File:AHM 2014 Engineering Retrospective.pptx

2014-01-09T18:10:09Z

Millerjv: uploaded a new version of "File:AHM 2014 Engineering Retrospective.pptx"

AHM2014-Engineering Updates

2014-01-09T00:45:08Z

Millerjv:

[http://cdn.knightlab.com/libs/timeline/latest/embed/index.html?source=0Aigzw56l1ZC-dHMwYWEzLW9tRFM1Sk5vbmZLU1FvNFE&font=Bevan-PotanoSans&maptype=TERRAIN&lang=en&hash_bookmark=true&height=850#0 NA-MIC Timeline]

* Retrospective from the entire program (Jim, [[Media:AHM 2014 Engineering Retrospective.pptx | Slides]])
** Highlights and watershed moments
* Accomplishments from the last year (Stephen)
** Highlights, best of 2013
** By the numbers: extensions, downloads, bugs, commits
* Plans for next 6 months (Steve)
** Mini-retreats: git big data, speed up slicer, overall cleanup of bug tracker
* Plans for after NA-MIC (Steve)

AHM2014-Engineering Updates

2014-01-09T00:44:47Z

Millerjv:

[http://cdn.knightlab.com/libs/timeline/latest/embed/index.html?source=0Aigzw56l1ZC-dHMwYWEzLW9tRFM1Sk5vbmZLU1FvNFE&font=Bevan-PotanoSans&maptype=TERRAIN&lang=en&hash_bookmark=true&height=850#0 NA-MIC Timeline]

* Retrospective from the entire program (Jim, [Media:AHM 2014 Engineering Retrospective.pptx
| Slides])
** Highlights and watershed moments
* Accomplishments from the last year (Stephen)
** Highlights, best of 2013
** By the numbers: extensions, downloads, bugs, commits
* Plans for next 6 months (Steve)
** Mini-retreats: git big data, speed up slicer, overall cleanup of bug tracker
* Plans for after NA-MIC (Steve)

2014-01-09T00:20:58Z

Millerjv:

[[AHM_2014#Agenda|Back to AHM_2014 Agenda]]

An optional dinner will be held on Wednesday evening, January 8, at 6:30pm, at Bambara, located at 202 S. Main St., SLC: http://www.bambara-slc.com/. The reservation for 14 people is under Ron's first and last name, and is in a private dining room.

Confirmed dinner attendees: 14
*Ron Kikinis
*Michael Ackerman
*Terry Yoo
*Greg Sharp
*Steve Pieper
*Sonia Pujol
*Hans Johnson
*Jack van Horn
*Sandy Wells
*Allen Tannenbaum
*Wiro Niessen
*Polina Golland
*Guido Gerig
*Jim Miller

2013-12-06T15:17:55Z

Millerjv: /* Infrastructure */

2014 Winter Project Week:MRB Extension Dependencies

2013-11-25T12:46:03Z

Millerjv: /* Project Description */

__NOTOC__
<gallery>
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

* Steve Pieper, Isomics
* Jean-Christophe Fillion-Robin, Kitware
* Jim Miller, GE
* Nicole Aucoin, BWH
* Alex Yarmarkovich, BWH

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
MRB's (and Scenes in general) may reference nodes or panels (via module selection) which may have been installed on the MRB author's machine via Extensions but not available on the machine of the person who downloaded the MRB. In this circumstance, the person who downloaded the MRB may not be able to access all the information in the MRB. For example, SceneView restores may not function properly. Furthermore, the user is not provided any guidance on how to rectify the situation.

The goal of this project is to develop a design whereby the Slicer will track a Scene's dependency on Extensions and provide a mechanism for the user to download the missing Extensions.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Talk through the issues in
# tracking (nodes, modules, extension) dependency information inside a MRML structure
# automatically downloading needed extensions at MRB download time
* Develop a preliminary design and plan
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
Options
# Track (nodes, modules, extension) dependency information inside MRML
# Record all Extensions available on MRB author's machine inside MRML

Notes
* Just because an Extension was used to author an MRB does not mean that Extension is needed to view the contents of the MRB.
</div>
</div>

2014 Winter Project Week:MRB Extension Dependencies

2013-11-25T12:45:03Z

Millerjv: /* Project Description */

2014 Winter Project Week:MRB Extension Dependencies

2013-11-25T12:44:42Z

Millerjv: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

* Steve Pieper, Isomics
* Jean-Christophe Fillion-Robin, Kitware
* Jim Miller, GE
* Nicole Aucoin, BWH
* Alex Yarmarkovich, BWH

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
MRB's (and Scenes in general) may reference nodes or panels (via module selection) which may have been installed on the MRB author's machine via Extensions but not available on the machine of the person who downloaded the MRB. In this circumstance, the person who downloaded the MRB may not be able to access all the information in the MRB. For example, SceneView restores may not function properly. Furthermore, the user is not provided any guidance on how to rectify the situation.

