New upstream release for camp
Hi Andreas, Can you have a look on my last changes on the camp package ? I integrated the new upstream release of camp this morning. These changes are needed for fw4spl 0.10.2. Best regards, Corentin
Re: New upstream release for camp
Hi Correntin, On Tue, Jan 12, 2016 at 02:25:54PM +0100, Corentin Desfarges wrote: > Can you have a look on my last changes on the camp package ? > I integrated the new upstream release of camp this morning. Thanks for your work on this. Could you please create a proper description for debian/patches/support_c++11.patch which is currently just an auto-generated template. Kind regards Andreas. -- http://fam-tille.de
Re: New upstream release for camp
Hi Andreas 2016-01-12 14:37 GMT+01:00 Andreas Tille : > Hi Correntin, > > On Tue, Jan 12, 2016 at 02:25:54PM +0100, Corentin Desfarges wrote: > > Can you have a look on my last changes on the camp package ? > > I integrated the new upstream release of camp this morning. > > Thanks for your work on this. Could you please create a proper > description for > > debian/patches/support_c++11.patch > > which is currently just an auto-generated template. > It is done! > > Kind regards > >Andreas. > > -- > http://fam-tille.de > Best regards, Corentin
Re: New upstream release for camp
Uploaded. Thanks for your work. Andreas. On Tue, Jan 12, 2016 at 02:47:58PM +0100, Corentin Desfarges wrote: > Hi Andreas > > > 2016-01-12 14:37 GMT+01:00 Andreas Tille : > > > Hi Correntin, > > > > On Tue, Jan 12, 2016 at 02:25:54PM +0100, Corentin Desfarges wrote: > > > Can you have a look on my last changes on the camp package ? > > > I integrated the new upstream release of camp this morning. > > > > Thanks for your work on this. Could you please create a proper > > description for > > > > debian/patches/support_c++11.patch > > > > which is currently just an auto-generated template. > > > > It is done! > > > > > > Kind regards > > > >Andreas. > > > > -- > > http://fam-tille.de > > > > Best regards, > > Corentin -- http://fam-tille.de
understanding DICOM workflow
Hi, I work in a hospital and I would like to see whether it is pssible to migrate our departments DICOM workflow to OSS. I am quite new to internal DICOM stuff, sorry. What I would like to do: We have four ultrasound maschines which can be connected to a DICOM server. It would be nice to create an worklist so the examiner can chose the patient's name on the maschine. The pictures taken during an examination schould been stored in some archive (PACS). We would like to write down thhe findings an store them together with the images of an examination. I just tried to connect one of our ultraound devices to Orthanc and could recieve the images. Very nice. I didn't figure out whether I can create a worklist. I suppose I cannot describe the findings using orthanc. I am not sure what DICOM-storage to use for good reliabilty and interoperability. I am pretty clueless to the concepts behind it. Sorry. Would you mind to give me any hints how to get a clue, do you have suggestions of any packages I might consider to complete my task? Thank you very much, Sebastian
Re: understanding DICOM workflow
Hi Sebastian,
> What I would like to do: [typical imaging workflow]
This can indeed be covered by Open Source tools. One well-known Open
Source DICOM toolkit is DCMTK [1] which is developed in Germany. Since I
am one the developers, I focus on these (and I am biased;). Of course
there are other (great!) tools but others probably know more about them.
These are the DCMTK tools that specifically deal with your use case:
- storescu: Send images ("DICOM Storage SCU")
- storescp: Receive images ("DICOM Storage SCP")
- wlmscpfs: Worklist server, serves Worklist jobs from file
system ("DICOM Modality Worklist SCP").
The following tools could also be interesting for you:
- findscu: Worklist client ("DICOM Modality Worklist SCU")
- movescu/getscu/findscu: Find and download images ("DICOM Q/R SCU")
- dcmqrscp: Image archive ("DICOM Q/R SCP"), i.e. mini PACS
All the tools are command line tools written in C++ and can be compiled
for Linux, Mac and Windows (besides others). Of course they are
available via apt in Debian. Note that if you need Storage Commitment
(another DICOM service on top of DICOM Storage) there is no ready-to-use
Open Source tool in DCMTK.
In order to get an idea how the tools work, you might read through a
tutorial describing their use for PACS communication [2] that I wrote
some months ago for a research project. All DCMTK tools have man pages.
They are part of the documentation that is also online here [3]. There
is also a well active discussion forum [4].
If you want to read more deeply into the standard you can find it here
for download [5]. But be aware, it's usually not known as an
easy read for beginners ;) A good place for DICOM questions (not DCMTK
questions) is the DICOM newsgroup [6] though probably one should get a
basic understanding before posting.
Actually there is another technical specification which connects DICOM
and standards like HL7 for complete workflows (services and options
used, restrictions, data mapping between standards, ...). It is called
IHE and you can download the specifications here [7]. If you're from the
radiology department, look into Radiology section on the site, open
Volume 1 and read through "Scheduled Workflow" which is the regular
Radiology workflow mapped to DICOM and HL7.
Happy reading, learning and using!
Viele Grüße
Michael
[1] http://dicom.offis.de/dcmtk.php.en
[2]
http://support.dcmtk.org/redmine/projects/dcmtk/wiki/Howto_PACSDebuggingWithDCMTK
[3] http://support.dcmtk.org/
[4] http://forum.dcmtk.org
[5] http://medical.nema.org/ (yes, that is the official web site...)
