GWEReallyQuickStartGuide - Revision history

Fedorov: /* Steps */

2010-09-29T23:26:19Z

Steps

2010-06-25T19:55:35Z

Examples

2010-06-24T13:00:31Z

Examples

2010-06-24T04:08:37Z

Examples

2010-06-24T03:16:47Z

2010-06-24T00:06:21Z

Examples

2010-06-23T23:44:49Z

2010-06-23T23:25:18Z

2009-06-15T14:36:59Z

Wish list

2009-06-15T14:29:05Z

Wish list

@@ Line 71: / Line 71: @@
 ${grad_EXPLORATION_ID}=${CONDUCT}-${TIME}-${ITER}
-${output}=$out(sftp://localhost.bwh.harvard.edu/projects/birn/fedorov/data/Testing/${grad_EXPLORATION_ID}.nrrd)
+${output}=$out(sftp://opel.bwh.harvard.edu/projects/birn/fedorov/data/Testing/${grad_EXPLORATION_ID}.nrrd)
-${input}=$in(sftp://localhost.bwh.harvard.edu/projects/birn/fedorov/data/Testing/MRMeningioma1.nrrd) ${grad}=$const(${grad_SLICER} --conductance ${CONDUCT} --timeStep ${TIME} --iterations ${ITER}) ${grad_SLICER}=$const(${SLICER_HOME}/Slicer3 --launch ${SLICER_HOME}/lib/Slicer3/Plugins/GradientAnisotropicDiffusion)
+${input}=$in(sftp://opel.bwh.harvard.edu/projects/birn/fedorov/data/Testing/MRMeningioma1.nrrd) ${grad}=$const(${grad_SLICER} --conductance ${CONDUCT} --timeStep ${TIME} --iterations ${ITER}) ${grad_SLICER}=$const(${SLICER_HOME}/Slicer3 --launch ${SLICER_HOME}/lib/Slicer3/Plugins/GradientAnisotropicDiffusion)
 ${grad} ${input} ${output}

@@ Line 119: / Line 119: @@
 ${SLICING_CMD}=$sliceGen(${SLICER_HOME},${output},2,17)
-${SLICER_HOME}/Slicer3 --launch BRAINSFit --fixedVolume ${f} --movingVolume ${m} --outputVolume ${output} --transformType Rigid,ScaleVersor3D,Affine,BSpline --useCenterOfHeadAlign --splineGridSize ${DIM1},${DIM2},${DIM3} --maskProcessingMode ROI --fixedBinaryVolume ${fb} --movingBinaryVolume ${mb} --maskProcessingMode ROI && ${SLICING_CMD}
+${SLICER_HOME}/Slicer3 --launch BRAINSFit --fixedVolume ${f} --movingVolume ${m} --outputVolume ${output} --transformType Rigid,ScaleVersor3D,Affine,BSpline --useCenterOfHeadAlign --splineGridSize ${DIM1},${DIM2},${DIM3} --maskProcessingMode ROI --fixedBinaryVolume ${fb} --movingBinaryVolume ${mb} && ${SLICING_CMD}
 </pre>

@@ Line 103: / Line 103: @@
 <pre>
 ${DIM1}=$range(3,4,1)
 ${DIM2}=$range(3,4,1)

@@ Line 103: / Line 103: @@
 <pre>
-${DIM1}=$range(3,6,1)
+${DIM1}=$range(3,4,1)
-${DIM2}=$range(3,6,1)
+${DIM2}=$range(3,4,1)
-${DIM3}=$range(3,6,1)
+${DIM3}=$range(3,4,1)
 ${output}=/scratch/tmp/gwe-tmp/${SYSTEM_JOB_NUM}.nrrd
 ${m}=/home/andrey/NAMICBoston2010/ProstateRegistration/Data/Case003_scene/BRAINSFitRegistration/t2ax-N4.nrrd
-${f}=/home/andrey/NAMICBoston2010/ProstateRegistration/Data/Case003_scene/t2ax-intraop-N4.nrrd
+${f}=/home/andrey/NAMICBoston2010/ProstateRegistration/Data/Case003_scene/t2ax-intraop.nrrd
-${mb}=/home/andrey/NAMICBoston2010/ProstateRegistration/Data/Case003_scene/BRAINSFitRegistration/t2ax-TG.nrrd
+${mb}=/home/andrey/NAMICBoston2010/ProstateRegistration/Data/Case003_scene/t2ax-TG.nrrd
 ${fb}=/home/andrey/NAMICBoston2010/ProstateRegistration/Data/Case003_scene/t2ax-intraop-TG.nrrd

