[mjackson@workstation] $ MosaicExporter Required Parameters: --help Produce help message --help Produce help message -i [ --inputfile ] arg MXA File to be used as input -r [ --recname ] arg Name of the Data Record to Export -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 Path to a log file to write output messages to. -L [ --listRecords ] arg List the possible Data Model Records for the given MXA file -o [ --outputPrefix ] arg The path to where the image files will be written. -d [ --description ] arg Description to be used for the tiff_tag 'IMAGE_DESCRIPTION' -z [ --rescale ] arg Scaling Factor - 100.0 is full size. 50.0 is half the size --voiOrigin Use VOI Origin -x [ --originx ] arg X Origin of the VOI -y [ --originy ] arg Y Origin of the VOI --voiSize Use VOI Size -w [ --width ] arg Width (Microns) of VOI -h [ --height ] arg Height (Microns) of VOI --working_volume Compute the largest Volume that would encompass the maximum area from each slice. -v [ --verbose ] Verbose Output
-o [--outputprefix] The path + partial file name that will start each exported slice. This can be a path + a partial file name or just a partial filename. If a relative path is give then it is relative to the directory where the executale is being run from. Some examples that this input parameter can have are:
/tmp/MyExperiment_ C:\Data\MyExperiment-Images\MyExperimentImage-
-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".
-d [ --description ] A short sentence describing the data. This is placed in the TIFF_COMMENT section of the tif header. (Currently not used).
-s [ --sliceStart ] The first slice of data to export
-e [ --sliceEnd ] The last slice of data to export
-z [ --rescale ] Rescale the images exported by the given percent. 100.0 is full size, 50.0 is half size, 200.0 is double the size of the original
--voiOrigin Use this flag followed by the -x (--originx) and -y (--originy) to denote that a specified volume of interest is to be used. If this parameter left out then the entire mosaic is exported and alignment of each slice is only as good as the original data aquisition. Arguments for these parameters are given in microns. For example:
--voiOrigin -x 46590 -y 47892
--voiSize Use this flag followed by the -w (--width) and -h (--height) flags to specify the size in Microns of the Mosaic being exported. If you would like an aligned set of images then you must use this parameter along with the --voiOrigin parameter.
-l [ --logfile ] The path to a file to store debugging messages into.
-L [--listRecords] Returns a list of the MXA Data Records in the MXA File.
--working_volume Calculates the working volume of the data set which is the largest volume that contains valid data.
-v [ --verbose ] Determines how many debugging messages are written to the log file
The R3DMosaicExporter GUI Application Showing the Main Input/Output Tab
If you only want a subvolume, need more verbose output or want to resize the images being produced you can click the "Options" tab to set those variables.
The R3DMosaicExporter GUI Application Showing the Options Tab
If you would like to calculate the working volume of the data set then use the "Working Volume" tab.
The R3DMosaicExporter GUI Application Showing the Working Volume Calculation Tab