Commontk - User contributions [en]

DICOM de-identification tool overview

2014-11-06T16:39:12Z

Andreas Fetzer: /* Requirements */

== Specific use cases and requirements for de-identification ==

=== Requirements ===
* Client side processing
* Offline processing
* Platform and browser independent
* Provided as commandline tool?
* In-application processing should be possible?
** e.g. in MITK and Slicer?
* Specify conditions like if tag value is equal to XYZ then remove all private tags except of <tag list>

Some issues, which anonymization tools often have, found on the [http://plastimatch.org/dicom_comparison.html Plastimatch homepage], also providing a comparison:

* Some date fields cannot be changed (duh)
* It is not possible to preserve relative dates (for example, we would like to set StudyDate to Jan 1, 2000, but preserve the fact that StructureSetDate occurred 35 days later)
* Private tags are always deleted (on our GE scanner, these contain important acquisition details)
* Comments, diagnosis descriptions, or other fields cannot be reset (may contain protected information)
* It is not possible to modify strings (for example, the physician might type “smith-final” into the StructureSetName field, and we would like to delete “smith” but preserve “final” )
* UIDs are not changed, or relationships between UIDs are not preserved (duh)

=== Usecases ===

*

== Available tools for DICOM de-identification ==

{| class="wikitable"
! Toolname
! Language
! Available as cmd line?
! Features
! URL
|-
| Clinical Trial Processor
| Java
|
|
| http://mircwiki.rsna.org/index.php?title=CTP-The_RSNA_Clinical_Trial_Processor
|-
| DICOM Cleaner
| Java
|
|
| http://www.dclunie.com/pixelmed/software/webstart/DicomCleanerUsage.html
|-
| DICOM Confidential
| Java
|
|
| http://sourceforge.net/projects/privacyguard/
|-
| DICOM Browser
| Java
| [http://nrg.wustl.edu/software/dicom-browser/instructions/batch-anonymizations/ Yes]
| Script based processing: Assignment / Deletion / Constraint and condition based / Built-in functions / Generators / user defined variables
| http://nrg.wustl.edu/software/dicom-browser/
|-
| GDCM Anon
| C++
| Yes
|
| http://gdcm.sourceforge.net/html/gdcmanon.html
|-
| DCMTK
| C++
|
|
|
|-
| DICOM anon
| Python
| Yes
|
| https://github.com/cbmi/dicom-anon
|-
|}

DICOM de-identification tool overview

2014-11-06T09:06:30Z

Andreas Fetzer:

== Specific use cases and requirements for de-identification ==

=== Requirements ===
* Client side processing
* Offline processing
* Platform and browser independent
* Provided as commandline tool?
* In-application processing should be possible?
** e.g. in MITK and Slicer?
* Specify conditions like if tag value is equal to XYZ then remove all private tags except of <tag list>

Some issue anonymization tools often have found on the [http://plastimatch.org/dicom_comparison.html Plastimatch homepage] also providing a comparison:

* Some date fields cannot be changed (duh)
* It is not possible to preserve relative dates (for example, we would like to set StudyDate to Jan 1, 2000, but preserve the fact that StructureSetDate occurred 35 days later)
* Private tags are always deleted (on our GE scanner, these contain important acquisition details)
* Comments, diagnosis descriptions, or other fields cannot be reset (may contain protected information)
* It is not possible to modify strings (for example, the physician might type “smith-final” into the StructureSetName field, and we would like to delete “smith” but preserve “final” )
* UIDs are not changed, or relationships between UIDs are not preserved (duh)

=== Usecases ===

*

== Available tools for DICOM de-identification ==

{| class="wikitable"
! Toolname
! Language
! Available as cmd line?
! Features
! URL
|-
| Clinical Trial Processor
| Java
|
|
| http://mircwiki.rsna.org/index.php?title=CTP-The_RSNA_Clinical_Trial_Processor
|-
| DICOM Cleaner
| Java
|
|
| http://www.dclunie.com/pixelmed/software/webstart/DicomCleanerUsage.html
|-
| DICOM Confidential
| Java
|
|
| http://sourceforge.net/projects/privacyguard/
|-
| DICOM Browser
| Java
| [http://nrg.wustl.edu/software/dicom-browser/instructions/batch-anonymizations/ Yes]
| Script based processing: Assignment / Deletion / Constraint and condition based / Built-in functions / Generators / user defined variables
| http://nrg.wustl.edu/software/dicom-browser/
|-
| GDCM Anon
| C++
| Yes
|
| http://gdcm.sourceforge.net/html/gdcmanon.html
|-
| DCMTK
| C++
|
|
|
|-
| DICOM anon
| Python
| Yes
|
| https://github.com/cbmi/dicom-anon
|-
|}

DICOM de-identification tool overview

2014-11-06T08:30:16Z

Andreas Fetzer:

== Specific use cases and requirements for de-identification ==

=== Requirements ===
* Client side processing
* Offline processing
* Platform and browser independent
* Provided as commandline tool?
* In-application processing should be possible?
** e.g. in MITK and Slicer?
* Specify conditions like if tag value is equal to XYZ then remove all private tags except of <tag list>

Some issue anonymization tools often have found on the [http://plastimatch.org/dicom_comparison.html Plastimatch homepage] also providing a comparison:

* Some date fields cannot be changed (duh)
* It is not possible to preserve relative dates (for example, we would like to set StudyDate to Jan 1, 2000, but preserve the fact that StructureSetDate occurred 35 days later)
* Private tags are always deleted (on our GE scanner, these contain important acquisition details)
* Comments, diagnosis descriptions, or other fields cannot be reset (may contain protected information)
* It is not possible to modify strings (for example, the physician might type “smith-final” into the StructureSetName field, and we would like to delete “smith” but preserve “final” )
* UIDs are not changed, or relationships between UIDs are not preserved (duh)