@@ Line 107: / Line 107: @@
 ${DIM3}=$range(3,6,1)
-${EXPLORATION_ID}=${CONDUCT}-${TIME}-${ITER}
+${output}=/scratch/tmp/gwe-tmp/${SYSTEM_JOB_NUM}.nrrd
 ${m}=/home/andrey/NAMICBoston2010/ProstateRegistration/Data/Case003_scene/BRAINSFitRegistration/t2ax-N4.nrrd
@@ Line 116: / Line 114: @@
 ${mb}=/home/andrey/NAMICBoston2010/ProstateRegistration/Data/Case003_scene/BRAINSFitRegistration/t2ax-TG.nrrd
 ${fb}=/home/andrey/NAMICBoston2010/ProstateRegistration/Data/Case003_scene/t2ax-intraop-TG.nrrd
 ${SLICING_CMD}=$sliceGen(${SLICER_HOME},${output},2,17)
-${reg} && ${SLICING_CMD}
+${SLICER_HOME}/Slicer3 --launch BRAINSFit --fixedVolume ${f} --movingVolume ${m} --outputVolume ${output} --transformType Rigid,ScaleVersor3D,Affine,BSpline --useCenterOfHeadAlign --splineGridSize ${DIM1},${DIM2},${DIM3} --maskProcessingMode ROI --fixedBinaryVolume ${fb} --movingBinaryVolume ${mb} --maskProcessingMode ROI && ${SLICING_CMD}
 </pre>

← Older revision		Revision as of 23:44, 23 June 2010
Line 99:		Line 99:
	* When you restart the demon on the local machine, kill the process		* When you restart the demon on the local machine, kill the process
	* If there is an error in the conf file, there is no error message, so if demon exists w/o error, check your conf files		* If there is an error in the conf file, there is no error message, so if demon exists w/o error, check your conf files
		+
		+	==Examples==
		+
		+	<pre>
		+	${DIM1}=$range(3,6,1)
		+	${DIM2}=$range(3,6,1)
		+	${DIM3}=$range(3,6,1)
		+
		+	${EXPLORATION_ID}=${CONDUCT}-${TIME}-${ITER}
		+
		+	${output}=$out(/scratch/tmp/gwe-tmp/${EXPLORATION_ID}.nrrd)
		+	${m}=/home/andrey/NAMICBoston2010/ProstateRegistration/Data/Case003_scene/BRAINSFitRegistration/t2ax-N4.nrrd
		+	${f}=/home/andrey/NAMICBoston2010/ProstateRegistration/Data/Case003_scene/t2ax-intraop-N4.nrrd
		+
		+	${reg}=$const(${SLICER_HOME}/Slicer3 --launch BRAINSFit --fixedVolume ${f} --movingVolume ${m} --outputVolume ${output})
		+
		+	${SLICING_CMD}=$sliceGen(${SLICER_HOME},${output},1,40)
		+
		+	${reg} && ${SLICING_CMD}
		+	</pre>

← Older revision		Revision as of 23:25, 23 June 2010
Line 94:		Line 94:

	* Changes to variables in gwe-grid.xml are not propagated to the remote daemon, even if the daemon is manually restarted. The only means to propagate is to re-deploy. This is OK, but should be stated in the docs.		* Changes to variables in gwe-grid.xml are not propagated to the remote daemon, even if the daemon is manually restarted. The only means to propagate is to re-deploy. This is OK, but should be stated in the docs.
		+
		+	==Tricks==
		+
		+	* When you restart the demon on the local machine, kill the process
		+	* If there is an error in the conf file, there is no error message, so if demon exists w/o error, check your conf files

@@ Line 80: / Line 80: @@
 == Wish list ==
-* improved error handling: exception stack trace like below is not helping in finding the source of the problem:
+* improved error handling: exception stack trace like below is not helping in finding the source of the problem.
 <pre>
@@ Line 91: / Line 91: @@
 </pre>
-* what is the variable update policy for GWE? i.e., if I change SLICER_HOME in conf, should I manually kill the daemon and restart for the changes to take effect?
+Possible improvement: give the exact command line back to the user to try manual launch to debug the problem.

← Older revision		Revision as of 14:29, 15 June 2009
Line 90:		Line 90:
	at org.gwe.app.agent.AgentApp.main(AgentApp.java:44)		at org.gwe.app.agent.AgentApp.main(AgentApp.java:44)
	</pre>		</pre>
		+
		+	* what is the variable update policy for GWE? i.e., if I change SLICER_HOME in conf, should I manually kill the daemon and restart for the changes to take effect?