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From: <zk...@us...> - 2007-11-04 23:41:00
|
Revision: 146
http://pyphant.svn.sourceforge.net/pyphant/?rev=146&view=rev
Author: zklaus
Date: 2007-11-04 15:41:03 -0800 (Sun, 04 Nov 2007)
Log Message:
-----------
r1304@zaphodb: ford | 2007-11-05 00:38:36 +0100
- Fixed NoneObject bug in __imod__ of Connectors.
- Fixed typo in Param.py
- Made ListSelect return unicode instead of string, thus correcting selection handling.
- Split OscLoader and other osc workers.
- Refactored OscMapper into a general mapper. Will be separated from Osc toolbox after some polishing.
Modified Paths:
--------------
trunk/src/pyphant/pyphant/core/Connectors.py
trunk/src/pyphant/pyphant/core/Param.py
trunk/src/pyphant/pyphant/wxgui2/paramvisualization/ListSelect.py
trunk/src/workers/OSC/OSC/OscLoader.py
trunk/src/workers/OSC/OSC/__init__.py
Added Paths:
-----------
trunk/src/workers/OSC/OSC/OscAbsorption.py
Property Changed:
----------------
trunk/
Property changes on: trunk
___________________________________________________________________
Name: svk:merge
- 3321fe91-ea1f-0410-9b6b-81c2d13ccd49:/branches/PyTablesHack:135
6f7b97d4-f842-44fd-9373-9f8d51b2dfcf:/local/pyphant/sourceforge:2719
8bf637c1-38a7-4b57-b48d-fce0f21498c5:/local/pyphant:1303
bece090c-e03b-4a9e-a238-bce0435dd73a:/local/pyphant:409
e121922d-4398-4060-8276-e26c71b599e4:/local/pyphant/sourceforge:367
ffafd7c2-a18e-42a0-a535-81fd4436fb1c:/local/pyphant/sourceforge/trunk:3267
+ 3321fe91-ea1f-0410-9b6b-81c2d13ccd49:/branches/PyTablesHack:135
6f7b97d4-f842-44fd-9373-9f8d51b2dfcf:/local/pyphant/sourceforge:2719
8bf637c1-38a7-4b57-b48d-fce0f21498c5:/local/pyphant:1304
bece090c-e03b-4a9e-a238-bce0435dd73a:/local/pyphant:409
e121922d-4398-4060-8276-e26c71b599e4:/local/pyphant/sourceforge:367
ffafd7c2-a18e-42a0-a535-81fd4436fb1c:/local/pyphant/sourceforge/trunk:3267
Modified: trunk/src/pyphant/pyphant/core/Connectors.py
===================================================================
--- trunk/src/pyphant/pyphant/core/Connectors.py 2007-11-04 23:40:42 UTC (rev 145)
+++ trunk/src/pyphant/pyphant/core/Connectors.py 2007-11-04 23:41:03 UTC (rev 146)
@@ -121,7 +121,8 @@
self.process = process
def __imod__(self, percentage):
- self.subscriber.updateProcess(self.process, percentage)
+ if self.subscriber:
+ self.subscriber.updateProcess(self.process, percentage)
return self
class CalculatingPlug(Plug):
Modified: trunk/src/pyphant/pyphant/core/Param.py
===================================================================
--- trunk/src/pyphant/pyphant/core/Param.py 2007-11-04 23:40:42 UTC (rev 145)
+++ trunk/src/pyphant/pyphant/core/Param.py 2007-11-04 23:41:03 UTC (rev 146)
@@ -95,7 +95,7 @@
return self.getPossibleValues()
def setPossibleValues(self, values):
- self._possibleValue=values
+ self._possibleValues=values
def __setPossibleValues(self, values):
oldValues=self.possibleValues
Modified: trunk/src/pyphant/pyphant/wxgui2/paramvisualization/ListSelect.py
===================================================================
--- trunk/src/pyphant/pyphant/wxgui2/paramvisualization/ListSelect.py 2007-11-04 23:40:42 UTC (rev 145)
+++ trunk/src/pyphant/pyphant/wxgui2/paramvisualization/ListSelect.py 2007-11-04 23:41:03 UTC (rev 146)
@@ -48,4 +48,4 @@
if self.GetSelection()==wx.NOT_FOUND:
raise ValueError("Invalid value")
else:
- return str(self.GetStringSelection())
+ return unicode(self.GetStringSelection())
Added: trunk/src/workers/OSC/OSC/OscAbsorption.py
===================================================================
--- trunk/src/workers/OSC/OSC/OscAbsorption.py (rev 0)
+++ trunk/src/workers/OSC/OSC/OscAbsorption.py 2007-11-04 23:41:03 UTC (rev 146)
@@ -0,0 +1,199 @@
+# -*- 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"""
+"""
+
+__id__ = "$Id$"
+__author__ = "$Author$"
+__version__ = "$Revision$"
+# $Source$
+
+import numpy
+from pyphant.core import (Worker, Connectors,
+ Param, DataContainer)
+
+import scipy.interpolate
+from Scientific.Physics import PhysicalQuantities
+
+class OscAbsorptionCalculator(Worker.Worker):
+ API = 2
+ VERSION = 1
+ REVISION = "$Revision$"[11:-1]
+ name = "Osc Absorption Calculator"
+
+ _sockets = [("osc", Connectors.TYPE_ARRAY)]
+ _params = [("clipping", "Clipping", 1, None)]
+
+ @Worker.plug(Connectors.TYPE_ARRAY)
+ def calcAbsorption(self, osc, subscriber=0):
+ cont = osc.recreateFieldContainers()
+ I = cont[u'ScopRaw[counts]']
+ I_d = cont[u'DarkRef[counts]']
+ I_0 = cont[u'WhiteRef[counts]']
+ A = -((I.data-I_d.data)/(I_0.data-I_d.data)-1)
+ if self.paramClipping.value==1:
+ A[A>1] = 0
+ A[A<0] = 0
+ Abso = DataContainer.FieldContainer(A, longname=u'Absorption', shortname=u'A')
+ result = DataContainer.SampleContainer(cont.values()+[Abso], longname=osc.longname, shortname=osc.shortname)
+ result.seal()
+ return result
+
+
+class OscAbsorptionExtractor(Worker.Worker):
+ API = 2
+ VERSION = 1
+ REVISION = "$Revision$"[11:-1]
+ name = "Single Spectrum Viewer"
+
+ _sockets = [("osc", Connectors.TYPE_ARRAY)]
+ _params = [("index", "Index", 1, None)]
+
+ @Worker.plug(Connectors.TYPE_ARRAY)
+ def extractSpec(self, osc, subscriber=0):
+ data = osc.recreateFieldContainers()
+ a = data[u'Absorption']
+ l = data[u'Wellenlänge[nm]']
+ lam = DataContainer.FieldContainer(l.data[self.paramIndex.value-1], l.unit, l.error, l.dimensions, l.longname, u"\lambda")
+ Abso = DataContainer.FieldContainer(a.data[self.paramIndex.value-1], a.unit, a.error, [lam], osc.longname+u", Abs Pixel %i"%self.paramIndex.value, u"A")
+ Abso.seal()
+ return Abso
+
+
+class OscMinimumFinder(Worker.Worker):
+ API = 2
+ VERSION = 1
+ REVISION = "$Revision$"[11:-1]
+ name = "Minimum finder"
+
+ _sockets = [("osc", Connectors.TYPE_ARRAY)]
+ _params = [("lower", "Lower Bound", 380, None),
+ ("upper", "Upper Bound", 500, None),
+ ("a", "a", 14000, None),
+ ("b", "b", -4270000, None),
+ ("s", "Fit smoothing (0 no smoothing, larger value more smoothing)", 150, None)]
+
+ @Worker.plug(Connectors.TYPE_ARRAY)
+ def findMinimum(self, osc, subscriber=0):
+ data = osc.recreateFieldContainers()
+ Abso = data[u'Absorption']
+ lam = data[u'Wellenlänge[nm]']
+ as = []
+ ls = []
+ mins = []
+ l = lam.data[0]
+ hs = []
+ lower = numpy.argwhere(l>self.paramLower.value)[0][0]
+ upper = numpy.argwhere(l<self.paramUpper.value)[-1][0]
+ count = len(lam.data)
+ for i in xrange(count):
+ l = lam.data[i][lower:upper]
+ ls.append(l)
+ a = Abso.data[i][lower:upper]
+ tck = scipy.interpolate.splrep(l, a, s=self.paramS.value)
+ a = scipy.interpolate.splev(l, tck, 0)
+ as.append(a)
+ imin = a.argmin()
+ if imin>0 and imin<len(l)-1:
+ mins.append(l[imin])
+ hs.append(l[imin]*float(self.paramA.value)/10000.0+float(self.paramB.value)/10000.0)
+ else:
+ mins.append(0)
+ hs.append(0)
+ subscriber %= float(i)*100.0/float(count)
+ data[u'Absorption'] = DataContainer.FieldContainer(numpy.array(as), longname=u'Absorption', shortname=u'A')
+ data[u'Wellenlänge[nm]'] = DataContainer.FieldContainer(numpy.array(ls), unit=lam.unit,
+ longname=u'Wavelength', shortname=u'\lambda')
+ data[u'Minima'] = DataContainer.FieldContainer(numpy.array(mins), unit=lam.unit,
+ longname=u'Minima', shortname='m')
+ data[u'Höhe'] = DataContainer.FieldContainer(numpy.array(hs), unit=lam.unit,
+ longname=u'Höhe', shortname='h')
+ result = DataContainer.SampleContainer(data.values(), longname=osc.longname, shortname=osc.shortname)
+ result.seal()
+ return result
+
+
+class OscMapper(Worker.Worker):
+ API = 2
+ VERSION = 1
+ REVISION = "$Revision$"[11:-1]
+ name = "Osc Mapper"
+
+ _sockets = [("osc", Connectors.TYPE_ARRAY)]
+ _params = [("xAxis", u"x-Axis", [u"TISCH_POS_X", u"TISCH_POS_Y"], None),
+ ("yAxis", u"y-Axis", [u"TISCH_POS_Y", u"TISCH_POS_X"], None),
+ ("field", u"Field", [u"Höhe", u"Strom"], None)]
+
+ def inithook(self):
+ self.isInvalidating=False
+
+ def invalidate(self, event=None):
+ if self.isInvalidating:
+ return
+ self.isInvalidating=True
+ if self.socketOsc.isFull():
+ templ = self.socketOsc.value
+ colNames = [ d[0][0] for d in templ.data.dtype.descr ]
+ self.paramXAxis.possibleValues=colNames
+ self.paramYAxis.possibleValues=colNames
+ self.paramField.possibleValues=colNames
+ super(OscMapper, self).invalidate(event)
+ self.isInvalidating=False
+
+ @Worker.plug(Connectors.TYPE_IMAGE)
+ def mapHeights(self, osc, subscriber=0):
+ d = 9
+ data = osc.recreateFieldContainers()
+ xCon = data[self.paramXAxis.value]
+ xCon.longname=xCon.longname.replace('_', ' ').title()
+ yCon = data[self.paramYAxis.value]
+ yCon.longname=yCon.longname.replace('_', ' ').title()
+ fCon = data[self.paramField.value]
+ fCon.longname=fCon.longname.replace('_', ' ').title()
+ xCon.data = xCon.data.astype('float')
+ xf = xCon.data
+ yCon.data = yCon.data.astype('float')
+ yf = yCon.data
+ x = (xf*10).astype('int')
+ y = (yf*10).astype('int')
+ x = x-x.min()
+ y = y-y.min()
+ fCon.data = fCon.data.astype('float')
+ h = fCon.data
+ m = h[h>0].min()
+ img = numpy.ones((y.max()+d, x.max()+d))*m
+ for i in xrange(len(x)):
+ img[y[i]:y[i]+d,x[i]:x[i]+d]=max(h[i], m)
+ result = DataContainer.FieldContainer(img, fCon.unit, dimensions=[xCon, yCon],
+ longname=u'Map of %s for %s'%(fCon.longname, osc.longname), shortname=fCon.shortname)
+ result.seal()
+ return result
Property changes on: trunk/src/workers/OSC/OSC/OscAbsorption.py
