View Issue Details
|ID||Project||Category||View Status||Date Submitted||Last Update|
|0002352||Slicer4||Core: Scripting (Wrapping, Python)||public||2012-07-25 11:15||2014-10-08 07:10|
|Priority||normal||Severity||feature||Reproducibility||have not tried|
|Target Version||Fixed in Version|
|Summary||0002352: Include more python packages in standard install|
Several very useful modules could be added if we had a better baseline of python functionality.
With some additional python modules included in the slicer core package, we could access other packages as optional installs.
Suggested core modules:
Tools that could be used if these were included in slicer python:
NiPy: http://nipy.sourceforge.net/ - in particular nipype and nibable have often been requested (nipype would also give a bridge to fsl and spm).
iPython: http://ipython.org/ - would be an improved developer interface, plus it could support parallel processing and web notebooks
pydicom: http://code.google.com/p/pydicom/ - for efficient processing of dicom files (read/write)
Some design work and analysis is required to see what is feasible on different platforms. Note that freely available binaries are already available for windows, many of which could be bundled with slicer or downloaded on-demand at runtime.
|Tags||No tags attached.|
|related to||0001718||closed||jcfr||SSL / HTTPS Issues with Python Interactor and QT - Windows 7|
|related to||0003100||closed||jcfr||cannot install extra python library|
|related to||0003158||closed||jcfr||Building Slicer with numpy-1.4.1 failed using VS2010|
|related to||0002637||acknowledged||jcfr||Include all Python header files with nightly binary build|
Some emails describing one set of use cases that require this feature.
---------- Forwarded message ----------
From my (very biased) point of view, there is a cascade of updates that
1) Add SimpleITK (i.e. Move to ITKv4)
Iowa City, Iowa 52242
I'm with Hans - I think nipype has a great potential to unify the
On Wed, Jul 25, 2012 at 9:43 AM, Johnson, Hans J <firstname.lastname@example.org>
I think that Nipype will be a great addition. I'm all for this and chipping in
PyXNAT (and its dependencies) would be awesome. The dependencies are as follows:
Package site: http://packages.python.org/pyxnat/index.html
SSL should also be added to the standard python build if possible:
Kumar, Sunil email@example.com via bwh.harvard.edu
My question pertains specifically to OSX 10.8 64-bit.
I've tried several different approaches to get SSL to build with Python (via a Slicer build). I can't get any to work. They are as follows:
1) SSL is not found in the default Slicer build. (I get errors when typing "import ssl" in the Python command prompt.)
2) If I try to "make" Slicer's Python alone, the SSL directories are incorrect and Python builds without it.
3) When I direct "Slicer4-superbuild/python/Modules/Setup" and "Slicer4-superbuild/python/setup.py" to the native install of SSL, I get architecture errors when I build Python.
4) When I direct "Slicer4-superbuild/python/Modules/Setup" and "Slicer4-superbuild/python/setup.py" to a 64-bit build of OpenSSL, I also get architecture errors when I build Python.
Would you know of a way to get around this? Any suggestions are appreciated.
Is there a suggested workaround how to compile Slicer with OpenSSL enabled?
Will keep you posted of the progress soon. Thanks. Jc
I'd also like to add pyMC and pyZMQ to my wish list of python packages.
it seems that Lauren would need it in addition to numpy
On 5/2/13 2:05 PM, Steve Pieper wrote:
Nothing has changed yet except that the package is now based on python
Here's the bug report:
we can add joblib to the list.
On Thu, May 2, 2013 at 9:32 AM, Ron Kikinis <firstname.lastname@example.org
I agree that a way to fork multiple python processes such as done by the package joblib, would be useful. This is impossible from the current Slicer python interpreter. Alternatively, a tutorial/examples on how best to do multiprocessing in python-slicer would be helpful.
Other packages I am using are within scipy. These include scipy.optimize, scipy.cluster, scipy.stats
Is there a good reason for not just adding pydicom into Slicer superbuild? It is a small package, and the capability to access DICOM is pretty much essential for Slicer tasks, but not possible from python!
I understand I can install pydicom, but on some systems I am unable to build Slicer, since they don't have a GUI head and X related libraries -- so I cannot use Slicer in batch mode for DICOM related tasks in my scripts. I am also unable to compile Slicer on the machines of my clinical users.
DICOM support is such a basic and essential functionality that I do not see why we can't just integrate it.
+1 for integrating pydicom in the superbuild.
@jc: can you give some hints what should be done to include this package into the superbuild? It does not have any dependencies.
for the reference, pydicom has been integrated a while ago
|2012-07-25 11:15||pieper||New Issue|
|2012-07-25 11:15||pieper||Status||new => assigned|
|2012-07-25 11:15||pieper||Assigned To||=> jcfr|
|2012-07-25 11:17||pieper||Note Added: 0005235|
|2012-07-25 11:24||jcfr||Target Version||=> Slicer 4.3.0|
|2012-08-15 06:04||demian||Note Added: 0005555|
||Note Added: 0005559|
|2012-08-16 11:22||pieper||Note Added: 0005560|
|2012-08-16 11:27||pieper||Target Version||Slicer 4.3.0 => Slicer 4.2.0 - October 1st 2012|
|2012-08-20 10:36||jcfr||Target Version||Slicer 4.2.0 - Feature freeze Sept 1st 2012 => Slicer 4.2.5|
|2012-08-21 09:40||jcfr||Target Version||Slicer 4.2.5 => Slicer 4.3.0|
|2012-08-27 05:29||pieper||Relationship added||related to 0001718|
|2012-08-27 05:30||pieper||Note Added: 0005794|
|2013-03-08 07:44||fedorov||Note Added: 0008097|
|2013-03-08 10:05||jcfr||Note Added: 0008098|
|2013-03-08 12:14||pieper||Note Added: 0008099|
|2013-05-03 03:24||pieper||Relationship added||related to 0003100|
|2013-05-03 05:05||pieper||Note Added: 0008558|
|2013-05-23 12:56||lauren||Note Added: 0008670|
|2013-05-23 12:59||lauren||Note Edited: 0008670|
|2013-05-23 13:00||lauren||Note Edited: 0008670|
|2013-06-13 13:43||pieper||Relationship added||related to 0003158|
|2013-08-30 12:48||jcfr||Target Version||Slicer 4.3.0 => Slicer 4.3.1|
|2013-09-12 11:04||jcfr||Target Version||Slicer 4.3.1 => Slicer 4.3.2|
|2013-10-03 13:07||fedorov||Note Added: 0010128|
|2013-10-04 00:41||pieper||Note Added: 0010129|
|2013-10-04 12:26||fedorov||Note Added: 0010135|
|2014-03-06 10:15||nicole||Target Version||Slicer 4.3.2 => Slicer 4.4.0|
|2014-05-12 23:57||jcfr||Status||assigned => acknowledged|
|2014-05-12 23:57||jcfr||Target Version||Slicer 4.4.0 =>|
|2014-05-13 00:35||jcfr||Relationship added||related to 0002637|
|2014-10-08 07:10||fedorov||Note Added: 0012609|