=== Usecases ===

*

== Available tools for DICOM de-identification ==

{| class="wikitable"
! Toolname
! Language
! Available as cmd line?
! Features
! URL
|-
| Clinical Trial Processor
| Java
|
|
| http://mircwiki.rsna.org/index.php?title=CTP-The_RSNA_Clinical_Trial_Processor
|-
| DICOM Cleaner
| Java
|
|
| http://www.dclunie.com/pixelmed/software/webstart/DicomCleanerUsage.html
|-
| DICOM Confidential
| Java
|
|
| http://sourceforge.net/projects/privacyguard/
|-
| DICOM Browser
| Java
| [http://nrg.wustl.edu/software/dicom-browser/instructions/batch-anonymizations/ Yes]
| Script based processing: Assignment / Deletion / Constraint and condition based / Built-in functions / Generators / user defined variables
| http://nrg.wustl.edu/software/dicom-browser/
|-
| GDCM Anon
| C++
| Yes
|
| http://gdcm.sourceforge.net/html/gdcmanon.html
|-
| DCMTK
| C++
|
|
|
|-
|}

DICOM de-identification tool overview

2014-11-05T08:16:34Z

Andreas Fetzer:

DICOM de-identification tool overview

2014-11-03T14:11:31Z

Andreas Fetzer: /* Available tools for DICOM de-identification */

DICOM de-identification tool overview

2014-11-03T13:33:18Z

Andreas Fetzer:

DICOM de-identification tool overview

2014-11-03T13:11:46Z

Andreas Fetzer:

DICOM de-identification tool overview

2014-11-03T11:04:05Z

Andreas Fetzer:

DICOM de-identification tool overview

2014-11-03T11:03:20Z

Andreas Fetzer:

== Specific use cases and requirements for de-identification ==
* Client side processing
* Offline processing
* Platform and browser independent
* Provided as commandline tool?
* In-application processing should be possible?
** e.g. in MITK and Slicer?

== Available tools for DICOM de-identification ==

{| class="wikitable"
! Toolname
! Language
! Available as cmd line?
! URL
|-
| Clinical Trial Processor
| Java
|
| http://mircwiki.rsna.org/index.php?title=CTP-The_RSNA_Clinical_Trial_Processor
|-
| DICOM Cleaner
| Java
|
| http://www.dclunie.com/pixelmed/software/webstart/DicomCleanerUsage.html
|-
| DICOM Confidential
| Java
|
| http://sourceforge.net/projects/privacyguard/
|-
| DICOM Browser
| Java
|
| http://nrg.wustl.edu/software/dicom-browser/
|-
| GDCM Anon
| C++
| Yes
| http://gdcm.sourceforge.net/html/gdcmanon.html
|-
| DCMTK
| C++
|
|
|-
|}

DICOM de-identification tool overview

2014-11-03T11:02:32Z

Andreas Fetzer:

Specific use cases and requirements for de-identification:
* Client side processing
* Offline processing
* Platform and browser independent
* Provided as commandline tool?
* In-application processing should be possible?
** e.g. in MITK and Slicer?

Available tools for DICOM de-identification:

{| class="wikitable"
! Toolname
! Language
! Available as cmd line?
! URL
|-
| Clinical Trial Processor
| Java
|
| http://mircwiki.rsna.org/index.php?title=CTP-The_RSNA_Clinical_Trial_Processor
|-
| DICOM Cleaner
| Java
|
| http://www.dclunie.com/pixelmed/software/webstart/DicomCleanerUsage.html
|-
| DICOM Confidential
| Java
|
| http://sourceforge.net/projects/privacyguard/
|-
| DICOM Browser
| Java
|
| http://nrg.wustl.edu/software/dicom-browser/
|-
| GDCM Anon
| C++
| Yes
| http://gdcm.sourceforge.net/html/gdcmanon.html
|-
| DCMTK
| C++
|
|
|-
|}

DICOM de-identification tool overview

2014-11-03T11:00:31Z

Andreas Fetzer:

Specific use cases and requirements for de-identification:
* Client side processing
* Offline processing
* Platform and browser independent
* Cmdline tool?
* In-application processing?
** In MITK and Slicer?

Available tools for DICOM de-identification:

{| class="wikitable"
! Toolname
! Language
! Available as cmd line?
! URL
|-
| Clinical Trial Processor
| Java
|
| http://mircwiki.rsna.org/index.php?title=CTP-The_RSNA_Clinical_Trial_Processor
|-
| DICOM Cleaner
| Java
|
| http://www.dclunie.com/pixelmed/software/webstart/DicomCleanerUsage.html
|-
| DICOM Confidential
| Java
|
| http://sourceforge.net/projects/privacyguard/
|-
| GDCM Anon
| C++
| Yes
| http://gdcm.sourceforge.net/html/gdcmanon.html
|-
| DCMTK
| C++
|
|
|-
|}

DICOM de-identification tool overview

2014-11-03T10:58:09Z

Andreas Fetzer:

Specific use cases and requirements for de-identification:
* Client side processing
* Platform and browser independent
* Cmdline tool?
* In-application processing?
** In MITK and Slicer?