___________________________________________________________________
Name: svn:keywords
+ Id Author Revision
Modified: trunk/src/workers/OSC/OSC/OscLoader.py
===================================================================
--- trunk/src/workers/OSC/OSC/OscLoader.py 2007-11-04 23:40:42 UTC (rev 145)
+++ trunk/src/workers/OSC/OSC/OscLoader.py 2007-11-04 23:41:03 UTC (rev 146)
@@ -37,11 +37,10 @@
__version__ = "$Revision$"
# $Source$
-import zipfile, numpy, copy, re
+import zipfile, numpy, re
from pyphant.core import (Worker, Connectors,
Param, DataContainer)
-import scipy.interpolate
from Scientific.Physics import PhysicalQuantities
def makeRoot(pixelName, ll):
@@ -138,130 +137,3 @@
result.seal()
return result
-class OscAbsorptionCalculator(Worker.Worker):
- API = 2
- VERSION = 1
- REVISION = "$Revision$"[11:-1]
- name = "Osc Absorption Calculator"
-
- _sockets = [("osc", Connectors.TYPE_ARRAY)]
- _params = [("clipping", "Clipping", 1, None)]
-
- @Worker.plug(Connectors.TYPE_ARRAY)
- def calcAbsorption(self, osc, subscriber=0):
- cont = osc.recreateFieldContainers()
- I = cont[u'ScopRaw[counts]']
- I_d = cont[u'DarkRef[counts]']
- I_0 = cont[u'WhiteRef[counts]']
- A = -((I.data-I_d.data)/(I_0.data-I_d.data)-1)
- if self.paramClipping.value==1:
- A[A>1] = 0
- A[A<0] = 0
- Abso = DataContainer.FieldContainer(A, longname='Absorption', shortname='A')
- result = DataContainer.SampleContainer(cont.values()+[Abso], longname=osc.longname, shortname=osc.shortname)
- result.seal()
- return result
-
-
-class OscAbsorptionExtractor(Worker.Worker):
- API = 2
- VERSION = 1
- REVISION = "$Revision$"[11:-1]
- name = "Single Spectrum Viewer"
-
- _sockets = [("osc", Connectors.TYPE_ARRAY)]
- _params = [("index", "Index", 1, None)]
-
- @Worker.plug(Connectors.TYPE_ARRAY)
- def extractSpec(self, osc, subscriber=0):
- data = osc.recreateFieldContainers()
- a = data[u'Absorption']
- l = data[u'Wellenlänge[nm]']
- lam = DataContainer.FieldContainer(l.data[self.paramIndex.value-1], l.unit, l.error, l.dimensions, l.longname, u"\lambda")
- Abso = DataContainer.FieldContainer(a.data[self.paramIndex.value-1], a.unit, a.error, [lam], osc.longname+u", Abs Pixel %i"%self.paramIndex.value, u"A")
- Abso.seal()
- return Abso
-
-
-class OscMinimumFinder(Worker.Worker):
- API = 2
- VERSION = 1
- REVISION = "$Revision$"[11:-1]
- name = "Minimum finder"
-
- _sockets = [("osc", Connectors.TYPE_ARRAY)]
- _params = [("lower", "Lower Bound", 380, None),
- ("upper", "Upper Bound", 500, None),
- ("a", "a", 14000, None),
- ("b", "b", -4270000, None),
- ("s", "Fit smoothing (0 no smoothing, larger value more smoothing)", 150, None)]
-
- @Worker.plug(Connectors.TYPE_ARRAY)
- def findMinimum(self, osc, subscriber=0):
- data = osc.recreateFieldContainers()
- Abso = data[u'Absorption']
- lam = data[u'Wellenlänge[nm]']
- as = []
- ls = []
- mins = []
- l = lam.data[0]
- hs = []
- lower = numpy.argwhere(l>self.paramLower.value)[0][0]
- upper = numpy.argwhere(l<self.paramUpper.value)[-1][0]
- count = len(lam.data)
- for i in xrange(count):
- l = lam.data[i][lower:upper]
- ls.append(l)
- a = Abso.data[i][lower:upper]
- tck = scipy.interpolate.splrep(l, a, s=self.paramS.value)
- a = scipy.interpolate.splev(l, tck, 0)
- as.append(a)
- imin = a.argmin()
- if imin>0 and imin<len(l)-1:
- mins.append(l[imin])
- hs.append(l[imin]*float(self.paramA.value)/10000.0+float(self.paramB.value)/10000.0)
- else:
- mins.append(0)
- hs.append(0)
- subscriber %= float(i)*100.0/float(count)
- data[u'Absorption'] = DataContainer.FieldContainer(numpy.array(as), longname=u'Absorption', shortname=u'A')
- data[u'Wellenlänge[nm]'] = DataContainer.FieldContainer(numpy.array(ls), unit=lam.unit,
- longname=u'Wavelength', shortname=u'\lambda')
- data[u'Minima'] = DataContainer.FieldContainer(numpy.array(mins), unit=lam.unit,
- longname=u'Minima', shortname='m')
- data[u'Höhe'] = DataContainer.FieldContainer(numpy.array(hs), unit=lam.unit,
- longname=u'Höhe', shortname='h')
- result = DataContainer.SampleContainer(data.values(), longname=osc.longname, shortname=osc.shortname)
- result.seal()
- return result
-
-
-class OscMapper(Worker.Worker):
- API = 2
- VERSION = 1
- REVISION = "$Revision$"[11:-1]
- name = "Osc Mapper"
-
- _sockets = [("osc", Connectors.TYPE_ARRAY)]
-
- @Worker.plug(Connectors.TYPE_IMAGE)
- def mapHeights(self, osc, subscriber=0):
- d = 9
- data = osc.recreateFieldContainers()
- xf = numpy.array(data[u'TISCH_POS_X'].data, dtype='float')
- yf = numpy.array(data[u'TISCH_POS_Y'].data, dtype='float')
- x = (xf*10).astype('int')
- y = (yf*10).astype('int')
- x = x-x.min()
- y = y-y.min()
- h = data[u'Höhe'].data
- m = h[h>0].min()
- img = numpy.ones((y.max()+d, x.max()+d))*m
- for i in xrange(len(x)):
- img[y[i]:y[i]+d,x[i]:x[i]+d]=max(h[i], m)
- xdim = DataContainer.FieldContainer(xf, PhysicalQuantities.PhysicalQuantity('1 mm'), longname=u'x-Axis', shortname="x")
- ydim = DataContainer.FieldContainer(yf, PhysicalQuantities.PhysicalQuantity('1 mm'), longname=u'y-Axis', shortname="y")
- result = DataContainer.FieldContainer(img, PhysicalQuantities.PhysicalQuantity('1 nm'), dimensions=[xdim, ydim],
- longname=u'Heightmap for '+osc.longname, shortname='h')
- result.seal()
- return result
Modified: trunk/src/workers/OSC/OSC/__init__.py
===================================================================
--- trunk/src/workers/OSC/OSC/__init__.py 2007-11-04 23:40:42 UTC (rev 145)
+++ trunk/src/workers/OSC/OSC/__init__.py 2007-11-04 23:41:03 UTC (rev 146)
@@ -37,5 +37,6 @@
__version__ = "$Revision$"
# $Source$
-workers=[ "OscLoader" ]
+workers=[ "OscLoader",
+ "OscAbsorption" ]
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <zk...@us...> - 2007-11-04 23:40:45
|
Revision: 145
http://pyphant.svn.sourceforge.net/pyphant/?rev=145&view=rev
Author: zklaus
Date: 2007-11-04 15:40:42 -0800 (Sun, 04 Nov 2007)
Log Message:
-----------
r1303@zaphodb: ford | 2007-11-04 16:03:58 +0100
- Made the loader data-agnostic.
Modified Paths:
--------------
trunk/src/workers/OSC/OSC/OscLoader.py
Property Changed:
----------------
trunk/
Property changes on: trunk
___________________________________________________________________
Name: svk:merge
- 3321fe91-ea1f-0410-9b6b-81c2d13ccd49:/branches/PyTablesHack:135
6f7b97d4-f842-44fd-9373-9f8d51b2dfcf:/local/pyphant/sourceforge:2719
8bf637c1-38a7-4b57-b48d-fce0f21498c5:/local/pyphant:1301
bece090c-e03b-4a9e-a238-bce0435dd73a:/local/pyphant:409
e121922d-4398-4060-8276-e26c71b599e4:/local/pyphant/sourceforge:367
ffafd7c2-a18e-42a0-a535-81fd4436fb1c:/local/pyphant/sourceforge/trunk:3267
+ 3321fe91-ea1f-0410-9b6b-81c2d13ccd49:/branches/PyTablesHack:135
6f7b97d4-f842-44fd-9373-9f8d51b2dfcf:/local/pyphant/sourceforge:2719
8bf637c1-38a7-4b57-b48d-fce0f21498c5:/local/pyphant:1303
bece090c-e03b-4a9e-a238-bce0435dd73a:/local/pyphant:409
e121922d-4398-4060-8276-e26c71b599e4:/local/pyphant/sourceforge:367
ffafd7c2-a18e-42a0-a535-81fd4436fb1c:/local/pyphant/sourceforge/trunk:3267
Modified: trunk/src/workers/OSC/OSC/OscLoader.py
===================================================================
--- trunk/src/workers/OSC/OSC/OscLoader.py 2007-10-31 13:18:25 UTC (rev 144)
+++ trunk/src/workers/OSC/OSC/OscLoader.py 2007-11-04 23:40:42 UTC (rev 145)
@@ -50,6 +50,8 @@
def startSection(root, l):
if l == u'MESSDATEN':
root[l] = []
+ elif l == u'SPALTENBESCHRIFTUNG':
+ root[l] = []
else:
root[l] = {}
return root[l], l
@@ -58,6 +60,10 @@
ff = l.split('=')
section[ff[0]] = ff[1]
+def addDataColumn(section, l):
+ ff = l.split('=')
+ section.append(ff[1])
+
def addTableLine(section, l):
ff = l.split('\t')
section.append([float(f) for f in ff])
@@ -65,7 +71,7 @@
LINE_HANDLER = { u'Section': startSection,
u'GLOBAL': addAttributeLine,
u'MESSUNG': addAttributeLine,
- u'SPALTENBESCHRIFTUNG': addAttributeLine,
+ u'SPALTENBESCHRIFTUNG': addDataColumn,
u'MESSDATEN': addTableLine }
def loadOscFromFile(filename, subscriber=0):
@@ -88,10 +94,8 @@
for dicname in (u'GLOBAL',u'MESSUNG'):
for k in d[dicname].keys():
container[k].append(d[dicname][k])
- for i in xrange(1,6):
- col = "SPALTE%i" % i
- container[d[u'SPALTENBESCHRIFTUNG'][col]].append(d[u'MESSDATEN'][:,i-1])
- #container[u'WhiteRef[counts]'].append(d[u'MESSDATEN'][:,4])
+ for i, col in enumerate(d[u'SPALTENBESCHRIFTUNG']):
+ container[col].append(d[u'MESSDATEN'][:,i])
cols = [DataContainer.FieldContainer(numpy.array(v), unit=longname2unit(k), longname=k) for k,v in container.iteritems()]
return DataContainer.SampleContainer(cols, longname=container[u'KOMMENTAR'][0])
@@ -99,12 +103,8 @@
def constructTemplate(data):
template = data[0]
container = {}
- for k in template[u'GLOBAL'].keys()+template[u'MESSUNG'].keys():
+ for k in template[u'GLOBAL'].keys()+template[u'MESSUNG'].keys()+template[u'SPALTENBESCHRIFTUNG']:
container[k] = []
- for i in xrange(1,5):
- k = "SPALTE%i" % i
- container[template[u'SPALTENBESCHRIFTUNG'][k]] = []
- container[u'WhiteRef[counts]'] = []
return container
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <zk...@us...> - 2007-10-31 13:18:22
|
Revision: 144
http://pyphant.svn.sourceforge.net/pyphant/?rev=144&view=rev
Author: zklaus
Date: 2007-10-31 06:18:25 -0700 (Wed, 31 Oct 2007)
Log Message:
-----------
r1301@zaphodb: ford | 2007-10-31 14:16:24 +0100
- Added shortlabel to DataContainer.
