diff --git a/code/compiler/AxonSeg_Linux/PackagingLog.html b/code/compiler/AxonSeg_Linux/PackagingLog.html new file mode 100644 index 0000000..299b785 --- /dev/null +++ b/code/compiler/AxonSeg_Linux/PackagingLog.html @@ -0,0 +1,158 @@ +
+mcc -o AxonSeg -W main:AxonSeg -T link:exe -d /autofs/cluster/msilab/users/Tanguy/code/axonseg/code/compiler/AxonSeg/for_testing -v /autofs/cluster/msilab/users/Tanguy/code/axonseg/AxonSeg.m -a /autofs/cluster/msilab/users/Tanguy/code/axonseg/code/GUI/AxonSeg.fig -a /autofs/cluster/msilab/users/Tanguy/code/axonseg/code/utils/ind2rgb8.mexa64 -a /autofs/cluster/msilab/users/Tanguy/code/axonseg/code/utils/ind2rgb8.mexmaci64 -a /autofs/cluster/msilab/users/Tanguy/code/axonseg/code/utils/ind2rgb8.mexw64 
+Compiler version: 6.2 (R2016a)
+
+Dependency analysis by REQUIREMENTS.
+
+[Warning: Adding path "/autofs/cluster/msilab/users/Tanguy/code/axonseg" to
+Compiler path instance.] 
+Parsing file "/autofs/cluster/msilab/users/Tanguy/code/axonseg/AxonSeg.m"
+	(Referenced from: "Compiler Command Line").
+Deleting 139 temporary MEX authorization files.
+Removing: '/tmp/04f039yQ75W_20227.auth'.
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+Removing: '/tmp/04f03HBISWO_20227.auth'.
+Removing: '/tmp/04f03A60qSO_20227.auth'.
+Generating file "/autofs/cluster/msilab/users/Tanguy/code/axonseg/code/compiler/AxonSeg/for_testing/readme.txt".
+Generating file "/autofs/cluster/msilab/users/Tanguy/code/axonseg/code/compiler/AxonSeg/for_testing/run_AxonSeg.sh".
+Packaging...
+Creating the bundle...
+Web based installer created at /autofs/cluster/msilab/users/Tanguy/code/axonseg/code/compiler/AxonSeg/for_redistribution/MyAppInstaller_web.install.
+Packaging complete.
+Elapsed packaging time was: 7 minutes and 57 seconds.
+
diff --git a/code/compiler/AxonSeg_Linux/PackagingLog.txt b/code/compiler/AxonSeg_Linux/PackagingLog.txt new file mode 100644 index 0000000..2fd849f --- /dev/null +++ b/code/compiler/AxonSeg_Linux/PackagingLog.txt @@ -0,0 +1,173 @@ +mcc -o AxonSeg -W main:AxonSeg -T link:exe -d /autofs/cluster/msilab/users/Tanguy/code/axonseg/code/compiler/AxonSeg/for_testing -v /autofs/cluster/msilab/users/Tanguy/code/axonseg/AxonSeg.m -a /autofs/cluster/msilab/users/Tanguy/code/axonseg/code/utils/ind2rgb8.mexa64 -a /autofs/cluster/msilab/users/Tanguy/code/axonseg/code/utils/ind2rgb8.mexmaci64 -a /autofs/cluster/msilab/users/Tanguy/code/axonseg/code/utils/ind2rgb8.mexw64 +Compiler version: 6.1 (R2015b) + +Dependency analysis by REQUIREMENTS. + +[Warning: Name is nonexistent or not a directory: +/autofs/cluster/matlab/8.6/toolbox/shared/dastudio/depviewer] +[> In path (line 33) + In startup (line 18) + In matlabrc (line 227)] +[Warning: Name is nonexistent or not a directory: +/autofs/cluster/matlab/8.6/toolbox/simulink/simharness/simharness] +[> In path (line 33) + In startup (line 18) + In matlabrc (line 227)] +[Warning: Name is nonexistent or not a directory: +/autofs/cluster/matlab/8.6/toolbox/slvnv/reqmgt/RTExplorer] +[> In path (line 33) + In startup (line 18) + In matlabrc (line 227)] +[Warning: Name is nonexistent or not a directory: +/autofs/cluster/matlab/8.6/toolbox/target/extensions/processor/tic2000/blks/mex] +[> In path (line 33) + In startup (line 18) + In matlabrc (line 227)] +[Warning: Name is nonexistent or