pyphant-devel Mailing List for Pyphant

Status: Alpha

Brought to you by: liehr, sgwissinfo, zklaus

pyphant-devel — Discussions about the inner workings and future developments.

You can subscribe to this list here.

2007	_Jan	_Feb	_Mar	_Apr	_May	_Jun	_Jul	_Aug	_Sep	_Oct (13)	_Nov (50)	_Dec (40)
2008	_Jan (49)	_Feb (72)	_Mar (18)	_Apr (27)	_May (40)	_Jun (52)	_Jul (26)	_Aug (8)	_Sep (12)	_Oct (26)	_Nov (13)	_Dec (14)
2009	_Jan (13)	_Feb (7)	_Mar (8)	_Apr (11)	_May (4)	_Jun (2)	_Jul (7)	_Aug (1)	_Sep (3)	_Oct	_Nov (1)	_Dec (1)
2010	_Jan (1)	_Feb (8)	_Mar (3)	_Apr (9)	_May (16)	_Jun (8)	_Jul (7)	_Aug	_Sep (1)	_Oct	_Nov	_Dec
2011	_Jan	_Feb	_Mar	_Apr	_May (1)	_Jun	_Jul	_Aug	_Sep	_Oct	_Nov (6)	_Dec (12)

Flat | Threaded

1 2 3 .. 24 > >> (Page 1 of 24)

[Pyphant-devel] SF.net SVN: pyphant:[718] branches/pyphant-1.0/

From: <ah...@us...> - 2011-12-09 09:45:36

Revision: 718
          http://pyphant.svn.sourceforge.net/pyphant/?rev=718&view=rev
Author:   aheld84
Date:     2011-12-09 09:45:30 +0000 (Fri, 09 Dec 2011)
Log Message:
-----------
cloned pyphant-1.0b1

Added Paths:
-----------
    branches/pyphant-1.0/

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Pyphant-devel] SF.net SVN: pyphant:[717] branches/pyphant-0.8/

From: <ah...@us...> - 2011-12-09 09:42:39

Revision: 717
          http://pyphant.svn.sourceforge.net/pyphant/?rev=717&view=rev
Author:   aheld84
Date:     2011-12-09 09:42:33 +0000 (Fri, 09 Dec 2011)
Log Message:
-----------
cloned pyphant-0.8a2

Added Paths:
-----------
    branches/pyphant-0.8/

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Pyphant-devel] SF.net SVN: pyphant:[716] tags/pyphant-0.8a1/src

From: <ah...@us...> - 2011-12-08 17:18:01

Revision: 716
          http://pyphant.svn.sourceforge.net/pyphant/?rev=716&view=rev
Author:   aheld84
Date:     2011-12-08 17:17:55 +0000 (Thu, 08 Dec 2011)
Log Message:
-----------
Merge commit '38194039bb04c97cb0a7962c8b0427e7f54f6b85' into svn-tag-pyphant-0.8a1

* commit '38194039bb04c97cb0a7962c8b0427e7f54f6b85':
  Configured release (version numbering, no .dev tagging).

Modified Paths:
--------------
    tags/pyphant-0.8a1/src/pyphant/setup.cfg
    tags/pyphant-0.8a1/src/pyphant/setup.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/setup.cfg
    tags/pyphant-0.8a1/src/workers/ImageProcessing/setup.py
    tags/pyphant-0.8a1/src/workers/OSC/setup.cfg
    tags/pyphant-0.8a1/src/workers/OSC/setup.py
    tags/pyphant-0.8a1/src/workers/Statistics/setup.cfg
    tags/pyphant-0.8a1/src/workers/Statistics/setup.py
    tags/pyphant-0.8a1/src/workers/fmfile/setup.cfg
    tags/pyphant-0.8a1/src/workers/fmfile/setup.py
    tags/pyphant-0.8a1/src/workers/tools/setup.cfg
    tags/pyphant-0.8a1/src/workers/tools/setup.py

Modified: tags/pyphant-0.8a1/src/pyphant/setup.cfg
===================================================================
--- tags/pyphant-0.8a1/src/pyphant/setup.cfg	2011-12-08 17:15:44 UTC (rev 715)
+++ tags/pyphant-0.8a1/src/pyphant/setup.cfg	2011-12-08 17:17:55 UTC (rev 716)
@@ -1,4 +1 @@
 # -*- coding: utf-8 -*-
-[egg_info]
-tag_build = .dev
-tag_svn_revision = 1

Modified: tags/pyphant-0.8a1/src/pyphant/setup.py
===================================================================
--- tags/pyphant-0.8a1/src/pyphant/setup.py	2011-12-08 17:15:44 UTC (rev 715)
+++ tags/pyphant-0.8a1/src/pyphant/setup.py	2011-12-08 17:17:55 UTC (rev 716)
@@ -4,7 +4,7 @@
 __id__ = '$Id: $'
 __revision__ = '$Revision: 25 $'
 
-VERSION = '0.5'
+VERSION = '0.8a1'
 
 
 from setuptools import setup, find_packages

Modified: tags/pyphant-0.8a1/src/workers/ImageProcessing/setup.cfg
===================================================================
--- tags/pyphant-0.8a1/src/workers/ImageProcessing/setup.cfg	2011-12-08 17:15:44 UTC (rev 715)
+++ tags/pyphant-0.8a1/src/workers/ImageProcessing/setup.cfg	2011-12-08 17:17:55 UTC (rev 716)
@@ -1,4 +1 @@
 # -*- coding: utf-8 -*-
-[egg_info]
-tag_build = .dev
-tag_svn_revision = 1

Modified: tags/pyphant-0.8a1/src/workers/ImageProcessing/setup.py
===================================================================
--- tags/pyphant-0.8a1/src/workers/ImageProcessing/setup.py	2011-12-08 17:15:44 UTC (rev 715)
+++ tags/pyphant-0.8a1/src/workers/ImageProcessing/setup.py	2011-12-08 17:17:55 UTC (rev 716)
@@ -14,7 +14,7 @@
 __id__ = '$Id$'
 __revision__ = '$Revision: 25 $'
 
-VERSION = '0.1'
+VERSION = '0.8a1'
 
 import setuptools
 

Modified: tags/pyphant-0.8a1/src/workers/OSC/setup.cfg
===================================================================
--- tags/pyphant-0.8a1/src/workers/OSC/setup.cfg	2011-12-08 17:15:44 UTC (rev 715)
+++ tags/pyphant-0.8a1/src/workers/OSC/setup.cfg	2011-12-08 17:17:55 UTC (rev 716)
@@ -1,4 +1 @@
 # -*- coding: utf-8 -*-
-[egg_info]
-tag_build = .dev
-tag_svn_revision = 1

Modified: tags/pyphant-0.8a1/src/workers/OSC/setup.py
===================================================================
--- tags/pyphant-0.8a1/src/workers/OSC/setup.py	2011-12-08 17:15:44 UTC (rev 715)
+++ tags/pyphant-0.8a1/src/workers/OSC/setup.py	2011-12-08 17:17:55 UTC (rev 716)
@@ -11,7 +11,7 @@
 __id__ = '$Id$'
 __revision__ = '$Revision: 25 $'
 
-VERSION = '0.1'
+VERSION = '0.8a1'
 
 import setuptools
 

Modified: tags/pyphant-0.8a1/src/workers/Statistics/setup.cfg
===================================================================
--- tags/pyphant-0.8a1/src/workers/Statistics/setup.cfg	2011-12-08 17:15:44 UTC (rev 715)
+++ tags/pyphant-0.8a1/src/workers/Statistics/setup.cfg	2011-12-08 17:17:55 UTC (rev 716)
@@ -1,4 +1 @@
 # -*- coding: utf-8 -*-
-[egg_info]
-tag_build = .dev
-tag_svn_revision = 1

Modified: tags/pyphant-0.8a1/src/workers/Statistics/setup.py
===================================================================
--- tags/pyphant-0.8a1/src/workers/Statistics/setup.py	2011-12-08 17:15:44 UTC (rev 715)
+++ tags/pyphant-0.8a1/src/workers/Statistics/setup.py	2011-12-08 17:17:55 UTC (rev 716)
@@ -14,7 +14,7 @@
 __id__ = '$Id$'
 __revision__ = '$Revision: 25 $'
 
-VERSION = '0.1'
+VERSION = '0.8a1'
 
 import setuptools
 

Modified: tags/pyphant-0.8a1/src/workers/fmfile/setup.cfg
===================================================================
--- tags/pyphant-0.8a1/src/workers/fmfile/setup.cfg	2011-12-08 17:15:44 UTC (rev 715)
+++ tags/pyphant-0.8a1/src/workers/fmfile/setup.cfg	2011-12-08 17:17:55 UTC (rev 716)
@@ -1,4 +1 @@
 # -*- coding: utf-8 -*-
-[egg_info]
-tag_build = .dev
-tag_svn_revision = 1

Modified: tags/pyphant-0.8a1/src/workers/fmfile/setup.py
===================================================================
--- tags/pyphant-0.8a1/src/workers/fmfile/setup.py	2011-12-08 17:15:44 UTC (rev 715)
+++ tags/pyphant-0.8a1/src/workers/fmfile/setup.py	2011-12-08 17:17:55 UTC (rev 716)
@@ -11,7 +11,7 @@
 __id__ = '$Id$'
 __revision__ = '$Revision: 25 $'
 
-VERSION = '0.1'
+VERSION = '0.8a1'
 
 import setuptools
 

Modified: tags/pyphant-0.8a1/src/workers/tools/setup.cfg
===================================================================
--- tags/pyphant-0.8a1/src/workers/tools/setup.cfg	2011-12-08 17:15:44 UTC (rev 715)
+++ tags/pyphant-0.8a1/src/workers/tools/setup.cfg	2011-12-08 17:17:55 UTC (rev 716)
@@ -1,4 +1 @@
 # -*- coding: utf-8 -*-
-[egg_info]
-tag_build = .dev
-tag_svn_revision = 1

Modified: tags/pyphant-0.8a1/src/workers/tools/setup.py
===================================================================
--- tags/pyphant-0.8a1/src/workers/tools/setup.py	2011-12-08 17:15:44 UTC (rev 715)
+++ tags/pyphant-0.8a1/src/workers/tools/setup.py	2011-12-08 17:17:55 UTC (rev 716)
@@ -11,7 +11,7 @@
 __id__ = '$Id$'
 __revision__ = '$Revision: 25 $'
 
-VERSION = '0.1'
+VERSION = '0.8a1'
 
 import setuptools
 
@@ -20,7 +20,7 @@
     version = VERSION,
     author = __author__,
     description = __doc__,
-    install_requires=['pyphant>=0.4alpha3'],
+    install_requires=['pyphant>=0.8a1'],
     packages = ['tools'],
     entry_points = """
     [pyphant.workers]

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Pyphant-devel] SF.net SVN: pyphant:[715] tags/pyphant-0.8a1/

From: <ah...@us...> - 2011-12-08 17:15:53

Revision: 715
          http://pyphant.svn.sourceforge.net/pyphant/?rev=715&view=rev
Author:   aheld84
Date:     2011-12-08 17:15:44 +0000 (Thu, 08 Dec 2011)
Log Message:
-----------
cloned r699

Revision Links:
--------------
    http://pyphant.svn.sourceforge.net/pyphant/?rev=699&view=rev

Added Paths:
-----------
    tags/pyphant-0.8a1/

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Pyphant-devel] SF.net SVN: pyphant:[714] tags/pyphant-0.8a2/src

From: <ah...@us...> - 2011-12-08 17:12:44

Revision: 714
          http://pyphant.svn.sourceforge.net/pyphant/?rev=714&view=rev
Author:   aheld84
Date:     2011-12-08 17:12:37 +0000 (Thu, 08 Dec 2011)
Log Message:
-----------
Merge branch 'v0.8' into svn-tag-pyphant-0.8a2

* v0.8:
  Configured release for v0.8a2
  Fix: Bin centers of Histogram worker
  Fix: wxPyphant hangs upon exiting
  Configured release (version numbering, no .dev tagging).

Modified Paths:
--------------
    tags/pyphant-0.8a2/src/pyphant/pyphant/wxgui2/wxPyphantApplication.py
    tags/pyphant-0.8a2/src/pyphant/setup.py
    tags/pyphant-0.8a2/src/workers/ImageProcessing/setup.py
    tags/pyphant-0.8a2/src/workers/OSC/setup.py
    tags/pyphant-0.8a2/src/workers/Statistics/Statistics/Histogram.py
    tags/pyphant-0.8a2/src/workers/Statistics/setup.py
    tags/pyphant-0.8a2/src/workers/fmfile/setup.py
    tags/pyphant-0.8a2/src/workers/tools/setup.py

Removed Paths:
-------------
    tags/pyphant-0.8a2/src/pyphant/setup.cfg
    tags/pyphant-0.8a2/src/workers/ImageProcessing/setup.cfg
    tags/pyphant-0.8a2/src/workers/OSC/setup.cfg
    tags/pyphant-0.8a2/src/workers/Statistics/setup.cfg
    tags/pyphant-0.8a2/src/workers/fmfile/setup.cfg
    tags/pyphant-0.8a2/src/workers/tools/setup.cfg

Modified: tags/pyphant-0.8a2/src/pyphant/pyphant/wxgui2/wxPyphantApplication.py
===================================================================
--- tags/pyphant-0.8a2/src/pyphant/pyphant/wxgui2/wxPyphantApplication.py	2011-12-08 17:05:59 UTC (rev 713)
+++ tags/pyphant-0.8a2/src/pyphant/pyphant/wxgui2/wxPyphantApplication.py	2011-12-08 17:12:37 UTC (rev 714)
@@ -35,7 +35,7 @@
 
 __id__ = "$Id$"
 __author__ = "$Author$"
-__version__ = "Sprint"
+__version__ = "0.8a2"
 # $Source$
 
 import os, os.path, pkg_resources
@@ -614,9 +614,10 @@
         # wxPyphantFrame is the main frame.
         self.parent._frame = wxPyphantFrame(self.parent)
         self.parent._frame.Show()
-                
+
         # The program will freeze without this line.
         evt.Skip()  # Make sure the default handler runs too...
+        self.Destroy()
 
 
 import optparse

Deleted: tags/pyphant-0.8a2/src/pyphant/setup.cfg
===================================================================
--- tags/pyphant-0.8a2/src/pyphant/setup.cfg	2011-12-08 17:05:59 UTC (rev 713)
+++ tags/pyphant-0.8a2/src/pyphant/setup.cfg	2011-12-08 17:12:37 UTC (rev 714)
@@ -1,4 +0,0 @@
-# -*- coding: utf-8 -*-
-[egg_info]
-tag_build = .dev
-tag_svn_revision = 1

Modified: tags/pyphant-0.8a2/src/pyphant/setup.py
===================================================================
--- tags/pyphant-0.8a2/src/pyphant/setup.py	2011-12-08 17:05:59 UTC (rev 713)
+++ tags/pyphant-0.8a2/src/pyphant/setup.py	2011-12-08 17:12:37 UTC (rev 714)
@@ -4,33 +4,38 @@
 __id__ = '$Id: $'
 __revision__ = '$Revision: 25 $'
 
-VERSION = '0.5'
+VERSION = '0.8a2'
 
 
 from setuptools import setup, find_packages
 
-setup( name='pyphant',
-       version = VERSION,
-       description='Workflow modelling app',
-       author='Klaus Zimmermann, Andreas W. Liehr',
-       author_email='kla...@fm...',
-       maintainer='Klaus Zimmermann',
-       maintainer_email='zk...@so...',
-       license = "BSD",
-       url='http://pyphant.sourceforge.net/',
-       install_requires=['sogl>=0.2.0',
-                         'egenix-mx-base',
-			 'paste',
-                         'simplejson',
-                         ## The following are required, but currently not setuptools enabled.
-                         #'ScientificPython>=2.6',
-                         #'matplotlib>=0.90.1',
-                         #'scipy>=0.5.2',
-                         #'tables>=1.4',
-                         #'wxPython>=2.6.3.2',
-                         ],
-       packages = find_packages(),
-       entry_points={'gui_scripts':['wxPyphant = pyphant.wxgui2.wxPyphantApplication:startWxPyphant']},
-       include_package_data = True,
-       test_suite = 'pyphant.tests'
-       )
+setup(
+    name='pyphant',
+    version=VERSION,
+    description='Workflow modelling app',
+    author='Alexander Held, Andreas W. Liehr, Klaus Zimmermann',
+    author_email='ale...@fm...',
+    maintainer='Alexander Held',
+    maintainer_email='ale...@fm...',
+    license="BSD",
+    url='http://pyphant.sourceforge.net/',
+    install_requires=[
+        'sogl>=0.2.0',
+        'paste',
+        'simplejson',
+        ## The following are required,
+        ## but currently not setuptools enabled.
+        #'ScientificPython',
+        #'matplotlib',
+        #'scipy',
+        #'tables',
+        #'wxPython',
+        #'egenix-mx-base',
+        ],
+    packages=find_packages(),
+    entry_points={'gui_scripts':[
+        'wxPyphant = pyphant.wxgui2.wxPyphantApplication:startWxPyphant'
+        ]},
+    include_package_data=True,
+    test_suite='pyphant.tests'
+    )

Deleted: tags/pyphant-0.8a2/src/workers/ImageProcessing/setup.cfg
===================================================================
--- tags/pyphant-0.8a2/src/workers/ImageProcessing/setup.cfg	2011-12-08 17:05:59 UTC (rev 713)
+++ tags/pyphant-0.8a2/src/workers/ImageProcessing/setup.cfg	2011-12-08 17:12:37 UTC (rev 714)
@@ -1,4 +0,0 @@
-# -*- coding: utf-8 -*-
-[egg_info]
-tag_build = .dev
-tag_svn_revision = 1

Modified: tags/pyphant-0.8a2/src/workers/ImageProcessing/setup.py
===================================================================
--- tags/pyphant-0.8a2/src/workers/ImageProcessing/setup.py	2011-12-08 17:05:59 UTC (rev 713)
+++ tags/pyphant-0.8a2/src/workers/ImageProcessing/setup.py	2011-12-08 17:12:37 UTC (rev 714)
@@ -9,25 +9,29 @@
 http://pyphant.sourceforge.net for more information.
 """
 
-__author__ = "Klaus Zimmermann, Andreas W. Liehr"
+__author__ = "Alexander Held, Andreas W. Liehr, Klaus Zimmermann"
 
 __id__ = '$Id$'
 __revision__ = '$Revision: 25 $'
 
-VERSION = '0.1'
+VERSION = '0.8a2'
 
 import setuptools
 
 setuptools.setup(
-    name = "pyphant.imageprocessing",
-    version = VERSION,
-    author = __author__,
-    description = __doc__,
-    install_requires=['pyphant>=0.4alpha3'],
-    packages = ['ImageProcessing'],
-    entry_points = """
+    name="pyphant.imageprocessing",
+    version=VERSION,
+    author=__author__,
+    author_email='ale...@fm...',
+    maintainer='Alexander Held',
+    maintainer_email='ale...@fm...',
+    license="BSD",
+    description=__doc__,
+    install_requires=['pyphant>=0.8a2'],
+    packages=['ImageProcessing'],
+    entry_points="""
     [pyphant.workers]
     myeentry = ImageProcessing
     """,
-    test_suite = 'ImageProcessing.tests')
-
+    test_suite='ImageProcessing.tests'
+    )

Deleted: tags/pyphant-0.8a2/src/workers/OSC/setup.cfg
===================================================================
--- tags/pyphant-0.8a2/src/workers/OSC/setup.cfg	2011-12-08 17:05:59 UTC (rev 713)
+++ tags/pyphant-0.8a2/src/workers/OSC/setup.cfg	2011-12-08 17:12:37 UTC (rev 714)
@@ -1,4 +0,0 @@
-# -*- coding: utf-8 -*-
-[egg_info]
-tag_build = .dev
-tag_svn_revision = 1

Modified: tags/pyphant-0.8a2/src/workers/OSC/setup.py
===================================================================
--- tags/pyphant-0.8a2/src/workers/OSC/setup.py	2011-12-08 17:05:59 UTC (rev 713)
+++ tags/pyphant-0.8a2/src/workers/OSC/setup.py	2011-12-08 17:12:37 UTC (rev 714)
@@ -6,24 +6,29 @@
 Visit http://pyphant.sourceforge.net for more information.
 """
 
-__author__ = "Klaus Zimmermann, Andreas W. Liehr"
+__author__ = "Andreas W. Liehr, Klaus Zimmermann"
 
 __id__ = '$Id$'
 __revision__ = '$Revision: 25 $'
 
-VERSION = '0.1'
+VERSION = '0.8a2'
 
 import setuptools
 
 setuptools.setup(
-    name = "pyphant.osc",
-    version = VERSION,
-    author = __author__,
-    description = __doc__,
-    install_requires=['pyphant>=0.4alpha3'],
-    packages = ['OSC'],
-    entry_points = """
+    name="pyphant.osc",
+    version=VERSION,
+    author=__author__,
+    author_email='kla...@fm...',
+    maintainer='Klaus Zimmermann',
+    maintainer_email='kla...@fm...',
+    license="BSD",
+    description=__doc__,
+    install_requires=['pyphant>=0.8a2'],
+    packages=['OSC'],
+    entry_points="""
     [pyphant.workers]
     myeentry = OSC
     """,
-    test_suite='OSC.tests')
+    test_suite='OSC.tests'
+    )

Modified: tags/pyphant-0.8a2/src/workers/Statistics/Statistics/Histogram.py
===================================================================
--- tags/pyphant-0.8a2/src/workers/Statistics/Statistics/Histogram.py	2011-12-08 17:05:59 UTC (rev 713)
+++ tags/pyphant-0.8a2/src/workers/Statistics/Statistics/Histogram.py	2011-12-08 17:12:37 UTC (rev 714)
@@ -42,31 +42,33 @@
 # $Source$
 
 from pyphant.core import (Connectors, DataContainer,
-                          Param, Worker)
-import scipy, scipy.stats
+                          Worker)
 import numpy
 
 class Histogram(Worker.Worker):
     API = 2
     VERSION = 1
     REVISION = "$Revision$"[11:-1]
-    name = u"Histogram"
+    name = "Histogram"
     _sockets=[("vector", Connectors.TYPE_IMAGE)]
     _params = [("bins", "Bins", 10, None)]
 
     @Worker.plug(Connectors.TYPE_IMAGE)
     def calculateHistogram(self, vector, subscriber=0):
         bins = self.paramBins.value
+        assert bins >= 2
+        # numpy 1.3
         try:
             histo = numpy.histogram(vector.data.flat, bins, new=True,
                                     range=(numpy.floor(vector.data.min()),
                                            numpy.ceil(vector.data.max())))
-            binCenters = histo[1][:-1]+(numpy.diff(histo[1])/2.0)
+        # newer numpy versions
         except TypeError:
             histo = numpy.histogram(vector.data.flat, bins,
                                     range=(numpy.floor(vector.data.min()),
                                            numpy.ceil(vector.data.max())))
-            binCenters = histo[1]+((histo[1][1]-histo[1][0])/2.0)
+        binCenters = histo[1][:-1] + (numpy.diff(histo[1]) / 2.0)
+        assert len(binCenters) == bins == len(histo[0])
         xdim = DataContainer.FieldContainer(binCenters, vector.unit,
                                             longname=vector.longname,
                                             shortname=vector.shortname)

Deleted: tags/pyphant-0.8a2/src/workers/Statistics/setup.cfg
===================================================================
--- tags/pyphant-0.8a2/src/workers/Statistics/setup.cfg	2011-12-08 17:05:59 UTC (rev 713)
+++ tags/pyphant-0.8a2/src/workers/Statistics/setup.cfg	2011-12-08 17:12:37 UTC (rev 714)
@@ -1,4 +0,0 @@
-# -*- coding: utf-8 -*-
-[egg_info]
-tag_build = .dev
-tag_svn_revision = 1

Modified: tags/pyphant-0.8a2/src/workers/Statistics/setup.py
===================================================================
--- tags/pyphant-0.8a2/src/workers/Statistics/setup.py	2011-12-08 17:05:59 UTC (rev 713)
+++ tags/pyphant-0.8a2/src/workers/Statistics/setup.py	2011-12-08 17:12:37 UTC (rev 714)
@@ -2,32 +2,36 @@
 # -*- coding: utf-8 -*-
 
 """
-Pyphant ImageProcessing toolbox
-This is the ImageProcessing toolbox, that serves as an example off a
-toolbox for the Pyphant framework. In order to use it you must have
+Pyphant Statistics toolbox
+This is the Statistics toolbox, that provides workers
+for the Pyphant framework. In order to use it you must have
 the Pyphant framework installed first. Visit
 http://pyphant.sourceforge.net for more information.
 """
 
-__author__ = "Klaus Zimmermann, Andreas W. Liehr"
+__author__ = "Alexander Held, Andreas W. Liehr, Klaus Zimmermann"
 
 __id__ = '$Id$'
 __revision__ = '$Revision: 25 $'
 
-VERSION = '0.1'
+VERSION = '0.8a2'
 
 import setuptools
 
 setuptools.setup(
-    name = "pyphant.statistics",
-    version = VERSION,
-    author = __author__,
-    description = __doc__,
-    install_requires=['pyphant>=0.4alpha3'],
-    packages = ['Statistics'],
-    entry_points = """
+    name="pyphant.statistics",
+    version=VERSION,
+    author=__author__,
+    author_email='ale...@fm...',
+    maintainer='Alexander Held',
+    maintainer_email='ale...@fm...',
+    license="BSD",
+    description=__doc__,
+    install_requires=['pyphant>=0.8a2'],
+    packages=['Statistics'],
+    entry_points="""
     [pyphant.workers]
     myeentry = Statistics
     """,
-    test_suite = 'Statistics.tests')
-
+    test_suite='Statistics.tests'
+    )

Deleted: tags/pyphant-0.8a2/src/workers/fmfile/setup.cfg
===================================================================
--- tags/pyphant-0.8a2/src/workers/fmfile/setup.cfg	2011-12-08 17:05:59 UTC (rev 713)
+++ tags/pyphant-0.8a2/src/workers/fmfile/setup.cfg	2011-12-08 17:12:37 UTC (rev 714)
@@ -1,4 +0,0 @@
-# -*- coding: utf-8 -*-
-[egg_info]
-tag_build = .dev
-tag_svn_revision = 1

Modified: tags/pyphant-0.8a2/src/workers/fmfile/setup.py
===================================================================
--- tags/pyphant-0.8a2/src/workers/fmfile/setup.py	2011-12-08 17:05:59 UTC (rev 713)
+++ tags/pyphant-0.8a2/src/workers/fmfile/setup.py	2011-12-08 17:12:37 UTC (rev 714)
@@ -6,28 +6,35 @@
 Visit http://pyphant.sourceforge.net for more information.
 """
 
-__author__ = "Klaus Zimmermann, Andreas W. Liehr"
+__author__ = "Alexander Held, Andreas W. Liehr, Rolf Wuerdemann, " +\
+             "Klaus Zimmermann"
 
 __id__ = '$Id$'
 __revision__ = '$Revision: 25 $'
 
-VERSION = '0.1'
+VERSION = '0.8a2'
 
 import setuptools
 
 setuptools.setup(
-    name = "pyphant.fmf",
-    version = VERSION,
-    author = __author__,
-    description = __doc__,
-    install_requires=['pyphant>=0.4alpha3',
-                      'ConfigObj'
-                      ],
-    packages = ['fmfile'],
-    entry_points = """
+    name="pyphant.fmf",
+    version=VERSION,
+    author=__author__,
+    author_email='ale...@fm...',
+    maintainer='Alexander Held',
+    maintainer_email='ale...@fm...',
+    license="BSD",
+    description=__doc__,
+    install_requires=[
+        'pyphant>=0.8a2',
+        'ConfigObj'
+        ],
+    packages=['fmfile'],
+    entry_points="""
     [pyphant.workers]
     myeentry = fmfile
     [pyphant.visualizers]
     pil.image = fmfile.FMFWriter:FMFWriter
     """,
-    test_suite='fmfile.tests')
+    test_suite='fmfile.tests'
+    )

Deleted: tags/pyphant-0.8a2/src/workers/tools/setup.cfg
===================================================================
--- tags/pyphant-0.8a2/src/workers/tools/setup.cfg	2011-12-08 17:05:59 UTC (rev 713)
+++ tags/pyphant-0.8a2/src/workers/tools/setup.cfg	2011-12-08 17:12:37 UTC (rev 714)
@@ -1,4 +0,0 @@
-# -*- coding: utf-8 -*-
-[egg_info]
-tag_build = .dev
-tag_svn_revision = 1

Modified: tags/pyphant-0.8a2/src/workers/tools/setup.py
===================================================================
--- tags/pyphant-0.8a2/src/workers/tools/setup.py	2011-12-08 17:05:59 UTC (rev 713)
+++ tags/pyphant-0.8a2/src/workers/tools/setup.py	2011-12-08 17:12:37 UTC (rev 714)
@@ -2,28 +2,33 @@
 # -*- coding: utf-8 -*-
 
 """
-Pyphant Organic Solar Cells toolbox
+Pyphant Tools toolbox
 Visit http://pyphant.sourceforge.net for more information.
 """
 
-__author__ = "Klaus Zimmermann, Kai Kaminski"
+__author__ = "Alexander Held, Klaus Zimmermann"
 
 __id__ = '$Id$'
 __revision__ = '$Revision: 25 $'
 
-VERSION = '0.1'
+VERSION = '0.8a2'
 
 import setuptools
 
 setuptools.setup(
-    name = "pyphant.tools",
-    version = VERSION,
-    author = __author__,
-    description = __doc__,
-    install_requires=['pyphant>=0.4alpha3'],
-    packages = ['tools'],
-    entry_points = """
+    name="pyphant.tools",
+    version=VERSION,
+    author=__author__,
+    author_email='ale...@fm...',
+    maintainer='Alexander Held',
+    maintainer_email='ale...@fm...',
+    license="BSD",
+    description=__doc__,
+    install_requires=['pyphant>=0.8a2'],
+    packages=['tools'],
+    entry_points="""
     [pyphant.workers]
     myeentry = tools
     """,
-    test_suite='tools.tests')
+    test_suite='tools.tests'
+    )

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Pyphant-devel] SF.net SVN: pyphant:[713] tags/pyphant-0.8a2/

From: <ah...@us...> - 2011-12-08 17:06:10

Revision: 713
          http://pyphant.svn.sourceforge.net/pyphant/?rev=713&view=rev
Author:   aheld84
Date:     2011-12-08 17:05:59 +0000 (Thu, 08 Dec 2011)
Log Message:
-----------
cloned r699

Revision Links:
--------------
    http://pyphant.svn.sourceforge.net/pyphant/?rev=699&view=rev

Added Paths:
-----------
    tags/pyphant-0.8a2/

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Pyphant-devel] SF.net SVN: pyphant:[712] tags/pyphant-0.8a1/

From: <ah...@us...> - 2011-12-02 16:19:59

Revision: 712
          http://pyphant.svn.sourceforge.net/pyphant/?rev=712&view=rev
Author:   aheld84
Date:     2011-12-02 16:19:53 +0000 (Fri, 02 Dec 2011)
Log Message:
-----------
Remove pyphant-0.8a1 tag created by git

git does not allow to branch from anything else than
trunk, so pyphant-0.8a1 is a copy and no link, which
is bad.
pyphant-0.8a1 should be tagged using pure svn

Removed Paths:
-------------
    tags/pyphant-0.8a1/

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Pyphant-devel] SF.net SVN: pyphant:[711] tags/pyphant-0.8a1

From: <ah...@us...> - 2011-12-02 16:10:10

Revision: 711
          http://pyphant.svn.sourceforge.net/pyphant/?rev=711&view=rev
Author:   aheld84
Date:     2011-12-02 16:09:56 +0000 (Fri, 02 Dec 2011)
Log Message:
-----------
Hack: Recreated pyphant 0.8a1

Added Paths:
-----------
    tags/pyphant-0.8a1/.gitignore
    tags/pyphant-0.8a1/.project
    tags/pyphant-0.8a1/.pydevproject
    tags/pyphant-0.8a1/doc/demo/README
    tags/pyphant-0.8a1/doc/demo/Sim_abs_210nm.fmf
    tags/pyphant-0.8a1/doc/demo/demo.h5
    tags/pyphant-0.8a1/doc/demo/demo.png
    tags/pyphant-0.8a1/doc/demo/demoFMF.py
    tags/pyphant-0.8a1/doc/demo/example.fmf
    tags/pyphant-0.8a1/doc/demo/example_delimiter.fmf
    tags/pyphant-0.8a1/doc/demo/example_delimiter2.fmf
    tags/pyphant-0.8a1/doc/demo/features.png
    tags/pyphant-0.8a1/doc/demo/fmf2h5.h5
    tags/pyphant-0.8a1/doc/demo/fmf2h5.py
    tags/pyphant-0.8a1/doc/demo/plotter.py
    tags/pyphant-0.8a1/doc/demo/pyphant-shade-Information-Analysis-Framework.png
    tags/pyphant-0.8a1/doc/demo/readfmf.py
    tags/pyphant-0.8a1/doc/demo/simpleScripting.py
    tags/pyphant-0.8a1/doc/demo/viewOSC.py
    tags/pyphant-0.8a1/doc/demo/visualizeImage.py
    tags/pyphant-0.8a1/doc/grammarDoc.py
    tags/pyphant-0.8a1/doc/grammarDoc.txt
    tags/pyphant-0.8a1/doc/knowledge-ideas.org
    tags/pyphant-0.8a1/doc/logo/mklogo.py
    tags/pyphant-0.8a1/doc/logo/pyphant-shade-Information-Analysis-Framework-ARTS-small.png
    tags/pyphant-0.8a1/doc/logo/pyphantLogo.py
    tags/pyphant-0.8a1/doc/test_numpy1.0.1Bug.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/__init__.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/cli/createExecutionOrder.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/cli/demo.h5
    tags/pyphant-0.8a1/src/pyphant/pyphant/cli/demo.png
    tags/pyphant-0.8a1/src/pyphant/pyphant/cli/pyphant_exec.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/cli/simpleCLI.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/CompositeWorker.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/Connectors.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/DataContainer.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/EventDispatcher.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/FieldContainer.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/H5FileHandler.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/Helpers.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/KnowledgeManager.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/KnowledgeNode.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/Param.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/PyTablesPersister.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/RoutingHTTPServer.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/SQLiteWrapper.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/UpdateManager.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/WebInterface.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/Worker.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/WorkerRegistry.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/XMLHandler.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/ZStackManager.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/__init__.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/bottle.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/singletonmixin.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/quantities/ParseQuantities.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/quantities/PhysicalQuantities.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/quantities/__init__.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/TestChart.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/TestCompositeWorker.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/TestDataContainer.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/TestEventDispatcher.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/TestH5FileHandler.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/TestImageVisualizer.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/TestKnowledgeManager.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/TestKnowledgeNode.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/TestParam.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/TestParseQuantities.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/TestPyTablesPersister.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/TestQuantities.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/TestSQLiteWrapper.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/TestZStacks.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/__init__.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/resources/zstack/TestZStack_z00.tif
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/resources/zstack/TestZStack_z01.tif
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/resources/zstack/TestZStack_z02.tif
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/resources/zstack/TestZStack_z03.tif
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/resources/zstack/TestZStack_z04.tif
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/resources/zstack/TestZStack_z05.tif
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/resources/zstack/TestZStack_z06.tif
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/resources/zstack/_meta.xml
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/resources/zstack/single_meta.xml
    tags/pyphant-0.8a1/src/pyphant/pyphant/visualizers/Chart.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/visualizers/ConfigurablePlot.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/visualizers/External.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/visualizers/ImageVisualizer.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/visualizers/KMVisualizer.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/visualizers/NonUniformImage.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/visualizers/PrimitiveVisualizer.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/visualizers/SingleValueVisualizer.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/visualizers/ZStackVisualizer.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/visualizers/__init__.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/web/images/disabled.gif
    tags/pyphant-0.8a1/src/pyphant/pyphant/web/images/favicon.ico
    tags/pyphant-0.8a1/src/pyphant/pyphant/web/images/offline.gif
    tags/pyphant-0.8a1/src/pyphant/pyphant/web/images/online.gif
    tags/pyphant-0.8a1/src/pyphant/pyphant/web/images/pyphant.png
    tags/pyphant-0.8a1/src/pyphant/pyphant/web/script/LaTeXMathML.js
    tags/pyphant-0.8a1/src/pyphant/pyphant/web/templates/back.tpl
    tags/pyphant-0.8a1/src/pyphant/pyphant/web/templates/disabled.tpl
    tags/pyphant-0.8a1/src/pyphant/pyphant/web/templates/fieldcontainer.tpl
    tags/pyphant-0.8a1/src/pyphant/pyphant/web/templates/frontpage.tpl
    tags/pyphant-0.8a1/src/pyphant/pyphant/web/templates/htmlhead.tpl
    tags/pyphant-0.8a1/src/pyphant/pyphant/web/templates/log.tpl
    tags/pyphant-0.8a1/src/pyphant/pyphant/web/templates/mathhead.tpl
    tags/pyphant-0.8a1/src/pyphant/pyphant/web/templates/message.tpl
    tags/pyphant-0.8a1/src/pyphant/pyphant/web/templates/ordermathhead.tpl
    tags/pyphant-0.8a1/src/pyphant/pyphant/web/templates/remotes.tpl
    tags/pyphant-0.8a1/src/pyphant/pyphant/web/templates/samplecontainer.tpl
    tags/pyphant-0.8a1/src/pyphant/pyphant/web/templates/search.tpl
    tags/pyphant-0.8a1/src/pyphant/pyphant/wxgui2/ConfigureFrame.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/wxgui2/DataVisReg.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/wxgui2/PyphantCanvas.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/wxgui2/PyphantDiagram.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/wxgui2/WorkerFactoryPool.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/wxgui2/WorkerRepository.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/wxgui2/__init__.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/wxgui2/paramvisualization/BoundedIntegerTextField.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/wxgui2/paramvisualization/CheckBox.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/wxgui2/paramvisualization/FileButton.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/wxgui2/paramvisualization/ListSelect.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/wxgui2/paramvisualization/OneLineStringField.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/wxgui2/paramvisualization/ParamVisReg.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/wxgui2/paramvisualization/__init__.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/wxgui2/pyphantLogo.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/wxgui2/wxPyphantApplication.py
    tags/pyphant-0.8a1/src/pyphant/setup.cfg
    tags/pyphant-0.8a1/src/pyphant/setup.py
    tags/pyphant-0.8a1/src/support/xmlrunner.py
    tags/pyphant-0.8a1/src/test-all.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/ApplyMask.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/AutoFocus.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/BiThresholdingWorker.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/ConetworkSeparator.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/ConetworkThresholdingPOC.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/CoverageWorker.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/DiffWorker.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/DistanceMapper.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/EdgeFillWorker.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/EdgeTouchingFeatureRemover.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/EnhanceContrast.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/FeatureRatio.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/FilterWorker.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/FindLocalExtrema.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/FitBackground.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/Gradient.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/ImageLoaderWorker.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/InvertWorker.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/MarkAF.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/Medianiser.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/NDImageWorker.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/OptimalContrastWorker.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/Reduce.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/SkeletonizeFeature.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/SliceSelector.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/SlopeCalculator.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/ThresholdingWorker.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/UltimatePointsCalculator.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/Watershed.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/__init__.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/tests/TestApplyMask.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/tests/TestDistanceMapper.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/tests/TestImageLoader.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/tests/TestMedianiser.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/tests/TestSkeletonizeFeature.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/tests/TestSlopeCalculator.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/tests/TestThresholdingWorker.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/tests/__init__.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/tests/demo.png
    tags/pyphant-0.8a1/src/workers/ImageProcessing/setup.cfg
    tags/pyphant-0.8a1/src/workers/ImageProcessing/setup.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/AddColumn.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/CompareFields.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/ComputeFunctional.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/ErrorEstimator.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/EstimateParameter.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/EstimateParameterFromValues.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/ExtremumFinder.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/MRA.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/OscAbsorption.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/OscCurrent.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/OscLoader.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/OscThicknessCorrection.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/OscVisualisers.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/Slicing.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/Smoother.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/ThicknessModeller.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/__init__.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/convert2FMF.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/data.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/tests/TestErrorEstimator.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/tests/TestExtremumFinder.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/tests/TestMRA.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/tests/TestOscAbsorption.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/tests/__init__.py
    tags/pyphant-0.8a1/src/workers/OSC/setup.cfg
    tags/pyphant-0.8a1/src/workers/OSC/setup.py
    tags/pyphant-0.8a1/src/workers/Statistics/Statistics/Histogram.py
    tags/pyphant-0.8a1/src/workers/Statistics/Statistics/__init__.py
    tags/pyphant-0.8a1/src/workers/Statistics/Statistics/tests/TestHistogram.py
    tags/pyphant-0.8a1/src/workers/Statistics/Statistics/tests/__init__.py
    tags/pyphant-0.8a1/src/workers/Statistics/setup.cfg
    tags/pyphant-0.8a1/src/workers/Statistics/setup.py
    tags/pyphant-0.8a1/src/workers/fmfile/fmfile/FMFLoader.py
    tags/pyphant-0.8a1/src/workers/fmfile/fmfile/FMFWriter.py
    tags/pyphant-0.8a1/src/workers/fmfile/fmfile/__init__.py
    tags/pyphant-0.8a1/src/workers/fmfile/fmfile/fmfgen.py
    tags/pyphant-0.8a1/src/workers/fmfile/fmfile/tests/TestFMFLoader.py
    tags/pyphant-0.8a1/src/workers/fmfile/fmfile/tests/__init__.py
    tags/pyphant-0.8a1/src/workers/fmfile/fmfile/tests/resources/fmf/dep.fmf
    tags/pyphant-0.8a1/src/workers/fmfile/setup.cfg
    tags/pyphant-0.8a1/src/workers/fmfile/setup.py
    tags/pyphant-0.8a1/src/workers/tools/setup.cfg
    tags/pyphant-0.8a1/src/workers/tools/setup.py
    tags/pyphant-0.8a1/src/workers/tools/tools/DCSource.py
    tags/pyphant-0.8a1/src/workers/tools/tools/Emd5Src.py
    tags/pyphant-0.8a1/src/workers/tools/tools/FCSource.py
    tags/pyphant-0.8a1/src/workers/tools/tools/SCSource.py
    tags/pyphant-0.8a1/src/workers/tools/tools/__init__.py
    tags/pyphant-0.8a1/src/workers/tools/tools/tests/TestEmd5Source.py
    tags/pyphant-0.8a1/src/workers/tools/tools/tests/__init__.py