- Simple charts now use shortlabel as ylabel, since the longname is in the title anyway.
- Hacked Chart to accomodate for Osc changes.
- Removed matplotlib ion. That slowed things horribly down. Further investigation needed.
- Removed special treatment of WhiteRef in OscLoader. The format was changed to make this unnecessary. WARNING: This breaks compatibility with older data files. Use T14 or later.
- Renamed Osc Absorption Spectrum to Single Spectrum Viewer.
- Added more meaningful short- and longnames in Single Spectrum Viewer.
- Added smoothing parameter to Minimum Finder.
- Minimumfinder changes 'Wellenl?\195?\164nge[nm]' to Wavelength.
Modified Paths:
--------------
trunk/src/pyphant/pyphant/core/DataContainer.py
trunk/src/pyphant/pyphant/visualizers/Chart.py
trunk/src/pyphant/pyphant/visualizers/ImageVisualizer.py
trunk/src/workers/OSC/OSC/OscLoader.py
Property Changed:
----------------
trunk/
Property changes on: trunk
___________________________________________________________________
Name: svk:merge
- 3321fe91-ea1f-0410-9b6b-81c2d13ccd49:/branches/PyTablesHack:135
6f7b97d4-f842-44fd-9373-9f8d51b2dfcf:/local/pyphant/sourceforge:2719
8bf637c1-38a7-4b57-b48d-fce0f21498c5:/local/pyphant:1298
bece090c-e03b-4a9e-a238-bce0435dd73a:/local/pyphant:409
e121922d-4398-4060-8276-e26c71b599e4:/local/pyphant/sourceforge:367
ffafd7c2-a18e-42a0-a535-81fd4436fb1c:/local/pyphant/sourceforge/trunk:3267
+ 3321fe91-ea1f-0410-9b6b-81c2d13ccd49:/branches/PyTablesHack:135
6f7b97d4-f842-44fd-9373-9f8d51b2dfcf:/local/pyphant/sourceforge:2719
8bf637c1-38a7-4b57-b48d-fce0f21498c5:/local/pyphant:1301
bece090c-e03b-4a9e-a238-bce0435dd73a:/local/pyphant:409
e121922d-4398-4060-8276-e26c71b599e4:/local/pyphant/sourceforge:367
ffafd7c2-a18e-42a0-a535-81fd4436fb1c:/local/pyphant/sourceforge/trunk:3267
Modified: trunk/src/pyphant/pyphant/core/DataContainer.py
===================================================================
--- trunk/src/pyphant/pyphant/core/DataContainer.py 2007-10-30 00:47:47 UTC (rev 143)
+++ trunk/src/pyphant/pyphant/core/DataContainer.py 2007-10-31 13:18:25 UTC (rev 144)
@@ -205,6 +205,13 @@
return u"%s $%s$ / %s" % (self.longname, self.shortname, self.unit)
label=property(_getLabel)
+ def _getShortLabel(self):
+ if not isPhysicalQuantity(self.unit) and self.unit == 1:
+ return u"$%s$ / a.u." % self.shortname
+ else:
+ return u"$%s$ / %s" % (self.shortname, self.unit)
+ shortlabel=property(_getShortLabel)
+
def __deepcopy__(self, memo):
self.lock.acquire()
data=copy.deepcopy(self.data, memo)
Modified: trunk/src/pyphant/pyphant/visualizers/Chart.py
===================================================================
--- trunk/src/pyphant/pyphant/visualizers/Chart.py 2007-10-30 00:47:47 UTC (rev 143)
+++ trunk/src/pyphant/pyphant/visualizers/Chart.py 2007-10-31 13:18:25 UTC (rev 144)
@@ -64,23 +64,28 @@
if isinstance(self.dataContainer, DataContainer.FieldContainer):
self.addFieldContainer(self.dataContainer)
pylab.xlabel(self.dataContainer.dimensions[0].label)
- pylab.ylabel(self.dataContainer.label)
+ pylab.ylabel(self.dataContainer.shortlabel)
pylab.title(self.dataContainer.longname)
else:
data = self.dataContainer.recreateFieldContainers()
- lam = data[u'Wellenlänge[nm]']
+ if u'Wellenlänge[nm]' in data.keys():
+ lam = data[u'Wellenlänge[nm]']
+ else:
+ lam = data[u'Wavelength']
abso = data[u'Absorption']
- mins = data[u'Minima']
for i in xrange(len(lam.data)):
self.ordinates.append(abso.data[i])
self.abscissae.append(lam.data[i])
- self.mins.append(mins.data[i])
+ if u'Minima' in data.keys():
+ mins = data[u'Minima']
+ for i in xrange(len(lam.data)):
+ self.mins.append(mins.data[i])
pylab.xlabel(lam.label)
pylab.ylabel(abso.label)
pylab.title(self.dataContainer.longname)
def finalize(self):
- pylab.ion()
+ #pylab.ion()
pylab.show()
Modified: trunk/src/pyphant/pyphant/visualizers/ImageVisualizer.py
===================================================================
--- trunk/src/pyphant/pyphant/visualizers/ImageVisualizer.py 2007-10-30 00:47:47 UTC (rev 143)
+++ trunk/src/pyphant/pyphant/visualizers/ImageVisualizer.py 2007-10-31 13:18:25 UTC (rev 144)
@@ -69,7 +69,7 @@
return str(x)
ax=pylab.gca()
pylab.colorbar(format=F(self.fieldContainer))
- pylab.ion()
+ #pylab.ion()
pylab.show()
DataVisReg.getInstance().registerVisualizer(TYPE_IMAGE, ImageVisualizer)
Modified: trunk/src/workers/OSC/OSC/OscLoader.py
===================================================================
--- trunk/src/workers/OSC/OSC/OscLoader.py 2007-10-30 00:47:47 UTC (rev 143)
+++ trunk/src/workers/OSC/OSC/OscLoader.py 2007-10-31 13:18:25 UTC (rev 144)
@@ -88,10 +88,10 @@
for dicname in (u'GLOBAL',u'MESSUNG'):
for k in d[dicname].keys():
container[k].append(d[dicname][k])
- for i in xrange(1,5):
+ for i in xrange(1,6):
col = "SPALTE%i" % i
container[d[u'SPALTENBESCHRIFTUNG'][col]].append(d[u'MESSDATEN'][:,i-1])
- container[u'WhiteRef[counts]'].append(d[u'MESSDATEN'][:,4])
+ #container[u'WhiteRef[counts]'].append(d[u'MESSDATEN'][:,4])
cols = [DataContainer.FieldContainer(numpy.array(v), unit=longname2unit(k), longname=k) for k,v in container.iteritems()]
return DataContainer.SampleContainer(cols, longname=container[u'KOMMENTAR'][0])
@@ -167,7 +167,7 @@
API = 2
VERSION = 1
REVISION = "$Revision$"[11:-1]
- name = "Osc Absorption Spectrum"
+ name = "Single Spectrum Viewer"
_sockets = [("osc", Connectors.TYPE_ARRAY)]
_params = [("index", "Index", 1, None)]
@@ -177,8 +177,8 @@
data = osc.recreateFieldContainers()
a = data[u'Absorption']
l = data[u'Wellenlänge[nm]']
- lam = DataContainer.FieldContainer(l.data[self.paramIndex.value], l.unit, l.error, l.dimensions, l.longname, l.shortname)
- Abso = DataContainer.FieldContainer(a.data[self.paramIndex.value], a.unit, a.error, [lam], a.longname, l.shortname)
+ lam = DataContainer.FieldContainer(l.data[self.paramIndex.value-1], l.unit, l.error, l.dimensions, l.longname, u"\lambda")
+ Abso = DataContainer.FieldContainer(a.data[self.paramIndex.value-1], a.unit, a.error, [lam], osc.longname+u", Abs Pixel %i"%self.paramIndex.value, u"A")
Abso.seal()
return Abso
@@ -193,7 +193,8 @@
_params = [("lower", "Lower Bound", 380, None),
("upper", "Upper Bound", 500, None),
("a", "a", 14000, None),
- ("b", "b", -4270000, None)]
+ ("b", "b", -4270000, None),
+ ("s", "Fit smoothing (0 no smoothing, larger value more smoothing)", 150, None)]
@Worker.plug(Connectors.TYPE_ARRAY)
def findMinimum(self, osc, subscriber=0):
@@ -212,7 +213,7 @@
l = lam.data[i][lower:upper]
ls.append(l)
a = Abso.data[i][lower:upper]
- tck = scipy.interpolate.splrep(l, a, s=len(l)-numpy.sqrt(2*len(l)))
+ tck = scipy.interpolate.splrep(l, a, s=self.paramS.value)
a = scipy.interpolate.splev(l, tck, 0)
as.append(a)
imin = a.argmin()
@@ -225,7 +226,7 @@
subscriber %= float(i)*100.0/float(count)
data[u'Absorption'] = DataContainer.FieldContainer(numpy.array(as), longname=u'Absorption', shortname=u'A')
data[u'Wellenlänge[nm]'] = DataContainer.FieldContainer(numpy.array(ls), unit=lam.unit,
- longname=lam.longname, shortname=lam.shortname)
+ longname=u'Wavelength', shortname=u'\lambda')
data[u'Minima'] = DataContainer.FieldContainer(numpy.array(mins), unit=lam.unit,
longname=u'Minima', shortname='m')
data[u'Höhe'] = DataContainer.FieldContainer(numpy.array(hs), unit=lam.unit,
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <zk...@us...> - 2007-10-30 00:47:44
|
Revision: 143
http://pyphant.svn.sourceforge.net/pyphant/?rev=143&view=rev
Author: zklaus
Date: 2007-10-29 17:47:47 -0700 (Mon, 29 Oct 2007)
Log Message:
-----------
r1298@zaphodb: ford | 2007-10-30 01:45:37 +0100
- Latexified the handling of shortname.
- Improved line chart labeling.
- Improved longname handling of osc data.