not a directory: +/autofs/cluster/matlab/8.6/toolbox/idelink/extensions/ticcs/lic] +[> In path (line 33) + In startup (line 18) + In matlabrc (line 227)] +[Warning: Adding path "/autofs/cluster/msilab/users/Tanguy/code/axonseg" to +Compiler path instance.] +[] +Parsing file "/autofs/cluster/msilab/users/Tanguy/code/axonseg/AxonSeg.m" + (Referenced from: "Compiler Command Line"). +Deleting 130 temporary MEX authorization files. +Removing: '/tmp/02b06V7DxZ5_11014.auth'. +Removing: '/tmp/02b06eMLtQi_11014.auth'. +Removing: '/tmp/02b06t1H9Iv_11014.auth'. +Removing: '/tmp/02b06JOQIHt_11014.auth'. +Removing: '/tmp/02b06f9MGQF_11014.auth'. +Removing: '/tmp/02b061nCj0R_11014.auth'. +Removing: '/tmp/02b06k5SAa4_11014.auth'. +Removing: '/tmp/02b066KFwlg_11014.auth'. +Removing: '/tmp/02b06eL16ws_11014.auth'. +Removing: '/tmp/02b061ojmJE_11014.auth'. +Removing: '/tmp/02b06zhigWQ_11014.auth'. +Removing: '/tmp/02b06q2fbb3_11014.auth'. +Removing: '/tmp/02b06lBEKqf_11014.auth'. +Removing: '/tmp/02b06DR8rLI_11014.auth'. +Removing: '/tmp/02b06uKJvUV_11014.auth'. +Removing: '/tmp/02b06okeg48_11014.auth'. +Removing: '/tmp/02b06TPdXmm_11014.auth'. +Removing: '/tmp/02b069LFbIz_11014.auth'. +Removing: '/tmp/02b06Sx0h4M_11014.auth'. +Removing: '/tmp/02b06HjLwq0_11014.auth'. +Removing: '/tmp/02b060MPtNd_11014.auth'. +Removing: '/tmp/02b06frX0br_11014.auth'. +Removing: '/tmp/02b06xgDjBE_11014.auth'. +Removing: 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+Removing: '/tmp/02b06DSldg9_11014.auth'. +Removing: '/tmp/02b06NsOR2m_11014.auth'. +Removing: '/tmp/02b06KCFcQA_11014.auth'. +Removing: '/tmp/02b06BxXdEO_11014.auth'. +Removing: '/tmp/02b06dTqVs2_11014.auth'. +Removing: '/tmp/02b06wneiig_11014.auth'. +Removing: '/tmp/02b06SQgn8t_11014.auth'. +Removing: '/tmp/02b06I0TeZH_11014.auth'. +Removing: '/tmp/02b064UUQQV_11014.auth'. +Removing: '/tmp/02b06F2ebJ9_11014.auth'. +Removing: '/tmp/02b06qplcCn_11014.auth'. +Removing: '/tmp/02b06FA9TvB_11014.auth'. +Removing: '/tmp/02b06SSTlqP_11014.auth'. +Removing: '/tmp/02b06TDrtl3_11014.auth'. +Removing: '/tmp/02b06NrVfhh_11014.auth'. +Removing: '/tmp/02b06yWXHdv_11014.auth'. +Removing: '/tmp/02b0630ROaJ_11014.auth'. +Removing: '/tmp/02b06YCkB8W_11014.auth'. +Removing: '/tmp/02b06WNz26a_11014.auth'. +Removing: '/tmp/02b06Ibi85o_11014.auth'. +Removing: '/tmp/02b06aDDT5C_11014.auth'. +Removing: '/tmp/02b0691Yj6Q_11014.auth'. +Removing: '/tmp/02b06PnTo74_11014.auth'. +Removing: '/tmp/02b06ZTo98i_11014.auth'. +Removing: '/tmp/02b06FyPybx_11014.auth'. +Removing: '/tmp/02b06cysFeL_11014.auth'. +Removing: '/tmp/02b06U9FxiZ_11014.auth'. +Removing: '/tmp/02b06HI14md_11014.auth'. +Removing: '/tmp/02b06ivjhsr_11014.auth'. +Removing: '/tmp/02b06HwL9xF_11014.auth'. +Removing: '/tmp/02b06C7iIET_11014.auth'. +Removing: '/tmp/02b06eR9WL7_11014.auth'. +Removing: '/tmp/02b06J4wSTl_11014.auth'. +Removing: '/tmp/02b06MiSw2z_11014.auth'. +Removing: '/tmp/02b06zlu9cO_11014.auth'. +Removing: '/tmp/02b06RePso2_11014.auth'. +Removing: '/tmp/02b06To4UAg_11014.auth'. +Removing: '/tmp/02b066Gf5Nu_11014.auth'. +Removing: '/tmp/02b06x5od2I_11014.auth'. +Removing: '/tmp/02b06tUEnhX_11014.auth'. +Removing: '/tmp/02b06N3NaKr_11014.auth'. +Removing: '/tmp/02b0660Fj4D_11014.auth'. +Removing: '/tmp/02b06RdNbpQ_11014.auth'. +Removing: '/tmp/02b06HBjOK2_11014.auth'. +Removing: '/tmp/02b061GU86e_11014.auth'. +Removing: '/tmp/02b06ROZcur_11014.auth'. +Removing: '/tmp/02b06kz1WRD_11014.auth'. +Removing: '/tmp/02b06gV6ngQ_11014.auth'. +Removing: '/tmp/02b06cFUDF2_11014.auth'. +Removing: '/tmp/02b06nFHK7e_11014.auth'. +Removing: '/tmp/02b06NClwAr_11014.auth'. +Removing: '/tmp/02b06mKBY3D_11014.auth'. +Removing: '/tmp/02b066G25xQ_11014.auth'. +Removing: '/tmp/02b06L0IP22_11014.auth'. +Removing: '/tmp/02b0635Lfyf_11014.auth'. +Removing: '/tmp/02b06Gnmm4r_11014.auth'. +Removing: '/tmp/02b06bsv8AE_11014.auth'. +Removing: '/tmp/02b06MW0z8Q_11014.auth'. +Removing: '/tmp/02b06a5YEG3_11014.auth'. +Removing: '/tmp/02b06ne0mfg_11014.auth'. +Removing: '/tmp/02b060h1KOs_11014.auth'. +Removing: '/tmp/02b06BDUSoF_11014.auth'. +Removing: '/tmp/02b06MkrIZR_11014.auth'. +Removing: '/tmp/02b06aqmdB4_11014.auth'. +Removing: '/tmp/02b06t5bpdh_11014.auth'. +Removing: '/tmp/02b06EkfgQt_11014.auth'. +Removing: '/tmp/02b06SMhZuG_11014.auth'. +Removing: '/tmp/02b06XNJSJb_11014.auth'. +Removing: '/tmp/02b06zK1qcq_11014.auth'. +Removing: '/tmp/02b06mGL0EE_11014.auth'. +Removing: '/tmp/02b06P0IG7S_11014.auth'. +Removing: '/tmp/02b065W9nA7_11014.auth'. +Removing: '/tmp/02b06VQX62l_11014.auth'. +Removing: '/tmp/02b06Cal6vA_11014.auth'. +Removing: '/tmp/02b06GZCEZO_11014.auth'. +Removing: '/tmp/02b06DnnNt3_11014.auth'. +Removing: '/tmp/02b06YRLXXh_11014.auth'. +Removing: '/tmp/02b06K0Nisw_11014.auth'. +Removing: '/tmp/02b06tXyHWK_11014.auth'. +Removing: '/tmp/02b06q14FcT_11014.auth'. +Removing: '/tmp/02b06dY9hsT_11014.auth'. +Removing: '/tmp/02b06qvxov5_11014.auth'. +Removing: '/tmp/02b06u3TTAh_11014.auth'. +Generating file "/autofs/cluster/msilab/users/Tanguy/code/axonseg/code/compiler/AxonSeg/for_testing/readme.txt". +Generating file "/autofs/cluster/msilab/users/Tanguy/code/axonseg/code/compiler/AxonSeg/for_testing/run_AxonSeg.sh". +Packaging... +Creating the bundle... +Web based installer created at /autofs/cluster/msilab/users/Tanguy/code/axonseg/code/compiler/AxonSeg/for_redistribution/MyAppInstaller_web.install. +Packaging complete. +Elapsed packaging time was: 20 minutes and 24 seconds. diff --git a/code/compiler/AxonSeg_Linux/for_redistribution_files_only/AxonSeg b/code/compiler/AxonSeg_Linux/for_redistribution_files_only/AxonSeg new file mode 100755 index 0000000..fcbf492 Binary files /dev/null and b/code/compiler/AxonSeg_Linux/for_redistribution_files_only/AxonSeg differ diff --git a/code/compiler/AxonSeg_Linux/for_redistribution_files_only/icon.icns b/code/compiler/AxonSeg_Linux/for_redistribution_files_only/icon.icns new file mode 100644 index 0000000..b122d94 Binary files /dev/null and b/code/compiler/AxonSeg_Linux/for_redistribution_files_only/icon.icns differ diff --git a/code/compiler/AxonSeg_Linux/for_redistribution_files_only/readme.txt b/code/compiler/AxonSeg_Linux/for_redistribution_files_only/readme.txt new file mode 100644 index 0000000..74d8cbf --- /dev/null +++ b/code/compiler/AxonSeg_Linux/for_redistribution_files_only/readme.txt @@ -0,0 +1,115 @@ +MATLAB Compiler + +1. Prerequisites for Deployment + +. Verify the MATLAB Runtime is installed and ensure you + have installed version 9.0.1 (R2016a). + +. 