Commontk - User contributions [en]

CTK-Hackfest-Nov-2014

2014-11-03T09:07:23Z

Christian Askeland: /* Infrastructure */

== Event pictures ==

=== Progress ===

== Introduction ==

'''Date:''' November 3-7, 2014

'''Location:'''

German Cancer Research Center, Heidelberg, Germany

More details to follow.

'''Goal:''' A follow on to the [[Commontk:Current_events#Past_events|wildly successful previous hackfests!]]

'''Requirements:''' Attendees must be willing to spend their time during the event writing ctk code that contributes to the main [[CTK-Roadmap | ctk roadmap]]. This means spending the week immersed in C++, Qt, DCMTK, CMake, and related technologies. People who do not feel qualified for this task are politely not invited :)

'''Group size:''' Maximum 20 participants so we can have a manageable working meeting. The organizing committee will invite and select participants based on input from [[TheTeam]].

'''Site Hosts:''' Marco Nolden, Sascha Zelzer, Ivo Wolf

'''Organizing Committee:''' Steve Pieper, Ivo Wolf, Stephen Aylward

'''Future Events:''' Future hackfests will be announced in advance, and we hope lots of people will be interested in participating. The venue and activities at future hackfests will be determined based on the number of active participants in the project. We welcome participation via the CTK email lists, the source code repository, and this website.

== Attendees ==

* So far we have received confirmation for the following people (in no particular order).

Please fill in your intentions in terms of common accommodation.

{|class="wikitable alternance" style="text-align:left; border:1px solid black;"
|+ '''''Participants'''''
|-
! scope=col style="background:#cde6f8;"| Name
! scope=col style="background:#cde6f8;"| Organization
|-
|Marco Nolden
|German Cancer Research Center, Heidelberg, Germany
|-
|Sascha Zelzer
|German Cancer Research Center, Heidelberg, Germany
|-
|Andreas Fetzer
|German Cancer Research Center, Heidelberg, Germany
|-
|Stefan Kislinkiy
|German Cancer Research Center, Heidelberg, Germany
|-
|Ralf Floca
|German Cancer Research Center, Heidelberg, Germany
|-
|Ivo Wolf
|Mannheim University of Applied Sciences, Germany
|-
|Steve Pieper
|Isomics, Inc., USA
|-
|Michael Onken
|Open Connections GmbH / OFFIS
|-
|Jean-Christophe Fillion-Robin
|Kitware, Inc., USA
|-
|Miklos Espak
|University College London, UK
|-
|Nicolas Toussaint
|University College London, UK
|-
|Gergely Zombori
|University College London, UK
|-
|Christian Askeland
|SINTEF Medical Technology, Trondheim, Norway
|-
|Stefan Baumann
|Basel, Switzerland
|-
|Hans Meine
|Fraunhofer MEVIS, Germany
|-
|}

{|class="wikitable alternance" style="text-align:left; border:1px solid black;"
|+ '''''Google Hangout Participants'''''
|-
! scope=col style="background:#cde6f8;"| Name
! scope=col style="background:#cde6f8;"| Organization
! scope=col style="background:#cde6f8;"| Availablity (Central European Time)
|-
|}



{{Note}}There were also other invitations sent to active people on the community, and people who recently showed interest. When their intent will be known they will be added to the list.

== Preparation ==

Developers should bring a laptop with the [http://github.com/commontk/CTK current CTK source code] downloaded and [[Build_Instructions|built]].

Use the [http://public.kitware.com/cgi-bin/mailman/listinfo/ctk-developers CTK developers mailing list] to discuss build issues and topics for ongoing work.

Phone conferences have been scheduled in the weeks leading to the event:

'''https://plus.google.com/hangouts/_/g3vi3lz7sycalj74ys2xpnpr3ya'''

== Topics and Projects ==

Consider reading [http://www.commontk.org/index.php/Contributing_to_CTK#Integrate_your_new_feature Contributing_to_CTK#Integrate_your_new_feature]

Reminder: when integrating branches, remember to use --log --no-ff when merging.

We plan to have concrete hacking topics as well as dedicated discussions in smaller groups. People are encouraged to show their interest in a particular subject by adding their name to the list below.

