Date: 2014-12-04 22:19 |
Priority: more information 5 |
Submitted By:
Andrew Plassard (plassaaj)
|
Assigned To: more information
Stephen Damon (damons) |
Hardware: None | Product: None |
Operating System: None | Component: None |
Version: None | Severity: None |
Resolution: None |
Summary: more information stderr and stdout are not logical on command line output |
Detailed description |
When I run a command line module and there is a missing argument
the error about the missing arguments are illogical. For instance
when I run
edu.vanderbilt.masi.plugins.labelfusion.PluginStatisticalFusion
with no arguments the output is
Could not find library, using working directory
/home/local/VANDERBILT/plassaaj/jist-lib
cli
####################################################################
cli Initializing MIPAV/JIST Framework
cli
####################################################################
cli Interpretting command line arguments
cli
####################################################################
edu.vanderbilt.masi.plugins.labelfusion.PluginStatisticalFusion
inAtlas = =
inTarget = = Target Image Volume
inAtlas2 = =
inHierarchy = = None
inProbability = = None
inOutput = = None
inOutput2 = = None
inConsensus = = 0.99
inPrior = = Voxelwise
inConvergence = = 1.0E-4
inMaximum = = 100
inWindow = = 5
inWindow2 = = 5
inWindow3 = = 5
inWindow4 = = 0
inBias = = 0
inAugment = = false
inWeighting = = MSD
inSearch = = 3
inSearch2 = = 3
inSearch3 = = 3
inSearch4 = = 0
inPatch = = 2
inPatch2 = = 2
inPatch3 = = 2
inPatch4 = = 0
inSearch5 = = 1.5
inSearch6 = = 1.5
inSearch7 = = 1.5
inSearch8 = = 1.5
inDifference = = 0.25
inGlobal = = 0
inLocal = = 0.1
inUse = = true
inSelection = = Jaccard
inSelection2 = = 0.05
inNumber = = 150
outLabel = = Label Volume
outPerformance = =
outPerformance2 = = Performance Level Parameters Volume
outLabel2 = =
outLabel3 = = Label Probabilities Volume
outProc = /fs1/masi/plassaaj/MSSTAPLE/DeepBrainSegmentation
cli
####################################################################
Module Failed in an Ungraceful Manner. Please contact the developer
with the following message.
edu.vanderbilt.masi.plugins.labelfusion.PluginStatisticalFusionRuntime
Exception:0
edu.vanderbilt.masi.algorithms.labelfusion.ObservationBase.determine_cropping_information(ObservationBase.java:328)
edu.vanderbilt.masi.algorithms.labelfusion.ObservationVolume.(ObservationVolume.java:28)
edu.vanderbilt.masi.algorithms.labelfusion.ObservationVolume.(ObservationVolume.java:14)
edu.vanderbilt.masi.plugins.labelfusion.AbstractStatisticalFusionPlugin$AbstractExecuteWrapper.get_observation_type(AbstractStatisticalFusionPlugin.java:459)
edu.vanderbilt.masi.plugins.labelfusion.AbstractStatisticalFusionPlugin$AbstractExecuteWrapper.execute(AbstractStatisticalFusionPlugin.java:348)
edu.vanderbilt.masi.plugins.labelfusion.PluginStatisticalFusion.execute(PluginStatisticalFusion.java:66)
edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm.runAlgorithm(ProcessingAlgorithm.java:337)
edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm.runAlgorithm(ProcessingAlgorithm.java:321)
edu.jhu.ece.iacl.jist.cli.run.main(run.java:100)
edu.jhu.ece.iacl.jist.pipeline.CalculationMonitorCalculation
monitor shutting down by interrupt.
---------- Performance Summary ----------
1) Algorithm Calculation -- ELAPSED TIME: Actual: 0.02 sec / CPU:
0.01 sec
TOTAL ELAPSED TIME: Actual: 0.02 sec / CPU: 0.01 sec
CURRENT MEMORY: Used 28 MB, Free 332 MB, Total 361 MB
cli
####################################################################
cli Done:
edu.vanderbilt.masi.plugins.labelfusion.PluginStatisticalFusion
cli
####################################################################
Which says the error is the developer's fault. Inherently this is
true in that the cli does not validate the inputs at all, but this
error implies that the module developer is at fault.
| |
|
Response
Message |
Date: 2014-12-05 00:26
Sender: Stephen Damon
Hi Andrew,
I just pushed a fixed for this. There was a minor bug in the CLI. I
also started a new public build if you are eager to try. Here's the
new output of running the same command:
cli
####################################################################
cli Initializing MIPAV/JIST Framework
cli
####################################################################
cli Interpretting command line arguments
cli
####################################################################
edu.vanderbilt.masi.plugins.labelfusion.PluginStatisticalFusion
PARSE ERROR: Missing required tag: inAtlas
inAtlas = =
inTarget = = Target Image Volume
inAtlas2 = =
inHierarchy = = None
inProbability = = None
inOutput = = None
inOutput2 = = None
inConsensus = = 0.99
inPrior = = Voxelwise
inConvergence = = 1.0E-4
inMaximum = = 100
inWindow = = 5
inWindow2 = = 5
inWindow3 = = 5
inWindow4 = = 0
inBias = = 0
inAugment = = false
inWeighting = = MSD
inSearch = = 3
inSearch2 = = 3
inSearch3 = = 3
inSearch4 = = 0
inPatch = = 2
inPatch2 = = 2
inPatch3 = = 2
inPatch4 = = 0
inSearch5 = = 1.5
inSearch6 = = 1.5
inSearch7 = = 1.5
inSearch8 = = 1.5
inDifference = = 0.25
inGlobal = = 0
inLocal = = 0.1
inUse = = true
inSelection = = Jaccard
inSelection2 = = 0.05
inNumber = = 150
outLabel = = Label Volume
outPerformance = =
outPerformance2 = = Performance Level Parameters Volume
outLabel2 = =
outLabel3 = = Label Probabilities Volume
outProc = /home-nfs/local/VANDERBILT/damons/workspace/JIST Plugins
cli
####################################################################
cli Exiting with errors.
Cheers,
Steve
| |
|
Attached Files:
Name |
Download | No Files Currently Attached | |
|
No commits have been made.
Changes:
Field |
Old Value |
Date |
By |
status_id | Open | 2014-12-05 00:30 | damons |
New Message | | 2014-12-05 00:26 | damons |
priority | 3 | 2014-12-04 22:23 | plassaaj | |
|