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 R2016a +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 +================================ +-AxonSeg +-run_AxonSeg.sh (shell script for temporarily setting environment variables and executing + the application) + -to run the shell script, type + + ./run_AxonSeg.sh + + at Linux or Mac command prompt. is the directory + where version 9.0.1 of the MATLAB Runtime is installed or the directory where + MATLAB is installed on the machine. is all the + arguments you want to pass to your application. For example, + + If you have version 9.0.1 of the MATLAB Runtime installed in + /mathworks/home/application/v901, run the shell script as: + + ./run_AxonSeg.sh /mathworks/home/application/v901 + + If you have MATLAB installed in /mathworks/devel/application/matlab, + run the shell script as: + + ./run_AxonSeg.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/v901/X11/app-defaults + + +(2) If the environment variable LD_LIBRARY_PATH is undefined, set it to the concatenation + of the following strings: + + MCR_ROOT/v901/runtime/glnxa64: + MCR_ROOT/v901/bin/glnxa64: + MCR_ROOT/v901/sys/os/glnxa64: + MCR_ROOT/v901/sys/opengl/lib/glnxa64 + + If it is defined, set it to the concatenation of these strings: + + ${LD_LIBRARY_PATH}: + MCR_ROOT/v901/runtime/glnxa64: + MCR_ROOT/v901/bin/glnxa64: + MCR_ROOT/v901/sys/os/glnxa64: + MCR_ROOT/v901/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_AxonSeg.sh + instead of setting environment variables. See + section 2 "Files to Deploy and Package". + + + + + + diff --git a/code/compiler/AxonSeg_Linux/for_redistribution_files_only/run_AxonSeg.sh b/code/compiler/AxonSeg_Linux/for_redistribution_files_only/run_AxonSeg.sh new file mode 100755 index 0000000..8b551aa --- /dev/null +++ b/code/compiler/AxonSeg_Linux/for_redistribution_files_only/run_AxonSeg.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 \ 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}/AxonSeg\"" $args +fi +exit + diff --git a/code/compiler/AxonSeg_Linux/for_redistribution_files_only/splash.png b/code/compiler/AxonSeg_Linux/for_redistribution_files_only/splash.png new file mode 100644 index 0000000..d60c6fa Binary files /dev/null and b/code/compiler/AxonSeg_Linux/for_redistribution_files_only/splash.png differ diff --git a/code/compiler/AxonSeg_Linux/for_testing/AxonSeg b/code/compiler/AxonSeg_Linux/for_testing/AxonSeg new file mode 100755 index 0000000..fcbf492 Binary files /dev/null and b/code/compiler/AxonSeg_Linux/for_testing/AxonSeg differ diff --git a/code/compiler/AxonSeg_Linux/for_testing/mccExcludedFiles.log b/code/compiler/AxonSeg_Linux/for_testing/mccExcludedFiles.log new file mode 100644 index 0000000..85536f0 --- /dev/null +++ b/code/compiler/AxonSeg_Linux/for_testing/mccExcludedFiles.log @@ -0,0 +1,8 @@ +The List of Excluded Files +Excluded files Exclusion Message ID Reason For Exclusion Exclusion Rule +/autofs/cluster/matlab/9.0/toolbox/ident/nlident/@idnlarx/pem_.m MATLAB:Completion:ExcludedBy Cannot be packaged for use in the target environment MCR. Removed from the parts list by license Compiler. +/autofs/cluster/matlab/9.0/toolbox/ident/nlident/@idnlgrey/pem_.m MATLAB:Completion:ExcludedBy Cannot be packaged for use in the target environment MCR. Removed from the parts list by license Compiler. +/autofs/cluster/matlab/9.0/toolbox/local/+matlab/+internal/+toolboxes/addInstalledToolboxesToPath.m