Available tools for DICOM de-identification:

{| class="wikitable"
! Toolname
! Language
! Available as cmd line?
! URL
|-
| Clinical Trial Processor
| Java
|
| http://mircwiki.rsna.org/index.php?title=CTP-The_RSNA_Clinical_Trial_Processor
|-
| DICOM Cleaner
| Java
|
| http://www.dclunie.com/pixelmed/software/webstart/DicomCleanerUsage.html
|-
| DICOM Confidential
| Java
|
| http://sourceforge.net/projects/privacyguard/
|-
| GDCM Anon
| C++
| Yes
| http://gdcm.sourceforge.net/html/gdcmanon.html
|-
| DCMTK
| C++
|
|
|-
|}

DICOM de-identification tool overview

2014-11-03T10:54:27Z

Andreas Fetzer:

Specific use cases and requirements for de-identification:
* ...

Available tools for DICOM de-identification:

{| class="wikitable"
! Toolname
! Language
! Available as cmd line?
! URL
|-
| Clinical Trial Processor
| Java
|
| http://mircwiki.rsna.org/index.php?title=CTP-The_RSNA_Clinical_Trial_Processor
|-
| DICOM Cleaner
| Java
|
| http://www.dclunie.com/pixelmed/software/webstart/DicomCleanerUsage.html
|-
| DICOM Confidential
| Java
|
| http://sourceforge.net/projects/privacyguard/
|-
| GDCM Anon
| C++
| Yes
| http://gdcm.sourceforge.net/html/gdcmanon.html
|-
| DCMTK
| C++
|
|
|-
|}

DICOM de-identification tool overview

2014-11-03T10:54:15Z

Andreas Fetzer:

Specific use cases and requirements for de-identification:
*

Available tools for DICOM de-identification:

{| class="wikitable"
! Toolname
! Language
! Available as cmd line?
! URL
|-
| Clinical Trial Processor
| Java
|
| http://mircwiki.rsna.org/index.php?title=CTP-The_RSNA_Clinical_Trial_Processor
|-
| DICOM Cleaner
| Java
|
| http://www.dclunie.com/pixelmed/software/webstart/DicomCleanerUsage.html
|-
| DICOM Confidential
| Java
|
| http://sourceforge.net/projects/privacyguard/
|-
| GDCM Anon
| C++
| Yes
| http://gdcm.sourceforge.net/html/gdcmanon.html
|-
| DCMTK
| C++
|
|
|-
|}

DICOM de-identification tool overview

2014-11-03T10:41:03Z

Andreas Fetzer:

Available tools for DICOM de-identification:

{| class="wikitable"
! Toolname
! Language
! Available as cmd line?
! URL
|-
| Clinical Trial Processor
| Java
|
| http://mircwiki.rsna.org/index.php?title=CTP-The_RSNA_Clinical_Trial_Processor
|-
| DICOM Cleaner
| Java
|
| http://www.dclunie.com/pixelmed/software/webstart/DicomCleanerUsage.html
|-
| DICOM Confidential
| Java
|
| http://sourceforge.net/projects/privacyguard/
|-
| GDCM Anon
| C++
| Yes
| http://gdcm.sourceforge.net/html/gdcmanon.html
|-
| DCMTK
| C++
|
|
|-
|}

DICOM de-identification tool overview

2014-11-03T10:40:38Z

Andreas Fetzer:

DICOM de-identification tool overview

2014-11-03T10:22:47Z

Andreas Fetzer:

Available tools for DICOM de-identification:

{| class="wikitable"
! Toolname
! Language
! Available as cmd line?
! URL
|-
| Clinical Trial Processor
| Java
|
| http://mircwiki.rsna.org/index.php?title=CTP-The_RSNA_Clinical_Trial_Processor
|-
| DICOM Cleaner
| Java
|
| http://www.dclunie.com/pixelmed/software/webstart/DicomCleanerUsage.html
|-
| GDCM Anon
| C++
| Yes
| http://gdcm.sourceforge.net/html/gdcmanon.html
|-
|}

DICOM de-identification tool overview

2014-11-03T10:21:42Z

Andreas Fetzer:

Available tools for DICOM de-identification:

* Java based tools

* C++
* cmd-line based?

{| class="wikitable"
! Toolname
! Language
! URL
|-
| Clinical Trial Processor
| Java
| http://mircwiki.rsna.org/index.php?title=CTP-The_RSNA_Clinical_Trial_Processor
|-
| DICOM Cleaner
| Java
| http://www.dclunie.com/pixelmed/software/webstart/DicomCleanerUsage.html
|-
| GDCM Anon
| C++
| http://gdcm.sourceforge.net/html/gdcmanon.html
|-
|}

CTK-Hackfest-Nov-2014/DICOM de-identification tool overview

2014-11-03T09:59:32Z

Andreas Fetzer: moved CTK-Hackfest-Nov-2014/DICOM de-identification tool overview to DICOM de-identification tool overview over redirect

#REDIRECT [[DICOM de-identification tool overview]]

DICOM de-identification tool overview

2014-11-03T09:59:32Z

Andreas Fetzer: moved CTK-Hackfest-Nov-2014/DICOM de-identification tool overview to DICOM de-identification tool overview over redirect

Available tools for DICOM de-identification:

* Java
* C++
* cmd-line based?

DICOM de-identification tool overview

2014-11-03T09:56:15Z

Andreas Fetzer: moved DICOM de-identification tool overview to CTK-Hackfest-Nov-2014/DICOM de-identification tool overview: Make this page a subpage for the hackfest in heidelberg

Available tools for DICOM de-identification:

* Java
* C++
* cmd-line based?

DICOM de-identification tool overview

2014-11-03T09:54:15Z

Andreas Fetzer: Created page with "Available tools for DICOM de-identification: * Java * C++ * cmd-line based?"

Available tools for DICOM de-identification:

* Java
* C++
* cmd-line based?

