/usr/lib/python2.7/dist-packages/PyMca/XMCDWindow.py is in pymca 4.7.4+dfsg-1build1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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#/*##########################################################################
# Copyright (C) 2004-2013 European Synchrotron Radiation Facility
#
# This file is part of the PyMca X-ray Fluorescence Toolkit developed at
# the ESRF by the Software group.
#
# This toolkit is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the Free
# Software Foundation; either version 2 of the License, or (at your option)
# any later version.
#
# PyMca is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
# details.
#
# You should have received a copy of the GNU General Public License along with
# PyMca; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#
# PyMca follows the dual licensing model of Riverbank's PyQt and cannot be
# used as a free plugin for a non-free program.
#
# Please contact the ESRF industrial unit (industry@esrf.fr) if this license
# is a problem for you.
#############################################################################*/
__author__ = "T. Rueter - ESRF Data Analysis"
import numpy, copy
from os.path import splitext, basename, dirname, exists, join as pathjoin
from PyMca.PyMca_Icons import IconDict
from PyMca import PyMcaDirs, PyMcaFileDialogs
from PyMca import ConfigDict
from PyMca import PyMcaQt as qt
from PyMca.PyMcaIO import specfilewrapper as specfile
from PyMca import PyMcaDataDir
from PyMca import ScanWindow as sw
if hasattr(qt, "QString"):
QString = qt.QString
QStringList = qt.QStringList
else:
QString = str
QStringList = list
DEBUG = 0
if DEBUG:
numpy.set_printoptions(threshold=50)
NEWLINE = '\n'
class TreeWidgetItem(qt.QTreeWidgetItem):
__legendColumn = 1
def __init__(self, parent, itemList):
qt.QTreeWidgetItem.__init__(self, parent, itemList)
def __lt__(self, other):
col = self.treeWidget().sortColumn()
val = self.text(col)
valOther = other.text(col)
if val == '---':
ret = True
elif col > self.__legendColumn:
try:
ret = (float(val) < float(valOther))
except ValueError:
ret = qt.QTreeWidgetItem.__lt__(self, other)
else:
ret = qt.QTreeWidgetItem.__lt__(self, other)
return ret
class XMCDOptions(qt.QDialog):
def __init__(self, parent, mList, full=True):
qt.QDialog.__init__(self, parent)
self.setWindowTitle('XLD/XMCD Options')
self.setModal(True)
self.motorList = mList
self.saved = False
# Buttons
buttonOK = qt.QPushButton('OK')
buttonOK.setToolTip('Accept the configuration')
buttonCancel = qt.QPushButton('Cancel')
buttonCancel.setToolTip('Return to XMCD Analysis\nwithout changes')
if full:
buttonSave = qt.QPushButton('Save')
buttonSave.setToolTip('Save configuration to *.cfg-File')
buttonLoad = qt.QPushButton('Load')
buttonLoad.setToolTip('Load existing configuration from *.cfg-File')
# OptionLists and ButtonGroups
# GroupBox can be generated from self.getGroupBox
normOpts = ['No &normalization',
'Normalize &after average',
'Normalize &before average']
xrangeOpts = ['&First curve in sequence',
'Active &curve',
'&Use equidistant x-range']
# ButtonGroups
normBG = qt.QButtonGroup(self)
xrangeBG = qt.QButtonGroup(self)
# ComboBoxes
normMeth = qt.QComboBox()
normMeth.addItems(['(y-min(y))/trapz(max(y)-min(y),x)',
'y/max(y)',
'(y-min(y))/(max(y)-min(y))',
'(y-min(y))/sum(max(y)-min(y))'])
normMeth.setEnabled(False)
self.optsDict = {
'normalization' : normBG,
'normalizationMethod' : normMeth,
'xrange' : xrangeBG
}
for idx in range(5):
# key: motor0, motor1, ...
key = 'motor%d'%idx
tmp = qt.QComboBox()
tmp.addItems(mList)
self.optsDict[key] = tmp
# Subdivide into GroupBoxes
normGroupBox = self.getGroupBox('Normalization',
normOpts,
normBG)
xrangeGroupBox = self.getGroupBox('Interpolation x-range',
xrangeOpts,
xrangeBG)
motorGroupBox = qt.QGroupBox('Motors')
# Layouts
mainLayout = qt.QVBoxLayout()
buttonLayout = qt.QHBoxLayout()
normLayout = qt.QHBoxLayout()
motorLayout = qt.QGridLayout()
if full: buttonLayout.addWidget(buttonSave)
buttonLayout.addWidget(buttonLoad)
buttonLayout.addWidget(qt.HorizontalSpacer())
buttonLayout.addWidget(buttonOK)
buttonLayout.addWidget(buttonCancel)
normLayout.addWidget(qt.QLabel('Method:'))
normLayout.addWidget(normMeth)
for idx in range(5):
label = qt.QLabel('Motor %d:'%(idx+1))
cbox = self.optsDict['motor%d'%idx]
motorLayout.addWidget(label,idx,0)
motorLayout.addWidget(cbox,idx,1)
motorGroupBox.setLayout(motorLayout)
normGroupBox.layout().addLayout(normLayout)
mainLayout.addWidget(normGroupBox)
mainLayout.addWidget(xrangeGroupBox)
mainLayout.addWidget(motorGroupBox)
mainLayout.addLayout(buttonLayout)
self.setLayout(mainLayout)
# Connects
if full:
buttonOK.clicked.connect(self.accept)
else:
buttonOK.clicked[()].connect(self.saveOptionsAndClose)
buttonCancel.clicked.connect(self.close)
if full:
buttonSave.clicked[()].connect(self.saveOptions)
buttonLoad.clicked[()].connect(self.loadOptions)
# Keep normalization method selector disabled
# when 'no normalization' selected
normBG.button(0).toggled.connect(normMeth.setDisabled)
def showEvent(self, event):
# Plugin does not destroy Options Window when accepted
# Reset self.saved manually
self.saved = False
qt.QDialog.showEvent(self, event)
def updateMotorList(self, mList):
for (key, obj) in self.optsDict.items():
if key.startswith('motor') and isinstance(obj, qt.QComboBox):
curr = obj.currentText()
obj.clear()
obj.addItems(mList)
idx = obj.findText(curr)
if idx < 0:
obj.setCurrentIndex(idx)
else:
# Motor not found in Motorlist, set to default
obj.setCurrentIndex(idx)
def getGroupBox(self, title, optionList, buttongroup=None):
'''
title : string
optionList : List of strings
buttongroup : qt.QButtonGroup
Returns
-------
GroupBox of QRadioButtons build from a
given optionList. If buttongroup is
specified, the buttons are organized in
a QButtonGroup.