MATLAB:Completion:ExcludedBy Cannot be packaged for use in the target environment MCR. Removed from the parts list by license Compiler. /autofs/cluster/matlab/9\.0/toolbox/local/[+]matlab/[+]internal/[+]toolboxes/addInstalledToolboxesToPath[.]m +/autofs/cluster/matlab/9.0/toolbox/local/+matlab/+internal/+zipAddOns/addInstalledZipAddOnsToPath.m MATLAB:Completion:ExcludedBy Cannot be packaged for use in the target environment MCR. Removed from the parts list by license Compiler. /autofs/cluster/matlab/9\.0/toolbox/local/[+]matlab/[+]internal/[+]zipAddOns/addInstalledZipAddOnsToPath[.]m +/autofs/cluster/matlab/9.0/toolbox/matlab/codetools/@mtree/mtree.m MATLAB:Completion:ExcludedBy Cannot be packaged for use in the target environment MCR. Removed from the parts list by license Compiler. /autofs/cluster/matlab/9\.0/toolbox/matlab/codetools +/autofs/cluster/matlab/9.0/toolbox/matlab/codetools/initdesktoputils.m MATLAB:Completion:ExcludedBy Cannot be packaged for use in the target environment MCR. Removed from the parts list by license Compiler. /autofs/cluster/matlab/9\.0/toolbox/matlab/codetools diff --git a/code/compiler/AxonSeg_Linux/for_testing/readme.txt b/code/compiler/AxonSeg_Linux/for_testing/readme.txt new file mode 100644 index 0000000..74d8cbf --- /dev/null +++ b/code/compiler/AxonSeg_Linux/for_testing/readme.txt @@ -0,0 +1,115 @@ +MATLAB Compiler + +1. Prerequisites for Deployment + +. Verify the MATLAB Runtime is installed and ensure you + have installed version 9.0.1 (R2016a). + +. 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 R2016a +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 +================================ +-AxonSeg +-run_AxonSeg.sh (shell script for temporarily setting environment variables and executing + the application) + -to run the shell script, type + + ./run_AxonSeg.sh + + at Linux or Mac command prompt. is the directory + where version 9.0.1 of the MATLAB Runtime is installed or the directory where + MATLAB is installed on the machine. is all the + arguments you want to pass to your application. For example, + + If you have version 9.0.1 of the MATLAB Runtime installed in + /mathworks/home/application/v901, run the shell script as: + + ./run_AxonSeg.sh /mathworks/home/application/v901 + + If you have MATLAB installed in /mathworks/devel/application/matlab, + run the shell script as: + + ./run_AxonSeg.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/v901/X11/app-defaults + + +(2) If the environment variable LD_LIBRARY_PATH is undefined, set it to the concatenation + of the following strings: + + MCR_ROOT/v901/runtime/glnxa64: + MCR_ROOT/v901/bin/glnxa64: + MCR_ROOT/v901/sys/os/glnxa64: + MCR_ROOT/v901/sys/opengl/lib/glnxa64 + + If it is defined, set it to the concatenation of these strings: + + ${LD_LIBRARY_PATH}: + MCR_ROOT/v901/runtime/glnxa64: + MCR_ROOT/v901/bin/glnxa64: + MCR_ROOT/v901/sys/os/glnxa64: + MCR_ROOT/v901/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_AxonSeg.sh + instead of setting environment variables. See + section 2 "Files to Deploy and Package". + + + + + + diff --git a/code/compiler/AxonSeg_Linux/for_testing/readme.txt~ b/code/compiler/AxonSeg_Linux/for_testing/readme.txt~ new file mode 100644 index 0000000..74d8cbf --- /dev/null +++ b/code/compiler/AxonSeg_Linux/for_testing/readme.txt~ @@ -0,0 +1,115 @@ +MATLAB Compiler + +1. Prerequisites for Deployment + +. Verify the MATLAB Runtime is installed and ensure you + have installed version 9.0.1 (R2016a). + +. 