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===Key Investigators===
* Gary Christensen, Iowa
* Paul Song, Iowa
* Cheng Zhang, Iowa
*Bill Hoffman
*Will Schroeder, Kitware (license issues)
*Jim Miller
*Luis Ibanez, Kitware

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<h1>Objective</h1>
To develop applications for image registration that can be distributed easily to other sites.

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<h1>Approach, Plan</h1>
Our plan for the project week is to
*Convert the SICLE image registration algorithm to use VTK & ITK.
*Use CPack to package the SICLE program.
*Setup and use a DART Dashboard at Iowa
*Investigate integration of wxWidgets with ITK and VTK.
*Compare and contrast the performance of Kwwidgets and wxWidgets
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<h1>Progress</h1>

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===References===

Gec: /* Key Investigators */

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[[Image:AtlasProject Splash.png | thumb | center | 300px | Atlas Project Splash Image ]]

===Key Investigators===
* Gary Christensen, Iowa
* Nathan Fritze, Iowa
* Nathan Burnette, Iowa

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<h1>Objective</h1>

Develop a software tool for visualizing and querying an electronic atlas. We are developing atlases of the human lung R01 HL64368, the rat lung R01HL073598, and the mouse lung R01 HL080285. We want to make a common software tool that can be customized for specific atlases. The image data and semantic information will be stored in a database and will be indexed through a graphical user interface.

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<h1>Approach, Plan</h1>

Our plan for the project week is to
*Reduce bottlenecks for the atlas application
*Compare and contrast the performance of Kwwidgets and wxWidgets
*Discuss ideas for a data manager object that is used to read, organize, and manage memory issues for the atlas.
*Learn the best ways to visualize images, surface models, segmentations and symbolic information referenced by coordinate systems using the NA-MIC software
*Discuss registration methods for matching airway trees.

The database should contain the following information, plus additional information, for every region on the atlas:
*statistics – average length, width, surface area, etc.
*labels – floating labels above the atlas that is visible from all viewing angles.
*associated color – the associated color that marks particular regions on the atlas.
*description – detailed description of the region on the atlas.

When dealing with registration images, clicking on the template/target image should highlight and display the corresponding point on a transformed coordinate system.

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<h1>Progress</h1>

We have...

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===References===

2007-06-21T20:34:41Z

Gec:

Special topic breakout: KWWidgets

2007-06-21T20:32:57Z

Gec:

[[Image:ProjectWeek-2007.png|thumb|300px|left|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]]]]

<br><br><br><br>

KWWidgets Breakout Session

June 26th, 1-2pm

Location: [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]]

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Attendees:
* Yumin Yuan
* Steve Pieper
* Alex Yarmarkovich
* Wendy Plesniak
* Nicole Aucoin
* Curt Lisle
* Csaba Csoma
* Brad Davis
* David Gobbi
* Kiran Shivanna
* Kevin Teich
* Jeff Hawley
* Xiujuan Geng
* James Harris
* Gary Christensen
* Paul Song

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=== Agenda ===

* Roadmap (to help KWWidgets developers prioritize their work)
* Widget feature requests / feedback
* Talk about best approaches to making some widget behavior appear consistent across platforms.
* Separate Tutorial Session for New Users (to happen possibly on Wednesday)

=== Specific Issues ===

==== From Nicole Aucoin====
Directory selection dialog box on linux:

- it pops up with a default width such that the right scroll bar isn't visible.

- request: an entry box where I can type a path to reduce clicking through the tree (useful before setting up a favourite)

==== From Curtis Lisle====
idea #1 - I have had trouble initializing widgets to specific values
in advance of user input. For example, I've created interfaces with
sliders and buttons but I have had trouble getting the widgets to
initialize in a state different then the default state. For example,
setting a slider to value=26 in the middle of its range without
dragging the mouse. The API looks like it is there, but I couldn't
get it to work for me. I'm sure I tried setting the state before and
after creation, if I remember, but no luck. It may be that I'm not
updating the GUI successfully after changing values.

idea #2 - discuss when UI elements need to have Modified() / Update()
invoked to refresh their appearance. I used a histogram widget on a
project and had to experiment a lot calling the panel and
RenderWidowWidget, etc. before I finally got the histogram to update
when the input changed.

==== From Brad Davis ====
Bug: Double-clicking does not work with slicer3 and linux

Feature request: Tree with additional columns widget

File->Add Data does not use new file browser.

====From Alex:====
I would lile to address the performance of building GUI in slicer3 Modules: When selecting a module for the first time (Volumes or Models) it takes noticable time before the UI panel is displayed.

Customizable tree widget similar to slicer2 model hierarchy editor: allow to add push-buttons or check boxes for the individual tree leaves.

====From Wendy:====
mostly pesky things:
* Creating special versions of menubutton drop-down menus with scroll capability,
* checkbuttons and radiobuttons with consistent "on/off" visual representation across platforms. (either special Slicer widgets or KWWidgets).

It would be good to decide on a strategy for addressing these things.