Modified Paths:
--------------
trunk/src/pyphant/pyphant/core/DataContainer.py
trunk/src/pyphant/pyphant/visualizers/Chart.py
trunk/src/workers/OSC/OSC/OscLoader.py
Property Changed:
----------------
trunk/
Property changes on: trunk
___________________________________________________________________
Name: svk:merge
- 3321fe91-ea1f-0410-9b6b-81c2d13ccd49:/branches/PyTablesHack:135
6f7b97d4-f842-44fd-9373-9f8d51b2dfcf:/local/pyphant/sourceforge:2719
8bf637c1-38a7-4b57-b48d-fce0f21498c5:/local/pyphant:1296
bece090c-e03b-4a9e-a238-bce0435dd73a:/local/pyphant:409
e121922d-4398-4060-8276-e26c71b599e4:/local/pyphant/sourceforge:367
ffafd7c2-a18e-42a0-a535-81fd4436fb1c:/local/pyphant/sourceforge/trunk:3267
+ 3321fe91-ea1f-0410-9b6b-81c2d13ccd49:/branches/PyTablesHack:135
6f7b97d4-f842-44fd-9373-9f8d51b2dfcf:/local/pyphant/sourceforge:2719
8bf637c1-38a7-4b57-b48d-fce0f21498c5:/local/pyphant:1298
bece090c-e03b-4a9e-a238-bce0435dd73a:/local/pyphant:409
e121922d-4398-4060-8276-e26c71b599e4:/local/pyphant/sourceforge:367
ffafd7c2-a18e-42a0-a535-81fd4436fb1c:/local/pyphant/sourceforge/trunk:3267
Modified: trunk/src/pyphant/pyphant/core/DataContainer.py
===================================================================
--- trunk/src/pyphant/pyphant/core/DataContainer.py 2007-10-29 23:53:15 UTC (rev 142)
+++ trunk/src/pyphant/pyphant/core/DataContainer.py 2007-10-30 00:47:47 UTC (rev 143)
@@ -200,9 +200,9 @@
def _getLabel(self):
if not isPhysicalQuantity(self.unit) and self.unit == 1:
- return u"%s %s / a.u." % (self.longname,self.shortname)
+ return u"%s $%s$ / a.u." % (self.longname,self.shortname)
else:
- return u"%s %s / %s" % (self.longname, self.shortname, self.unit)
+ return u"%s $%s$ / %s" % (self.longname, self.shortname, self.unit)
label=property(_getLabel)
def __deepcopy__(self, memo):
@@ -291,7 +291,7 @@
for j in xrange(N):
pos = listing.index(topic)
if nameList:
- listing[pos] += str(j)
+ listing[pos] += "_{"+str(j)+"}"
else:
listing[pos] += names[j].capitalize()
nameList = False
Modified: trunk/src/pyphant/pyphant/visualizers/Chart.py
===================================================================
--- trunk/src/pyphant/pyphant/visualizers/Chart.py 2007-10-29 23:53:15 UTC (rev 142)
+++ trunk/src/pyphant/pyphant/visualizers/Chart.py 2007-10-30 00:47:47 UTC (rev 143)
@@ -65,6 +65,7 @@
self.addFieldContainer(self.dataContainer)
pylab.xlabel(self.dataContainer.dimensions[0].label)
pylab.ylabel(self.dataContainer.label)
+ pylab.title(self.dataContainer.longname)
else:
data = self.dataContainer.recreateFieldContainers()
lam = data[u'Wellenlänge[nm]']
@@ -76,6 +77,7 @@
self.mins.append(mins.data[i])
pylab.xlabel(lam.label)
pylab.ylabel(abso.label)
+ pylab.title(self.dataContainer.longname)
def finalize(self):
pylab.ion()
Modified: trunk/src/workers/OSC/OSC/OscLoader.py
===================================================================
--- trunk/src/workers/OSC/OSC/OscLoader.py 2007-10-29 23:53:15 UTC (rev 142)
+++ trunk/src/workers/OSC/OSC/OscLoader.py 2007-10-30 00:47:47 UTC (rev 143)
@@ -93,7 +93,7 @@
container[d[u'SPALTENBESCHRIFTUNG'][col]].append(d[u'MESSDATEN'][:,i-1])
container[u'WhiteRef[counts]'].append(d[u'MESSDATEN'][:,4])
cols = [DataContainer.FieldContainer(numpy.array(v), unit=longname2unit(k), longname=k) for k,v in container.iteritems()]
- return DataContainer.SampleContainer(cols)
+ return DataContainer.SampleContainer(cols, longname=container[u'KOMMENTAR'][0])
def constructTemplate(data):
@@ -158,7 +158,7 @@
A[A>1] = 0
A[A<0] = 0
Abso = DataContainer.FieldContainer(A, longname='Absorption', shortname='A')
- result = DataContainer.SampleContainer(cont.values()+[Abso], longname='Osc data', shortname='O')
+ result = DataContainer.SampleContainer(cont.values()+[Abso], longname=osc.longname, shortname=osc.shortname)
result.seal()
return result
@@ -230,7 +230,7 @@
longname=u'Minima', shortname='m')
data[u'Höhe'] = DataContainer.FieldContainer(numpy.array(hs), unit=lam.unit,
longname=u'Höhe', shortname='h')
- result = DataContainer.SampleContainer(data.values(), longname='Osc data', shortname='O')
+ result = DataContainer.SampleContainer(data.values(), longname=osc.longname, shortname=osc.shortname)
result.seal()
return result
@@ -257,10 +257,10 @@
m = h[h>0].min()
img = numpy.ones((y.max()+d, x.max()+d))*m
for i in xrange(len(x)):
- #img[y[i]-d:y[i]+d,x[i]-d:x[i]+d]=max(h[i], m)
img[y[i]:y[i]+d,x[i]:x[i]+d]=max(h[i], m)
xdim = DataContainer.FieldContainer(xf, PhysicalQuantities.PhysicalQuantity('1 mm'), longname=u'x-Axis', shortname="x")
ydim = DataContainer.FieldContainer(yf, PhysicalQuantities.PhysicalQuantity('1 mm'), longname=u'y-Axis', shortname="y")
- result = DataContainer.FieldContainer(img, PhysicalQuantities.PhysicalQuantity('1 nm'), dimensions=[xdim, ydim], longname='Osc Heightmap', shortname='h')
+ result = DataContainer.FieldContainer(img, PhysicalQuantities.PhysicalQuantity('1 nm'), dimensions=[xdim, ydim],
+ longname=u'Heightmap for '+osc.longname, shortname='h')
result.seal()
return result
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <zk...@us...> - 2007-10-29 23:53:12
|
Revision: 142
http://pyphant.svn.sourceforge.net/pyphant/?rev=142&view=rev
Author: zklaus
Date: 2007-10-29 16:53:15 -0700 (Mon, 29 Oct 2007)
Log Message:
-----------
r1296@zaphodb: ford | 2007-10-30 00:51:10 +0100
- Added unit parsing to OscLoader (from Columntitles with [unit]-tags).
- Sanitized minimum finder.
- Improved height-map generation.
Modified Paths:
--------------
trunk/src/workers/OSC/OSC/OscLoader.py
Property Changed:
----------------
trunk/
Property changes on: trunk
___________________________________________________________________
Name: svk:merge
- 3321fe91-ea1f-0410-9b6b-81c2d13ccd49:/branches/PyTablesHack:135
6f7b97d4-f842-44fd-9373-9f8d51b2dfcf:/local/pyphant/sourceforge:2719
8bf637c1-38a7-4b57-b48d-fce0f21498c5:/local/pyphant:1294
bece090c-e03b-4a9e-a238-bce0435dd73a:/local/pyphant:409
e121922d-4398-4060-8276-e26c71b599e4:/local/pyphant/sourceforge:367
ffafd7c2-a18e-42a0-a535-81fd4436fb1c:/local/pyphant/sourceforge/trunk:3267
+ 3321fe91-ea1f-0410-9b6b-81c2d13ccd49:/branches/PyTablesHack:135
6f7b97d4-f842-44fd-9373-9f8d51b2dfcf:/local/pyphant/sourceforge:2719
8bf637c1-38a7-4b57-b48d-fce0f21498c5:/local/pyphant:1296
bece090c-e03b-4a9e-a238-bce0435dd73a:/local/pyphant:409
e121922d-4398-4060-8276-e26c71b599e4:/local/pyphant/sourceforge:367
ffafd7c2-a18e-42a0-a535-81fd4436fb1c:/local/pyphant/sourceforge/trunk:3267
Modified: trunk/src/workers/OSC/OSC/OscLoader.py
===================================================================
--- trunk/src/workers/OSC/OSC/OscLoader.py 2007-10-27 20:50:39 UTC (rev 141)
+++ trunk/src/workers/OSC/OSC/OscLoader.py 2007-10-29 23:53:15 UTC (rev 142)
@@ -37,7 +37,7 @@
__version__ = "$Revision$"
# $Source$
-import zipfile, numpy, copy
+import zipfile, numpy, copy, re
from pyphant.core import (Worker, Connectors,
Param, DataContainer)
@@ -69,6 +69,13 @@
u'MESSDATEN': addTableLine }
def loadOscFromFile(filename, subscriber=0):
+ def longname2unit(name):
+ reg = re.compile(r"\[([^]]*)\]")
+ m = reg.search(name)
+ if not m or m.group(1)=="counts":
+ return 1.0
+ else:
+ return PhysicalQuantities.PhysicalQuantity('1 '+str(m.group(1)))
z = zipfile.ZipFile(filename, 'r')
data = []
names = z.namelist()
@@ -85,7 +92,7 @@
col = "SPALTE%i" % i
container[d[u'SPALTENBESCHRIFTUNG'][col]].append(d[u'MESSDATEN'][:,i-1])
container[u'WhiteRef[counts]'].append(d[u'MESSDATEN'][:,4])
- cols = [DataContainer.FieldContainer(numpy.array(v), longname=k) for k,v in container.iteritems()]
+ cols = [DataContainer.FieldContainer(numpy.array(v), unit=longname2unit(k), longname=k) for k,v in container.iteritems()]
return DataContainer.SampleContainer(cols)
@@ -203,26 +210,26 @@
count = len(lam.data)
for i in xrange(count):
l = lam.data[i][lower:upper]
+ ls.append(l)
a = Abso.data[i][lower:upper]
tck = scipy.interpolate.splrep(l, a, s=len(l)-numpy.sqrt(2*len(l)))
a = scipy.interpolate.splev(l, tck, 0)
- #d1 = scipy.interpolate.splev(l, tck, 1)
- d2 = scipy.interpolate.splev(l, tck, 2)
- #j = numpy.abs(d1).argmin()
- j = a.argmin()
- if d2[j]>0:
- mins.append(l[j])
- hs.append(l[j]*float(self.paramA.value)/10000.0+float(self.paramB.value)/10000.0)
+ as.append(a)
+ imin = a.argmin()
+ if imin>0 and imin<len(l)-1:
+ mins.append(l[imin])
+ hs.append(l[imin]*float(self.paramA.value)/10000.0+float(self.paramB.value)/10000.0)
else:
mins.append(0)
hs.append(0)
- as.append(a)
- ls.append(l)
subscriber %= float(i)*100.0/float(count)
- data[u'Absorption'] = DataContainer.FieldContainer(numpy.array(as), longname='Absorption', shortname='A')
- data[u'Wellenlänge[nm]'] = DataContainer.FieldContainer(numpy.array(ls), longname=lam.longname, shortname=lam.shortname)
- data[u'Minima'] = DataContainer.FieldContainer(numpy.array(mins), longname=u'Minima', shortname='m')
- data[u'Höhe'] = DataContainer.FieldContainer(numpy.array(hs), unit=PhysicalQuantities.PhysicalQuantity('1 nm'), longname=u'Höhe', shortname='h')
+ data[u'Absorption'] = DataContainer.FieldContainer(numpy.array(as), longname=u'Absorption', shortname=u'A')
+ data[u'Wellenlänge[nm]'] = DataContainer.FieldContainer(numpy.array(ls), unit=lam.unit,
+ longname=lam.longname, shortname=lam.shortname)
+ data[u'Minima'] = DataContainer.FieldContainer(numpy.array(mins), unit=lam.unit,
+ longname=u'Minima', shortname='m')
+ data[u'Höhe'] = DataContainer.FieldContainer(numpy.array(hs), unit=lam.unit,
+ longname=u'Höhe', shortname='h')
result = DataContainer.SampleContainer(data.values(), longname='Osc data', shortname='O')
result.seal()
return result
@@ -238,7 +245,7 @@
@Worker.plug(Connectors.TYPE_IMAGE)
def mapHeights(self, osc, subscriber=0):
- d = 4
+ d = 9
data = osc.recreateFieldContainers()
xf = numpy.array(data[u'TISCH_POS_X'].data, dtype='float')
yf = numpy.array(data[u'TISCH_POS_Y'].data, dtype='float')
@@ -248,9 +255,10 @@
y = y-y.min()
h = data[u'Höhe'].data
m = h[h>0].min()
- img = numpy.ones((y.max(), x.max()))*m
+ img = numpy.ones((y.max()+d, x.max()+d))*m
for i in xrange(len(x)):
- img[y[i]-d:y[i]+d,x[i]-d:x[i]+d]=max(h[i], m)
+ #img[y[i]-d:y[i]+d,x[i]-d:x[i]+d]=max(h[i], m)
+ img[y[i]:y[i]+d,x[i]:x[i]+d]=max(h[i], m)
xdim = DataContainer.FieldContainer(xf, PhysicalQuantities.PhysicalQuantity('1 mm'), longname=u'x-Axis', shortname="x")
ydim = DataContainer.FieldContainer(yf, PhysicalQuantities.PhysicalQuantity('1 mm'), longname=u'y-Axis', shortname="y")
result = DataContainer.FieldContainer(img, PhysicalQuantities.PhysicalQuantity('1 nm'), dimensions=[xdim, ydim], longname='Osc Heightmap', shortname='h')
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|
|
From: <zk...@us...> - 2007-10-27 20:50:40
|
Revision: 141
http://pyphant.svn.sourceforge.net/pyphant/?rev=141&view=rev
Author: zklaus
Date: 2007-10-27 13:50:39 -0700 (Sat, 27 Oct 2007)
Log Message:
-----------
r1294@zaphodb: ford | 2007-10-27 22:35:17 +0200
- Modified the minimum finder algorithm.