Added: tags/pyphant-0.8a1/.gitignore
===================================================================
--- tags/pyphant-0.8a1/.gitignore	                        (rev 0)
+++ tags/pyphant-0.8a1/.gitignore	2011-12-02 16:09:56 UTC (rev 711)
@@ -0,0 +1,20 @@
+*.py[co]
+*~
+DEBUG
+PKG-INFO
+SOURCES.txt
+dependency_links.txt
+entry_points.txt
+requires.txt
+top_level.txt
+.svn
+build
+dist
+*.egg-info
+\#*\#
+*.aux
+*.log
+*.out
+*.bst
+*.bbl
+.ropeproject/

Added: tags/pyphant-0.8a1/.project
===================================================================
--- tags/pyphant-0.8a1/.project	                        (rev 0)
+++ tags/pyphant-0.8a1/.project	2011-12-02 16:09:56 UTC (rev 711)
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>pyphant</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.python.pydev.PyDevBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.python.pydev.pythonNature</nature>
+	</natures>
+</projectDescription>

Added: tags/pyphant-0.8a1/.pydevproject
===================================================================
--- tags/pyphant-0.8a1/.pydevproject	                        (rev 0)
+++ tags/pyphant-0.8a1/.pydevproject	2011-12-02 16:09:56 UTC (rev 711)
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<?eclipse-pydev version="1.0"?>
+
+<pydev_project>
+<pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python 2.5</pydev_property>
+<pydev_pathproperty name="org.python.pydev.PROJECT_SOURCE_PATH">
+<path>/pyphant/src/pyphant</path>
+<path>/pyphant/src/workers/fmfile</path>
+<path>/pyphant/src/workers/ImageProcessing</path>
+<path>/pyphant/src/workers/OSC</path>
+</pydev_pathproperty>
+</pydev_project>

Added: tags/pyphant-0.8a1/doc/demo/README
===================================================================
--- tags/pyphant-0.8a1/doc/demo/README	                        (rev 0)
+++ tags/pyphant-0.8a1/doc/demo/README	2011-12-02 16:09:56 UTC (rev 711)
@@ -0,0 +1,6 @@
+#Start GUI with
+wxPythant demo.h5
+
+#Start scripting example with
+./simpleScripting.py
+

Added: tags/pyphant-0.8a1/doc/demo/Sim_abs_210nm.fmf
===================================================================
--- tags/pyphant-0.8a1/doc/demo/Sim_abs_210nm.fmf	                        (rev 0)
+++ tags/pyphant-0.8a1/doc/demo/Sim_abs_210nm.fmf	2011-12-02 16:09:56 UTC (rev 711)
@@ -0,0 +1,261 @@
+; -*- coding: utf-8 -*-
+[*reference]
+author: Kristian O. Sylvester-Hvid and Andreas W. Liehr
+date: 2007-12-07
+width: h = 210 nm
+title: Simulated abs spectrum for P3HT:PCBM solar cell - 210nm blend layer
+[*data definitions]
+wavelength: \lambda [nm]
+absorption: A(\lambda)
+[*data]
+300 0.94001276
+302 0.94052832
+304 0.94100929
+306 0.94144604
+308 0.94180794
+310 0.94206936
+312 0.9422048
+314 0.94226886
+316 0.94232466
+318 0.94250446
+320 0.94286269
+322 0.94339843
+324 0.94398425
+326 0.94434446
+328 0.94427402
+330 0.94353182
+332 0.94200658
+334 0.93963851
+336 0.93632749
+338 0.9321587
+340 0.92667119
+342 0.91986756
+344 0.91172259
+346 0.90177058
+348 0.89041845
+350 0.8775073
+352 0.86356483
+354 0.84936335
+356 0.83456895
+358 0.82062459
+360 0.8076951
+362 0.79614205
+364 0.78564803
+366 0.77755195
+368 0.77085322
+370 0.76677966
+372 0.76425721
+374 0.76322039
+376 0.76481169
+378 0.76822021
+380 0.77352729
+382 0.77995359
+384 0.78875682
+386 0.79887878
+388 0.81032685
+390 0.82164329
+392 0.83405087
+394 0.84724906
+396 0.86076354
+398 0.87312447
+400 0.88556675
+402 0.8975478
+404 0.90855741
+406 0.918659
+408 0.92730708
+410 0.9342962
+412 0.93988822
+414 0.94414255
+416 0.94665541
+418 0.9482054
+420 0.94895653
+422 0.94856192
+424 0.94709676
+426 0.94477955
+428 0.94172813
+430 0.93847747
+432 0.93522811
+434 0.93179879
+436 0.92875434
+438 0.9254059
+440 0.92240329
+442 0.91961551
+444 0.91700092
+446 0.91509408
+448 0.91307083
+450 0.91157556
+452 0.9100461
+454 0.90922433
+456 0.90849702
+458 0.90873161
+460 0.90918283
+462 0.90961624
+464 0.9103671
+466 0.91096396
+468 0.91174446
+470 0.91324641
+472 0.91475231
+474 0.9166557
+476 0.9184305
+478 0.92016726
+480 0.92199446
+482 0.92325293
+484 0.92476136
+486 0.92637909
+488 0.92800125
+490 0.92996184
+492 0.93139366
+494 0.9327197
+496 0.93383375
+498 0.93467089
+500 0.93529753
+502 0.93601335
+504 0.93691212
+506 0.93781723
+508 0.93874206
+510 0.93939636
+512 0.94003719
+514 0.94025198
+516 0.94035136
+518 0.94047114
+520 0.94073254
+522 0.94103714
+524 0.94130091
+526 0.94144813
+528 0.9415573
+530 0.94156843
+532 0.94138793
+534 0.94122204
+536 0.94099705
+538 0.94070117
+540 0.94035489
+542 0.9398703
+544 0.93954695
+546 0.93907971
+548 0.93853096
+550 0.93828818
+552 0.93770268
+554 0.93729021
+556 0.93682153
+558 0.93665619
+560 0.93660652
+562 0.9368939
+564 0.93710224
+566 0.93784482
+568 0.93866566
+570 0.93971
+572 0.94093727
+574 0.94231377
+576 0.94372178
+578 0.94516736
+580 0.94656231
+582 0.94775016
+584 0.94883467
+586 0.94980323
+588 0.95039466
+590 0.95043141
+592 0.95019453
+594 0.94949293
+596 0.94863656
+598 0.94729984
+600 0.9451777
+602 0.94231776
+604 0.93889644
+606 0.93402475
+608 0.9273553
+610 0.91887018
+612 0.90780796
+614 0.89401947
+616 0.87904645
+618 0.85919763
+620 0.83898752
+622 0.81322756
+624 0.7848802
+626 0.75385085
+628 0.71965866
+630 0.68307008
+632 0.64559891
+634 0.60841687
+636 0.57242972
+638 0.53468059
+640 0.50251968
+642 0.46947399
+644 0.44484263
+646 0.42004295
+648 0.39939842
+650 0.37870989
+652 0.36264726
+654 0.35232717
+656 0.33934159
+658 0.32502465
+660 0.31542268
+662 0.30824157
+664 0.2990077
+666 0.2947837
+668 0.28922591
+670 0.28658894
+672 0.28614721
+674 0.28202046
+676 0.28149016
+678 0.28040605
+680 0.27845176
+682 0.27654909
+684 0.27634083
+686 0.27617549
+688 0.27632291
+690 0.27384696
+692 0.27280758
+694 0.27443572
+696 0.27510338
+698 0.27512684
+700 0.27583487
+702 0.2729722
+704 0.27366256
+706 0.27463568
+708 0.27448946
+710 0.2767401
+712 0.27715502
+714 0.27797834
+716 0.27954103
+718 0.27946012
+720 0.28130034
+722 0.28056736
+724 0.28254809
+726 0.28456215
+728 0.28409837
+730 0.28531638
+732 0.2877751
+734 0.28996248
+736 0.2926061
+738 0.29527246
+740 0.29744612
+742 0.29808286
+744 0.29999903
+746 0.30224372
+748 0.30390019
+750 0.30599832
+752 0.30891292
+754 0.31095523
+756 0.31187227
+758 0.31412822
+760 0.315058
+762 0.31755964
+764 0.31919832
+766 0.32225542
+768 0.32428429
+770 0.32687193
+772 0.3273539
+774 0.32961995
+776 0.33199819
+778 0.33408599
+780 0.3366742
+782 0.33664265
+784 0.33911601
+786 0.3409073
+788 0.34362441
+790 0.34421251
+792 0.34616219
+794 0.34814186
+796 0.34946026
+798 0.35092394
+800 0.35234574

Added: tags/pyphant-0.8a1/doc/demo/demo.h5
===================================================================
--- tags/pyphant-0.8a1/doc/demo/demo.h5	                        (rev 0)
+++ tags/pyphant-0.8a1/doc/demo/demo.h5	2011-12-02 16:09:56 UTC (rev 711)
@@ -0,0 +1,68 @@
+\x89HDF
+
+

[Pyphant-devel] SF.net SVN: pyphant:[710] tags/pyphant-0.8a1

From: <ah...@us...> - 2011-12-02 15:59:44

Revision: 710
          http://pyphant.svn.sourceforge.net/pyphant/?rev=710&view=rev
Author:   aheld84
Date:     2011-12-02 15:59:33 +0000 (Fri, 02 Dec 2011)
Log Message:
-----------
Hack: cleared all files

this is necessary to recreate pyphant 0.8a1 in svn
since branches always branch from trunk

Removed Paths:
-------------
    tags/pyphant-0.8a1/.gitignore
    tags/pyphant-0.8a1/.project
    tags/pyphant-0.8a1/.pydevproject
    tags/pyphant-0.8a1/doc/demo/README
    tags/pyphant-0.8a1/doc/demo/Sim_abs_210nm.fmf
    tags/pyphant-0.8a1/doc/demo/demo.h5
    tags/pyphant-0.8a1/doc/demo/demo.png
    tags/pyphant-0.8a1/doc/demo/demoFMF.py
    tags/pyphant-0.8a1/doc/demo/example.fmf
    tags/pyphant-0.8a1/doc/demo/example_delimiter.fmf
    tags/pyphant-0.8a1/doc/demo/example_delimiter2.fmf
    tags/pyphant-0.8a1/doc/demo/features.png
    tags/pyphant-0.8a1/doc/demo/fmf2h5.h5
    tags/pyphant-0.8a1/doc/demo/fmf2h5.py
    tags/pyphant-0.8a1/doc/demo/plotter.py
    tags/pyphant-0.8a1/doc/demo/pyphant-shade-Information-Analysis-Framework.png
    tags/pyphant-0.8a1/doc/demo/readfmf.py
    tags/pyphant-0.8a1/doc/demo/simpleScripting.py
    tags/pyphant-0.8a1/doc/demo/viewOSC.py
    tags/pyphant-0.8a1/doc/demo/visualizeImage.py
    tags/pyphant-0.8a1/doc/grammarDoc.py
    tags/pyphant-0.8a1/doc/grammarDoc.txt
    tags/pyphant-0.8a1/doc/knowledge-ideas.org
    tags/pyphant-0.8a1/doc/logo/mklogo.py
    tags/pyphant-0.8a1/doc/logo/pyphant-shade-Information-Analysis-Framework-ARTS-small.png
    tags/pyphant-0.8a1/doc/logo/pyphantLogo.py
    tags/pyphant-0.8a1/doc/test_numpy1.0.1Bug.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/__init__.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/cli/createExecutionOrder.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/cli/demo.h5
    tags/pyphant-0.8a1/src/pyphant/pyphant/cli/demo.png
    tags/pyphant-0.8a1/src/pyphant/pyphant/cli/pyphant_exec.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/cli/simpleCLI.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/AstTransformers.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/CompositeWorker.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/Connectors.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/DataContainer.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/EventDispatcher.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/FieldContainer.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/H5FileHandler.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/Helpers.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/KnowledgeManager.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/KnowledgeNode.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/Param.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/PyTablesPersister.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/RoutingHTTPServer.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/SQLiteWrapper.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/UpdateManager.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/WebInterface.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/Worker.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/WorkerRegistry.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/__init__.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/bottle.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/core/singletonmixin.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/quantities/ParseQuantities.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/quantities/PhysicalQuantities.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/quantities/__init__.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/TestChart.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/TestCompositeWorker.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/TestDataContainer.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/TestEventDispatcher.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/TestH5FileHandler.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/TestImageVisualizer.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/TestKnowledgeManager.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/TestKnowledgeNode.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/TestParam.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/TestParseQuantities.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/TestPyTablesPersister.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/TestQuantities.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/TestSQLiteWrapper.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/TestTimestamp.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/tests/__init__.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/visualizers/Chart.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/visualizers/ConfigurablePlot.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/visualizers/External.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/visualizers/ImageVisualizer.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/visualizers/KMVisualizer.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/visualizers/NonUniformImage.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/visualizers/PrimitiveVisualizer.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/visualizers/ZStackVisualizer.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/visualizers/__init__.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/web/images/disabled.gif
    tags/pyphant-0.8a1/src/pyphant/pyphant/web/images/favicon.ico
    tags/pyphant-0.8a1/src/pyphant/pyphant/web/images/offline.gif
    tags/pyphant-0.8a1/src/pyphant/pyphant/web/images/online.gif
    tags/pyphant-0.8a1/src/pyphant/pyphant/web/images/pyphant.png
    tags/pyphant-0.8a1/src/pyphant/pyphant/web/script/LaTeXMathML.js
    tags/pyphant-0.8a1/src/pyphant/pyphant/web/templates/back.tpl
    tags/pyphant-0.8a1/src/pyphant/pyphant/web/templates/disabled.tpl
    tags/pyphant-0.8a1/src/pyphant/pyphant/web/templates/fieldcontainer.tpl
    tags/pyphant-0.8a1/src/pyphant/pyphant/web/templates/frontpage.tpl
    tags/pyphant-0.8a1/src/pyphant/pyphant/web/templates/htmlhead.tpl
    tags/pyphant-0.8a1/src/pyphant/pyphant/web/templates/log.tpl
    tags/pyphant-0.8a1/src/pyphant/pyphant/web/templates/mathhead.tpl
    tags/pyphant-0.8a1/src/pyphant/pyphant/web/templates/message.tpl
    tags/pyphant-0.8a1/src/pyphant/pyphant/web/templates/ordermathhead.tpl
    tags/pyphant-0.8a1/src/pyphant/pyphant/web/templates/remotes.tpl
    tags/pyphant-0.8a1/src/pyphant/pyphant/web/templates/samplecontainer.tpl
    tags/pyphant-0.8a1/src/pyphant/pyphant/web/templates/search.tpl
    tags/pyphant-0.8a1/src/pyphant/pyphant/wxgui2/ConfigureFrame.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/wxgui2/DataVisReg.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/wxgui2/PyphantCanvas.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/wxgui2/PyphantDiagram.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/wxgui2/WorkerFactoryPool.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/wxgui2/WorkerRepository.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/wxgui2/__init__.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/wxgui2/paramvisualization/BoundedIntegerTextField.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/wxgui2/paramvisualization/CheckBox.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/wxgui2/paramvisualization/FileButton.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/wxgui2/paramvisualization/ListSelect.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/wxgui2/paramvisualization/OneLineStringField.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/wxgui2/paramvisualization/ParamVisReg.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/wxgui2/paramvisualization/__init__.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/wxgui2/pyphantLogo.py
    tags/pyphant-0.8a1/src/pyphant/pyphant/wxgui2/wxPyphantApplication.py
    tags/pyphant-0.8a1/src/pyphant/setup.cfg
    tags/pyphant-0.8a1/src/pyphant/setup.py
    tags/pyphant-0.8a1/src/support/xmlrunner.py
    tags/pyphant-0.8a1/src/test-all.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/ApplyMask.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/AutoFocus.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/BiThresholdingWorker.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/ConetworkSeparator.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/ConetworkThresholdingPOC.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/CoverageWorker.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/DiffWorker.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/DistanceMapper.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/EdgeFillWorker.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/EdgeTouchingFeatureRemover.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/EnhanceContrast.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/FindLocalExtrema.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/FitBackground.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/Gradient.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/ImageLoaderWorker.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/InvertWorker.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/LoadZStack.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/MarkInclusions.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/Medianiser.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/OptimalContrastWorker.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/SkeletonizeFeature.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/SlopeCalculator.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/ThresholdingWorker.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/UltimatePointsCalculator.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/Watershed.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/__init__.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/tests/TestApplyMask.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/tests/TestAutoFocus.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/tests/TestCoverage.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/tests/TestDiffWorker.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/tests/TestDistanceMapper.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/tests/TestETFR.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/tests/TestEdgeFill.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/tests/TestEnhanceContrast.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/tests/TestFitBackground.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/tests/TestGradient.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/tests/TestImageLoader.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/tests/TestInvert.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/tests/TestLocalExtrema.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/tests/TestMedianiser.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/tests/TestSkeletonizeFeature.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/tests/TestSlopeCalculator.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/tests/TestThresholdingWorker.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/tests/TestUltimatePoints.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/tests/TestWatershed.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/tests/__init__.py
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/tests/demo.png
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/tests/resources/zstack/TestZStack_z00.tif
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/tests/resources/zstack/TestZStack_z01.tif
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/tests/resources/zstack/TestZStack_z02.tif
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/tests/resources/zstack/TestZStack_z03.tif
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/tests/resources/zstack/TestZStack_z04.tif
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/tests/resources/zstack/TestZStack_z05.tif
    tags/pyphant-0.8a1/src/workers/ImageProcessing/ImageProcessing/tests/resources/zstack/TestZStack_z06.tif
    tags/pyphant-0.8a1/src/workers/ImageProcessing/setup.cfg
    tags/pyphant-0.8a1/src/workers/ImageProcessing/setup.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/CompareFields.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/ComputeFunctional.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/ErrorEstimator.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/EstimateParameter.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/EstimateParameterFromValues.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/ExtremumFinder.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/MRA.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/OscAbsorption.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/OscCurrent.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/OscLoader.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/OscMapper.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/OscThicknessCorrection.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/OscVisualisers.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/Smoother.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/ThicknessModeller.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/__init__.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/convert2FMF.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/data.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/tests/TestErrorEstimator.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/tests/TestExtremumFinder.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/tests/TestInstantiation.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/tests/TestMRA.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/tests/TestOscAbsorption.py
    tags/pyphant-0.8a1/src/workers/OSC/OSC/tests/__init__.py
    tags/pyphant-0.8a1/src/workers/OSC/setup.cfg
    tags/pyphant-0.8a1/src/workers/OSC/setup.py
    tags/pyphant-0.8a1/src/workers/Statistics/Statistics/Histogram.py
    tags/pyphant-0.8a1/src/workers/Statistics/Statistics/__init__.py
    tags/pyphant-0.8a1/src/workers/Statistics/Statistics/tests/TestHistogram.py
    tags/pyphant-0.8a1/src/workers/Statistics/Statistics/tests/__init__.py
    tags/pyphant-0.8a1/src/workers/Statistics/setup.cfg
    tags/pyphant-0.8a1/src/workers/Statistics/setup.py
    tags/pyphant-0.8a1/src/workers/fmfile/fmfile/FMFLoader.py
    tags/pyphant-0.8a1/src/workers/fmfile/fmfile/FMFWriter.py
    tags/pyphant-0.8a1/src/workers/fmfile/fmfile/__init__.py
    tags/pyphant-0.8a1/src/workers/fmfile/fmfile/fmfgen.py
    tags/pyphant-0.8a1/src/workers/fmfile/fmfile/tests/TestFMFLoader.py
    tags/pyphant-0.8a1/src/workers/fmfile/fmfile/tests/__init__.py
    tags/pyphant-0.8a1/src/workers/fmfile/fmfile/tests/resources/fmf/dep.fmf
    tags/pyphant-0.8a1/src/workers/fmfile/fmfile/tests/resources/fmf/hash_test.fmf
    tags/pyphant-0.8a1/src/workers/fmfile/fmfile/tests/resources/fmf/multitable.fmf
    tags/pyphant-0.8a1/src/workers/fmfile/fmfile/tests/resources/fmf/onecolumn.fmf
    tags/pyphant-0.8a1/src/workers/fmfile/fmfile/tests/resources/fmf/onerow.fmf
    tags/pyphant-0.8a1/src/workers/fmfile/fmfile/tests/resources/fmf/onerow_dep.fmf
    tags/pyphant-0.8a1/src/workers/fmfile/fmfile/tests/resources/fmf/onevalue.fmf
    tags/pyphant-0.8a1/src/workers/fmfile/fmfile/tests/resources/fmf/semi_test.fmf
    tags/pyphant-0.8a1/src/workers/fmfile/setup.cfg
    tags/pyphant-0.8a1/src/workers/fmfile/setup.py
    tags/pyphant-0.8a1/src/workers/tools/setup.cfg
    tags/pyphant-0.8a1/src/workers/tools/setup.py
    tags/pyphant-0.8a1/src/workers/tools/tools/AddColumn.py
    tags/pyphant-0.8a1/src/workers/tools/tools/AlgebraWorker.py
    tags/pyphant-0.8a1/src/workers/tools/tools/ColumnExtractor.py
    tags/pyphant-0.8a1/src/workers/tools/tools/DCSource.py
    tags/pyphant-0.8a1/src/workers/tools/tools/Emd5Src.py
    tags/pyphant-0.8a1/src/workers/tools/tools/ExtractRows.py
    tags/pyphant-0.8a1/src/workers/tools/tools/FCSource.py
    tags/pyphant-0.8a1/src/workers/tools/tools/SCSource.py
    tags/pyphant-0.8a1/src/workers/tools/tools/Slicing.py
    tags/pyphant-0.8a1/src/workers/tools/tools/__init__.py
    tags/pyphant-0.8a1/src/workers/tools/tools/tests/TestEmd5Source.py
    tags/pyphant-0.8a1/src/workers/tools/tools/tests/TestInstantiation.py
    tags/pyphant-0.8a1/src/workers/tools/tools/tests/__init__.py

Deleted: tags/pyphant-0.8a1/.gitignore
===================================================================
--- tags/pyphant-0.8a1/.gitignore	2011-12-02 15:25:53 UTC (rev 709)
+++ tags/pyphant-0.8a1/.gitignore	2011-12-02 15:59:33 UTC (rev 710)
@@ -1,20 +0,0 @@
-*.py[co]
-*~
-DEBUG
-PKG-INFO
-SOURCES.txt
-dependency_links.txt
-entry_points.txt
-requires.txt
-top_level.txt
-.svn
-build
-dist
-*.egg-info
-\#*\#
-*.aux
-*.log
-*.out
-*.bst
-*.bbl
-.ropeproject/

Deleted: tags/pyphant-0.8a1/.project
===================================================================
--- tags/pyphant-0.8a1/.project	2011-12-02 15:25:53 UTC (rev 709)
+++ tags/pyphant-0.8a1/.project	2011-12-02 15:59:33 UTC (rev 710)
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
-	<name>pyphant</name>
-	<comment></comment>
-	<projects>
-	</projects>
-	<buildSpec>
-		<buildCommand>
-			<name>org.python.pydev.PyDevBuilder</name>
-			<arguments>
-			</arguments>
-		</buildCommand>
-	</buildSpec>
-	<natures>
-		<nature>org.python.pydev.pythonNature</nature>
-	</natures>
-</projectDescription>

Deleted: tags/pyphant-0.8a1/.pydevproject
===================================================================
--- tags/pyphant-0.8a1/.pydevproject	2011-12-02 15:25:53 UTC (rev 709)
+++ tags/pyphant-0.8a1/.pydevproject	2011-12-02 15:59:33 UTC (rev 710)
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<?eclipse-pydev version="1.0"?>
-
-<pydev_project>
-<pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python 2.5</pydev_property>
-<pydev_pathproperty name="org.python.pydev.PROJECT_SOURCE_PATH">
-<path>/pyphant/src/pyphant</path>
-<path>/pyphant/src/workers/fmfile</path>
-<path>/pyphant/src/workers/ImageProcessing</path>
-<path>/pyphant/src/workers/OSC</path>
-</pydev_pathproperty>
-</pydev_project>

Deleted: tags/pyphant-0.8a1/doc/demo/README
===================================================================
--- tags/pyphant-0.8a1/doc/demo/README	2011-12-02 15:25:53 UTC (rev 709)
+++ tags/pyphant-0.8a1/doc/demo/README	2011-12-02 15:59:33 UTC (rev 710)
@@ -1,6 +0,0 @@
-#Start GUI with
-wxPythant demo.h5
-
-#Start scripting example with
-./simpleScripting.py
-

Deleted: tags/pyphant-0.8a1/doc/demo/Sim_abs_210nm.fmf
===================================================================
--- tags/pyphant-0.8a1/doc/demo/Sim_abs_210nm.fmf	2011-12-02 15:25:53 UTC (rev 709)
+++ tags/pyphant-0.8a1/doc/demo/Sim_abs_210nm.fmf	2011-12-02 15:59:33 UTC (rev 710)
@@ -1,261 +0,0 @@
-; -*- coding: utf-8 -*-
-[*reference]
-author: Kristian O. Sylvester-Hvid and Andreas W. Liehr
-date: 2007-12-07
-width: h = 210 nm
-title: Simulated abs spectrum for P3HT:PCBM solar cell - 210nm blend layer
-[*data definitions]
-wavelength: \lambda [nm]
-absorption: A(\lambda)
-[*data]
-300 0.94001276
-302 0.94052832
-304 0.94100929
-306 0.94144604
-308 0.94180794
-310 0.94206936
-312 0.9422048
-314 0.94226886
-316 0.94232466
-318 0.94250446
-320 0.94286269
-322 0.94339843
-324 0.94398425
-326 0.94434446
-328 0.94427402
-330 0.94353182
-332 0.94200658
-334 0.93963851
-336 0.93632749
-338 0.9321587
-340 0.92667119
-342 0.91986756
-344 0.91172259
-346 0.90177058
-348 0.89041845
-350 0.8775073
-352 0.86356483
-354 0.84936335
-356 0.83456895
-358 0.82062459
-360 0.8076951
-362 0.79614205
-364 0.78564803
-366 0.77755195
-368 0.77085322
-370 0.76677966
-372 0.76425721
-374 0.76322039
-376 0.76481169
-378 0.76822021
-380 0.77352729
-382 0.77995359
-384 0.78875682
-386 0.79887878
-388 0.81032685
-390 0.82164329
-392 0.83405087
-394 0.84724906
-396 0.86076354
-398 0.87312447
-400 0.88556675
-402 0.8975478
-404 0.90855741
-406 0.918659
-408 0.92730708
-410 0.9342962
-412 0.93988822
-414 0.94414255
-416 0.94665541
-418 0.9482054
-420 0.94895653
-422 0.94856192
-424 0.94709676
-426 0.94477955
-428 0.94172813
-430 0.93847747
-432 0.93522811
-434 0.93179879
-436 0.92875434
-438 0.9254059
-440 0.92240329
-442 0.91961551
-444 0.91700092
-446 0.91509408
-448 0.91307083
-450 0.91157556
-452 0.9100461
-454 0.90922433
-456 0.90849702
-458 0.90873161
-460 0.90918283
-462 0.90961624
-464 0.9103671
-466 0.91096396
-468 0.91174446
-470 0.91324641
-472 0.91475231
-474 0.9166557
-476 0.9184305
-478 0.92016726
-480 0.92199446
-482 0.92325293
-484 0.92476136
-486 0.92637909
-488 0.92800125
-490 0.92996184
-492 0.93139366
-494 0.9327197
-496 0.93383375
-498 0.93467089
-500 0.93529753
-502 0.93601335
-504 0.93691212
-506 0.93781723
-508 0.93874206
-510 0.93939636
-512 0.94003719
-514 0.94025198
-516 0.94035136
-518 0.94047114
-520 0.94073254
-522 0.94103714
-524 0.94130091
-526 0.94144813
-528 0.9415573
-530 0.94156843
-532 0.94138793
-534 0.94122204
-536 0.94099705
-538 0.94070117
-540 0.94035489
-542 0.9398703
-544 0.93954695
-546 0.93907971
-548 0.93853096
-550 0.93828818
-552 0.93770268
-554 0.93729021
-556 0.93682153
-558 0.93665619
-560 0.93660652
-562 0.9368939
-564 0.93710224
-566 0.93784482
-568 0.93866566
-570 0.93971
-572 0.94093727
-574 0.94231377
-576 0.94372178
-578 0.94516736
-580 0.94656231
-582 0.94775016
-584 0.94883467
-586 0.94980323
-588 0.95039466
-590 0.95043141
-592 0.95019453
-594 0.94949293
-596 0.94863656
-598 0.94729984
-600 0.9451777
-602 0.94231776
-604 0.93889644
-606 0.93402475
-608 0.9273553
-610 0.91887018
-612 0.90780796
-614 0.89401947
-616 0.87904645
-618 0.85919763
-620 0.83898752
-622 0.81322756
-624 0.7848802
-626 0.75385085
-628 0.71965866
-630 0.68307008
-632 0.64559891
-634 0.60841687
-636 0.57242972
-638 0.53468059
-640 0.50251968
-642 0.46947399
-644 0.44484263
-646 0.42004295
-648 0.39939842
-650 0.37870989
-652 0.36264726
-654 0.35232717
-656 0.33934159
-658 0.32502465
-660 0.31542268
-662 0.30824157
-664 0.2990077
-666 0.2947837
-668 0.28922591
-670 0.28658894
-672 0.28614721
-674 0.28202046
-676 0.28149016
-678 0.28040605
-680 0.27845176
-682 0.27654909
-684 0.27634083
-686 0.27617549
-688 0.27632291
-690 0.27384696
-692 0.27280758
-694 0.27443572
-696 0.27510338
-698 0.27512684
-700 0.27583487
-702 0.2729722
-704 0.27366256
-706 0.27463568
-708 0.27448946
-710 0.2767401
-712 0.27715502
-714 0.27797834
-716 0.27954103
-718 0.27946012
-720 0.28130034
-722 0.28056736
-724 0.28254809
-726 0.28456215
-728 0.28409837
-730 0.28531638
-732 0.2877751
-734 0.28996248
-736 0.2926061
-738 0.29527246
-740 0.29744612
-742 0.29808286
-744 0.29999903
-746 0.30224372
-748 0.30390019
-750 0.30599832
-752 0.30891292
-754 0.31095523
-756 0.31187227
-758 0.31412822
-760 0.315058
-762 0.31755964
-764 0.31919832
-766 0.32225542
-768 0.32428429
-770 0.32687193
-772 0.3273539
-774 0.32961995
-776 0.33199819
-778 0.33408599
-780 0.3366742
-782 0.33664265
-784 0.33911601
-786 0.3409073
-788 0.34362441
-790 0.34421251
-792 0.34616219
-794 0.34814186
-796 0.34946026
-798 0.35092394
-800 0.35234574

Deleted: tags/pyphant-0.8a1/doc/demo/demo.h5
===================================================================
(Binary files differ)

Deleted: tags/pyphant-0.8a1/doc/demo/demo.png
===================================================================
(Binary files differ)

Deleted: tags/pyphant-0.8a1/doc/demo/demoFMF.py
===================================================================
--- tags/pyphant-0.8a1/doc/demo/demoFMF.py	2011-12-02 15:25:53 UTC (rev 709)
+++ tags/pyphant-0.8a1/doc/demo/demoFMF.py	2011-12-02 15:59:33 UTC (rev 710)
@@ -1,57 +0,0 @@
-# -*- coding: utf-8 -*-
-
-# Copyright (c) 2006-2008, Rectorate of the University of Freiburg
-# All rights reserved.
-#
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions are met:
-#
-# * Redistributions of source code must retain the above copyright
-#   notice, this list of conditions and the following disclaimer.
-# * Redistributions in binary form must reproduce the above copyright
-#   notice, this list of conditions and the following disclaimer in the
-#   documentation and/or other materials provided with the distribution.
-# * Neither the name of the Freiburg Materials Research Center,
-#   University of Freiburg nor the names of its contributors may be used to
-#   endorse or promote products derived from this software without specific
-#   prior written permission.
-#
-#
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
-# IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
-# TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
-# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
-# OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
-# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
-# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
-# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-u"""
-"""
-
-__id__ = "$Id$"
-__author__ = "$Author$"
-__version__ = "$Revision$"
-# $Source$
-
-
-import sys
-import unittest
-sys.path.append("..")
-
-import pkg_resources
-
-pkg_resources.require("Pyphant")
-
-from fmfile import FMFLoader
-import pyphant.visualizers.Chart as cv
-
-loader = FMFLoader.FMFLoader()
-loader.paramFilename.value = 'Sim_abs_210nm.fmf'
-data = loader.loadFMF()
-
-v = cv.LineChart(data['absorption'])
-v.figure.savefig('demoFMF.png')

Deleted: tags/pyphant-0.8a1/doc/demo/example.fmf
===================================================================
--- tags/pyphant-0.8a1/doc/demo/example.fmf	2011-12-02 15:25:53 UTC (rev 709)
+++ tags/pyphant-0.8a1/doc/demo/example.fmf	2011-12-02 15:59:33 UTC (rev 710)
@@ -1,111 +0,0 @@
-# -*- fmf-version: 1.0; coding: utf-8 -*-
-[*reference]
-title: Demonstrating the flexibility of the Full-Metadata-Format
-creator: Andreas W. Liehr
-created: 2008-10-29
-place: Freiburger Materialforschungszentrum, Universität Freiburg, Deutschland
-[Textual values]
-word: Hello!
-sentence: Hello World!
-timestamp: 2008-10-31 12:00:59.438151
-comma separated list: world, die Welt, el mundo, monde
-inside quotation: Arthur C. Clarke's "The Sentinel"
-single quote: 'Freiburger Materialforschungszentrum, Universität Freiburg, Deutschland'
-double quotation mark: "Freiburger Materialforschungszentrum, Universität Freiburg, Deutschland"
-multiline: '''A multiline value, 
-that spans more than one line :-)
-The line breaks are included in the value.'''
-Another multiline: """A multiline value, 
-that spans more than one line :-)"""
-Enclosed quotation marks: """ Andreas says: "Hello World!" """
-[Numerical values]
-#Note, that the 'key' is arbitrary, but has to be unique within a section
-integer: 1
-list of integers: 1, 2, 3, 4, 5
-float: 1.0
-float with leading dot: .1
-float with exponential: 1e-10
-float with Exponential: -1.1E10
-list of floats: 1.0, .1, 1e-10, -1.1E10
-complex: 1+2j
-Complex: 1.1+2j
-Complex number with zero real part : 2j
-Complex number with zero imaginary part: 1+0j
-list of complex: 1+2j, 1.1+2j
-[Boolean values]
-true1: True
-true2: true
-true3: TRUE
-false1: False
-false2: false
-false3: FALSE
-list of booleans: True, true, TRUE, False, false, FALSE
-[Quantities]
-voltage: 1V
-temperature in Celsius: 22 degC
-resistance: 2.0 kg*m^2*A^-2*s^-3
-arbitrary units: 10 a.u.
-distance from Earth to Sun: 1 AU
-[Quantities with error]
-voltage: 1 V +- 1 mV
-current: 1 A +/- 0.001 A
-energy:  1 J \pm 1 mJ
-work:    1 W +- 0.1%
-voltage in brackets: (1 +- 0.001) V
-current in brackets: (1 +- 0.1%)  A
-trailing amplitude: (1 +- 0.01) 2 ohm
-trailing amplitude, relative error: (1 +- 1%) 2 ohm
-estimated parameter: 1 \pm 0.1
-another estimated parameter: 1 \pm 1%
-list of quantities: 1V, 22 degC,(1 +- 1%) 2 ohm
-[Variables]
-number: N = 2
-voltage: U = 1V
-temperature in Celsius: T_C = 22 degC
-temperature in Fahrenheit: T = 22 degF
-resistance: \omega = 2.0 kg*m^2*A^-2*s^-3
-resistance 2: \omega = 2.0 kg*m**2*A**-2*s**-3
-normed variable: n = 10 a.u.
-[Physical Quantities with error]
-voltage: U = 1 V +- 1 mV
-current: I = 1 A +/- 0.001 A
-energy:  E = 1 J \pm 1 mJ
-work:    A = 1 W +- 0.1%
-voltage in brackets: U = (1 +- 0.001) V
-current in brackets: I = (1 +- 0.1%)  A
-trailing amplitude: \omega = (1 +- 0.01) 2 ohm
-trailing amplitude, relative error: \omega = (1 +- 1%) 2 ohm
-estimated parameter: p = 1 \pm 0.1
-another estimated parameter: p = 1 \pm 1%
-list of quantities: number: N = 2, U = 1V, T_C = 22 degC
-[Datetime stamps]
-date: 2008-12-16
-week date: 2008-W47-1 
-list of dates: 2008-11-17,2008-1-3,2006-2-17,2008-W47-1
-datetime: 2008-12-16T16:51
-another datetime: 2008-12-16 16:51
-datetime with second: 2008-12-16T16:51:05
-datetime UTC: 2008-12-16T16:51Z
-datetime+2h: 2006-04-23 14:25:51+02:00
-[*table definitions]
-table: T
-mixed: M
-[*data definitions: T]
-String: S
-Integer: I
-Float with dot: Fd
-Float with exponent: Fe
-Complex: C
-Missing Value: V_m
-Infinite Value: V_i
-[*data: T]
-H_2	1	1.	1e1	1+0j	nan	inf	
-O_2	2	.2	2E1	2+.1j	NaN	INF
-O 2	2	.2	2E1	2.+2j	NAN	Inf
-[*data definitions: M]
-String: S
-Complex: C
-Float: F
-[*data: M]
-N_2	1	2
-2	1+1j	2.1

Deleted: tags/pyphant-0.8a1/doc/demo/example_delimiter.fmf
===================================================================
--- tags/pyphant-0.8a1/doc/demo/example_delimiter.fmf	2011-12-02 15:25:53 UTC (rev 709)
+++ tags/pyphant-0.8a1/doc/demo/example_delimiter.fmf	2011-12-02 15:59:33 UTC (rev 710)
@@ -1,56 +0,0 @@
-# -*- fmf-version: 1.0; coding: utf-8; delimiter: whitespace -*-
-[*reference]
-title: Demonstrating the flexibility of the Full-Metadata-Format
-creator: Andreas W. Liehr
-created: 2008-10-29
-place: Freiburger Materialforschungszentrum, Universität Freiburg, Deutschland
-[String Examples]
-word: Hello!
-sentence: Hello World!
-comma separated list: world, die Welt, el mundo, monde
-multiline: '''A multiline value, 
-that spans more than one line :-)
-The line breaks are included in the value.'''
-[Numbers]
-#Note, that the 'key' is arbitrary, but has to be unique within a section
-integer: 1
-float: 1.0
-float with leading dot: .1
-float with exponential: 1e-10
-float with Exponential: -1.1E10
-complex: 1+2j
-[Physical Quantities]
-number: N = 2
-voltage: U = 1V
-temperature in Celsius: T_C = 22 degC
-temperature in Fahrenheit: T = 22 degF
-[Physical Quantities with error]
-voltage: U = 1 V +- 1 mV
-current: I = 1 A +/- 0.001 A
-energy:  E = 1 J \pm 1 mJ
-work:    A = 1 W +- 0.1%
-voltage in brackets: U = (1 +- 0.001) V
-current in brackets: I = (1 +- 0.1%)  A
-estimated parameter: p = 1 \pm 0.1
-another estimated parameter: p = 1 \pm 1%
-[*table definitions]
-table: T
-mixed: M
-[*data definitions: T]
-String: S
-Integer: I
-Float with dot: Fd
-Float with exponent: Fe
-Complex: C
-Missing Value: V_m
-Infinite Value: V_i
-[*data: T]
-H_2 1 1. 1e1 1+0j nan inf	
-O_2 2 .2 2E1 2+.1j NaN INF
-[*data definitions: M]
-String: S
-Complex: C
-Float: F
-[*data: M]
-N_2 1 2
-2 1+1j 2.1

