Updated README files

Modified run.bat files

README.md

@@ -11,7 +11,11 @@ GA-AEM is a repository for Geoscience Australia's C++ programs and utilities for
 The majority of the development for this project was carried out by the authors whilst employed at Geoscience Australia. A significant part of the development was however carried out as part of a Geoscience Australia-CSIRO placement. The CSIRO Deep Earth Imaging Future Science Platform (DEI-FSP), CSIRO Discovery Program and CSIRO Research Office is acknowledged for funding and facilitating that placement.
 
 ## Pre-built Windows binaries
-For Windows users whom do not wish to compile the programs themselves a package of pre-built Windows binaries are available to be downloaded from GitHub [*here*](https://github.com/GeoscienceAustralia/ga-aem/releases/tag/v2.0.0-Release-20240424). Although the package does not require compiling it does requires the installation of some third-party dependencies. See the section on [*third party software dependencies*](#third-party-software-dependencies) for details.
+For Windows users whom do not wish to compile the programs themselves a package of pre-built Windows binaries are available to be downloaded from GitHub [*here*](https://github.com/GeoscienceAustralia/ga-aem/releases/tag/v2.0.0-Release-20240424).
+- Although the pre-built Windows package does not require compiling, it will require the installation of some third-party dependencies. See the section on [*third party software dependencies*](#third-party-software-dependencies) for details.
+- Then, once installed you will need to set or modify the user's *`PATH`* (and possibly *`GDAL_DATA`* and *`PROJ_LIB`*) environment variables. These may be set in the user's environment or using the example `ga-aem_vars.bat` batch file, which will probably need to be modified depending on which versions of, and where, you install ga-aem and the third-party packages.
+- See [*scripts/ga-aem_vars.bat*](scripts/ga-aem_vars.bat) and [*scripts/test_ga-aem_paths.bat*](scripts/test_ga-aem_paths.bat) for guidance on setting Windows environment variables for ga-aem.
+- Ideally you would set the variables in the user environment (e.g. *`Start Menu | search "edit environment variable for your account"`*). After setting, be sure to open a fresh command window or Windows Explorer window.
 