'''
first = True
groupBox = qt.QGroupBox(title, None)
gbLayout = qt.QVBoxLayout(None)
gbLayout.addStretch(1)
for (idx, radioText) in enumerate(optionList):
radio = qt.QRadioButton(radioText)
gbLayout.addWidget(radio)
if buttongroup:
buttongroup.addButton(radio, idx)
if first:
radio.setChecked(True)
first = False
groupBox.setLayout(gbLayout)
return groupBox
def normalizationMethod(self, ident):
ret = None
normDict = {
'toMaximum' : r'y/max(y)',
'offsetAndMaximum': r'(y-min(y))/(max(y)-min(y))',
'offsetAndCounts' : r'(y-min(y))/sum(max(y)-min(y))',
'offsetAndArea' : r'(y-min(y))/trapz(max(y)-min(y),x)'
}
for (name, eq) in normDict.items():
if ident == name:
return eq
if ident == eq:
return name
raise ValueError("'%s' not found.")
def saveOptionsAndClose(self):
if not self.saved:
if not self.saveOptions():
return
self.accept()
def saveOptions(self, filename=None):
saveDir = PyMcaDirs.outputDir
filter = ['PyMca (*.cfg)']
if filename is None:
try:
filename = PyMcaFileDialogs.\
getFileList(parent=self,
filetypelist=filter,
message='Save XLD/XMCD Analysis Configuration',
mode='SAVE',
single=True)[0]
except IndexError:
# Returned list is empty
return
if DEBUG:
print('saveOptions -- Filename: "%s"' % filename)
if len(filename) == 0:
self.saved = False
return False
if not str(filename).endswith('.cfg'):
filename += '.cfg'
confDict = ConfigDict.ConfigDict()
tmp = self.getOptions()
for (key, value) in tmp.items():
if key.startswith('Motor') and len(value) == 0:
tmp[key] = 'None'
confDict['XMCDOptions'] = tmp
try:
confDict.write(filename)
except IOError:
msg = qt.QMessageBox()
msg.setWindowTitle('XLD/XMCD Options Error')
msg.setText('Unable to write configuration to \'%s\''%filename)
msg.exec_()
self.saved = True
return True
def loadOptions(self):
openDir = PyMcaDirs.outputDir
filter = 'PyMca (*.cfg)'
filename = qt.QFileDialog.\
getOpenFileName(self,
'Load XLD/XMCD Analysis Configuration',
openDir,
filter)
confDict = ConfigDict.ConfigDict()
try:
confDict.read(filename)
except IOError:
msg = qt.QMessageBox()
msg.setTitle('XMCD Options Error')
msg.setText('Unable to read configuration file \'%s\''%filename)
return
if 'XMCDOptions'not in confDict:
return
try:
self.setOptions(confDict['XMCDOptions'])
except ValueError as e:
if DEBUG:
print('loadOptions -- int conversion failed:',)
print('Invalid value for option \'%s\'' % e)
else:
msg = qt.QMessageBox()
msg.setWindowTitle('XMCD Options Error')
msg.setText('Configuration file \'%s\' corruted' % filename)
msg.exec_()
return
except KeyError as e:
if DEBUG:
print('loadOptions -- invalid identifier:',)
print('option \'%s\' not found' % e)
else:
msg = qt.QMessageBox()
msg.setWindowTitle('XMCD Options Error')
msg.setText('Configuration file \'%s\' corruted' % filename)
msg.exec_()
return
self.saved = True
def getOptions(self):
ddict = {}
for (option, obj) in self.optsDict.items():
if isinstance(obj, qt.QButtonGroup):
ddict[option] = obj.checkedId()
elif isinstance(obj, qt.QComboBox):
tmp = str(obj.currentText())
if option == 'normalizationMethod':
tmp = self.normalizationMethod(tmp)
if option.startswith('motor') and (not len(tmp)):
tmp = 'None'
ddict[option] = tmp
else:
ddict[option] = 'None'
return ddict
def getMotors(self):
motors = sorted([key for key in self.optsDict.keys()\
if key.startswith('motor')])
return [str(self.optsDict[motor].currentText()) \
for motor in motors]
def setOptions(self, ddict):
for option in ddict.keys():
obj = self.optsDict[option]
if isinstance(obj, qt.QComboBox):
name = ddict[option]
if option == 'normalizationMethod':
name = self.normalizationMethod(name)
if option.startswith('Motor') and name == 'None':
name = ''
idx = obj.findText(QString(name))
obj.setCurrentIndex(idx)
elif isinstance(obj, qt.QButtonGroup):
try:
idx = int(ddict[option])
except ValueError:
raise ValueError(option)
button = self.optsDict[option].button(idx)
if type(button) == type(qt.QRadioButton()):
button.setChecked(True)
class XMCDScanWindow(sw.ScanWindow):