The goal of this project is to develop a design whereby the Slicer will track a Scene's dependency on Extensions and provide a mechanism for the user to download the missing Extensions.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Talk through the issues in
# tracking (nodes, modules, extension) information inside a MRML structure
# automatically downloading needed extensions at MRB download time
* Develop a preliminary design and plan
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
Options
# Track (nodes, modules, extension) dependency information inside MRML
# Record all Extensions available on MRB author's machine inside MRML
</div>
</div>

2014 Winter Project Week:MRB Extension Dependencies

2013-11-25T12:43:17Z

Millerjv: /* Project Description */

__NOTOC__
<gallery>
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

Steve Pieper, Isomics
Jean-Christophe Fillion-Robin, Kitware
Jim Miller, GE
Nicole Aucoin, BWH
Alex Yarmarkovich, BWH

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
MRB's (and Scenes in general) may reference nodes or panels (via module selection) which may have been installed on the MRB author's machine via Extensions but not available on the machine of the person who downloaded the MRB. In this circumstance, the person who downloaded the MRB may not be able to access all the information in the MRB. For example, SceneView restores may not function properly. Furthermore, the user is not provided any guidance on how to rectify the situation.

The goal of this project is to develop a design whereby the Slicer will track a Scene's dependency on Extensions and provide a mechanism for the user to download the missing Extensions.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Talk through the issues in
# tracking (nodes, modules, extension) information inside a MRML structure
# automatically downloading needed extensions at MRB download time
* Develop a preliminary design and plan
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
Options
# Track (nodes, modules, extension) dependency information inside MRML
# Record all Extensions available on MRB author's machine inside MRML
</div>
</div>

2014 Winter Project Week:MRB Extension Dependencies

2013-11-25T12:39:22Z

Millerjv:

__NOTOC__
<gallery>
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

Steve Pieper, Isomics
Jean-Christophe Fillion-Robin, Kitware
Jim Miller, GE
Nicole Aucoin, BWH
Alex Yarmarkovich, BWH

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
MRB's (and Scenes in general) may reference nodes or panels (via module selection) which may have been installed on the MRB author's machine but not available on the machine of the person who downloaded the MRB. In this circumstance, the person who downloaded the MRB may not be able to access all the information in the MRB. For example, SceneView restores may not function properly. Furthermore, the user is not provided an guidance on how to rectify the situation.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Talk through the issues in
# tracking (nodes, modules, extension) information inside a MRML structure
# automatically downloading needed extensions at MRB download time
* Develop a preliminary design and plan
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2014 Winter Project Week:MRB Extension Dependencies

2013-11-25T12:39:10Z

Millerjv: Created page with '__NOTOC__ <gallery> Image:PW-SLC2014.png|Projects List </gallery> ==Key Investigators== Steve Pieper, Isomics Jean-Christophe Fillion-Robi…'

__NOTOC__
<gallery>
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

Steve Pieper, Isomics
Jean-Christophe Fillion-Robin, Kitware
Jim Miller, GE
Nicole Aucoin, BWH
Alex Yarmarkovich, BWH

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* MRB's (and Scenes in general) may reference nodes or panels (via module selection) which may have been installed on the MRB author's machine but not available on the machine of the person who downloaded the MRB. In this circumstance, the person who downloaded the MRB may not be able to access all the information in the MRB. For example, SceneView restores may not function properly. Furthermore, the user is not provided an guidance on how to rectify the situation.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Talk through the issues in
# tracking (nodes, modules, extension) information inside a MRML structure
# automatically downloading needed extensions at MRB download time
* Develop a preliminary design and plan
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

Engineering:TCON 2013

2013-11-21T19:31:51Z

Millerjv: /* 2013-11-21 */

Back to [[TCON:Main|TCON:Main]], [[Events]]

__TOC__

==2013-11-21==

Attendees: Jim

Agenda:
* DBP projects for [http://wiki.na-mic.org/Wiki/index.php/AHM_2014#Agenda Project Week]

==2013-11-07==

Attendees: Tina, Nicole

Agenda:
* [http://wiki.na-mic.org/Wiki/index.php/AHM_2014#Agenda Project Week] - hotel link is live, registration to come soon

==2013-10-31==

Attendees: Jim, JC, Nicole, Tina, Ron, Andrey

Agenda:
* Engineering projects for [http://wiki.na-mic.org/Wiki/index.php/2014_Winter_Project_Week 2014 Winter Project Week]

==2013-10-24==

No Meeting today.