Deleted: tags/pyphant-0.8a1/doc/demo/example_delimiter2.fmf
===================================================================
--- tags/pyphant-0.8a1/doc/demo/example_delimiter2.fmf	2011-12-02 15:25:53 UTC (rev 709)
+++ tags/pyphant-0.8a1/doc/demo/example_delimiter2.fmf	2011-12-02 15:59:33 UTC (rev 710)
@@ -1,57 +0,0 @@
-# -*- fmf-version: 1.0; coding: utf-8; delimiter:, -*-
-[*reference]
-title: Demonstrating the flexibility of the Full-Metadata-Format
-creator: Andreas W. Liehr
-created: 2008-10-29
-place: Freiburger Materialforschungszentrum, Universität Freiburg, Deutschland
-[String Examples]
-word: Hello!
-sentence: Hello World!
-comma separated list: world, die Welt, el mundo, monde
-multiline: '''A multiline value, 
-that spans more than one line :-)
-The line breaks are included in the value.'''
-[Numbers]
-#Note, that the 'key' is arbitrary, but has to be unique within a section
-integer: 1
-float: 1.0
-float with leading dot: .1
-float with exponential: 1e-10
-float with Exponential: -1.1E10
-complex: 1+2j
-[Physical Quantities]
-number: N = 2
-voltage: U = 1V
-temperature in Celsius: T_C = 22 degC
-temperature in Fahrenheit: T = 22 degF
-[Physical Quantities with error]
-voltage: U = 1 V +- 1 mV
-current: I = 1 A +/- 0.001 A
-energy:  E = 1 J \pm 1 mJ
-work:    A = 1 W +- 0.1%
-voltage in brackets: U = (1 +- 0.001) V
-current in brackets: I = (1 +- 0.1%)  A
-estimated parameter: p = 1 \pm 0.1
-another estimated parameter: p = 1 \pm 1%
-[*table definitions]
-table: T
-mixed: M
-[*data definitions: T]
-String: S
-Integer: I
-Float with dot: Fd
-Float with exponent: Fe
-Complex: C
-Missing Value: V_m
-Infinite Value: V_i
-[*data: T]
-H_2,1,1.,1e1,1+0j,nan,inf	
-O_2,2,.2,2E1,2+.1j,NaN,INF
-O 2,2,.2,2E1,2+.1j,NAN,Inf
-[*data definitions: M]
-String: S
-Complex: C
-Float: F
-[*data: M]
-N_2,1,2
-2,1+1j,2.1

Deleted: tags/pyphant-0.8a1/doc/demo/features.png
===================================================================
--- tags/pyphant-0.8a1/doc/demo/features.png	2011-12-02 15:25:53 UTC (rev 709)
+++ tags/pyphant-0.8a1/doc/demo/features.png	2011-12-02 15:59:33 UTC (rev 710)
@@ -1,14 +0,0 @@
-\x89PNG
-
-

[Pyphant-devel] SF.net SVN: pyphant:[709] tags/pyphant-0.8a1/

From: <ah...@us...> - 2011-12-02 15:26:03

Revision: 709
          http://pyphant.svn.sourceforge.net/pyphant/?rev=709&view=rev
Author:   aheld84
Date:     2011-12-02 15:25:53 +0000 (Fri, 02 Dec 2011)
Log Message:
-----------
cloned trunk

Added Paths:
-----------
    tags/pyphant-0.8a1/

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Pyphant-devel] SF.net SVN: pyphant:[708] tags/pyphant-1.0b1/src

From: <ah...@us...> - 2011-12-02 13:42:20

Revision: 708
          http://pyphant.svn.sourceforge.net/pyphant/?rev=708&view=rev
Author:   aheld84
Date:     2011-12-02 13:42:09 +0000 (Fri, 02 Dec 2011)
Log Message:
-----------
Merge branch 'v1.0' into svn-tag-pyphant-1.0b1

* v1.0:
  Configured release for v1.0b1

Modified Paths:
--------------
    tags/pyphant-1.0b1/src/pyphant/pyphant/wxgui2/wxPyphantApplication.py
    tags/pyphant-1.0b1/src/pyphant/setup.py
    tags/pyphant-1.0b1/src/workers/ImageProcessing/setup.py
    tags/pyphant-1.0b1/src/workers/OSC/setup.py
    tags/pyphant-1.0b1/src/workers/Statistics/setup.py
    tags/pyphant-1.0b1/src/workers/fmfile/setup.py
    tags/pyphant-1.0b1/src/workers/tools/setup.py

Removed Paths:
-------------
    tags/pyphant-1.0b1/src/pyphant/setup.cfg
    tags/pyphant-1.0b1/src/workers/ImageProcessing/setup.cfg
    tags/pyphant-1.0b1/src/workers/OSC/setup.cfg
    tags/pyphant-1.0b1/src/workers/Statistics/setup.cfg
    tags/pyphant-1.0b1/src/workers/fmfile/setup.cfg
    tags/pyphant-1.0b1/src/workers/tools/setup.cfg

Modified: tags/pyphant-1.0b1/src/pyphant/pyphant/wxgui2/wxPyphantApplication.py
===================================================================
--- tags/pyphant-1.0b1/src/pyphant/pyphant/wxgui2/wxPyphantApplication.py	2011-12-02 13:21:01 UTC (rev 707)
+++ tags/pyphant-1.0b1/src/pyphant/pyphant/wxgui2/wxPyphantApplication.py	2011-12-02 13:42:09 UTC (rev 708)
@@ -35,7 +35,7 @@
 
 __id__ = "$Id$"
 __author__ = "$Author$"
-__version__ = "Sprint"
+__version__ = "1.0b1"
 # $Source$
 
 import os, os.path, pkg_resources

Deleted: tags/pyphant-1.0b1/src/pyphant/setup.cfg
===================================================================
--- tags/pyphant-1.0b1/src/pyphant/setup.cfg	2011-12-02 13:21:01 UTC (rev 707)
+++ tags/pyphant-1.0b1/src/pyphant/setup.cfg	2011-12-02 13:42:09 UTC (rev 708)
@@ -1,4 +0,0 @@
-# -*- coding: utf-8 -*-
-[egg_info]
-tag_build = .dev
-tag_svn_revision = 1

Modified: tags/pyphant-1.0b1/src/pyphant/setup.py
===================================================================
--- tags/pyphant-1.0b1/src/pyphant/setup.py	2011-12-02 13:21:01 UTC (rev 707)
+++ tags/pyphant-1.0b1/src/pyphant/setup.py	2011-12-02 13:42:09 UTC (rev 708)
@@ -4,33 +4,38 @@
 __id__ = '$Id: $'
 __revision__ = '$Revision: 25 $'
 
-VERSION = '0.5'
+VERSION = '1.0b1'
 
 
 from setuptools import setup, find_packages
 
-setup( name='pyphant',
-       version = VERSION,
-       description='Workflow modelling app',
-       author='Klaus Zimmermann, Andreas W. Liehr',
-       author_email='kla...@fm...',
-       maintainer='Klaus Zimmermann',
-       maintainer_email='zk...@so...',
-       license = "BSD",
-       url='http://pyphant.sourceforge.net/',
-       install_requires=['sogl>=0.2.0',
-                         'egenix-mx-base',
-			 'paste',
-                         'simplejson',
-                         ## The following are required, but currently not setuptools enabled.
-                         #'ScientificPython>=2.6',
-                         #'matplotlib>=0.90.1',
-                         #'scipy>=0.5.2',
-                         #'tables>=1.4',
-                         #'wxPython>=2.6.3.2',
-                         ],
-       packages = find_packages(),
-       entry_points={'gui_scripts':['wxPyphant = pyphant.wxgui2.wxPyphantApplication:startWxPyphant']},
-       include_package_data = True,
-       test_suite = 'pyphant.tests'
-       )
+setup(
+    name='pyphant',
+    version=VERSION,
+    description='Workflow modelling app',
+    author='Alexander Held, Andreas W. Liehr, Klaus Zimmermann',
+    author_email='ale...@fm...',
+    maintainer='Alexander Held',
+    maintainer_email='ale...@fm...',
+    license="BSD",
+    url='http://pyphant.sourceforge.net/',
+    install_requires=[
+        'sogl>=0.2.0',
+        'paste',
+        'simplejson',
+        ## The following are required,
+        ## but currently not setuptools enabled.
+        #'ScientificPython',
+        #'matplotlib',
+        #'scipy',
+        #'tables',
+        #'wxPython',
+        #'egenix-mx-base',
+        ],
+    packages=find_packages(),
+    entry_points={'gui_scripts':[
+        'wxPyphant = pyphant.wxgui2.wxPyphantApplication:startWxPyphant'
+        ]},
+    include_package_data=True,
+    test_suite='pyphant.tests'
+    )

Deleted: tags/pyphant-1.0b1/src/workers/ImageProcessing/setup.cfg
===================================================================
--- tags/pyphant-1.0b1/src/workers/ImageProcessing/setup.cfg	2011-12-02 13:21:01 UTC (rev 707)
+++ tags/pyphant-1.0b1/src/workers/ImageProcessing/setup.cfg	2011-12-02 13:42:09 UTC (rev 708)
@@ -1,4 +0,0 @@
-# -*- coding: utf-8 -*-
-[egg_info]
-tag_build = .dev
-tag_svn_revision = 1

Modified: tags/pyphant-1.0b1/src/workers/ImageProcessing/setup.py
===================================================================
--- tags/pyphant-1.0b1/src/workers/ImageProcessing/setup.py	2011-12-02 13:21:01 UTC (rev 707)
+++ tags/pyphant-1.0b1/src/workers/ImageProcessing/setup.py	2011-12-02 13:42:09 UTC (rev 708)
@@ -9,24 +9,29 @@
 http://pyphant.sourceforge.net for more information.
 """
 
-__author__ = "Klaus Zimmermann, Andreas W. Liehr"
+__author__ = "Alexander Held, Andreas W. Liehr, Klaus Zimmermann"
 
 __id__ = '$Id$'
 __revision__ = '$Revision: 25 $'
 
-VERSION = '0.1'
+VERSION = '1.0b1'
 
 import setuptools
 
 setuptools.setup(
-    name = "pyphant.imageprocessing",
-    version = VERSION,
-    author = __author__,
-    description = __doc__,
-    install_requires=['pyphant>=0.4alpha3'],
-    packages = ['ImageProcessing'],
-    entry_points = """
+    name="pyphant.imageprocessing",
+    version=VERSION,
+    author=__author__,
+    author_email='ale...@fm...',
+    maintainer='Alexander Held',
+    maintainer_email='ale...@fm...',
+    license="BSD",
+    description=__doc__,
+    install_requires=['pyphant>=1.0b1'],
+    packages=['ImageProcessing'],
+    entry_points="""
     [pyphant.workers]
     myeentry = ImageProcessing
     """,
-    test_suite = 'ImageProcessing.tests')
+    test_suite='ImageProcessing.tests'
+    )

Deleted: tags/pyphant-1.0b1/src/workers/OSC/setup.cfg
===================================================================
--- tags/pyphant-1.0b1/src/workers/OSC/setup.cfg	2011-12-02 13:21:01 UTC (rev 707)
+++ tags/pyphant-1.0b1/src/workers/OSC/setup.cfg	2011-12-02 13:42:09 UTC (rev 708)
@@ -1,4 +0,0 @@
-# -*- coding: utf-8 -*-
-[egg_info]
-tag_build = .dev
-tag_svn_revision = 1

Modified: tags/pyphant-1.0b1/src/workers/OSC/setup.py
===================================================================
--- tags/pyphant-1.0b1/src/workers/OSC/setup.py	2011-12-02 13:21:01 UTC (rev 707)
+++ tags/pyphant-1.0b1/src/workers/OSC/setup.py	2011-12-02 13:42:09 UTC (rev 708)
@@ -6,24 +6,29 @@
 Visit http://pyphant.sourceforge.net for more information.
 """
 
-__author__ = "Klaus Zimmermann, Andreas W. Liehr"
+__author__ = "Andreas W. Liehr, Klaus Zimmermann"
 
 __id__ = '$Id$'
 __revision__ = '$Revision: 25 $'
 
-VERSION = '0.1'
+VERSION = '1.0b1'
 
 import setuptools
 
 setuptools.setup(
-    name = "pyphant.osc",
-    version = VERSION,
-    author = __author__,
-    description = __doc__,
-    install_requires=['pyphant>=0.4alpha3'],
-    packages = ['OSC'],
-    entry_points = """
+    name="pyphant.osc",
+    version=VERSION,
+    author=__author__,
+    author_email='kla...@fm...',
+    maintainer='Klaus Zimmermann',
+    maintainer_email='kla...@fm...',
+    license="BSD",
+    description=__doc__,
+    install_requires=['pyphant>=1.0b1'],
+    packages=['OSC'],
+    entry_points="""
     [pyphant.workers]
     myeentry = OSC
     """,
-    test_suite='OSC.tests')
+    test_suite='OSC.tests'
+    )

Deleted: tags/pyphant-1.0b1/src/workers/Statistics/setup.cfg
===================================================================
--- tags/pyphant-1.0b1/src/workers/Statistics/setup.cfg	2011-12-02 13:21:01 UTC (rev 707)
+++ tags/pyphant-1.0b1/src/workers/Statistics/setup.cfg	2011-12-02 13:42:09 UTC (rev 708)
@@ -1,4 +0,0 @@
-# -*- coding: utf-8 -*-
-[egg_info]
-tag_build = .dev
-tag_svn_revision = 1

Modified: tags/pyphant-1.0b1/src/workers/Statistics/setup.py
===================================================================
--- tags/pyphant-1.0b1/src/workers/Statistics/setup.py	2011-12-02 13:21:01 UTC (rev 707)
+++ tags/pyphant-1.0b1/src/workers/Statistics/setup.py	2011-12-02 13:42:09 UTC (rev 708)
@@ -9,24 +9,29 @@
 http://pyphant.sourceforge.net for more information.
 """
 
-__author__ = "Klaus Zimmermann, Andreas W. Liehr"
+__author__ = "Alexander Held, Andreas W. Liehr, Klaus Zimmermann"
 
 __id__ = '$Id$'
 __revision__ = '$Revision: 25 $'
 
-VERSION = '0.1'
+VERSION = '1.0b1'
 
 import setuptools
 
 setuptools.setup(
-    name = "pyphant.statistics",
-    version = VERSION,
-    author = __author__,
-    description = __doc__,
-    install_requires=['pyphant>=0.4alpha3'],
-    packages = ['Statistics'],
-    entry_points = """
+    name="pyphant.statistics",
+    version=VERSION,
+    author=__author__,
+    author_email='ale...@fm...',
+    maintainer='Alexander Held',
+    maintainer_email='ale...@fm...',
+    license="BSD",
+    description=__doc__,
+    install_requires=['pyphant>=1.0b1'],
+    packages=['Statistics'],
+    entry_points="""
     [pyphant.workers]
     myeentry = Statistics
     """,
-    test_suite = 'Statistics.tests')
+    test_suite='Statistics.tests'
+    )

Deleted: tags/pyphant-1.0b1/src/workers/fmfile/setup.cfg
===================================================================
--- tags/pyphant-1.0b1/src/workers/fmfile/setup.cfg	2011-12-02 13:21:01 UTC (rev 707)
+++ tags/pyphant-1.0b1/src/workers/fmfile/setup.cfg	2011-12-02 13:42:09 UTC (rev 708)
@@ -1,4 +0,0 @@
-# -*- coding: utf-8 -*-
-[egg_info]
-tag_build = .dev
-tag_svn_revision = 1

Modified: tags/pyphant-1.0b1/src/workers/fmfile/setup.py
===================================================================
--- tags/pyphant-1.0b1/src/workers/fmfile/setup.py	2011-12-02 13:21:01 UTC (rev 707)
+++ tags/pyphant-1.0b1/src/workers/fmfile/setup.py	2011-12-02 13:42:09 UTC (rev 708)
@@ -6,28 +6,35 @@
 Visit http://pyphant.sourceforge.net for more information.
 """
 
-__author__ = "Klaus Zimmermann, Andreas W. Liehr"
+__author__ = "Alexander Held, Andreas W. Liehr, Rolf Wuerdemann, " +\
+             "Klaus Zimmermann"
 
 __id__ = '$Id$'
 __revision__ = '$Revision: 25 $'
 
-VERSION = '0.1'
+VERSION = '1.0b1'
 
 import setuptools
 
 setuptools.setup(
-    name = "pyphant.fmf",
-    version = VERSION,
-    author = __author__,
-    description = __doc__,
-    install_requires=['pyphant>=0.4alpha3',
-                      'ConfigObj'
-                      ],
-    packages = ['fmfile'],
-    entry_points = """
+    name="pyphant.fmf",
+    version=VERSION,
+    author=__author__,
+    author_email='ale...@fm...',
+    maintainer='Alexander Held',
+    maintainer_email='ale...@fm...',
+    license="BSD",
+    description=__doc__,
+    install_requires=[
+        'pyphant>=1.0b1',
+        'ConfigObj'
+        ],
+    packages=['fmfile'],
+    entry_points="""
     [pyphant.workers]
     myeentry = fmfile
     [pyphant.visualizers]
     pil.image = fmfile.FMFWriter:FMFWriter
     """,
-    test_suite='fmfile.tests')
+    test_suite='fmfile.tests'
+    )

Deleted: tags/pyphant-1.0b1/src/workers/tools/setup.cfg
===================================================================
--- tags/pyphant-1.0b1/src/workers/tools/setup.cfg	2011-12-02 13:21:01 UTC (rev 707)
+++ tags/pyphant-1.0b1/src/workers/tools/setup.cfg	2011-12-02 13:42:09 UTC (rev 708)
@@ -1,4 +0,0 @@
-# -*- coding: utf-8 -*-
-[egg_info]
-tag_build = .dev
-tag_svn_revision = 1

Modified: tags/pyphant-1.0b1/src/workers/tools/setup.py
===================================================================
--- tags/pyphant-1.0b1/src/workers/tools/setup.py	2011-12-02 13:21:01 UTC (rev 707)
+++ tags/pyphant-1.0b1/src/workers/tools/setup.py	2011-12-02 13:42:09 UTC (rev 708)
@@ -6,24 +6,29 @@
 Visit http://pyphant.sourceforge.net for more information.
 """
 
-__author__ = "Klaus Zimmermann, Kai Kaminski"
+__author__ = "Alexander Held, Klaus Zimmermann"
 
 __id__ = '$Id$'
 __revision__ = '$Revision: 25 $'
 
-VERSION = '0.1'
+VERSION = '1.0b1'
 
 import setuptools
 
 setuptools.setup(
-    name = "pyphant.tools",
-    version = VERSION,
-    author = __author__,
-    description = __doc__,
-    install_requires=['pyphant>=0.4alpha3'],
-    packages = ['tools'],
-    entry_points = """
+    name="pyphant.tools",
+    version=VERSION,
+    author=__author__,
+    author_email='ale...@fm...',
+    maintainer='Alexander Held',
+    maintainer_email='ale...@fm...',
+    license="BSD",
+    description=__doc__,
+    install_requires=['pyphant>=1.0b1'],
+    packages=['tools'],
+    entry_points="""
     [pyphant.workers]
     myeentry = tools
     """,
-    test_suite='tools.tests')
+    test_suite='tools.tests'
+    )

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Pyphant-devel] SF.net SVN: pyphant:[707] tags/pyphant-1.0b1/

From: <ah...@us...> - 2011-12-02 13:21:07

Revision: 707
          http://pyphant.svn.sourceforge.net/pyphant/?rev=707&view=rev
Author:   aheld84
Date:     2011-12-02 13:21:01 +0000 (Fri, 02 Dec 2011)
Log Message:
-----------
cloned svn-trunk

Added Paths:
-----------
    tags/pyphant-1.0b1/

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Pyphant-devel] SF.net SVN: pyphant:[706] trunk/src/pyphant/pyphant/cli

From: <ah...@us...> - 2011-11-30 16:16:16

Revision: 706
          http://pyphant.svn.sourceforge.net/pyphant/?rev=706&view=rev
Author:   aheld84
Date:     2011-11-30 16:16:10 +0000 (Wed, 30 Nov 2011)
Log Message:
-----------
Merge branch 'master' into svn-trunk

* master:
  Fix: simpleCLI.py
  Fix: Removed broken cli/demo.h5

Modified Paths:
--------------
    trunk/src/pyphant/pyphant/cli/demo.h5
    trunk/src/pyphant/pyphant/cli/simpleCLI.py

Modified: trunk/src/pyphant/pyphant/cli/demo.h5
===================================================================
(Binary files differ)

Modified: trunk/src/pyphant/pyphant/cli/simpleCLI.py
===================================================================
--- trunk/src/pyphant/pyphant/cli/simpleCLI.py	2011-11-29 09:19:11 UTC (rev 705)
+++ trunk/src/pyphant/pyphant/cli/simpleCLI.py	2011-11-30 16:16:10 UTC (rev 706)
@@ -42,14 +42,14 @@
     recipe = handler.loadRecipe()
 
 #Configure ImageLoaderWorker
-inputWorker = recipe.getWorkers('Image Loader')[0]
+inputWorker = recipe.getWorker('Load Image')
 imageName = 'demo.png'
 inputWorker.getParam('filename').value=imageName
 
 #Fetch Result
-worker = recipe.getWorkers('Apply Mask')[0]
-result = worker.plugCreateMaskedImage.getResult()
+worker = recipe.getWorker('Invert')
+result = worker.plugInvert.getResult()
 
 #Visualise result
 visualizer = ImageVisualizer(result)
-visualizer.figure.savefig('result-'+imageName)
+visualizer.figure.savefig('result-' + imageName)

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Pyphant-devel] SF.net SVN: pyphant:[705] trunk/src

From: <ah...@us...> - 2011-11-29 09:19:18

Revision: 705
          http://pyphant.svn.sourceforge.net/pyphant/?rev=705&view=rev
Author:   aheld84
Date:     2011-11-29 09:19:11 +0000 (Tue, 29 Nov 2011)
Log Message:
-----------
Merge branch 'master' into svn-trunk

* master:
  Cosm: Cleaned up code
  Bugfix: Gravitational constant 'Grav' of FMFversion 1.0 is correctly interpreted.
  Refactoring ParseQuantities: Explicitely checking for changed units has the disadvantage to fail on combined units.
  Refactoring str2unit: The function has been refactured in order to fix some bugs, but this is just a work around, because other bugs keep crawling out of their holes.
  ParseQuantities: Bugfix, reading FMF 1.0 does not accidentially convert some values to base units due to floating point accuracy.
  ParseQuantity: Refactored str2unit

Modified Paths:
--------------
    trunk/src/pyphant/pyphant/quantities/ParseQuantities.py
    trunk/src/pyphant/pyphant/tests/TestParseQuantities.py
    trunk/src/workers/fmfile/fmfile/tests/TestFMFLoader.py

Modified: trunk/src/pyphant/pyphant/quantities/ParseQuantities.py
===================================================================
--- trunk/src/pyphant/pyphant/quantities/ParseQuantities.py	2011-11-18 15:34:32 UTC (rev 704)
+++ trunk/src/pyphant/pyphant/quantities/ParseQuantities.py	2011-11-29 09:19:11 UTC (rev 705)
@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 
 # Copyright (c) 2008-2009, Rectorate of the University of Freiburg
-# Copyright (c) 2009-2010, Andreas W. Liehr (li...@us...)
+# Copyright (c) 2009-2011, Andreas W. Liehr (li...@us...)
 # All rights reserved.
 #
 # Redistribution and use in source and binary forms, with or without
@@ -45,52 +45,70 @@
 import logging
 _logger = logging.getLogger("pyphant")
 
-def str2unit(unit,FMFversion='1.1'):
-    """The function str2unit returns either a quantity or a float from a given string."""
+def str2unit(unitStr, FMFversion='1.1'):
+    """return float or Quantity instance
+
+    The function str2unit is a factory, which either returns a float
+    or a Quantity instance from a given string.
+    Because the definition of units and physical constants is not unique for
+    FMFversion 1.0 (http://arxiv.org/abs/0904.1299) and
+    FMFversion 1.1 (http://dx.doi.org/10.1016/j.cpc.2009.11.014),
+    the result of str2unit() depends on FMFversion.
+    """
+    if FMFversion not in ['1.0', '1.1']:
+        raise ValueError('FMFversion %s not supported.' % (FMFversion, ))
+    # Deal with exceptional units like '%' or 'a.u.'
+    if unitStr.endswith('%'):
+        if len(unitStr.strip()) == 1:
+            return 0.01
+        else:
+            return float(unitStr[:-1]) / 100.0
+    elif unitStr.endswith('a.u.'):
+        if len(unitStr.strip()) == 4:
+            return 1.0
+        else:
+            return float(unitStr[:-4])
     # Prepare conversion to quantity
-    if unit.startswith('.'):
-        unit = '0'+unit
-    elif unit.endswith('%'):
+    if unitStr.startswith('.'):
+        unitStr = '0' + unitStr
+    elif not (unitStr[0].isdigit() or unitStr[0] == '-'):
+        unitStr = '1' + unitStr
+    # Convert input to quantity or float
+    unitStr = unitStr.replace('^', '**')
+    try: #FMFversion == '1.1'
+        unit = Quantity(unitStr.encode('utf-8'))
+    except:
+        unit = None
+    if FMFversion == '1.0':
         try:
-            unit = float(unit[:-1])/100.0
-        except: 
-            unit = 0.01
-    elif unit.endswith('a.u.'):
+            unit1_0 = PhysicalQuantity(unitStr.encode('utf-8'))
+            unit1_1 = Quantity(str(unit1_0.inBaseUnits()))
+        except:
+            unit1_1 = None
+        if isinstance(unit1_1, Quantity): # Unit exists in 1.0
+            if isinstance(unit, Quantity): # Unit also exists in 1.1
+                if unit.isCompatible(unit1_1.unit):
+                    # Interpretation of unit has not changed
+                    unit = unit1_1.inUnitsOf(unit.unit)
+                else:
+                    unit = unit1_1
+                    _logger.warn('Usage of old unit "%s" required '
+                                 'conversion to base units.' % (unitStr, ))
+            else:
+                unit = unit1_1
+                _logger.warn('Usage of old unit "%s" required '
+                             'conversion to base units.' % (unitStr, ))
+    if unit is None:
         try:
-            unit = float(unit[:-4])
+            if 'j' in unitStr:
+                unit = complex(unitStr)
+            else:
+                unit = float(unitStr)
         except:
-            unit = 1.0
-    elif not (unit[0].isdigit() or unit[0]=='-'):
-        unit = '1'+unit
-    # Convert input to quantity or float
-    if FMFversion not in ['1.0','1.1']:
-        raise ValueError, 'FMFversion %s not supported.' % FMFversion
-    else:
-        try:
-            unit = unit.replace('^', '**')
-            if FMFversion=='1.1':
-                unit = Quantity(unit.encode('utf-8'))
-            elif FMFversion=='1.0':
-                unit1_0 = PhysicalQuantity(unit.encode('utf-8'))
-                unit = Quantity(str(unit1_0.inBaseUnits()))
-                try:
-                    unit_new = Quantity(str(unit1_0))
-                    if unit_new == unit:
-                        unit = unit_new
-                    else:
-                        _logger.warn('Usage of old unit "%s" required '
-                                     'conversion to base units.' % unit1_0)
-                except:
-                    _logger.warn('Usage of old unit "%s" required '
-                                 'conversion to base units.' % unit1_0)
-        except Exception, e:
-            try:
-                unit = float(unit)
-            except:
-                raise e
+            raise ValueError("Unit %s cannot be interpreted." % (unitStr, ))
     return unit
 
-def parseQuantity(value,FMFversion='1.1'):
+def parseQuantity(value, FMFversion='1.1'):
     import re
     pm = re.compile(ur"(?:\\pm|\+-|\+/-)")
     try:
@@ -106,36 +124,39 @@
         value = str2unit(value,FMFversion)
     if error != None:
         if error.endswith('%'):
-            error = value*float(error[:-1])/100.0
+            error = value * float(error[:-1]) / 100.0
         else:
             try:
-                error = float(error)*unit
+                error = float(error) * unit
             except:
-                error = str2unit(error,FMFversion)
+                error = str2unit(error, FMFversion)
     return value, error
 
-def parseVariable(oldVal,FMFversion='1.1'):
+def parseVariable(oldVal, FMFversion='1.1'):
     shortname, value = tuple([s.strip() for s in oldVal.split('=')])
-    value, error = parseQuantity(value,FMFversion)
+    value, error = parseQuantity(value, FMFversion)
     return (shortname, value, error)
 
-def parseDateTime(value,FMFversion='1.1'):
+def parseDateTime(value, FMFversion='1.1'):
     """
     >>>parseDateTime('2004-08-21 12:00:00+-12hr')
-    (Quantity(731814.5,'d'), Quantity(0.5,'d'))
+    (Quantity(731814.5, 'd'), Quantity(0.5, 'd'))
     >>>parseDateTime('2004-08-21 12:00:00')
-    (Quantity(731814.5,'d'), None)
+    (Quantity(731814.5, 'd'), None)
     """
     datetimeWithError = value.split('+-')
-    if len(datetimeWithError)==2:
+    if len(datetimeWithError) == 2:
         datetime = mx.DateTime.ISO.ParseAny(datetimeWithError[0])
-        uncertainty = parseQuantity(datetimeWithError[1],FMFversion)[0]
+        uncertainty = parseQuantity(datetimeWithError[1], FMFversion)[0]
         if uncertainty.isCompatible('h'):
-            _logger.warning("The uncertainty of timestamp %s has the unit 'h', which is deprecated. The correct abbreviation for hour is 'hr'." % value)
-            uncertainty = uncertainty*Quantity('1hr/h')
+            _logger.warning(
+                "The uncertainty of timestamp %s has the unit 'h', "
+                "which is deprecated. "
+                "The correct abbreviation for hour is 'hr'." % (value, ))
+            uncertainty = uncertainty * Quantity('1hr/h')
         error = uncertainty.inUnitsOf('d')
     else:
         datetime = mx.DateTime.ISO.ParseAny(value)
         error = None
-    days,seconds = datetime.absvalues()
-    return (Quantity(days,'d')+Quantity(seconds,'s'),error)
+    days, seconds = datetime.absvalues()
+    return (Quantity(days, 'd') + Quantity(seconds, 's'), error)

Modified: trunk/src/pyphant/pyphant/tests/TestParseQuantities.py
===================================================================
--- trunk/src/pyphant/pyphant/tests/TestParseQuantities.py	2011-11-18 15:34:32 UTC (rev 704)
+++ trunk/src/pyphant/pyphant/tests/TestParseQuantities.py	2011-11-29 09:19:11 UTC (rev 705)
@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 
 # Copyright (c) 2009, Rectorate of the University of Freiburg
-# Copyright (c) 2009-2010, Andreas W. Liehr (li...@us...)
+# Copyright (c) 2009-2011, Andreas W. Liehr (li...@us...)
 # All rights reserved.
 #
 # Redistribution and use in source and binary forms, with or without
@@ -35,54 +35,86 @@
 
 import pkg_resources
 pkg_resources.require('pyphant')
-
-import unittest, numpy
+import unittest
 from pyphant.quantities.ParseQuantities import parseDateTime,str2unit
 from pyphant.quantities import Quantity
-"""
+
+
+class TestParseDateTime(unittest.TestCase):
+    """
     >>>parseDateTime('2004-08-21 12:00:00+-12hr')
-    (Quantity(731814.5,'d'), Quantity(0.5,'d'))
+    (Quantity(731814.5, 'd'), Quantity(0.5, 'd'))
     >>>parseDateTime('2004-08-21 12:00:00')
-    (Quantity(731814.5,'d'), None)
-"""
-class TestParseDateTime(unittest.TestCase):
+    (Quantity(731814.5, 'd'), None)
+    """
+
     def testWithError(self):
         self.assertEqual(parseDateTime('2004-08-21 12:00:00+-12hr'),
-                         (Quantity(731814.5,'d'), Quantity(0.5,'d'))
+                         (Quantity(731814.5, 'd'), Quantity(0.5, 'd'))
                          )
 
     def testWithErrorOldDeprecatedAbbreviation(self):
         self.assertEqual(parseDateTime('2004-08-21 12:00:00+-12h'),
-                         (Quantity(731814.5,'d'), Quantity(0.5,'d'))
+                         (Quantity(731814.5, 'd'), Quantity(0.5, 'd'))
                          )
 
+
 class TestStr2unit(unittest.TestCase):
     """Test the correct conversion of strings to quantities or floats."""
+
+    def setUp(self):
+        self.inputDict = {'complexJ':'1.0j', 'Joule':'1.0J'}
+
     def testSimpleQuantity(self):
-        """The the conversion of a simple textual quantity specification to a quantity object."""
+        """
+        The the conversion of a simple textual quantity specification
+        to a quantity object.
+        """
         expected = Quantity('1V')
         result = str2unit('1V')
-        self.assertEqual(expected,result)
+        self.assertEqual(expected, result)
 
-    def setUp(self):
-        self.inputDict = {'complexJ':'1.0j','Joule':'1.0J'}
+    def testComplexNumber(self):
+        """
+        Complex numbers have to be denoted by small 'j',
+        in oder to discriminate them from Joule.
+        """
+        result = str2unit(self.inputDict['complexJ'])
+        self.assertEqual(result, complex(self.inputDict['complexJ']))
 
     def testJouleValue(self):
         """Physical quantities with unit Joule are indicated by 'J'."""
         result = str2unit(self.inputDict['Joule'])
-        self.assertEqual(result,Quantity(self.inputDict['Joule']))
+        self.assertEqual(result, Quantity(self.inputDict['Joule']))
 
     def testHourPlanck(self):
-        """In FMF 1.0 unit 'h' denotes hours, while in FMF 1.1 'h' denotes the Planck constant."""
+        """
+        In FMF 1.0 unit 'h' denotes hours,
+        while in FMF 1.1 'h' denotes the Planck constant.
+        """
         result = str2unit('1h')
-        self.assertEqual(result,Quantity('6.62606896e-34 J*s'))
-        result = str2unit('1h',FMFversion='1.0')
-        self.assertEqual(result,Quantity('3600s'))
+        self.assertEqual(result, Quantity('6.62606896e-34 J*s'))
+        result = str2unit('1h', FMFversion='1.0')
+        self.assertEqual(result, Quantity('3600s'))
 
+    def testFloatAccuracy(self):
+        result = str2unit('16.8 mm', FMFversion='1.0')
+        diff = result - Quantity('16.8 mm')
+        self.assertEqual(abs(diff.value) < 2e-14,True)
+        result = str2unit('16.8 mm', FMFversion='1.0')
+        diff = Quantity('16.8 mm')
+        self.assertEqual(result, diff)
+
+    def testGravitationalConstant(self):
+        result = str2unit("1 Grav", FMFversion="1.0")
+        self.assertEqual(result, str2unit('6.67259e-11 m**3/kg/s**2'))
+
+
 if __name__ == "__main__":
     import sys
     if len(sys.argv) == 1:
         unittest.main()
     else:
-        suite = unittest.TestLoader().loadTestsFromTestCase(eval(sys.argv[1:][0]))
+        suite = unittest.TestLoader().loadTestsFromTestCase(
+            eval(sys.argv[1:][0]))
         unittest.TextTestRunner().run(suite)

Modified: trunk/src/workers/fmfile/fmfile/tests/TestFMFLoader.py
===================================================================
--- trunk/src/workers/fmfile/fmfile/tests/TestFMFLoader.py	2011-11-18 15:34:32 UTC (rev 704)
+++ trunk/src/workers/fmfile/fmfile/tests/TestFMFLoader.py	2011-11-29 09:19:11 UTC (rev 705)
@@ -1,8 +1,8 @@
-#!/usr/bin/env python2.5
+#!/usr/bin/env python2.6
 # -*- coding: utf-8 -*-
 
 # Copyright (c) 2008-2009,  Rectorate of the University of Freiburg
-# Copyright (c) 2009-2010, Andreas W. Liehr (li...@us...)
+# Copyright (c) 2009-2011, Andreas W. Liehr (li...@us...)
 # All rights reserved.
 #
 # Redistribution and use in source and binary forms, with or without
@@ -45,15 +45,22 @@
 from pyphant.quantities.ParseQuantities import str2unit
 from copy import deepcopy
 
+#Estimate floating point accuracy
+ACCURACY = 1.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.
+
 class FieldContainerCondenseDim(unittest.TestCase):
     def setUp(self):
         self.x = numpy.linspace(0,0.9,10)
         m = numpy.meshgrid(self.x, self.x*5)
         self.valid = numpy.tile(self.x, (10,1))
-        self.invalid = [ a.squeeze() for a in numpy.vsplit(m[0]+m[1], len(m[0])) ]
+        self.invalid = [
+            a.squeeze() for a in numpy.vsplit(m[0] + m[1], len(m[0]))
+            ]
 
     def testInvalid(self):
-        self.assertRaises(AssertionError, FMFLoader.checkAndCondense, self.invalid)
+        self.assertRaises(
+            AssertionError, FMFLoader.checkAndCondense, self.invalid
+            )
 
     def testValid(self):
         result = FMFLoader.checkAndCondense(self.valid)
@@ -61,75 +68,100 @@
 
 class TestColumn2FieldContainer(unittest.TestCase):
     def testStrings(self):
-        column = ['Hello','World']
-        result = FMFLoader.column2FieldContainer('simple string',column)
-        expectedResult = FieldContainer(numpy.array(column),longname='simple string')
-        assertEqual(result,expectedResult)
+        column = ['Hello', 'World']
+        result = FMFLoader.column2FieldContainer('simple string', column)
+        expectedResult = FieldContainer(
+            numpy.array(column), longname='simple string'
+            )
+        assertEqual(result, expectedResult)
 
     def testListofStrings(self):
-        column = ['World',['Hello', 'World'],'World']
-        result = FMFLoader.column2FieldContainer('simple string',column)
-        expectedResult = FieldContainer(numpy.array(['World','Hello, World','World']),longname='simple string')
-        assertEqual(result,expectedResult)
+        column = ['World', ['Hello', 'World'], 'World']
+        result = FMFLoader.column2FieldContainer('simple string', column)
+        expectedResult = FieldContainer(
+            numpy.array(['World', 'Hello, World', 'World']),
+            longname='simple string'
+            )
+        assertEqual(result, expectedResult)
 
     def testListofStrings2(self):
-        column = [['Hello', 'World'],'World']
-        result = FMFLoader.column2FieldContainer('simple string',column)
-        expectedResult = FieldContainer(numpy.array(['Hello, World','World']),longname='simple string')
-        assertEqual(result,expectedResult)
+        column = [['Hello', 'World'], 'World']
+        result = FMFLoader.column2FieldContainer('simple string', column)
+        expectedResult = FieldContainer(
+            numpy.array(['Hello, World', 'World']), longname='simple string'
+            )
+        assertEqual(result, expectedResult)
 
     def testVariable(self):
-        column = [('T',Quantity('22.4 degC'),Quantity('0.5 degC')),
-                  ('T',Quantity('11.2 degC'),Quantity('0.5 degC'))
-                  ]
-        result = FMFLoader.column2FieldContainer('temperature',column)
-        expectedResult = FieldContainer(numpy.array([22.4,11.2]),error=numpy.array([0.5,0.5]),
-                                        mask = numpy.array([False,False]),
-                                        unit='1 degC',longname='temperature',shortname='T')
-        assertEqual(result,expectedResult)
+        column = [
+            ('T', Quantity('22.4 degC'), Quantity('0.5 degC')),
+            ('T', Quantity('11.2 degC'), Quantity('0.5 degC'))
+            ]
+        result = FMFLoader.column2FieldContainer('temperature', column)
+        expectedResult = FieldContainer(
+            numpy.array([22.4, 11.2]) ,error=numpy.array([0.5, 0.5]),
+            mask=numpy.array([False, False]),
+            unit='1 degC', longname='temperature', shortname='T'
+            )
+        assertEqual(result, expectedResult)
 
     def testVariableWithNaN(self):
-        column = [('T',Quantity('22.4 degC'),Quantity('0.5 degC')),
-                  ('T',Quantity('11.2 degC'),None)
-                  ]
-        result = FMFLoader.column2FieldContainer('temperature',column)
-        expectedResult = FieldContainer(numpy.array([22.4,11.2]),error=numpy.array([0.5,0.0]),
-                                        mask = numpy.array([False,False]),
-                                        unit='1 degC',longname='temperature',shortname='T')
-        assertEqual(result,expectedResult)
+        column = [
+            ('T', Quantity('22.4 degC'), Quantity('0.5 degC')),
+            ('T', Quantity('11.2 degC'), None)
+            ]
+        result = FMFLoader.column2FieldContainer('temperature', column)
+        expectedResult = FieldContainer(
+            numpy.array([22.4, 11.2]), error=numpy.array([0.5, 0.0]),
+            mask = numpy.array([False, False]),
+            unit='1 degC', longname='temperature', shortname='T'
+            )
+        assertEqual(result, expectedResult)
 
     def testVariableFirstNaN(self):
-        column = [('T','NaN',Quantity('0.5 degC')),
-                  ('T',Quantity('11.2 degC'),None)
-                  ]
-        result = FMFLoader.column2FieldContainer('temperature',column)
-        expectedResult = FieldContainer(numpy.array([numpy.NaN,11.2]),error=numpy.array([0.5,0.0]),
-                                        mask = numpy.array([True,False]),
-                                        unit='1 degC',longname='temperature',shortname='T')
-        assertEqual(result,expectedResult)
+        column = [
+            ('T', 'NaN', Quantity('0.5 degC')),
+            ('T', Quantity('11.2 degC'), None)
+            ]
+        result = FMFLoader.column2FieldContainer('temperature', column)
+        expectedResult = FieldContainer(
+            numpy.array([numpy.NaN, 11.2]), error=numpy.array([0.5, 0.0]),
+            mask = numpy.array([True, False]),
+            unit='1 degC', longname='temperature', shortname='T')
+        assertEqual(result, expectedResult)
 
 class TestDiscriminatingJouleAndImaginary(unittest.TestCase):
-    """In order to discriminate between an imaginary number and unit Joule, imaginary numbers have to be indicated only by a minor capital 'j', while a major capital 'J' indicates the unit Joule.
     """
+    In order to discriminate between an imaginary number and unit Joule,
+    imaginary numbers have to be indicated only by a minor capital 'j',
+    while a major capital 'J' indicates the unit Joule.
+    """
     def setUp(self):
-        self.inputDict = {'complexJ':'1.0j','Joule':'1.0J'}
+        self.inputDict = {'complexJ':'1.0j', 'Joule':'1.0J'}
 