 ## Languages
 - Mostly C++.
@@ -103,7 +107,7 @@ For full functionality and to build all programs, and ultimately run them, the f
 	- GNU compiler on Ubuntu [*`cmake_build_script_ubuntu.sh`*](cmake_build_script_ubuntu.sh)  (including for the Ubuntu emulator on Windows).
 	- GNU compiler on Gadi cluster [*`cmake_build_script_gadi-gnu.sh`*](cmake_build_script_gadi-gnu.sh).
 	- Intel compiler on Gadi cluster [*`cmake_build_script_gadi-intel.sh`*](cmake_build_script_gadi-intel.sh).
-- It is highly likely that you will need to set some environment variables, particularly on Windows, to help CMake find the various third-party packages. These include ***`FFTW_DIR, NETCDF_DIR, GDAL_DIR, PETSC_DIR`***. They may be set either inside the build script or in the user-environment. See [*here*](visualstudio/README.md) and [*here*](scripts/ga-aem_vars.bat) for hints.
+- It is highly likely that you will need to set some environment variables, particularly on Windows, to help CMake find the various third-party packages. These include ***`FFTW_DIR, NETCDF_DIR, GDAL_DIR, PETSC_DIR`***. They may be set either inside the build script or in the user-environment. See [*here*](visualstudio/README.md) and [*here*](scripts/ga-aem_vars.bat) for tips.
 ### CMake generate step
 - To choose a specific compiler, replace the line,
 	```bash

examples/GeoTEM3-GSQ823-1996/galeisbstdem/run.bat

@@ -1,9 +1,11 @@
 @echo off
 
-REM Add executable and FFTW directories to your search path
-REM (Ideally you would add these to your PATH environment variable)
-set path=..\..\..\bin\x64\Release\;%path%
-set path=..\..\..\third_party\fftw3.2.2.dlls\64bit;%path%
+REM Ideally you would set GA-AEM_ROOT as a variable in you user environment (e.g. Start | Edit environment variable for your account)
+REM set GA-AEM_ROOT=C:\Users\[YourUserName]\AppData\Local\GA-AEM
+REM set GA-AEM_ROOT=%LocalAppData%\GA-AEM
+
+REM Call "ga-aem_vars.bat" batch script to add executables and dependencies to your search path
+CALL %GA-AEM_ROOT%\scripts\ga-aem_vars.bat
 
 REM Run standalone on a single CPU
 galeisbstdem.exe galeisbstdem.con	&:: Invert amplitude of total-field data in the X&Z-component plane and do not solve Dx and Dz Tx-Rx offsets

examples/SkyTEM-BHMAR-2009/gaforwardmodeltdem/run.bat

@@ -1,9 +1,11 @@
 echo off
 
-REM Add executable and FFTW directories to yo search path
-REM (Ideally you would add these to your PATH environment variable)
-set path=..\..\..\bin\x64\Release\;%path%
-set path=..\..\..\third_party\fftw3.2.2.dlls\64bit;%path%
+REM Ideally you would set GA-AEM_ROOT as a variable in you user environment (e.g. Start | Edit environment variable for your account)
+REM set GA-AEM_ROOT=C:\Users\[YourUserName]\AppData\Local\GA-AEM
+REM set GA-AEM_ROOT=%LocalAppData%\GA-AEM
+
+REM Call "ga-aem_vars.bat" batch script to add executables and dependencies to your search path
+CALL %GA-AEM_ROOT%\scripts\ga-aem_vars.bat
 
 gaforwardmodeltdem.exe skytem_lm.con
 gaforwardmodeltdem.exe skytem_hm.con

examples/SkyTEM-BHMAR-2009/galeisbstdem/run.bat

@@ -8,13 +8,13 @@ REM Call "ga-aem_vars.bat" batch script to add executables and dependencies to y
 CALL %GA-AEM_ROOT%\scripts\ga-aem_vars.bat
 
 REM Run standalone on a single CPU
-galeisbstdem.exe galeisbstdem.con	
+REM galeisbstdem.exe galeisbstdem.con
 
 REM Run using 4 OpenMP threads
 REM galeisbstdem.exe galeisbstdem.con 4	
 
 REM Use 4 MPI processes
-REM mpiexec -np 4 galeisbstdem.exe galeisbstdem.con	
+mpiexec -np 4 galeisbstdem.exe galeisbstdem.con	
 
 REM If you do not have MPI installed substitute galeisbstdem-nompi.exe in place of galeisbstdem.exe
 REM galeisbstdem-nompi.exe galeisbstdem.con

examples/SkyTEM-BHMAR-2009/galeisbstdem/run_pbs.sh

@@ -14,7 +14,7 @@
 #PBS -e galeisbstdem.err
 #PBS -j oe
 
-module load ga-aem-csiro/dev
+module load ga-aem/v2.0.0-Release20240424
 module list
 
 cat run_pbs.sh

examples/Tempest-Frome-2010/gaforwardmodeltdem/run.bat

@@ -1,9 +1,11 @@
 echo off
 
-REM Add executable and FFTW directories to yo search path
-REM (Ideally you would add these to your PATH environment variable)
-set path=..\..\..\bin\x64\Release\;%path%
-set path=..\..\..\third_party\fftw3.2.2.dlls\64bit;%path%
+REM Ideally you would set GA-AEM_ROOT as a variable in you user environment (e.g. Start | Edit environment variable for your account)
+REM set GA-AEM_ROOT=C:\Users\[YourUserName]\AppData\Local\GA-AEM
+REM set GA-AEM_ROOT=%LocalAppData%\GA-AEM
+
+REM Call "ga-aem_vars.bat" batch script to add executables and dependencies to your search path
+CALL %GA-AEM_ROOT%\scripts\ga-aem_vars.bat
 
 gaforwardmodeltdem.exe tempest_standard.con
 gaforwardmodeltdem.exe tempest_hisample.con

examples/VTEM-Thomson-2014/gaforwardmodeltdem/run.bat

@@ -1,9 +1,11 @@
 echo off
 
-REM Add executable and FFTW directories to yo search path
-REM (Ideally you would add these to your PATH environment variable)
-set path=..\..\..\bin\x64\Release\;%path%
-set path=..\..\..\third_party\fftw3.2.2.dlls\64bit;%path%
+REM Ideally you would set GA-AEM_ROOT as a variable in you user environment (e.g. Start | Edit environment variable for your account)
+REM set GA-AEM_ROOT=C:\Users\[YourUserName]\AppData\Local\GA-AEM
+REM set GA-AEM_ROOT=%LocalAppData%\GA-AEM
+