==2013-10-17==
Attendees: Jim, Steve, Dirk, Tina, Ron, Nicole

*Albert's problem

==2013-10-03==
Attendees: Jim, JC, Nicole, Tina

Agenda:

* Testing

Notes:

* Don't check in a test that will fail for more than 24 hours
** Nicole: will check in a test showing failing behaviour but not failing the test via ctest
* JC script for patch release is ready, fixing last few tests
* Winter project week is set, start thinking of projects in mid to late October
** http://wiki.na-mic.org/Wiki/index.php/AHM_2014

==2013-09-26==
Attendees: Jim, Dave, Nicole, JC

Notes:
* update from JC on the release
* Jim, JC and Nicole discussed layout changes and attendant bugs

==2013-09-19==
Attendees: Tina, Nicole, JC

Agenda:
* From Nicole: Adding a MRML scene flag for when changing the layout
** see back trace here in comment 9733: [http://www.na-mic.org/Bug/view.php?id=1690 Bug 1690]. Need to be able to know in my displayble manager that the layout is in the process of changing so as not to try and set renderers on widgets (active camera may also not be set)
** name? LayoutChangeState, LayoutChangeEvent?
** for which Slicer release? Bug 1690 probably won't get closed without this change and will need to be retargeted
* Slicer 4.3.1 release on Monday
** [http://na-mic.org/Mantis/roadmap_page.php Roadmap]

Notes:
* Nicole will post a topic to github and send the url for feedback
** [https://github.com/naucoin/Slicer/commit/50a20e429f5d4033a6984e2d7a5b5bcb47f7d578 commit link]

==2013-09-12==
Attendees: Jim, Ayesha, Nicole, Tina, JC

Agenda:
* Slicer 4.3.1 release
** [http://na-mic.org/Mantis/roadmap_page.php Roadmap]

Notes:
* Tina announced we will have a project week at MIT next summer, Jun 23-27
* Jim talked about redoing the process read node data method
** MRML node changes to support creating default display and storage nodes
** to let extensions define new nodes and have them get passed to CLIs
** Nicole will test once it's ready for review

==2013-09-05==
Attendees: Jim, Nicole, JC, Tina

Agenda:
* Slicer 4.3 release
** [http://na-mic.org/Mantis/roadmap_page.php Roadmap]
** SVN branch was made this afternoon

==2013-08-29==
Attendees: Jim, Steve, Nicole, Sunil, JC

Agenda:
* Slicer 4.3 release
** [http://na-mic.org/Mantis/roadmap_page.php Roadmap]

Notes:
* talked about the light box bug, Jim says cross hair displayable manager is good as a base
** http://na-mic.org/Bug/view.php?id=1690
* Nicole to change Markups documentation xml file to take out a layer of nesting, JC can extend the wiki settings after the release
* talked about the dti analysis bug, Steve can reproduce now and will try to fix
** http://na-mic.org/Bug/bug_view_advanced_page.php?bug_id=3323
* ITK tag has been updated

==2013-08-22==

Attendees: Steve, Nicole, JC, Dave

Agenda:
* Slicer 4.3 release
** [http://na-mic.org/Mantis/roadmap_page.php Roadmap]

==2013-08-15==
Attendees: Steve, Nicole, Ayesha, Ron, Tina, JC

Agenda:
* Slicer 4.3 release
** [http://na-mic.org/Mantis/roadmap_page.php Roadmap]

==2013-08-08==
Attendees: Ron, Nicole, Jim, Tina

==2013-07-18==
Attendees: Ron, Nicole, Steve, Jim, Tina, JC

Agenda:
* Slicer 4.3 release [http://na-mic.org/Mantis/roadmap_page.php Road map]

==2013-07-11==
Attendees: Nicole, Dave, Steve, Tina

*visualization of pediatric cardiac patients using 3d slicer has been underway at Children's (a brief tutorial was provided to them a few years ago and it turns out that they have been using it extensively. They are preparing an educational website for clinicians, which will be launched this year.)

==2013-07-04==

No mtg

==2013-06-27==
Attendees: Ron, Steve, Nicole, Dave, Tina

* Summary stats from project week: http://wiki.na-mic.org/Wiki/index.php/2013_Summer_Project_Week#Summary

==2013-06-20==

Project Week!

==2013-06-13==

Attendees: Tina, Nicole, Sneha, Steve, JC, Dave

Agenda:
*[[2013_Summer_Project_Week#Projects | Project Week]]

==2013-06-07==

Attendees: Hans Meine, Steve, Jim, Ayesha, Tina, Dirk

*Hans Meine project

==2013-05-30==

Attendees: Ayesha, Lilla, Steve, Tina, Nicole, Dirk, JC, Matt Tosch

* [[2013_Summer_Project_Week#Projects | Project Week]]
**Lilla Zollei
**Hans Meine

*https://sites.google.com/site/nihbtrc2/resources

==2013-05-23==

Attendees:
Jim, Tina, Nicole, Jason (UCSF), Beck (USCF), Aiyesha, Tamas, Dave, JC, Adriana (Univ of Mexico)

Agenda:

* [[2013_Summer_Project_Week#Projects | Project Week]]
** HD projects added
**UCSF team will not be able to join this project week, but SLC possible
**U of Mexico team will complete their project pages and join next call

==2013-05-16==

Attendees:
Jim, Steve, Tina, Nicole, JC, Aiyesha, Josh, Dirk, Jack

Agenda:

* [[2013_Summer_Project_Week#Projects | Project Week]]

==2013-05-02==

Attendees: Jim, Nicole, Aiyesha, Dave

Agenda:

* [[2013_Summer_Project_Week#Projects | Project Week]]