-    def testComplexVale(self):
+    def testComplexValue(self):
         """Imaginary numbers are indicated by 'j'."""
         result = FMFLoader.item2value(self.inputDict['complexJ'])
-        self.assertEqual(result,complex(self.inputDict['complexJ']))
+        self.assertEqual(result, (complex(self.inputDict['complexJ']), None))
 
     def testJouleValue1_1(self):
         """Physical quantities with unit Joule are indicated by 'J'."""
         result = FMFLoader.item2value(self.inputDict['Joule'])
-        self.assertEqual(result,(Quantity(self.inputDict['Joule']),None))
+        self.assertEqual(result, (Quantity(self.inputDict['Joule']), None))
 
     def testJouleValue1_0(self):
         """Physical quantities with unit Joule are indicated by 'J'."""
-        result = FMFLoader.item2value(self.inputDict['Joule'],FMFversion='1.0')
-        self.assertEqual(result,(Quantity(self.inputDict['Joule']),None))
+        result = FMFLoader.item2value(
+            self.inputDict['Joule'], FMFversion='1.0'
+            )
+        self.assertEqual(result, (Quantity(self.inputDict['Joule']), None))
 
 class TestFMFversion1_0(unittest.TestCase):
+    def almostEqual(self, a, b):
+        diff = a - b
+        mean = 0.5 * (a + b)
+        self.assertTrue(abs(diff / mean) < ACCURACY)
+
     def setUp(self):
         self.FMFinput = """# -*- fmf-version: 1.0; coding: utf-8 -*-
 [*reference]
@@ -178,31 +210,84 @@
 2	1+1j	2.
 """
     def testReadSingleFile(self):
-        """Test the correct interpretation of physical constants as definied in FMF version 1.0."""
-        consts = FMFLoader.readSingleFile(self.FMFinput,"testReadSingleFile")[0].attributes['Mathematical and Physical Constants']
-        self.assertEqual(consts[u'Speed of light'][1],str2unit("1 c",FMFversion="1.0"))
-        self.assertEqual(consts[u'Speed of light'][1],str2unit("1 c"))
-        self.assertEqual(consts[u'Permeability of vacuum'][1],str2unit("1 mu0",FMFversion="1.0"))
-        self.assertEqual(consts[u'Permittivity of vacuum'][1],str2unit("1 eps0",FMFversion="1.0"))
-        self.assertEqual(consts[u'Gravitational constant'][1],str2unit("1 Grav",FMFversion="1.0"))
-        self.assertEqual(consts[u'Planck constant'][1],str2unit("1 hplanck",FMFversion="1.0"))
-        self.assertEqual(consts[u'Planck constant / 2pi'][1],str2unit("1 hbar",FMFversion="1.0"))
-        self.assertEqual(consts[u'Elementary charge'][1],str2unit("1 e",FMFversion="1.0"))
-        self.assertNotEqual(consts[u'Elementary charge'][1],str2unit("1 e"),
-                         "Elementary charge has been adapted to new CODATA recommendations.")
-        self.assertEqual(consts[u'Electron mass'][1],str2unit("1 me",FMFversion="1.0"))
-        self.assertNotEqual(consts[u'Electron mass'][1],str2unit("1 me"),
-                            "Electron mass has been adapted to new CODATA recommendations.")
-        self.assertEqual(consts[u'Proton mass'][1],str2unit("1 mp",FMFversion="1.0"))
-        self.assertNotEqual(consts[u'Proton mass'][1],str2unit("1 mp"),
-                            "Proton mass has been adapted to new CODATA recommendations.")
-        self.assertEqual(consts[u'Avogadro number'][1],str2unit("1 Nav",FMFversion="1.0"))
-        self.assertEqual(consts[u'Boltzmann constant'][1],str2unit("1 k",FMFversion="1.0"))
-        consts = FMFLoader.readSingleFile(self.FMFinput,"testReadSingleFile")[0].attributes['Additional constants changed from FMF version 1.0 to 1.1']
-        self.assertEqual(consts[u'Parsec'][1],str2unit("1 pc",FMFversion="1.0"))
-        self.assertEqual(consts[u'US gallon'][1],str2unit("1 galUS",FMFversion="1.0"))
-        self.assertEqual(consts[u'Atomic mass units'][1],str2unit("1 amu",FMFversion="1.0"))
+        """
+        Test the correct interpretation of physical constants
+        as definied in FMF version 1.0.
+        """
+        consts = FMFLoader.readSingleFile(
+            self.FMFinput,
+            "testReadSingleFile")[0].attributes[
+            'Mathematical and Physical Constants'
+            ]
+        self.assertEqual(
+            consts[u'Speed of light'][1], str2unit("1 c", FMFversion="1.0")
+            )
+        self.assertEqual(consts[u'Speed of light'][1], str2unit("1 c"))
+        self.assertEqual(
+            consts[u'Permeability of vacuum'][1],
+            str2unit("1 mu0", FMFversion="1.0")
+            )
+        self.assertEqual(
+            consts[u'Permittivity of vacuum'][1],
+            str2unit("1 eps0", FMFversion="1.0")
+            )
+        self.assertEqual(
+            consts[u'Gravitational constant'][1],
+            str2unit("1 Grav", FMFversion="1.0")
+            )
+        self.assertTrue(
+            consts[u'Planck constant'][1],
+            str2unit("1 hplanck", FMFversion="1.0")
+            )
+        self.almostEqual(
+            consts[u'Planck constant / 2pi'][1],
+            str2unit("1 hbar", FMFversion="1.0")
+            )
+        self.almostEqual(
+            consts[u'Elementary charge'][1],
+            str2unit("1 e", FMFversion="1.0")
+            )
+        self.assertNotEqual(
+            consts[u'Elementary charge'][1], str2unit("1 e"),
+            "Elementary charge has been adapted to new CODATA recommendations."
+            )
+        self.assertEqual(
+            consts[u'Electron mass'][1], str2unit("1 me", FMFversion="1.0")
+            )
+        self.assertNotEqual(
+            consts[u'Electron mass'][1], str2unit("1 me"),
+            "Electron mass has been adapted to new CODATA recommendations."
+            )
+        self.assertEqual(
+            consts[u'Proton mass'][1], str2unit("1 mp", FMFversion="1.0")
+            )
+        self.assertNotEqual(
+            consts[u'Proton mass'][1], str2unit("1 mp"),
+            "Proton mass has been adapted to new CODATA recommendations."
+            )
+        self.assertEqual(
+            consts[u'Avogadro number'][1], str2unit("1 Nav", FMFversion="1.0")
+            )
+        self.assertEqual(
+            consts[u'Boltzmann constant'][1], str2unit("1 k", FMFversion="1.0")
+            )
+        consts = FMFLoader.readSingleFile(
+            self.FMFinput,
+            "testReadSingleFile")[0].attributes[
+            'Additional constants changed from FMF version 1.0 to 1.1'
+            ]
+        self.almostEqual(
+            consts[u'Parsec'][1], str2unit("1 pc", FMFversion="1.0")
+            )
+        self.almostEqual(
+            consts[u'US gallon'][1], str2unit("1 galUS", FMFversion="1.0")
+            )
+        self.assertEqual(
+            consts[u'Atomic mass units'][1],
+            str2unit("1 amu", FMFversion="1.0")
+            )
 
+
 class TestFMFversion1_1(unittest.TestCase):
     def setUp(self):
         self.FMFinput = """# -*- fmf-version: 1.1; coding: utf-8 -*-
@@ -255,26 +340,76 @@
 2	1+1j	2.
 """
     def testReadSingleFile(self):
-        """Test the correct interpretation of physical constants as definied in FMF version 1.1."""
-        consts = FMFLoader.readSingleFile(self.FMFinput,"testReadSingleFile")[0].attributes['Mathematical and Physical Constants']
-        self.assertEqual(consts[u'Speed of light'][1],str2unit("1 c",FMFversion="1.1"))
-        self.assertEqual(consts[u'Permeability of vacuum'][1],str2unit("1 mu0",FMFversion="1.1"),
-                         'The values differ by %s.' % (consts[u'Permeability of vacuum'][1]-str2unit("1 mu0",FMFversion="1.1"),))
-        self.assertEqual(consts[u'Permittivity of vacuum'][1],str2unit("1 eps0",FMFversion="1.1"))
-        self.assertEqual(consts[u'Gravitational constant'][1],str2unit("1 G",FMFversion="1.1"))
-        self.assertEqual(consts[u'Planck constant'][1],str2unit("1 h",FMFversion="1.1"))
-        self.assertEqual(consts[u'Planck constant / 2pi'][1],str2unit("1 hbar",FMFversion="1.1"))
-        self.assertEqual(consts[u'Elementary charge'][1],str2unit("1 e",FMFversion="1.1"),
-                         'The elements %s and %s do not match.' % (consts[u'Elementary charge'][1],str2unit("1 e",FMFversion="1.1")))
-        self.assertEqual(consts[u'Electron mass'][1],str2unit("1 me",FMFversion="1.1"))
-        self.assertEqual(consts[u'Proton mass'][1],str2unit("1 mp",FMFversion="1.1"))
-        self.assertEqual(consts[u'Avogadro number'][1],str2unit("1 NA",FMFversion="1.1"))
-        self.assertEqual(consts[u'Boltzmann constant'][1],str2unit("1 k",FMFversion="1.1"))
-        self.assertEqual(consts[u'Rydberg constant'][1],str2unit("1 Ryd",FMFversion="1.1"))
-        consts = FMFLoader.readSingleFile(self.FMFinput,"testReadSingleFile")[0].attributes['Additional constants changed from FMF version 1.0 to 1.1']
-        self.assertEqual(consts[u'Parsec'][1],str2unit("1 pc",FMFversion="1.1"))
-        self.assertEqual(consts[u'US gallon'][1],str2unit("1 galUS",FMFversion="1.1"))
-        self.assertEqual(consts[u'Atomic mass units'][1],str2unit("1 u",FMFversion="1.1"))
+        """
+        Test the correct interpretation of physical constants
+        as definied in FMF version 1.1.
+        """
+        consts = FMFLoader.readSingleFile(
+            self.FMFinput, "testReadSingleFile")[0].attributes[
+            'Mathematical and Physical Constants'
+            ]
+        self.assertEqual(
+            consts[u'Speed of light'][1], str2unit("1 c", FMFversion="1.1")
+            )
+        self.assertEqual(
+            consts[u'Permeability of vacuum'][1],
+            str2unit("1 mu0", FMFversion="1.1"),
+            'The values differ by %s.' % (
+                consts[u'Permeability of vacuum'][1] -\
+                str2unit("1 mu0", FMFversion="1.1"),
+                )
+            )
+        self.assertEqual(
+            consts[u'Permittivity of vacuum'][1],
+            str2unit("1 eps0", FMFversion="1.1")
+            )
+        self.assertEqual(
+            consts[u'Gravitational constant'][1],
+            str2unit("1 G", FMFversion="1.1")
+            )
+        self.assertEqual(
+            consts[u'Planck constant'][1],
+            str2unit("1 h", FMFversion="1.1")
+            )
+        self.assertEqual(
+            consts[u'Planck constant / 2pi'][1],
+            str2unit("1 hbar", FMFversion="1.1")
+            )
+        self.assertEqual(
+            consts[u'Elementary charge'][1], str2unit("1 e",FMFversion="1.1"),
+            'The elements %s and %s do not match.' % (
+                consts[u'Elementary charge'][1],
+                str2unit("1 e", FMFversion="1.1")
+                )
+            )
+        self.assertEqual(
+            consts[u'Electron mass'][1], str2unit("1 me", FMFversion="1.1")
+            )
+        self.assertEqual(
+            consts[u'Proton mass'][1], str2unit("1 mp", FMFversion="1.1")
+            )
+        self.assertEqual(
+            consts[u'Avogadro number'][1], str2unit("1 NA", FMFversion="1.1")
+            )
+        self.assertEqual(
+            consts[u'Boltzmann constant'][1], str2unit("1 k",FMFversion="1.1")
+            )
+        self.assertEqual(
+            consts[u'Rydberg constant'][1], str2unit("1 Ryd", FMFversion="1.1")
+            )
+        consts = FMFLoader.readSingleFile(
+            self.FMFinput, "testReadSingleFile")[0].attributes[
+            'Additional constants changed from FMF version 1.0 to 1.1'
+            ]
+        self.assertEqual(
+            consts[u'Parsec'][1], str2unit("1 pc", FMFversion="1.1")
+            )
+        self.assertEqual(
+            consts[u'US gallon'][1], str2unit("1 galUS", FMFversion="1.1")
+            )
+        self.assertEqual(
+            consts[u'Atomic mass units'][1], str2unit("1 u", FMFversion="1.1")
+            )
 
 
 class Emd5ConsistencyTestCase(unittest.TestCase):
@@ -379,7 +514,6 @@
         self.assertEqual(result.attributes['*reference']['title'], title)
 
 
-
 if __name__ == "__main__":
     import sys
     import logging

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Pyphant-devel] SF.net SVN: pyphant:[704] trunk/src/pyphant/pyphant

From: <ah...@us...> - 2011-11-18 15:34:44

Revision: 704
          http://pyphant.svn.sourceforge.net/pyphant/?rev=704&view=rev
Author:   aheld84
Date:     2011-11-18 15:34:32 +0000 (Fri, 18 Nov 2011)
Log Message:
-----------
Merge branch 'master' into svn-trunk

* master:
  Fix: PyTablesPersister: Annotations of Recipes

Modified Paths:
--------------
    trunk/src/pyphant/pyphant/core/PyTablesPersister.py
    trunk/src/pyphant/pyphant/tests/TestH5FileHandler.py

Modified: trunk/src/pyphant/pyphant/core/PyTablesPersister.py
===================================================================
--- trunk/src/pyphant/pyphant/core/PyTablesPersister.py	2011-11-18 15:01:02 UTC (rev 703)
+++ trunk/src/pyphant/pyphant/core/PyTablesPersister.py	2011-11-18 15:34:32 UTC (rev 704)
@@ -109,6 +109,7 @@
 def saveRecipe(h5, recipe, saveResults=True):
     recipeGroup = h5.createGroup("/", "recipe")
     h5.createGroup("/", "results")
+    h5.setNodeAttr(recipeGroup, "Annotations", recipe._annotations)
     workers = recipe.getWorkers()
     for worker in workers:
         saveWorker(h5, recipeGroup, worker, saveResults)
@@ -257,7 +258,11 @@
 
 def loadRecipe(h5):
     recipeGroup = h5.root.recipe
-    recipe = CompositeWorker.CompositeWorker()
+    try:
+        annotations = recipeGroup._v_attrs.Annotations
+    except AttributeError:
+        annotations = {}
+    recipe = CompositeWorker.CompositeWorker(annotations=annotations)
     workers = {}
     createWorkerGraph(recipeGroup, workers, recipe)
     restoreResultsToWorkers(recipeGroup, workers, h5)

Modified: trunk/src/pyphant/pyphant/tests/TestH5FileHandler.py
===================================================================
--- trunk/src/pyphant/pyphant/tests/TestH5FileHandler.py	2011-11-18 15:01:02 UTC (rev 703)
+++ trunk/src/pyphant/pyphant/tests/TestH5FileHandler.py	2011-11-18 15:34:32 UTC (rev 704)
@@ -244,7 +244,7 @@
         from pyphant.core.CompositeWorker import CompositeWorker
         from pyphant.core.WorkerRegistry import WorkerRegistry
         from itertools import chain
-        recipe = CompositeWorker()
+        recipe = CompositeWorker(annotations={'foo':42.0, 'bar':u'Hääh?'})
         wreg = WorkerRegistry.getInstance()
         workerInfos = [t.workerInfos for t in wreg.getToolBoxInfoList()]
         for wInfo in chain(*workerInfos):
@@ -261,6 +261,7 @@
         loadedWorkerNames = [w.name for w in loadedWorkers]
         for name in loadedWorkerNames:
             self.assertTrue(name in workerNames)
+        self.assertEqual(recipe._annotations, loadedRecipe._annotations)
 
 
 if __name__ == "__main__":

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Pyphant-devel] SF.net SVN: pyphant:[703] trunk/src/pyphant/pyphant

From: <ah...@us...> - 2011-11-18 15:01:16

Revision: 703
          http://pyphant.svn.sourceforge.net/pyphant/?rev=703&view=rev
Author:   aheld84
Date:     2011-11-18 15:01:02 +0000 (Fri, 18 Nov 2011)
Log Message:
-----------
Merge branch 'master' into svn-trunk

* master:
  Fix: Removed direct usage of PyTablesPersister

Modified Paths:
--------------
    trunk/src/pyphant/pyphant/cli/createExecutionOrder.py
    trunk/src/pyphant/pyphant/cli/simpleCLI.py
    trunk/src/pyphant/pyphant/core/H5FileHandler.py
    trunk/src/pyphant/pyphant/core/PyTablesPersister.py
    trunk/src/pyphant/pyphant/tests/TestH5FileHandler.py
    trunk/src/pyphant/pyphant/tests/TestPyTablesPersister.py
    trunk/src/pyphant/pyphant/wxgui2/wxPyphantApplication.py

Modified: trunk/src/pyphant/pyphant/cli/createExecutionOrder.py
===================================================================
--- trunk/src/pyphant/pyphant/cli/createExecutionOrder.py	2011-11-17 11:10:52 UTC (rev 702)
+++ trunk/src/pyphant/pyphant/cli/createExecutionOrder.py	2011-11-18 15:01:02 UTC (rev 703)
@@ -1,6 +1,7 @@
 import pkg_resources
 pkg_resources.require('pyphant')
 from pyphant.core import PyTablesPersister
+from pyphant.core.H5FileHandler import H5FileHandler
 import optparse
 import sys
 
@@ -105,7 +106,8 @@
     orderLists.append(orders[i:])
     for i, orderList in enumerate(orderLists):
         filename = os.path.basename(sourcefile)[:-3]+'_%i.h5'%i
-        PyTablesPersister.saveRecipeToHDF5File(recipe, filename)
+        with H5FileHandler(filename, 'w') as handler:
+            handler.saveRecipe(recipe)
         h5 = tables.openFile(filename, 'r+')
         for o in orderList:
             PyTablesPersister.saveExecutionOrder(h5, o)

Modified: trunk/src/pyphant/pyphant/cli/simpleCLI.py
===================================================================
--- trunk/src/pyphant/pyphant/cli/simpleCLI.py	2011-11-17 11:10:52 UTC (rev 702)
+++ trunk/src/pyphant/pyphant/cli/simpleCLI.py	2011-11-18 15:01:02 UTC (rev 703)
@@ -34,11 +34,12 @@
 __author__ = "$Author: liehr $"
 __version__ = "$Revision: 29 $"
 
-import pyphant.core.PyTablesPersister
+from pyphant.core.H5FileHandler import H5FileHandler
 from pyphant.visualizers.ImageVisualizer import ImageVisualizer
 
 #Load recipe from hdf file
-recipe = pyphant.core.PyTablesPersister.loadRecipeFromHDF5File('demo.h5')
+with H5FileHandler('demo.h5', 'r') as handler:
+    recipe = handler.loadRecipe()
 
 #Configure ImageLoaderWorker
 inputWorker = recipe.getWorkers('Image Loader')[0]
@@ -52,7 +53,3 @@
 #Visualise result
 visualizer = ImageVisualizer(result)
 visualizer.figure.savefig('result-'+imageName)
-
-
-
-

Modified: trunk/src/pyphant/pyphant/core/H5FileHandler.py
===================================================================
--- trunk/src/pyphant/pyphant/core/H5FileHandler.py	2011-11-17 11:10:52 UTC (rev 702)
+++ trunk/src/pyphant/pyphant/core/H5FileHandler.py	2011-11-18 15:01:02 UTC (rev 703)
@@ -39,10 +39,8 @@
 # $Source$:
 import tables
 from pyphant.core import DataContainer
-from tables import StringCol
 from pyphant.quantities import Quantity
 PhysicalQuantity = Quantity
-import scipy
 import logging
 import os
 from pyphant.core import PyTablesPersister
@@ -261,7 +259,7 @@
                        in the file.
         result -- SampleContainer instance to be saved
         """
-        PyTablesPersister.saveSample(self.handle, resultGroup, result)
+        return PyTablesPersister.saveSample(self.handle, resultGroup, result)
 
     def saveField(self, resultGroup, result):
         """
@@ -271,4 +269,13 @@
                        in the file.
         result -- FieldContainer instance to be saved
         """
-        PyTablesPersister.saveField(self.handle, resultGroup, result)
+        return PyTablesPersister.saveField(self.handle, resultGroup, result)
+
+    def saveRecipe(self, recipe, saveResults=True):
+        """
+        Saves a recipe
+
+        recipe -- CompositeWorker to be saved
+        saveResults -- Whether to save results of the workers
+        """
+        return PyTablesPersister.saveRecipe(self.handle, recipe, saveResults)

Modified: trunk/src/pyphant/pyphant/core/PyTablesPersister.py
===================================================================
--- trunk/src/pyphant/pyphant/core/PyTablesPersister.py	2011-11-17 11:10:52 UTC (rev 702)
+++ trunk/src/pyphant/pyphant/core/PyTablesPersister.py	2011-11-18 15:01:02 UTC (rev 703)
@@ -106,15 +106,12 @@
     input.flush()
     orderGroup._v_attrs.resultPlug = order[1]
 
-def saveRecipeToHDF5File(recipe, filename, saveResults=True):
-    _logger.info( "Saving to %s" % filename )
-    h5 = tables.openFile(filename, 'w')
+def saveRecipe(h5, recipe, saveResults=True):
     recipeGroup = h5.createGroup("/", "recipe")
-    resultsGroup = h5.createGroup("/", "results")
-    workers=recipe.getWorkers()
+    h5.createGroup("/", "results")
+    workers = recipe.getWorkers()
     for worker in workers:
         saveWorker(h5, recipeGroup, worker, saveResults)
-    h5.close()
 
 def saveWorker(h5, recipeGroup, worker, saveResults=True):
     workerGroup = h5.createGroup(recipeGroup, "worker_"+str(hash(worker)))
@@ -258,12 +255,6 @@
             except KeyError:
                 _logger.warning(u'Could not restore "%s" to parameter: "%s"'%(param,paramName))
 
-def loadRecipeFromHDF5File( filename ):
-    h5 = tables.openFile(filename, 'r')
-    recipe = loadRecipe(h5)
-    h5.close()
-    return recipe
-
 def loadRecipe(h5):
     recipeGroup = h5.root.recipe
     recipe = CompositeWorker.CompositeWorker()

Modified: trunk/src/pyphant/pyphant/tests/TestH5FileHandler.py
===================================================================
--- trunk/src/pyphant/pyphant/tests/TestH5FileHandler.py	2011-11-17 11:10:52 UTC (rev 702)
+++ trunk/src/pyphant/pyphant/tests/TestH5FileHandler.py	2011-11-18 15:01:02 UTC (rev 703)
@@ -45,8 +45,7 @@
 import pkg_resources
 pkg_resources.require("pyphant")
 from pyphant.quantities import Quantity as PQ
-from pyphant.core.DataContainer import FieldContainer, SampleContainer,\
-    assertEqual
+from pyphant.core.DataContainer import FieldContainer, SampleContainer
 from pyphant.core.H5FileHandler import H5FileHandler as H5FH
 from numpy import array as NPArray
 import os
@@ -56,7 +55,7 @@
 class BasicTestCase(unittest.TestCase):
     def testReadOnlyFileNotFound(self):
         try:
-            handler = H5FH('', 'r')
+            H5FH('', 'r')
             assert False
         except IOError:
             pass
@@ -78,8 +77,8 @@
 class FCSaveLoadTestCase(FieldContainerTestCase):
     def setUp(self):
         FieldContainerTestCase.setUp(self)
-        osHandle, self.fcFilename = mkstemp(suffix = '.h5',
-                                            prefix = 'pyphantH5FileHandlerTest')
+        osHandle, self.fcFilename = mkstemp(
+            suffix = '.h5', prefix = 'pyphantH5FileHandlerTest')
         os.close(osHandle)
 
     def tearDown(self):
@@ -96,8 +95,8 @@
 class FCReadOnlyTestCase(FieldContainerTestCase):
     def setUp(self):
         FieldContainerTestCase.setUp(self)
-        osHandle, self.rofcFilename = mkstemp(suffix = '.h5',
-                                            prefix = 'pyphantH5FileHandlerTest')
+        osHandle, self.rofcFilename = mkstemp(
+            suffix = '.h5', prefix = 'pyphantH5FileHandlerTest')
         os.close(osHandle)
         handler = H5FH(self.rofcFilename, 'w')
         with handler:
@@ -137,11 +136,10 @@
 class SCSaveLoadTestCase(SampleContainerTestCase):
     def setUp(self):
         SampleContainerTestCase.setUp(self)
-        osHandle, self.scFilename = mkstemp(suffix = '.h5',
-                                            prefix = 'pyphantH5FileHandlerTest')
+        osHandle, self.scFilename = mkstemp(
+            suffix = '.h5', prefix = 'pyphantH5FileHandlerTest')
         os.close(osHandle)
 
-
     def tearDown(self):
         os.remove(self.scFilename)
 
@@ -156,8 +154,8 @@
 class SCReadOnlyTestCase(SampleContainerTestCase):
     def setUp(self):
         SampleContainerTestCase.setUp(self)
-        osHandle, self.roscFilename = mkstemp(suffix = '.h5',
-                                            prefix = 'pyphantH5FileHandlerTest')
+        osHandle, self.roscFilename = mkstemp(
+            suffix = '.h5', prefix = 'pyphantH5FileHandlerTest')
         os.close(osHandle)
         handler = H5FH(self.roscFilename, 'w')
         with handler:
@@ -176,8 +174,8 @@
 class MixedAppendTestCase(SampleContainerTestCase):
     def setUp(self):
         SampleContainerTestCase.setUp(self)
-        osHandle, self.appscFilename = mkstemp(suffix = '.h5',
-                                            prefix = 'pyphantH5FileHandlerTest')
+        osHandle, self.appscFilename = mkstemp(
+            suffix = '.h5', prefix = 'pyphantH5FileHandlerTest')
         os.close(osHandle)
         handler = H5FH(self.appscFilename, 'w')
         with handler:
@@ -199,8 +197,8 @@
 class SummaryTestCase(SampleContainerTestCase):
     def setUp(self):
         SampleContainerTestCase.setUp(self)
-        osHandle, self.summFilename = mkstemp(suffix = '.h5',
-                                            prefix = 'pyphantH5FileHandlerTest')
+        osHandle, self.summFilename = mkstemp(
+            suffix = '.h5', prefix = 'pyphantH5FileHandlerTest')
         os.close(osHandle)
         handler = H5FH(self.summFilename, 'w')
         with handler:
@@ -233,6 +231,38 @@
         self.assertEqual(fcsummary['dimensions'], [im_id])
 
 
+class RecipeTestCase(unittest.TestCase):
+    def setUp(self):
+        osHandle, self.path = mkstemp(
+            suffix='.h5', prefix='pyphantH5RecipeTest')
+        os.close(osHandle)
+
+    def tearDown(self):
+        os.remove(self.path)
+
+    def testSaveLoadRecipe(self):
+        from pyphant.core.CompositeWorker import CompositeWorker
+        from pyphant.core.WorkerRegistry import WorkerRegistry
+        from itertools import chain
+        recipe = CompositeWorker()
+        wreg = WorkerRegistry.getInstance()
+        workerInfos = [t.workerInfos for t in wreg.getToolBoxInfoList()]
+        for wInfo in chain(*workerInfos):
+            worker = wInfo.createWorker()
+            recipe.addWorker(worker)
+        with H5FH(self.path, 'w') as handler:
+            handler.saveRecipe(recipe)
+        with H5FH(self.path, 'r') as handler:
+            loadedRecipe = handler.loadRecipe()
+        loadedWorkers = loadedRecipe.getWorkers()
+        workers = recipe.getWorkers()
+        self.assertEqual(len(loadedWorkers), len(workers))
+        workerNames = [w.name for w in workers]
+        loadedWorkerNames = [w.name for w in loadedWorkers]
+        for name in loadedWorkerNames:
+            self.assertTrue(name in workerNames)
+
+
 if __name__ == "__main__":
     import sys
     if len(sys.argv) == 1:

Modified: trunk/src/pyphant/pyphant/tests/TestPyTablesPersister.py
===================================================================
--- trunk/src/pyphant/pyphant/tests/TestPyTablesPersister.py	2011-11-17 11:10:52 UTC (rev 702)
+++ trunk/src/pyphant/pyphant/tests/TestPyTablesPersister.py	2011-11-18 15:01:02 UTC (rev 703)
@@ -46,11 +46,10 @@
 import scipy
 import copy, datetime
 from pyphant.quantities import Quantity
-from pyphant.core.DataContainer import FieldContainer, SampleContainer, assertEqual
+from pyphant.core.DataContainer import FieldContainer, SampleContainer
 from pyphant.core.PyTablesPersister import (saveField, loadField, saveSample,
                                             loadSample, saveExecutionOrder,
                                             loadExecutionOrders)
-import numpy.testing as nt
 import numpy
 import tables
 

Modified: trunk/src/pyphant/pyphant/wxgui2/wxPyphantApplication.py
===================================================================
--- trunk/src/pyphant/pyphant/wxgui2/wxPyphantApplication.py	2011-11-17 11:10:52 UTC (rev 702)
+++ trunk/src/pyphant/pyphant/wxgui2/wxPyphantApplication.py	2011-11-18 15:01:02 UTC (rev 703)
@@ -61,8 +61,7 @@
 import wx.aui
 import sogl
 import pyphant.wxgui2.paramvisualization.ParamVisReg as ParamVisReg
-from pyphant.core.PyTablesPersister import (loadRecipeFromHDF5File,
-                                            saveRecipeToHDF5File)
+from pyphant.core.H5FileHandler import H5FileHandler
 import WorkerRepository
 import ConfigureFrame
 import platform
@@ -226,8 +225,9 @@
         if self._wxPyphantApp.pathToRecipe[-3:] == '.h5':
             if os.path.exists(self._wxPyphantApp.pathToRecipe):
                 try:
-                    recipe = loadRecipeFromHDF5File(
-                        self._wxPyphantApp.pathToRecipe)
+                    with H5FileHandler(self._wxPyphantApp.pathToRecipe, 'r') \
+                             as handler:
+                        recipe = handler.loadRecipe()
                     self._remainingSpace = PyphantCanvas.PyphantCanvas(
                         self, recipe)
                 except:
@@ -259,9 +259,9 @@
         self.recipeState = 'dirty'
 
     def onSaveCompositeWorker(self, event=None):
-        saveRecipeToHDF5File(self._remainingSpace.diagram.recipe,
-                             self._wxPyphantApp.pathToRecipe,
-                             self._fileMenu.IsChecked(wx.ID_FILE4))
+        with H5FileHandler(self._wxPyphantApp.pathToRecipe, 'w') as handler:
+            handler.saveRecipe(self._remainingSpace.diagram.recipe,
+                               self._fileMenu.IsChecked(wx.ID_FILE4))
         self.recipeState = 'clean'
 
     def onSaveAsCompositeWorker(self, event=None):
@@ -273,9 +273,10 @@
             filename = dlg.GetPath()
             if not filename.endswith(".h5"):
                 filename += ".h5"
-            saveRecipeToHDF5File(
-                self._remainingSpace.diagram.recipe,
-                filename, self._fileMenu.IsChecked(wx.ID_FILE4))
+            with H5FileHandler(filename, 'w') as handler:
+                handler.saveRecipe(
+                    self._remainingSpace.diagram.recipe,
+                    self._fileMenu.IsChecked(wx.ID_FILE4))
             self._wxPyphantApp.pathToRecipe = filename
             self.recipeState = 'clean'
             from pyphant.core.WebInterface import shorten

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Pyphant-devel] SF.net SVN: pyphant:[702] trunk/src/workers/ImageProcessing/ImageProcessing /tests/TestCoverage.py

From: <ah...@us...> - 2011-11-17 11:10:59

Revision: 702
          http://pyphant.svn.sourceforge.net/pyphant/?rev=702&view=rev
Author:   aheld84
Date:     2011-11-17 11:10:52 +0000 (Thu, 17 Nov 2011)
Log Message:
-----------
Merge branch 'master' into svn-trunk

* master:
  Fix: removed python 2.7 specific unittest features

Modified Paths:
--------------
    trunk/src/workers/ImageProcessing/ImageProcessing/tests/TestCoverage.py

Modified: trunk/src/workers/ImageProcessing/ImageProcessing/tests/TestCoverage.py
===================================================================
--- trunk/src/workers/ImageProcessing/ImageProcessing/tests/TestCoverage.py	2011-11-17 10:26:46 UTC (rev 701)
+++ trunk/src/workers/ImageProcessing/ImageProcessing/tests/TestCoverage.py	2011-11-17 11:10:52 UTC (rev 702)
@@ -75,7 +75,7 @@
                 stuff1 = (stuff1 * rho1).inUnitsOf('C / m ** 3').value
                 stuff2 = (stuff2 * rho2).inUnitsOf('C / m ** 3').value
                 actualRatio = stuff1 / (stuff1 + stuff2)
-                self.assertAlmostEqual(ratio, actualRatio, delta=delta)
+                self.assertTrue(abs(ratio - actualRatio) <= delta)
 
 
 if __name__ == "__main__":

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Pyphant-devel] SF.net SVN: pyphant:[701] trunk/src

From: <ah...@us...> - 2011-11-17 10:26:56

Revision: 701
          http://pyphant.svn.sourceforge.net/pyphant/?rev=701&view=rev
Author:   aheld84
Date:     2011-11-17 10:26:46 +0000 (Thu, 17 Nov 2011)
Log Message:
-----------
Merge branch 'master' into svn-trunk

* master: (24 commits)
  Fix: CommentChar in FMFLoader
  Fix for ;/# error in FMFLoader - see #52
  Fix for #/; error in FMFLoader - see #52
  Fix: Pathological fmf tables
  Fix: Unique timestamps
  Fix: Bin centers of Histogram worker
  Enh: Addes simple instantiation tests for tools and OSC
  Enh: Added tests for ImageProcessing toolbox
  Enh: Added / updated ImageProcessing tests
  Enh: Added test for thresholding with units
  Enh: Added simple LoadZStack worker
  Fix: Logical Operators for SampleContainers
  Enh: Adopted tests for intended logical operators
  Fix: Removed unnecessary imports from DataContainer
  Enh: Added optional unit support to ThresholdingWorker
  Enh: Changed deprecated interpretation of multi dim images
  Cosm: Changed display name of some workers
  Fix: Broken import in InvertWorker
  Cosm: Cleaned up OscMapper.py
  Fix: wxPyphant crash upon exit
  ...