Modified Paths:
--------------
trunk/src/workers/OSC/OSC/OscLoader.py
Property Changed:
----------------
trunk/
Property changes on: trunk
___________________________________________________________________
Name: svk:merge
- 3321fe91-ea1f-0410-9b6b-81c2d13ccd49:/branches/PyTablesHack:135
6f7b97d4-f842-44fd-9373-9f8d51b2dfcf:/local/pyphant/sourceforge:2719
8bf637c1-38a7-4b57-b48d-fce0f21498c5:/local/pyphant:1291
bece090c-e03b-4a9e-a238-bce0435dd73a:/local/pyphant:409
e121922d-4398-4060-8276-e26c71b599e4:/local/pyphant/sourceforge:367
ffafd7c2-a18e-42a0-a535-81fd4436fb1c:/local/pyphant/sourceforge/trunk:3267
+ 3321fe91-ea1f-0410-9b6b-81c2d13ccd49:/branches/PyTablesHack:135
6f7b97d4-f842-44fd-9373-9f8d51b2dfcf:/local/pyphant/sourceforge:2719
8bf637c1-38a7-4b57-b48d-fce0f21498c5:/local/pyphant:1294
bece090c-e03b-4a9e-a238-bce0435dd73a:/local/pyphant:409
e121922d-4398-4060-8276-e26c71b599e4:/local/pyphant/sourceforge:367
ffafd7c2-a18e-42a0-a535-81fd4436fb1c:/local/pyphant/sourceforge/trunk:3267
Modified: trunk/src/workers/OSC/OSC/OscLoader.py
===================================================================
--- trunk/src/workers/OSC/OSC/OscLoader.py 2007-10-24 23:48:42 UTC (rev 140)
+++ trunk/src/workers/OSC/OSC/OscLoader.py 2007-10-27 20:50:39 UTC (rev 141)
@@ -206,9 +206,10 @@
a = Abso.data[i][lower:upper]
tck = scipy.interpolate.splrep(l, a, s=len(l)-numpy.sqrt(2*len(l)))
a = scipy.interpolate.splev(l, tck, 0)
- d1 = scipy.interpolate.splev(l, tck, 1)
+ #d1 = scipy.interpolate.splev(l, tck, 1)
d2 = scipy.interpolate.splev(l, tck, 2)
- j = numpy.abs(d1).argmin()
+ #j = numpy.abs(d1).argmin()
+ j = a.argmin()
if d2[j]>0:
mins.append(l[j])
hs.append(l[j]*float(self.paramA.value)/10000.0+float(self.paramB.value)/10000.0)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <zk...@us...> - 2007-10-24 23:48:38
|
Revision: 140
http://pyphant.svn.sourceforge.net/pyphant/?rev=140&view=rev
Author: zklaus
Date: 2007-10-24 16:48:42 -0700 (Wed, 24 Oct 2007)
Log Message:
-----------
r1291@zaphodb: ford | 2007-10-25 01:45:37 +0200
- Removed pysvn code completely from setup.py. This is another dependency with very little gain, especially in the light of setuptools subversion capabilities.
Modified Paths:
--------------
trunk/src/pyphant/setup.py
Property Changed:
----------------
trunk/
Property changes on: trunk
___________________________________________________________________
Name: svk:merge
- 3321fe91-ea1f-0410-9b6b-81c2d13ccd49:/branches/PyTablesHack:135
6f7b97d4-f842-44fd-9373-9f8d51b2dfcf:/local/pyphant/sourceforge:2719
8bf637c1-38a7-4b57-b48d-fce0f21498c5:/local/pyphant:1290
bece090c-e03b-4a9e-a238-bce0435dd73a:/local/pyphant:409
e121922d-4398-4060-8276-e26c71b599e4:/local/pyphant/sourceforge:367
ffafd7c2-a18e-42a0-a535-81fd4436fb1c:/local/pyphant/sourceforge/trunk:3267
+ 3321fe91-ea1f-0410-9b6b-81c2d13ccd49:/branches/PyTablesHack:135
6f7b97d4-f842-44fd-9373-9f8d51b2dfcf:/local/pyphant/sourceforge:2719
8bf637c1-38a7-4b57-b48d-fce0f21498c5:/local/pyphant:1291
bece090c-e03b-4a9e-a238-bce0435dd73a:/local/pyphant:409
e121922d-4398-4060-8276-e26c71b599e4:/local/pyphant/sourceforge:367
ffafd7c2-a18e-42a0-a535-81fd4436fb1c:/local/pyphant/sourceforge/trunk:3267
Modified: trunk/src/pyphant/setup.py
===================================================================
--- trunk/src/pyphant/setup.py 2007-10-24 23:48:29 UTC (rev 139)
+++ trunk/src/pyphant/setup.py 2007-10-24 23:48:42 UTC (rev 140)
@@ -8,13 +8,7 @@
from setuptools import setup, find_packages
-try:
- import pysvn
- client = pysvn.Client()
- head_rev = client.update('.')
- version='%s-%s'%(VERSION, head_rev[0].number)
-except:
- version='%s-%s'%(VERSION, __revision__[11:-2])
+version='%s-%s'%(VERSION, __revision__[11:-2])
setup( name='Pyphant',
version = version,
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <zk...@us...> - 2007-10-24 23:48:26
|
Revision: 139
http://pyphant.svn.sourceforge.net/pyphant/?rev=139&view=rev
Author: zklaus
Date: 2007-10-24 16:48:29 -0700 (Wed, 24 Oct 2007)
Log Message:
-----------
r1290@zaphodb: ford | 2007-10-25 01:44:16 +0200
- Added proper titleing to ImageVisualizer.
- Extended bounds of BoundedIntegerTextField.
- Made pyphants setup.py independent of pysvn
- Fixed various typos in OscLoader.py.
Modified Paths:
--------------
trunk/src/pyphant/pyphant/visualizers/ImageVisualizer.py
trunk/src/pyphant/pyphant/wxgui2/paramvisualization/BoundedIntegerTextField.py
trunk/src/pyphant/setup.py
trunk/src/workers/OSC/OSC/OscLoader.py
Property Changed:
----------------
trunk/
Property changes on: trunk
___________________________________________________________________
Name: svk:merge
- 3321fe91-ea1f-0410-9b6b-81c2d13ccd49:/branches/PyTablesHack:135
6f7b97d4-f842-44fd-9373-9f8d51b2dfcf:/local/pyphant/sourceforge:2719
8bf637c1-38a7-4b57-b48d-fce0f21498c5:/local/pyphant:1286
bece090c-e03b-4a9e-a238-bce0435dd73a:/local/pyphant:409
e121922d-4398-4060-8276-e26c71b599e4:/local/pyphant/sourceforge:367
ffafd7c2-a18e-42a0-a535-81fd4436fb1c:/local/pyphant/sourceforge/trunk:3267
+ 3321fe91-ea1f-0410-9b6b-81c2d13ccd49:/branches/PyTablesHack:135
6f7b97d4-f842-44fd-9373-9f8d51b2dfcf:/local/pyphant/sourceforge:2719
8bf637c1-38a7-4b57-b48d-fce0f21498c5:/local/pyphant:1290
bece090c-e03b-4a9e-a238-bce0435dd73a:/local/pyphant:409
e121922d-4398-4060-8276-e26c71b599e4:/local/pyphant/sourceforge:367
ffafd7c2-a18e-42a0-a535-81fd4436fb1c:/local/pyphant/sourceforge/trunk:3267
Modified: trunk/src/pyphant/pyphant/visualizers/ImageVisualizer.py
===================================================================
--- trunk/src/pyphant/pyphant/visualizers/ImageVisualizer.py 2007-10-24 23:33:16 UTC (rev 138)
+++ trunk/src/pyphant/pyphant/visualizers/ImageVisualizer.py 2007-10-24 23:48:29 UTC (rev 139)
@@ -57,6 +57,7 @@
pylab.imshow(self.fieldContainer.data, extent=(xmin, xmax, ymin, ymax))
pylab.xlabel(self.fieldContainer.dimensions[0].label)
pylab.ylabel(self.fieldContainer.dimensions[1].label)
+ pylab.title(self.fieldContainer.longname)
class F(pylab.Formatter):
def __init__(self, container, *args, **kwargs):
Modified: trunk/src/pyphant/pyphant/wxgui2/paramvisualization/BoundedIntegerTextField.py
===================================================================
--- trunk/src/pyphant/pyphant/wxgui2/paramvisualization/BoundedIntegerTextField.py 2007-10-24 23:33:16 UTC (rev 138)
+++ trunk/src/pyphant/pyphant/wxgui2/paramvisualization/BoundedIntegerTextField.py 2007-10-24 23:48:29 UTC (rev 139)
@@ -41,8 +41,8 @@
class BoundedIntegerTextField(wx.lib.masked.NumCtrl):
def __init__(self, parent, param):
- min=0
- max=5000
+ min = -50000000
+ max = 50000000
if min and min>=0: allowNegative=False
else: allowNegative=True
if min or max: limited=True
Modified: trunk/src/pyphant/setup.py
===================================================================
--- trunk/src/pyphant/setup.py 2007-10-24 23:33:16 UTC (rev 138)
+++ trunk/src/pyphant/setup.py 2007-10-24 23:48:29 UTC (rev 139)
@@ -8,9 +8,9 @@
from setuptools import setup, find_packages
-import pysvn
-client = pysvn.Client()
try:
+ import pysvn
+ client = pysvn.Client()
head_rev = client.update('.')
version='%s-%s'%(VERSION, head_rev[0].number)
except:
Modified: trunk/src/workers/OSC/OSC/OscLoader.py
===================================================================
--- trunk/src/workers/OSC/OSC/OscLoader.py 2007-10-24 23:33:16 UTC (rev 138)
+++ trunk/src/workers/OSC/OSC/OscLoader.py 2007-10-24 23:48:29 UTC (rev 139)
@@ -184,7 +184,9 @@
_sockets = [("osc", Connectors.TYPE_ARRAY)]
_params = [("lower", "Lower Bound", 380, None),
- ("upper", "Upper Bound", 500, None)]
+ ("upper", "Upper Bound", 500, None),
+ ("a", "a", 14000, None),
+ ("b", "b", -4270000, None)]
@Worker.plug(Connectors.TYPE_ARRAY)
def findMinimum(self, osc, subscriber=0):
@@ -209,7 +211,7 @@
j = numpy.abs(d1).argmin()
if d2[j]>0:
mins.append(l[j])
- hs.append(l[j]*1.4-427.0)
+ hs.append(l[j]*float(self.paramA.value)/10000.0+float(self.paramB.value)/10000.0)
else:
mins.append(0)
hs.append(0)
@@ -248,8 +250,8 @@
img = numpy.ones((y.max(), x.max()))*m
for i in xrange(len(x)):
img[y[i]-d:y[i]+d,x[i]-d:x[i]+d]=max(h[i], m)
- xdim = DataContainer.FieldContainer(xf, PhysicalQuantities.PhysicalQuantity('1 cm'), longname=u'x-Axis', shortname="x")
- ydim = DataContainer.FieldContainer(yf, PhysicalQuantities.PhysicalQuantity('1 cm'), longname=u'y-Axis', shortname="y")
+ xdim = DataContainer.FieldContainer(xf, PhysicalQuantities.PhysicalQuantity('1 mm'), longname=u'x-Axis', shortname="x")
+ ydim = DataContainer.FieldContainer(yf, PhysicalQuantities.PhysicalQuantity('1 mm'), longname=u'y-Axis', shortname="y")
result = DataContainer.FieldContainer(img, PhysicalQuantities.PhysicalQuantity('1 nm'), dimensions=[xdim, ydim], longname='Osc Heightmap', shortname='h')
result.seal()
return result
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <zk...@us...> - 2007-10-24 23:33:18
|
Revision: 138
http://pyphant.svn.sourceforge.net/pyphant/?rev=138&view=rev
Author: zklaus
Date: 2007-10-24 16:33:16 -0700 (Wed, 24 Oct 2007)
Log Message:
-----------
r1286@zaphodb: ford | 2007-10-25 01:31:12 +0200
- Added some unicode marker.