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 R2016a +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 +================================ +-AxonSeg +-run_AxonSeg.sh (shell script for temporarily setting environment variables and executing + the application) + -to run the shell script, type + + ./run_AxonSeg.sh + + at Linux or Mac command prompt. is the directory + where version 9.0.1 of the MATLAB Runtime is installed or the directory where + MATLAB is installed on the machine. is all the + arguments you want to pass to your application. For example, + + If you have version 9.0.1 of the MATLAB Runtime installed in + /mathworks/home/application/v901, run the shell script as: + + ./run_AxonSeg.sh /mathworks/home/application/v901 + + If you have MATLAB installed in /mathworks/devel/application/matlab, + run the shell script as: + + ./run_AxonSeg.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/v901/X11/app-defaults + + +(2) If the environment variable LD_LIBRARY_PATH is undefined, set it to the concatenation + of the following strings: + + MCR_ROOT/v901/runtime/glnxa64: + MCR_ROOT/v901/bin/glnxa64: + MCR_ROOT/v901/sys/os/glnxa64: + MCR_ROOT/v901/sys/opengl/lib/glnxa64 + + If it is defined, set it to the concatenation of these strings: + + ${LD_LIBRARY_PATH}: + MCR_ROOT/v901/runtime/glnxa64: + MCR_ROOT/v901/bin/glnxa64: + MCR_ROOT/v901/sys/os/glnxa64: + MCR_ROOT/v901/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_AxonSeg.sh + instead of setting environment variables. See + section 2 "Files to Deploy and Package". + + + + + + diff --git a/code/compiler/AxonSeg_Linux/for_testing/requiredMCRProducts.txt b/code/compiler/AxonSeg_Linux/for_testing/requiredMCRProducts.txt new file mode 100644 index 0000000..973a120 --- /dev/null +++ b/code/compiler/AxonSeg_Linux/for_testing/requiredMCRProducts.txt @@ -0,0 +1 @@ +35000 35001 35010 \ No newline at end of file diff --git a/code/compiler/AxonSeg_Linux/for_testing/run_AxonSeg.sh b/code/compiler/AxonSeg_Linux/for_testing/run_AxonSeg.sh new file mode 100755 index 0000000..8b551aa --- /dev/null +++ b/code/compiler/AxonSeg_Linux/for_testing/run_AxonSeg.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 \ 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}/AxonSeg\"" $args +fi +exit + diff --git a/code/compiler/AxonSeg_Linux/for_testing/run_AxonSeg.sh~ b/code/compiler/AxonSeg_Linux/for_testing/run_AxonSeg.sh~ new file mode 100644 index 0000000..96159d8 --- /dev/null +++ b/code/compiler/AxonSeg_Linux/for_testing/run_AxonSeg.sh~ @@ -0,0 +1,35 @@ +#!/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 \ 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; + MCR_CACHE_ROOT=/autofs/cluster/msilab/users/Tanguy/code/tmp; + export LD_LIBRARY_PATH; + export MCR_CACHE_ROOT; +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}/AxonSeg\"" $args +fi +exit + diff --git a/code/compiler/AxonSeg_Linux/for_testing/splash.png b/code/compiler/AxonSeg_Linux/for_testing/splash.png new file mode 100644 index 0000000..d60c6fa Binary files /dev/null and b/code/compiler/AxonSeg_Linux/for_testing/splash.png