Modified Paths:
--------------
    trunk/src/pyphant/pyphant/core/CompositeWorker.py
    trunk/src/pyphant/pyphant/core/DataContainer.py
    trunk/src/pyphant/pyphant/core/Helpers.py
    trunk/src/pyphant/pyphant/tests/TestDataContainer.py
    trunk/src/pyphant/pyphant/wxgui2/wxPyphantApplication.py
    trunk/src/workers/ImageProcessing/ImageProcessing/EnhanceContrast.py
    trunk/src/workers/ImageProcessing/ImageProcessing/FitBackground.py
    trunk/src/workers/ImageProcessing/ImageProcessing/InvertWorker.py
    trunk/src/workers/ImageProcessing/ImageProcessing/Medianiser.py
    trunk/src/workers/ImageProcessing/ImageProcessing/ThresholdingWorker.py
    trunk/src/workers/ImageProcessing/ImageProcessing/Watershed.py
    trunk/src/workers/ImageProcessing/ImageProcessing/__init__.py
    trunk/src/workers/ImageProcessing/ImageProcessing/tests/TestAutoFocus.py
    trunk/src/workers/ImageProcessing/ImageProcessing/tests/TestThresholdingWorker.py
    trunk/src/workers/OSC/OSC/OscMapper.py
    trunk/src/workers/OSC/OSC/__init__.py
    trunk/src/workers/OSC/OSC/tests/TestMRA.py
    trunk/src/workers/Statistics/Statistics/Histogram.py
    trunk/src/workers/Statistics/Statistics/tests/TestHistogram.py
    trunk/src/workers/fmfile/fmfile/FMFLoader.py
    trunk/src/workers/fmfile/fmfile/tests/TestFMFLoader.py
    trunk/src/workers/tools/tools/__init__.py

Added Paths:
-----------
    trunk/src/pyphant/pyphant/core/AstTransformers.py
    trunk/src/pyphant/pyphant/tests/TestTimestamp.py
    trunk/src/workers/ImageProcessing/ImageProcessing/LoadZStack.py
    trunk/src/workers/ImageProcessing/ImageProcessing/tests/TestCoverage.py
    trunk/src/workers/ImageProcessing/ImageProcessing/tests/TestDiffWorker.py
    trunk/src/workers/ImageProcessing/ImageProcessing/tests/TestETFR.py
    trunk/src/workers/ImageProcessing/ImageProcessing/tests/TestEdgeFill.py
    trunk/src/workers/ImageProcessing/ImageProcessing/tests/TestEnhanceContrast.py
    trunk/src/workers/ImageProcessing/ImageProcessing/tests/TestFitBackground.py
    trunk/src/workers/ImageProcessing/ImageProcessing/tests/TestGradient.py
    trunk/src/workers/ImageProcessing/ImageProcessing/tests/TestInvert.py
    trunk/src/workers/ImageProcessing/ImageProcessing/tests/TestLocalExtrema.py
    trunk/src/workers/ImageProcessing/ImageProcessing/tests/TestUltimatePoints.py
    trunk/src/workers/ImageProcessing/ImageProcessing/tests/TestWatershed.py
    trunk/src/workers/OSC/OSC/MRA.py
    trunk/src/workers/OSC/OSC/tests/TestInstantiation.py
    trunk/src/workers/fmfile/fmfile/tests/resources/fmf/hash_test.fmf
    trunk/src/workers/fmfile/fmfile/tests/resources/fmf/multitable.fmf
    trunk/src/workers/fmfile/fmfile/tests/resources/fmf/onecolumn.fmf
    trunk/src/workers/fmfile/fmfile/tests/resources/fmf/onerow.fmf
    trunk/src/workers/fmfile/fmfile/tests/resources/fmf/onerow_dep.fmf
    trunk/src/workers/fmfile/fmfile/tests/resources/fmf/onevalue.fmf
    trunk/src/workers/fmfile/fmfile/tests/resources/fmf/semi_test.fmf
    trunk/src/workers/tools/tools/tests/TestInstantiation.py

Removed Paths:
-------------
    trunk/src/workers/ImageProcessing/ImageProcessing/NDImageWorker.py
    trunk/src/workers/tools/tools/MRA.py

Added: trunk/src/pyphant/pyphant/core/AstTransformers.py
===================================================================
--- trunk/src/pyphant/pyphant/core/AstTransformers.py	                        (rev 0)
+++ trunk/src/pyphant/pyphant/core/AstTransformers.py	2011-11-17 10:26:46 UTC (rev 701)
@@ -0,0 +1,211 @@
+from pyphant.quantities import Quantity
+from ast import (NodeTransformer, fix_missing_locations, Name, Load,
+                 BinOp, Num, Mult, Compare, BoolOp, And, Add, Sub, Div, Or,
+                 Call, Not, Expression)
+
+
+class LocationFixingNodeTransformer(NodeTransformer):
+    def visit(self, *args, **kargs):
+        result = NodeTransformer.visit(self, *args, **kargs)
+        fix_missing_locations(result)
+        return result
+
+
+class ReplaceName(LocationFixingNodeTransformer):
+    def __init__(self, sampleContainer):
+        self.localDict = {}
+        self.count = 0
+        self.sc = sampleContainer
+
+    def visit_Call(self, node):
+        if isinstance(node.func, Name) and node.func.id.lower() == 'col':
+            newName = self.getName(self.sc[node.args[0].s])
+            return Name(newName, Load())
+
+    def visit_Str(self, node):
+        quantity = Quantity(node.s)
+        class QuantityDummy(object):
+            pass
+        dummy = QuantityDummy()
+        dummy.unit = Quantity(1.0, quantity.unit)
+        dummy.data = quantity.value
+        dummy.dimensions = None
+        newName = self.getName(dummy)
+        return Name(newName, Load())
+
+    def getName(self, ref):
+        newName = "N%s" % self.count
+        self.count += 1
+        self.localDict[newName] = ref
+        return newName
+
+
+def withFactor(factor, node):
+    if not isinstance(factor, float):
+        raise ValueError('Incompatible units!')
+    if factor == 1.0:
+        return node
+    return BinOp(Num(factor), Mult(), node)
+
+
+class ReplaceCompare(LocationFixingNodeTransformer):
+    def __init__(self, localDict):
+        self.localDict = localDict
+
+    def visit_Compare(self, node):
+        self.generic_visit(node)
+        unitcalc = UnitCalculator(self.localDict)
+        leftUD = unitcalc.getUnitAndDim(node.left)
+        listUD = [unitcalc.getUnitAndDim(comp) for comp in node.comparators]
+        nonNoneDims = [ud[1] for ud in listUD + [leftUD] if ud[1] is not None]
+        for dims in nonNoneDims:
+            checkDimensions(nonNoneDims[0], dims)
+        factorlist = [ud[0] / leftUD[0] for ud in listUD]
+        newComplist = [withFactor(*t) \
+                       for t in zip(factorlist, node.comparators)]
+        compOp = Compare(node.left, node.ops, newComplist)
+        compOpTrans = self.compBreaker(compOp)
+        return compOpTrans
+
+    def compBreaker(self, node):
+        assert isinstance(node, Compare)
+        if len(node.comparators) == 1:
+            return node
+        else:
+            comp1 = Compare(node.left, node.ops[0:1],
+                            node.comparators[0:1])
+            comp2 = Compare(node.comparators[0],
+                            node.ops[1:], node.comparators[1:])
+            newNode = BoolOp(And(), [comp1, self.compBreaker(comp2)])
+            return newNode
+
+
+class ReplaceOperator(LocationFixingNodeTransformer):
+    def __init__(self, localDict):
+        self.localDict = localDict
+
+    def visit_BinOp(self, node):
+        self.generic_visit(node)
+        unitcalc = UnitCalculator(self.localDict)
+        leftUD = unitcalc.getUnitAndDim(node.left)
+        rightUD = unitcalc.getUnitAndDim(node.right)
+        checkDimensions(leftUD[1], rightUD[1])
+        if isinstance(node.op, (Add, Sub)):
+            factor = rightUD[0] / leftUD[0]
+            right = withFactor(factor, node.right)
+            binOp = BinOp(node.left, node.op, right)
+            return binOp
+        elif isinstance(node.op, (Mult, Div)):
+            return node
+        else:
+            raise NotImplementedError('%s not implemented' % (node.op, ))
+
+    def visit_BoolOp(self, node):
+        self.generic_visit(node)
+        if isinstance(node.op, And):
+            func = 'logical_and'
+        elif isinstance(node.op, Or):
+            func = 'logical_or'
+        else:
+            raise NotImplementedError('%s not implemented' % (node.op, ))
+        return self.boolOpBreaker(node.values, func)
+
+    def boolOpBreaker(self, values, func):
+        if len(values) == 1:
+            return values[0]
+        else:
+            return Call(Name(func, Load()),
+                        [values[0], self.boolOpBreaker(values[1:], func)],
+                        [], None, None)
+
+    def visit_UnaryOp(self, node):
+        self.generic_visit(node)
+        if isinstance(node.op, Not):
+            return Call(Name('logical_not', Load()), [node.operand],
+                        [], None, None)
+        else:
+            raise NotImplementedError('%s not implemented' % (node.op, ))
+
+
+class UnitCalculator(object):
+    def __init__(self, localDict):
+        self.localDict = localDict
+
+    def getUnitAndDim(self, node):
+        if isinstance(node, Expression):
+            return self.getUnitAndDim(node.body)
+        elif isinstance(node, Name):
+            if node.id in ['True', 'False']:
+                return (1.0, None)
+            else:
+                column = self.localDict[node.id]
+                return (column.unit, column.dimensions)
+        elif isinstance(node, Num):
+            return (1.0, None)
+        elif isinstance(node, Call):
+            if not isinstance(node.func, Name):
+                raise NotImplementedError(
+                    'Dynamic functions are not implemented!')
+            funcId = node.func.id
+            if funcId in ['logical_and', 'logical_or']:
+                left = self.getUnitAndDim(node.args[0])
+                right = self.getUnitAndDim(node.args[1])
+                dimensions = checkDimensions(left[1], right[1])
+                if not isinstance(left[0], float):
+                    raise ValueError(
+                        "Type %s cannot be interpreted as a Boolean" % left)
+                if not isinstance(right[0], float):
+                    raise ValueError(
+                        "Type %s cannot be interpreted as a Boolean" % right)
+                return (1.0, dimensions)
+            elif funcId == 'logical_not':
+                return self.getUnitAndDim(node.args[0])
+            else:
+                raise NotImplementedError("Function '%s' not implemented" \
+                                          % (funcId, ))
+        elif isinstance(node, BinOp):
+            left = self.getUnitAndDim(node.left)
+            right = self.getUnitAndDim(node.right)
+            dimensions = checkDimensions(left[1], right[1])
+            if isinstance(node.op, (Add, Sub)):
+                if not isinstance(left[0] / right[0], float):
+                    raise ValueError("units %s, %s not compatible" \
+                                     % (left, right))
+                unit = left[0]
+            elif isinstance(node.op, Mult):
+                unit = left[0] * right[0]
+            elif isinstance(node.op, Div):
+                unit = left[0] / right[0]
+            else:
+                raise NotImplementedError()
+            return (unit, dimensions)
+        elif isinstance(node, Compare):
+            left = self.getUnitAndDim(node.left)
+            nonNoneDims = []
+            if left[1] is not None:
+                nonNoneDims.append(left[1])
+            for comparator in node.comparators:
+                right = self.getUnitAndDim(comparator)
+                if right[1] is not None:
+                    nonNoneDims.append(right[1])
+                if not isinstance(left[0] / right[0], float):
+                    raise ValueError("units %s, %s not compatible" \
+                                     % (left[0], right[0]))
+            if len(nonNoneDims) >= 1:
+                for dims in nonNoneDims:
+                    checkDimensions(nonNoneDims[0], dims)
+                dimensions = nonNoneDims[0]
+            else:
+                dimensions = None
+            return (1.0, dimensions)
+        else:
+            raise NotImplementedError()
+
+
+def checkDimensions(dimensions1, dimensions2):
+    if dimensions1 is not None and dimensions2 is not None and \
+           dimensions1 != dimensions2:
+        msg = 'Dimensions "%s" and "%s" do not match!' \
+              % (dimensions1, dimensions2)
+        raise ValueError(msg)
+    return dimensions1 or dimensions2

Modified: trunk/src/pyphant/pyphant/core/CompositeWorker.py
===================================================================
--- trunk/src/pyphant/pyphant/core/CompositeWorker.py	2011-05-23 12:48:36 UTC (rev 700)
+++ trunk/src/pyphant/pyphant/core/CompositeWorker.py	2011-11-17 10:26:46 UTC (rev 701)
@@ -84,7 +84,7 @@
     API = 2
     VERSION = 1
     REVISION = "$Revision: $"[11:-1]
-    name = "CompositeWorker"
+    name = "Composite"
     _params = [("noSockets", "Number of sockets", 0, None),
                ("noPlugs", "Number of plugs", 0, None)]
 

Modified: trunk/src/pyphant/pyphant/core/DataContainer.py
===================================================================
--- trunk/src/pyphant/pyphant/core/DataContainer.py	2011-05-23 12:48:36 UTC (rev 700)
+++ trunk/src/pyphant/pyphant/core/DataContainer.py	2011-11-17 10:26:46 UTC (rev 701)
@@ -70,10 +70,11 @@
 __version__ = "$Revision$"
 
 import copy, hashlib, threading, numpy, StringIO
-import os, platform, datetime, socket, urlparse
-from pyphant.quantities import (isQuantity, Quantity)
+import urlparse
+from pyphant.core.AstTransformers import (
+    ReplaceName, ReplaceCompare, ReplaceOperator, UnitCalculator,
+    checkDimensions)
 import Helpers
-from ast import (NodeTransformer, NodeVisitor)
 import logging
 _logger = logging.getLogger("pyphant")
 
@@ -175,7 +176,7 @@
                 self.id = id
             else:
                 self.hash = self.generateHash()
-                self.timestamp = datetime.datetime.utcnow()
+                self.timestamp = Helpers.getModuleUniqueTimestamp()
                 self.id = u"emd5://%s/%s/%s/%s.%s" % (self.machine,
                                                       self.creator,
                                                       enc(self.timestamp.isoformat('_')),
@@ -336,15 +337,15 @@
         sorted by precedence from lowest precedence (least binding) to highest
         precedence (most binding):
 
+        or
+        and
+        not
         Comparisons: <, <=, >, >=, <>, !=, ==
-        Bitwise OR: |
-        Bitwise XOR: ^
-        Bitwise AND: &
         Addition and Subtraction: +, -
         Multiplication, Division: *, /
-        Positive, Negative, Bitwise NOT: +x, -x, ~x
+        Positive, Negative: +x, -x
 
-        Not implemented: and, or, not, **, //, %, if - else
+        Not implemented: ~, &, |, **, //, %, <<, >>
 
         Examples
         --------
@@ -362,7 +363,7 @@
             exprStr = "col('Distance') / col('Time')"
             exprStr = "col('Distance') - '1 m'"
             exprStr = "col('t') >= '4 s'"
-            exprStr = "(col('s') > '1 m') & (COL('Time') == '3s')"
+            exprStr = "col('s') > '1 m' and COL('Time') == '3s'"
 
         """
         exprStr = exprStr or 'True'
@@ -370,10 +371,16 @@
         rpn = ReplaceName(self)
         expr = compile(exprStr, "<calcColumn>", 'eval', ast.PyCF_ONLY_AST)
         replacedExpr = rpn.visit(expr)
+        rpc = ReplaceCompare(rpn.localDict)
+        factorExpr = rpc.visit(replacedExpr)
         rpo = ReplaceOperator(rpn.localDict)
-        factorExpr = rpo.visit(replacedExpr)
+        factorExpr = rpo.visit(factorExpr)
         localDict = dict([(key, value.data) \
                           for key, value in rpn.localDict.iteritems()])
+        numpyDict = {'logical_and':numpy.logical_and,
+                     'logical_or':numpy.logical_or,
+                     'logical_not':numpy.logical_not}
+        localDict.update(numpyDict)
         data = eval(compile(factorExpr, '<calcColumn>', 'eval'), {}, localDict)
         unitcalc = UnitCalculator(rpn.localDict)
         unit, dims = unitcalc.getUnitAndDim(replacedExpr)
@@ -465,179 +472,3 @@
         return True
     else:
         raise AssertionError, diagnosis.getvalue()
-
-
-class LocationFixingNodeTransformer(NodeTransformer):
-    def visit(self, *args, **kargs):
-        result = NodeTransformer.visit(self, *args, **kargs)
-        from ast import fix_missing_locations
-        fix_missing_locations(result)
-        return result
-
-
-class ReplaceName(LocationFixingNodeTransformer):
-    def __init__(self, sampleContainer):
-        self.localDict = {}
-        self.count = 0
-        self.sc = sampleContainer
-
-    def visit_Call(self, node):
-        from ast import (Name, Load)
-        if isinstance(node.func, Name) and node.func.id.lower() == 'col':
-            newName = self.getName(self.sc[node.args[0].s])
-            return Name(newName, Load())
-
-    def visit_Str(self, node):
-        from ast import (Name, Load)
-        quantity = Quantity(node.s)
-        class QuantityDummy(object):
-            pass
-        dummy = QuantityDummy()
-        dummy.unit = Quantity(1.0, quantity.unit)
-        dummy.data = quantity.value
-        dummy.dimensions = None
-        newName = self.getName(dummy)
-        return Name(newName, Load())
-
-    def getName(self, ref):
-        newName = "N%s" % self.count
-        self.count += 1
-        self.localDict[newName] = ref
-        return newName
-
-
-class ReplaceOperator(LocationFixingNodeTransformer):
-    def __init__(self, localDict):
-        self.localDict = localDict
-
-    def visit_BinOp(self, node):
-        from ast import (Add, Sub, BinOp)
-        self.generic_visit(node)
-        unitcalc = UnitCalculator(self.localDict)
-        leftUD = unitcalc.getUnitAndDim(node.left)
-        rightUD = unitcalc.getUnitAndDim(node.right)
-        checkDimensions(leftUD[1], rightUD[1])
-        if isinstance(node.op,(Add, Sub)):
-            factor = rightUD[0] / leftUD[0]
-            right = self.withFactor(factor, node.right)
-            binOp = BinOp(node.left, node.op, right)
-            return binOp
-        else:
-            return node
-
-    def visit_Compare(self, node):
-        from ast import Compare
-        self.generic_visit(node)
-        unitcalc = UnitCalculator(self.localDict)
-        leftUD = unitcalc.getUnitAndDim(node.left)
-        listUD = [unitcalc.getUnitAndDim(comp) for comp in node.comparators]
-        nonNoneDims = [ud[1] for ud in listUD + [leftUD] if ud[1] is not None]
-        for dims in nonNoneDims:
-            checkDimensions(nonNoneDims[0], dims)
-        factorlist = [ud[0] / leftUD[0] for ud in listUD]
-        newComplist = [self.withFactor(*t) \
-                       for t in zip(factorlist, node.comparators)]
-        compOp = Compare(node.left, node.ops, newComplist)
-        compOpTrans = self.compBreaker(compOp)
-        return compOpTrans
-
-    def withFactor(self, factor, node):
-        from ast import (BinOp, Num, Mult)
-        if not isinstance(factor, float):
-            raise ValueError('Incompatible units!')
-        if factor == 1.0:
-            return node
-        return BinOp(Num(factor), Mult(), node)
-
-    def compBreaker(self, node):
-        from ast import (Compare, BinOp, BitAnd)
-        assert isinstance(node, Compare)
-        if len(node.comparators) == 1:
-            return node
-        else:
-            comp1 = Compare(node.left, node.ops[0:1],
-                            node.comparators[0:1])
-            comp2 = Compare(node.comparators[0],
-                            node.ops[1:], node.comparators[1:])
-            newNode = BinOp(comp1, BitAnd(), self.compBreaker(comp2))
-            return newNode
-
-
-class UnitCalculator(object):
-    def __init__(self, localDict):
-        self.localDict = localDict
-
-    def getUnitAndDim(self, node):
-        from ast import (Expression, Name, Num,
-                         BinOp, Add, Mult, Div, Sub,
-                         Compare, BoolOp, UnaryOp,
-                         BitOr, BitXor, BitAnd)
-        if isinstance(node, Expression):
-            return self.getUnitAndDim(node.body)
-        elif isinstance(node, Name):
-            if node.id in ['True', 'False']:
-                return (1.0, None)
-            else:
-                column = self.localDict[node.id]
-                return (column.unit, column.dimensions)
-        elif isinstance(node, Num):
-            return (1.0, None)
-        elif isinstance(node, BinOp):
-            left = self.getUnitAndDim(node.left)
-            right = self.getUnitAndDim(node.right)
-            dimensions = checkDimensions(left[1], right[1])
-            if isinstance(node.op, (Add, Sub)):
-                if not isinstance(left[0] / right[0], float):
-                    raise ValueError("units %s, %s not compatible" \
-                                     % (left, right))
-                unit = left[0]
-            elif isinstance(node.op, Mult):
-                unit = left[0] * right[0]
-            elif isinstance(node.op, Div):
-                unit = left[0] / right[0]
-            elif isinstance(node.op, (BitOr, BitXor, BitAnd)):
-                if not isinstance(left[0], float):
-                    raise ValueError(
-                        "Type %s cannot be interpreted as a Boolean" % left)
-                if not isinstance(right[0], float):
-                    raise ValueError(
-                        "Type %s cannot be interpreted as a Boolean" % right)
-                unit = 1.0
-            else:
-                raise NotImplementedError()
-            return (unit, dimensions)
-        elif isinstance(node, Compare):
-            left = self.getUnitAndDim(node.left)
-            nonNoneDims = []
-            if left[1] is not None:
-                nonNoneDims.append(left[1])
-            for comparator in node.comparators:
-                right = self.getUnitAndDim(comparator)
-                if right[1] is not None:
-                    nonNoneDims.append(right[1])
-                if not isinstance(left[0] / right[0], float):
-                    raise ValueError("units %s, %s not compatible" \
-                                     % (left[0], right[0]))
-            if len(nonNoneDims) >= 1:
-                for dims in nonNoneDims:
-                    checkDimensions(nonNoneDims[0], dims)
-                dimensions = nonNoneDims[0]
-            else:
-                dimensions = None
-            return (1.0, dimensions)
-        elif isinstance(node, BoolOp):
-            raise NotImplementedError(
-                'BoolOps not supported. Use bitwise ops instead (&, |)!')
-        elif isinstance(node, UnaryOp):
-            return self.getUnitAndDim(node.operand)
-        else:
-            raise NotImplementedError()
-
-
-def checkDimensions(dimensions1, dimensions2):
-    if dimensions1 is not None and dimensions2 is not None and \
-           dimensions1 != dimensions2:
-        msg = 'Dimensions "%s" and "%s" do not match!' \
-              % (dimensions1, dimensions2)
-        raise ValueError(msg)
-    return dimensions1 or dimensions2

Modified: trunk/src/pyphant/pyphant/core/Helpers.py
===================================================================
--- trunk/src/pyphant/pyphant/core/Helpers.py	2011-05-23 12:48:36 UTC (rev 700)
+++ trunk/src/pyphant/pyphant/core/Helpers.py	2011-11-17 10:26:46 UTC (rev 701)
@@ -183,3 +183,27 @@
                          attributes=attributes, columns=columns)
     sc.seal()
     return sc
+
+from threading import Lock
+TIMESTAMP_LOCK = Lock()
+LAST_TIMESTAMP = ''
+del Lock
+
+def getModuleUniqueTimestamp():
+    global TIMESTAMP_LOCK
+    global LAST_TIMESTAMP
+    TIMESTAMP_LOCK.acquire()
+    timestamp = None
+    try:
+        from datetime import datetime
+        while True:
+            timestamp = datetime.utcnow()
+            if timestamp != LAST_TIMESTAMP:
+                LAST_TIMESTAMP = timestamp
+                break
+            else:
+                from time import sleep
+                sleep(.001)
+    finally:
+        TIMESTAMP_LOCK.release()
+    return timestamp

Modified: trunk/src/pyphant/pyphant/tests/TestDataContainer.py
===================================================================
--- trunk/src/pyphant/pyphant/tests/TestDataContainer.py	2011-05-23 12:48:36 UTC (rev 700)
+++ trunk/src/pyphant/pyphant/tests/TestDataContainer.py	2011-11-17 10:26:46 UTC (rev 701)
@@ -557,17 +557,20 @@
 class AlgebraSampleContainerTests(SampleContainerTest):
 
     def testNodeTransformer(self):
-        from pyphant.core.DataContainer import (ReplaceName, ReplaceOperator)
+        from pyphant.core.AstTransformers import (ReplaceName, ReplaceOperator,
+                                                  ReplaceCompare)
         rpn = ReplaceName(self.sampleContainer)
         import ast
         exprStr = 'col("i") / (col("t") + col("t"))'
         expr = compile(exprStr, "<TestCase>", 'eval', ast.PyCF_ONLY_AST)
         replacedExpr = rpn.visit(expr)
-        #print rpn.localDict
-        #print ast.dump(replacedExpr)
-        rpb = ReplaceOperator(rpn.localDict)
-        factorExpr = rpb.visit(replacedExpr)
-        #print ast.dump(factorExpr)
+        print rpn.localDict
+        print ast.dump(replacedExpr)
+        rpc = ReplaceCompare(rpn.localDict)
+        factorExpr = rpc.visit(replacedExpr)
+        rpo = ReplaceOperator(rpn.localDict)
+        factorExpr = rpo.visit(factorExpr)
+        print ast.dump(factorExpr)
 
     def testCalcColumn(self):
         exprStr = 'col("i") / (col("t") + col("t")) + "1km/s"'
@@ -854,7 +857,7 @@
     #purely one dimensional Tests:
     def testConsistancy(self):
         result1 = self.sampleContainer.filter(
-            '("20m" < col("i")) & ("80m" > col("i"))')
+            '"20m" < col("i") and "80m" > col("i")')
         result2 = self.sampleContainer.filter('"20m" < col("i") < "80m"')
         self.assertEqual(result1[0], result2[0])
         self.assertEqual(result1[1], result2[1])
@@ -875,7 +878,7 @@
 
     def testANDExpression(self):
         result = self.sampleContainer.filter(
-            '(col("i") >= "20m") & (col("t") <= "98.5s")')
+            'col("i") >= "20m" and col("t") <= "98.5s"')
         expectedi = self.sampleContainer["i"][20:98]
         expectedt = self.sampleContainer["t"][20:98]
         expectedi.attributes = {}
@@ -916,21 +919,32 @@
                               [True, True, False, True, True])
 
     def testNot2dExpression(self):
-        self._compareExpected('~ (col("t") == "10s")',
+        self._compareExpected('not col("t") == "10s"',
                               [True, True, True, False, True])
 
     def testAnd2dExpression(self):
         self._compareExpected(
-            '(col("Zeit") == "60s") & ("20000m" == col("Strecke"))',
+            'col("Zeit") == "60s" and "20000m" == col("Strecke")',
             [False, False, True, False, False])
 
+    def testMultiAnd2dExpression(self):
+        self._compareExpected(
+            "col('l') >= '0 km' and col('l') < '20 km' and col('t') <= '60s'",
+            [False, True, False, True, False])
+
     def testOr2dExpression(self):
         self._compareExpected(
-            '(col("Zeit") < "60s") | (col("Strecke") == "5500m")',
+            'col("Zeit") < "60s" or col("Strecke") == "5500m"',
             [True, True, False, True, True])
 
+    def testMultiOr2dExpression(self):
+        self._compareExpected(
+            "col('t') == '20s' or col('l') == '0 km' or col('t') > '1000.2 s'",
+            [True, True, False, False, True]
+            )
+
     def testMultipleCompareOpPrecedence2dExpression(self):
-        self._compareExpected('~ ("0m" <= col("l") <= "10000m")',
+        self._compareExpected('not "0m" <= col("l") <= "10000m"',
                               [True, False, True, False, False])
 
     def testColumnToColumn2dExpression(self):

Copied: trunk/src/pyphant/pyphant/tests/TestTimestamp.py (from rev 700, trunk/src/workers/OSC/OSC/__init__.py)
===================================================================
--- trunk/src/pyphant/pyphant/tests/TestTimestamp.py	                        (rev 0)
+++ trunk/src/pyphant/pyphant/tests/TestTimestamp.py	2011-11-17 10:26:46 UTC (rev 701)
@@ -0,0 +1,56 @@
+# -*- coding: utf-8 -*-
+
+# Copyright (c) 2011, Rectorate of the University of Freiburg
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+# * Redistributions of source code must retain the above copyright
+#   notice, this list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above copyright
+#   notice, this list of conditions and the following disclaimer in the
+#   documentation and/or other materials provided with the distribution.
+# * Neither the name of the Freiburg Materials Research Center,
+#   University of Freiburg nor the names of its contributors may be used to
+#   endorse or promote products derived from this software without specific
+#   prior written permission.
+#
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+# IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+# TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
+# OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+u"""Provides test for unique timestamps
+"""
+
+__id__ = "$Id$"
+__author__ = "$Author$"
+__version__ = "$Revision$"
+# $Source$
+
+import unittest
+import pkg_resources
+
+pkg_resources.require("pyphant")
+
+
+class TestModuleUniqueTimestamp(unittest.TestCase):
+    def testUnique(self):
+        from pyphant.core.Helpers import getModuleUniqueTimestamp
+        for x in xrange(100):
+            self.assertNotEqual(
+                getModuleUniqueTimestamp(),
+                getModuleUniqueTimestamp())
+
+
+if __name__ == '__main__':
+    unittest.main()

Modified: trunk/src/pyphant/pyphant/wxgui2/wxPyphantApplication.py
===================================================================
--- trunk/src/pyphant/pyphant/wxgui2/wxPyphantApplication.py	2011-05-23 12:48:36 UTC (rev 700)
+++ trunk/src/pyphant/pyphant/wxgui2/wxPyphantApplication.py	2011-11-17 10:26:46 UTC (rev 701)
@@ -533,10 +533,10 @@
                 if isinstance(exep, socket_error):
                     try:
                         #Python 2.6
-                        eno = err.errno
+                        eno = exep.errno
                     except AttributeError:
                         #Python 2.5
-                        eno = err.args[0]
+                        eno = exep.args[0]
                     from errno import EADDRINUSE
                     if eno == EADDRINUSE:
                         msg += "\nReason: Could not find a free port."\
@@ -620,6 +620,7 @@
 
         # The program will freeze without this line.
         evt.Skip()  # Make sure the default handler runs too...
+        self.Destroy()
 
 
 import optparse

Modified: trunk/src/workers/ImageProcessing/ImageProcessing/EnhanceContrast.py
===================================================================
--- trunk/src/workers/ImageProcessing/ImageProcessing/EnhanceContrast.py	2011-05-23 12:48:36 UTC (rev 700)
+++ trunk/src/workers/ImageProcessing/ImageProcessing/EnhanceContrast.py	2011-11-17 10:26:46 UTC (rev 701)
@@ -38,8 +38,7 @@
 __version__ = "$Revision$"
 # $Source$
 
-from pyphant.core import (Worker, Connectors)
-from ImageProcessing.NDImageWorker import pile
+from pyphant.core import (Worker, Connectors, DataContainer)
 import scipy, copy
 
 def normalizeHistogram(data):
@@ -60,12 +59,12 @@
     API = 2
     VERSION = 1
     REVISION = "$Revision$"[11:-1]
-    name = "EnhanceContrast"
+    name = "Enhance Contrast"
     _sockets = [("image", Connectors.TYPE_IMAGE)]
 
     @Worker.plug(Connectors.TYPE_IMAGE)
     def enhance(self, image, subscriber=0):
-        newdata = pile(normalizeLinear, image.data)
+        newdata = normalizeLinear(image.data)
         longname = "Normalize"
         result = DataContainer.FieldContainer(
             newdata,
@@ -78,5 +77,4 @@
             copy.deepcopy(image.attributes),
             False)
         result.seal()
-        #print newdata.shape
         return result

Modified: trunk/src/workers/ImageProcessing/ImageProcessing/FitBackground.py
===================================================================
--- trunk/src/workers/ImageProcessing/ImageProcessing/FitBackground.py	2011-05-23 12:48:36 UTC (rev 700)
+++ trunk/src/workers/ImageProcessing/ImageProcessing/FitBackground.py	2011-11-17 10:26:46 UTC (rev 701)
@@ -47,7 +47,7 @@
     API = 2
     VERSION = 1
     REVISION = "$Revision$"[11:-1]
-    name = "FitBackground"
+    name = "Fit Background"
     _sockets = [("image", Connectors.TYPE_IMAGE)]
     _params = [("poldegree", "Polynomial degree (1 to 5)", 3, None),
                ("swidth", "sample width", 150, None),
@@ -102,34 +102,22 @@
         brightsize = int(self.paramBrightsize.value)
         brightruns = int(self.paramBrightruns.value)
         dopreview = self.paramDopreview.value
-        assert image.data.ndim in [2, 3]
-        if image.data.ndim == 2:
-            pile = [image.data]
-        else:
-            pile = image.data
+        data = image.data
         #Median:
         for run in xrange(medianruns):
-            pile = [ndimage.median_filter(data,
-                                          size=mediansize) for data in pile]
+            data = ndimage.median_filter(data, size=mediansize)
         #Suspend dark spots:
         for run in xrange(darkruns):
-            pile = [255 - ndimage.grey_erosion(255 - data,
-                                         size=darksize) for data in pile]
+            data = 255 - ndimage.grey_erosion(255 - data, size=darksize)
         #Suspend features:
         for run in xrange(brightruns):
-            pile = [ndimage.grey_erosion(data,
-                                         size=brightsize) for data in pile]
+            data = ndimage.grey_erosion(data, size=brightsize)
         #Fit background:
         if not dopreview:
-            pile = [self.fit(data, poldegree, swidth, sheight,
-                             threshold) for data in pile]
-        if image.data.ndim == 2:
-            newdata = pile[0]
-        else:
-            newdata = numpy.array(pile)
+            data = self.fit(data, poldegree, swidth, sheight, threshold)
         longname = "FitBackground"
         result = DataContainer.FieldContainer(
-            newdata,
+            data,
             copy.deepcopy(image.unit),
             copy.deepcopy(image.error),
             copy.deepcopy(image.mask),
@@ -139,4 +127,4 @@
             copy.deepcopy(image.attributes),
             False)
         result.seal()
-        return result
\ No newline at end of file
+        return result

Modified: trunk/src/workers/ImageProcessing/ImageProcessing/InvertWorker.py
===================================================================
--- trunk/src/workers/ImageProcessing/ImageProcessing/InvertWorker.py	2011-05-23 12:48:36 UTC (rev 700)
+++ trunk/src/workers/ImageProcessing/ImageProcessing/InvertWorker.py	2011-11-17 10:26:46 UTC (rev 701)
@@ -56,7 +56,7 @@
         max = scipy.amax(image.data)
         min = scipy.amin(image.data)
         data = max + min - image.data
-        from DataContainer import FieldContainer
+        from pyphant.core.DataContainer import FieldContainer
         result = FieldContainer(data, unit=image.unit,
                                 dimensions=copy.deepcopy(image.dimensions),
                                 mask=copy.deepcopy(image.mask),

Added: trunk/src/workers/ImageProcessing/ImageProcessing/LoadZStack.py
===================================================================
--- trunk/src/workers/ImageProcessing/ImageProcessing/LoadZStack.py	                        (rev 0)
+++ trunk/src/workers/ImageProcessing/ImageProcessing/LoadZStack.py	2011-11-17 10:26:46 UTC (rev 701)
@@ -0,0 +1,138 @@
+# -*- coding: utf-8 -*-
+
+# Copyright (c) 2006-2011, Rectorate of the University of Freiburg
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+# * Redistributions of source code must retain the above copyright
+#   notice, this list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above copyright
+#   notice, this list of conditions and the following disclaimer in the
+#   documentation and/or other materials provided with the distribution.
+# * Neither the name of the Freiburg Materials Research Center,
+#   University of Freiburg nor the names of its contributors may be used to
+#   endorse or promote products derived from this software without specific
+#   prior written permission.
+#
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+# IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+# TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
+# OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+u"""
+The Load ZStack worker is a class of Pyphant's Image Processing
+Toolbox. It simply loads a set of images from the location given in the
+worker's configuration as a 3d image.
+"""
+
+__id__ = "$Id$"
+__author__ = "$Author$"
+__version__ = "$Revision$"
+# $Source$
+
+from pyphant.core.Connectors import (SUBTYPE_FILE, TYPE_IMAGE)
+from pyphant.core import Worker
+
+
+class LoadZStack(Worker.Worker):
+    API = 2
+    VERSION = 1
+    REVISION = "$Revision$"[11:-1]
+    name = "Load ZStack"
+    _params = [
+        ("path", u"Path (select any file)", "", SUBTYPE_FILE),
+        ("regex", u"File Filter Regex", r'(?i)^.+\.tif$', None),
+        ("fieldUnit", u"Unit of the field", 1, None),
+        ("dz", u"z increment", '1 mum', None),
+        ("dy", u"y increment", '1 mum', None),
+        ("dx", u"x increment", '1 mum', None),
+        ("startz", u"z start", '0 mum', None),
+        ("starty", u"y start", '0 mum', None),
+        ("startx", u"x start", '0 mum', None),
+        ("zClip", u"Clipping of z-axis (pixels)", ':', None),
+        ("yClip", u"Clipping of y-axis (pixels)", ':', None),
+        ("xClip", u"Clipping of x-axis (pixels)", ':', None),
+        ("dtype", u"data type", 'uint8', None),
+        ("longname", u"Longname", 'ZStack', None),
+        ("shortname", u"Shortname", 'I', None)
+        ]
+
+    @Worker.plug(TYPE_IMAGE)
+    def loadImageAsGreyScale(self, subscriber=0):
+        import os
+        import re
+        from scipy.misc import imread
+        import numpy
+        from pyphant.core.DataContainer import FieldContainer
+        from pyphant.quantities import Quantity
+        path = os.path.realpath(self.paramPath.value)
+        if os.path.isfile(path):
+            path = os.path.dirname(path)
+        pattern = re.compile(self.paramRegex.value)
+        filenames = filter(
+            lambda x: pattern.match(x) is not None, os.listdir(path)
+            )
+        filenames.sort()
+        filenames = [os.path.join(path, fname) for fname in filenames]
+        print path
+        zClip = self.getClip(self.paramZClip.value)
+        filenames = filenames[zClip[0]:zClip[1]]
+        assert len(filenames) >= 1
+        yClip = self.getClip(self.paramYClip.value)
+        xClip = self.getClip(self.paramXClip.value)
+        dtype = self.paramDtype.value
+        data = []
+        for i, fn in enumerate(filenames):
+            subscriber %= 1 + 99 * i / len(filenames)
+            data.append(imread(fn, True)[yClip[0]:yClip[1], xClip[0]:xClip[1]])
+        data = numpy.array(data, dtype=dtype)
+        axes = ['z', 'y', 'x']
+        dimensions = [
+            self.getDimension(a, data.shape[i]) for i, a in enumerate(axes)
+            ]
+        try:
+            unit = Quantity(self.paramFieldUnit.value)
+        except AttributeError:
+            unit = self.paramFieldUnit.value
+        longname = self.paramLongname.value
+        shortname = self.paramShortname.value
+        image = FieldContainer(
+            data=data, dimensions=dimensions, unit=unit,
+            longname=longname, shortname=shortname,
+            attributes={'yFactor':Quantity(self.paramDy.value),
+                        'xFactor':Quantity(self.paramDx.value)}
+            )
+        image.seal()
+        subscriber %= 100
+        return image
+
+    def getClip(self, clipStr):
+        split = clipStr.split(':')
+        assert len(split) == 2
+        return [int(x) if len(x) else None for x in split]
+
+    def getDimension(self, axis, length):
+        from pyphant.quantities import Quantity
+        from pyphant.core.DataContainer import FieldContainer
+        import numpy
+        delta = Quantity(self.getParam('d' + axis).value)
+        start = Quantity(self.getParam('start' + axis).value)
+
+        start = start.inUnitsOf(delta.unit)
+        data = start.value + numpy.arange(0, length, dtype=float) * delta.value
+        dim = FieldContainer(
+            data, unit=Quantity(1.0, delta.unit),
+            shortname=axis,
+            longname='%s-Axis' % (axis.upper(), )
+            )
+        return dim

Modified: trunk/src/workers/ImageProcessing/ImageProcessing/Medianiser.py
===================================================================
--- trunk/src/workers/ImageProcessing/ImageProcessing/Medianiser.py	2011-05-23 12:48:36 UTC (rev 700)
+++ trunk/src/workers/ImageProcessing/ImageProcessing/Medianiser.py	2011-11-17 10:26:46 UTC (rev 701)
@@ -50,7 +50,7 @@
     API = 2
     VERSION = 1
     REVISION = "$Revision$"[11:-1]
-    name = "Medianiser"
+    name = "Median"
     _sockets = [("field", Connectors.TYPE_IMAGE)]
     _params = [("size", "Kernel Size", 5, None),
                ("runs", "Runs", 3, None)]
@@ -63,4 +63,4 @@
         for i in range(ru):
             im.data = scipy.ndimage.filters.median_filter(im.data, size=size)
         im.seal()
-        return im
\ No newline at end of file
+        return im

Deleted: trunk/src/workers/ImageProcessing/ImageProcessing/NDImageWorker.py
===================================================================
--- trunk/src/workers/ImageProcessing/ImageProcessing/NDImageWorker.py	2011-05-23 12:48:36 UTC (rev 700)
+++ trunk/src/workers/ImageProcessing/ImageProcessing/NDImageWorker.py	2011-11-17 10:26:46 UTC (rev 701)
@@ -1,183 +0,0 @@
-# -*- coding: utf-8 -*-
-
-# Copyright (c) 2006-2007, Rectorate of the University of Freiburg
-# All rights reserved.
-#
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions are met:
-#
-# * Redistributions of source code must retain the above copyright
-#   notice, this list of conditions and the following disclaimer.
-# * Redistributions in binary form must reproduce the above copyright
-#   notice, this list of conditions and the following disclaimer in the
-#   documentation and/or other materials provided with the distribution.
-# * Neither the name of the Freiburg Materials Research Center,
-#   University of Freiburg nor the names of its contributors may be used to
-#   endorse or promote products derived from this software without specific
-#   prior written permission.
-#
-#
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
-# IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
-# TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
-# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
-# OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
-# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
-# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
-# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-u"""
-TODO: Check units, repair functionality
-"""
-
-__id__ = "$Id$"
-__author__ = "$Author$"
-__version__ = "$Revision$"
-# $Source$
-
-from pyphant.core import Worker, Connectors,\
-                         Param, DataContainer
-import ImageProcessing
-import numpy, copy
-from scipy import ndimage
-
-def pile(func, imagedata, runs=1, dopile=True):
-    assert imagedata.ndim in [2, 3]
-    assert runs >= 0
-    if runs == 0:
-        return imagedata
-    if imagedata.ndim == 2 or not dopile:
-        pile = [imagedata]
-    else:
-        pile = imagedata
-    for run in xrange(runs):
-        pile = [func(data) for data in pile]
-    if imagedata.ndim == 2 or not dopile:
-        newdata = pile[0]
-    else:
-        newdata = numpy.array(pile)
-    return newdata
-
-
-class NDImage(Worker.Worker):
-    API = 2
-    VERSION = 1
-    REVISION = "$Revision$"[11:-1]
-    name = "ndimage"
-    _sockets = [("image", Connectors.TYPE_IMAGE)]
-    _filters = {"binary_closing":("iterations", ),
-                "binary_opening":("iterations", ),
-                "binary_fill_holes":(),
-                "binary_erosion":("iterations", ),
-                "binary_dilation":("iterations", ),
-                "maximum_filter":("size", "mode", "cval"),
-                "median_filter":("size", "mode", "cval"),
-                "grey_closing":("size", "mode", "cval"),
-                "grey_erosion":("size", "mode", "cval"),
-                "grey_opening":("size", "mode", "cval"),
-                "distance_transform_bf":("metric", ),
-                "sobel":("axis", "mode", "cval"),
-                "grey_invert":(None, ),
-                "cut_histogram":(None, "tolerance"),
-                "label":(None, "connectivity"),
-                "threshold":(None, "threshold"),
-                "area_opening":(None, "size")}
-    _ndparams = {"iterations":1,
-                 "size":5,
-                 "mode":["reflect",
-                         "nearest",
-                         "wrap",
-                         "constant"],
-                 "cval":0,
-                 "tolerance":1000,
-                 "connectivity":2,
-                 "metric":["euclidean",
-                           "taxicab",
-                           "chessboard"],
-                 "threshold":"1 m",
-                 "axis":-1}
-    _params = [("pile", "Treat 3d images as pile of 2d images", True, None),
-               ("ndfilter", "Filter", _filters.keys(), None)]
-    _params += [(pn, pn, dflt, None) for pn, dflt in _ndparams.iteritems()]
-
-    def area_opening(self, data, size):
-        structure = ndimage.morphology.generate_binary_structure(data.ndim,
-                                                                 2)
-        labels = ndimage.label(data, structure=structure)[0]
-        slices = ndimage.find_objects(labels)
-        areas = [numpy.where(labels[sli] == label + 1, True, False).sum() \
-                     for label, sli in enumerate(slices)]
-        print areas
-        output = numpy.zeros(data.shape, dtype=data.dtype)
-        for label, sli, area in zip(range(len(slices)), slices, areas):
-            if area >= size:
-                output[sli] |= numpy.where(labels[sli] == label + 1, data[sli], 0)
-        return output
-
-    def threshold(self, data, threshold):
-        from pyphant.quantities import (Quantity,
-                                                           isQuantity)
-        from pyphant.core.Helpers import uc2utf8
-        try:
-            thp = Quantity(uc2utf8(threshold))
-        except:
-            thp = float(threshold)
-        thp /= self._unit
-        assert not isQuantity(thp)
-        return numpy.where(data < thp, False, True)
-
-    def grey_invert(self, data):
-        return 255 - data
-
-    def label(self, data, connectivity):
-        structure = ndimage.morphology.generate_binary_structure(data.ndim,
-                                                               connectivity)
-        return ndimage.label(data, structure=structure)[0]
-
-    def cut_histogram(self, data, tolerance):
-        hist = ndimage.histogram(data, 0, 256, 256)
-        csum = numpy.cumsum(hist)
-        cut = csum[255] / tolerance
-        for i in xrange(len(csum)):
-            if csum[i] > cut:
-                newmin = i
-                break
-        meanvalue = data.mean()
-        return numpy.where(data < newmin, meanvalue, data)
-
-    def applyfilter(self, data):
-        if None in self._filters[self.paramNdfilter.value]:
-            call = getattr(self, self.paramNdfilter.value)
-        else:
-            call = getattr(ndimage, self.paramNdfilter.value)
-        args = {}
-        for par in self._filters[self.paramNdfilter.value]:
-            if par != None:
-                args[par] = self.getParam(par).value
-        #print args
-        return call(data, **args)
-
-    @Worker.plug(Connectors.TYPE_IMAGE)
-    def ndimage(self, image, subscriber=0):
-        self._unit = image.unit
-        if "iterations" in self._filters[self.paramNdfilter.value]:
-            runs = 1
-        else:
-            runs = self.paramIterations.value
-        newdata = pile(self.applyfilter, image.data, runs, self.paramPile.value)
-        longname = "%s" % (self.paramNdfilter.value, )
-        result = DataContainer.FieldContainer(
-            newdata,
-            copy.deepcopy(image.unit),
-            None,
-            copy.deepcopy(image.mask),
-            copy.deepcopy(image.dimensions),
-            longname,
-            image.shortname,
-            copy.deepcopy(image.attributes),
-            False)
-        result.seal()
-        return result