Meeting Notes:
* Jim and Nicole discussed qMRMLNodeComboBoxes, events, and mrml updates on entering modules
** workaround: disable widget until ready to update from MRML. Look into blockSignals.
* discussed Dave's project and storing/distributing large data for extensions

==2013-4-25==

Attendees:

Agenda:

* [[2013_Summer_Project_Week#Projects | Project Week]] Kickoff: list projects

Meeting Notes:

==2013-04-18==

Attendees: Jim, Steve, Nicole, Tina, Andriy, Aiyesha, JC

Agenda:

* [[2013_Summer_Project_Week | Project Week]]
* Virtual functional pointer tables
See: [https://github.com/BRAINSia/BRAINSTools/commit/31beee592eba2d98655b864e6dc704ac9bf995e8 Hans's test example]

Meeting Notes:

==2013-04-11==

Attendees: Jim, JC, Hans, Nicole, Brad

Meeting notes:
* BRAINS and EMSegment
* Building on Mac
* [[2013_Summer_Project_Week | Project Week]]: filling in the page

==2013-04-04==

Attendees: Jim, Nicole, JC, Ayesha

==2013-3-28==

Attendees: Jim, Steve, Nicole, JC, Ayesha

Agenda:
*Project Week Kickoff:List engineering projects

Meeting Notes:
* discussed general outlines of engineering projects:
** Annotations rewrite
** Brain atlas optimisations (Marianna to do a demo)
** Provenance
** Patient hierarchies
** Sample data - content addressable data, in external data processing in Slicer, cmake file for external data, when write test can decorate the data file name with macro keywords saying it's external
* Next slicer release?
**post namic submission late May
** itkv4 version - use for project week development, not ready for users though
** need to go through the targetted bugs to decide what goes in the next release
* Slicer prereqs
** qt(? or cmake?) version - no time to update it now
** VS2010: cmake-ified python testing, delayed by the double convert and dcmtk build problems, but should be done by project week

==2013-3-21==

No call today. Several participants in DC. Please join next tcon to kickoff engineering project discussion for project week.

==2013-3-14==
Attendees: Steve, Ron, Tina, Nicole, Ayesha,

Agenda:
* CHECK YOUR EMAIL (SLICER-DEVELOPERS, NAMIC-ENG) FOR NEW TCON NUMBER
* OpenSSL status update
* Reorg menus in Slicer - deferred to when JC is on the call
* india update (nicole)
* Training Events http://wiki.na-mic.org/Wiki/index.php/Training:Events_Timeline
* Project Week kickoff in two weeks with engineering projects.

==2013-3-7==
Attendees: Jim, Steve, Tina, Aisha

Agenda:
* CHECK YOUR EMAIL (NAMIC-ENG) FOR NEW TCON NUMBER

==2013-2-28==
Attendees: Jim, Steve, Tina, Hans, JC, Sunil, Dave

Agenda:
*

==2013-2-21==
Attendees: Jim, Steve, Tina, Hans, JC, Sunil, Dave

Agenda:
*

==2013-2-14==

Attendees: Nicole, Sunil, Tina, Jim, JC, Ron, Dave,

Agenda:
*utility python script to parse a file to make MRML file for modelmaker - where is the best place to put it (Nicole)

==2013-2-7==

Attendees: Nicole, Sunil, Tina, Steve, Andriy

Agenda:
*(Ann will review progress report materials with core/site PIs offline)
*

==2013-1-31==

Attendees: Jim, Steve, Nicole, Tina, Sunil, Ruiy, Stephen

Agenda:
* Python external libraries discussion (Ron, Steve, JC, Sunil)
**SSL, setuptools, etc.
**Bug report: http://na-mic.org/Bug/view.php?id=2352
*In the next TCON, Ann will review draft of engineering core progress report. All site PIs should plan to attend.

=== Extending Slicer with more python packages ===

==== Different approaches ====
Multiple and non-exclusive approach can be considered.

* (1) Bundling of package within Slicer installed (i.e. NUMPY)

If the package require compilation steps and is recognized of general interest, it probably make sens to bundle it within Slicer.

* (2) Installation of additional python packages from an *installed* Slicer

Few cases should be considered here:

a) *NO* compilation - *NO* libraries - It means the user does *NOT* have to install any compiler to be able to install the package. It is basically a pure python implementation.

b) *NO* compilation - *WITH* dependencies/libraries - It means the user does *NOT* have to install any compiler *BUT* have to install some external library to be able to install/use the package. This could reveal to be challenging for some user, especially to get the PATH, ... right.

c) *WITH* compilation - *NO* libraries - On unix like system, it is generally easier to install compiler but if we consider that most of our user works on windows, we should probably not require them to install Visual Studio to be able to install a python package ...

* (3) Installation of additional python packages from a *built* Slicer

The researched having a lot of experience in development usually have a build tree of Slicer and know enough to be able to tinker and install things.

==== Runtime installation ====

In the python ecosystem, the usage of a tool named [http://pypi.python.org/pypi/pip pip] became the standard regarding installation of additional module and packages. There are currently around 27500 packages available on the Python Package Index. See http://pypi.python.org/pypi

Most of these packages are served from server using <code>https</code> protocol. To support such protocol, we would have to include the [http://www.openssl.org/ OpenSSL library].