plotModifiedSignal = qt.pyqtSignal()
saveOptionsSignal = qt.pyqtSignal('QString')
def __init__(self,
origin,
parent=None):
'''
Input
-----
origin : ScanWindow instance
Plot window containing the data on which
the analysis is performed
parent : QWidgit instance
'''
sw.ScanWindow.__init__(self,
parent,
name='XLD/XMCD Analysis',
specfit=None)
self.plotWindow = origin
self.scanWindowInfoWidget.hide()
# Buttons to push spectra to main Window
buttonWidget = qt.QWidget()
buttonAdd = qt.QPushButton('Add', self)
buttonAdd.setToolTip('Add active curve to main window')
buttonReplace = qt.QPushButton('Replace', self)
buttonReplace.setToolTip(
'Replace all curves in main window '
+'with active curve in analysis window')
buttonAddAll = qt.QPushButton('Add all', self)
buttonAddAll.setToolTip(
'Add all curves in analysis window '
+'to main window')
buttonReplaceAll = qt.QPushButton('Replace all', self)
buttonReplaceAll.setToolTip(
'Replace all curves in main window '
+'with all curves from analysis window')
self.graphBottomLayout.addWidget(qt.HorizontalSpacer())
self.graphBottomLayout.addWidget(buttonAdd)
self.graphBottomLayout.addWidget(buttonAddAll)
self.graphBottomLayout.addWidget(buttonReplace)
self.graphBottomLayout.addWidget(buttonReplaceAll)
buttonAdd.clicked.connect(self.add)
buttonReplace.clicked.connect(self.replace)
buttonAddAll.clicked.connect(self.addAll)
buttonReplaceAll.clicked.connect(self.replaceAll)
# Copy spectra from origin
self.selectionDict = {'A':[], 'B':[]}
self.curvesDict = {}
self.optsDict = {
'normAfterAvg' : False,
'normBeforeAvg' : False,
'useActive' : False,
'equidistant' : False,
'normalizationMethod' : self.NormOffsetAndArea
}
self.xRange = None
# Keep track of Averages, XMCD and XAS curves by label
self.avgA = None
self.avgB = None
self.xmcd = None
self.xas = None
def processOptions(self, options):
tmp = { 'equidistant': False,
'useActive': False,
'normAfterAvg': False,
'normBeforeAvg': False,
'normalizationMethod': None
}
xRange = options['xrange']
normalization = options['normalization']
normMethod = options['normalizationMethod']
# xRange Options. Default: Use first scan
if xRange == 1:
tmp['useActive'] = True
elif xRange == 2:
tmp['equidistant'] = True
# Normalization Options. Default: No Normalization
if normalization == 1:
tmp['normAfterAvg'] = True
elif normalization == 2:
tmp['normBeforeAvg'] = True
# Normalization Method. Default: offsetAndArea
tmp['normalizationMethod'] = self.setNormalizationMethod(normMethod)
# Trigger reclaculation
self.optsDict = tmp
groupA = self.selectionDict['A']
groupB = self.selectionDict['B']
self.processSelection(groupA, groupB)
def setNormalizationMethod(self, fname):
if fname == 'toMaximum':
func = self.NormToMaximum
elif fname == 'offsetAndMaximum':
func = self.NormToOffsetAndMaximum
elif fname == 'offsetAndCounts':
func = self.NormOffsetAndCounts
else:
func = self.NormOffsetAndArea
return func
def NormToMaximum(self,x,y):
ymax = numpy.max(y)
ynorm = y/ymax
return ynorm
def NormToOffsetAndMaximum(self,x,y):
ynorm = y - numpy.min(y)
ymax = numpy.max(ynorm)
ynorm /= ymax
return ynorm
def NormOffsetAndCounts(self, x, y):
ynorm = y - numpy.min(y)
ymax = numpy.sum(ynorm)
ynorm /= ymax
return ynorm
def NormOffsetAndArea(self, x, y):
ynorm = y - numpy.min(y)
ymax = numpy.trapz(ynorm, x)
ynorm /= ymax
return ynorm
def interpXRange(self,
xRange=None,
equidistant=False,
xRangeList=None):
'''
Input
-----
xRange : ndarray
x-range on which all curves are interpolated
If set to none, the first curve in xRangeList
is used
equidistant : Bool
Determines equidistant xrange on which
all curves are interpolated
xRangeList : List
List of ndarray from which the overlap
is determined. If set to none, self.curvesDict
is used.
Determines the interpolation x-range used for XMCD
Analysis specified by the provided parameters. The
interpolation x-range is limited by the maximal
overlap between the curves present in the plot window.