Modified: trunk/src/workers/ImageProcessing/ImageProcessing/ThresholdingWorker.py
===================================================================
--- trunk/src/workers/ImageProcessing/ImageProcessing/ThresholdingWorker.py	2011-05-23 12:48:36 UTC (rev 700)
+++ trunk/src/workers/ImageProcessing/ImageProcessing/ThresholdingWorker.py	2011-11-17 10:26:46 UTC (rev 701)
@@ -53,14 +53,28 @@
     REVISION = "$Revision$"[11:-1]
     name = "Threshold"
     _sockets = [("image", Connectors.TYPE_IMAGE)]
-    _params = [("threshold", "Threshold", 160, None),
+    _params = [("threshold", "Threshold", "160.0", None),
+               ("unit", "Unit", "ignore", None)
 #               ("mode", "Mode(absolute/coverage)",
 #                ["absolute", "coverage"], None)
                ]
 
     @Worker.plug(Connectors.TYPE_IMAGE)
     def threshold(self, image, subscriber=0):
-        th = self.paramThreshold.value
+        th = float(self.paramThreshold.value)
+        if self.paramUnit.value.lower() != 'ignore':
+            from pyphant.quantities import Quantity, isQuantity
+            try:
+                unit = float(self.paramUnit.value)
+                assert not isQuantity(image.unit)
+            except ValueError:
+                try:
+                    unit = Quantity(self.paramUnit.value)
+                except TypeError:
+                    unit = Quantity(1.0, self.paramUnit.value)
+                assert isQuantity(image.unit)
+                assert unit.isCompatible(image.unit.unit)
+            th *= unit / image.unit
         resultArray = scipy.where(image.data < th,
                                   ImageProcessing.FEATURE_COLOR,
                                   ImageProcessing.BACKGROUND_COLOR)
@@ -68,4 +82,4 @@
                                     dimensions=copy.deepcopy(image.dimensions),
                                     longname=u"Binary Image", shortname=u"B")
         result.seal()
-        return result
\ No newline at end of file
+        return result

Modified: trunk/src/workers/ImageProcessing/ImageProcessing/Watershed.py
===================================================================
--- trunk/src/workers/ImageProcessing/ImageProcessing/Watershed.py	2011-05-23 12:48:36 UTC (rev 700)
+++ trunk/src/workers/ImageProcessing/ImageProcessing/Watershed.py	2011-11-17 10:26:46 UTC (rev 701)
@@ -39,7 +39,6 @@
 # $Source$
 
 from pyphant.core import (Worker, Connectors, DataContainer)
-from ImageProcessing.NDImageWorker import pile
 import copy
 import heapq
 import scipy
@@ -96,7 +95,7 @@
     @Worker.plug(Connectors.TYPE_IMAGE)
     def wsworker(self, image, markers, subscriber=0):
         self._markers = markers.data
-        newdata = pile(self.watershed, image.data)
+        newdata = self.watershed(image.data)
         longname = "Watershed"
         result = DataContainer.FieldContainer(newdata,
                                               copy.deepcopy(image.unit),

Modified: trunk/src/workers/ImageProcessing/ImageProcessing/__init__.py
===================================================================
--- trunk/src/workers/ImageProcessing/ImageProcessing/__init__.py	2011-05-23 12:48:36 UTC (rev 700)
+++ trunk/src/workers/ImageProcessing/ImageProcessing/__init__.py	2011-11-17 10:26:46 UTC (rev 701)
@@ -56,9 +56,9 @@
     "Gradient",
     "ImageLoaderWorker",
     "InvertWorker",
+    "LoadZStack",
     "MarkInclusions",
     "Medianiser",
-    "NDImageWorker",
     "SkeletonizeFeature",
     "ThresholdingWorker",
     "UltimatePointsCalculator",

Modified: trunk/src/workers/ImageProcessing/ImageProcessing/tests/TestAutoFocus.py
===================================================================
--- trunk/src/workers/ImageProcessing/ImageProcessing/tests/TestAutoFocus.py	2011-05-23 12:48:36 UTC (rev 700)
+++ trunk/src/workers/ImageProcessing/ImageProcessing/tests/TestAutoFocus.py	2011-11-17 10:26:46 UTC (rev 701)
@@ -31,7 +31,8 @@
 # NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 # SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
-u"""Provides unittest classes for AutoFocus worker.
+u"""Provides unittest classes for AutoFocus, LoadZStack
+and MarkInclusions worker.
 """
 
 __id__ = "$Id$".replace('$','')
@@ -46,32 +47,8 @@
 from ImageProcessing import __path__ as ppath
 importDir = os.path.join(ppath[0], "tests", "resources",
                          "zstack")
-from pyphant.quantities import Quantity
-import numpy
-import scipy
 
 
-def importZStack(filenames, zUnit, zValues):
-    from pyphant.core.DataContainer import FieldContainer
-    zDim = FieldContainer(data=zValues, unit=zUnit,
-                          shortname='z', longname='Z Axis')
-    yDim = FieldContainer(data=numpy.arange(.0, 400.0, 1.0) * 1.29,
-                          unit=Quantity('1.0 mum'),
-                          shortname='y', longname='Y Axis')
-    xDim = FieldContainer(data=numpy.arange(.0, 400.0, 1.0) * 1.29,
-                          unit=Quantity('1.0 mum'),
-                          shortname='x', longname='X Axis')
-    imgData = numpy.zeros((zDim.data.shape[0], yDim.data.shape[0],
-                           xDim.data.shape[0]), dtype='uint8')
-    for i, filename in enumerate(filenames):
-        imgData[i] = scipy.misc.imread(os.path.join(importDir, filename),
-                                       flatten=True)
-    zStack = FieldContainer(data=imgData, dimensions=[zDim, yDim, xDim],
-                            shortname='I', longname='ZStack')
-    zStack.seal()
-    return zStack
-
-
 class ZStackTestCase(unittest.TestCase):
     def setUp(self):
         pass
@@ -87,12 +64,13 @@
 
     def testZStack(self):
         print "Importing ZStack..."
-        zstack = importZStack(
-            filenames=filter(lambda x: x.endswith('.tif'),
-                             sorted(os.listdir(importDir))),
-            zUnit=Quantity('1.0 mum'),
-            zValues = numpy.arange(0.0, 601.0, 100.0)
-            )
+        from ImageProcessing.LoadZStack import LoadZStack
+        loader = LoadZStack()
+        loader.paramPath.value = importDir
+        loader.paramDz.value = '100.0 mum'
+        loader.paramDy.value = '1.29 mum'
+        loader.paramDx.value = '1.29 mum'
+        zstack = loader.loadImageAsGreyScale()
         print "Done."
         print "Calculating ZStack-statistics..."
         from ImageProcessing.AutoFocus import AutoFocus
@@ -114,11 +92,15 @@
 
     def testSingle(self):
         print "Importing single image..."
-        zstack = importZStack(
-            filenames=['TestZStack_z03.tif'],
-            zUnit=Quantity('1.0 mum'),
-            zValues = numpy.array([300.0, ])
-            )
+        from ImageProcessing.LoadZStack import LoadZStack
+        loader = LoadZStack()
+        loader.paramPath.value = os.path.join(importDir, 'TestZStack_z00.tif')
+        loader.paramDz.value = '100.0 mum'
+        loader.paramDy.value = '1.29 mum'
+        loader.paramDx.value = '1.29 mum'
+        loader.paramStartz.value = '300.0 mum'
+        loader.paramZClip.value = '3:4'
+        zstack = loader.loadImageAsGreyScale()
         print "Done."
         print "Calculating single image statistics..."
         from ImageProcessing.AutoFocus import AutoFocus
@@ -138,7 +120,24 @@
         self.check((300.0, 0.0), statistics['zPos'].data[imin])
         self.check((7.0 * mul, mul), statistics['diameter'].data[imin])
 
+    def testMarkInclusions(self):
+        from ImageProcessing.LoadZStack import LoadZStack
+        from ImageProcessing.MarkInclusions import MarkInclusions
+        loader = LoadZStack()
+        loader.paramPath.value = importDir
+        loader.paramDz.value = '100.0 mum'
+        loader.paramDy.value = '1.29 mum'
+        loader.paramDx.value = '1.29 mum'
+        zstack = loader.loadImageAsGreyScale()
+        from ImageProcessing.AutoFocus import AutoFocus
+        afw = AutoFocus()
+        statistics = afw.getStatistics(zstack)
+        minc = MarkInclusions()
+        marked = minc.markInclusions(zstack, statistics)
+        self.assertEqual(zstack.dimensions, marked.dimensions)
+        self.assertEqual(zstack.unit, marked.unit)
 
+
 if __name__ == "__main__":
     import sys
     if len(sys.argv) == 1:

Added: trunk/src/workers/ImageProcessing/ImageProcessing/tests/TestCoverage.py
===================================================================
--- trunk/src/workers/ImageProcessing/ImageProcessing/tests/TestCoverage.py	                        (rev 0)
+++ trunk/src/workers/ImageProcessing/ImageProcessing/tests/TestCoverage.py	2011-11-17 10:26:46 UTC (rev 701)
@@ -0,0 +1,88 @@
+# -*- coding: utf-8 -*-
+
+# Copyright (c) 2006-2007, Rectorate of the University of Freiburg
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+# * Redistributions of source code must retain the above copyright
+#   notice, this list of conditions and the following disclaimer.
+# * Redistributions in binary form must...
 
[truncated message content]

[Pyphant-devel] SF.net SVN: pyphant:[700] trunk/src

From: <zk...@us...> - 2011-05-23 12:48:46

Revision: 700
          http://pyphant.svn.sourceforge.net/pyphant/?rev=700&view=rev
Author:   zklaus
Date:     2011-05-23 12:48:36 +0000 (Mon, 23 May 2011)

Log Message:
-----------
Merge branch 'master' into svn-trunk

* master: (42 commits)
  Enh: Added loadRecipe method to H5FileHandler
  Fix: Workaround for Statistics.Histogram
  Fix: Worker.py: unwanted sharing of annotations
  Fix: KM: removed ProgressDialog if no wx present
  Enh: Faster hashing for FieldContainers
  Fix: Docstrings in toolboxes
  Merge: Autofocus
  Fix: Type of name parameter of workers
  Bar chart: Increase range from [0:ymax] to [min(ymin,0):ymax]
  MRA: - Bugfix: Local Extrema Systematically Shifted
  - "OSC.MRA" Bugfix: Removed systematic error in calculation of local extrema
  Fix: Dimensions in AlgebraWorker
  Revert: Undo last 2 commits
  Fix: tried to fix dimensions in AlgebraWorker
  Fix: started working on dimensions in AlgebraWorker
  Fix: AlgebraWorker: Sealing of DCs
  Enh: Added wildcard support to FileButton
  Test: Tried working on the FileButton of FMFLoader
  Fix: Put workers back into the ImageProcessing toolbox
  Fix: Made OscMapper worker independent of OscAbsorption
  ...

Modified Paths:
--------------
    trunk/src/pyphant/pyphant/core/DataContainer.py
    trunk/src/pyphant/pyphant/core/FieldContainer.py
    trunk/src/pyphant/pyphant/core/H5FileHandler.py
    trunk/src/pyphant/pyphant/core/Helpers.py
    trunk/src/pyphant/pyphant/core/KnowledgeManager.py
    trunk/src/pyphant/pyphant/core/Worker.py
    trunk/src/pyphant/pyphant/tests/TestDataContainer.py
    trunk/src/pyphant/pyphant/visualizers/Chart.py
    trunk/src/pyphant/pyphant/visualizers/ZStackVisualizer.py
    trunk/src/pyphant/pyphant/visualizers/__init__.py
    trunk/src/pyphant/pyphant/wxgui2/paramvisualization/FileButton.py
    trunk/src/pyphant/pyphant/wxgui2/wxPyphantApplication.py
    trunk/src/workers/ImageProcessing/ImageProcessing/ApplyMask.py
    trunk/src/workers/ImageProcessing/ImageProcessing/AutoFocus.py
    trunk/src/workers/ImageProcessing/ImageProcessing/BiThresholdingWorker.py
    trunk/src/workers/ImageProcessing/ImageProcessing/CoverageWorker.py
    trunk/src/workers/ImageProcessing/ImageProcessing/DiffWorker.py
    trunk/src/workers/ImageProcessing/ImageProcessing/DistanceMapper.py
    trunk/src/workers/ImageProcessing/ImageProcessing/EdgeFillWorker.py
    trunk/src/workers/ImageProcessing/ImageProcessing/EdgeTouchingFeatureRemover.py
    trunk/src/workers/ImageProcessing/ImageProcessing/EnhanceContrast.py
    trunk/src/workers/ImageProcessing/ImageProcessing/FindLocalExtrema.py
    trunk/src/workers/ImageProcessing/ImageProcessing/FitBackground.py
    trunk/src/workers/ImageProcessing/ImageProcessing/Gradient.py
    trunk/src/workers/ImageProcessing/ImageProcessing/ImageLoaderWorker.py
    trunk/src/workers/ImageProcessing/ImageProcessing/InvertWorker.py
    trunk/src/workers/ImageProcessing/ImageProcessing/Medianiser.py
    trunk/src/workers/ImageProcessing/ImageProcessing/NDImageWorker.py
    trunk/src/workers/ImageProcessing/ImageProcessing/OptimalContrastWorker.py
    trunk/src/workers/ImageProcessing/ImageProcessing/SkeletonizeFeature.py
    trunk/src/workers/ImageProcessing/ImageProcessing/ThresholdingWorker.py
    trunk/src/workers/ImageProcessing/ImageProcessing/UltimatePointsCalculator.py
    trunk/src/workers/ImageProcessing/ImageProcessing/Watershed.py
    trunk/src/workers/ImageProcessing/ImageProcessing/__init__.py
    trunk/src/workers/ImageProcessing/setup.py
    trunk/src/workers/OSC/OSC/ErrorEstimator.py
    trunk/src/workers/OSC/OSC/EstimateParameterFromValues.py
    trunk/src/workers/OSC/OSC/ExtremumFinder.py
    trunk/src/workers/OSC/OSC/OscAbsorption.py
    trunk/src/workers/OSC/OSC/__init__.py
    trunk/src/workers/OSC/OSC/tests/TestMRA.py
    trunk/src/workers/Statistics/Statistics/Histogram.py
    trunk/src/workers/Statistics/setup.py
    trunk/src/workers/fmfile/fmfile/FMFLoader.py
    trunk/src/workers/tools/setup.py
    trunk/src/workers/tools/tools/__init__.py

Added Paths:
-----------
    trunk/src/workers/ImageProcessing/ImageProcessing/MarkInclusions.py
    trunk/src/workers/ImageProcessing/ImageProcessing/tests/TestAutoFocus.py
    trunk/src/workers/ImageProcessing/ImageProcessing/tests/resources/
    trunk/src/workers/ImageProcessing/ImageProcessing/tests/resources/zstack/
    trunk/src/workers/ImageProcessing/ImageProcessing/tests/resources/zstack/TestZStack_z00.tif
    trunk/src/workers/ImageProcessing/ImageProcessing/tests/resources/zstack/TestZStack_z01.tif
    trunk/src/workers/ImageProcessing/ImageProcessing/tests/resources/zstack/TestZStack_z02.tif
    trunk/src/workers/ImageProcessing/ImageProcessing/tests/resources/zstack/TestZStack_z03.tif
    trunk/src/workers/ImageProcessing/ImageProcessing/tests/resources/zstack/TestZStack_z04.tif
    trunk/src/workers/ImageProcessing/ImageProcessing/tests/resources/zstack/TestZStack_z05.tif
    trunk/src/workers/ImageProcessing/ImageProcessing/tests/resources/zstack/TestZStack_z06.tif
    trunk/src/workers/OSC/OSC/OscMapper.py
    trunk/src/workers/tools/tools/AddColumn.py
    trunk/src/workers/tools/tools/AlgebraWorker.py
    trunk/src/workers/tools/tools/ColumnExtractor.py
    trunk/src/workers/tools/tools/ExtractRows.py
    trunk/src/workers/tools/tools/MRA.py
    trunk/src/workers/tools/tools/Slicing.py

Removed Paths:
-------------
    trunk/src/pyphant/pyphant/core/XMLHandler.py
    trunk/src/pyphant/pyphant/core/ZStackManager.py
    trunk/src/pyphant/pyphant/tests/TestZStacks.py
    trunk/src/pyphant/pyphant/tests/resources/zstack/TestZStack_z00.tif
    trunk/src/pyphant/pyphant/tests/resources/zstack/TestZStack_z01.tif
    trunk/src/pyphant/pyphant/tests/resources/zstack/TestZStack_z02.tif
    trunk/src/pyphant/pyphant/tests/resources/zstack/TestZStack_z03.tif
    trunk/src/pyphant/pyphant/tests/resources/zstack/TestZStack_z04.tif
    trunk/src/pyphant/pyphant/tests/resources/zstack/TestZStack_z05.tif
    trunk/src/pyphant/pyphant/tests/resources/zstack/TestZStack_z06.tif
    trunk/src/pyphant/pyphant/tests/resources/zstack/_meta.xml
    trunk/src/pyphant/pyphant/tests/resources/zstack/single_meta.xml
    trunk/src/pyphant/pyphant/visualizers/SingleValueVisualizer.py
    trunk/src/workers/ImageProcessing/ImageProcessing/FeatureRatio.py
    trunk/src/workers/ImageProcessing/ImageProcessing/FilterWorker.py
    trunk/src/workers/ImageProcessing/ImageProcessing/MarkAF.py
    trunk/src/workers/ImageProcessing/ImageProcessing/Reduce.py
    trunk/src/workers/ImageProcessing/ImageProcessing/SliceSelector.py
    trunk/src/workers/OSC/OSC/AddColumn.py
    trunk/src/workers/OSC/OSC/MRA.py
    trunk/src/workers/OSC/OSC/Slicing.py

Modified: trunk/src/pyphant/pyphant/core/DataContainer.py
===================================================================
--- trunk/src/pyphant/pyphant/core/DataContainer.py	2010-09-13 08:56:34 UTC (rev 699)
+++ trunk/src/pyphant/pyphant/core/DataContainer.py	2011-05-23 12:48:36 UTC (rev 700)
@@ -36,7 +36,7 @@
 =============================================================================
 
 The *DataContainer* is Pypahnt's preferred data exchange class. It is
-designed to maximise the interoperability of the various workers
+designed to maximize the interoperability of the various workers
 provided by Pyphant.
 
 It can be seen as an interface for exchanging data between workers and
@@ -58,7 +58,7 @@
 =============================================================
 
 The *SampleContainer* combines different FieldContainers that have the
-same numer of sample points to a table-like representation. It stores
+same number of sample points to a table-like representation. It stores
 different observations on the same subject per row whereby each column
 comprises a quantity of the same kind. Each row can be regarded as the
 realization of a random variable.
@@ -71,10 +71,9 @@
 
 import copy, hashlib, threading, numpy, StringIO
 import os, platform, datetime, socket, urlparse
-from pyphant.quantities import (isQuantity,
-                                                   Quantity)
+from pyphant.quantities import (isQuantity, Quantity)
 import Helpers
-
+from ast import (NodeTransformer, NodeVisitor)
 import logging
 _logger = logging.getLogger("pyphant")
 
@@ -83,7 +82,7 @@
 enc = lambda s: unicode(s, "utf-8")
 
 def parseId(id):
-    u"""Returns tupple (HASH, TYPESTRING) from given .id attribute."""
+    u"""Returns tuple (HASH, TYPESTRING) from given .id attribute."""
     resUri = urlparse.urlsplit(id)
     return resUri[2].split('/')[-1].split('.') #(hash, uriType)
 
@@ -293,446 +292,152 @@
     def numberOfColumns(self):
         return len(self.columns)
 
-    def _getCommands(self, expression):
+    def calcColumn(self, exprStr, shortname, longname):
         """
-        This method generates nested tuples of filter commands to be applied
-        to a SampleContainer out of a string expression. For details of the
-        output see SampleContainer.filter()
-        expression -- String describing the filter commands. For details
-                      see SampleContainer.filter(expression)
+        Return an unsealed FieldContainer generated from `exprStr`.
+
+        Parameters
+        ----------
+        exprStr : str
+            Expression has to be a string. Specifies the mathematical
+            operations which will be evaluated to generate a new FieldContainer
+            containing the result. `exprStr` may contain FieldContainers,
+            PhysicalQuantities, Booleans and Numbers as well as the operators
+            listed below.
+
+        shortname : str
+            The `shortname` of the returned FieldContainer.
+
+        longname : str
+            The `longname`of the returned FieldContainer.
+
+        Syntax
+        ------
+        FieldContainer
+            FieldContainers can be adressed by their `shortname`or `longname`.
+            For a FieldContainer with shortname="exampleFC" the syntax within
+            `exprStr` is:
+                col("exampleFC")
+            where `col` stands for column and may be `Col` or `COL` as well.
+            Adressing by `longname` works analogously.
+
+        PhysicalQuantity
+            Within the expression PhysicalQuantities have to be enquoted:
+                "10kg", "100 m", "5 kg * m / s ** 2"
+            where the whitespaces are optional.
+
+        Booleans and Numbers
+            Can just be used without quotes or braces within `exprStr`:
+                True, False, 1.2, 10
+
+        Operators
+        ---------
+        A list of all implemented operations that can be used within `exprStr`
+        sorted by precedence from lowest precedence (least binding) to highest
+        precedence (most binding):
+
+        Comparisons: <, <=, >, >=, <>, !=, ==
+        Bitwise OR: |
+        Bitwise XOR: ^
+        Bitwise AND: &
+        Addition and Subtraction: +, -
+        Multiplication, Division: *, /
+        Positive, Negative, Bitwise NOT: +x, -x, ~x
+
+        Not implemented: and, or, not, **, //, %, if - else
+
+        Examples
+        --------
+        Some examples of valid expressions will be given.
+        Data:
+            distance = FieldContainer(scipy.array([5., 10., 1.]),
+                                    Quantity('1.0 m'),
+                                    longname=u"Distance",
+                                    shortname=u"s")
+            time = FieldContainer(scipy.array([3., 4., 5.]),
+                                    Quantity('1.0 s'),
+                                    longname=u"Time",
+                                    shortname=u"t")
+        Examplary expressions:
+            exprStr = "col('Distance') / col('Time')"
+            exprStr = "col('Distance') - '1 m'"
+            exprStr = "col('t') >= '4 s'"
+            exprStr = "(col('s') > '1 m') & (COL('Time') == '3s')"
+
         """
-        #TODO: compare SCColumns with each other,
-        #      allow multi dimensional columns (think up new syntax)
-        import re
-        #test for expressions containing whitespaces only:
-        if len(re.findall(r'\S', expression)) == 0:
-            return ()
-        #prepare regular expressions
-        reDoubleQuotes = re.compile(r'("[^"][^"]*")')
-        reSplit = re.compile(
-            r'(<(?!=)|<=|>(?!=)|>=|==|!=|not|NOT|and|AND|or|OR|\(|\))'
-            )
-        reCompareOp = re.compile(r'<|>|==|!=')
-        #split the expression
-        DQList = reDoubleQuotes.split(expression)
-        splitlist = []
-        for dq in DQList:
-            if reDoubleQuotes.match(dq) != None: splitlist.append(dq)
-            else: splitlist.extend(reSplit.split(dq))
-        #identify splitted Elements
-        al = [] #<-- abstractlist containing tuples of (type, expression)
-        for e in splitlist:
-            if len(re.findall(r'\S', e)) == 0: pass #<-- skip whitespaces
-            elif reCompareOp.match(e) != None:
-                al.append(('CompareOp', e))
-            elif reSplit.match(e) != None:
-                al.append(('Delimiter', e.lower()))
-            elif reDoubleQuotes.match(e) != None:
-                column = None
-                try:
-                    column = self[e[1:-1]]
-                except:
-                    raise IndexError(
-                        'Could not find column ' + e + ' in "'
-                        + self.longname + '".'
-                        )
-                al.append(('SCColumn', column))
+        exprStr = exprStr or 'True'
+        import ast
+        rpn = ReplaceName(self)
+        expr = compile(exprStr, "<calcColumn>", 'eval', ast.PyCF_ONLY_AST)
+        replacedExpr = rpn.visit(expr)
+        rpo = ReplaceOperator(rpn.localDict)
+        factorExpr = rpo.visit(replacedExpr)
+        localDict = dict([(key, value.data) \
+                          for key, value in rpn.localDict.iteritems()])
+        data = eval(compile(factorExpr, '<calcColumn>', 'eval'), {}, localDict)
+        unitcalc = UnitCalculator(rpn.localDict)
+        unit, dims = unitcalc.getUnitAndDim(replacedExpr)
+        if dims is None:
+            assert not isinstance(data, numpy.ndarray)
+            for col in self.columns:
+                checkDimensions(col.dimensions[0],
+                                self.columns[0].dimensions[0])
+            shape = self.columns[0].dimensions[0].data.shape
+            if data:
+                data = numpy.ones(shape, dtype=bool)
             else:
-                try:
-                    phq = Quantity(e)
-                    al.append(('PhysQuant', phq))
-                    continue
-                except:
-                    try:
-                        number = Quantity(e+' m')
-                        al.append(('Number', eval(e)))
-                        continue
-                    except: pass
-                    raise ValueError, "Error parsing expression: " + e
-        #resolve multiple CompareOps like a <= b <= c == d:
-        i = 0
-        values = ['PhysQuant', 'SCColumn', 'Number']
-        start_sequence = -1
-        while i < len(al) - 4:
-            if ((al[i][0] in values) and (al[i+1][0] == 'CompareOp')
-                and (al[i+2][0] in values) and (al[i+3][0] == 'CompareOp')
-                and (al[i+4][0] in values)):
-                if start_sequence == -1:
-                    start_sequence = i
-                al.insert(i+3, ('Delimiter', 'and'))
-                al.insert(i+4, al[i+2])
-                i += 4
-            else:
-                #'not' has higher precedence than 'and':
-                if start_sequence != -1:
-                    al.insert(start_sequence, ('Delimiter', '('))
-                    al.insert(i+4, ('Delimiter', ')'))
-                    start_sequence = -1
-                    i += 3
-                else:
-                    i += 1
-        if start_sequence != -1:
-            al.insert(start_sequence, ('Delimiter', '('))
-            al.insert(i+4, ('Delimiter', ')'))
-        #identify atomar components like "a" <= 10m, 10s > "b",
-        #... and compress them:
-        if al[0][0] == 'CompareOp':
-            raise ValueError(
-                al[0][1] + " may not stand at the beginning of an expression!"
-                )
-        i = 1
-        valid = False
-        while i < len(al):
-            if al[i][0] == 'CompareOp':
-                left = al.pop(i-1)
-                middle = al.pop(i-1)
-                right = al.pop(i-1)
-                if left[0] not in values:
-                    raise TypeError, str(left[1]) + " is not a proper value."
-                if right[0] not in values:
-                    raise TypeError, str(right[1]) + " is not a proper value."
-                al.insert(i-1, ('Atomar', left, middle[1], right))
-                valid = True
-            i += 1
-        if not valid:
-            raise ValueError(
-                "There has to be at least one valid comparison: " + expression
-                )
+                data = numpy.zeros(shape, dtype=bool)
+            dims = [self.columns[0].dimensions[0]]
+        field = FieldContainer(data, unit, dimensions=dims,
+                               longname=longname, shortname=shortname)
+        return field
 
-        def compressBraces(sublist):
-            """
-            Identifies braces and compresses them recursively.
-            sublist -- list of filter commands
-            """
-            openbraces = 0
-            start = 0
-            end = 0
-            finished = False
-            for i in range(len(sublist)):
-                if sublist[i] == ('Delimiter', '('):
-                    openbraces += 1
-                    if openbraces == 1 and not finished:
-                        start = i
-                elif sublist[i] == ('Delimiter', ')'):
-                    openbraces -= 1
-                    if openbraces == 0 and not finished:
-                        end = i
-                        finished = True
-            if openbraces != 0:
-                raise ValueError(
-                    "There are unmatched braces within the expression: "
-                    + expression
-                    )
-            if start == 0 and end == 0:
-                #no more braces found: end of recursion
-                return sublist[:]
-            else:
-                if end-start == 1:
-                    raise ValueError(
-                        "There are braces enclosing nothing in the expression: "
-                        + expression
-                        )
-                middle = None
-                if end-start == 2:
-                    #discard unnecessary braces in order to reduce
-                    #recursion depth later on:
-                    middle = sublist[start+1:start+2]
-                else:
-                    middle = [('Brace', compressBraces(sublist[start+1:end]))]
-                return sublist[0:start]+middle+compressBraces(sublist[end+1:])
-        #TODO: The following three methods could be merged into one generalized
-        #method for compressing unitary and binary operators. This would be
-        #useful in a future version when there are lots of operators to be
-        #supported.
+    def filter(self, exprStr, shortname='', longname=''):
+        """
+        Return an unsealed SampleContainer containing only those rows where
+        `exprStr` was evaluated to be True. This method replaces the old
+        filter method and is mostly capable of the same operations, yet the
+        syntax has changed slightly.
 
-        def compressNot(sublist):
-            """
-            Identifies "not"s and compresses them recursively.
-            sublist -- list of filter commands
-            """
-            i = 0
-            while i < len(sublist):
-                if sublist[i] == ('Delimiter', 'not'):
-                    if i+1 >= len(sublist):
-                        raise ValueError(
-                            "'not' must not stand at the end of an expression: "
-                            + expression
-                            )
-                    x = sublist[i+1]
-                    if x[0] == 'Atomar':
-                        retlist = sublist[0:i] + [('NOT', x)]
-                        retlist += compressNot(sublist[i+2:])
-                        return retlist
-                    elif x[0] == 'Brace':
-                        retlist = sublist[0:i]
-                        retlist += [('NOT', ('Brace', compressNot(x[1])))]
-                        retlist += compressNot(sublist[i+2:])
-                        return retlist
-                    else:
-                        raise ValueError(
-                            "'not' cannot be applied to " + str(x) + "."
-                            )
-                elif sublist[i][0] == 'Brace':
-                    retlist = sublist[0:i]
-                    retlist += [('Brace', compressNot(sublist[i][1]))]
-                    retlist += compressNot(sublist[i+1:])
-                    return retlist
-                i += 1
-            return sublist[:]
+        Parameters
+        ----------
+        exprStr : str
+            A string with a logical expression that has to evaluate to be
+            either True or False. This can be for example an inequality or
+            a comparison. For all possible operations and a description of
+            the syntax as well as examples see `calcColumn`.
 
-        def compressAnd(sublist, start=0):
-            """
-            Identifies "and"s and compresses them recursively:
-            start -- start == 1 indicates that the 1st element of sublist
-                     has already been compressed. This is necessary for
-                     binary operators.
-            sublist -- list of filter commands
-            """
-            i = start
-            while i < len(sublist):
-                if sublist[i] == ('Delimiter', 'and'):
-                    left = None
-                    if start == 1 and i == 1: left = sublist[i-1]
-                    else: left = compressAnd(sublist[i-1:i])[0]
-                    if left[0] not in ['NOT', 'AND', 'Brace', 'Atomar']:
-                        raise ValueError(
-                            "'and' cannot be applied to " + str(left) + "."
-                            )
-                    right = compressAnd(sublist[i+1:i+2])[0]
-                    if right[0] not in ['NOT', 'AND', 'Brace', 'Atomar']:
-                        raise ValueError(
-                            "'and' cannot be applied to " + str(right) + "."
-                            )
-                    retlist = sublist[0:i-1]
-                    retlist += compressAnd([('AND', left, right)]+sublist[i+2:],
-                                           1)
-                    return retlist
-                elif sublist[i][0] == 'Brace':
-                    retlist = sublist[0:i]
-                    retlist += compressAnd([('Brace',
-                                             compressAnd(sublist[i][1]))]
-                                           + sublist[i+1:], 1)
-                    return retlist
-                elif sublist[i][0] == 'NOT':
-                    retlist = sublist[0:i]
-                    retlist += compressAnd([('NOT',
-                                             compressAnd([sublist[i][1]])[0])]
-                                           + sublist[i+1:], 1)
-                    return retlist
-                i += 1
-            return sublist[:]
+        shortname, longname : str, default=''
+            Specify the short and long name of the resulting FC.
 
-        def compressOrDCB(sublist, start=0):
-            """
-            Identifies "or"s and compresses them recursively.
-            Decompresses braces in order to reduce recursion depth later on.
-            start -- start == 1 indicates that the 1st element of sublist
-                     has already been compressed. This is necessary for
-                     binary operators.
-            sublist -- list of filter commands
-            """
-            i = start
-            while i < len(sublist):
-                if sublist[i] == ('Delimiter', 'or'):
-                    left = None
-                    if start == 1 and i == 1: left = sublist[i-1]
-                    else: left = compressOrDCB(sublist[i-1:i])[0]
-                    if left[0] not in ['NOT', 'AND', 'Atomar', 'OR']:
-                        raise ValueError(
-                            "'or' cannot be applied to " + str(left) + "."
-                            )
-                    right = compressOrDCB(sublist[i+1:i+2])[0]
-                    if right[0] not in ['NOT', 'AND', 'Atomar', 'OR']:
-                        raise ValueError(
-                            "'or' cannot be applied to " + str(right) + "."
-                            )
-                    retlist = sublist[0:i-1]
-                    retlist += compressOrDCB([('OR', left, right)]
-                                             + sublist[i+2:], 1)
-                    return retlist
-                elif sublist[i][0] == 'Brace':
-                    inner = compressOrDCB(sublist[i][1])
-                    if len(inner) != 1:
-                        raise ValueError(
-                            "Expression could not be parsed completely."
-                            "(probably missing keyword): " + expression
-                            )
-                    retlist = sublist[0:i]
-                    retlist += compressOrDCB(inner + sublist[i+1:], 1)
-                    return retlist
-                elif sublist[i][0] == 'NOT':
-                    retlist = sublist[0:i]
-                    retlist += compressOrDCB(
-                        [('NOT', compressOrDCB([sublist[i][1]])[0])]
-                        + sublist[i+1:], 1
-                        )
-                    return retlist
-                elif sublist[i][0] == 'AND':
-                    retlist = sublist[0:i]
-                    retlist += compressOrDCB(
-                        [('AND',
-                          compressOrDCB([sublist[i][1]])[0],
-                          compressOrDCB([sublist[i][2]])[0])]
-                        + sublist[i+1:], 1)
-                    return retlist
-                i += 1
-            return sublist[:]
-        compressed = compressOrDCB(compressAnd(compressNot(compressBraces(al))))
-        if len(compressed) != 1:
-            raise ValueError(
-                "Expression could not be parsed completely"
-                "(probably missing keyword): " + expression
-                )
-        return compressed[0]
+        """
+        shortname = shortname or self.shortname
+        longname = longname or self.longname
+        mask = self.calcColumn(exprStr, 'm', 'mask')
+        assert isinstance(mask.unit, float)
+        mask = mask.data
+        return self.extractRows(mask, shortname, longname)
 
-    def filter(self, expression):
+    def extractRows(self, mask, shortname, longname):
         """
-        Returns a new SampleContainer with filter commands applied to it.
-        expression -- can be either a string expression or nested tuples
-                      of commands. In case expression is a string (or unicode),
-                      the following syntax holds:
-                      Let's define
-                      <atomar> := <value> <CompareOp> <value>
-                      where <value> is either a SC Column accessed as
-                      "longname" or "shortname" (including the double quotes)
-                      or a number or a string representing a Quantity
-                      (e.g. 300nm). And <CompareOp> can be ==, !=, <, <=, >, >=.
-                      Then a valid expression <expression> is:
-                      - <atomar>
-                      - (<expression>)
-                      - not <expression>
-                      - <expression> and <expression>
-                      - <expression> or <expression>
-                      - NOT, AND, OR is equivalent to not, and, or
-                      Precedence is as follows:
-                      - multiple CompareOps are evaluated:
-                        e.g. a <= b < c --> (a <= b and b < c)
-                      - <atomar>
-                      - braces
-                      - not
-                      - and
-                      - or
-                      If expression is a nested tuple, syntax is as follows:
-                      <value> is either ('SCColumn', FieldContainer instance)
-                      or ('PhysQuant', Quantity instance)
-                      or ('Number', int float etc.)
-                      <CompareOp> is in ['==', '!=', ...]
-                      A valid nested tuple <nt> can be:
-                      - ('Atomar', <value>, <CompareOp>, <value>)
-                      - ('NOT', <nt>)
-                      - ('AND', <nt>, <nt>)
-                      - ('OR', <nt>, <nt>)
-                      Precedence is obtained from the way the tuples are nested.
-        """
-        #determine type of expression:
-        from types import StringType, UnicodeType, TupleType
-        commands = None
-        if isinstance(expression, UnicodeType):
-            commands = self._getCommands(expression.encode('utf-8'))
-        elif isinstance(expression, StringType):
-            commands = self._getCommands(expression)
-        elif isinstance(expression, TupleType) or expression == None:
-            commands = expression
-        else:
-            raise TypeError(
-                "Expression has to be of StringType, UnicodeType,"
-                "TupleType or None. Found " + str(type(expression))
-                + " instead!"
-                )
-        #check for empty commands:
-        if commands == None or commands == ():
-            return copy.deepcopy(self)
-        #generate boolean numpymask from commands using fast numpy methods:
-        def evaluateAtomar(atomar):
-            left = atomar[1]
-            if left[0] == 'SCColumn':
-                if left[1].data.ndim != 1:
-                    raise NotImplementedError(
-                        'Comparing columns of dimensions other than one '
-                        'is not yet implemented: "' + left[1].longname + '"'
-                        )
-            right = atomar[3]
-            if right[0] == 'SCColumn':
-                if right[1].data.ndim != 1:
-                    raise NotImplementedError(
-                        'Comparing columns of dimensions other than one '
-                        'is not yet implemented: "' + right[1].longname + '"'
-                        )
-            leftvalue = None
-            rightvalue = None
-            if left[0] == 'SCColumn' and right[0] == 'SCColumn':
-                number = right[1].unit/left[1].unit
-                if isQuantity(number):
-                    raise TypeError(
-                        'Cannot compare "' + left[1].longname + '" to "'
-                        + right[1].longname + '".'
-                        )
-                leftvalue = left[1].data
-                rightvalue = right[1].data*number
-            elif left[0] == 'SCColumn':
-                number = right[1]/left[1].unit
-                if isQuantity(number):
-                    raise TypeError(
-                        'Cannot compare "' + left[1].longname
-                        + '" to ' + str(right[1]) + '".'
-                        )
-                leftvalue = left[1].data
-                rightvalue = number
-            elif right[0] == 'SCColumn':
-                number = left[1]/right[1].unit
-                if isQuantity(number):
-                    raise TypeError(
-                        "Cannot compare " + str(left[1]) + ' to "'
-                        + right[1].longname + '".'
-                        )
-                leftvalue = number
-                rightvalue = right[1].data
-            else:
-                raise ValueError(
-                    "At least one argument of '" + atomar[2][1]
-                    + "' has to be a column."
-                    )
-            if   atomar[2] == '==': return leftvalue == rightvalue
-            elif atomar[2] == '!=': return leftvalue != rightvalue
-            elif atomar[2] == '<=': return leftvalue <= rightvalue
-            elif atomar[2] == '<' : return leftvalue <  rightvalue
-            elif atomar[2] == '>=': return leftvalue >= rightvalue
-            elif atomar[2] == '>' : return leftvalue >  rightvalue
-            raise ValueError, "Invalid atomar expression: " + str(atomar)
+        Return an unsealed SampleContainer that contains only selected rows. The
+        selection is specified via the `mask`.
 
