2011 Winter Project Week:SPECTRE Integration - Revision history

Naucoin: /* Key Investigators */

2011-01-14T17:14:13Z

Key Investigators

2011-01-14T17:04:12Z

2011-01-14T00:08:26Z

Key Investigators

2011-01-11T21:49:59Z

Key Investigators

2011-01-11T00:30:09Z

Key Investigators

2011-01-11T00:02:27Z

Key Investigators

2011-01-10T21:27:02Z

Key Investigators

2011-01-05T16:10:39Z

Key Investigators

2010-12-29T19:43:06Z

Key Investigators

2010-12-29T18:56:55Z

Key Investigators

@@ Line 84: / Line 84: @@
 ** Changes checked in to Slicer3 trunk, Slicer3_USE_JAVA set to OFF by default
 ** Would be ideal to pass the cmake variable's value to extend.tcl so that it can be passed to the extensions modules via cmake.
-** Steve says that Slicer4 will use CMake to build extensions, but put the passing into extend.tcl so it can be ported, preliminary changes made, testing required
+** Steve says that Slicer4 will use CMake to build extensions, but put the passing into extend.tcl so it can be ported, preliminary changes made and checked in to extend.tcl and SPECTRE's CMakeLists.txt file (will stop building if Slicer3_USE_JAVA is false).
 Pre-project week:

@@ Line 2: / Line 2: @@
 <gallery>
 Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
 </gallery>
@@ Line 81: / Line 84: @@
 ** Changes checked in to Slicer3 trunk, Slicer3_USE_JAVA set to OFF by default
 ** Would be ideal to pass the cmake variable's value to extend.tcl so that it can be passed to the extensions modules via cmake.
-** Steve says that Slicer4 will use CMake to build extensions, but put the passing into extend.tcl so it can be ported
+** Steve says that Slicer4 will use CMake to build extensions, but put the passing into extend.tcl so it can be ported, preliminary changes made, testing required
 Pre-project week:

@@ Line 64: / Line 64: @@
 **Min hard coded the memory argument in JistCLI.java, working well in tests
 * Y flip
@@ Line 73: / Line 81: @@
 ** Changes checked in to Slicer3 trunk, Slicer3_USE_JAVA set to OFF by default
 ** Would be ideal to pass the cmake variable's value to extend.tcl so that it can be passed to the extensions modules via cmake.
 Pre-project week:

@@ Line 62: / Line 62: @@
 **Checked in new SPECTRE.tcl.in to NITRC repository using the new argument
 **To avoid the JVM crash when passing in a too large heap size, put in an if/else to call it with a small heap size if the argument is --xml
 * Y flip
 ** SPECTRE reorients the input image to be axially aligned and isotropic, then it does output a realigned original image
 ** Can Slicer use the output realigned original as the default bg/fg volume?
 Pre-project week:

@@ Line 69: / Line 69: @@
 Pre-project week:
 <ul>
 <li>Memory
 <ul>

← Older revision		Revision as of 21:27, 10 January 2011
Line 54:		Line 54:

	<h3>Progress</h3>		<h3>Progress</h3>
		+
		+	During Project Week:
		+
		+	*Memory argument
		+	**It will be difficult to add this argument to SPECTRE (SPECTRE won't use it, so adding it to the auto generated xml is tricky, and hard coding it in would be non optimal).
		+	**For now, keep it as a command line module option that is stripped out before calling SPECTRE
		+	**Checked in new SPECTRE.tcl.in to NITRC repository using the new argument
		+
		+	* Y flip
		+	** SPECTRE reorients the input image to be axially aligned and isotropic, then it does output a realigned original image
		+	** Can Slicer use the output realigned original as the default bg/fg volume?

	Pre-project week:		Pre-project week:

@@ Line 46: / Line 46: @@
 <li>Remove the requirement to have to run MIPAV before running the SPECTRE extension in Slicer.
 <li>Set volume types in SPECTRE outputs
 </ul>

@@ Line 54: / Line 54: @@
 <h3>Progress</h3>
 <ul>
 <li>Y flip
 <ul>

@@ Line 58: / Line 58: @@
 <ul>
 <li>Atlas file OAS1_0001_MR1_original.hdr & .img loaded into Slicer using Add Data. Saved in .nhdr nrrd format, .nhdr contains:
-<pre>space: left-posterior-superior
+<pre>
 sizes: 176 208 176
 space directions: (1,0,0) (0,-1,0) (0,0,1)
-space origin: (0,0,0)</pre>
+kinds: domain domain domain
 <li>Loading the .nhdr file back into Slicer, volume aligns with .hdr/.img
 <li>Turning off deleting intermediate files for SPECTRE:
     [$::slicer3::CommandLineModuleGUI_SPECTRE_2009 GetLogic] DeleteTemporaryFilesOff
 <li>Running the algorithm, generating only stripped image. unu head on input image BJAIF_vtkMRMLScalarVolumeNodeB.nrrd:
-<pre>space: left-posterior-superior
+<pre>
 sizes: 176 208 176
 space directions: (1,0,0) (0,-1,0) (0,0,1)
 space origin: (0,0,0)
 </pre>
 <li>unu head on output stripped image BJAIF_vtkMRMLScalarVolumeNodeD.nrrd:
 <pre>
+type: float
 </pre>
 </ul>
 </ul>