Returns
-------
out : numpy array
x-range between xmin and xmax containing n points
'''
if not xRangeList:
# Default xRangeList: curvesDict sorted for legends
keys = sorted(self.curvesDict.keys())
xRangeList = [self.curvesDict[k].x[0] for k in keys]
if not len(xRangeList):
if DEBUG:
print('interpXRange -- Nothing to do')
return None
num = 0
xmin, xmax = self.plotWindow.getGraphXLimits()
for x in xRangeList:
if x.min() > xmin:
xmin = x.min()
if x.max() < xmax:
xmax = x.max()
if xmin >= xmax:
raise ValueError('No overlap between curves')
pass
if equidistant:
for x in xRangeList:
curr = numpy.nonzero((x >= xmin) &
(x <= xmax))[0].size
num = curr if curr>num else num
# Exclude first and last point
out = numpy.linspace(xmin, xmax, num, endpoint=False)[1:]
else:
if xRange is not None:
x = xRange
else:
x = xRangeList[0]
# Ensure monotonically increasing x-range
if not numpy.all(numpy.diff(x)>0.):
mask = numpy.nonzero(numpy.diff(x)>0.)[0]
x = numpy.take(x, mask)
# Exclude the endpoints
mask = numpy.nonzero((x > xmin) &
(x < xmax))[0]
out = numpy.sort(numpy.take(x, mask))
if DEBUG:
print('interpXRange -- Resulting xrange:')
print('\tmin = %f' % out.min())
print('\tmax = %f' % out.max())
print('\tnum = %f' % len(out))
return out
def processSelection(self, groupA, groupB):
'''
Input
-----
groupA, groupB : Lists of strings
Contain the legends of curves selected
to Group A resp. B
'''
# Clear analysis window
all = self.getAllCurves(just_legend=True)
self.removeCurves(all)
self.avgB, self.avgA = None, None
self.xas, self.xmcd = None, None
self.selectionDict['A'] = groupA[:]
self.selectionDict['B'] = groupB[:]
self.curvesDict = self.copyCurves(groupA + groupB)
if (len(self.curvesDict) == 0) or\
((len(self.selectionDict['A']) == 0) and\
(len(self.selectionDict['B']) == 0)):
# Nothing to do
return
# Make sure to use active curve when specified
if self.optsDict['useActive']:
# Get active curve
active = self.plotWindow.getActiveCurve()
if active:
if DEBUG:
print('processSelection -- xrange: use active')
x, y, leg, info = active[0:4]
xRange = self.interpXRange(xRange=x)
else:
return
elif self.optsDict['equidistant']:
if DEBUG:
print('processSelection -- xrange: use equidistant')
xRange = self.interpXRange(equidistant=True)
else:
if DEBUG:
print('processSelection -- xrange: use first')
xRange = self.interpXRange()
activeLegend = self.plotWindow.graph.getActiveCurve(justlegend=True)
if (not activeLegend) or (activeLegend not in self.curvesDict.keys()):
# Use first curve in the series as xrange
activeLegend = sorted(self.curvesDict.keys())[0]
active = self.curvesDict[activeLegend]
xlabel, ylabel = self.extractLabels(active.info)
# Calculate averages and add them to the plot
normalization = self.optsDict['normalizationMethod']
normBefore = self.optsDict['normBeforeAvg']
normAfter = self.optsDict['normAfterAvg']
for idx in ['A','B']:
sel = self.selectionDict[idx]
if not len(sel):
continue
xvalList = []
yvalList = []
for legend in sel:
tmp = self.curvesDict[legend]
if normBefore:
xVals = tmp.x[0]
yVals = normalization(xVals, tmp.y[0])
else:
xVals = tmp.x[0]
yVals = tmp.y[0]
xvalList.append(xVals)
yvalList.append(yVals)
avg_x, avg_y = self.specAverage(xvalList,
yvalList,
xRange)
if normAfter:
avg_y = normalization(avg_x, avg_y)
avgName = 'avg_' + idx
info = {'xlabel': xlabel, 'ylabel': ylabel}
self.addCurve(avg_x, avg_y, avgName, info)
if idx == 'A':
self.avgA = self.dataObjectsList[-1]
if idx == 'B':
self.avgB = self.dataObjectsList[-1]
if (self.avgA and self.avgB):
self.performXMCD()
self.performXAS()
def copyCurves(self, selection):
'''
Input
-----
selection : List
Contains legends of curves to be processed
Creates a deep copy of the curves present in the
plot window. In order to avoid interpolation
errors later on, it is ensured that the xranges
of the data is strictly monotonically increasing.
Returns
-------
out : Dictionary
Contains legends as keys and dataObjects
as values.
'''
if not len(selection):
return {}
out = {}
for legend in selection:
tmp = self.plotWindow.dataObjectsDict.get(legend, None)
if tmp:
tmp = copy.deepcopy(tmp)
xarr, yarr = tmp.x, tmp.y
#if len(tmp.x) == len(tmp.y):
xprocArr, yprocArr = [], []
for (x,y) in zip(xarr,yarr):
# Sort
idx = numpy.argsort(x, kind='mergesort')
xproc = numpy.take(x, idx)
yproc = numpy.take(y, idx)
# Ravel, Increase
xproc = xproc.ravel()
idx = numpy.nonzero((xproc[1:] > xproc[:-1]))[0]
xproc = numpy.take(xproc, idx)
yproc = numpy.take(yproc, idx)
xprocArr += [xproc]
yprocArr += [yproc]
tmp.x = xprocArr
tmp.y = yprocArr
out[legend] = tmp
else:
# TODO: Errorhandling, curve not found
if DEBUG:
print("copyCurves -- Retrieved none type curve")
continue
return out
def specAverage(self, xarr, yarr, xRange=None):
'''
xarr : list
List containing x-Values in 1-D numpy arrays
yarr : list
List containing y-Values in 1-D numpy arrays
xRange : Numpy array
x-Values used for interpolation. Must overlap
with all arrays in xarr
From the spectra given in xarr & yarr, the method
determines the overlap in the x-range. For spectra
with unequal x-ranges, the method interpolates all
spectra on the values given in xRange and averages
them.
Returns
-------
xnew, ynew : Numpy arrays or None
Average spectrum. In case of invalid input,
(None, None) tuple is returned.
'''
if (len(xarr) != len(yarr)) or\
(len(xarr) == 0) or (len(yarr) == 0):
if DEBUG:
print('specAverage -- invalid input!')
print('Array lengths do not match or are 0')
return None, None
same = True
if xRange == None:
x0 = xarr[0]
else:
x0 = xRange
for x in xarr:
if len(x0) == len(x):
if numpy.all(x0 == x):
pass
else:
same = False
break
else:
same = False
break
xsort = []
ysort = []
for (x,y) in zip(xarr, yarr):
if numpy.all(numpy.diff(x) > 0.):
# All values sorted
xsort.append(x)
ysort.append(y)
else:
# Sort values
mask = numpy.argsort(x)
xsort.append(x.take(mask))
ysort.append(y.take(mask))
if xRange != None:
xmin0 = xRange.min()
xmax0 = xRange.max()
else:
xmin0 = xsort[0][0]
xmax0 = xsort[0][-1]
if (not same) or (xRange == None):
# Determine global xmin0 & xmax0
for x in xsort:
xmin = x.min()
xmax = x.max()
if xmin > xmin0:
xmin0 = xmin
if xmax < xmax0:
xmax0 = xmax
if xmax <= xmin:
if DEBUG:
print('specAverage -- ')
print('No overlap between spectra!')