=== Hacking Topics ===

==== Infrastructure ====

* Qt5 migration (Christian)
** compile and run on Mac
* Packaging / install support (Marco, Jc)
* Fix issue related to [https://github.com/commontk/Artichoke Artichoke] and improve documentation (Jc)
* Dashboard
** General Situation: Continuous/Nightly clients, coverage
** Configurations: Qt4, Qt5, etc.
** Travis CI (Sascha, Steve)
* Incomplete doxygen on the website (Christian)

==== DICOM ====

* Multi-frame support (Steve, Christian, Michael)
** SEG support
*** Investigate compatibility of DCMTK seg functionality with BrainLab segmentations; [http://slicer.kitware.com/midas3/item/162562 sample dataset] (QIICR community, Steve has access) - RLE compressed
*** Investigate DCMTK RLE compression tools applied to segmentations; trying to apply it to sample objects generates "F: No conversion to transfer syntax RLE Lossless possible!" error; [http://slicer.kitware.com/midas3/item/162428 SPL segmentation dataset example], [http://slicer.kitware.com/midas3/item/161740 PET segmentation example]
* Making CLIs read and write valid DICOM (Steve, Michael)
* Anonymization (Andreas Fetzer, Marco, Steve, Stefan)
** Client-side options: gdcmanon, dcmtk (?), dcmjs, DicomCleaner, CTP...

==== XNAT ====

* Improve and extend the XNAT API (Sascha Zelzer, Miklos Espak)
** Data editing
** Caching
** Filtered data query based on data type and/or properties
** Launch pipelines (remote) and follow progress

==== CLI ====

* Make it customisable what options to generate to the final command (Gergely Zombori)

* Finalize integration of CTK CLI frontend into Slicer and investigate how to integrate the backend (Jc)

==== ?? ====

=== Planned Discussions ===
* Possible extensions of CTK to the IGT domain
** OpenIGT link
** ...
* QIICR Presentation
==== ... ====

== Agenda ==

==== Monday ====

Start: The meeting room will be open starting at 9am. Official start and kick-off will be early afternoon after everybody arrived.

Opening discussion
* Review topics and projects
* Plans for the week
* Review [https://github.com/commontk/CTK/issues?state=open open issues on github].

Evening:

==== Tuesday ====

During the day: hack, hack, hack...

Evening:

==== Wednesday ====

During the day: hack, hack, hack...

16:00 Famous Old City tour guided by Hans-Peter Meinzer

==== Thursday ====

During the day: hack, hack, hack…

'''Around 2:00 pm:'''
* Lab visit at the department for Medical and Biological Informatics
* Duration approx. 2h
* Planned Demos:
** Organ + tumor segmentation
** Diffusion Imaging
** CAI

Evening:

==== Friday ====

During the day: hack, hack, hack...

11:00: Closing discussion

Afternoon: hack or travel

== Travel & Hotel ==

===Local contacts===

* Marco Nolden (m.nolden@dkfz-heidelberg.de)
* Sascha Zelzer (s.zelzer@dkfz-heidelberg.de) [[File:Sascha_phone.png|130px]]
* Andreas Fetzer (a.fetzer@dkfz-heidelberg.de)

===Transportation===

It takes about an hour from Frankfurt Airport (FRA) to Heidelberg Main Station with one change in Mannheim. If you stay in the Old Town you can also look for connections going to "Heidelberg Altstadt". You can look it up at [http://www.bahn.de/p_en/view/index.shtml Deutsche Bahn], but they run quite frequently.

'''Local:''' from the Old Town, "Universitätsplatz", runs [http://www.vrn.de/mam/vrn/einfach-ankommen/dokumente/stadtlinienplaene/heidelberg_schematisch.pdf bus number 32] ([http://www.vrn.de/mam/vrn/einfach-ankommen/dokumente/stadtlinienplaene/heidelberg.pdf geographic map]) via Main Station to DKFZ, exit at "Chirurgische Klinik", bus direction is "Neuenheim". After you exit, DKFZ is on your right.