+REM Call "ga-aem_vars.bat" batch script to add executables and dependencies to your search path
+CALL %GA-AEM_ROOT%\scripts\ga-aem_vars.bat
 
 gaforwardmodeltdem.exe vtem.con
 gaforwardmodeltdem.exe vtem-hisample.con

examples/VTEM-Thomson-2014/gaforwardmodeltdem_ip/run.bat

@@ -1,9 +1,11 @@
 echo off
 
-REM Add executable and FFTW directories to yo search path
-REM (Ideally you would add these to your PATH environment variable)
-set path=..\..\..\bin\x64\Release\;%path%
-set path=..\..\..\third_party\fftw3.2.2.dlls\64bit;%path%
+REM Ideally you would set GA-AEM_ROOT as a variable in you user environment (e.g. Start | Edit environment variable for your account)
+REM set GA-AEM_ROOT=C:\Users\[YourUserName]\AppData\Local\GA-AEM
+REM set GA-AEM_ROOT=%LocalAppData%\GA-AEM
+
+REM Call "ga-aem_vars.bat" batch script to add executables and dependencies to your search path
+CALL %GA-AEM_ROOT%\scripts\ga-aem_vars.bat
 
 gaforwardmodeltdem.exe vtem.con
 

examples/VTEM-Thomson-2014/galeiallatonce/run.bat

@@ -1,11 +1,11 @@
 @echo off
 
-REM Add executable and FFTW directories to yo search path
-REM (Ideally you would add these to your PATH environment variable)
-set path=C:\Microsoft_HPC_Pack_2012\Bin;%path%
-REM set path=..\..\..\..\fftw3.2.2.dlls\64bit;%path%
-set path=..\..\..\..\petsc\3.9.4\vs2017\win64_release\lib;%path%
-set path=..\..\..\bin\x64\Release\;%path%
+REM Ideally you would set GA-AEM_ROOT as a variable in you user environment (e.g. Start | Edit environment variable for your account)
+REM set GA-AEM_ROOT=C:\Users\[YourUserName]\AppData\Local\GA-AEM
+REM set GA-AEM_ROOT=%LocalAppData%\GA-AEM
+
+REM Call "ga-aem_vars.bat" batch script to add executables and dependencies to your search path
+CALL %GA-AEM_ROOT%\scripts\ga-aem_vars.bat
 
 REM Using 4 MPI processes
 mpiexec -np 4 galeiallatonce.exe galeiallatonce.con

examples/VTEM-Thomson-2014/galeisbstdem/run.bat

@@ -1,9 +1,11 @@
 @echo off
 
-REM Add executable and FFTW directories to your search path
-REM (Ideally you would add these to your PATH environment variable)
-set path=..\..\..\bin\x64\Release\;%path%
-set path=..\..\..\third_party\fftw3.2.2.dlls\64bit;%path%
+REM Ideally you would set GA-AEM_ROOT as a variable in you user environment (e.g. Start | Edit environment variable for your account)
+REM set GA-AEM_ROOT=C:\Users\[YourUserName]\AppData\Local\GA-AEM
+REM set GA-AEM_ROOT=%LocalAppData%\GA-AEM
+
+REM Call "ga-aem_vars.bat" batch script to add executables and dependencies to your search path
+CALL %GA-AEM_ROOT%\scripts\ga-aem_vars.bat
 
 REM Standalone
 REM galeisbstdem.exe galeisbstdem.con

examples/ctlinedata-programs/README.md

@@ -0,0 +1,4 @@
+# Example inversion dataset
+This small and non-sensical example inversion output dataset *`example-inversion-output/inversion.output.dat`* is really just one line of AEM inversion results, with line 3001401 duplicated as line 4001401. It is used to demonstrating the ctlinedata programs. Thus the gridding results from *`ctlinedata2slicegrids.exe`* will not make sense because of it being one duplicated line.
+
+The script *`example-inversion-output/splitlines.bat`* uses a utility program for splitting up ASCII datafiles by column number called *`splitasciibycolumn.exe`*. These are the files in the *`lines`* sub-directory. *`Splitasciibycolumn.exe`* can be found in the open-source GitHub repository [*utility-programs*](https://github.com/rcb547/utility-programs). The Windows executables are available [*here*](https://github.com/rcb547/utility-programs/releases/tag/v1.0).

examples/ctlinedata-programs/ctlinedata2curtainimage.bat

@@ -1,6 +1,10 @@
 echo off
 
-REM execute (Call) "ga-aem_vars.bat" batch script to add executables and dependencies to your search path
+REM Ideally you would set GA-AEM_ROOT as a variable in you user environment (e.g. Start | Edit environment variable for your account)
+REM set GA-AEM_ROOT=C:\Users\[YourUserName]\AppData\Local\GA-AEM
+REM set GA-AEM_ROOT=%LocalAppData%\GA-AEM
+
+REM Call "ga-aem_vars.bat" batch script to add executables and dependencies to your search path
 CALL %GA-AEM_ROOT%\scripts\ga-aem_vars.bat
 
 REM using column numbers to define fields 

examples/ctlinedata-programs/ctlinedata2georefimage-log-stretch-columns.con

@@ -1,8 +1,9 @@
 Control Begin
 
 	Input Begin
-		DataFiles    = example-inversion-output\lines\*.asc
-		//DataFiles    = example-inversion-output\inversion.output.dat
+		HeaderFile   = example-inversion-output\inversion.output.hdr
+		DataFiles    = example-inversion-output\inversion.output.dat
+		//DataFiles    = example-inversion-output\lines\*.asc
 		Subsample    = 1
 		Line         = Column 5
 		Easting      = Column 9

examples/ctlinedata-programs/ctlinedata2georefimage.bat

@@ -1,6 +1,10 @@
 echo off
 
-REM execute (Call) "ga-aem_vars.bat" batch script to add executables and dependencies to your search path
+REM Ideally you would set GA-AEM_ROOT as a variable in you user environment (e.g. Start | Edit environment variable for your account)
+REM set GA-AEM_ROOT=C:\Users\[YourUserName]\AppData\Local\GA-AEM
+REM set GA-AEM_ROOT=%LocalAppData%\GA-AEM
+
+REM Call "ga-aem_vars.bat" batch script to add executables and dependencies to your search path
 CALL %GA-AEM_ROOT%\scripts\ga-aem_vars.bat
 
 REM using column numbers to define fields