==== Integrating OpenSSL into Slicer ====

Considering the [http://www.openssl.org/source/license.html license of OpenSSL] (BSD style) is compatible with the Slicer one, there should not be any problem distributing it within Slicer. That said, is still presents few challenges.

===== Build system integration =====

* Download of the binaries on windows
* Build or download of binaries on macosx/linux
* As part of this integration, integrating a CMake'ified version of python would also make sens.

Some work and testing would be required to make sure everything works as expected.

===== Legal mention on the download page =====
We would have to probably have some mention on our page. That said, I found an article mentioning that it should now be fine to distribute strong cryptographic algorithm library within open-source project:
* http://www.theregister.co.uk/2011/01/07/open_source_crypto_curbs/
* https://www.federalregister.gov/articles/2011/01/07/2010-32803/publicly-available-mass-market-encryption-software-and-other-specified-publicly-available-encryption

===== Certificate Authority =====
To ensure Slicer is authenticated, we would have to create appropriate certificate and bundle them within Slicer. Some testing/research is required to exactly find out what need to be done. There is also probably a (not ideal) way of ignoring CA ...

==2013-01-24==

Attendees: Jim, Ron, Nicole, Sunil, JC, Steve

Agenda:
* ITK v4
* ssl issues with python

Minutes:
* ITK v4
** JC found the problem with dcmtk
* Xnat folks need to install some python package => Need openssl to pip install most of the package
** What is the legal aspect of having openssl bundled ?
** OpenSSL is build by CMake folks on all platform ... it could be re-used
* Difference between ITK 3.20.0 and ITK 3.20.1. See https://github.com/Kitware/ITK/compare/v3.20.0...v3.20.1
* Talked about Stan langage. See http://mc-stan.org/

==2013-01-17==

Attendees: Ron, Steve, Tina, Nicole, JC, Sunil, Dave, Jim

*Project week results review: http://wiki.na-mic.org/Wiki/index.php/2013_Winter_Project_Week

Agenda:

==2013-01-10==

No call due to [[2013_Winter_Project_Week]]

==2013-01-03==

Attendees: Jim, Steve, Stephen, Nicole, Tina,

Agenda:
* Project week: http://wiki.na-mic.org/Wiki/index.php/2013_Winter_Project_Week
** Engineering core presentation: http://wiki.na-mic.org/Wiki/index.php/AHM2013-Engineering_Updates

Engineering:TCON 2013

2013-11-21T19:31:39Z

Millerjv: /* 2013-11-07 */

Back to [[TCON:Main|TCON:Main]], [[Events]]

__TOC__

==2013-11-21==

Attendees: Jim

Agenda:
* DBP Projects for [http://wiki.na-mic.org/Wiki/index.php/AHM_2014#Agenda Project Week]

==2013-11-07==

Attendees: Tina, Nicole

Agenda:
* [http://wiki.na-mic.org/Wiki/index.php/AHM_2014#Agenda Project Week] - hotel link is live, registration to come soon

==2013-10-31==

Attendees: Jim, JC, Nicole, Tina, Ron, Andrey

Agenda:
* Engineering projects for [http://wiki.na-mic.org/Wiki/index.php/2014_Winter_Project_Week 2014 Winter Project Week]

==2013-10-24==

No Meeting today.

==2013-10-17==
Attendees: Jim, Steve, Dirk, Tina, Ron, Nicole

*Albert's problem

==2013-10-03==
Attendees: Jim, JC, Nicole, Tina

Agenda:

* Testing

Notes:

* Don't check in a test that will fail for more than 24 hours
** Nicole: will check in a test showing failing behaviour but not failing the test via ctest
* JC script for patch release is ready, fixing last few tests
* Winter project week is set, start thinking of projects in mid to late October
** http://wiki.na-mic.org/Wiki/index.php/AHM_2014

==2013-09-26==
Attendees: Jim, Dave, Nicole, JC

Notes:
* update from JC on the release
* Jim, JC and Nicole discussed layout changes and attendant bugs

==2013-09-19==
Attendees: Tina, Nicole, JC

Agenda:
* From Nicole: Adding a MRML scene flag for when changing the layout
** see back trace here in comment 9733: [http://www.na-mic.org/Bug/view.php?id=1690 Bug 1690]. Need to be able to know in my displayble manager that the layout is in the process of changing so as not to try and set renderers on widgets (active camera may also not be set)
** name? LayoutChangeState, LayoutChangeEvent?
** for which Slicer release? Bug 1690 probably won't get closed without this change and will need to be retargeted
* Slicer 4.3.1 release on Monday
** [http://na-mic.org/Mantis/roadmap_page.php Roadmap]

Notes:
* Nicole will post a topic to github and send the url for feedback
** [https://github.com/naucoin/Slicer/commit/50a20e429f5d4033a6984e2d7a5b5bcb47f7d578 commit link]