[[File:Heidelberg_map.png|700px]]

During the day the bus runs every 10 minutes in both directions, timetables are also available at [http://fahrplanauskunft.vrn.de/vrn/XSLT_TRIP_REQUEST2?language=en VRN].

===Lodging===

We recommend to stay in the historic Old Town. There is an easy direct bus ride every 10 minutes from there to DKFZ.

We have reserved a number of rooms at the [http://www.hollaender-hof.de/en/ Holländer Hof] ([http://www.openstreetmap.org/?mlat=49.41317&mlon=8.70925#map=19/49.41317/8.70925 map]) hotel! Please use "CTK 2014" when you do a reservation there. Of course there are plenty of other hotels in that area, e.g. [http://www.hotel-goldener-hecht.de/ Goldener Hecht] or the oldest house in town, [http://www.ritter-heidelberg.de/ Hotel zum Ritter].

===Meeting Room===

The full address for the DKFZ is

Deutsches Krebsforschungszentrum
Im Neuenheimer Feld 280
69120 Heidelberg

We will meet in the main building on the second floor (European counting!). The cryptic room number is D0.02.032. Follow the description below to find it.

When leaving bus 32, you will see something similar to

[[File:DKFZ_Bus.jpg|600px]]

The large building on the right is the DKFZ main bulding

[[File:DKFZ_Hauptgebaeude_neu_600x402.jpg|600px]]

Walk through the main entrance and follow the map

[[File:DKFZ_Hackfest_map.jpg|600px]]

Ask the nice guys at the reception or call us in case of any problems.

===Weather===

November is a rather wet month. [http://www.weather-and-climate.com/average-monthly-Rainfall-Temperature-Sunshine,heidelberg,Germany Average weather in Heidelberg]

===Food===

Plan on having breakfast at your hotel before the meeting. Please email the organizers if you have any allergies or dietary restrictions.

Being a university and hospital campus, there are several lunch possibilities, including cafeterias, a students mensa, and two restaurants.

===Optional Activities in the Area===

CTK-Hackfest-Nov-2014

2014-11-03T09:00:03Z

Christian Askeland: /* Hacking Topics */

== Event pictures ==

=== Progress ===

== Introduction ==

'''Date:''' November 3-7, 2014

'''Location:'''

German Cancer Research Center, Heidelberg, Germany

More details to follow.

'''Goal:''' A follow on to the [[Commontk:Current_events#Past_events|wildly successful previous hackfests!]]

'''Requirements:''' Attendees must be willing to spend their time during the event writing ctk code that contributes to the main [[CTK-Roadmap | ctk roadmap]]. This means spending the week immersed in C++, Qt, DCMTK, CMake, and related technologies. People who do not feel qualified for this task are politely not invited :)

'''Group size:''' Maximum 20 participants so we can have a manageable working meeting. The organizing committee will invite and select participants based on input from [[TheTeam]].

'''Site Hosts:''' Marco Nolden, Sascha Zelzer, Ivo Wolf

'''Organizing Committee:''' Steve Pieper, Ivo Wolf, Stephen Aylward

'''Future Events:''' Future hackfests will be announced in advance, and we hope lots of people will be interested in participating. The venue and activities at future hackfests will be determined based on the number of active participants in the project. We welcome participation via the CTK email lists, the source code repository, and this website.

== Attendees ==

* So far we have received confirmation for the following people (in no particular order).

Please fill in your intentions in terms of common accommodation.

{|class="wikitable alternance" style="text-align:left; border:1px solid black;"
|+ '''''Participants'''''
|-
! scope=col style="background:#cde6f8;"| Name
! scope=col style="background:#cde6f8;"| Organization
|-
|Marco Nolden
|German Cancer Research Center, Heidelberg, Germany
|-
|Sascha Zelzer
|German Cancer Research Center, Heidelberg, Germany
|-
|Andreas Fetzer
|German Cancer Research Center, Heidelberg, Germany
|-
|Stefan Kislinkiy
|German Cancer Research Center, Heidelberg, Germany
|-
|Ralf Floca
|German Cancer Research Center, Heidelberg, Germany
|-
|Ivo Wolf
|Mannheim University of Applied Sciences, Germany
|-
|Steve Pieper
|Isomics, Inc., USA
|-
|Michael Onken
|Open Connections GmbH / OFFIS
|-
|Jean-Christophe Fillion-Robin
|Kitware, Inc., USA
|-
|Miklos Espak
|University College London, UK
|-
|Nicolas Toussaint
|University College London, UK
|-
|Gergely Zombori
|University College London, UK
|-
|Christian Askeland
|SINTEF Medical Technology, Trondheim, Norway
|-
|Stefan Baumann
|Basel, Switzerland
|-
|Hans Meine
|Fraunhofer MEVIS, Germany
|-
|}