CTK-Hackfest-Nov-2014

2014-11-03T09:52:45Z

Andreas Fetzer:

== 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...
** Testing can use [[File:PieperMRI.tar.gz | this freely sharable identified MR scan]]
** Goal is to de-identify with various tools and compare results with [ftp://medical.nema.org/medical/dicom/Final/sup142_ft.pdf supplement 142 of the DICOM standard].
** There is a separate page, which provides an overview of existing de-identification tools: [[DICOM de-identification tool overview]]

==== 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

2014-11-03T07:47:21Z

Andreas Fetzer: /* Thursday */

== 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)
* 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-May-2014

2014-02-18T08:41:20Z

Andreas Fetzer:

== Event pictures ==

Images from the hackfest:
<gallery widths=300 px heights=200px perrow=3>
</gallery>



=== Progress ===

<gallery widths=400px heights=300px perrow=2>

</gallery>

== Introduction ==

'''Date:''' May 5-9, 2014

'''Location:'''

ERL conference room, [http://www.wustl.edu/ Washington University Saint Louis].

[[#location|How to get here.]]

'''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:''' Lawrence Tarbox and Dan Marcus

'''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
|-
|Steve Pieper
|Isomics, Inc. Cambridge, USA.
|-
|Stephen Aylward
|Kitware, Inc. North Carolina, USA.
|-
|Jean-Christophe Fillion-Robin
|Kitware, Inc. North Carolina, USA.
|-
|-
|Marco Nolden
|German Cancer Research Center, Heidelberg, Germany
|-
|-
|Sascha Zelzer
|German Cancer Research Center, Heidelberg, Germany
|-
|-
|Andreas Fetzer
|German Cancer Research Center, Heidelberg, Germany
|-
|-
|Ivo Wolf
|Mannheim University of Applied Sciences, 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 (St. Louis time)
|-
|[http://en.wikipedia.org/wiki/Jeremy_Bentham#Death_and_the_Auto-Icon Jeremy Bentham's auto-icon]
|University College, London
| Anytime
|-
|}



{{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:
* To be announced

== Topics and Projects ==

TBD (probably XNAT, DICOM, CLIs, Hosting...)

== Agenda ==

==== Monday ====

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 ====

10:00 Roadmap discussion

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

Evening:

==== Thursday ====

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

Evening:

==== Friday ====

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

10:00; Closing discussion

Afternoon: hack or travel

== Travel & Hotel ==

===Local contacts===

* Lawrence Tarbox (tarboxl@mir.wustl.edu)
* Dan Marcus (dmarcus@wustl.edu)

===Transportation===

The facility is easy to get to from the airport via the Metrorail light rail system, with stations at the airport terminals and just around the corner from our building. We do not recommend renting a car due to parking headaches, but if one chooses to rent a car, there are parking garages available that are not terribly expensive (e.g. $6 - $8 per day, no in and out).

===Lodging===

Within walking distance is the Parkway Hotel (83% thumbs up and ranked #23 out of 123 hotels in St. Louis on tripadvisor.com). If we were to reserve a room block, the Parkway would be very convenient. The Parkway is affiliated with the medical campus, and one can use enclosed skyways to walk to our building (though the routing is a bit confusing). There are other good hotels in the area. Fred Prior likes the Chase Park Plaza, even though it is more expensive than the Parkway, and a several blocks longer walk. A nearby Drury Inn said that they would provide a shuttle if enough people stayed there. And of course there are several downtown hotels that are only a few Metrorail stops away.

===Weather===

[http://www.weather.com/weather/wxclimatology/monthly/graph/USMO0787 Average weather in St. Louis]

===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 several cafeterias and a daily show of high end food trucks just outside our door. And both the nearby Grove and Central West neighborhoods have several restaurant choices for any meal and at multiple budget levels. Naturally, we could also have pizza or Chinese food or sandwiches or whatever brought in if participants are interested, and don’t want to be bothered with going out.

===Optional Activities in the Area===
Fred did offer to host an outing to his country club (Meadowbrook), if there is interest. The pool would not be open until Memorial Day (May 26th), but golf, tennis, and of course excellent food would be available. While a country club outing would not be inexpensive, it would be less expensive than many other similar, high quality outings. Other outing options could include a Cardinals game, if they are in town, or any of the museums and gardens in the area.

User:Andreas Fetzer

2014-02-18T08:37:23Z

Andreas Fetzer: Blanked the page

File:CtkDicomWidgetsInMITK.png

2013-11-08T10:51:52Z

Andreas Fetzer:

CTK-Hackfest-Nov-2013

2013-11-08T10:35:29Z

Andreas Fetzer:

== Event pictures ==

Images from the hackfest
<gallery widths=300 px heights=200px perrow=3>
File:20131107_192029.jpg|<big>Hacking</big>
File:Bentham.png|<big>[http://en.wikipedia.org/wiki/Jeremy_Bentham#Death_and_the_Auto-Icon Honorary CTK Hacker]</big>
</gallery>



=== Progress ===

<gallery widths=400px heights=300px perrow=2>
File:Screen Shot 2013-11-07 at 1.24.00 PM.png|DICOM Table Interface integrated in 3D Slicer's nightly build [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DICOM (Documentation)]
File:DICOM Header Browser.png|DICOM Header Browser
File:ctkDicomWidgetsInMITK.png|New ctkDicomTableWidgets in the MITK Dicom Editor
</gallery>

== Introduction ==

'''Date:''' Nov 4-8, 2013

'''Location:'''

Room 1.19 (Monday, Friday) and Room 2.14 (other days)
Malet Place Engineering Building, University College London.

[[#location|How to get here.]]