[6] comp.protocols.dicom, also mirrored here:
https://groups.google.com/forum/#!topic/comp.protocols.dicom/
[7] http://ihe.net/Technical_Frameworks/
--
Michael Onken, Open Connections GmbH
Please use a free license for blimps and sift
Dear Andreas, The Henikoffs and I received your email about regarding changing the license of blimps and SIFT to GPL. We are willing to consider it if SIFT can be easily distributed. Do you have a working version of SIFT on debian? My old version of SIFT uses a very old version of blast and calls a binary of blimps --I think the source code has been since lost. If you can can confirm that SIFT works in debian, then Dr. Henikoff will talk to the FHCRC tech transfer office to start the process. Thanks, Pauline Hello, I'm writing you on behalf of the Debian Med team which is a group inside Debian with the objective to make Debian the best distribution for biology and medical care. We try to package free software that is relevant in these fields for main Debian. You might know that there are packages of blimps and sift for some time which are not part of the official Debian distribution due to its license which is considered non-free since it violates the Debian Free Software Guidelines[1]. We would really make blimps and sift part of the official Debian distribution which has several advantages for users as well even for you as developers since the wider spreading of your code might lead to enhancements that will be send to you. We would like you to reconsider the restriction under the following considerations: - Did you earned a mentionable amount of money by selling mssstest yourself? - Do you consider that anybody else would earn a mentionable amount of money by selling a freely licensed program? - Would you agree that it is in the interest of mssstest code and the users to have a free distribution inside Debian? Please keep in mind that the restriction implies that the programs cannot be included as part of a distribution that is sold (even if it's just to compensate for the cost of the storage media). Your intention is almost certainly to prevent people to sell the program standalone. To our experience authors who used this kind of license (for instance Joe Felsenstein as author of PHYLIP) did not considered this as a success. May be you reconsider the license to choose some free license like GPL; BSD or MPL - feel free to discuss this here on our mailing list. It would be great if you would simply drop the restriction and enable us to integrate blimps and sift into Debian properly. Kind regards Andreas. [1] https://www.debian.org/social_contract#guidelines -- http://fam-tille.de
Re: understanding DICOM workflow
Hi Michael, On Tue, Jan 12, 2016 at 06:45:00PM -0500, Michael Onken wrote: > > What I would like to do: [typical imaging workflow] > > This can indeed be covered by Open Source tools. One well-known Open > Source DICOM toolkit is DCMTK [1] which is developed in Germany. Since I > am one the developers, ... Thanks for this very valuable contribution which is a sign that Debian (Med) can connect users and developers. Its good to know that upstream is reading our list. Please make sure that the packaging we are doing is perfectly in line with what you like to distribute to your users. Kind regards Andreas. -- http://fam-tille.de
Re: Please use a free license for blimps and sift
Dear Pauline, On Wed, Jan 13, 2016 at 09:59:14AM +0800, Pauline Ng wrote: > The Henikoffs and I received your email about regarding changing the > license of blimps and SIFT to GPL. We are willing to consider it if SIFT > can be easily distributed. Do you have a working version of SIFT on > debian? Currently version 4.0.3b is packaged and I know that this is not the latest released version. One reason for this lag behind is the fact that SIFT remains in non-free which does not receive the apropriate care - thus the motivation for my mail to tackle the latest version if there would be a free license. > My old version of SIFT uses a very old version of blast and calls a binary > of blimps --I think the source code has been since lost. The Debian version of SIFT is linked against a separately packaged version of blimps 3.9. I noticed that the downloadable tarball sift5.2.2.tar.gz contains a dir blimps/blimps with C sources (and even *.o files which should not be distributed inside a tarball). I also see a dir blimps/bin which we would clean up from the tarball since we usually do not ship precompiled binaries in the source tarball. > If you can can confirm that SIFT works in debian, then Dr. Henikoff will > talk to the FHCRC tech transfer office to start the process. I can confirm that the Debian Med team got the old version of SIFT working and we will try or best to get also the latest version working. However, please make sure that the license change is not only for the purpose of distribution inside Debian but rather in general since a specific free Debian license is also considered as non-free by the Debian Free Software Guidelines. > Thanks, > Pauline Thanks a lot for your fast response Andreas. > Hello, > > > > I'm writing you on behalf of the Debian Med team which is a group inside > Debian with the objective to make Debian the best distribution for biology > and medical care. We try to package free software that is relevant in > these fields for main Debian. > > > > You might know that there are packages of blimps and sift for some time > which are not part of the official Debian distribution due to its license > which is considered non-free since it violates the Debian Free Software > Guidelines[1]. We would really make blimps and sift part of the official > Debian distribution which has several advantages for users as well even for > you as developers since the wider spreading of your code might lead to > enhancements that will be send to you. > > > > We would like you to reconsider the restriction under the following > > considerations: > > > > - Did you earned a mentionable amount of money by selling mssstest > >yourself? > > - Do you consider that anybody else would earn a mentionable amount > >of money by selling a freely licensed program? > > - Would you agree that it is in the interest of mssstest code and > >the users to have a free distribution inside Debian? > > > > Please keep in mind that the restriction implies that the programs cannot > be included as part of a distribution that is sold (even if it's just to > compensate for the cost of the storage media). Your intention is almost > certainly to prevent people to sell the program standalone. > > > > To our experience authors who used this kind of license (for instance Joe > Felsenstein as author of PHYLIP) did not considered this as a success. May > be you reconsider the license to choose some free license like GPL; BSD or > MPL - feel free to discuss this here on our mailing list. > > > > It would be great if you would simply drop the restriction and enable us to > integrate blimps and sift into Debian properly. > > > > Kind regards > > > > Andreas. > > > > > > [1] https://www.debian.org/social_contract#guidelines > > > > -- > http://fam-tille.de -- http://fam-tille.de
