MCR_ROOT/v92/sys/opengl/lib/glnxa64
+
+    If it is defined, set it to the concatenation of these strings:
+
+    ${LD_LIBRARY_PATH}: 
+    MCR_ROOT/v92/runtime/glnxa64:
+    MCR_ROOT/v92/bin/glnxa64:
+    MCR_ROOT/v92/sys/os/glnxa64:
+    MCR_ROOT/v92/sys/opengl/lib/glnxa64
+
+   For more detail information about setting the MATLAB Runtime paths, see Package and 
+   Distribute in the MATLAB Compiler documentation in the MathWorks Documentation Center.
+
+
+
+        NOTE: To make these changes persistent after logout on Linux 
+              or Mac machines, modify the .cshrc file to include this  
+              setenv command.
+        NOTE: The environment variable syntax utilizes forward 
+              slashes (/), delimited by colons (:).  
+        NOTE: When deploying standalone applications, it is possible 
+              to run the shell script file run_dtiinitDiffusionMaps.sh 
+              instead of setting environment variables. See 
+              section 2 "Files to Deploy and Package".    
+
+
+
+
+
+

src/bin/requiredMCRProducts.txt

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+35000	35010	

src/bin/run_dtiinitDiffusionMaps.sh

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+#!/bin/sh
+# script for execution of deployed applications
+#
+# Sets up the MATLAB Runtime environment for the current $ARCH and executes 
+# the specified command.
+#
+exe_name=$0
+exe_dir=`dirname "$0"`
+echo "------------------------------------------"
+if [ "x$1" = "x" ]; then
+  echo Usage:
+  echo    $0 \<deployedMCRroot\> args
+else
+  echo Setting up environment variables
+  MCRROOT="$1"
+  echo ---
+  LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ;
+  LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ;
+  LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64;
+  LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/opengl/lib/glnxa64;
+  export LD_LIBRARY_PATH;
+  echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH};
+  shift 1
+  args=
+  while [ $# -gt 0 ]; do
+      token=$1
+      args="${args} \"${token}\"" 
+      shift
+  done
+  eval "\"${exe_dir}/dtiinitDiffusionMaps\"" $args
+fi
+exit
+