Difference between revisions of "2008 Winter Project Week:PythonSupport"

From NAMIC Wiki
Jump to: navigation, search
 
(3 intermediate revisions by the same user not shown)
Line 18: Line 18:
 
* Python command line modules (advantages: easy to write, access to Python libraries, don't need a compiler to write new modules)
 
* Python command line modules (advantages: easy to write, access to Python libraries, don't need a compiler to write new modules)
 
* matplotlib and scipy Python modules (they provide a matlab-like processing environment for images directly within Slicer).
 
* matplotlib and scipy Python modules (they provide a matlab-like processing environment for images directly within Slicer).
−
* Python as Slicer's scripting language (for automating task and programmatically access modules - this is Dan's new baby!)
+
* Python as Slicer's scripting language (for automating tasks, programmatically access modules - this is Dan's new baby! - enabling staged processing)
  
 
</div>
 
</div>
Line 26: Line 26:
 
<h1>Approach, Plan </h1>
 
<h1>Approach, Plan </h1>
 
In the project week, we plan to
 
In the project week, we plan to
−
* consolidate Python support in Slicer3 from a design point of view (eg. can we allow Python command line modules to modify the MRML scene in a thread-safe way? ) (can we provide a Python equivalent to ScriptedModules?)
+
* solve building issues, check stability on different platforms
 +
* threading issues: modifying the MRML scene from Python command line modules in a thread-safe way
 +
* stabilize calling modules from Python, write example on staged processing
 +
* provide a Python equivalent to ScriptedModules
 
* define what aspects will end up in the next release
 
* define what aspects will end up in the next release
−
* solve issues (building issues, threading issues, etc)
+
* propose a working set of Python command line modules (interact with Sonia's breakout session on Tuesday?) to be included in the next release
−
* propose a working set of Python command line modules (interact with Sonia's breakout session on Tuesday?) to be included in the next release.
+
* write documentation on how to write Python command line modules
 
</div>
 
</div>
  
Line 35: Line 38:
  
 
<h1>Progress</h1>
 
<h1>Progress</h1>
 +
 +
====January 2008 Project Week====
 +
 +
* Matplotlib with a Cairo backend is almost there
 +
* Python command line modules now work correctly (handling arguments multiple=true has been fixed)
 +
* A set of working Python command line modules has been committed
 +
* Scripted modules have been extended to Python, and a sample scripted module has been written
 +
* Meta-modules are now possible; the first meta-modules will be written soon
  
 
====June 2007 Project Week====
 
====June 2007 Project Week====
Line 51: Line 62:
  
 
Later on, after the meeting
 
Later on, after the meeting
−
* command line parsing has been completed (in a very simple way, without needing access to XML)
+
* command line parsing has been completed
−
* API has been simplified
+
* Python scripting and Python modules have been made independent of Numpy
 +
* Python command line modules are now run in the main thread (allows interaction with MRML scene)
 +
* a set of Python command line modules has been written
  
 
</div>
 
</div>

Latest revision as of 11:03, 14 January 2008

Home < 2008 Winter Project Week:PythonSupport
Return to 2008_Winter_Project_Week
[1]
Python module


Key Investigators

  • Mario Negri Institute: Luca Antiga
  • UCSD: Bryan Smith

Objective

Python has a great potential in Slicer3. Its uses span:

  • Python command line modules (advantages: easy to write, access to Python libraries, don't need a compiler to write new modules)
  • matplotlib and scipy Python modules (they provide a matlab-like processing environment for images directly within Slicer).
  • Python as Slicer's scripting language (for automating tasks, programmatically access modules - this is Dan's new baby! - enabling staged processing)

Approach, Plan

In the project week, we plan to

  • solve building issues, check stability on different platforms
  • threading issues: modifying the MRML scene from Python command line modules in a thread-safe way
  • stabilize calling modules from Python, write example on staged processing
  • provide a Python equivalent to ScriptedModules
  • define what aspects will end up in the next release
  • propose a working set of Python command line modules (interact with Sonia's breakout session on Tuesday?) to be included in the next release
  • write documentation on how to write Python command line modules

Progress

January 2008 Project Week

  • Matplotlib with a Cairo backend is almost there
  • Python command line modules now work correctly (handling arguments multiple=true has been fixed)
  • A set of working Python command line modules has been committed
  • Scripted modules have been extended to Python, and a sample scripted module has been written
  • Meta-modules are now possible; the first meta-modules will be written soon

June 2007 Project Week

These are the results of the MIT project week (largely Dan's work)

  • Implemented Python Modules
    • Add search for Python in ModuleFactory
      • Can put .py files in the CommandLine Module path
    • Execute Python within Slicer
      • Full access to VTK, vtkTEEM, vtkITK, etc.
    • If the Python module provides an XML description, and an Execute function, will be added as a CommandLine Module
  • ToDo
    • Check-in (needs USE_PYTHON guards)
    • Progress reporting
    • Simplify the API
    • Automate command line parsing using XML description

Later on, after the meeting

  • command line parsing has been completed
  • Python scripting and Python modules have been made independent of Numpy
  • Python command line modules are now run in the main thread (allows interaction with MRML scene)
  • a set of Python command line modules has been written


Retrieved from "https://www.na-mic.org/w/index.php?title=2008_Winter_Project_Week:PythonSupport&oldid=21337"