* Also, if a radiobutton's indicator visibility is off, the widget gets rendered with a 3D effect (even if we're using an icon to display the button's on/off state). Can we turn that 3D effect off?

==== From KWW-Users mailing list====
http://public.kitware.com/pipermail/kwwidgets/2007-June/000456.html

http://public.kitware.com/pipermail/kwwidgets/2007-June/000461.html

http://public.kitware.com/pipermail/kwwidgets/2007-May/000433.html

==== From Steve:====

I'd like to have a discussion of [http://www.kwwidgets.org/Wiki/KWWidgets/Tracing GUI Tracing]. In slicer3 we've started to experiment with a MRML-based tracing structure using the scene snapshot infrastructure, but we should consider if this is preferable to a GUI-based solution or not. See, for example, [http://www.na-mic.org/ViewVC/index.cgi/trunk/Base/GUI/vtkSlicerRecordSnapshotWidget.cxx?annotate=3621 the vtkSlicerRecordSnapshotWidget].

Performance of the file browser could be improved (request for multi-threaded solution or a helper process that does the glob'ing so the main application does not block).

Look and feel issues:
* On windows, the menu bar and scroll bar do not get the appearance
* On linux, font size is sometimes way too small

Maybe just me, but I find the new file browser sometimes ignores doubleclicks -- perhaps it is more picky about any small mouse movement between clicks?

Configure event management is still a problem - dragging the split frame or hiding the left panel (with F5) causes a lot of extraneous ConfigureEvents.

==== From Gary:====

I'd like to have a discussion of how to make a widget that reads one image plane at a time from a volume to make a multi-data set display. We have an implementation in wxWidgets that reads data from multiple files and has a slider that changes the slice number without having to read the entire volumes into memory.

When displaying multiple vtkKWRenderWindows at once, the KWwidgets base class generates an error. Being able to display multiple renderwindows at one time is an essential requirement for our project.

The order of linking the ITK, VTK, TCL, TK and KWwidget libraries so that they do not conflict.

Special topic breakout: ITK

2007-06-21T20:19:43Z

Gec:

'''Tutorial Session on ITK'''

= Topics =
*How do you efficiently integrate VTK and ITK with respect to reading and writing images? Is there one class that can be used to hold data sets for both libraries?
*How to do FFTs in ITK?
*What type of coordinate space should be used, voxels vs. real space?
*What type of image formats should be used?
*Is there any standard way to read in coefficient files, i.e., algorithm specific parameters?
*How are XML/MRML files parced in ITK/VTK?
*What are the memory and performance issues with ITK?

= Participants =
*Jeff Hawley
*Kunlin Cao
*Kai Ding
*Xiujuan Geng
*James Harris
*Gary Christensen
*Paul Song
*Jake Nickel
*Nick Kiguta

Collaboration/UIowa/Developing a GUI for non-rigid image registration programs using NA-MIC Kit

2007-06-20T20:52:59Z

Gec:

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===Key Investigators===
*Gary Christensen, The University of Iowa
*Kunlin Cao, The University of Iowa
*Kai Ding, The University of Iowa
*Xiujuan Geng, The University of Iowa
*Paul Song, The University of Iowa
*Hans Jonson, The University of Iowa
*Yumin, Kitware
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<h1>Objective</h1>
Learn how to use a professional software development process. Learn how to create GUIs to make our tools easier for others to use. Learn how to port our existing image registration & image processing libraries and tools to the ITK and VTK model. Learn how to package our programs so they run on different computer operating systems such as Windows, Linux, and Macintosh.

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<h1>Approach, Plan</h1>

Our plan for the project week is to:
*Learn about the image processing pipeline and memory management issues.
*Learn about ITK file formats.
*Learn how to read, write, and visualize images using NA-MIC tools.
*Learn how to make GUIs ( Evaluate whether or not we need to write our own GUI using KWWidgets or can take advantage of slicer3 )
*Develop an Analyze object map reader.
*Learn how to use cpack.

The GUI should provide the following functionality:
*Display the template and target images in 2D and 3D before registration for verification.
*Display landmarks, contours, and surfaces to be used for registration and validation.
*Allow the user to set various parameters.
*Allow the user to label corresponding landmarks and contours (possibly surfaces in the future).
*Display status and instant messages while the program is running, i.e., deforming images, difference images, Jacobian, displacement fields, deforming grid, graphs, etc.

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<h1>Progress</h1>

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===References===
This work is supported in part by NIH grants EB004126, HL079406, HL64368, HL080285, and HL073598.

*G.E. Christensen, H.J. Johnson. Consistent Image Registration, IEEE TMI, 20(7), 2001, pp 568-582.
*H.J. Johnson, G.E. Christensen. Consistent Landmark and Intensity-based Image Registration, IEEE TMI, 21(5), 2002, pp. 450-461.
*G.E. Christensen, H.J. Johnson and M.W. Vannier, Synthesizing average 3D anatomical shapes, NeuroImage, 32, 2006, pp. 146-158.