{|class="wikitable alternance" style="text-align:left; border:1px solid black;"
|+ '''''Google Hangout Participants'''''
|-
! scope=col style="background:#cde6f8;"| Name
! scope=col style="background:#cde6f8;"| Organization
! scope=col style="background:#cde6f8;"| Availablity (Central European Time)
|-
|}



{{Note}}There were also other invitations sent to active people on the community, and people who recently showed interest. When their intent will be known they will be added to the list.

== Preparation ==

Developers should bring a laptop with the [http://github.com/commontk/CTK current CTK source code] downloaded and [[Build_Instructions|built]].

Use the [http://public.kitware.com/cgi-bin/mailman/listinfo/ctk-developers CTK developers mailing list] to discuss build issues and topics for ongoing work.

Phone conferences have been scheduled in the weeks leading to the event:

'''https://plus.google.com/hangouts/_/g3vi3lz7sycalj74ys2xpnpr3ya'''

== Topics and Projects ==

Consider reading [http://www.commontk.org/index.php/Contributing_to_CTK#Integrate_your_new_feature Contributing_to_CTK#Integrate_your_new_feature]

Reminder: when integrating branches, remember to use --log --no-ff when merging.

We plan to have concrete hacking topics as well as dedicated discussions in smaller groups. People are encouraged to show their interest in a particular subject by adding their name to the list below.

=== Hacking Topics ===

==== Infrastructure ====

* Qt5 migration (Christian)
** compile and run on Mac
* Packaging / install support (Marco, Jc)
* Fix issue related to [https://github.com/commontk/Artichoke Artichoke] and improve documentation (Jc)
* Dashboard
** General Situation: Continuous/Nightly clients, coverage
** Configurations: Qt4, Qt5, etc.
** Travis CI (Sascha, Steve)

==== DICOM ====

* Multi-frame support (Steve, Christian, Michael)
** SEG support
*** Investigate compatibility of DCMTK seg functionality with BrainLab segmentations; [http://slicer.kitware.com/midas3/item/162562 sample dataset] (QIICR community, Steve has access) - RLE compressed
*** Investigate DCMTK RLE compression tools applied to segmentations; trying to apply it to sample objects generates "F: No conversion to transfer syntax RLE Lossless possible!" error; [http://slicer.kitware.com/midas3/item/162428 SPL segmentation dataset example], [http://slicer.kitware.com/midas3/item/161740 PET segmentation example]
* Making CLIs read and write valid DICOM (Steve, Michael)
* Anonymization (Andreas Fetzer, Marco, Steve, Stefan)
** Client-side options: gdcmanon, dcmtk (?), dcmjs, DicomCleaner, CTP...

==== XNAT ====

* Improve and extend the XNAT API (Sascha Zelzer, Miklos Espak)
** Data editing
** Caching
** Filtered data query based on data type and/or properties
** Launch pipelines (remote) and follow progress

==== CLI ====

* Make it customisable what options to generate to the final command (Gergely Zombori)

* Finalize integration of CTK CLI frontend into Slicer and investigate how to integrate the backend (Jc)

==== ?? ====

=== Planned Discussions ===
* Possible extensions of CTK to the IGT domain
** OpenIGT link
** ...
* QIICR Presentation
==== ... ====

== Agenda ==

==== Monday ====

Start: The meeting room will be open starting at 9am. Official start and kick-off will be early afternoon after everybody arrived.