return numpy.array([]), numpy.array([])
# Clip xRange to maximal overlap in spectra
if xRange is None:
xRange = xsort[0]
mask = numpy.nonzero((xRange>=xmin0) &
(xRange<=xmax0))[0]
xnew = numpy.take(xRange, mask)
ynew = numpy.zeros(len(xnew))
# Perform average
for (x, y) in zip(xsort, ysort):
if same:
ynew += y
else:
yinter = numpy.interp(xnew, x, y)
ynew += numpy.asarray(yinter)
num = len(yarr)
ynew /= num
return xnew, ynew
def extractLabels(self, info):
xlabel = 'X'
ylabel = 'Y'
sel = info.get('selection', None)
labelNames = info.get('LabelNames',[])
if not len(labelNames):
pass
elif len(labelNames) == 2:
[xlabel, ylabel] = labelNames
elif sel:
xsel = sel.get('x',[])
ysel = sel.get('y',[])
if len(xsel) > 0:
x = xsel[0]
xlabel = labelNames[x]
if len(ysel) > 0:
y = ysel[0]
ylabel = labelNames[y]
return xlabel, ylabel
def performXAS(self):
keys = self.dataObjectsDict.keys()
if (self.avgA in keys) and (self.avgB in keys):
a = self.dataObjectsDict[self.avgA]
b = self.dataObjectsDict[self.avgB]
else:
if DEBUG:
print('performXAS -- Data not found: ')
print('\tavg_m = %f' % self.avgA)
print('\tavg_p = %f' % self.avgB)
return
if numpy.all( a.x[0] == b.x[0] ):
avg = .5*(b.y[0] + a.y[0])
else:
if DEBUG:
print('performXAS -- x ranges are not the same! ')
print('Force interpolation')
avg = self.performAverage([a.x[0], b.x[0]],
[a.y[0], b.y[0]],
b.x[0])
xmcdLegend = 'XAS'
xlabel, ylabel = self.extractLabels(a.info)
info = {'xlabel': xlabel, 'ylabel': ylabel}
self.addCurve(a.x[0], avg, xmcdLegend, info)
self.xas = self.dataObjectsList[-1]
def performXMCD(self):
keys = self.dataObjectsDict.keys()
if (self.avgA in keys) and (self.avgB in keys):
a = self.dataObjectsDict[self.avgA]
b = self.dataObjectsDict[self.avgB]
else:
if DEBUG:
print('performXMCD -- Data not found:')
return
if numpy.all( a.x[0] == b.x[0] ):
diff = b.y[0] - a.y[0]
else:
if DEBUG:
print('performXMCD -- x ranges are not the same! ')
print('Force interpolation using p Average xrange')
# Use performAverage d = 2 * avg(y1, -y2)
# and force interpolation on p-xrange
diff = 2. * self.performAverage([a.x[0], b.x[0]],
[-a.y[0], b.y[0]],
b.x[0])
xmcdLegend = 'XMCD'
xlabel, ylabel = self.extractLabels(a.info)
info = {'xlabel': xlabel, 'ylabel': ylabel}
self.addCurve(b.x[0], diff, xmcdLegend, info)
self.graph.mapToY2(' '.join([xmcdLegend, ylabel]))
self._zoomReset()
self.xmcd = self.dataObjectsList[-1]
def selectionInfo(self, idx, key):
'''
Convenience function to retrieve values
from the info dictionaries of the curves
stored selectionDict.
'''
sel = self.selectionDict[idx]
ret = '%s: '%idx
for legend in sel:
curr = self.curvesDict[legend]
value = curr.info.get(key, None)
if value:
ret = ' '.join([ret, value])
return ret
def _saveIconSignal(self):
saveDir = PyMcaDirs.outputDir
filter = 'spec File (*.spec);;Any File (*.*)'
try:
(filelist, append, comment) = getSaveFileName(parent=self,
caption='Save XMCD Analysis',
filter=filter,
directory=saveDir)
filename = filelist[0]
except IndexError:
# Returned list is empty
return
except ValueError:
# Returned list is empty
return
if append:
specf = specfile.Specfile(filename)
scanno = specf.scanno() + 1
else:
scanno = 1
ext = splitext(filename)[1]
if not len(ext):
ext = '.spec'
filename += ext
try:
if append:
sepFile = splitext(basename(filename))
sepFileName = sepFile[0] + '_%.2d'%scanno + sepFile[1]
sepFileName = pathjoin(dirname(filename),sepFileName)
if scanno == 2:
# Case: Scan appended to file containing
# a single scan. Make sure, that the first
# scan is also written to seperate file and
# the corresponding cfg-file is copied
# 1. Create filename of first scan
sepFirstFileName = sepFile[0] + '_01' + sepFile[1]
sepFirstFileName = pathjoin(dirname(filename),sepFirstFileName)
# 2. Guess filename of first config
confname = sepFile[0] + '.cfg'
confname = pathjoin(dirname(filename),confname)
# 3. Create new filename of first config
sepFirstConfName = sepFile[0] + '_01' + '.cfg'
sepFirstConfName = pathjoin(dirname(filename),sepFirstConfName)
# Copy contents
firstSeperateFile = open(sepFirstFileName, 'wb')
firstSeperateConf = open(sepFirstConfName, 'wb')
filehandle = open(filename, 'rb')
confhandle = open(confname, 'rb')
firstFile = filehandle.read()
firstConf = confhandle.read()
firstSeperateFile.write(firstFile)
firstSeperateConf.write(firstConf)
firstSeperateFile.close()
firstSeperateConf.close()
filehandle = open(filename, 'ab')
seperateFile = open(sepFileName, 'wb')
else:
filehandle = open(filename, 'wb')
seperateFile = None
except IOError:
msg = qt.QMessageBox(text="Unable to open '%s'"%filename)
msg.exec_()
return
title = ''
legends = self.dataObjectsList
tmpLegs = sorted(self.curvesDict.keys())
if len(tmpLegs) > 0:
title += self.curvesDict[tmpLegs[0]].info.get('selectionlegend','')