Modified Paths:
--------------
trunk/src/workers/OSC/OSC/OscLoader.py
Property Changed:
----------------
trunk/
Property changes on: trunk
___________________________________________________________________
Name: svk:merge
- 3321fe91-ea1f-0410-9b6b-81c2d13ccd49:/branches/PyTablesHack:135
6f7b97d4-f842-44fd-9373-9f8d51b2dfcf:/local/pyphant/sourceforge:2719
8bf637c1-38a7-4b57-b48d-fce0f21498c5:/local/pyphant:429
bece090c-e03b-4a9e-a238-bce0435dd73a:/local/pyphant:409
e121922d-4398-4060-8276-e26c71b599e4:/local/pyphant/sourceforge:367
ffafd7c2-a18e-42a0-a535-81fd4436fb1c:/local/pyphant/sourceforge/trunk:3267
+ 3321fe91-ea1f-0410-9b6b-81c2d13ccd49:/branches/PyTablesHack:135
6f7b97d4-f842-44fd-9373-9f8d51b2dfcf:/local/pyphant/sourceforge:2719
8bf637c1-38a7-4b57-b48d-fce0f21498c5:/local/pyphant:1286
bece090c-e03b-4a9e-a238-bce0435dd73a:/local/pyphant:409
e121922d-4398-4060-8276-e26c71b599e4:/local/pyphant/sourceforge:367
ffafd7c2-a18e-42a0-a535-81fd4436fb1c:/local/pyphant/sourceforge/trunk:3267
Modified: trunk/src/workers/OSC/OSC/OscLoader.py
===================================================================
--- trunk/src/workers/OSC/OSC/OscLoader.py 2007-10-23 14:24:28 UTC (rev 137)
+++ trunk/src/workers/OSC/OSC/OscLoader.py 2007-10-24 23:33:16 UTC (rev 138)
@@ -48,7 +48,7 @@
return {}
def startSection(root, l):
- if l == 'MESSDATEN':
+ if l == u'MESSDATEN':
root[l] = []
else:
root[l] = {}
@@ -62,11 +62,11 @@
ff = l.split('\t')
section.append([float(f) for f in ff])
-LINE_HANDLER = { 'Section': startSection,
- 'GLOBAL': addAttributeLine,
- 'MESSUNG': addAttributeLine,
- 'SPALTENBESCHRIFTUNG': addAttributeLine,
- 'MESSDATEN': addTableLine }
+LINE_HANDLER = { u'Section': startSection,
+ u'GLOBAL': addAttributeLine,
+ u'MESSUNG': addAttributeLine,
+ u'SPALTENBESCHRIFTUNG': addAttributeLine,
+ u'MESSDATEN': addTableLine }
def loadOscFromFile(filename, subscriber=0):
z = zipfile.ZipFile(filename, 'r')
@@ -78,13 +78,13 @@
subscriber %= float(i)/total*100.0
container = constructTemplate(data)
for d in data:
- for dicname in ('GLOBAL','MESSUNG'):
+ for dicname in (u'GLOBAL',u'MESSUNG'):
for k in d[dicname].keys():
container[k].append(d[dicname][k])
for i in xrange(1,5):
col = "SPALTE%i" % i
- container[d['SPALTENBESCHRIFTUNG'][col]].append(d['MESSDATEN'][:,i-1])
- container['WhiteRef[counts]'].append(d['MESSDATEN'][:,4])
+ container[d[u'SPALTENBESCHRIFTUNG'][col]].append(d[u'MESSDATEN'][:,i-1])
+ container[u'WhiteRef[counts]'].append(d[u'MESSDATEN'][:,4])
cols = [DataContainer.FieldContainer(numpy.array(v), longname=k) for k,v in container.iteritems()]
return DataContainer.SampleContainer(cols)
@@ -92,12 +92,12 @@
def constructTemplate(data):
template = data[0]
container = {}
- for k in template['GLOBAL'].keys()+template['MESSUNG'].keys():
+ for k in template[u'GLOBAL'].keys()+template[u'MESSUNG'].keys():
container[k] = []
for i in xrange(1,5):
k = "SPALTE%i" % i
- container[template['SPALTENBESCHRIFTUNG'][k]] = []
- container['WhiteRef[counts]'] = []
+ container[template[u'SPALTENBESCHRIFTUNG'][k]] = []
+ container[u'WhiteRef[counts]'] = []
return container
@@ -110,10 +110,10 @@
secId = 'root'
for l in ll:
if l.startswith('[') and l.endswith(']'):
- section, secId = LINE_HANDLER['Section'](root, l[1:-1])
+ section, secId = LINE_HANDLER[u'Section'](root, l[1:-1])
else:
LINE_HANDLER[secId](section, l)
- root['MESSDATEN'] = numpy.array(root['MESSDATEN'])
+ root[u'MESSDATEN'] = numpy.array(root[u'MESSDATEN'])
return root
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <li...@us...> - 2007-10-23 14:24:28
|
Revision: 137
http://pyphant.svn.sourceforge.net/pyphant/?rev=137&view=rev
Author: liehr
Date: 2007-10-23 07:24:28 -0700 (Tue, 23 Oct 2007)
Log Message:
-----------
r3267@orion: obi | 2007-10-23 16:14:00 +0200
- Added test checking the creation of SampleContainers with string elements (uncomplete).
- Added test checking the creation of a SampleContainer from a single FieldContainer (fails).
Modified Paths:
--------------
trunk/src/pyphant/pyphant/tests/TestDataContainer.py
Property Changed:
----------------
trunk/
Property changes on: trunk
___________________________________________________________________
Name: svk:merge
- 3321fe91-ea1f-0410-9b6b-81c2d13ccd49:/branches/PyTablesHack:135
6f7b97d4-f842-44fd-9373-9f8d51b2dfcf:/local/pyphant/sourceforge:2719
8bf637c1-38a7-4b57-b48d-fce0f21498c5:/local/pyphant:429
bece090c-e03b-4a9e-a238-bce0435dd73a:/local/pyphant:409
e121922d-4398-4060-8276-e26c71b599e4:/local/pyphant/sourceforge:367
ffafd7c2-a18e-42a0-a535-81fd4436fb1c:/local/pyphant/sourceforge/trunk:2958
+ 3321fe91-ea1f-0410-9b6b-81c2d13ccd49:/branches/PyTablesHack:135
6f7b97d4-f842-44fd-9373-9f8d51b2dfcf:/local/pyphant/sourceforge:2719
8bf637c1-38a7-4b57-b48d-fce0f21498c5:/local/pyphant:429
bece090c-e03b-4a9e-a238-bce0435dd73a:/local/pyphant:409
e121922d-4398-4060-8276-e26c71b599e4:/local/pyphant/sourceforge:367
ffafd7c2-a18e-42a0-a535-81fd4436fb1c:/local/pyphant/sourceforge/trunk:3267
Modified: trunk/src/pyphant/pyphant/tests/TestDataContainer.py
===================================================================
--- trunk/src/pyphant/pyphant/tests/TestDataContainer.py 2007-10-23 14:23:45 UTC (rev 136)
+++ trunk/src/pyphant/pyphant/tests/TestDataContainer.py 2007-10-23 14:24:28 UTC (rev 137)
@@ -176,6 +176,21 @@
else:
self.fail("Modification of sealed FieldContainer was not prohibited.")
+ def testSingleSample(self):
+ #string = numpy.rec.fromrecords([(s,) for s in [u'Hello',u'World!',u'Bäh!']])
+# strings =
+ uField = FieldContainer(scipy.array([u'Hello',u'World!',u'Bäh!']),longname=u'Text',shortname='\gamma')
+ table = SampleContainer(uField)
+
+ def testStringSample(self):
+ #string = numpy.rec.fromrecords([(s,) for s in [u'Hello',u'World!',u'Bäh!']])
+# strings =
+ uField = FieldContainer(scipy.array([u'Hello',u'World!',u'Bäh!']),longname=u'Text',shortname='\gamma')
+ sample = SampleContainer([uField])
+ sample.seal()
+ print sample,sample.data
+
+
class TestCreateDType(unittest.TestCase):
def setUp(self):
self.dim = 11
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <li...@us...> - 2007-10-23 14:23:42
|
Revision: 136
http://pyphant.svn.sourceforge.net/pyphant/?rev=136&view=rev
Author: liehr
Date: 2007-10-23 07:23:45 -0700 (Tue, 23 Oct 2007)
Log Message:
-----------
r3235@orion (orig r135): liehr | 2007-10-18 15:40:46 +0200
First attempts to fix the bug.
Modified Paths:
--------------
trunk/src/pyphant/pyphant/core/PyTablesPersister.py
Property Changed:
----------------
trunk/
Property changes on: trunk
___________________________________________________________________
Name: svk:merge
- 6f7b97d4-f842-44fd-9373-9f8d51b2dfcf:/local/pyphant/sourceforge:2719
8bf637c1-38a7-4b57-b48d-fce0f21498c5:/local/pyphant:429
bece090c-e03b-4a9e-a238-bce0435dd73a:/local/pyphant:409
e121922d-4398-4060-8276-e26c71b599e4:/local/pyphant/sourceforge:367
ffafd7c2-a18e-42a0-a535-81fd4436fb1c:/local/pyphant/sourceforge/trunk:2958
+ 3321fe91-ea1f-0410-9b6b-81c2d13ccd49:/branches/PyTablesHack:135
6f7b97d4-f842-44fd-9373-9f8d51b2dfcf:/local/pyphant/sourceforge:2719
8bf637c1-38a7-4b57-b48d-fce0f21498c5:/local/pyphant:429
bece090c-e03b-4a9e-a238-bce0435dd73a:/local/pyphant:409
e121922d-4398-4060-8276-e26c71b599e4:/local/pyphant/sourceforge:367
ffafd7c2-a18e-42a0-a535-81fd4436fb1c:/local/pyphant/sourceforge/trunk:2958
Modified: trunk/src/pyphant/pyphant/core/PyTablesPersister.py
===================================================================
--- trunk/src/pyphant/pyphant/core/PyTablesPersister.py 2007-10-18 13:40:46 UTC (rev 135)
+++ trunk/src/pyphant/pyphant/core/PyTablesPersister.py 2007-10-23 14:23:45 UTC (rev 136)
@@ -138,16 +138,23 @@
return resId
def saveSample(h5, resultGroup, result):
- desc=buildDescription(result.desc)
+ desc = result.desc
+ descDict = {}
+ for name in desc.names:
+ origDType = desc.fields[name][0]
+ if origDType.char == 'U':
+ strings = result.data[name].tolist()
+ utfLen = [len(string.encode('utf-8')) for string in strings]
+ maxLen = max(utfLen)
+ descDict["col_"+name.encode("utf-8")]=StringCol(maxLen)
+
+ else:
+ descDict["col_"+name.encode("utf-8")]=Col.from_dtype(desc.fields[name][0])#Col(dtype=descStr.capitalize())
+ desc = descDict
dataTable = h5.createTable(resultGroup, "data", desc, result.longname.encode("utf-8"))
keys = [key[4:] for key in desc.keys()]
- data=scipy.transpose(scipy.array([result.data[key].tolist() for key in keys]))
header=[key.encode("utf-8") for key in keys]
- for line in data:
- row=dataTable.row
- for i, key in enumerate(header):
- row["col_"+key]=line[i]
- row.append()
+ dataTable.append(result.data)
dataTable.flush()
h5.setNodeAttr(resultGroup, "desc", result.desc)
units = [repr(unit).encode("utf-8") for unit in result.units]
@@ -165,14 +172,6 @@
u.append()
unitsTable.flush()
-def buildDescription(desc):
- descDict = {}
- for name in desc.names:
- descStr = str(desc.fields[name][0])
- print desc.fields[name], ";",descStr
- descDict["col_"+name.encode("utf-8")]=Col.from_dtype(desc.fields[name][0])#Col(dtype=descStr.capitalize())
- return descDict
-
def saveField(h5, resultGroup, result):
h5.createArray(resultGroup, "data", result.data, result.longname.encode("utf-8"))
if result.error:
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|
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From: <li...@us...> - 2007-10-18 13:40:41
|
Revision: 135
http://pyphant.svn.sourceforge.net/pyphant/?rev=135&view=rev
Author: liehr
Date: 2007-10-18 06:40:46 -0700 (Thu, 18 Oct 2007)
Log Message:
-----------
First attempts to fix the bug.
