2013 Project Week:Threaded SimpleITK Modules - Revision history

Blowekamp: /* Project Description */

2013-01-11T16:33:07Z

Project Description

Blowekamp: /* Preliminary Work */

2013-01-11T16:31:57Z

Preliminary Work

Blowekamp: /* Project Description */

2013-01-11T15:24:57Z

Project Description

Pieper: /* Project Description */

2012-12-24T23:09:40Z

Project Description

Pieper: /* Project Description */

2012-12-24T23:09:13Z

Project Description

Pieper: /* Project Description */

2012-12-18T22:31:47Z

Project Description

Pieper: /* Project Description */

2012-12-18T22:30:54Z

Project Description

Pieper: /* Preliminary Work */

2012-12-18T22:26:50Z

Preliminary Work

Pieper: Created page with 'NOTOC Image:PW-SLC2013.png|Projects List Image:yourimagehere.png| Image description ==Key Investigators== * Brad …'

2012-12-18T22:19:22Z

Created page with '__NOTOC__ <gallery> Image:PW-SLC2013.png|Projects List Image:yourimagehere.png| Image description </gallery> ==Key Investigators== * Brad …'

New page

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
Image:yourimagehere.png| Image description
</gallery>

==Key Investigators==

* Brad Lowekamp, NLM
* Steve Pieper, Isomics

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Support multi-threaded execution of SimpleITK filters.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Review other threading implementations in slicer, vtk, and itk to look for best practices
** Processing tasks (for CLIs) [https://github.com/Slicer/Slicer/blob/master/Base/Logic/vtkSlicerApplicationLogic.cxx#L312 in vtkSlicerApplicationLogic]
** ITK MultiThreader
** VTK MultiThreader
** [http://docs.python.org/2/library/threading.html Python threading]

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Progress here
</div>
</div>

== Preliminary Work ==

The example code below calls two different python functions from inside threads. One function calls the 'time.sleep' method, and one uses VTK to do some processing. As you can see from the output printed below, the VTK threads block, and a new thread is not started until the last one completes. On the other hand, the sleep based thread does return right away. The behavior is based on the [http://docs.python.org/2/glossary.html#term-global-interpreter-lock CPython global interpreter lock].

<pre>
import vtk
import threading
import Queue
import time, datetime
import os

class ThreadClass(threading.Thread):
def __init__(self, queue, work):
threading.Thread.__init__(self)
self.queue = queue
self.work = work

def run(self):
now = datetime.datetime.now()
self.queue.put( "start %s, time: %s" % (self.getName(), now) )
self.work()
now = datetime.datetime.now()
self.queue.put( "end %s, time: %s" % (self.getName(), now) )

def process():
e = vtk.vtkImageEllipsoidSource()
e.SetWholeExtent(0,300,0,300,0,300)
s = vtk.vtkImageGaussianSmooth()
s.SetInputConnection(e.GetOutputPort())
s.Update()

def sleep():
time.sleep(1)

for work,message in ((process,'vtk'), (sleep,'sleep')):
print ('threading test with %s:' % message)
threads = 3
queue = Queue.Queue()
for i in range(threads):
t = ThreadClass(queue,work)
t.start()
print('started:')

for i in range(2*threads):
print(queue.get())
print('finished\n')
</pre>

<pre>
#8 Slicer-superbuild $ ./VTK-build/bin/vtkpython /Users/pieper/Dropbox/hacks/threadVTK.py
threading test with vtk:
started:
start Thread-1, time: 2012-12-18 17:13:17.047282
end Thread-1, time: 2012-12-18 17:13:18.006989
start Thread-2, time: 2012-12-18 17:13:18.007318
end Thread-2, time: 2012-12-18 17:13:18.953446
start Thread-3, time: 2012-12-18 17:13:18.953762
end Thread-3, time: 2012-12-18 17:13:19.897673
finished

threading test with sleep:
started:
start Thread-4, time: 2012-12-18 17:13:19.898124
start Thread-5, time: 2012-12-18 17:13:19.898346
start Thread-6, time: 2012-12-18 17:13:19.898506
end Thread-4, time: 2012-12-18 17:13:20.899137
end Thread-6, time: 2012-12-18 17:13:20.899378
end Thread-5, time: 2012-12-18 17:13:20.899469
finished
</pre>