# Keep plots in the order they were added!
curves = [self.dataObjectsDict[leg] for leg in legends]
yVals = [curve.y[0] for curve in curves]
# xrange is the same for every curve
xVals = [curves[0].x[0]]
else:
yVals = []
xVals = []
outArray = numpy.vstack([xVals, yVals]).T
if not len(outArray):
ncols = 0
elif len(outArray.shape) > 1:
ncols = outArray.shape[1]
else:
ncols = 1
delim = ' '
title = 'XMCD Analysis ' + title
header = '#S %d %s'%(scanno,title) + NEWLINE
header += ('#U00 Selected in Group ' +\
self.selectionInfo('A', 'Key') + NEWLINE)
header += ('#U01 Selected in Group ' +\
self.selectionInfo('B', 'Key') + NEWLINE)
# Write Comments
if len(comment) > 0:
header += ('#U02 User commentary:' + NEWLINE)
lines = comment.splitlines()[:97]
for (idx, line) in enumerate(lines):
header += ('#U%.2d %s'%(idx+3, line) + NEWLINE)
header += '#N %d'%ncols + NEWLINE
if ext == '.spec':
header += ('#L ' + self.getGraphXTitle() + ' ' + ' '.join(legends) + NEWLINE)
else:
header += ('#L ' + self.getGraphXTitle() + ' ' + delim.join(legends) + NEWLINE)
for fh in [filehandle, seperateFile]:
if fh is not None:
fh.write(NEWLINE)
fh.write(header)
for line in outArray:
tmp = delim.join(['%f'%num for num in line])
fh.write(tmp + NEWLINE)
fh.write(NEWLINE)
fh.close()
# Emit saveOptionsSignal to save config file
self.saveOptionsSignal.emit(splitext(filename)[0])
if seperateFile is not None:
self.saveOptionsSignal.emit(splitext(sepFileName)[0])
def add(self):
activeCurve = self.getActiveCurve()
if activeCurve is None:
return
(xVal, yVal, legend, info) = activeCurve
#if 'selectionlegend' in info:
# newLegend = info['selectionlegend']
#elif 'operation' in info:
# newLegend = (str(operation) + ' ' + self.title)
#else:
# newLegend = (legend + ' ' + self.title)
newLegend = legend
self.plotWindow.addCurve(xVal,
yVal,
newLegend,
info)
self.plotModifiedSignal.emit()
def addAll(self):
for (xVal, yVal, legend, info) in self.getAllCurves():
#if 'selectionlegend' in info:
# newLegend = info['selectionlegend']
#elif 'operation' in info:
# newLegend = (str(operation) + ' ' + self.title)
#else:
# newLegend = (legend + ' ' + self.title)
newLegend = legend
self.plotWindow.addCurve(xVal,
yVal,
newLegend,
info)
self.plotModifiedSignal.emit()
def replace(self):
activeCurve = self.getActiveCurve()
if activeCurve is None:
return
(xVal, yVal, legend, info) = activeCurve
if 'selectionlegend' in info:
newLegend = info['selectionlegend']
elif 'operation' in info:
newLegend = (str(operation) + ' ' + self.title)
else:
newLegend = (legend + self.title)
self.plotWindow.addCurve(xVal,
yVal,
newLegend,
info,
replace=True)
self.plotModifiedSignal.emit()
def replaceAll(self):
allCurves = self.getAllCurves()
for (idx, (xVal, yVal, legend, info)) in enumerate(allCurves):
if 'selectionlegend' in info:
newLegend = info['selectionlegend']
elif 'operation' in info:
newLegend = (str(operation) + ' ' + self.title)
else:
newLegend = (legend + ' ' + self.title)
if idx == 0:
self.plotWindow.addCurve(xVal,
yVal,
newLegend,
info,
replace=True)
else:
self.plotWindow.addCurve(xVal,
yVal,
newLegend,
info)
self.plotModifiedSignal.emit()
class XMCDMenu(qt.QMenu):
def __init__(self, parent, title=None):
qt.QMenu.__init__(self, parent)
if title:
self.setTitle(title)
def setActionList(self, actionList, update=False):
'''
List functions has to have the form (functionName, function)
Default is ('', function)
'''
if not update:
self.clear()
for (name, function) in actionList:
if name == '$SEPARATOR':
self.addSeparator()
continue
if name != '':
fName = name
else:
fName = function.func_name
act = qt.QAction(fName, self)
# Force triggered() instead of triggered(bool)
# to ensure proper interaction with default parameters
act.triggered[()].connect(function)
self.addAction(act)
class XMCDTreeWidget(qt.QTreeWidget):
__colGroup = 0
__colLegend = 1
__colScanNo = 2
__colCounter = 3
selectionModifiedSignal = qt.pyqtSignal()
def __init__(self, parent, groups = ['B','A','D'], color=True):
qt.QTreeWidget.__init__(self, parent)
# Last identifier in groups is the ignore instruction
self.groupList = groups
self.actionList = []
self.contextMenu = qt.QMenu('Perform', self)
self.color = color
self.colorDict = {
groups[0] : qt.QBrush(qt.QColor(220, 220, 255)),
groups[1] : qt.QBrush(qt.QColor(255, 210, 210)),
'': qt.QBrush(qt.QColor(255, 255, 255))
}
def sizeHint(self):
vscrollbar = self.verticalScrollBar()
width = vscrollbar.width()
for i in range(self.columnCount()):
width += (2 + self.columnWidth(i))
return qt.QSize( width, 20*22)
def setContextMenu(self, menu):
self.contextMenu = menu
def contextMenuEvent(self, event):
if event.reason() == event.Mouse:
pos = event.globalPos()
item = self.itemAt(event.pos())
else:
pos = None
sel = self.selectedItems()
if sel:
item = sel[0]
else:
item = self.currentItem()
if item is None:
self.invisibleRootItem().child(0)
if item is not None:
itemrect = self.visualItemRect(item)
portrect = self.viewport().rect()
itemrect.setLeft(portrect.left())
itemrect.setWidth(portrect.width())
pos = self.mapToGlobal(itemrect.bottomLeft())
if pos is not None:
self.contextMenu.popup(pos)
event.accept()
def invertSelection(self):
root = self.invisibleRootItem()
for i in range(root.childCount()):
if root.child(i).isSelected():
root.child(i).setSelected(False)
else:
root.child(i).setSelected(True)
def getColumn(self, ncol, selectedOnly=False, convertType=str):
'''
Returns items in tree column ncol and converts them
to convertType. If the conversion fails, the default
type is a python string.