Modified Paths:
--------------
branches/PyTablesHack/src/pyphant/pyphant/core/PyTablesPersister.py
Modified: branches/PyTablesHack/src/pyphant/pyphant/core/PyTablesPersister.py
===================================================================
--- branches/PyTablesHack/src/pyphant/pyphant/core/PyTablesPersister.py 2007-10-18 13:39:01 UTC (rev 134)
+++ branches/PyTablesHack/src/pyphant/pyphant/core/PyTablesPersister.py 2007-10-18 13:40:46 UTC (rev 135)
@@ -138,16 +138,23 @@
return resId
def saveSample(h5, resultGroup, result):
- desc=buildDescription(result.desc)
+ desc = result.desc
+ descDict = {}
+ for name in desc.names:
+ origDType = desc.fields[name][0]
+ if origDType.char == 'U':
+ strings = result.data[name].tolist()
+ utfLen = [len(string.encode('utf-8')) for string in strings]
+ maxLen = max(utfLen)
+ descDict["col_"+name.encode("utf-8")]=StringCol(maxLen)
+
+ else:
+ descDict["col_"+name.encode("utf-8")]=Col.from_dtype(desc.fields[name][0])#Col(dtype=descStr.capitalize())
+ desc = descDict
dataTable = h5.createTable(resultGroup, "data", desc, result.longname.encode("utf-8"))
keys = [key[4:] for key in desc.keys()]
- data=scipy.transpose(scipy.array([result.data[key].tolist() for key in keys]))
header=[key.encode("utf-8") for key in keys]
- for line in data:
- row=dataTable.row
- for i, key in enumerate(header):
- row["col_"+key]=line[i]
- row.append()
+ dataTable.append(result.data)
dataTable.flush()
h5.setNodeAttr(resultGroup, "desc", result.desc)
units = [repr(unit).encode("utf-8") for unit in result.units]
@@ -165,14 +172,6 @@
u.append()
unitsTable.flush()
-def buildDescription(desc):
- descDict = {}
- for name in desc.names:
- descStr = str(desc.fields[name][0])
- print desc.fields[name], ";",descStr
- descDict["col_"+name.encode("utf-8")]=Col.from_dtype(desc.fields[name][0])#Col(dtype=descStr.capitalize())
- return descDict
-
def saveField(h5, resultGroup, result):
h5.createArray(resultGroup, "data", result.data, result.longname.encode("utf-8"))
if result.error:
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|
From: <li...@us...> - 2007-10-18 13:38:57
|
Revision: 134
http://pyphant.svn.sourceforge.net/pyphant/?rev=134&view=rev
Author: liehr
Date: 2007-10-18 06:39:01 -0700 (Thu, 18 Oct 2007)
Log Message:
-----------
On-going bug fixes for saving of complex recarrays.
Added Paths:
-----------
branches/PyTablesHack/
Copied: branches/PyTablesHack (from rev 133, trunk)
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|
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From: <zk...@us...> - 2007-10-12 10:15:04
|
Revision: 133
http://pyphant.svn.sourceforge.net/pyphant/?rev=133&view=rev
Author: zklaus
Date: 2007-10-12 03:14:50 -0700 (Fri, 12 Oct 2007)
Log Message:
-----------
r429@localhost: ford | 2007-10-12 11:46:18 +0200
- Moved createDType in DataContainer.py to a more reasonable place.
- Added various OscWorkers in OscLoader.py, all in all allowing for the creation of heightmaps from osc data.
- Modified SampleContainer and ChartVisualiser to better cope with sample like data.
Modified Paths:
--------------
trunk/src/pyphant/pyphant/core/DataContainer.py
trunk/src/pyphant/pyphant/visualizers/Chart.py
trunk/src/workers/OSC/OSC/OscLoader.py
Property Changed:
----------------
trunk/
Property changes on: trunk
___________________________________________________________________
Name: svk:merge
- 6f7b97d4-f842-44fd-9373-9f8d51b2dfcf:/local/pyphant/sourceforge:2719
8bf637c1-38a7-4b57-b48d-fce0f21498c5:/local/pyphant:411
bece090c-e03b-4a9e-a238-bce0435dd73a:/local/pyphant:409
e121922d-4398-4060-8276-e26c71b599e4:/local/pyphant/sourceforge:367
ffafd7c2-a18e-42a0-a535-81fd4436fb1c:/local/pyphant/sourceforge/trunk:2958
+ 6f7b97d4-f842-44fd-9373-9f8d51b2dfcf:/local/pyphant/sourceforge:2719
8bf637c1-38a7-4b57-b48d-fce0f21498c5:/local/pyphant:429
bece090c-e03b-4a9e-a238-bce0435dd73a:/local/pyphant:409
e121922d-4398-4060-8276-e26c71b599e4:/local/pyphant/sourceforge:367
ffafd7c2-a18e-42a0-a535-81fd4436fb1c:/local/pyphant/sourceforge/trunk:2958
Modified: trunk/src/pyphant/pyphant/core/DataContainer.py
===================================================================
--- trunk/src/pyphant/pyphant/core/DataContainer.py 2007-10-08 17:31:17 UTC (rev 132)
+++ trunk/src/pyphant/pyphant/core/DataContainer.py 2007-10-12 10:14:50 UTC (rev 133)
@@ -104,33 +104,6 @@
resUri = urlparse.urlsplit(id)
return resUri[2].split('/')[-1].split('.') #(hash, uriType)
-def createDType(columns):
- """Returns numpy.dtype object describing the provided list of
- FieldContainers."""
- names = [col.shortname for col in columns]
- formats = [numpy.dtype(str(col.data.shape[1:])+col.data.dtype.str) for col in columns]
- titles = [col.longname for col in columns]
-
- nameList = True
- for listing in [names,titles]:
- for topic in listing:
- N = listing.count(topic)
- if N > 1:
- for j in xrange(N):
- pos = listing.index(topic)
- if nameList:
- listing[pos] += str(j)
- else:
- listing[pos] += names[j].capitalize()
- nameList = False
-
- #Workaround for numpy ticket 485
- if numpy.__version__ == '1.0.1':
- result = scipy.dtype({'names':names, 'formats':formats})
- else:
- result = scipy.dtype({'names':names, 'formats':formats, 'titles':titles})
- return result
-
class DataContainer(object):
u"""DataContainer \t- A Pyphant base class for self-explanatory scientific data
\nDataContainer presents the following attributes:
@@ -303,6 +276,34 @@
return not self.__eq__(other)
+def createDType(columns):
+ """Returns numpy.dtype object describing the provided list of
+ FieldContainers."""