==2013-09-12==
Attendees: Jim, Ayesha, Nicole, Tina, JC

Agenda:
* Slicer 4.3.1 release
** [http://na-mic.org/Mantis/roadmap_page.php Roadmap]

Notes:
* Tina announced we will have a project week at MIT next summer, Jun 23-27
* Jim talked about redoing the process read node data method
** MRML node changes to support creating default display and storage nodes
** to let extensions define new nodes and have them get passed to CLIs
** Nicole will test once it's ready for review

==2013-09-05==
Attendees: Jim, Nicole, JC, Tina

Agenda:
* Slicer 4.3 release
** [http://na-mic.org/Mantis/roadmap_page.php Roadmap]
** SVN branch was made this afternoon

==2013-08-29==
Attendees: Jim, Steve, Nicole, Sunil, JC

Agenda:
* Slicer 4.3 release
** [http://na-mic.org/Mantis/roadmap_page.php Roadmap]

Notes:
* talked about the light box bug, Jim says cross hair displayable manager is good as a base
** http://na-mic.org/Bug/view.php?id=1690
* Nicole to change Markups documentation xml file to take out a layer of nesting, JC can extend the wiki settings after the release
* talked about the dti analysis bug, Steve can reproduce now and will try to fix
** http://na-mic.org/Bug/bug_view_advanced_page.php?bug_id=3323
* ITK tag has been updated

==2013-08-22==

Attendees: Steve, Nicole, JC, Dave

Agenda:
* Slicer 4.3 release
** [http://na-mic.org/Mantis/roadmap_page.php Roadmap]

==2013-08-15==
Attendees: Steve, Nicole, Ayesha, Ron, Tina, JC

Agenda:
* Slicer 4.3 release
** [http://na-mic.org/Mantis/roadmap_page.php Roadmap]

==2013-08-08==
Attendees: Ron, Nicole, Jim, Tina

==2013-07-18==
Attendees: Ron, Nicole, Steve, Jim, Tina, JC

Agenda:
* Slicer 4.3 release [http://na-mic.org/Mantis/roadmap_page.php Road map]

==2013-07-11==
Attendees: Nicole, Dave, Steve, Tina

*visualization of pediatric cardiac patients using 3d slicer has been underway at Children's (a brief tutorial was provided to them a few years ago and it turns out that they have been using it extensively. They are preparing an educational website for clinicians, which will be launched this year.)

==2013-07-04==

No mtg

==2013-06-27==
Attendees: Ron, Steve, Nicole, Dave, Tina

* Summary stats from project week: http://wiki.na-mic.org/Wiki/index.php/2013_Summer_Project_Week#Summary

==2013-06-20==

Project Week!

==2013-06-13==

Attendees: Tina, Nicole, Sneha, Steve, JC, Dave

Agenda:
*[[2013_Summer_Project_Week#Projects | Project Week]]

==2013-06-07==

Attendees: Hans Meine, Steve, Jim, Ayesha, Tina, Dirk

*Hans Meine project

==2013-05-30==

Attendees: Ayesha, Lilla, Steve, Tina, Nicole, Dirk, JC, Matt Tosch

* [[2013_Summer_Project_Week#Projects | Project Week]]
**Lilla Zollei
**Hans Meine

*https://sites.google.com/site/nihbtrc2/resources

==2013-05-23==

Attendees:
Jim, Tina, Nicole, Jason (UCSF), Beck (USCF), Aiyesha, Tamas, Dave, JC, Adriana (Univ of Mexico)

Agenda:

* [[2013_Summer_Project_Week#Projects | Project Week]]
** HD projects added
**UCSF team will not be able to join this project week, but SLC possible
**U of Mexico team will complete their project pages and join next call

==2013-05-16==

Attendees:
Jim, Steve, Tina, Nicole, JC, Aiyesha, Josh, Dirk, Jack

Agenda:

* [[2013_Summer_Project_Week#Projects | Project Week]]

==2013-05-02==

Attendees: Jim, Nicole, Aiyesha, Dave

Agenda:

* [[2013_Summer_Project_Week#Projects | Project Week]]

Meeting Notes:
* Jim and Nicole discussed qMRMLNodeComboBoxes, events, and mrml updates on entering modules
** workaround: disable widget until ready to update from MRML. Look into blockSignals.
* discussed Dave's project and storing/distributing large data for extensions

==2013-4-25==

Attendees:

Agenda:

* [[2013_Summer_Project_Week#Projects | Project Week]] Kickoff: list projects

Meeting Notes:

==2013-04-18==

Attendees: Jim, Steve, Nicole, Tina, Andriy, Aiyesha, JC

Agenda:

* [[2013_Summer_Project_Week | Project Week]]
* Virtual functional pointer tables
See: [https://github.com/BRAINSia/BRAINSTools/commit/31beee592eba2d98655b864e6dc704ac9bf995e8 Hans's test example]

Meeting Notes:

==2013-04-11==

Attendees: Jim, JC, Hans, Nicole, Brad

Meeting notes:
* BRAINS and EMSegment
* Building on Mac
* [[2013_Summer_Project_Week | Project Week]]: filling in the page