'''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:''' Matt Clarkson (m.clarkson@ucl.ac.uk), Miklos Espak (m.espak@ucl.ac.uk)

'''Organizing Committee:''' (need to ask people)

'''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
|-
|Matt Clarkson
|University College London, UK.
|-
|Miklos Espak
|University College London, UK.
|-
|Nicolas Toussaint
|University College London, UK.
|-
|Marco Nolden
|German Cancer Research Center, Heidelberg, Germany.
|-
|Sascha Zelzer
|German Cancer Research Center, Heidelberg, Germany.
|-
|Andreas Fetzer
|German Cancer Research Center, Heidelberg, Germany.
|-
|Steve Pieper
|Isomics, Inc. Cambridge, USA.
|-
|Florian Vichot
|INRIA, Sophia-Antipolis, France
|-
|Ivo Wolf
|Mannheim University of Applied Sciences, Germany
|-
| Ernesto Coto
| University of Sheffield, UK.
|-
|}

{|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 (London time)
|-
|Jean-Christophe Fillion-Robin
|Kitware Inc, North Carolina, USA
| 1pm to 6pm
|-
|Michael Onken (planned)
|OFFIS, Germany.
| as needed. Skype: "michaeloffis"
|-
|Csaba Pinter
|Queen's University, Kingston, ON
| TBD
|-
|}



{{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:
* To be announced

== Topics and Projects ==

=== XNAT Library ===

Interested people: Miklos, Nicolas, Florian, Ivo, Sascha

* Stabilize API and make it more robust
* Merge to master

Open topics

* Error handling (Miklos)
* Timeout handling (Miklos)
* Unit tests for ctkXnatCore
* Zip support (Sascha)
* Up/Download support in the API (Sascha / Miklos)
* SSL support (ask about disabling SSL) (Florian?)
* Support browsing files attached to assessments
* General API review (Sascha, Miklos, Ivo, Florian)
* Add API documentation

=== CLI Library ===

Florian, Sascha, Ernesto, Steve, Marco

Open Topics

* Add a CTK "test" for validating the XML of external CLIs
** Maybe a "web service" for quickly validating the XML files
* CTK should become the official CTK schema hosting site
* Default values for some elements are problematic (e.g. for SpinBox)
** Have a best practices document how to handle optional default values
* CLIs depending on external dependencies (shared libraries) are problematic
** Probably nothing we can solve inside CTK
* The UiLoader should be more customizable (JC did that in a branch for the Slicer integration)
* Maybe have a way to check for long running modules during the XML retrieval and cancel them (more of a developer thing)
* Add a method for clearing the XML cache (probably in ctkCmdLineModuleManager)
* Having a new web services front-end could be interesting

Discussion

* Make GIMIAS CLI modules work with the ctkCmdLineModuleExplorer (Ernesto)

=== DICOM Application Hosting ===

Ivo, Sascha

=== DICOM Libraries ===

Andreas, Steve

* Improve and finish the widgets
* DICOM Database backend (Marco, Steve)

=== CTK packaging ===

Marco, Sascha

* continue [[Debian_Packaging | Debian packaging support]]

=== General Discussion ===

* Create support for CLI Web Services in CTK?
* Could we make CLI modules run in Osirix?

== Agenda ==

==== Monday ====

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...

15:00 Google Hangout with US and other participants

* Talk about DCMTK_DIR ([https://github.com/commontk/CTK/issues/382 Issue 382])
** Michael: Would integrate the DCMTKConfig.cmake file but needs more time to check the changes and make sure it works for everyone
** Jc: NO_DEFAULT_PATH in FindDCMTK.cmake would work for Slicer, CTK, etc. but in the future (when all distributions contain a DCMTK package with a DCMTKConfig.cmake) FindDCMTK.cmake should not be needed anymore
** Marco: We still need a way to find the system installed DCMTK
** Steve: We should be able to tell the scripts that it should find a specific DCMTK version and not automatically prefer one version over another. E.g. there could be a system DCMTK but we would still want to use a developer DCMTK build
** Jc: Is not sure why it failed at all on Csaba's machine. Will look remotely at the concrete problem on that machine.
** Marco: NO_DEFAULT_PATH would still work for the Debian packages if we pass DCMTK_DIR=/usr
** Steve: Mentions that find_program was gone from FindDCMTK.cmake leading to test failures. It is probably okay to add the find_program paths to the CMakeLists.txt file of the CTK tests.
** Jc: The DCMTK fixes are in the commontk DCMTK fork
** Marco: We should not depend on the commontk DCMTK fork since it makes compatibility with official snapshots difficult
** Jc: We should set-up a dashboard for DCMTK builds on cdash.org
* Discuss CTK install and Debian package support
** Marco: Let's have a separate hangout for that
* Failing tests on Steves machine (and others like Ivos)
** Steve: ctkCrosshairTest2 is failing on all platforms.
** Jc: It is not used anymore in Slicer
** Steve: We could remove the class and the test if nobody is using it
** General agreement
* Dashboard
** Jc suggests to move back to a traditional dashboard style (no splitting by library)
** Everyone agrees

Evening:

