new HASL function

Former-commit-id: 9c43e384a6397b3fefe0ee1deafad9143c620fd7

app_old/for_redistribution_files_only/readme.txt

@@ -0,0 +1,102 @@
+full_analysis Executable
+
+1. Prerequisites for Deployment 
+
+Verify that version 9.6 (R2019a) 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.
+
+Alternatively, download and install the Linux version of the MATLAB Runtime for R2019a 
+from the following link on the MathWorks website:
+
+    http://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 
+================================
+-full_analysis 
+-run_full_analysis.sh (shell script for temporarily setting environment variables and 
+                       executing the application)
+   -to run the shell script, type
+
+       ./run_full_analysis.sh <mcr_directory> <argument_list>
+
+    at Linux or Mac command prompt. <mcr_directory> is the directory 
+    where version 9.6 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 9.6 of the MATLAB Runtime installed in 
+    /mathworks/home/application/v96, run the shell script as:
+
+       ./run_full_analysis.sh /mathworks/home/application/v96
+
+    If you have MATLAB installed in /mathworks/devel/application/matlab, 
+    run the shell script as:
+
+       ./run_full_analysis.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.
+-This readme file 
+
+
+
+3. Definitions
+
+For information on deployment terminology, go to
+http://www.mathworks.com/help and select MATLAB Compiler >
+Getting Started > About Application Deployment >
+Deployment Product Terms in the MathWorks Documentation
+Center.
+
+4. Appendix 
+
+A. Linux systems:
+In the following directions, replace MR/v96 by the directory on the target machine where 
+   MATLAB is installed, or MR by the directory where the MATLAB Runtime is installed.
+
+(1) Set the environment variable XAPPLRESDIR to this value:
+
+MR/v96/X11/app-defaults
+
+
+(2) If the environment variable LD_LIBRARY_PATH is undefined, set it to the following:
+
+MR/v96/runtime/glnxa64:MR/v96/bin/glnxa64:MR/v96/sys/os/glnxa64:MR/v96/sys/opengl/lib/glnxa64
+
+If it is defined, set it to the following:
+
+${LD_LIBRARY_PATH}:MR/v96/runtime/glnxa64:MR/v96/bin/glnxa64:MR/v96/sys/os/glnxa64:MR/v96/sys/opengl/lib/glnxa64
+
+    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_full_analysis.sh 
+              instead of setting environment variables. See 
+              section 2 "Files to Deploy and Package".    
+
+
+
+
+
+

app_old/for_redistribution_files_only/run_full_analysis.sh

@@ -0,0 +1,33 @@
+#!/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}/full_analysis\"" $args
+fi
+exit
+

app_old/for_testing/full_analysis.REMOVED.git-id

@@ -0,0 +1 @@
+25876135238101de79313ba4587e06f6e944a134

app_old/for_testing/readme.txt

@@ -0,0 +1,102 @@
+full_analysis Executable
+
+1. Prerequisites for Deployment 
+
+Verify that version 9.6 (R2019a) 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.
+
+Alternatively, download and install the Linux version of the MATLAB Runtime for R2019a 
+from the following link on the MathWorks website:
+
+    http://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 
+================================
+-full_analysis 
+-run_full_analysis.sh (shell script for temporarily setting environment variables and 
+                       executing the application)
+   -to run the shell script, type
+
+       ./run_full_analysis.sh <mcr_directory> <argument_list>
+
+    at Linux or Mac command prompt. <mcr_directory> is the directory 
+    where version 9.6 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 9.6 of the MATLAB Runtime installed in 
+    /mathworks/home/application/v96, run the shell script as:
+
+       ./run_full_analysis.sh /mathworks/home/application/v96
+
+    If you have MATLAB installed in /mathworks/devel/application/matlab, 
+    run the shell script as:
+
+       ./run_full_analysis.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.
+-This readme file 
+
+
+
+3. Definitions
+
+For information on deployment terminology, go to
+http://www.mathworks.com/help and select MATLAB Compiler >
+Getting Started > About Application Deployment >
+Deployment Product Terms in the MathWorks Documentation
+Center.
+
+4. Appendix 
+
+A. Linux systems:
+In the following directions, replace MR/v96 by the directory on the target machine where 
+   MATLAB is installed, or MR by the directory where the MATLAB Runtime is installed.
+
+(1) Set the environment variable XAPPLRESDIR to this value:
+
+MR/v96/X11/app-defaults
+
+
+(2) If the environment variable LD_LIBRARY_PATH is undefined, set it to the following:
+
+MR/v96/runtime/glnxa64:MR/v96/bin/glnxa64:MR/v96/sys/os/glnxa64:MR/v96/sys/opengl/lib/glnxa64
+
+If it is defined, set it to the following:
+
+${LD_LIBRARY_PATH}:MR/v96/runtime/glnxa64:MR/v96/bin/glnxa64:MR/v96/sys/os/glnxa64:MR/v96/sys/opengl/lib/glnxa64
+
+    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_full_analysis.sh 
+              instead of setting environment variables. See 
+              section 2 "Files to Deploy and Package".    
+
+
+
+
+
+

app_old/for_testing/run_full_analysis.sh

@@ -0,0 +1,33 @@
+#!/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}/full_analysis\"" $args
+fi
+exit
+

run

@@ -56,8 +56,6 @@ time ${CODE_DIR}/run_full_analysis.sh "${MCR_ROOT}"\
                                       "${aslFile}"\
                                       "${m0File}"\
                                       "${mprageFile}"\
-                                      "${hyperCO2_flag}" \
-                                      "${config_stimulus_start}" \
                                       "${OUTPUT_DIR}"
 
 # Check exit status