differ diff --git a/code/compiler/MCR_cache b/code/compiler/MCR_cache new file mode 100644 index 0000000..5339a18 --- /dev/null +++ b/code/compiler/MCR_cache @@ -0,0 +1,5 @@ +# if MCR cache(CTF extraction path) gets corrupted --> change dir +setenv MCR_CACHE_ROOT /folderofyourchoice/tmp; + +# if MyAppInstaller_web.install fails extracting.. Might be because you are on remote server, and no space. change your home to a bigger space: +setenv HOME /folderofyourchoic diff --git a/code/compiler/as_Segmentation_full_image.prj b/code/compiler/as_Segmentation_full_image.prj deleted file mode 100644 index c566fac..0000000 --- a/code/compiler/as_Segmentation_full_image.prj +++ /dev/null @@ -1,193 +0,0 @@ - - - as_Segmentation_full_image - ${PROJECT_ROOT}/as_Segmentation_full_image_resources/icon.icns - - ${PROJECT_ROOT}/as_Segmentation_full_image_resources/icon_48.png - ${PROJECT_ROOT}/as_Segmentation_full_image_resources/icon_32.png - ${PROJECT_ROOT}/as_Segmentation_full_image_resources/icon_24.png - ${PROJECT_ROOT}/as_Segmentation_full_image_resources/icon_16.png - - 1.0 - NeuroPoly and DCClab - - - as_Segmentation_full_image('image.tif','SegParameters.mat') -as_Segmentation_full_image({'image.tif', 'mask_axon.tif'},'SegParameters.mat') - Reference: Zaimi A, Duval T, Gasecka A, Côté D, Stikov N and Cohen-Adad J (2016). AxonSeg: open source software for axon and myelin segmentation and morphometric analysis. Front. Neuroinform. 10:37. doi: 10.3389/fninf.2016.00037 - -Copyright (c) 2017 NeuroPoly (Polytechnique Montreal) and DCClab (Université Laval) - ${PROJECT_ROOT}/AxonSeg_mac/for_testing/splash.png - - /as_Segmentation_full_image/ - option.installpath.systemwideapp - - In the following directions, replace MCR_ROOT by the directory where the MATLAB Runtime is installed on the target machine. - -If the environment variable DYLD_LIBRARY_PATH is undefined, set it to the concatenation of the following strings: - - MCR_ROOT/v91/runtime/maci64: - MCR_ROOT/v91/sys/os/maci64: - MCR_ROOT/v91/bin/maci64 - -If it is defined, set it to the concatenation of these strings: - - ${LD_LIBRARY_PATH}: - MCR_ROOT/v91/runtime/maci64: - MCR_ROOT/v91/sys/os/maci64: - MCR_ROOT/v91/bin/maci64 - - ${PROJECT_ROOT}/as_Segmentation_full_image/for_testing - ${PROJECT_ROOT}/as_Segmentation_full_image/for_redistribution_files_only - ${PROJECT_ROOT}/as_Segmentation_full_image/for_redistribution - ${PROJECT_ROOT}/as_Segmentation_full_image - false - - true - subtarget.standalone - - true - false - false - MyAppInstaller_web - MyAppInstaller_mcr - MyAppInstaller_app - false - false - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - /Users/Tanguy/code/axon_segmentation/code/as_Segmentation_full_image.m - - - - - ${MATLAB_ROOT}/toolbox/matlab/demos/gatlin.mat - ${MATLAB_ROOT}/toolbox/matlab/demos/mandrill.mat - ${MATLAB_ROOT}/toolbox/matlab/demos/mri.mat - /Users/Tanguy/code/axon_segmentation/code/Blockprocessing/as_listcell2axonlist.m - /Users/Tanguy/code/axon_segmentation/code/Seg_axon/axonInitialSegmentation.m - /Users/Tanguy/code/axon_segmentation/code/Seg_axon/axon_stats_step2.m - /Users/Tanguy/code/axon_segmentation/code/Seg_myelin/MinimalPath/minimalPath.m - /Users/Tanguy/code/axon_segmentation/code/Seg_myelin/MinimalPath/minimalpath_reg.m - /Users/Tanguy/code/axon_segmentation/code/Seg_myelin/Snake/BasicSnake_version2f/DrawSegmentedArea2D.m - /Users/Tanguy/code/axon_segmentation/code/Seg_myelin/Snake/BasicSnake_version2f/ImageDerivatives2D.m - /Users/Tanguy/code/axon_segmentation/code/Seg_myelin/Snake/BasicSnake_version2f/Snake2D.m - /Users/Tanguy/code/axon_segmentation/code/Seg_myelin/Snake/BasicSnake_version2f/SnakeMoveIteration2D.m - /Users/Tanguy/code/axon_segmentation/code/Seg_myelin/Snake/as_myelinFindBoundary2.m - /Users/Tanguy/code/axon_segmentation/code/Seg_myelin/as_myelinseg2axonlist.m - /Users/Tanguy/code/axon_segmentation/code/Seg_myelin/as_stats.m - /Users/Tanguy/code/axon_segmentation/code/Seg_myelin/myelinInitialSegmention.m - /Users/Tanguy/code/axon_segmentation/code/Stats/as_AxonSeg_predict.m - /Users/Tanguy/code/axon_segmentation/code/Stats/as_stats_axons.m - /Users/Tanguy/code/axon_segmentation/code/Stats/as_stats_downsample.m - /Users/Tanguy/code/axon_segmentation/code/Stats/as_stats_fields.m - /Users/Tanguy/code/axon_segmentation/code/axonlist/as_axonlist_changeorigin.m - /Users/Tanguy/code/axon_segmentation/code/axonlist/as_axonlist_distance_closerthandiameter.m - /Users/Tanguy/code/axon_segmentation/code/axonlist/as_axonlist_distancematrix.m - /Users/Tanguy/code/axon_segmentation/code/axonlist/as_display_label.m - /Users/Tanguy/code/axon_segmentation/code/axonlist/as_index2mask.m - /Users/Tanguy/code/axon_segmentation/code/axonlist/as_myelin2axon.m - /Users/Tanguy/code/axon_segmentation/code/imageprocessing/RemoveBorder.m - /Users/Tanguy/code/axon_segmentation/code/imageprocessing/as_gaussian_smoothing.m - /Users/Tanguy/code/axon_segmentation/code/imageprocessing/as_improc_blockwising.m - /Users/Tanguy/code/axon_segmentation/code/pipeline/Deconv.m - /Users/Tanguy/code/axon_segmentation/code/pipeline/histeq.m - /Users/Tanguy/code/axon_segmentation/code/pipeline/step1_full.m - /Users/Tanguy/code/axon_segmentation/code/pipeline/step2_full.m - /Users/Tanguy/code/axon_segmentation/code/utils/findmaxima.m - /Users/Tanguy/code/axon_segmentation/code/utils/findminima.m - /Users/Tanguy/code/axon_segmentation/code/utils/imzoom.m - /Users/Tanguy/code/axon_segmentation/code/utils/ind2rgb8.mexmaci64 - /Users/Tanguy/code/axon_segmentation/code/utils/j_progress.m - /Users/Tanguy/code/axon_segmentation/code/utils/matlabCentral/qinterp2/qinterp2.m - /Users/Tanguy/code/axon_segmentation/code/utils/matlabCentral/sc/gray.m - /Users/Tanguy/code/axon_segmentation/code/utils/matlabCentral/sc/hot.m - /Users/Tanguy/code/axon_segmentation/code/utils/matlabCentral/sc/imdisp.m - /Users/Tanguy/code/axon_segmentation/code/utils/matlabCentral/sc/jet.m - /Users/Tanguy/code/axon_segmentation/code/utils/matlabCentral/sc/private/colormap_helper.m - /Users/Tanguy/code/axon_segmentation/code/utils/matlabCentral/sc/private/rescale.m - /Users/Tanguy/code/axon_segmentation/code/utils/matlabCentral/sc/real2rgb.m - /Users/Tanguy/code/axon_segmentation/code/utils/matlabCentral/sc/sc.m - /Users/Tanguy/code/axon_segmentation/code/utils/reshape2D.m - - - /Users/Tanguy/code/axon_segmentation/code/compiler/as_Segmentation_full_image/for_testing/readme.txt - /Users/Tanguy/code/axon_segmentation/code/compiler/as_Segmentation_full_image/for_testing/as_Segmentation_full_image.app - 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