@@ Line 33: / Line 33: @@
 <h3>Progress</h3>
 * Able to patch SimpleITK to enable threading in all SimpleITK methods
-* Compiled patch into Slice and confirmed able to run ITK filters in background
+* Compiled patch into Slicer and confirmed able to run ITK filters in background
 **https://github.com/blowekamp/Slicer/tree/EnableSimpleITKThreads
 </div>
 </div>

← Older revision		Revision as of 22:30, 18 December 2012
Line 11:		Line 11:

	==Project Description==		==Project Description==
		+
		+	For some filters and segmentation algorithms written using SimpleITK in slicer, it would be nice to let them run in the background while letting slicer's main thread continue to process events. But the python byte code interpreter only allow a single path of python code to run at a time (see the discussion in the Preliminary Work section below). However since SimpleITK's implementation is in C++, it could release the GIL to allow the rest of the application to run while it processes.

	<div style="margin: 20px;">		<div style="margin: 20px;">

@@ Line 108: / Line 108: @@
 end Thread-6, time: 2012-12-18 17:13:20.899378
 end Thread-5, time: 2012-12-18 17:13:20.899469
 finished
 </pre>

@@ Line 32: / Line 32: @@
 <div style="width: 27%; float: left; padding-right: 3%;">
 <h3>Progress</h3>
-* Progress here
+* Able to patch SimpleITK to enable threading in all SimpleITK methods
 </div>
 </div>

@@ Line 12: / Line 12: @@
 ==Project Description==
-For some filters and segmentation algorithms written using SimpleITK in slicer it would be nice to let them run in the background while letting slicer's main thread continue to process events.  But the python byte code interpreter only allows a single path of python code to run at a time (see the discussion in the Preliminary Work section below).  However since SimpleITK's implementation is in C++, it could release the GIL to allow the rest of the application to run while it processes.
+For some filters and segmentation algorithms written using SimpleITK in slicer it would be nice to let them run in the background while letting slicer's main thread continue to process events.  But the python byte code interpreter only allows a single path of python code to run at a time (see the discussion in the Preliminary Work section below).  However since SimpleITK's implementation is in C++, it could release the GIL to allow the rest of the application to run while it processes.  Care must be taken when processing progress events or modifying variables that are shared with the main thread.
 <div style="margin: 20px;">
 <div style="width: 27%; float: left; padding-right: 3%;">

@@ Line 18: / Line 18: @@
 <h3>Objective</h3>
 * Support multi-threaded execution of SimpleITK filters.
 </div>
 <div style="width: 27%; float: left; padding-right: 3%;">

@@ Line 34: / Line 34: @@
 == Preliminary Work ==
-The example code below calls two different python functions from inside threads.  One function calls the 'time.sleep' method, and one uses VTK to do some processing.  As you can see from the output printed below, the VTK threads block, and a new thread is not started until the last one completes.  On the other hand, the sleep based thread does return right away.  The behavior is based on the [http://docs.python.org/2/glossary.html#term-global-interpreter-lock CPython global interpreter lock].
+The example code below calls two different python functions from inside threads.  One function calls the 'time.sleep' method, and one uses VTK to do some processing.  As you can see from the output printed below, the VTK threads block, and a new thread is not started until the last one completes.  On the other hand, the sleep based thread does return right away.  The behavior is based on the [http://docs.python.org/2/glossary.html#term-global-interpreter-lock CPython global interpreter lock].  The topic was [http://web.archiveorange.com/archive/v/aysypJwvM9H8MY8BtpyP discussed in detail] on the vtk developers list back in 2005.
 <pre>

2013 Project Week:Threaded SimpleITK Modules - Revision history

Blowekamp: /* Project Description */

Blowekamp: /* Preliminary Work */

Blowekamp: /* Project Description */

Pieper: /* Project Description */

Pieper: /* Project Description */

Pieper: /* Project Description */

Pieper: /* Project Description */

Pieper: /* Preliminary Work */

Pieper: Created page with '__NOTOC__ Image:PW-SLC2013.png|Projects List Image:yourimagehere.png| Image description ==Key Investigators== * Brad …'

Pieper: Created page with 'NOTOC Image:PW-SLC2013.png|Projects List Image:yourimagehere.png| Image description ==Key Investigators== * Brad …'