1. GS Run Processor
:
1.2 Image Processing
: 1.2.1 Launching the image processing pipeline
1.2.1
Launching the image processing pipeline
There are three ways to launch the image processing step of the GS Run Processor application:
•
As part of the automated pipeline processing system of the GS Junior or GS FLX+ Instruments (see GS Sequencer application, in Part A of this manual)
•
From the GS Run Processor Manager tool accessed via the GS RunBrowser application (see section
3.4.3
)
•
From the command line interface (CLI)
The command line application can be launched by the runImagePipe command, which has the following command line structure:
runImagePipe [options] RUN_DIRECTORY
The
RUN_DIRECTORY
specified must contain a dataRunParams.parse file, the imageLog.parse file and the complete contents of the rawImages subdirectory. The options for the runImagePipe command are listed in
Table 5
.
Option
Description
--progress
Displays real-time progress of the job’s processing.
--pipe=XMLFILE
Specifies a pipeline processing script file. (Specifying the .xml extension is optional.)
--reg=REGION_NUM
Specifies processing of data from a particular region of the PTP. Regions can be specified as a range or as a comma-separated list ("1-4" or "1,2,5,9"). (Note: Multiple regions are only supported on the GS FLX+ Instrument.)
-verbose
Provides verbose log output useful for troubleshooting.
Table 5: runImagePipe command options