==== Wednesday ====

10:00 Roadmap discussion

* Matt: Right now we have Widgets, DICOM, etc. is that still how we see CTK?
* Steve:
** Generally we factor out common stuff. Mainly project driven requirements
** Adding JavaScript widgets for image processing (on top of e.g. jQuery) would be nice
* Marco:
** Currently we are focusing on data management aspects (XNAT, DICOM RT, CLIs, etc.)
** Image guided therapy applications are driving the requirements for us
** New data structures for imaging are hard to agree on
* Marco:
** How CTK is presented to the outside is important
** CTK could provide standardized approaches to develop e.g. CLIs
* Florian:
** Students ask what they could CTK use for - has to tell them that it is rather for application/platform developers
* Matt:
** Pushing the XNAT work is important for us
** Also interested in mor DICOM data structure support
** Wrapping algorithms inside a proper DICOM workflow would be interesting
** What about Application Hosting?
* Steve:
** Its not directly in the QIICR proposal
* Sascha:
** We are still not ready for a production grade implementation
** Same goes for probably any other implementation
* Steve:
** Syngo Via does not seem to see a role for application hosting (they have a kind of distributed client server architecture)
** Doesn't fit with running applications locally on the workstation supporting application hosting
* Marco:
** Physicians are not really happy with proprietary solutions so there is some pressure for a more open system
** There is an IHE profile which contains application hosting, so there is also some interest
* Matt:
** We are working on XNAT support which also supports pipelines. But there is also Nipype, the GIMIAS Taverna approach, etc.
** Having XNAT in CTK is nice since people converge somehow to using the same type of database
* Marco:
** What is QIICR using as a data backend?
** Having a more light-weight, easily installable and searchable PACS would be nice
* Steve:
** The plan is to use TCIA
** It is unclear which backend technology is used for it

Conclusion:

* We are pretty much happy as it is
* A light-weight database solution would be really nice to have
* Same goes for a pipeline system

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

Evening:

==== Thursday ====

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

Evening:

==== Friday ====

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

10:00; Closing discussion

Afternoon: hack or travel

== Travel & Hotel ==

'''Local contact'''

Need any help in organizing your visit, contact Miklos Espak (m.espak@ucl.ac.uk).
If you have any troubles during your visit, call +44 792 6656 927.

'''Transportation'''

[http://www.ucl.ac.uk/maps/public-transport How to get to the UCL.]

'''Lodging'''

Hotels in central London can be expensive, this one seems reasonably priced:

* [http://www.imperialhotels.co.uk/tavistock The Tavistock Hotel]

<div id="location">'''Meeting Location'''</div>

Malet Place Engineering Building, University College London
[http://goo.gl/maps/2encP]

Monday and Friday: room 1.19
Other days: room 2.14

The reception is at the '''Engineering Front Building''' right at the gate, so please come there and refer to the CTK hackfest.

[http://www.ucl.ac.uk/maps UCL Bloomsbury campus map]

[http://crf.casa.ucl.ac.uk/ UCL campus route finder]

'''Weather'''

Daily temperature will be around 12-15C (53-59F), mostly dry, light rain is possible some days.

'''Food'''

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

File:TableView Vertical Sorting.png

2013-05-24T15:42:25Z

Andreas Fetzer: ctkDICOMTableView with vertical layout

ctkDICOMTableView with vertical layout

File:TableView Horizontal Sorting.png

2013-05-24T15:41:35Z

Andreas Fetzer: New ctkDICOMTableView with horizontal layout

New ctkDICOMTableView with horizontal layout

CTK-Hackfest-May-2013

2013-05-24T15:39:44Z

Andreas Fetzer: /* Gallery of Results */

== Event pictures ==
Images from the hackfest
<gallery widths=300 px heights=200px perrow=3>

File:2013-05-20_16.16.28.jpg|<big>Discussions on Monday</big>
File:2013-05-21_11.33.58.jpg|<big>Planning on Tuesday</big>
</gallery>

== Introduction ==

'''Date:''' May 20-24, 2013

'''Location:''' [http://en.wikipedia.org/wiki/Kingston,_Ontario Kingston, Ontario, Canada]. In a classroom at Queens University.

'''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:''' Gabor Fichtinger, Csaba Pinter, Andras Lasso

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

'''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
|-
|Steve Pieper
|Isomics, Inc., Cambridge, MA, USA
|-
|Ivo Wolf
|Hochschule Mannheim
|-
|Marco Nolden
|German Cancer Research Center (DKFZ)
|-
|Sascha Zelzer
|German Cancer Research Center (DKFZ)
|-
|Andreas Fetzer
|German Cancer Research Center (DKFZ)
|-
|Florian Vichot
|INRIA
|-
|Lawrence Tarbox
|Washington University, St. Louis
|-
|Andras Lasso
|Queen's University, Kingston, ON
|-
|Csaba Pinter
|Queen's University, Kingston, ON
|-
|Alberto Biancardi
|The University of Sheffield, UK
|-
| Xenios Papademetris
| Yale University US
|-
|}

{|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
|-
| Jean-Christophe Fillion-Robin
| Kitware Inc.
|-
|}



{{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:
* To be announced

== Topics and Projects ==

==== DICOM Application Hosting ====
* Results:
** Merged DAH branch into master
** Slicer as Hosted Application (Ivo, Lawrence, Steve)
*** launch hosted app, send data
*** loaded into slicer for manipulation
*** changed data detected automatically
*** TODO: data sent back to host
*** TODO: act on bringToFront events (includes resizing)
** pushed corresponding CTK-based MITK hosted/host application
** Started to develop integration tests
* Plans
** finish data return to host by end of next hackfest ;)
** Interoperability testing of CTK with other Application Hosting code
** Lawrence to test CTK code against the XIP hosting implementation
** Testing framework to be continued

==== DICOM Database and Networking ====

* Review implementation issues when using CTK DICOM
** DICOM issues in github [https://github.com/commontk/CTK/issues?labels=DICOM&state=open]
** <del> Incorrect import when DICOMDIR is present [http://na-mic.org/Bug/view.php?id=3111]. Should we skip DICOMDIR when it is not picked explicitly? </del> {{done}}
** Incorrect/slow database behavior when multiple processes access it simultaneously [http://na-mic.org/Bug/view.php?id=3106] (interference between ctkDICOMIndexer and ctkDICOMModel)
* Discuss DICOM-RT for CTK
* Discuss DICOM Export options
** CLI outputs converted into real DICOM
** RT and other non-imaging types
*** GUI Issues
*** Lower-level dcmrt issues, possible use of DKFZ toolkit
*** Use of various tools (VTK, ITK, Plastimatch), validation