+ names = [col.shortname for col in columns]
+ formats = [numpy.dtype(str(col.data.shape[1:])+col.data.dtype.str) for col in columns]
+ titles = [col.longname for col in columns]
+
+ nameList = True
+ for listing in [names,titles]:
+ for topic in listing:
+ N = listing.count(topic)
+ if N > 1:
+ for j in xrange(N):
+ pos = listing.index(topic)
+ if nameList:
+ listing[pos] += str(j)
+ else:
+ listing[pos] += names[j].capitalize()
+ nameList = False
+
+ #Workaround for numpy ticket 485
+ if numpy.__version__ == '1.0.1':
+ result = scipy.dtype({'names':names, 'formats':formats})
+ else:
+ result = scipy.dtype({'names':names, 'formats':formats, 'titles':titles})
+ return result
+
+
class SampleContainer(DataContainer):
u"""SampleContainer(columns, longname='Realizations of random variable', shortname='X')
\t Class of tables storing realizations of random variables as recarray
@@ -329,6 +330,9 @@
self.desc = createDType(columns)
self.data = scipy.rec.fromarrays([col.data for col in columns], self.desc)
self.units= [col.unit for col in columns]
+ self._units = {}
+ for i in xrange(len(self.units)):
+ self._units[self.data.dtype.descr[i][0][1]] = columns[i].unit
def _getLabel(self):
@@ -364,3 +368,13 @@
super(SampleContainer, self).seal(id)
self.lock.release()
+ def recreateFieldContainers(self):
+ fields = [ d[0] for d in self.data.dtype.descr ]
+ containers = {}
+ for field in fields:
+ container = FieldContainer( self.data[field[1]],
+ unit = self._units[field[1]],
+ longname=field[0],
+ shortname=field[1])
+ containers[field[0]]=container
+ return containers
Modified: trunk/src/pyphant/pyphant/visualizers/Chart.py
===================================================================
--- trunk/src/pyphant/pyphant/visualizers/Chart.py 2007-10-08 17:31:17 UTC (rev 132)
+++ trunk/src/pyphant/pyphant/visualizers/Chart.py 2007-10-12 10:14:50 UTC (rev 133)
@@ -39,6 +39,7 @@
import pylab
import pyphant.core.Connectors
+from pyphant.core import DataContainer
from pyphant.wxgui2.DataVisReg import DataVisReg
from Scientific.Physics.PhysicalQuantities import isPhysicalQuantity
@@ -46,16 +47,35 @@
name='General chart'
def __init__(self, dataContainer):
self.dataContainer = dataContainer
+ self.ordinates = []
+ self.abscissae = []
+ self.mins = []
+
+ def addFieldContainer(self, fieldContainer):
+ if not isPhysicalQuantity(fieldContainer.unit):
+ self.ordinates.append(fieldContainer.data*self.dataContainer.unit)
+ else:
+ self.ordinates.append(fieldContainer.data*fieldContainer.unit.value)
+ self.abscissae.append(fieldContainer.dimensions[0].data)
+
def prepare(self):
pylab.figure()
- if not isPhysicalQuantity(self.dataContainer.unit):
- self.ordinate = self.dataContainer.data*self.dataContainer.unit
+ if isinstance(self.dataContainer, DataContainer.FieldContainer):
+ self.addFieldContainer(self.dataContainer)
+ pylab.xlabel(self.dataContainer.dimensions[0].label)
+ pylab.ylabel(self.dataContainer.label)
else:
- self.ordinate = self.dataContainer.data*self.dataContainer.unit.value
- self.abscissa = self.dataContainer.dimensions[0]
- pylab.xlabel(self.abscissa.label)
- pylab.ylabel(self.dataContainer.label)
+ data = self.dataContainer.recreateFieldContainers()
+ lam = data[u'Wellenlänge[nm]']
+ abso = data[u'Absorption']
+ mins = data[u'Minima']
+ for i in xrange(len(lam.data)):
+ self.ordinates.append(abso.data[i])
+ self.abscissae.append(lam.data[i])
+ self.mins.append(mins.data[i])
+ pylab.xlabel(lam.label)
+ pylab.ylabel(abso.label)
def finalize(self):
pylab.ion()
@@ -69,10 +89,11 @@
self.prepare()
# xerr and yerr added due to error in matplotlib 0.87.4
self.error = pylab.zeros(len(self.abscissa.data))
- pylab.bar(self.abscissa.data,self.ordinate,
- xerr = self.error,yerr = self.error,
- capsize=0,
- width=pylab.min(pylab.diff(self.abscissa.data)))
+ for i in xrange(len(self.ordinates)):
+ pylab.bar(self.abscissae[i],self.ordinates[i],
+ xerr = self.error,yerr = self.error,
+ capsize=0,
+ width=pylab.min(pylab.diff(self.abscissae[i])))
self.finalize()
@@ -81,7 +102,10 @@
def __init__(self, dataContainer):
Chart.__init__(self, dataContainer)
self.prepare()
- pylab.plot(self.abscissa.data,self.ordinate)
+ for i in xrange(len(self.ordinates)):
+ pylab.plot(self.abscissae[i],self.ordinates[i])
+ for i in xrange(len(self.mins)):
+ pylab.axvline(self.mins[i])
self.finalize()
Modified: trunk/src/workers/OSC/OSC/OscLoader.py
===================================================================
--- trunk/src/workers/OSC/OSC/OscLoader.py 2007-10-08 17:31:17 UTC (rev 132)
+++ trunk/src/workers/OSC/OSC/OscLoader.py 2007-10-12 10:14:50 UTC (rev 133)
@@ -41,6 +41,8 @@
from pyphant.core import (Worker, Connectors,
Param, DataContainer)
+import scipy.interpolate
+from Scientific.Physics import PhysicalQuantities
def makeRoot(pixelName, ll):
return {}
@@ -136,25 +138,118 @@
name = "Osc Absorption Calculator"
_sockets = [("osc", Connectors.TYPE_ARRAY)]
+ _params = [("clipping", "Clipping", 1, None)]
@Worker.plug(Connectors.TYPE_ARRAY)
def calcAbsorption(self, osc, subscriber=0):
- #resArr = copy.deepcopy(osc.data)
- resArr = osc.data
- I = resArr[u'ScopRaw[counts]']
- print I.shape
- #del resArr[u'ScopRaw[counts]'][0]
- I_d = resArr[u'DarkRef[counts]']
- #del resArr[u'DarkRef[counts]'][0]
- I_0 = resArr[u'WhiteRef[counts]']
- #del resArr[u'WhiteRef[counts]'][0]
- c = resArr[u'Unkorrigierte Reflexion[counts]']
- #del resArr[u'Unkorrigierte Reflexion[counts]'][0]
- l = resArr[u'Wellenlänge[nm]']
- #del resArr[u'Wellenlänge[nm]'][0]
- A = -((I-I_d)/(I_0-I_d)-1)
- lam = DataContainer.FieldContainer(l, 'nm', longname=u'Wellenlänge', shortname=u'\\lambda')
- result = DataContainer.FieldContainer(A[20], dimensions=[lam], longname='Absorption', shortname='A')
+ cont = osc.recreateFieldContainers()
+ I = cont[u'ScopRaw[counts]']
+ I_d = cont[u'DarkRef[counts]']
+ I_0 = cont[u'WhiteRef[counts]']
+ A = -((I.data-I_d.data)/(I_0.data-I_d.data)-1)
+ if self.paramClipping.value==1:
+ A[A>1] = 0
+ A[A<0] = 0
+ Abso = DataContainer.FieldContainer(A, longname='Absorption', shortname='A')
+ result = DataContainer.SampleContainer(cont.values()+[Abso], longname='Osc data', shortname='O')
result.seal()
return result
+
+class OscAbsorptionExtractor(Worker.Worker):
+ API = 2
+ VERSION = 1
+ REVISION = "$Revision$"[11:-1]
+ name = "Osc Absorption Spectrum"
+
+ _sockets = [("osc", Connectors.TYPE_ARRAY)]
+ _params = [("index", "Index", 1, None)]
+
+ @Worker.plug(Connectors.TYPE_ARRAY)
+ def extractSpec(self, osc, subscriber=0):
+ data = osc.recreateFieldContainers()
+ a = data[u'Absorption']
+ l = data[u'Wellenlänge[nm]']
+ lam = DataContainer.FieldContainer(l.data[self.paramIndex.value], l.unit, l.error, l.dimensions, l.longname, l.shortname)
+ Abso = DataContainer.FieldContainer(a.data[self.paramIndex.value], a.unit, a.error, [lam], a.longname, l.shortname)
+ Abso.seal()
+ return Abso
+
+
+class OscMinimumFinder(Worker.Worker):
+ API = 2
+ VERSION = 1
+ REVISION = "$Revision$"[11:-1]
+ name = "Minimum finder"
+
+ _sockets = [("osc", Connectors.TYPE_ARRAY)]
+ _params = [("lower", "Lower Bound", 380, None),
+ ("upper", "Upper Bound", 500, None)]
+
+ @Worker.plug(Connectors.TYPE_ARRAY)
+ def findMinimum(self, osc, subscriber=0):
+ data = osc.recreateFieldContainers()
+ Abso = data[u'Absorption']
+ lam = data[u'Wellenlänge[nm]']
+ as = []
+ ls = []
+ mins = []
+ l = lam.data[0]
+ hs = []
+ lower = numpy.argwhere(l>self.paramLower.value)[0][0]
+ upper = numpy.argwhere(l<self.paramUpper.value)[-1][0]
+ count = len(lam.data)
+ for i in xrange(count):
+ l = lam.data[i][lower:upper]
+ a = Abso.data[i][lower:upper]
+ tck = scipy.interpolate.splrep(l, a, s=len(l)-numpy.sqrt(2*len(l)))
+ a = scipy.interpolate.splev(l, tck, 0)
+ d1 = scipy.interpolate.splev(l, tck, 1)
+ d2 = scipy.interpolate.splev(l, tck, 2)
+ j = numpy.abs(d1).argmin()
+ if d2[j]>0:
+ mins.append(l[j])
+ hs.append(l[j]*1.4-427.0)
+ else:
+ mins.append(0)
+ hs.append(0)
+ as.append(a)
+ ls.append(l)
+ subscriber %= float(i)*100.0/float(count)
+ data[u'Absorption'] = DataContainer.FieldContainer(numpy.array(as), longname='Absorption', shortname='A')
+ data[u'Wellenlänge[nm]'] = DataContainer.FieldContainer(numpy.array(ls), longname=lam.longname, shortname=lam.shortname)
+ data[u'Minima'] = DataContainer.FieldContainer(numpy.array(mins), longname=u'Minima', shortname='m')
+ data[u'Höhe'] = DataContainer.FieldContainer(numpy.array(hs), unit=PhysicalQuantities.PhysicalQuantity('1 nm'), longname=u'Höhe', shortname='h')
+ result = DataContainer.SampleContainer(data.values(), longname='Osc data', shortname='O')
+ result.seal()
+ return result
+
+
+class OscMapper(Worker.Worker):
+ API = 2
+ VERSION = 1
+ REVISION = "$Revision$"[11:-1]
+ name = "Osc Mapper"
+
+ _sockets = [("osc", Connectors.TYPE_ARRAY)]
+
+ @Worker.plug(Connectors.TYPE_IMAGE)
+ def mapHeights(self, osc, subscriber=0):
+ d = 4
+ data = osc.recreateFieldContainers()
+ xf = numpy.array(data[u'TISCH_POS_X'].data, dtype='float')
+ yf = numpy.array(data[u'TISCH_POS_Y'].data, dtype='float')
+ x = (xf*10).astype('int')
+ y = (yf*10).astype('int')
+ x = x-x.min()
+ y = y-y.min()
+ h = data[u'Höhe'].data
+ m = h[h>0].min()
+ img = numpy.ones((y.max(), x.max()))*m
+ for i in xrange(len(x)):
+ img[y[i]-d:y[i]+d,x[i]-d:x[i]+d]=max(h[i], m)
+ xdim = DataContainer.FieldContainer(xf, PhysicalQuantities.PhysicalQuantity('1 cm'), longname=u'x-Axis', shortname="x")
+ ydim = DataContainer.FieldContainer(yf, PhysicalQuantities.PhysicalQuantity('1 cm'), longname=u'y-Axis', shortname="y")
+ result = DataContainer.FieldContainer(img, PhysicalQuantities.PhysicalQuantity('1 nm'), dimensions=[xdim, ydim], longname='Osc Heightmap', shortname='h')
+ result.seal()
+ return result
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|
|
From: <zk...@us...> - 2007-10-08 17:31:13
|
Revision: 132
http://pyphant.svn.sourceforge.net/pyphant/?rev=132&view=rev
Author: zklaus
Date: 2007-10-08 10:31:17 -0700 (Mon, 08 Oct 2007)
Log Message:
-----------
r409@charon: zklaus | 2007-10-08 19:31:01 +0200
- Removed old debug code.
Modified Paths:
--------------
trunk/src/pyphant/pyphant/core/CompositeWorker.py
Property Changed:
----------------
trunk/
Property changes on: trunk
___________________________________________________________________
Name: svk:merge
- 6f7b97d4-f842-44fd-9373-9f8d51b2dfcf:/local/pyphant/sourceforge:2719
8bf637c1-38a7-4b57-b48d-fce0f21498c5:/local/pyphant:411
e121922d-4398-4060-8276-e26c71b599e4:/local/pyphant/sourceforge:367
ffafd7c2-a18e-42a0-a535-81fd4436fb1c:/local/pyphant/sourceforge/trunk:2958
+ 6f7b97d4-f842-44fd-9373-9f8d51b2dfcf:/local/pyphant/sourceforge:2719
8bf637c1-38a7-4b57-b48d-fce0f21498c5:/local/pyphant:411
bece090c-e03b-4a9e-a238-bce0435dd73a:/local/pyphant:409
e121922d-4398-4060-8276-e26c71b599e4:/local/pyphant/sourceforge:367
ffafd7c2-a18e-42a0-a535-81fd4436fb1c:/local/pyphant/sourceforge/trunk:2958
Modified: trunk/src/pyphant/pyphant/core/CompositeWorker.py
===================================================================
--- trunk/src/pyphant/pyphant/core/CompositeWorker.py 2007-10-01 08:01:50 UTC (rev 131)
+++ trunk/src/pyphant/pyphant/core/CompositeWorker.py 2007-10-08 17:31:17 UTC (rev 132)
@@ -40,9 +40,6 @@
from pyphant.core import EventDispatcher, Worker, Connectors
import copy, pkg_resources
-pkg_resources.require('Pyphant_ImageProcessing')
-import ImageProcessing.ThresholdingWorker
-
class CompositeWorkerChangedEvent(object):
def __init__(self, worker, message, data=None):
self.worker = worker
@@ -81,13 +78,6 @@
_params = [("noSockets", "Number of sockets", 1, None),
("noPlugs", "Number of plugs", 1, None)]
-# def __init__(self, parent=None, annotations={}):
-# Worker.Worker.__init__(self, parent, annotations)
-# th = ImageProcessing.ThresholdingWorker.ThresholdingWorker()
-# self.addWorker(th)
-# (th.getSockets()[0]).insert(self.socketSocket0)
-# self.plugPlug0.insert(th.getPlugs()[0])
-
def inithook(self):
self._workers = []
self._sources = []
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