Hi there,
thanks for the good work to maintain such a useful tool.
My current setup is MIPAV 7.4.0 with JIST-CRUISE-2014Dec12-03-37PM
(v 3.2) and PyJIST 2014-03-27
Executing modules from the CLI I get errors about missing
parameters if I skip them, even if default values are specified.
This is also true if not using PyJIST, but directly calling Java as
described here:
http://www.nitrc.org/plugins/mwiki/index...
Using an older version of JIST (MIPAV 7.2.0 and JIST
v2.0-2013Nov06) this is not the case
e.g.(this would execute perfectly under JIST v2.0)
JIST-run module -c edu.jhu.bme.smile.demo.RandomVol -- -outRand1
./testrand.nii.gz
cli
####################################################################
cli Initializing MIPAV/JIST Framework
cli
####################################################################
cli Interpretting command line arguments
cli
####################################################################
edu.jhu.bme.smile.demo.RandomVol
PARSE ERROR: Missing required tag: inSize
inSize = = 100
PARSE ERROR: Missing required tag: inSize2
inSize2 = = 100
PARSE ERROR: Missing required tag: inSize3
inSize3 = = 20
PARSE ERROR: Missing required tag: inSize4
inSize4 = = 1
PARSE ERROR: Missing required tag: inStandard
inStandard = = 1
PARSE ERROR: Missing required tag: inLambda
inLambda = = 5
PARSE ERROR: Missing required tag: inMaximum
inMaximum = = 1
PARSE ERROR: Missing required tag: inMinimum
inMinimum = = 0
PARSE ERROR: Missing required tag: inField
inField = = Uniform
outRand1 = ./testrand.nii.gz
outProc = /home/johndoe/Downloads/PyJIST
cli
####################################################################
cli Exiting with errors.
Specifying all parameters works perfectly in any version
bin/JIST-run module -c
edu.jhu.bme.smile.demo.RandomVol -- -outRand1 ./testrand.nii.gz
-inSize 100 -inSize2 100 -inSize3 20 -inSize4 1 -inStandard 1
-inLambda 5 -inMaximum 1 -inMinimum 0 -inField Uniform
cli
####################################################################
cli Initializing MIPAV/JIST Framework
cli
####################################################################
cli Interpretting command line arguments
cli
####################################################################
edu.jhu.bme.smile.demo.RandomVol
inSize = 100
inSize2 = 100
inSize3 = 20
inSize4 = 1
inStandard = 1
inLambda = 5
inMaximum = 1
inMinimum = 0
inField = Uniform
outRand1 = ./testrand.nii.gz
outProc = /home/johndoe/Downloads/PyJIST
cli
####################################################################
edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat
ImageDataFloat: 0New image:100x100x20x1
edu.jhu.bme.smile.demo.RandomVol FINISHED
edu.jhu.ece.iacl.jist.pipeline.CalculationMonitorCalculation
Monitor not running. Punting stop.
---------- Performance Summary ----------
1) Algorithm Calculation -- ELAPSED TIME: Actual: 0.03 sec / CPU:
0.03 sec
TOTAL ELAPSED TIME: Actual: 0.03 sec / CPU: 0.03 sec
CURRENT MEMORY: Used 45 MB, Free 918 MB, Total 963 MB
edu.jhu.ece.iacl.jist.pipeline.view.input.RefresherRefresher
finished.
Argument for outRand1 Absolute path required for output files.
cli
####################################################################
cli Done: edu.jhu.bme.smile.demo.RandomVol
cli
####################################################################