* GUI
** https://bigfiles.assembla.com/spaces/slicerrt/documents/download/DicomPatientBrowsersReview.pptx

* Results
** New DB table of display overrides
** New table view of patient/study/series - ctkDICOMTableView
** New Layout control for ctkDICOMBrowser to replace tree and ctkDICOMModel
** New signals to match use cases
** New signals for ctkDICOMDatabase during imports and new dialog in app widget to show summary results
* Plans
** issue #336 - create replacement for ctkDICOMAppWidget and deprecate old (Marco)
** issue #337 - implement signals from table view (Marco and Andras with Steve)
** issue #331 - to be completed soon by Andreas
** issue #332 - ctkDICOMTableManager to control layouts (also Andreas)
** issue #276 - fix up RT use cases (Andras and Csaba)
** Review naming View vs. Widget
** Look into re-using http://www.commontk.org/index.php/File:CtkSearchBox3.png
** Marco is making ctkDICOM2

==== Widgets ====
* Spin box development [http://public.kitware.com/pipermail/ctk-developers/2013-May/001125.html]
* <del>ctkDICOMModel and display of real-world patient data (RT special cases for example)</del> - {{done}}
* Compare [[Documentation/WidgetPlans|widget plans]] with [[Documentation/ImageGallery |current set]].
* Qt5 Compatibility?
** <del>Working on VTK / Qt5 compatibility</del> - {{done}} VTK6 topic : http://review.source.kitware.com/#/t/2803

* Results
** Miklos and Julien developed plan for resolving spin box features: there will be a ctkDoubleSpinBox with new precision features migrated from current ctkSpinBox and Miklos's changes to expose more of the QSpinBox features.
** Jc was Qt5+VTK6 issues and plans to backport them to VTK5.10

==== Tests Framework ====
* Qt testing framework
** Checkpoint verification
** Possibly help debugging when a test is failing and fixing a test
* Check log for warnings and errors
* Integrate with Error Log widget and the app launcher (but won't work on mac)
* Suggest as something for student at CREATIS
** Rotating log files
** capturing screen during test to help diagnose failures
** capturing all output to log files and flushing
** report crash utility for user to send all files to file issue
** auto-detect crashes using some kind of token
** track the exact version of libraries and stack traces (platform specific) Look into google crashpad.
** Review squish video: http://www.froglogic.com/squish/gui-testing/squish-qt-webinar-qanda.php

* Results & Plans
** CREATIS group attended hangout and plans to contribute to QtTesting

==== Build Systems & Software process ====
* <del>DCMTK build issues [http://public.kitware.com/pipermail/ctk-developers/2013-May/001122.html] [http://public.kitware.com/pipermail/ctk-developers/2013-May/001120.html]</del> {{done}} Fixed by [https://github.com/commontk/CTK/commit/74b4b07b92f2a3ac492fef6dcb429bd08c513d59 74b4b07b9]
* A drop-in CMake module allowing to easily setup Superbuild project.
** Consolidate CTK, Slicer, .. approach
* Collection of "External_XXX.cmake" file that could easily be re-used ? (See https://github.com/BRAINSia/NAMICExternalProjects)
* <del>Finalize work related to qRestAPI project (pending since Bologna hackfest)</del> {{done}} History cleaned and pushed: https://github.com/commontk/qRestAPI
* Results
** Fixed and tested the DCMTK build issues
** Windows build issues identified for PythonQt on windows vs 2010/2012 (include order of std vector header)
** Still some more issues, likely also to do with include order

==== Command Line Modules ====
* Using CLI XML to build stand-alone widget [https://github.com/pieper/CTK/blob/8391b2f54e18e68e6672a4d3a54da38bc9c77b79/Libs/CommandLineModules/Widgets/Testing/Cpp/ctkCmdLineModuleWidgetTest1.cpp#L86][http://www.commontk.org/index.php/File:Cli-widget-prototype-2012-12-14.png]
* Contribute Slicer fixes to CLI infrastructure. See https://github.com/jcfr/CTK/tree/279-tweak-cmdlinemodule-library-for-slicer-integration
* Hierarchy nodes preserved on CLI execution
** keep the CLI simple.
** xinclude to allow people to centralize their grant support and other boilerplate info

* Results
** Xenios and Sascha performed tests and discussed many options
*** Explored C++ tools for generating the CLI XML on the fly
*** Lots of ideas and Xenios has some TODO items and he will push to a fork for review.

==== qRestAPI and XNAT API ====

* Results
** Sascha and Florian built on Miklos's work from last hackfest
** Many C++ level accessors are now available in a rough application
** Can login to XNAT, list projects, lists subjects in project
** Florian and Sascha contacted Tim Olsen and Dan Marcus to work through some questions on the REST API of XNAT
* Plans
** Work will continue and people will stay in touch.
** Now there is a CTK library outside the plugin framework
** New widgets and models reflecting status
** The XNAT group expressed enthusiasm to work with CTK
** INRIA is researching and evaluating XNAT to see if it will fill needs
** Maxime is in contact with the CVI (cardiovascular) group associated with the XNAT developers (http://cvrgrid.org/featured/xnat-cvi)
** DKFZ is likely to deploy XNAT instances unless there are unforeseen roadblocks
*** Want to take advantage of distributed project sharing
*** Pushing from PACS into common space
** BWH also has internal XNAT implementations with several years worth of prostate biopsy databases.