==2013-04-04==

Attendees: Jim, Nicole, JC, Ayesha

==2013-3-28==

Attendees: Jim, Steve, Nicole, JC, Ayesha

Agenda:
*Project Week Kickoff:List engineering projects

Meeting Notes:
* discussed general outlines of engineering projects:
** Annotations rewrite
** Brain atlas optimisations (Marianna to do a demo)
** Provenance
** Patient hierarchies
** Sample data - content addressable data, in external data processing in Slicer, cmake file for external data, when write test can decorate the data file name with macro keywords saying it's external
* Next slicer release?
**post namic submission late May
** itkv4 version - use for project week development, not ready for users though
** need to go through the targetted bugs to decide what goes in the next release
* Slicer prereqs
** qt(? or cmake?) version - no time to update it now
** VS2010: cmake-ified python testing, delayed by the double convert and dcmtk build problems, but should be done by project week

==2013-3-21==

No call today. Several participants in DC. Please join next tcon to kickoff engineering project discussion for project week.

==2013-3-14==
Attendees: Steve, Ron, Tina, Nicole, Ayesha,

Agenda:
* CHECK YOUR EMAIL (SLICER-DEVELOPERS, NAMIC-ENG) FOR NEW TCON NUMBER
* OpenSSL status update
* Reorg menus in Slicer - deferred to when JC is on the call
* india update (nicole)
* Training Events http://wiki.na-mic.org/Wiki/index.php/Training:Events_Timeline
* Project Week kickoff in two weeks with engineering projects.

==2013-3-7==
Attendees: Jim, Steve, Tina, Aisha

Agenda:
* CHECK YOUR EMAIL (NAMIC-ENG) FOR NEW TCON NUMBER

==2013-2-28==
Attendees: Jim, Steve, Tina, Hans, JC, Sunil, Dave

Agenda:
*

==2013-2-21==
Attendees: Jim, Steve, Tina, Hans, JC, Sunil, Dave

Agenda:
*

==2013-2-14==

Attendees: Nicole, Sunil, Tina, Jim, JC, Ron, Dave,

Agenda:
*utility python script to parse a file to make MRML file for modelmaker - where is the best place to put it (Nicole)

==2013-2-7==

Attendees: Nicole, Sunil, Tina, Steve, Andriy

Agenda:
*(Ann will review progress report materials with core/site PIs offline)
*

==2013-1-31==

Attendees: Jim, Steve, Nicole, Tina, Sunil, Ruiy, Stephen

Agenda:
* Python external libraries discussion (Ron, Steve, JC, Sunil)
**SSL, setuptools, etc.
**Bug report: http://na-mic.org/Bug/view.php?id=2352
*In the next TCON, Ann will review draft of engineering core progress report. All site PIs should plan to attend.

=== Extending Slicer with more python packages ===

==== Different approaches ====
Multiple and non-exclusive approach can be considered.

* (1) Bundling of package within Slicer installed (i.e. NUMPY)

If the package require compilation steps and is recognized of general interest, it probably make sens to bundle it within Slicer.

* (2) Installation of additional python packages from an *installed* Slicer

Few cases should be considered here:

a) *NO* compilation - *NO* libraries - It means the user does *NOT* have to install any compiler to be able to install the package. It is basically a pure python implementation.

b) *NO* compilation - *WITH* dependencies/libraries - It means the user does *NOT* have to install any compiler *BUT* have to install some external library to be able to install/use the package. This could reveal to be challenging for some user, especially to get the PATH, ... right.

c) *WITH* compilation - *NO* libraries - On unix like system, it is generally easier to install compiler but if we consider that most of our user works on windows, we should probably not require them to install Visual Studio to be able to install a python package ...

* (3) Installation of additional python packages from a *built* Slicer

The researched having a lot of experience in development usually have a build tree of Slicer and know enough to be able to tinker and install things.

==== Runtime installation ====

In the python ecosystem, the usage of a tool named [http://pypi.python.org/pypi/pip pip] became the standard regarding installation of additional module and packages. There are currently around 27500 packages available on the Python Package Index. See http://pypi.python.org/pypi

Most of these packages are served from server using <code>https</code> protocol. To support such protocol, we would have to include the [http://www.openssl.org/ OpenSSL library].

==== Integrating OpenSSL into Slicer ====

Considering the [http://www.openssl.org/source/license.html license of OpenSSL] (BSD style) is compatible with the Slicer one, there should not be any problem distributing it within Slicer. That said, is still presents few challenges.

===== Build system integration =====

* Download of the binaries on windows
* Build or download of binaries on macosx/linux
* As part of this integration, integrating a CMake'ified version of python would also make sens.

Some work and testing would be required to make sure everything works as expected.

===== Legal mention on the download page =====
We would have to probably have some mention on our page. That said, I found an article mentioning that it should now be fine to distribute strong cryptographic algorithm library within open-source project:
* http://www.theregister.co.uk/2011/01/07/open_source_crypto_curbs/
* https://www.federalregister.gov/articles/2011/01/07/2010-32803/publicly-available-mass-market-encryption-software-and-other-specified-publicly-available-encryption

===== Certificate Authority =====
To ensure Slicer is authenticated, we would have to create appropriate certificate and bundle them within Slicer. Some testing/research is required to exactly find out what need to be done. There is also probably a (not ideal) way of ignoring CA ...