If selectedOnly is set to True, only the selected
the items of selected rows are returned.
'''
out = []
convert = (convertType != str)
if ncol > (self.columnCount()-1):
if DEBUG:
print('getColum -- Selected column out of bounds')
raise IndexError("Selected column '%d' out of bounds" % ncol)
return out
if selectedOnly:
sel = self.selectedItems()
else:
root = self.invisibleRootItem()
sel = [root.child(i) for i in range(root.childCount())]
for item in sel:
tmp = str(item.text(ncol))
if convert:
try:
tmp = convertType(tmp)
except (TypeError, ValueError):
if convertType == float:
tmp = float('NaN')
else:
if DEBUG:
print('getColum -- Conversion failed!')
raise TypeError
out += [tmp]
return out
def build(self, items, headerLabels):
'''
(Re-) Builds the tree display
headerLabels must be of type QStringList
items must be of type [QStringList] (List of Lists)
'''
# Remember selection, then clear list
sel = self.getColumn(self.__colLegend, True)
self.clear()
self.setHeaderLabels(headerLabels)
for item in items:
treeItem = TreeWidgetItem(self, item)
if self.color:
idx = str(treeItem.text(self.__colGroup))
for i in range(self.columnCount()):
treeItem.setBackground(i, self.colorDict[idx])
if treeItem.text(self.__colLegend) in sel:
treeItem.setSelected(True)
def setSelectionAs(self, idx):
'''
Sets the items currently selected to
the identifier given in idx.
'''
if idx not in self.groupList:
raise ValueError('XMCDTreeWidget: invalid identifer \'%s\'' % idx)
sel = self.selectedItems()
if idx == self.groupList[-1]:
# Last identifier in self.groupList
# is the dummy identifier
idx = ''
for item in sel:
item.setText(self.__colGroup, idx)
if self.color:
for i in range(self.columnCount()):
item.setBackground(i, self.colorDict[idx])
self.selectionModifiedSignal.emit()
def setSelectionToSequence(self, seq=None, selectedOnly=False):
'''
Sets the group column (col 0) to seq.
If sequence is None, a dialog window is
shown.
'''
chk = True
if selectedOnly:
sel = self.selectedItems()
else:
root = self.invisibleRootItem()
sel = [root.child(i) for i in range(root.childCount())]
# Try to sort for scanNo
#self.sortItems(self.__colLegend, qt.Qt.AscendingOrder)
self.sortItems(self.__colScanNo, qt.Qt.AscendingOrder)
if not seq:
seq, chk = qt.QInputDialog.\
getText(None,
'Sequence Dialog',
'Valid identifiers are: ' + ', '.join(self.groupList),
qt.QLineEdit.Normal,
'Enter sequence')
seq = str(seq).upper()
if not chk:
return
for idx in seq:
if idx not in self.groupList:
invalidMsg = qt.QMessageBox(None)
invalidMsg.setText('Invalid identifier. Try again.')
invalidMsg.setStandardButtons(qt.QMessageBox.Ok)
invalidMsg.exec_()
return
if len(sel) != len(seq):
# Assume pattern and repeat
seq = seq * (len(sel)//len(seq) + 1)
#invalidMsg = qt.QMessageBox(None)
#invalidMsg.setText('Sequence length does not match item count.')
#invalidMsg.setStandardButtons(qt.QMessageBox.Ok)
#invalidMsg.exec_()
for (idx, item) in zip(seq, sel):
if idx == self.groupList[-1]:
idx = ''
item.setText(self.__colGroup, idx)
if self.color:
for i in range(self.columnCount()):
item.setBackground(i, self.colorDict[idx])
self.selectionModifiedSignal.emit()
def clearSelection(self, selectedOnly=True):
'''
Empties the groups column for the selected rows.
'''
if selectedOnly:
sel = self.selectedItems()
else:
root = self.invisibleRootItem()
sel = [root.child(i) for i in range(root.childCount())]
for item in sel:
item.setText(self.__colGroup,'')
if self.color:
for i in range(self.columnCount()):
item.setBackground(i, self.colorDict[''])
self.selectionModifiedSignal.emit()
def getSelection(self):
'''
Returns dictionary with where the keys
are the identifiers ('D', 'A', 'B') and
the values are (sorted) lists containing
legends to which the respective identifier is
assigned to.
'''
out = dict((group, []) for group in self.groupList)
root = self.invisibleRootItem()
for i in range(root.childCount()):
item = root.child(i)
group = str(item.text(0))
legend = str(item.text(1))
#nCols = item.columnCount()
#legend = str(item.text(nCols-1))
if len(group) == 0:
group = self.groupList[-1]
out[group] += [legend]
for value in out.values():
value.sort()
return out
class XMCDWidget(qt.QWidget):
setSelectionSignal = qt.pyqtSignal(object, object)
def __init__(self, parent,
plotWindow,
beamline,
nSelectors = 5):
"""
Input
-----
plotWindow : ScanWindow instance
ScanWindow from which curves are passed for
XLD/XMCD Analysis
nSelectors : Int
Number of columns show in the widget. Per default
these are
<Group> <Legend> <ScanNo> <Counter> <Motor 1> ... <Motor5>
"""
qt.QWidget.__init__(self, parent)
self.setWindowIcon(qt.QIcon(IconDict['peak']))
self.plotWindow = plotWindow
self.legendList = []
self.motorsList = []
self.infoList = []
