added macOS compiled version 1.1

SASHIMISegmentation-v1.1.prj

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+<deployment-project plugin="plugin.ezdeploy" plugin-version="1.0">
+  <configuration file="/Users/brianchow/Documents/GitHub/SASHIMI/SASHIMISegmentation-v1.1.prj" location="/Users/brianchow/Documents/GitHub/SASHIMI" name="SASHIMISegmentation-v1.1" target="target.ezdeploy.standalone" target-name="Application Compiler">
+    <param.appname>SASHIMI_Segmentation</param.appname>
+    <param.icon />
+    <param.icons />
+    <param.version>1.1</param.version>
+    <param.authnamewatermark>Bart Bolsterlee</param.authnamewatermark>
+    <param.email>b.bolsterlee@neura.edu.au</param.email>
+    <param.company>NeuRA</param.company>
+    <param.summary />
+    <param.description />
+    <param.screenshot>${PROJECT_ROOT}/sashimi-logo.png</param.screenshot>
+    <param.guid />
+    <param.installpath.string>/NeuRA/SASHIMI_Segmentation/</param.installpath.string>
+    <param.installpath.combo>option.installpath.systemwideapp</param.installpath.combo>
+    <param.logo>${PROJECT_ROOT}/sashimi-logo.png</param.logo>
+    <param.install.notes />
+    <param.target.install.notes>In the following directions, replace MR/v97 by the directory on the target machine where MATLAB is installed, or MR by the directory where the MATLAB Runtime is installed.
+
+If the environment variable DYLD_LIBRARY_PATH is undefined, set it to the following string:
+
+MR/v97/runtime/maci64:MR/v97/sys/os/maci64:MR/v97/bin/maci64
+
+If it is defined, set it to the following:
+
+${DYLD_LIBRARY_PATH}:MR/v97/runtime/maci64:MR/v97/sys/os/maci64:MR/v97/bin/maci64</param.target.install.notes>
+    <param.intermediate>${PROJECT_ROOT}/SASHIMISegmentation-v1.1/for_testing</param.intermediate>
+    <param.files.only>${PROJECT_ROOT}/SASHIMISegmentation-v1.1/for_redistribution_files_only</param.files.only>
+    <param.output>${PROJECT_ROOT}/SASHIMISegmentation-v1.1/for_redistribution</param.output>
+    <param.logdir>${PROJECT_ROOT}/SASHIMISegmentation-v1.1</param.logdir>
+    <param.enable.clean.build>false</param.enable.clean.build>
+    <param.user.defined.mcr.options />
+    <param.target.type>subtarget.standalone</param.target.type>
+    <param.support.packages />
+    <param.web.mcr>true</param.web.mcr>
+    <param.package.mcr>false</param.package.mcr>
+    <param.no.mcr>false</param.no.mcr>
+    <param.web.mcr.name>MyAppInstaller_web</param.web.mcr.name>
+    <param.package.mcr.name>MyAppInstaller_mcr</param.package.mcr.name>
+    <param.no.mcr.name>MyAppInstaller_app</param.no.mcr.name>
+    <param.windows.command.prompt>false</param.windows.command.prompt>
+    <param.create.log>false</param.create.log>
+    <param.log.file />
+    <param.native.matlab>false</param.native.matlab>
+    <param.checkbox>false</param.checkbox>
+    <param.example />
+    <param.help.text>Syntax 
+	  -? 
+
+ Input Arguments 
+	 -?  print help on how to use the application 
+	 input arguments</param.help.text>
+    <unset>
+      <param.icon />
+      <param.icons />
+      <param.summary />
+      <param.description />
+      <param.guid />
+      <param.installpath.string />
+      <param.installpath.combo />
+      <param.install.notes />
+      <param.intermediate />
+      <param.files.only />
+      <param.output />
+      <param.logdir />
+      <param.enable.clean.build />
+      <param.user.defined.mcr.options />
+      <param.target.type />
+      <param.support.packages />
+      <param.web.mcr />
+      <param.package.mcr />
+      <param.no.mcr />
+      <param.web.mcr.name />
+      <param.package.mcr.name />
+      <param.no.mcr.name />
+      <param.windows.command.prompt />
+      <param.create.log />
+      <param.log.file />
+      <param.native.matlab />
+      <param.checkbox />
+      <param.example />
+    </unset>
+    <fileset.main>
+      <file>${PROJECT_ROOT}/SASHIMI_v1_1.mlapp</file>
+    </fileset.main>
+    <fileset.resources />
+    <fileset.package />
+    <fileset.depfun>
+      <file>${PROJECT_ROOT}/convertObjects.m</file>
+      <file>${PROJECT_ROOT}/fit_spline.m</file>
+      <file>${PROJECT_ROOT}/register_slices.m</file>
+      <file>${PROJECT_ROOT}/sashimi-logo.png</file>
+      <file>${PROJECT_ROOT}/snap_to_edge.m</file>
+    </fileset.depfun>
+    <build-deliverables>
+      <file location="${PROJECT_ROOT}/SASHIMISegmentation-v1.1/for_testing" name="SASHIMI_Segmentation.app" optional="false">/Users/brianchow/Documents/GitHub/SASHIMI/SASHIMISegmentation-v1.1/for_testing/SASHIMI_Segmentation.app</file>
+      <file location="${PROJECT_ROOT}/SASHIMISegmentation-v1.1/for_testing" name="splash.png" optional="false">/Users/brianchow/Documents/GitHub/SASHIMI/SASHIMISegmentation-v1.1/for_testing/splash.png</file>
+      <file location="${PROJECT_ROOT}/SASHIMISegmentation-v1.1/for_testing" name="run_SASHIMI_Segmentation.sh" optional="false">/Users/brianchow/Documents/GitHub/SASHIMI/SASHIMISegmentation-v1.1/for_testing/run_SASHIMI_Segmentation.sh</file>
+      <file location="${PROJECT_ROOT}/SASHIMISegmentation-v1.1/for_testing" name="readme.txt" optional="true">/Users/brianchow/Documents/GitHub/SASHIMI/SASHIMISegmentation-v1.1/for_testing/readme.txt</file>
+    </build-deliverables>
+    <workflow />
+    <matlab>
+      <root>/Applications/MATLAB_R2019b.app</root>
+      <toolboxes />
+    </matlab>
+    <platform>
+      <unix>true</unix>
+      <mac>true</mac>
+      <windows>false</windows>
+      <win2k>false</win2k>
+      <winxp>false</winxp>
+      <vista>false</vista>
+      <linux>false</linux>
+      <solaris>false</solaris>
+      <osver>10.15.4</osver>
+      <os32>false</os32>
+      <os64>true</os64>
+      <arch>maci64</arch>
+      <matlab>true</matlab>
+    </platform>
+  </configuration>
+</deployment-project>

