Archiver User Manual

Introduction

The R3D Image Tools executables work on data that is stored in an HDF5 file and more specifically, an MXA formatted HDF5 file. In oder to create a proper data archive there are 2 programs to use. The GUI based R3DArchiver and the command line based Archiver utility. Please note that the format of the .rms file must be in a key=value style. This format looks like the following:
CurrentSlice = 0
PolishTime = 1200
TrackNumber = 67.5
TrackWidth = 0.5
RPM = 100

Command Line

The command line version of the data archiver 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] $ Archiver
Required Parameters:
  --help                  Produce help message
  -r [ --rms ] arg        RoboMet.3D settings file
  -m [ --model ] arg      XML file describing data model
  -o [ --outputfile ] arg File name to be used for writing archive file
  -s [ --sliceStart ] arg The value of the starting slice to export
  -e [ --sliceEnd ] arg   The value of the ending slice to export
  -l [ --logfile ] arg    Name of the Log file to store any output into

Each argument is required and should be filled in correctly. If there are spaces in either the filename or the path to and of the file names then they should be surrounded with double quotes.

Argument Details

-r [ --rms ]The RoboMet.3D .rms file that is exported from the RoboMet.3D run.

-m [ --model ] The path to the RoboMet.3D xml file that describes the basic MXADataModel.

-o [ --outputfile ] The path to the MXA archive file that is to be produced. Usually this file has an extension of .mxa (or .h5).

-s [ --sliceStart ] The first slice of data to export

-e [ --sliceEnd ] The last slice of data to export

-l [--logfile] The path to a file to store debugging messages into.

An example of the invocation would be the following (from a Unix machine):


[mjackson@workstation] $ Archiver -r /Users/Data/RoboMet/MyExperiment/MyExperiment.rms -x \
/Users/Data/RoboMet/RoboMetModel.xml -m /Users/Data/RoboMet/MyExperiment/MyData.mxa -s 100 -e 289 -l /tmp/MyExperiment.log

This would import slices 100 through 289 inclusive into a file called MyData.mxa located in the /Users/Data/RoboMet/MyExperiment/ directory. Inspecting the log file for any errors is also helpfule if there are problems reading the data in later processing steps.

GUI Application

To use the GUI version of the Archiver double click the R3DArchiver.exe (Windows), R3DArchiver.app (OS X) or R3DArchiver (Linux).

R3DArchiver.jpg

The R3DArchiver GUI Application

Simply fill out the text fields and use the buttons to select the various outputs. When you are ready to import your data, click the "Start" button and wait for the process to complete. You may click cancel at any time during the archiving 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