== Agenda ==

==== Monday ====

Opening discussion
* Review topics and projects
* Plans for the week

Evening: BBQ at the Fichtinger residence

==== Tuesday ====

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

Evening: Dinner and beers at the [http://www.kingstonbrewing.ca/ Kingston Brewery]

==== Wednesday ====

During the day: hack, hack, hack...
10:30 Hangout to review status

Evening: [http://www.hauntedwalk.com/kingstontours.php Kingston Haunted Walks]

==== Thursday ====

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

Evening: BBQ by the [http://farm5.staticflickr.com/4042/4276978263_96c7a234ff_b.jpg gazebo] on the waterfront

==== Friday ====

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

Late morning; Closing discussion

https://plus.google.com/hangouts/_/33c4f3b6fd88ee2330172c2c91439632c7d6e9b6?authuser=0&hl=en

* [http://public.kitware.com/pipermail/ctk-developers/2013-May/001126.html Next hackfest in London, UK]!?!
* Then back in North America - St. Louis - when?

Afternoon: hack or travel

== Gallery of Results ==
Images from the hackfest
<gallery widths=300 px heights=200px perrow=3>
File:Screen Shot 2013-05-24 at 10.23.16 AM.png |<big>Slicer running as DICOM Hosted Application using CTK infrastructure</big>
Image:MITKasHostedApp-and-asHost-withCLIasHostedApp.jpg|For comparison image from Bologna Hackfest: MITK running as DICOM Application Hosting hosted application (hosted by ctkDICOMHost) as well as hosting system with CTK-CLI as hosted application
File:Screen Shot 2013-05-24 at 11.27.52 AM.png |<big>Summary dialog after DICOM import shown in use in slicer. Uses new signals from ctkDICOMDatabase and the signal tracking in ctkDICOMAppWidget</big>
File:TableView_Horizontal_Sorting.png |<big>New DICOMWidgets with horizontal orientation. The ctkDICOMTableView uses the QSqlQueryModel to display the database content</big>
File:TableView_Vertical_Sorting.png |<big>New DICOMWidgets with vertical orientation.</big>

</gallery>

== Travel & Hotel ==

'''Local contact'''

Need any help in organizing your visit, contact Andras Lasso (lasso@cs.queensu.ca).
If you have any troubles during your visit, call ''TBD''.

'''Airport'''

* Option A: Fly into Kingston via Toronto
* Option B: Fly into Toronto, take a bus to Kingston
** Recommended: Coach Canada direct bus from Toronto Airport to Kingston, leaves twice a day: 2.30pm and 7pm. You can buy the ticket from a Kiosk at the airport or [http://www.coachcanada.com/coachcanada/index.asp?_lp.lang=en buy online]
** Megabus from Toronto downtown: [http://www.tripadvisor.ca/Travel-g155019-c116016/Toronto:Ontario:Getting.Downtown.From.Pearson.Airport.html get to the Toronto Coach Terminal], take a bus to Kingston, leaves in about every hour. [http://ca.megabus.com/default.aspx Online reservation] is strongly recommended, as early as possible, because the prices are continuously increasing (starts from $1 and increased to about $40).

'''Transportation on Site'''

Take a cab at the Kingston airport or bus terminal to your hotel. After that everything is in walking distance.

'''Lodging'''

Be aware there is a Queen's event during the week of the hackfest so try to book your hotel early

* Frontenac http://www.frontenacclub.com Queen’s rate $143 per day (plus tax)
* The Belvedere http://www.hotelbelvedere.com is a small hotel of Colonial character, they only have 20 rooms.
* Holiday Inn Kingston Waterfront, http://www.hikingstonwaterfront.com/ about $140
* There are cheaper motels (Super-8 for $100 / night)

'''Meeting Location'''

[https://maps.google.ca/maps?q=Queen's+University&hl=en&sll=44.225024,-76.493151&sspn=0.010379,0.026157&t=v&hq=Queen's+University&z=16&iwloc=A Queen's University], [http://www.queensu.ca/campusmap/?mapquery=kinesiology Kinesiology building], room #107.

'''Weather'''

Can be still chilly in May, average temperature is about 15°C.

'''Food'''

Plan on having breakfast at your hotel before the meeting. A variety of lunch options will be available, as will access to snacks and beverages during the day. Please email the organizers if you have any allergies or dietary restrictions.

'''Optional Activities in the Area'''

* [http://www.ganboatline.com/LostShipsTour.asp Boat Cruise in Thousand Islands]
* [http://www.niagarafallstourism.com/ Trip to Niagara Falls (Sat-Sun)]
* Wildlife Canoeing ([http://www.1000islandskayaking.com/ Thousand Islands], [http://www.ontarioparks.com/english/bone.html Bon Echo], [http://www.ontarioparks.com/english/char.html Charleston Lake], etc.)
* [http://www.hauntedwalk.com/kingstontours.php Kingston Haunted Walks]
* Art after dark:
** http://www.downtownkingston.ca/files/13%20Art%20After%20Dark_Spring%20Featured%20Artists.pdf
** http://www.downtownkingston.ca/files/13%20Art%20After%20Dark_Spring%20Gallery%20Map.pdf
* Canadian Souvenirs: [https://maps.google.ca/maps?ie=UTF-8&q=red+maple+kingston&fb=1&gl=ca&hq=red+maple&hnear=0x4cd2ab0674408ea9:0x76a5497715d6d9ea,Kingston,+ON&cid=0,0,6137054689914097153&ei=ZkOeUbWiI8PWygGD0YG4Cg&ved=0CIEBEPwSMAA Red Maple], some stuff they sell: http://shop.red-maple.ca/