standalone/MacOS/SASHIMI_Segmentation.app/Contents/Info.plist

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+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
+<plist version="1.0">
+<dict>
+	<key>CFBundleDevelopmentRegion</key>
+	<string>English</string>
+	<key>CFBundleExecutable</key>
+	<string>prelaunch</string>
+	<key>CFBundleIconFile</key>
+	<string>membrane.icns</string>
+	<key>CFBundleIdentifier</key>
+	<string>SASHIMI_Segmentation</string>
+	<key>CFBundleInfoDictionaryVersion</key>
+	<string>6.0</string>
+	<key>CFBundleName</key>
+	<string>SASHIMI_Segmentation</string>
+	<key>CFBundlePackageType</key>
+	<string>APPL</string>
+	<key>CFBundleShortVersionString</key>
+	<string>1.1.0.0</string>
+	<key>CFBundleSignature</key>
+	<string>SASHIMI_Segmentation</string>
+	<key>CFBundleVersion</key>
+	<string>1</string>
+	<key>CFBundleVersionString</key>
+	<string>1.1.0.0</string>
+	<key>CFResourcesFileMapped</key>
+	<true/>
+	<key>LSMinimumSystemVersion</key>
+	<string>10.13.6</string>
+	<key>NSCameraUsageDescription</key>
+	<string>This app requires camera access to capture photos</string>
+	<key>NSMainNibFile</key>
+	<string>MainMenu</string>
+	<key>NSMicrophoneUsageDescription</key>
+	<string>This app requires microphone access to capture sound</string>
+	<key>NSPrincipalClass</key>
+	<string>NSApplication</string>
+</dict>
+</plist>