-        def getMaskFromCommands(cmds):
-            """
-            Returns a boolean numpy mask from given commands.
-            cmds -- nested tuples of commands (see SampleContainer.filter())
-            """
-            if cmds[0] == 'Atomar':
-                return evaluateAtomar(cmds)
-            elif cmds[0] == 'AND':
-                left = getMaskFromCommands(cmds[1])
-                right = getMaskFromCommands(cmds[2])
-                if left.shape != right.shape:
-                    raise TypeError(
-                        "Cannot apply 'and' to columns of different shape: "
-                        + str(left.shape) + ", " + str(right.shape)
-                        )
-                return numpy.logical_and(left, right)
-            elif cmds[0] == 'OR':
-                left = getMaskFromCommands(cmds[1])
-                right = getMaskFromCommands(cmds[2])
-                if left.shape != right.shape:
-                    raise TypeError(
-                        "Cannot apply 'or' to columns of different shape: "
-                        + str(left.shape) + ", " + str(right.shape)
-                        )
-                return numpy.logical_or(left, right)
-            elif cmds[0] == 'NOT':
-                return numpy.logical_not(getMaskFromCommands(cmds[1]))
-        numpymask = getMaskFromCommands(commands)
+        Parameters
+        ----------
+        mask : numpy array of Boolean values
+            The length of the array has to be equal to the length of the columns
+            of the SampleContainer. If the value of mask[n] is
+            True, the nth row is part of the result, else it is discarded.
+
+        shortname, longname : str
+            Specify the short and long name of the resulting FC.
+
+        """
         maskedcolumns = []
         for col in self.columns:
-            maskedcol = None
             try:
-                maskedcol = col.getMaskedFC(numpymask)
+                maskedcol = col.getMaskedFC(mask)
             except ValueError:
                 raise ValueError(
                     'Column "' + col.longname + '" has not enough rows!'
@@ -744,11 +449,12 @@
             maskedcolumns.append(maskedcol)
         #build new SampleContainer from masked columns and return it
         result = SampleContainer(maskedcolumns,
-                                 longname=self.longname,
-                                 shortname=self.shortname,
+                                 longname=longname,
+                                 shortname=shortname,
                                  attributes=copy.deepcopy(self.attributes))
         return result
 
+
 def assertEqual(con1, con2, rtol=1e-5, atol=1e-8):
     diagnosis = StringIO.StringIO()
     testReport = logging.StreamHandler(diagnosis)
@@ -759,3 +465,179 @@
         return True
     else:
         raise AssertionError, diagnosis.getvalue()
+
+
+class LocationFixingNodeTransformer(NodeTransformer):
+    def visit(self, *args, **kargs):
+        result = NodeTransformer.visit(self, *args, **kargs)
+        from ast import fix_missing_locations
+        fix_missing_locations(result)
+        return result
+
+
+class ReplaceName(LocationFixingNodeTransformer):
+    def __init__(self, sampleContainer):
+        self.localDict = {}
+        self.count = 0
+        self.sc = sampleContainer
+
+    def visit_Call(self, node):
+        from ast import (Name, Load)
+        if isinstance(node.func, Name) and node.func.id.lower() == 'col':
+            newName = self.getName(self.sc[node.args[0].s])
+            return Name(newName, Load())
+
+    def visit_Str(self, node):
+        from ast import (Name, Load)
+        quantity = Quantity(node.s)
+        class QuantityDummy(object):
+            pass
+        dummy = QuantityDummy()
+        dummy.unit = Quantity(1.0, quantity.unit)
+        dummy.data = quantity.value
+        dummy.dimensions = None
+        newName = self.getName(dummy)
+        return Name(newName, Load())
+
+    def getName(self, ref):
+        newName = "N%s" % self.count
+        self.count += 1
+        self.localDict[newName] = ref
+        return newName
+
+
+class ReplaceOperator(LocationFixingNodeTransformer):
+    def __init__(self, localDict):
+        self.localDict = localDict
+
+    def visit_BinOp(self, node):
+        from ast import (Add, Sub, BinOp)
+        self.generic_visit(node)
+        unitcalc = UnitCalculator(self.localDict)
+        leftUD = unitcalc.getUnitAndDim(node.left)
+        rightUD = unitcalc.getUnitAndDim(node.right)
+        checkDimensions(leftUD[1], rightUD[1])
+        if isinstance(node.op,(Add, Sub)):
+            factor = rightUD[0] / leftUD[0]
+            right = self.withFactor(factor, node.right)
+            binOp = BinOp(node.left, node.op, right)
+            return binOp
+        else:
+            return node
+
+    def visit_Compare(self, node):
+        from ast import Compare
+        self.generic_visit(node)
+        unitcalc = UnitCalculator(self.localDict)
+        leftUD = unitcalc.getUnitAndDim(node.left)
+        listUD = [unitcalc.getUnitAndDim(comp) for comp in node.comparators]
+        nonNoneDims = [ud[1] for ud in listUD + [leftUD] if ud[1] is not None]
+        for dims in nonNoneDims:
+            checkDimensions(nonNoneDims[0], dims)
+        factorlist = [ud[0] / leftUD[0] for ud in listUD]
+        newComplist = [self.withFactor(*t) \
+                       for t in zip(factorlist, node.comparators)]
+        compOp = Compare(node.left, node.ops, newComplist)
+        compOpTrans = self.compBreaker(compOp)
+        return compOpTrans
+
+    def withFactor(self, factor, node):
+        from ast import (BinOp, Num, Mult)
+        if not isinstance(factor, float):
+            raise ValueError('Incompatible units!')
+        if factor == 1.0:
+            return node
+        return BinOp(Num(factor), Mult(), node)
+
+    def compBreaker(self, node):
+        from ast import (Compare, BinOp, BitAnd)
+        assert isinstance(node, Compare)
+        if len(node.comparators) == 1:
+            return node
+        else:
+            comp1 = Compare(node.left, node.ops[0:1],
+                            node.comparators[0:1])
+            comp2 = Compare(node.comparators[0],
+                            node.ops[1:], node.comparators[1:])
+            newNode = BinOp(comp1, BitAnd(), self.compBreaker(comp2))
+            return newNode
+
+
+class UnitCalculator(object):
+    def __init__(self, localDict):
+        self.localDict = localDict
+
+    def getUnitAndDim(self, node):
+        from ast import (Expression, Name, Num,
+                         BinOp, Add, Mult, Div, Sub,
+                         Compare, BoolOp, UnaryOp,
+                         BitOr, BitXor, BitAnd)
+        if isinstance(node, Expression):
+            return self.getUnitAndDim(node.body)
+        elif isinstance(node, Name):
+            if node.id in ['True', 'False']:
+                return (1.0, None)
+            else:
+                column = self.localDict[node.id]
+                return (column.unit, column.dimensions)
+        elif isinstance(node, Num):
+            return (1.0, None)
+        elif isinstance(node, BinOp):
+            left = self.getUnitAndDim(node.left)
+            right = self.getUnitAndDim(node.right)
+            dimensions = checkDimensions(left[1], right[1])
+            if isinstance(node.op, (Add, Sub)):
+                if not isinstance(left[0] / right[0], float):
+                    raise ValueError("units %s, %s not compatible" \
+                                     % (left, right))
+                unit = left[0]
+            elif isinstance(node.op, Mult):
+                unit = left[0] * right[0]
+            elif isinstance(node.op, Div):
+                unit = left[0] / right[0]
+            elif isinstance(node.op, (BitOr, BitXor, BitAnd)):
+                if not isinstance(left[0], float):
+                    raise ValueError(
+                        "Type %s cannot be interpreted as a Boolean" % left)
+                if not isinstance(right[0], float):
+                    raise ValueError(
+                        "Type %s cannot be interpreted as a Boolean" % right)
+                unit = 1.0
+            else:
+                raise NotImplementedError()
+            return (unit, dimensions)
+        elif isinstance(node, Compare):
+            left = self.getUnitAndDim(node.left)
+            nonNoneDims = []
+            if left[1] is not None:
+                nonNoneDims.append(left[1])
+            for comparator in node.comparators:
+                right = self.getUnitAndDim(comparator)
+                if right[1] is not None:
+                    nonNoneDims.append(right[1])
+                if not isinstance(left[0] / right[0], float):
+                    raise ValueError("units %s, %s not compatible" \
+                                     % (left[0], right[0]))
+            if len(nonNoneDims) >= 1:
+                for dims in nonNoneDims:
+                    checkDimensions(nonNoneDims[0], dims)
+                dimensions = nonNoneDims[0]
+            else:
+                dimensions = None
+            return (1.0, dimensions)
+        elif isinstance(node, BoolOp):
+            raise NotImplementedError(
+                'BoolOps not supported. Use bitwise ops instead (&, |)!')
+        elif isinstance(node, UnaryOp):
+            return self.getUnitAndDim(node.operand)
+        else:
+            raise NotImplementedError()
+
+
+def checkDimensions(dimensions1, dimensions2):
+    if dimensions1 is not None and dimensions2 is not None and \
+           dimensions1 != dimensions2:
+        msg = 'Dimensions "%s" and "%s" do not match!' \
+              % (dimensions1, dimensions2)
+        raise ValueError(msg)
+    return dimensions1 or dimensions2

Modified: trunk/src/pyphant/pyphant/core/FieldContainer.py
===================================================================
--- trunk/src/pyphant/pyphant/core/FieldContainer.py	2010-09-13 08:56:34 UTC (rev 699)
+++ trunk/src/pyphant/pyphant/core/FieldContainer.py	2011-05-23 12:48:36 UTC (rev 700)
@@ -288,12 +288,15 @@
         if m == None:
             m = hashlib.md5()
         super(FieldContainer, self).generateHash(m)
-        m.update(str(self.data.tolist()))
+        #m.update(str(self.data.tolist()))
+        m.update(self.data.dumps())
         m.update(str(self.unit))
         if self.error!=None:
-            m.update(str(self.error.tolist()))
+            #m.update(str(self.error.tolist()))
+            m.update(self.error.dumps())
         if self.mask!=None:
-            m.update(str(self.mask.tolist()))
+            #m.update(str(self.mask.tolist()))
+            m.update(self.mask.dumps())
         [m.update(dim.hash) for dim in self._dimensions]
         return enc(m.hexdigest())
 
@@ -648,8 +651,8 @@
 
     def getMaskedFC(self, numpymask):
         """
-        Returns a new FieldContainer instance that emerges from this instance
-        by clipping along the primary axis according to the
+        Return an unsealed FieldContainer instance that emerges from
+        this instance by clipping along the primary axis according to the
         entries in the parameter numpymask, i.e. all entries where numpymask
         is set to False are discarded.
         numpymask -- Numpy array with Boolean values

Modified: trunk/src/pyphant/pyphant/core/H5FileHandler.py
===================================================================
--- trunk/src/pyphant/pyphant/core/H5FileHandler.py	2010-09-13 08:56:34 UTC (rev 699)
+++ trunk/src/pyphant/pyphant/core/H5FileHandler.py	2011-05-23 12:48:36 UTC (rev 700)
@@ -121,7 +121,7 @@
             try:
                 resNode._g_checkHasChild('dimensions')
             except tables.NoSuchNodeError:
-                return True         
+                return True
         return False
 
     def loadDataContainer(self, dcId):
@@ -220,6 +220,9 @@
             summary['attributes'] = attributes
         return summary
 
+    def loadRecipe(self):
+        return PyTablesPersister.loadRecipe(self.handle)
+
     def saveDataContainer(self, result):
         """
         Saves a given DataContainer instance to the HDF5 file.

Modified: trunk/src/pyphant/pyphant/core/Helpers.py
===================================================================
--- trunk/src/pyphant/pyphant/core/Helpers.py	2010-09-13 08:56:34 UTC (rev 699)
+++ trunk/src/pyphant/pyphant/core/Helpers.py	2011-05-23 12:48:36 UTC (rev 700)
@@ -40,8 +40,12 @@
     if homedir == '~':
         homedir = os.getcwdu()
     path = os.path.join(homedir, '.pyphant', subdir)
-    if not os.path.isdir(path):
-        os.makedirs(path)
+    # Create the dir in a multi process save way:
+    try:
+        os.makedirs(path) #<-- ignores EEXIST in all but top recursion levels
+    except OSError, ose:
+        if ose.errno != os.errno.EEXIST:
+            raise
     return path
 
 def getUsername():
@@ -154,3 +158,28 @@
         output = plug.getResult()
     socket.pullPlug()
     return output
+
+def makeSC(column_data, longnames, shortnames, longname, shortname,
+           attributes={}):
+    unzipped = zip(*column_data)
+    assert len(unzipped) == len(longnames) == len(shortnames)
+    def get_column_fc(col, ln, sn):
+        try:
+            from pyphant.quantities import Quantity
+            unit = Quantity(1.0, col[0].unit)
+            data = [quant.value for quant in col]
+        except (KeyError, AttributeError):
+            unit = 1
+            data = col
+        from numpy import array
+        from pyphant.core.DataContainer import FieldContainer
+        fc = FieldContainer(data=array(data), unit=unit,
+                            longname=ln, shortname=sn)
+        return fc
+    columns = [get_column_fc(col, ln, sn) for col, ln, sn \
+               in zip(unzipped, longnames, shortnames)]
+    from pyphant.core.DataContainer import SampleContainer
+    sc = SampleContainer(longname=longname, shortname=shortname,
+                         attributes=attributes, columns=columns)
+    sc.seal()
+    return sc

Modified: trunk/src/pyphant/pyphant/core/KnowledgeManager.py
===================================================================
--- trunk/src/pyphant/pyphant/core/KnowledgeManager.py	2010-09-13 08:56:34 UTC (rev 699)
+++ trunk/src/pyphant/pyphant/core/KnowledgeManager.py	2011-05-23 12:48:36 UTC (rev 700)
@@ -198,11 +198,14 @@
             for fname in [afname for afname in files if afname.endswith('.h5')]:
                 flist.append(os.path.realpath(os.path.join(directory, fname)))
         os.path.walk(getPyphantPath(KM_PATH), accumulate_files, file_list)
-        from wx import (ProgressDialog, PyNoAppError)
         try:
-            pdial = ProgressDialog('Rebuilding index...', ' ' * 100,
-                                   maximum=len(file_list))
-        except PyNoAppError:
+            from wx import (ProgressDialog, PyNoAppError)
+            try:
+                pdial = ProgressDialog('Rebuilding index...', ' ' * 100,
+                                       maximum=len(file_list))
+            except PyNoAppError:
+                pdial = None
+        except ImportError:
             pdial = None
         count = 1
         for realname in file_list:

Modified: trunk/src/pyphant/pyphant/core/Worker.py
===================================================================
--- trunk/src/pyphant/pyphant/core/Worker.py	2010-09-13 08:56:34 UTC (rev 699)
+++ trunk/src/pyphant/pyphant/core/Worker.py	2011-05-23 12:48:36 UTC (rev 700)
@@ -81,9 +81,12 @@
     _plugs=[]
     _params=[]
     DEFAULT_ANNOTATIONS={"pos":(0,0)}
-    def __init__(self, parent=None, annotations={}):
-        self._annotations=annotations
-        map(lambda k: self._annotations.setdefault(k, Worker.DEFAULT_ANNOTATIONS[k]),
+    def __init__(self, parent=None, annotations=None):
+        if annotations is None:
+            annotations = {}
+        self._annotations = annotations
+        map(lambda k: self._annotations.setdefault(
+            k, Worker.DEFAULT_ANNOTATIONS[k]),
             Worker.DEFAULT_ANNOTATIONS.keys())
         self.parent=parent
         self.initSockets(self._sockets)
@@ -144,7 +147,7 @@
         self._params={}
         self._order=[]
         self.addParam('name',Param.createParam(self,'name','Name',
-                                               self.__class__.__name__))
+                                               self.name))
         for (name, displayName, value, subtype) in params:
             p=Param.createParam(self, name, displayName, value, subtype)
             setattr(self, 'param'+self.upperFirstLetter(name), p)

Deleted: trunk/src/pyphant/pyphant/core/XMLHandler.py
===================================================================
--- trunk/src/pyphant/pyphant/core/XMLHandler.py	2010-09-13 08:56:34 UTC (rev 699)
+++ trunk/src/pyphant/pyphant/core/XMLHandler.py	2011-05-23 12:48:36 UTC (rev 700)
@@ -1,88 +0,0 @@
-# -*- coding: utf-8 -*-
-
-# Copyright (c) 2006-2009, Rectorate of the University of Freiburg
-# All rights reserved.
-#
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions are met:
-#
-# * Redistributions of source code must retain the above copyright
-#   notice, this list of conditions and the following disclaimer.
-# * Redistributions in binary form must reproduce the above copyright
-#   notice, this list of conditions and the following disclaimer in the
-#   documentation and/or other materials provided with the distribution.
-# * Neither the name of the Freiburg Materials Research Center,
-#   University of Freiburg nor the names of its contributors may be used to
-#   endorse or promote products derived from this software without specific
-#   prior written permission.
-#
-#
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
-# IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
-# TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
-# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
-# OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
-# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
-# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
-# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-"""
-TODO
-"""
-__id__ = "$Id$"
-__author__ = "$Author$"
-__version__ = "$Revision$"
-# $Source$:
-
-import xml.sax
-
-
-class XMLElement(object):
-
-    def __init__(self, name, attrs, parent, content=''):
-        self.name = name
-        self.attributes = attrs
-        self.parent = parent
-        self.children = {}
-        self.content = content
-        if parent != None:
-            parent[name] = self
-
-    def __getitem__(self, key):
-        return self.children[key]
-
-    def __setitem__(self, key, item):
-        self.children[key] = item
-
-
-class XMLHandler(xml.sax.handler.ContentHandler):
-
-    def __init__(self):
-        self.current_element = None
-        self.root_element = None
-
-    def startElement(self, name, attrs):
-        if self.root_element == None:
-            element = XMLElement(name, attrs, None)
-            self.root_element = element
-            self.current_element = element
-        else:
-            element = XMLElement(name, attrs, self.current_element)
-            self.current_element = element
-
-    def endElement(self, name):
-        assert name == self.current_element.name
-        self.current_element = self.current_element.parent
-
-    def characters(self, content):
-        if self.current_element != None:
-            self.current_element.content += content
-
-
-def getXMLRoot(filename_or_stream):
-    handler = XMLHandler()
-    xml.sax.parse(filename_or_stream, handler)
-    return handler.root_element

Deleted: trunk/src/pyphant/pyphant/core/ZStackManager.py
===================================================================
--- trunk/src/pyphant/pyphant/core/ZStackManager.py	2010-09-13 08:56:34 UTC (rev 699)
+++ trunk/src/pyphant/pyphant/core/ZStackManager.py	2011-05-23 12:48:36 UTC (rev 700)
@@ -1,300 +0,0 @@
-#!/usr/bin/env python2.5
-# -*- coding: utf-8 -*-
-
-# Copyright (c) 2006-2009, Rectorate of the University of Freiburg
-# All rights reserved.
-#
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions are met:
-#
-# * Redistributions of source code must retain the above copyright
-#   notice, this list of conditions and the following disclaimer.
-# * Redistributions in binary form must reproduce the above copyright
-#   notice, this list of conditions and the following disclaimer in the
-#   documentation and/or other materials provided with the distribution.
-# * Neither the name of the Freiburg Materials Research Center,
-#   University of Freiburg nor the names of its contributors may be used to
-#   endorse or promote products derived from this software without specific
-#   prior written permission.
-#
-#
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
-# IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
-# TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
-# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
-# OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
-# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
-# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
-# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-u"""Provides ZStackManager
-"""
-
-__id__ = "$Id$".replace('$','')
-__author__ = "$Author$".replace('$','')
-__version__ = "$Revision$".replace('$','')
-# $Source$
-
-
-from pyphant.quantities import Quantity
-from pyphant.core.DataContainer import (FieldContainer, SampleContainer)
-import scipy
-import Image
-from pyphant.core.KnowledgeManager import KnowledgeManager
-import os
-import re
-kmanager = KnowledgeManager.getInstance()
-
-
-class ZStack(object):
-    def __init__(self, sc_id=None, meta=None, temporary=False):
-        """Initializes a ZStack from an existing id or metadata"""
-        assert (sc_id is None) is not (meta is None)
-        self.temporary = temporary
-        if sc_id is not None:
-            self.repr_sc = kmanager.getDataContainer(sc_id)
-        else:
-            self.repr_sc = self._import_zstack(meta)
-
-    @staticmethod
-    def _get_image_fcs(images_meta, temporary=False):
-        zvalues = []
-        emd5s = []
-        files = []
-        from wx import (ProgressDialog, PyNoAppError)
-        try:
-            pdial = ProgressDialog('Importing ZStack...', ' ' * 50,
-                                   maximum=len(images_meta))
-        except PyNoAppError:
-            pdial = None
-        count = 1
-        for img_meta in images_meta:
-            if pdial is not None:
-                pdial.Update(count, os.path.basename(img_meta['imgFilename']))
-                count += 1
-            files.append(img_meta['xmlFilename'])
-            img = Image.open(img_meta['imgFilename'])
-            data = scipy.misc.fromimage(img, flatten=True)
-            zvalue = img_meta['z-pos']
-            yunit = Quantity(1.0, img_meta['height'].unit)
-            xunit = Quantity(1.0, img_meta['width'].unit)
-            ydata = scipy.arange(img_meta['height[pixel]']) \
-                    * img_meta['y-factor'].inUnitsOf(yunit.unit).value \
-                    + img_meta['y-pos'].inUnitsOf(yunit.unit).value
-            xdata = scipy.arange(img_meta['width[pixel]']) \
-                    * img_meta['x-factor'].inUnitsOf(xunit.unit).value \
-                    + img_meta['x-pos'].inUnitsOf(xunit.unit).value
-            dimensions = [FieldContainer(ydata,
-                                         unit=yunit,
-                                         longname=u'y-axis',
-                                         shortname=u'y'),
-                          FieldContainer(xdata,
-                                         unit=xunit,
-                                         longname=u'x-axis',
-                                         shortname=u'x')]
-            fcattr = {'vmin':0, 'vmax':255}
-            fcattr.update(img_meta)
-            img_fc = FieldContainer(data=data,
-                                    longname=os.path.basename(
-                                        img_meta['imgFilename']),
-                                    shortname="i",
-                                    dimensions=dimensions, attributes=fcattr)
-            img_fc.seal()
-            kmanager.registerDataContainer(img_fc, temporary=temporary)
-            emd5s.append(img_fc.id)
-            zvalues.append(zvalue.value)
-        if len(zvalues) == 0:
-            return None, None, None
-        zfc = FieldContainer(scipy.array(zvalues), longname='z-value',
-                             shortname='z', unit=Quantity(1.0, zvalue.unit))
-        filefc = FieldContainer(scipy.array(files), longname='filename',
-                                shortname='f')
-        emd5fc = FieldContainer(scipy.array(emd5s), longname='emd5',
-                                shortname='i')
-        if pdial is not None:
-            pdial.Destroy()
-        return zfc, filefc, emd5fc
-
-    def _import_zstack(self, meta):
-        zfc, filefc, emd5fc = ZStack._get_image_fcs(meta, self.temporary)
-        if zfc == None:
-            return None
-        attributes = {}
-        attributes['ZStackType'] = 'RawSC'
-        attributes['xmlFilename'] = meta[0]['xmlFilename']
-        attributes['crystal'] = meta[0]['crystal']
-        ssc = SampleContainer([zfc, filefc, emd5fc],
-                              meta[0]['ZStackName'],
-                              "z",
-                              attributes)
-        ssc.seal()
-        kmanager.registerDataContainer(ssc, temporary=self.temporary)
-        return ssc
-
-
-class ZStackManager(object):
-    def importZStack(self, xmlFName, name, crystal, temporary=False):
-        metaReader = getMetaReader(xmlFName, name, crystal)
-        meta = metaReader.getMeta()
-        return ZStack(meta=meta, temporary=temporary)
-
-    def getZStacks(self):
-        """Returns a list of all ZStacks in the pool"""
-        search_dict = {'type':'sample', 'attributes':{'ZStackType':'RawSC'}}
-        search_result = kmanager.search(['id'], search_dict)
-        if len(search_result) == 0:
-            return []
-        return [ZStack(zs_id[0]) for zs_id in search_result]
-
-    def getZStackByName(self, name):
-        search_dict = {'type':'sample', 'attributes':{'ZStackType':'RawSC'},
-                       'longname':name}
-        sresult = kmanager.search(['id'], search_dict)
-        if sresult == []:
-            raise ValueError("There is no ZStack called %s!" \
-                                 % name)
-        return ZStack(sc_id=sresult[0][0])
-
-
-class MetaReader(object):
-    def __init__(self, xmlFName, name, crystal):
-        self.xmlFN...
 
[truncated message content]

[Pyphant-devel] SF.net SVN: pyphant:[699] trunk

From: <zk...@us...> - 2010-09-13 08:56:43

Revision: 699
          http://pyphant.svn.sourceforge.net/pyphant/?rev=699&view=rev
Author:   zklaus
Date:     2010-09-13 08:56:34 +0000 (Mon, 13 Sep 2010)

Log Message:
-----------
Merge branch 'master' into svn-trunk

* master:
  removed unneeded variable setup
  Changed pyphant/Core/Helper.py to use getpass.
  Bugfix: Logo is loaded from base64 encoded string.
  Added splash screen: This version needs to be started in src/pyphant/pyphant/wxgui2 or doc/logo in order to find the splash screen image.
  pyphantLogo module with docstring.
  Base64 coded pyphant logo.
  Fix: ZStacks: refractive index
  Fix: Restore parameters to DCSource workers
  Cosm: Added line feed to README

Modified Paths:
--------------
    trunk/doc/demo/README
    trunk/src/pyphant/pyphant/core/Helpers.py
    trunk/src/pyphant/pyphant/core/ZStackManager.py
    trunk/src/pyphant/pyphant/tests/TestZStacks.py
    trunk/src/pyphant/pyphant/wxgui2/wxPyphantApplication.py
    trunk/src/workers/tools/tools/DCSource.py
    trunk/src/workers/tools/tools/FCSource.py
    trunk/src/workers/tools/tools/SCSource.py

Added Paths:
-----------
    trunk/doc/logo/
    trunk/doc/logo/mklogo.py
    trunk/doc/logo/pyphant-shade-Information-Analysis-Framework-ARTS-small.png
    trunk/doc/logo/pyphantLogo.py
    trunk/src/pyphant/pyphant/wxgui2/pyphantLogo.py

Modified: trunk/doc/demo/README
===================================================================
--- trunk/doc/demo/README	2010-07-18 18:51:16 UTC (rev 698)
+++ trunk/doc/demo/README	2010-09-13 08:56:34 UTC (rev 699)
@@ -2,4 +2,5 @@
 wxPythant demo.h5
 
 #Start scripting example with
-./simpleScripting.py
\ No newline at end of file
+./simpleScripting.py
+

Added: trunk/doc/logo/mklogo.py
===================================================================
--- trunk/doc/logo/mklogo.py	                        (rev 0)
+++ trunk/doc/logo/mklogo.py	2010-09-13 08:56:34 UTC (rev 699)
@@ -0,0 +1,49 @@
+copyright="""# -*- coding: utf-8 -*-
+
+# Copyright (c) 2010, Andreas W. Liehr (li...@us...)
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+# * Redistributions of source code must retain the above copyright
+#   notice, this list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above copyright
+#   notice, this list of conditions and the following disclaimer in the
+#   documentation and/or other materials provided with the distribution.
+# * Neither the name of the Freiburg Materials Research Center,
+#   University of Freiburg nor the names of its contributors may be used to
+#   endorse or promote products derived from this software without specific
+#   prior written permission.
+#
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+# IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+# TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
+# OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+"""
+
+"""Creates pyphantLogo.py, a python modul including a base 64 encoded PNG file of the Pyphant logo."""
+
+import base64
+picname = 'pyphant-shade-Information-Analysis-Framework-ARTS-small.png'
+file = open(picname,'rb')
+logo = file.read()
+file.close()
+pic_b64 = logo.encode('base64')
+
+file = open("pyphantLogo.py",'w')
+file.write(copyright)
+file.write("\"\"\""+
+"""Python modul including a base 64 encoded PNG file of the Pyphant logo based on %s.""" % picname +"\"\"\"\n\n" 
+           )
+file.write("pic_b64 = \"\"\"%s\"\"\"\n" % pic_b64)
+file.close()

Added: trunk/doc/logo/pyphant-shade-Information-Analysis-Framework-ARTS-small.png
===================================================================
--- trunk/doc/logo/pyphant-shade-Information-Analysis-Framework-ARTS-small.png	                        (rev 0)
+++ trunk/doc/logo/pyphant-shade-Information-Analysis-Framework-ARTS-small.png	2010-09-13 08:56:34 UTC (rev 699)
@@ -0,0 +1,978 @@
+\x89PNG
+
+

[Pyphant-devel] SF.net SVN: pyphant:[698] trunk

From: <zk...@us...> - 2010-07-18 18:51:22

Revision: 698
          http://pyphant.svn.sourceforge.net/pyphant/?rev=698&view=rev
Author:   zklaus
Date:     2010-07-18 18:51:16 +0000 (Sun, 18 Jul 2010)

Log Message:
-----------
Merge branch 'master' into svn-trunk

* master:
  Fix: Fix typo, remove debug print.
  Fix: Add proper handling of maskless fields to PlotFrame; better unit handling.
  Enh: Add legend to viewOSC script.

Modified Paths:
--------------
    trunk/doc/demo/viewOSC.py
    trunk/src/pyphant/pyphant/visualizers/ConfigurablePlot.py
    trunk/src/workers/OSC/OSC/EstimateParameterFromValues.py

Modified: trunk/doc/demo/viewOSC.py
===================================================================
--- trunk/doc/demo/viewOSC.py	2010-07-14 10:41:43 UTC (rev 697)
+++ trunk/doc/demo/viewOSC.py	2010-07-18 18:51:16 UTC (rev 698)
@@ -182,7 +182,7 @@
     residuum = (simulation.dimensions[0].data-thickness.data[index])**2
     absorption = simulation.data[residuum.argmin(),:]
     pylab.plot(simulation.dimensions[1].data,
-               absorption,label="$%s$"%simulation.shortname)
+               absorption,label="$%s$ functional"%simulation.shortname)
     title = "Functional based: " + title_template % (thickness[index].shortname,
                                                      thickness.data[index],
                                                      thickness.unit.unit.name())
@@ -194,7 +194,7 @@
         residuum = (simulation.dimensions[0].data-thickness.data[index])**2
         absorption = simulation.data[residuum.argmin(),:]
         pylab.plot(simulation.dimensions[1].data,
-                   absorption,label="$%s$"%simulation.shortname)
+                   absorption,label="$%s$ immediate"%simulation.shortname)
         title += "\nImmediate: " +  title_template % (thickness[index].shortname,
                                                       thickness.data[index],
                                                       thickness.unit.unit.name())
@@ -223,6 +223,7 @@
                      label ="$\\Delta%s$"%maximaPos.shortname, linestyle='dashed')
     pylab.title(title)
     pylab.xlabel(simulation.dimensions[1].label)
+    pylab.legend(loc="lower left")
 
 def noisyAbsorption(recipe, curvNo, noIndicators):
     worker = recipe.getWorker("Slicing")

Modified: trunk/src/pyphant/pyphant/visualizers/ConfigurablePlot.py
===================================================================
--- trunk/src/pyphant/pyphant/visualizers/ConfigurablePlot.py	2010-07-14 10:41:43 UTC (rev 697)
+++ trunk/src/pyphant/pyphant/visualizers/ConfigurablePlot.py	2010-07-18 18:51:16 UTC (rev 698)
@@ -49,8 +49,8 @@
 from pyphant.core import DataContainer
 from pyphant.wxgui2.DataVisReg import DataVisReg
 from pyphant.quantities import isQuantity, Quantity
+from pyphant.quantities.ParseQuantities import str2unit
 
-
 class PlotPanel (wx.PyPanel):
     """The PlotPanel has a Figure and a Canvas. OnSize events simply set a
     flag, and the actual resizing of the figure is triggered by an Idle event."""
@@ -122,10 +122,15 @@
         if not isinstance(aspect, Quantity):
             self.ax.set_aspect(aspect)
         try:
-            mask = numpy.logical_not(self.c.mask)
-            x = self.x.data[mask]
-            y = self.y.data[mask]
-            c = self.c.data[mask]
+            if self.c.mask!=None:
+                mask = numpy.logical_not(self.c.mask)
+                x = self.x.data[mask]
+                y = self.y.data[mask]
+                c = self.c.data[mask]
+            else:
+                x = self.x.data
+                y = self.y.data
+                c = self.c.data
             self.scat = self.ax.scatter(x,y,
                                         s=numpy.pi*(self.radius/self.x.unit)**2,
                                         c=c,
@@ -231,9 +236,9 @@
             self.vmin_text.Value=str(vmin)
             vmax = numpy.nanmax(field.data).round()*field.unit
             self.vmax_text.Value=str(vmax)
-        self.plot_panel.vmin = Quantity(self.vmin_text.Value)
-        self.plot_panel.vmax = Quantity(self.vmax_text.Value)
-        self.plot_panel.radius = Quantity(self.radius_text.Value)
+        self.plot_panel.vmin = str2unit(self.vmin_text.Value)
+        self.plot_panel.vmax = str2unit(self.vmax_text.Value)
+        self.plot_panel.radius = str2unit(self.radius_text.Value)
         self.plot_panel.draw()
         self.GetSizer().Fit(self)
 

Modified: trunk/src/workers/OSC/OSC/EstimateParameterFromValues.py
===================================================================
--- trunk/src/workers/OSC/OSC/EstimateParameterFromValues.py	2010-07-14 10:41:43 UTC (rev 697)
+++ trunk/src/workers/OSC/OSC/EstimateParameterFromValues.py	2010-07-18 18:51:16 UTC (rev 698)
@@ -75,14 +75,14 @@
         minima_model = model[self.paramMinima_model.value]
         maxima_model = model[self.paramMaxima_model.value]
         minima_experimental = experimental[self.paramMinima_experimental.value]
-        minima_experimantal = minima_experimental.inUnitsOf(minima_model)
+        minima_experimental = minima_experimental.inUnitsOf(minima_model)
         minima = minima_experimental.data.transpose()
         if minima_experimental.error != None:
             minima_error = iter(minima_experimental.error.transpose())
         else:
             minima_error = None
         maxima_experimental = experimental[self.paramMaxima_experimental.value]
-        maxima_experimantal = maxima_experimental.inUnitsOf(maxima_model)
+        maxima_experimental = maxima_experimental.inUnitsOf(maxima_model)
         maxima = maxima_experimental.data.transpose()
         if maxima_experimental.error != None:
             maxima_error = iter(maxima_experimental.error.transpose())
@@ -119,7 +119,6 @@
                     grades.append(numpy.nan)
                     continue
                 grades.append(grade)
-                print grades[-1]
             grades = numpy.array(grades)
             i = numpy.nanargmin(grades)
             if numpy.isnan(i):


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Pyphant-devel] SF.net SVN: pyphant:[697] trunk/doc/demo/viewOSC.py

From: <zk...@us...> - 2010-07-14 10:41:51

Revision: 697
          http://pyphant.svn.sourceforge.net/pyphant/?rev=697&view=rev
Author:   zklaus
Date:     2010-07-14 10:41:43 +0000 (Wed, 14 Jul 2010)

Log Message:
-----------
Merge branch 'master' into svn-trunk

* master:
  Enh: Now the viewOSC script also displays result from the alternative method.

Modified Paths:
--------------
    trunk/doc/demo/viewOSC.py

Modified: trunk/doc/demo/viewOSC.py
===================================================================
--- trunk/doc/demo/viewOSC.py	2010-07-12 21:47:51 UTC (rev 696)
+++ trunk/doc/demo/viewOSC.py	2010-07-14 10:41:43 UTC (rev 697)
@@ -166,30 +166,48 @@
         pylab.show()
 
 def compareAbsorption(recipe, curvNo, noIndicators):
-    worker = recipe.getWorker("Slicing")
-    noisyAbsorption = worker.plugExtract.getResult()
-    worker = recipe.getWorker("ThicknessModeller")
-    simulation = worker.plugCalcAbsorption.getResult()
-    worker = recipe.getWorker("MRA Exp")
-    minimaPos = worker.plugMra.getResult()[r'\lambda_{min}'].inUnitsOf(simulation.dimensions[1])
-    maximaPos = worker.plugMra.getResult()[r'\lambda_{max}'].inUnitsOf(simulation.dimensions[1])
     worker = recipe.getWorker("AddColumn")
-    table = worker.plugCompute.getResult(subscriber=TextSubscriber("Add Column"))
+    table = worker.plugCompute.getResult(subscriber=TextSubscriber("Result Functional"))
     xPos = table[u"x-position"]
     yPos = table[u"y-position"]
-    thickness = table[u"thickness"]
     index = curvNo2Index(table[u"pixel"], curvNo)
-    result = "$%s_{%s}$(%s %s,%s %s)=%s %s" % (thickness[index].shortname,curvNo,
+    title_template = "$%%s_{%s}$(%s %s,%s %s)=%%s %%s" % (curvNo,
                                                xPos.data[index],xPos.unit.unit.name(),
-                                               yPos.data[index],yPos.unit.unit.name(),
-                                               thickness.data[index],
-                                               thickness.unit.unit.name())
+                                               yPos.data[index],yPos.unit.unit.name())
+
+    worker = recipe.getWorker("ThicknessModeller")
+    simulation = worker.plugCalcAbsorption.getResult()
+
+    thickness = table[u"thickness"]
     residuum = (simulation.dimensions[0].data-thickness.data[index])**2
     absorption = simulation.data[residuum.argmin(),:]
+    pylab.plot(simulation.dimensions[1].data,
+               absorption,label="$%s$"%simulation.shortname)
+    title = "Functional based: " + title_template % (thickness[index].shortname,
+                                                     thickness.data[index],
+                                                     thickness.unit.unit.name())
+
+    try:
+        worker = recipe.getWorker("Res Direct")
+        table = worker.plugCompute.getResult(subscriber=TextSubscriber("Result without Functional"))
+        thickness = table[u"thickness"]
+        residuum = (simulation.dimensions[0].data-thickness.data[index])**2
+        absorption = simulation.data[residuum.argmin(),:]
+        pylab.plot(simulation.dimensions[1].data,
+                   absorption,label="$%s$"%simulation.shortname)
+        title += "\nImmediate: " +  title_template % (thickness[index].shortname,
+                                                      thickness.data[index],
+                                                      thickness.unit.unit.name())
+    except:
+        pass
+
+    worker = recipe.getWorker("Slicing")
+    noisyAbsorption = worker.plugExtract.getResult()
+    worker = recipe.getWorker("MRA Exp")
+    minimaPos = worker.plugMra.getResult()[r'\lambda_{min}'].inUnitsOf(simulation.dimensions[1])
+    maximaPos = worker.plugMra.getResult()[r'\lambda_{max}'].inUnitsOf(simulation.dimensions[1])
     pylab.plot(noisyAbsorption.dimensions[1].inUnitsOf(simulation.dimensions[1]).data,
                noisyAbsorption.data[index,:],label="$%s$"%noisyAbsorption.shortname)
-    pylab.plot(simulation.dimensions[1].data,
-               absorption,label="$%s$"%simulation.shortname)
     if not noIndicators:
         pylab.vlines(minimaPos.data[:,index],0.1,1.0,
                      label ="$%s$"%minimaPos.shortname)
@@ -203,7 +221,7 @@
                      label ="$\\Delta%s$"%maximaPos.shortname, linestyle='dashed')
         pylab.vlines(maximaPos.data[:,index]-maximaPos.error[:,index],0.1,1.0,
                      label ="$\\Delta%s$"%maximaPos.shortname, linestyle='dashed')
-    pylab.title(result)
+    pylab.title(title)
     pylab.xlabel(simulation.dimensions[1].label)
 
 def noisyAbsorption(recipe, curvNo, noIndicators):


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Pyphant-devel] SF.net SVN: pyphant:[696] trunk/src

From: <zk...@us...> - 2010-07-12 21:47:59

Revision: 696
          http://pyphant.svn.sourceforge.net/pyphant/?rev=696&view=rev
Author:   zklaus
Date:     2010-07-12 21:47:51 +0000 (Mon, 12 Jul 2010)

Log Message:
-----------
Merge branch 'master' into svn-trunk

* master:
  Enh: Add EstimateParameterFromValues.py
  Enh: Add removal of second lamp peak to Absorbtion calculation.
  Fix: Improve progress handling in Compute Functional.
  Enh: PlotFrame now takes the mask of the value column into account.
  Fix: MRA can now deal with curves without extrema.

