Tile Alignment User Manual

Introduction

Command Line

The command line version of the Tile Alignment is invoked using either a terminal (on Unix type systems) or using the "Command Prompt" on Windows. Simply invoking the command line utility with no arguments will produce a message that displays all the necessary arguments.

[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

Argument Details

-i [--inputfile] This is the complete path to the MXA data file that holds the RoboMet data to be processed.

-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.

GUI Application

To use the GUI version of the TileAlignment double click the R3DTileAlignment.exe (Windows), R3DTileAlignment.app (OS X) or R3DTileAlignment (Linux).

R3DTileAlignment.jpg

The R3DTileAlignment GUI Application

Simply fill out the text fields and use the buttons to select the various outputs. When you are ready to align your data, click the "Align" button and wait for the process to complete. You may click cancel at any time during the alignment process. The remnents of the output files will still remain though.
Generated on Fri Aug 28 14:04:33 2009 for R3DImageTools by  doxygen 1.5.2