standalone/MacOS/readme.txt

@@ -0,0 +1,108 @@
+SASHIMI_Segmentation Executable
+
+1. Prerequisites for Deployment 
+
+Verify that version 9.7 (R2019b) of the MATLAB Runtime is installed.   
+If not, you can run the MATLAB Runtime installer.
+To find its location, enter
+
+    >>mcrinstaller
+
+at the MATLAB prompt.
+NOTE: You will need administrator rights to run the MATLAB Runtime installer. 
+
+Alternatively, download and install the Macintosh version of the MATLAB Runtime for R2019b 
+from the following link on the MathWorks website:
+
+    https://www.mathworks.com/products/compiler/mcr/index.html
+
+For more information about the MATLAB Runtime and the MATLAB Runtime installer, see 
+"Distribute Applications" in the MATLAB Compiler documentation  
+in the MathWorks Documentation Center.
+
+2. Files to Deploy and Package
+
+Files to Package for Standalone 
+================================
+-run_SASHIMI_Segmentation.sh (shell script for temporarily setting environment variables 
+ and executing the application)
+   -to run the shell script, type
+
+       ./run_SASHIMI_Segmentation.sh <mcr_directory> <argument_list>
+
+    at Linux or Mac command prompt. <mcr_directory> is the directory 
+    where version 9.7 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 9.7 of the MATLAB Runtime installed in 
+    /mathworks/home/application/v97, run the shell script as:
+
+       ./run_SASHIMI_Segmentation.sh /mathworks/home/application/v97
+
+    If you have MATLAB installed in /mathworks/devel/application/matlab, 
+    run the shell script as:
+
+       ./run_SASHIMI_Segmentation.sh /mathworks/devel/application/matlab
+-MCRInstaller.zip 
+    Note: if end users are unable to download the MATLAB Runtime using the
+    instructions in the previous section, include it when building your 
+    component by clicking the "Runtime included in package" link in the
+    Deployment Tool.
+-The Macintosh bundle directory structure SASHIMI_Segmentation.app 
+    Note: this can be stored in an archive file with the zip command 
+    zip -r SASHIMI_Segmentation.zip SASHIMI_Segmentation.app
+    or the tar command 
+    tar -cvf SASHIMI_Segmentation.tar SASHIMI_Segmentation.app
+-This readme file 
+
+
+
+3. Definitions
+
+For information on deployment terminology, go to
+https://www.mathworks.com/help and select MATLAB Compiler >
+Getting Started > About Application Deployment >
+Deployment Product Terms in the MathWorks Documentation
+Center.
+
+4. Appendix 
+
+A. Mac systems:
+In the following directions, replace MR/v97 by the directory on the target machine where 
+   MATLAB is installed, or MR by the directory where the MATLAB Runtime is installed.
+
+If the environment variable DYLD_LIBRARY_PATH is undefined, set it to the following 
+   string:
+
+MR/v97/runtime/maci64:MR/v97/sys/os/maci64:MR/v97/bin/maci64
+
+If it is defined, set it to the following:
+
+${DYLD_LIBRARY_PATH}:MR/v97/runtime/maci64:MR/v97/sys/os/maci64:MR/v97/bin/maci64
+
+    For more detailed 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, you can
+              run the shell script file run_SASHIMI_Segmentation.sh 
+              instead of setting environment variables. See 
+              section 2 "Files to Deploy and Package".    
+
+
+
+5. Launching application using Macintosh finder
+
+If the application is purely graphical, that is, it doesn't read from standard in or 
+write to standard out or standard error, it may be launched in the finder just like any 
+other Macintosh application.
+
+
+

standalone/MacOS/run_SASHIMI_Segmentation.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="$1"
+  echo ---
+  DYLD_LIBRARY_PATH=.:${MCRROOT}/runtime/maci64 ;
+  DYLD_LIBRARY_PATH=${DYLD_LIBRARY_PATH}:${MCRROOT}/bin/maci64 ;
+  DYLD_LIBRARY_PATH=${DYLD_LIBRARY_PATH}:${MCRROOT}/sys/os/maci64;
+  export DYLD_LIBRARY_PATH;
+  echo DYLD_LIBRARY_PATH is ${DYLD_LIBRARY_PATH};
+  shift 1
+  args=
+  while [ $# -gt 0 ]; do
+      token=$1
+      args="${args} \"${token}\"" 
+      shift
+  done
+  eval "\"${exe_dir}/SASHIMI_Segmentation.app/Contents/MacOS/SASHIMI_Segmentation\"" $args
+fi
+exit
+