2011 Winter Project Week:MIDAS for data hosting - Revision history

Zach.mullen: /* Delivery Mechanism */

2011-01-10T15:08:18Z

Delivery Mechanism

Zach.mullen: /* Key Investigators */

2011-01-10T15:04:25Z

Key Investigators

Zach.mullen: /* Delivery Mechanism */

2011-01-10T15:01:59Z

Delivery Mechanism

Zach.mullen: /* Delivery Mechanism */

2011-01-10T15:01:28Z

Delivery Mechanism

Zach.mullen: /* Key Investigators */

2011-01-10T15:01:10Z

Key Investigators

Zach.mullen: /* Delivery Mechanism */

2011-01-10T14:48:34Z

Delivery Mechanism

Zach.mullen at 14:39, 10 January 2011

2011-01-10T14:39:36Z

Zach.mullen at 22:07, 6 January 2011

2011-01-06T22:07:36Z

Zach.mullen: Created page with 'NOTOC Image:PW-SLC2011.png|Projects List ==Key Investigators== * Kitware: Zach Mullen * Iowa: Hans Johnson

2011-01-06T22:06:29Z

Created page with 'NOTOC <gallery> Image:PW-SLC2011.png|Projects List </gallery> ==Key Investigators== * Kitware: Zach Mullen * Iowa: Hans Johnson <div s…'

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Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
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==Key Investigators==
* Kitware: Zach Mullen
* Iowa: Hans Johnson

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<h3>Objective</h3>
[http://public.kitware.com/Wiki/TubeTK TubeTK] is a new open-source toolkit that hosts algorithms for applications involving images of tubes.

Two driving applications:
* Surgical guidance: registering pre-operative vascular models with intra-operative images (e.g., ultrasound)
* Characterizing vascular patters: using graph theory to distinguish clinical populations based on vascular patterns (e.g., benign -vs- malignant tumors via tortuosity)

History
* June 2001, UNC released the patent on vessel extraction method from [Aylward, Bullitt 1996...]
* TubeTK released under Apache 2.0 license: includes rights to patents

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<h3>Approach, Plan</h3>
* Python module in Slicer 4 for centerline and radius estimation of vasculature in brain MRA
** Workflow: brain envelop segmentation, seeding, extraction
* Integration with VMTK

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<h3>Progress</h3>

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==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as follows:

* All software written during the project week will be contributed to TubeTK, and algorithms will be incorporated into 3D Slicer as CLI applications.

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 * Test data will be hosted publicly (with any necessary access control) on [http://midas.kitware.com midas.kitware.com]
-* That site will also host the Easy Upload page.
+* Test data in the Slicer4 repository will be replaced by a reference
-* MIDASDesktop lives in the svn repository here: [https://www.kitware.com/svn/KWPublic/trunk/MIDAS/MIDAScpp https://www.kitware.com/svn/KWPublic/trunk/MIDAS/MIDAScpp]
+* That site will also host the Slicer Easy Upload page.
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@@ Line 36: / Line 36: @@
 * MIDAS+CTest macro has been created and is currently in use successfully with the BRAINSTools test data.
 * Easy Upload page has a working prototype and requires further improvements and customization for Slicer
-* MIDASDesktop: svn repo is here [https://www.kitware.com/svn/KWPublic/trunk/MIDAS/MIDAScpp]
+* MIDASDesktop: svn repo is here [https://www.kitware.com/svn/KWPublic/trunk/MIDAS/MIDAScpp https://www.kitware.com/svn/KWPublic/trunk/MIDAS/MIDAScpp]
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@@ Line 45: / Line 45: @@
 ==Delivery Mechanism==
-* Test data will be hosted publicly (with any necessary access control) on [http://midas.kitware.com]
+* Test data will be hosted publicly (with any necessary access control) on [http://midas.kitware.com midas.kitware.com]
 * That site will also host the Easy Upload page.
 * MIDASDesktop lives in the svn repository here: [https://www.kitware.com/svn/KWPublic/trunk/MIDAS/MIDAScpp https://www.kitware.com/svn/KWPublic/trunk/MIDAS/MIDAScpp]
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@@ Line 47: / Line 47: @@
 * Test data will be hosted publicly (with any necessary access control) on [http://midas.kitware.com]
 * That site will also host the Easy Upload page.
-* MIDASDesktop lives in the svn repository here: [https://www.kitware.com/svn/KWPublic/trunk/MIDAS/MIDAScpp]
+* MIDASDesktop lives in the svn repository here: [https://www.kitware.com/svn/KWPublic/trunk/MIDAS/MIDAScpp https://www.kitware.com/svn/KWPublic/trunk/MIDAS/MIDAScpp]
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@@ Line 12: / Line 12: @@
 <h3>Objective</h3>
 Make use of the [http://www.kitware.com/midaswiki/index.php/Main_Page MIDAS] data archiving system to host data related to tests such as baseline and comparison images.
-Two driving applications:
+Motivation:
-* Surgical guidance: registering pre-operative vascular models with intra-operative images (e.g., ultrasound)
+* Not all users will want to build and test every module of Slicer, so they shouldn't have to download the testing data for every part of Slicer
-* Characterizing vascular patters: using graph theory to distinguish clinical populations based on vascular patterns (e.g., benign -vs- malignant tumors via tortuosity)
+* Encourage the optional use of testing with "large" datasets that aren't downloaded unless the "large-data" tests are configured to run
+* Don't download any duplicated test data more than once
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@@ Line 28: / Line 24: @@
 <h3>Approach, Plan</h3>
-* Python module in Slicer 4 for centerline and radius estimation of vasculature in brain MRA
+* MIDAS+CTest: create a thin wrapper for "add_test" calls that will allow for adding a test that references remote data on a MIDAS server in a human-readable way
-** Workflow: brain envelop segmentation, seeding, extraction
+* The underlying mechanism will address data by its checksum to ensure integrity and no duplication of downloads, but test creators and users shouldn't have to deal with checksums
-* Integration with VMTK
+* Create an "Easy Upload" page for the Slicer community to allow test data to be uploaded and ready to test against with as few clicks as possible
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@@ Line 37: / Line 34: @@
 <h3>Progress</h3>
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← Older revision		Revision as of 14:39, 10 January 2011
Line 12:		Line 12:

	<h3>Objective</h3>		<h3>Objective</h3>
		+	Make use of the [http://www.kitware.com/midaswiki/index.php/Main_Page MIDAS] data archiving system to host data related to tests such as baseline and comparison images.
	[http://public.kitware.com/Wiki/TubeTK TubeTK] is a new open-source toolkit that hosts algorithms for applications involving images of tubes.		[http://public.kitware.com/Wiki/TubeTK TubeTK] is a new open-source toolkit that hosts algorithms for applications involving images of tubes.

@@ Line 6: / Line 6: @@
 ==Key Investigators==
 * Kitware: Zach Mullen
-* Iowa: Hans Johnson
+* UIowa: Hans Johnson
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