Opening discussion
* Review topics and projects
* Plans for the week
* Review [https://github.com/commontk/CTK/issues?state=open open issues on github].

Evening:

==== Tuesday ====

During the day: hack, hack, hack...

Evening:

==== Wednesday ====

During the day: hack, hack, hack...

16:00 Famous Old City tour guided by Hans-Peter Meinzer

==== Thursday ====

During the day: hack, hack, hack…

'''Around 2:00 pm:'''
* Lab visit at the department for Medical and Biological Informatics
* Duration approx. 2h
* Planned Demos:
** Organ + tumor segmentation
** Diffusion Imaging
** CAI

Evening:

==== Friday ====

During the day: hack, hack, hack...

11:00: Closing discussion

Afternoon: hack or travel

== Travel & Hotel ==

===Local contacts===

* Marco Nolden (m.nolden@dkfz-heidelberg.de)
* Sascha Zelzer (s.zelzer@dkfz-heidelberg.de) [[File:Sascha_phone.png|130px]]
* Andreas Fetzer (a.fetzer@dkfz-heidelberg.de)

===Transportation===

It takes about an hour from Frankfurt Airport (FRA) to Heidelberg Main Station with one change in Mannheim. If you stay in the Old Town you can also look for connections going to "Heidelberg Altstadt". You can look it up at [http://www.bahn.de/p_en/view/index.shtml Deutsche Bahn], but they run quite frequently.

'''Local:''' from the Old Town, "Universitätsplatz", runs [http://www.vrn.de/mam/vrn/einfach-ankommen/dokumente/stadtlinienplaene/heidelberg_schematisch.pdf bus number 32] ([http://www.vrn.de/mam/vrn/einfach-ankommen/dokumente/stadtlinienplaene/heidelberg.pdf geographic map]) via Main Station to DKFZ, exit at "Chirurgische Klinik", bus direction is "Neuenheim". After you exit, DKFZ is on your right.

[[File:Heidelberg_map.png|700px]]

During the day the bus runs every 10 minutes in both directions, timetables are also available at [http://fahrplanauskunft.vrn.de/vrn/XSLT_TRIP_REQUEST2?language=en VRN].

===Lodging===

We recommend to stay in the historic Old Town. There is an easy direct bus ride every 10 minutes from there to DKFZ.

We have reserved a number of rooms at the [http://www.hollaender-hof.de/en/ Holländer Hof] ([http://www.openstreetmap.org/?mlat=49.41317&mlon=8.70925#map=19/49.41317/8.70925 map]) hotel! Please use "CTK 2014" when you do a reservation there. Of course there are plenty of other hotels in that area, e.g. [http://www.hotel-goldener-hecht.de/ Goldener Hecht] or the oldest house in town, [http://www.ritter-heidelberg.de/ Hotel zum Ritter].

===Meeting Room===

The full address for the DKFZ is

Deutsches Krebsforschungszentrum
Im Neuenheimer Feld 280
69120 Heidelberg

We will meet in the main building on the second floor (European counting!). The cryptic room number is D0.02.032. Follow the description below to find it.

When leaving bus 32, you will see something similar to

[[File:DKFZ_Bus.jpg|600px]]

The large building on the right is the DKFZ main bulding

[[File:DKFZ_Hauptgebaeude_neu_600x402.jpg|600px]]

Walk through the main entrance and follow the map

[[File:DKFZ_Hackfest_map.jpg|600px]]

Ask the nice guys at the reception or call us in case of any problems.

===Weather===

November is a rather wet month. [http://www.weather-and-climate.com/average-monthly-Rainfall-Temperature-Sunshine,heidelberg,Germany Average weather in Heidelberg]

===Food===

Plan on having breakfast at your hotel before the meeting. Please email the organizers if you have any allergies or dietary restrictions.

Being a university and hospital campus, there are several lunch possibilities, including cafeterias, a students mensa, and two restaurants.

===Optional Activities in the Area===

CTK-Hackfest-Nov-2014

2014-10-16T11:29:11Z

Christian Askeland: /* Topics and Projects */

CTK-Hackfest-Nov-2014

2014-10-15T08:42:33Z

Christian Askeland: /* Attendees */