Modified Paths:
--------------
    trunk/src/pyphant/pyphant/visualizers/ConfigurablePlot.py
    trunk/src/workers/OSC/OSC/ComputeFunctional.py
    trunk/src/workers/OSC/OSC/MRA.py
    trunk/src/workers/OSC/OSC/OscAbsorption.py
    trunk/src/workers/OSC/OSC/__init__.py

Added Paths:
-----------
    trunk/src/workers/OSC/OSC/EstimateParameterFromValues.py

Modified: trunk/src/pyphant/pyphant/visualizers/ConfigurablePlot.py
===================================================================
--- trunk/src/pyphant/pyphant/visualizers/ConfigurablePlot.py	2010-07-12 20:43:11 UTC (rev 695)
+++ trunk/src/pyphant/pyphant/visualizers/ConfigurablePlot.py	2010-07-12 21:47:51 UTC (rev 696)
@@ -122,9 +122,13 @@
         if not isinstance(aspect, Quantity):
             self.ax.set_aspect(aspect)
         try:
-            self.scat = self.ax.scatter(self.x.data, self.y.data,
+            mask = numpy.logical_not(self.c.mask)
+            x = self.x.data[mask]
+            y = self.y.data[mask]
+            c = self.c.data[mask]
+            self.scat = self.ax.scatter(x,y,
                                         s=numpy.pi*(self.radius/self.x.unit)**2,
-                                        c=self.c.data,
+                                        c=c,
                                         vmin=self.vmin, vmax=self.vmax)
             self.colorbar = self.figure.colorbar(self.scat, format=F(self.c),
                                                  ax=self.ax)
@@ -223,9 +227,9 @@
         if self.plot_panel.c_key != colorVariable:
             self.plot_panel.c_key = colorVariable
             field = self.dataContainer[colorVariable]
-            vmin = field.data.min().round()*field.unit
+            vmin = numpy.nanmin(field.data).round()*field.unit
             self.vmin_text.Value=str(vmin)
-            vmax = field.data.max().round()*field.unit
+            vmax = numpy.nanmax(field.data).round()*field.unit
             self.vmax_text.Value=str(vmax)
         self.plot_panel.vmin = Quantity(self.vmin_text.Value)
         self.plot_panel.vmax = Quantity(self.vmax_text.Value)

Modified: trunk/src/workers/OSC/OSC/ComputeFunctional.py
===================================================================
--- trunk/src/workers/OSC/OSC/ComputeFunctional.py	2010-07-12 20:43:11 UTC (rev 695)
+++ trunk/src/workers/OSC/OSC/ComputeFunctional.py	2010-07-12 21:47:51 UTC (rev 696)
@@ -57,7 +57,7 @@
     _params = [("extentX", u"Extension of x-axis [%%]", 10, None),
                ("extentY", u"Extension of y-axis [%%]", 10, None)]
 
-    def computeDistances(self, field, subscriber=1):
+    def computeDistances(self, field, subscriber=1, percentage=0):
         xGrid,yGrid = numpy.meshgrid(field.dimensions[-1].data,field.dimensions[-2].data)
         x    = numpy.extract(numpy.logical_not(numpy.isnan(field.data)),xGrid)
         xCon = DataContainer.FieldContainer(x,unit=field.dimensions[-1].unit,
@@ -80,8 +80,7 @@
         distances = numpy.zeros(x.shape,'f')
         ni = functional.shape[0]
         nj = functional.shape[1]
-        increment = 100.0/(ni*nj)
-        percentage = 0
+        increment = 50.0/(ni*nj)
         for i in xrange(ni):
             for j in xrange(nj):
                 for k in xrange(len(x)):
@@ -99,7 +98,8 @@
 
     @Worker.plug(Connectors.TYPE_ARRAY)
     def compute(self, field, subscriber=1):
-        functionals = DataContainer.SampleContainer([self.computeDistances(column, subscriber) for column in field],
+        percentage = 0
+        functionals = DataContainer.SampleContainer([self.computeDistances(column, subscriber, percentage) for column in field],
                                                     longname='Functionals of %s'%field.longname,
                                                     shortname='F_{%s}'%field.shortname)
         functionals.seal()

Added: trunk/src/workers/OSC/OSC/EstimateParameterFromValues.py
===================================================================
--- trunk/src/workers/OSC/OSC/EstimateParameterFromValues.py	                        (rev 0)
+++ trunk/src/workers/OSC/OSC/EstimateParameterFromValues.py	2010-07-12 21:47:51 UTC (rev 696)
@@ -0,0 +1,140 @@
+# -*- coding: utf-8 -*-
+
+# Copyright (c) 2008-2009, Rectorate of the University of Freiburg
+# Copyright (c) 2009, Andreas W. Liehr (li...@us...)
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+# * Redistributions of source code must retain the above copyright
+#   notice, this list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above copyright
+#   notice, this list of conditions and the following disclaimer in the
+#   documentation and/or other materials provided with the distribution.
+# * Neither the name of the Freiburg Materials Research Center,
+#   University of Freiburg nor the names of its contributors may be used to
+#   endorse or promote products derived from this software without specific
+#   prior written permission.
+#
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+# IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+# TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
+# OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+u"""
+"""
+
+__id__ = "$Id$"
+__author__ = "$Author$"
+__version__ = "$Revision$"
+# $Source$
+
+import numpy
+from pyphant.core import (Worker, Connectors,
+                          Param, DataContainer)
+import scipy.interpolate
+from pyphant import quantities
+import copy
+
+class EstimateParameterFromValues(Worker.Worker):
+    API = 2
+    VERSION = 1
+    REVISION = "$Revision$"[11:-1]
+    name = "Estimate Parameter"
+
+    _sockets = [("model", Connectors.TYPE_ARRAY),
+                ("experimental", Connectors.TYPE_ARRAY)]
+    _params = [("minima_model", u"Minima in the model", [u"Minima"], None),
+               ("maxima_model", u"Maxima in the model", [u"Maxima"], None),
+               ("minima_experimental", u"Minima in the experiment", [u"Minima"], None),
+               ("maxima_experimental", u"Maxima in the experiment", [u"Maxima"], None),
+               ("extentX", u"Extension of x-axis [%%]", 10, None),
+               ("extentY", u"Extension of y-axis [%%]", 10, None)]
+
+    def refreshParams(self, subscriber=None):
+        if self.socketModel.isFull():
+            templ = self.socketModel.getResult( subscriber )
+            self.paramMinima_model.possibleValues = templ.longnames.keys()
+            self.paramMaxima_model.possibleValues = templ.longnames.keys()
+        if self.socketExperimental.isFull():
+            templ = self.socketExperimental.getResult( subscriber )
+            self.paramMinima_experimental.possibleValues = templ.longnames.keys()
+            self.paramMaxima_experimental.possibleValues = templ.longnames.keys()
+
+    @Worker.plug(Connectors.TYPE_IMAGE)
+    def compute(self, model, experimental, subscriber=1):
+        minima_model = model[self.paramMinima_model.value]
+        maxima_model = model[self.paramMaxima_model.value]
+        minima_experimental = experimental[self.paramMinima_experimental.value]
+        minima_experimantal = minima_experimental.inUnitsOf(minima_model)
+        minima = minima_experimental.data.transpose()
+        if minima_experimental.error != None:
+            minima_error = iter(minima_experimental.error.transpose())
+        else:
+            minima_error = None
+        maxima_experimental = experimental[self.paramMaxima_experimental.value]
+        maxima_experimantal = maxima_experimental.inUnitsOf(maxima_model)
+        maxima = maxima_experimental.data.transpose()
+        if maxima_experimental.error != None:
+            maxima_error = iter(maxima_experimental.error.transpose())
+        else:
+            maxima_error = None
+        parameter = []
+        inc = 100.0/float(len(minima))
+        acc = inc
+        subscriber %= acc
+        mask = []
+        for row_minima, row_maxima in zip(minima, maxima):
+            if minima_error:
+                filtered_minima_error = filter(
+                    lambda c: not numpy.isnan(c), minima_error.next())
+            else:
+                filtered_minima_error = None
+            if maxima_error:
+                filtered_maxima_error = filter(
+                    lambda c: not numpy.isnan(c), maxima_error.next())
+            else:
+                filtered_maxima_error = None
+            row_minima = numpy.array(filter(lambda c: not numpy.isnan(c), row_minima))
+            row_maxima = numpy.array(filter(lambda c: not numpy.isnan(c), row_minima))
+            grades = []
+            for rm_minima, rm_maxima in zip(minima_model.data.transpose(), maxima_model.data.transpose()):
+                rm_minima = filter(lambda c: not numpy.isnan(c), rm_minima)
+                rm_maxima = filter(lambda c: not numpy.isnan(c), rm_maxima)
+                grade = 0
+                if len(rm_minima) == len(row_minima):
+                    grade = sum(numpy.abs(numpy.array(rm_minima)-row_minima))
+                if len(rm_maxima) == len(row_maxima):
+                    grade += sum(numpy.abs(numpy.array(rm_maxima)-row_maxima))
+                if grade == 0:
+                    grades.append(numpy.nan)
+                    continue
+                grades.append(grade)
+                print grades[-1]
+            grades = numpy.array(grades)
+            i = numpy.nanargmin(grades)
+            if numpy.isnan(i):
+                mask.append(True)
+                parameter.append(numpy.nan)
+            else:
+                mask.append(False)
+                parameter.append(minima_model.dimensions[1].data[i])
+            acc += inc
+            subscriber %= acc
+        result = DataContainer.FieldContainer(
+            numpy.array(parameter),
+            mask = numpy.array(mask),
+            longname = minima_model.dimensions[-1].longname,
+            shortname = minima_model.dimensions[-1].shortname,
+            unit = minima_model.dimensions[-1].unit)
+        result.seal()
+        return result

Modified: trunk/src/workers/OSC/OSC/MRA.py
===================================================================
--- trunk/src/workers/OSC/OSC/MRA.py	2010-07-12 20:43:11 UTC (rev 695)
+++ trunk/src/workers/OSC/OSC/MRA.py	2010-07-12 21:47:51 UTC (rev 696)
@@ -116,10 +116,18 @@
         convolvedField = convolveMRA(field, sigma)
         lastMinima = findMinima(convolvedField, numb_edge, lastMinima)
         lastMaxima = findMaxima(convolvedField, numb_edge, lastMaxima)
-    pos_minima = dim.data[numpy.array(lastMinima)+1]
-    error_minima = numpy.abs(pos_minima - dim.data[numpy.array(firstMinima)+1])
-    pos_maxima = dim.data[numpy.array(lastMaxima)+1]
-    error_maxima = numpy.abs(pos_maxima - dim.data[numpy.array(firstMaxima)+1])
+    if len(lastMinima)>0 and len(firstMinima)>0:
+        pos_minima = dim.data[numpy.array(lastMinima)+1]
+        error_minima = numpy.abs(pos_minima - dim.data[numpy.array(firstMinima)+1])
+    else:
+        pos_minima = numpy.array([],dtype=dim.data.dtype)
+        error_minima = numpy.array([],dtype=dim.data.dtype)
+    if len(lastMaxima)>0 and len(firstMaxima)>0:
+        pos_maxima = dim.data[numpy.array(lastMaxima)+1]
+        error_maxima = numpy.abs(pos_maxima - dim.data[numpy.array(firstMaxima)+1])
+    else:
+        pos_maxima = numpy.array([],dtype=dim.data.dtype)
+        error_maxima = numpy.array([],dtype=dim.data.dtype)
     return ((pos_minima, error_minima), (pos_maxima, error_maxima))
 
 def pos_error_to_data_container(p_e):

Modified: trunk/src/workers/OSC/OSC/OscAbsorption.py
===================================================================
--- trunk/src/workers/OSC/OSC/OscAbsorption.py	2010-07-12 20:43:11 UTC (rev 695)
+++ trunk/src/workers/OSC/OSC/OscAbsorption.py	2010-07-12 21:47:51 UTC (rev 696)
@@ -73,6 +73,22 @@
         indexDict = IndexDict(offset,fmax,fstep)
     return (offset, fstep, indexDict)
 
+def removePeak(Abso, lower, upper):
+    dim = Abso.dimensions[-1]
+    minVal = lower/dim.unit
+    maxVal = upper/dim.unit
+    high_part = numpy.argwhere(minVal<dim.data).flatten()
+    low_part = numpy.argwhere(dim.data<maxVal).flatten()
+    lamp_interval = numpy.intersect1d(high_part, low_part)
+    min_index = lamp_interval[0]
+    max_index = lamp_interval[-1]
+    steps = max_index-min_index
+    for row in Abso.data:
+        min_value = row[min_index]
+        max_value = row[max_index]
+        step_size = (max_value-min_value)/steps
+        row[lamp_interval] = min_value + (lamp_interval-min_index)*step_size
+
 class OscAbsorptionCalculator(Worker.Worker):
     API = 2
     VERSION = 1
@@ -100,20 +116,12 @@
                                             shortname=ur'\tilde{A}')
         Abso.dimensions[-1] = I.dimensions[-1]
         if self.paramMask_lamp.value==1:
-            dim = Abso.dimensions[-1]
-            minVal = quantities.Quantity('654nm')/dim.unit
-            maxVal = quantities.Quantity('660nm')/dim.unit
-            high_part = numpy.argwhere(minVal<dim.data).flatten()
-            low_part = numpy.argwhere(dim.data<maxVal).flatten()
-            lamp_interval = numpy.intersect1d(high_part, low_part)
-            min_index = lamp_interval[0]
-            max_index = lamp_interval[-1]
-            steps = max_index-min_index
-            for row in Abso.data:
-                min_value = row[min_index]
-                max_value = row[max_index]
-                step_size = (max_value-min_value)/steps
-                row[lamp_interval] = min_value + (lamp_interval-min_index)*step_size
+            removePeak(Abso,
+                       quantities.Quantity('654nm'),
+                       quantities.Quantity('660nm'))
+            removePeak(Abso,
+                       quantities.Quantity('920nm'),
+                       quantities.Quantity('980nm'))
         Abso.seal()
         return Abso
 

Modified: trunk/src/workers/OSC/OSC/__init__.py
===================================================================
--- trunk/src/workers/OSC/OSC/__init__.py	2010-07-12 20:43:11 UTC (rev 695)
+++ trunk/src/workers/OSC/OSC/__init__.py	2010-07-12 21:47:51 UTC (rev 696)
@@ -45,6 +45,7 @@
     "ComputeFunctional",
     "ErrorEstimator",
     "EstimateParameter",
+    "EstimateParameterFromValues",
     "ExtremumFinder",
     "MRA",
     "OscAbsorption",


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Pyphant-devel] SF.net SVN: pyphant:[695] trunk/src

From: <zk...@us...> - 2010-07-12 20:43:18

Revision: 695
          http://pyphant.svn.sourceforge.net/pyphant/?rev=695&view=rev
Author:   zklaus
Date:     2010-07-12 20:43:11 +0000 (Mon, 12 Jul 2010)

Log Message:
-----------
Merge branch 'master' into svn-trunk

* master:
  Enh: Import of single microscopy images

Modified Paths:
--------------
    trunk/src/pyphant/pyphant/core/ZStackManager.py
    trunk/src/pyphant/pyphant/tests/TestZStacks.py
    trunk/src/pyphant/pyphant/tests/resources/zstack/_meta.xml
    trunk/src/pyphant/pyphant/wxgui2/wxPyphantApplication.py
    trunk/src/workers/ImageProcessing/ImageProcessing/MarkAF.py

Added Paths:
-----------
    trunk/src/pyphant/pyphant/tests/resources/zstack/single_meta.xml

Modified: trunk/src/pyphant/pyphant/core/ZStackManager.py
===================================================================
--- trunk/src/pyphant/pyphant/core/ZStackManager.py	2010-07-08 13:13:29 UTC (rev 694)
+++ trunk/src/pyphant/pyphant/core/ZStackManager.py	2010-07-12 20:43:11 UTC (rev 695)
@@ -39,65 +39,27 @@
 # $Source$
 
 
-from pyphant.core.XMLHandler import getXMLRoot
 from pyphant.quantities import Quantity
 from pyphant.core.DataContainer import (FieldContainer, SampleContainer)
 import scipy
 import Image
 from pyphant.core.KnowledgeManager import KnowledgeManager
 import os
+import re
 kmanager = KnowledgeManager.getInstance()
 
 
 class ZStack(object):
-    def __init__(self, sc_id=None, name=None, xml_file=None, temporary=False):
-        """Initializes a ZStack from an existing id or a local source"""
-        assert (sc_id is None) is not (xml_file is None)
+    def __init__(self, sc_id=None, meta=None, temporary=False):
+        """Initializes a ZStack from an existing id or metadata"""
+        assert (sc_id is None) is not (meta is None)
         self.temporary = temporary
-        self._recipe_path = None
         if sc_id is not None:
             self.repr_sc = kmanager.getDataContainer(sc_id)
         else:
-            assert name is not None
-            self.repr_sc = self._import_zstack(name,
-                                               os.path.realpath(xml_file))
+            self.repr_sc = self._import_zstack(meta)
 
     @staticmethod
-    def _get_images_meta(xml_file):
-        def getFloat(xmlelement):
-            return float(xmlelement.content.strip().replace(',', '.'))
-
-        def getMum(xmlelement):
-            return Quantity(getFloat(xmlelement), 'mum')
-
-        base_path = os.path.dirname(xml_file)
-        xml_root = getXMLRoot(xml_file)
-        images_meta = []
-        for ztag in [value for key, value in xml_root.children.iteritems()\
-                     if key.startswith('z')]:
-            meta = {}
-            fname = xml_root['Tags']['V5'].content.strip()
-            root, ext = os.path.splitext(fname)
-            fname = "%s_%s%s" % (root, ztag.name, ext)
-            meta['img_filename'] = os.path.join(base_path, fname)
-            meta['zvi_filename'] = os.path.join(
-                base_path, xml_root['Tags']['V150'].content.strip())
-            meta['xml_filename'] = xml_file
-            meta['zid'] = ztag.name
-            ztag = ztag['Tags']
-            meta['timestamp'] = ztag['V44'].content.strip()
-            meta['width'] = int(ztag['V3'].content.strip())
-            meta['height'] = int(ztag['V4'].content.strip())
-            meta['x-pos'] = getMum(ztag['V15'])
-            meta['y-pos'] = getMum(ztag['V16'])
-            meta['z-pos'] = getMum(ztag['V93'])
-            meta['pixel_width'] = getMum(xml_root['Scaling']['Factor_0'])
-            meta['pixel_height'] = getMum(xml_root['Scaling']['Factor_1'])
-            images_meta.append(meta)
-        images_meta.sort(key = lambda x: x['z-pos'].value)
-        return images_meta
-
-    @staticmethod
     def _get_image_fcs(images_meta, temporary=False):
         zvalues = []
         emd5s = []
@@ -111,47 +73,43 @@
         count = 1
         for img_meta in images_meta:
             if pdial is not None:
-                pdial.Update(count, os.path.basename(img_meta['img_filename']))
+                pdial.Update(count, os.path.basename(img_meta['imgFilename']))
                 count += 1
-            files.append(img_meta['xml_filename'])
-            img = Image.open(img_meta['img_filename'])
+            files.append(img_meta['xmlFilename'])
+            img = Image.open(img_meta['imgFilename'])
             data = scipy.misc.fromimage(img, flatten=True)
             zvalue = img_meta['z-pos']
-            ydata = scipy.arange(img_meta['height']) \
-                    * img_meta['pixel_height'].inUnitsOf('mum').value \
-                    + img_meta['y-pos'].inUnitsOf('mum').value
-            xdata = scipy.arange(img_meta['width']) \
-                    * img_meta['pixel_width'].inUnitsOf('mum').value \
-                    + img_meta['x-pos'].inUnitsOf('mum').value
+            yunit = Quantity(1.0, img_meta['height'].unit)
+            xunit = Quantity(1.0, img_meta['width'].unit)
+            ydata = scipy.arange(img_meta['height[pixel]']) \
+                    * img_meta['y-factor'].inUnitsOf(yunit.unit).value \
+                    + img_meta['y-pos'].inUnitsOf(yunit.unit).value
+            xdata = scipy.arange(img_meta['width[pixel]']) \
+                    * img_meta['x-factor'].inUnitsOf(xunit.unit).value \
+                    + img_meta['x-pos'].inUnitsOf(xunit.unit).value
             dimensions = [FieldContainer(ydata,
-                                         unit=Quantity(1.0, 'mum'),
+                                         unit=yunit,
                                          longname=u'y-axis',
                                          shortname=u'y'),
                           FieldContainer(xdata,
-                                         unit=Quantity(1.0, 'mum'),
+                                         unit=xunit,
                                          longname=u'x-axis',
                                          shortname=u'x')]
-            fcattr = {'img_filename':img_meta['img_filename'],
-                      'xml_filename':img_meta['xml_filename'],
-                      'zvi_filename':img_meta['zvi_filename'],
-                      'zvalue':zvalue,
-                      'timestamp':img_meta['timestamp'],
-                      'zid':img_meta['zid'],
-                      'ZStackType':'RawImage',
-                      'vmin':0, 'vmax':255}
+            fcattr = {'vmin':0, 'vmax':255}
+            fcattr.update(img_meta)
             img_fc = FieldContainer(data=data,
                                     longname=os.path.basename(
-                                        img_meta['img_filename']),
+                                        img_meta['imgFilename']),
                                     shortname="i",
                                     dimensions=dimensions, attributes=fcattr)
             img_fc.seal()
             kmanager.registerDataContainer(img_fc, temporary=temporary)
             emd5s.append(img_fc.id)
-            zvalues.append(zvalue.inUnitsOf('mum').value)
+            zvalues.append(zvalue.value)
         if len(zvalues) == 0:
             return None, None, None
         zfc = FieldContainer(scipy.array(zvalues), longname='z-value',
-                             shortname='z', unit=Quantity(1.0, 'mum'))
+                             shortname='z', unit=Quantity(1.0, zvalue.unit))
         filefc = FieldContainer(scipy.array(files), longname='filename',
                                 shortname='f')
         emd5fc = FieldContainer(scipy.array(emd5s), longname='emd5',
@@ -160,26 +118,16 @@
             pdial.Destroy()
         return zfc, filefc, emd5fc
 
-    @staticmethod
-    def _estimate_ztol(zfc):
-        zmums = [(float(zvalue) * zfc.unit).inUnitsOf('mum').value \
-                 for zvalue in zfc.data]
-        zmums.sort()
-        diffs = []
-        for index in xrange(len(zmums) - 1):
-            diffs.append(zmums[index + 1] - zmums[index])
-        return Quantity(2.0 * sum(diffs) / float(len(diffs)), 'mum')
-
-    def _import_zstack(self, name, xml_file):
-        images_meta = ZStack._get_images_meta(xml_file)
-        zfc, filefc, emd5fc = ZStack._get_image_fcs(images_meta, self.temporary)
+    def _import_zstack(self, meta):
+        zfc, filefc, emd5fc = ZStack._get_image_fcs(meta, self.temporary)
         if zfc == None:
             return None
         attributes = {}
-        attributes['ztol'] = ZStack._estimate_ztol(zfc)
         attributes['ZStackType'] = 'RawSC'
+        attributes['xmlFilename'] = meta[0]['xmlFilename']
+        attributes['crystal'] = meta[0]['crystal']
         ssc = SampleContainer([zfc, filefc, emd5fc],
-                              name,
+                              meta[0]['ZStackName'],
                               "z",
                               attributes)
         ssc.seal()
@@ -188,9 +136,10 @@
 
 
 class ZStackManager(object):
-    def addZStack(self, zstack):
-        """Adds a given zstack to the pool"""
-        kmanager.registerDataContainer(zstack.repr_sc)
+    def importZStack(self, xmlFName, name, crystal, temporary=False):
+        metaReader = getMetaReader(xmlFName, name, crystal)
+        meta = metaReader.getMeta()
+        return ZStack(meta=meta, temporary=temporary)
 
     def getZStacks(self):
         """Returns a list of all ZStacks in the pool"""
@@ -208,3 +157,141 @@
             raise ValueError("There is no ZStack called %s!" \
                                  % name)
         return ZStack(sc_id=sresult[0][0])
+
+
+class MetaReader(object):
+    def __init__(self, xmlFName, name, crystal):
+        self.xmlFName = xmlFName
+        from pyphant.core.XMLHandler import getXMLRoot
+        self.xmlRoot = getXMLRoot(xmlFName)
+        self.zStackName = name
+        self.crystal = crystal
+
+    def getMeta(self):
+        getStr = lambda x: x.content.strip()
+        def getTag(tag, tagstr):
+            for subtag in tagstr.split(':'):
+                tag = tag[subtag]
+            return tag
+        common_meta = {}
+        for key, tagstr in self.commonTagDict.iteritems():
+            common_meta[key] = getStr(getTag(self.xmlRoot, tagstr))
+        common_meta['xmlFilename'] = self.xmlFName
+        images_meta = []
+        for ztag in [value for key, value in self.xmlRoot.children.iteritems()\
+                     if self.tagRe.match(key) is not None]:
+            meta = common_meta.copy()
+            for key, tagstr in self.imageTagDict.iteritems():
+                meta[key] = getStr(getTag(ztag, tagstr))
+            meta['zid'] = self.getZId(ztag.name)
+            meta['pid'] = self.getPId(ztag.name)
+            meta['imgFilename'] = self.getImgFName(ztag.name)
+            meta['ZStackName'] = self.zStackName
+            meta['crystal'] = self.crystal
+            images_meta.append(meta)
+        self.validateMeta(images_meta)
+        images_meta.sort(key = lambda x: x['z-pos'].value)
+        return images_meta
+
+
+class ZStackMetaReader(MetaReader):
+    commonTagDict = {'scalingfactor 0':'Scaling:Factor_0',
+                     'scalingfactor 1':'Scaling:Factor_1',
+                     'SF type 0':'Scaling:Type_0',
+                     'SF type 1':'Scaling:Type_1',
+                     'width[pixel]':'Tags:V25',
+                     'height[pixel]':'Tags:V26',
+                     'width':'Tags:V30',
+                     'height':'Tags:V33',
+                     'width type':'Tags:V28',
+                     'height type':'Tags:V31',
+                     'x-factor':'Tags:V29',
+                     'y-factor':'Tags:V32',
+                     'x-pos':'Tags:V48',
+                     'y-pos':'Tags:V49',
+                     'objective':'Tags:V101'}
+    imageTagDict = {'timestamp':'Tags:V44',
+                    'z-pos':'Tags:V93'}
+    tagRe = re.compile(r'^z[0-9]+$')
+
+    def getImgFName(self, ztagname):
+        fname = self.xmlRoot['Tags']['V5'].content.strip()
+        root, ext = os.path.splitext(fname)
+        fname = "%s_%s%s" % (root, ztagname, ext)
+        return os.path.join(os.path.dirname(self.xmlFName), fname)
+
+    def getZId(self, ztagname):
+        return int(ztagname[1:])
+
+    def getPId(self, ztagname):
+        return 0
+
+    def validateMeta(self, meta):
+        getFloat = lambda x: float(x.replace(',', '.'))
+        getMum = lambda x: Quantity(getFloat(x), 'mum')
+        mumErr = 'Expected micrometre but got different unit!'
+        for img_meta in meta:
+            assert img_meta.pop('SF type 0') == '76', mumErr
+            assert img_meta.pop('SF type 1') == '76', mumErr
+            assert img_meta.pop('width type') == '76', mumErr
+            assert img_meta.pop('height type') == '76', mumErr
+            assert getFloat(img_meta.pop('scalingfactor 0')) \
+                   == getFloat(img_meta['x-factor'])
+            assert getFloat(img_meta.pop('scalingfactor 1')) \
+                   == getFloat(img_meta['y-factor'])
+            for key in ['width', 'height', 'x-factor', 'y-factor', 'x-pos',
+                        'y-pos', 'z-pos']:
+                img_meta[key] = getMum(img_meta[key])
+            for key in ['width[pixel]', 'height[pixel]']:
+                img_meta[key] = int(img_meta[key])
+            assert img_meta['width[pixel]'] == int(round(img_meta['width'] /\
+                   img_meta['x-factor'])), "x scaling is void"
+            assert img_meta['height[pixel]'] == int(round(img_meta['height'] /\
+                   img_meta['y-factor'])), "y scaling is void"
+
+
+class SingleMetaReader(ZStackMetaReader):
+    commonTagDict = {'scalingfactor 0':'Scaling:Factor_0',
+                     'scalingfactor 1':'Scaling:Factor_1',
+                     'SF type 0':'Scaling:Type_0',
+                     'SF type 1':'Scaling:Type_1',
+                     'width[pixel]':'Tags:V11',
+                     'height[pixel]':'Tags:V12',
+                     'width':'Tags:V16',
+                     'height':'Tags:V19',
+                     'width type':'Tags:V14',
+                     'height type':'Tags:V17',
+                     'x-factor':'Tags:V15',
+                     'y-factor':'Tags:V18',
+                     'x-pos':'Tags:V41',
+                     'y-pos':'Tags:V42',
+                     'objective':'Tags:V93',
+                     'timestamp':'Tags:V50',
+                     'z-pos':'Tags:V99'}
+    imageTagDict = {}
+    tagRe = re.compile(r'^_single$')
+
+    def getZId(self, ztagname):
+        return 0
+
+    def getImgFName(self, ztagname):
+        fname = self.xmlRoot['Tags']['V5'].content.strip()
+        return os.path.join(os.path.dirname(self.xmlFName), fname)
+
+META_READERS = [ZStackMetaReader, SingleMetaReader]
+
+def getMetaReader(xml, name, crystal):
+    from pyphant.core.XMLHandler import getXMLRoot
+    root = getXMLRoot(xml)
+    matched = False
+    for key in root.children.iterkeys():
+        for mreader in META_READERS:
+            if mreader.tagRe.match(key) is not None:
+                matched = True
+                break
+        if matched:
+            break
+    if matched:
+        return mreader(xml, name, crystal)
+    else:
+        raise ValueError("Unknown file format in file: %s" % xml)

Modified: trunk/src/pyphant/pyphant/tests/TestZStacks.py
===================================================================
--- trunk/src/pyphant/pyphant/tests/TestZStacks.py	2010-07-08 13:13:29 UTC (rev 694)
+++ trunk/src/pyphant/pyphant/tests/TestZStacks.py	2010-07-12 20:43:11 UTC (rev 695)
@@ -60,12 +60,12 @@
         import os
         from pyphant.core import KnowledgeManager
         from pyphant import __path__ as ppath
-        from pyphant.core.ZStackManager import ZStack
+        from pyphant.core.ZStackManager import ZStackManager
         print "Importing ZStack..."
-        zstack = ZStack(name="TestCase_ZStack",
-                        xml_file=os.path.join(ppath[0], "tests", "resources",
+        zstack = ZStackManager().importZStack(name="TestCase_ZStack",
+                        xmlFName=os.path.join(ppath[0], "tests", "resources",
                                               "zstack", "_meta.xml"),
-                        temporary=True)
+                        temporary=True, crystal='TestCrystal')
         print "Done."
         print "Calculating ZStack-statistics..."
         from ImageProcessing.AutoFocus import AutoFocus
@@ -84,7 +84,25 @@
         self.check((300.0, 0.0), statistics['z-pos'].data[imin])
         self.check((7.0, 1.0), statistics['diameter'].data[imin])
 
+    def testSingle(self):
+        import os
+        from pyphant.core import KnowledgeManager
+        from pyphant import __path__ as ppath
+        from pyphant.core.ZStackManager import ZStackManager
+        print "Importing single image..."
+        zstack = ZStackManager().importZStack(name="TestCase_Single",
+                        xmlFName=os.path.join(ppath[0], "tests", "resources",
+                                              "zstack", "single_meta.xml"),
+                        temporary=True, crystal='TestCrystal2')
+        print "Done."
+        print "Calculating single image statistics..."
+        from ImageProcessing.AutoFocus import AutoFocus
+        afw = AutoFocus()
+        statistics = afw.get_statistics_sc(zstack.repr_sc)
+        print "Done."
+        assert len(statistics['diameter'].data) == 2
 
+
 if __name__ == "__main__":
     import sys
     if len(sys.argv) == 1:

Modified: trunk/src/pyphant/pyphant/tests/resources/zstack/_meta.xml
===================================================================
--- trunk/src/pyphant/pyphant/tests/resources/zstack/_meta.xml	2010-07-08 13:13:29 UTC (rev 694)
+++ trunk/src/pyphant/pyphant/tests/resources/zstack/_meta.xml	2010-07-12 20:43:11 UTC (rev 695)
@@ -2,11 +2,23 @@
 <ROOT>
    <Tags>
      <V5>TestZStack.tif</V5>
-     <V150></V150>
+     <V25>400</V25>
+     <V26>400</V26>
+     <V29>1,0</V29>
+     <V30>400,0</V30>
+     <V28>76</V28>
+     <V32>1,0</V32>
+     <V33>400,0</V33>
+     <V31>76</V31>
+     <V48>0,0</V48>
+     <V49>0,0</V49>
+     <V101>TestObjective</V101>
    </Tags>
    <Scaling>
      <Factor_0>1,00</Factor_0>
      <Factor_1>1,00</Factor_1>
+     <Type_0>76</Type_0>
+     <Type_1>76</Type_1>
    </Scaling>
    <z00>
      <Tags>

Added: trunk/src/pyphant/pyphant/tests/resources/zstack/single_meta.xml
===================================================================
--- trunk/src/pyphant/pyphant/tests/resources/zstack/single_meta.xml	                        (rev 0)
+++ trunk/src/pyphant/pyphant/tests/resources/zstack/single_meta.xml	2010-07-12 20:43:11 UTC (rev 695)
@@ -0,0 +1,29 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<ROOT>
+   <Tags>
+     <V5>TestZStack_z04.tif</V5>
+     <V11>400</V11>
+     <V12>400</V12>
+     <V15>1,0</V15>
+     <V16>400,0</V16>
+     <V14>76</V14>
+     <V18>1,0</V18>
+     <V19>400,0</V19>
+     <V17>76</V17>
+     <V41>0,0</V41>
+     <V42>0,0</V42>
+     <V93>TestObjective</V93>
+     <V50>12.07.2010 09:40:00</V50>
+     <V99>0,0</V99>
+   </Tags>
+   <Scaling>
+     <Factor_0>1,00</Factor_0>
+     <Factor_1>1,00</Factor_1>
+     <Type_0>76</Type_0>
+     <Type_1>76</Type_1>
+   </Scaling>
+   <_single>
+     <Tags>
+     </Tags>
+   </_single>
+</ROOT>

Modified: trunk/src/pyphant/pyphant/wxgui2/wxPyphantApplication.py
===================================================================
--- trunk/src/pyphant/pyphant/wxgui2/wxPyphantApplication.py	2010-07-08 13:13:29 UTC (rev 694)
+++ trunk/src/pyphant/pyphant/wxgui2/wxPyphantApplication.py	2010-07-12 20:43:11 UTC (rev 695)
@@ -480,7 +480,7 @@
                             defaultFile="", wildcard=wc, style=wx.OPEN)
         if dlg.ShowModal() == wx.ID_OK:
             filename = os.path.realpath(dlg.GetPath())
-            from pyphant.core.ZStackManager import (ZStack, ZStackManager)
+            from pyphant.core.ZStackManager import ZStackManager
             tedlg = wx.TextEntryDialog(self, "Enter name for ZStack:",
                                        "", "ZStack")
             if tedlg.ShowModal() == wx.ID_OK:
@@ -491,10 +491,15 @@
                     cpt2 = "Error"
                     msg2 = "ZStack %s already exists!" % name
                 except ValueError:
-                    zstack = ZStack(name=name, xml_file=filename)
-                    zsm.addZStack(zstack)
-                    cpt2 = "Info"
-                    msg2 = "Successfully imported ZStack."
+                    tedlg2 = wx.TextEntryDialog(self, "Enter crystal name:",
+                                                "", "Crystal01")
+                    if tedlg2.ShowModal() == wx.ID_OK:
+                        crystal = tedlg2.GetValue()
+                        zsm.importZStack(name=name, xmlFName=filename,
+                                         crystal=crystal)
+                        cpt2 = "Info"
+                        msg2 = "Successfully imported ZStack."
+                    tedlg2.Destroy()
                 dlg2 = wx.MessageDialog(self, msg2, cpt2, wx.OK)
                 dlg2.ShowModal()
                 dlg2.Destroy()

Modified: trunk/src/workers/ImageProcessing/ImageProcessing/MarkAF.py
===================================================================
--- trunk/src/workers/ImageProcessing/ImageProcessing/MarkAF.py	2010-07-08 13:13:29 UTC (rev 694)
+++ trunk/src/workers/ImageProcessing/ImageProcessing/MarkAF.py	2010-07-12 20:43:11 UTC (rev 695)
@@ -106,7 +106,7 @@
         output_img = deepcopy(image)
         if vmin is not None:
             output_img.attributes.update({'vmin':vmin, 'vmax':vmax})
-        mf_z = int(image.attributes['zid'][-2:])
+        mf_z = image.attributes['zid']
         slicess = [(slice(yt, yp), slice(xt, xp)) \
                    for yt, yp, xt, xp, z in zip(
             statistics['yt'].data, statistics['yp'].data,
@@ -125,7 +125,7 @@
         output_img = deepcopy(image)
         output_img.data = numpy.zeros(image.data.shape,
                                       dtype=image.data.dtype)
-        mf_z = int(image.attributes['zid'][-2:])
+        mf_z = image.attributes['zid']
         labelslicess = [(label, (slice(yt, yp), slice(xt, xp))) \
                        for label, yt, yp, xt, xp, z in zip(
             statistics['label'].data,


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Pyphant-devel] SF.net SVN: pyphant:[694] trunk/src/pyphant/pyphant/quantities/ ParseQuantities.py

From: <zk...@us...> - 2010-07-08 13:13:35

Revision: 694
          http://pyphant.svn.sourceforge.net/pyphant/?rev=694&view=rev
Author:   zklaus
Date:     2010-07-08 13:13:29 +0000 (Thu, 08 Jul 2010)

Log Message:
-----------
Merge branch 'master' into svn-trunk

* master:
  Fix: Fixes problem in ParseQuantities.

Modified Paths:
--------------
    trunk/src/pyphant/pyphant/quantities/ParseQuantities.py

Modified: trunk/src/pyphant/pyphant/quantities/ParseQuantities.py
===================================================================
--- trunk/src/pyphant/pyphant/quantities/ParseQuantities.py	2010-07-07 10:24:27 UTC (rev 693)
+++ trunk/src/pyphant/pyphant/quantities/ParseQuantities.py	2010-07-08 13:13:29 UTC (rev 694)
@@ -66,7 +66,6 @@
     if FMFversion not in ['1.0','1.1']:
         raise ValueError, 'FMFversion %s not supported.' % FMFversion
     else:
-        unit = unit.replace('^', '**')
         try:
             unit = unit.replace('^', '**')
             if FMFversion=='1.1':


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Flat | Threaded

1 2 3 .. 24 > >> (Page 1 of 24)

2007	Jan	Feb	Mar	Apr	May	Jun	Jul	Aug	Sep	Oct (13)	Nov (50)	Dec (40)
2008	Jan (49)	Feb (72)	Mar (18)	Apr (27)	May (40)	Jun (52)	Jul (26)	Aug (8)	Sep (12)	Oct (26)	Nov (13)	Dec (14)
2009	Jan (13)	Feb (7)	Mar (8)	Apr (11)	May (4)	Jun (2)	Jul (7)	Aug (1)	Sep (3)	Oct	Nov (1)	Dec (1)
2010	Jan (1)	Feb (8)	Mar (3)	Apr (9)	May (16)	Jun (8)	Jul (7)	Aug	Sep (1)	Oct	Nov	Dec
2011	Jan	Feb	Mar	Apr	May (1)	Jun	Jul	Aug	Sep	Oct	Nov (6)	Dec (12)