==2013-01-24==

Attendees: Jim, Ron, Nicole, Sunil, JC, Steve

Agenda:
* ITK v4
* ssl issues with python

Minutes:
* ITK v4
** JC found the problem with dcmtk
* Xnat folks need to install some python package => Need openssl to pip install most of the package
** What is the legal aspect of having openssl bundled ?
** OpenSSL is build by CMake folks on all platform ... it could be re-used
* Difference between ITK 3.20.0 and ITK 3.20.1. See https://github.com/Kitware/ITK/compare/v3.20.0...v3.20.1
* Talked about Stan langage. See http://mc-stan.org/

==2013-01-17==

Attendees: Ron, Steve, Tina, Nicole, JC, Sunil, Dave, Jim

*Project week results review: http://wiki.na-mic.org/Wiki/index.php/2013_Winter_Project_Week

Agenda:

==2013-01-10==

No call due to [[2013_Winter_Project_Week]]

==2013-01-03==

Attendees: Jim, Steve, Stephen, Nicole, Tina,

Agenda:
* Project week: http://wiki.na-mic.org/Wiki/index.php/2013_Winter_Project_Week
** Engineering core presentation: http://wiki.na-mic.org/Wiki/index.php/AHM2013-Engineering_Updates

User:Millerjv

2013-10-17T15:45:51Z

Millerjv:

[[Image:JimMiller.JPG]]
=James V. Miller=
Jim Miller is a Senior Scientist in the Interventional and Therapy Laboratory at [http://www.ge.com/research/ GE Research]. In this role, Jim has developed techniques for segmentation, registration, detection, and quantification for oncology, pulmonology, cardiology, neurology and surgery applications in CT, PET, MR, and X-Ray. This technology has been deployed on review workstations as well as integrated into the scanner platforms. Jim was the architect of the image processing pipeline for the Insight Toolkit ([http://www.itk.org ITK]) and architect for the 3D Slicer [http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation generic execution model].

Before joining GE Research, Jim received a PhD in Computer Engineering from [http://www.rpi.edu Rensselaer Polytechnic Institute] where he developed segmentation techniques based on robust statistics.

Within NA-MIC, Jim is part of the Engineering Core and Site PI for GE Research. Here, he is adding technology to ITK to support the needs of NA-MIC and developing a module plugin and scheduling architecture for the 3D Slicer.

Jim's technology interests include
* statistical methods for segmentation, quantification, and detection
* atlas based methods for clinical applications
* registration methods for longitudinal analysis and motion compensation

Jim has extensive experience in C++, object oriented programming, software architectures, software testing, and open source software. Jim has 20 US Patents and 40 publications in the field.

= Contact =
'''Email:''' millerjv at ge dot com

'''Websites:''' [http://www.researchgate.net/profile/James_Miller14/?ev=prf_highl Research Gate], [http://www.linkedin.com/pub/james-miller/6/230/850 LinkedIn], [http://www.ohloh.net/accounts/millerjv Ohloh], [http://github.com/millerjv github]

User:Millerjv

2013-10-17T13:32:44Z

Millerjv:

[[Image:JimMiller.JPG]]
=James V. Miller=
Jim Miller is a Senior Scientist in the Interventional and Therapy Laboratory at [http://www.ge.com/research/ GE Research]. In this role, Jim has developed techniques for segmentation, registration, detection, and quantification for oncology, pulmonology, cardiology, neurology and surgery applications in CT, PET, MR, and X-Ray. This technology has been deployed on review workstations as well as integrated into the scanner platforms. Jim was the architect of the image processing pipeline for the Insight Toolkit ([http://www.itk.org ITK]) and architect for the 3D Slicer [http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation generic execution model].

Before joining GE Research, Jim received a PhD in Computer Engineering from [http://www.rpi.edu Rensselaer Polytechnic Institute] where he developed segmentation techniques based on robust statistics.

Within NA-MIC, Jim is part of the Engineering Core and Site PI for GE Research. Here, he is adding technology to ITK to support the needs of NA-MIC and developing a module plugin and scheduling architecture for the 3D Slicer.

Jim's technology interests include
* statistical methods for segmentation, quantification, and detection
* atlas based methods for clinical applications
* registration methods for longitudinal analysis and motion compensation

Jim has extensive experience in C++, object oriented programming, software architectures, software testing, and open source software. Jim has 20 US Patents and 40 publications in the field.

= Contact =
'''Email:''' millerjv at ge dot com

'''Websites:''' [http://www.researchgate.net/profile/James_Miller14/?ev=prf_highl Research Gate], [http://www.linkedin.com/pub/james-miller/6/230/850 LinkedIn], [http://www.ohloh.net/accounts/millerjv Ohlo], [http://github.com/millerjv github]