[mjackson@workstation] $ TileAlignment Required Parameters: --help Produce help message -i [ --inputfile ] arg MXA File to be used as input -r [ --recname ] arg Name of the Data Record to Register -s [ --sliceStart ] arg The value of the starting slice to fix -e [ --sliceEnd ] arg The value of the ending slice to fix -t [ --numThreads ] arg The number of threads to use when registering -l [ --logfile ] arg Name of the Log file to store any output into -R [ --restartfile ] arg Location of the restartfile file to initialize from. -L [ --listRecords ] arg List the possible Data Model Records for the given MXA file -v [ --verbose ] Verbose Output
-r [--recname] You will need to know the name of the MXA Data Record that represents the image that you would like to process. Typically this is "Zeiss Image". You can invoke the PCMRegistration program with the --listRecords argument to obtain a list of the MXA Data Records in the MXA File.
-s [--sliceStart] The first slice of data to export
-e [--sliceEnd] The last slice of data to export
-t [--numThreads] The number of threads to use to process the MXA Data file. Each thread should have access to about 200 MB of memory.
-l [--logfile] The path to a file to store debugging messages into.
-R [--restartfile] Path to a temporary file that holds intermediate data. This can help debug if something goes wrong during the process. The file is written in binary so computer codes would need to be written to parse the file.
-L [--listRecords] Returns a list of the MXA Data Records in the MXA File.
-v [--verbose] Determines how many debugging messages are written to the log file
An example of the invocation would be the following (from a Unix machine):
[mjackson@workstation] $ TileAlignment -i /Users/Data/RoboMet/MyExperiment/MyData.mxa \ -r "Zeiss Image" --logfile /tmp/TileAlignment-MyExperiment.log --tempfile /tmp/TileAlignment.dat \ --numThreads 16 -s 100 -e 289 -v
You will need to know the name of the MXA Data Record that represents the image that you would like to export. Typically this is "Zeiss Image". You can invoke the TileAlignment program with the --listRecords argument to obtain a list of the MXA Data Records in the MXA File.
The TileAlignment program multi-core/multi-cpu aware through the use of threads. If you are running the program on a multi-core cpu a safe number for the "--numThreads" argument is the number of physical cores or cpus that are available on the system. For example, if you have a Quad Core CPU that does NOT support HyperThreading then "4" is a good number to use. If your CPU supports HyperThreading or another model where each core supports more than 1 physical thread you can try increasing the number of threads that TileAlignment will use. Good results have been obtained using 16 threads on an 8 core/16 thread Intel Xeon 5500 series CPU.
The "tempfile" argument is just to hold some temporary binary data. This data is not user readable and can be discarded when the program exits. If something happens during the execution this file can sometimes have data that the programmer can use to diagnose the issue.
The R3DTileAlignment GUI Application