# Set self.plotWindow before calling self._setLists!
self._setLists()
self.motorNamesList = [''] + self._getAllMotorNames()
self.motorNamesList.sort()
self.numCurves = len(self.legendList)
#self.cBoxList = []
self.analysisWindow = XMCDScanWindow(origin=plotWindow,
parent=None)
self.optsWindow = XMCDOptions(self, self.motorNamesList)
helpFileName = pathjoin(PyMcaDataDir.PYMCA_DOC_DIR,
"HTML",
"XMCDInfotext.html")
self.helpFileBrowser = qt.QTextBrowser()
self.helpFileBrowser.setWindowTitle("XMCD Help")
self.helpFileBrowser.setLineWrapMode(qt.QTextEdit.FixedPixelWidth)
self.helpFileBrowser.setLineWrapColumnOrWidth(500)
self.helpFileBrowser.resize(520,300)
try:
helpFileHandle = open(helpFileName)
helpFileHTML = helpFileHandle.read()
helpFileHandle.close()
self.helpFileBrowser.setHtml(helpFileHTML)
except IOError:
if DEBUG:
print('XMCDWindow -- init: Unable to read help file')
self.helpFileBrowser = None
self.selectionDict = {'D': [],
'B': [],
'A': []}
self.setSizePolicy(qt.QSizePolicy.MinimumExpanding,
qt.QSizePolicy.Expanding)
self.setWindowTitle("XLD/XMCD Analysis")
buttonOptions = qt.QPushButton('Options', self)
buttonOptions.setToolTip(
'Set normalization and interpolation\n'
+'method and motors shown')
buttonInfo = qt.QPushButton('Info')
buttonInfo.setToolTip(
'Shows a describtion of the plugins features\n'
+'and gives instructions on how to use it')
updatePixmap = qt.QPixmap(IconDict["reload"])
buttonUpdate = qt.QPushButton(
qt.QIcon(updatePixmap), '', self)
buttonUpdate.setIconSize(qt.QSize(21,21))
buttonUpdate.setToolTip(
'Update curves in XMCD Analysis\n'
+'by checking the plot window')
self.list = XMCDTreeWidget(self)
labels = ['Group', 'Legend', 'S#','Counter']+\
(['']*nSelectors)
ncols = len(labels)
self.list.setColumnCount(ncols)
self.list.setHeaderLabels(labels)
self.list.setSortingEnabled(True)
self.list.setSelectionMode(
qt.QAbstractItemView.ExtendedSelection)
listContextMenu = XMCDMenu(None)
listContextMenu.setActionList(
[('Perform analysis', self.triggerXMCD),
('$SEPARATOR', None),
('Set as A', self.setAsA),
('Set as B', self.setAsB),
('Enter sequence', self.list.setSelectionToSequence),
('Remove selection', self.list.clearSelection),
('$SEPARATOR', None),
('Invert selection', self.list.invertSelection),
('Remove curve(s)', self.removeCurve_)])
self.list.setContextMenu(listContextMenu)
self.expCBox = qt.QComboBox(self)
self.expCBox.setToolTip('Select configuration of predefined\n'
+'experiment or configure new experiment')
self.experimentsDict = {
'Generic Dichorism': {
'xrange': 0,
'normalization': 0,
'normalizationMethod': 'offsetAndArea',
'motor0': '',
'motor1': '',
'motor2': '',
'motor3': '',
'motor4': ''
},
'ID08: XMCD 9 Tesla Magnet': {
'xrange': 0,
'normalization': 0,
'normalizationMethod': 'offsetAndArea',
'motor0': 'phaseD',
'motor1': 'magnet',
'motor2': '',
'motor3': '',
'motor4': ''
},
'ID08: XMCD 5 Tesla Magnet': {
'xrange': 0,
'normalization': 0,
'normalizationMethod': 'offsetAndArea',
'motor0': 'PhaseD',
'motor1': 'oxPS',
'motor2': '',
'motor3': '',
'motor4': ''
},
'ID08: XLD 5 Tesla Magnet': {
'xrange': 0,
'normalization': 0,
'normalizationMethod': 'offsetAndArea',
'motor0': 'PhaseD',
'motor1': '',
'motor2': '',
'motor3': '',
'motor4': ''
},
'ID08: XLD 9 Tesla Magnet': {
'xrange': 0,
'normalization': 0,
'normalizationMethod': 'offsetAndArea',
'motor0': 'phaseD',
'motor1': '',
'motor2': '',
'motor3': '',
'motor4': ''
},
'ID12: XMCD (Flipper)': {
'xrange': 0,
'normalization': 0,
'normalizationMethod': 'offsetAndArea',
'motor0': 'BRUKER',
'motor1': 'OXFORD',
'motor2': 'CRYO',
'motor3': '',
'motor4': ''
},
'ID12: XMCD': {
'xrange': 0,
'normalization': 0,
'normalizationMethod': 'offsetAndArea',
'motor0': 'Phase',
'motor1': 'PhaseA',
'motor2': 'BRUKER',
'motor3': 'OXFORD',
'motor4': 'CRYO'
},
'ID12: XLD (quater wave plate)': {
'xrange': 0,
'normalization': 0,
'normalizationMethod': 'offsetAndArea',
'motor0': '',
'motor1': '',
'motor2': '',
'motor3': '',
'motor4': ''
}
}
self.expCBox.addItems(
['Generic Dichorism',
'ID08: XLD 9 Tesla Magnet',
'ID08: XLD 5 Tesla Magnet',
'ID08: XMCD 9 Tesla Magnet',
'ID08: XMCD 5 Tesla Magnet',
'ID12: XLD (quater wave plate)',
'ID12: XMCD (Flipper)',
'ID12: XMCD',
'Add new configuration'])
self.expCBox.insertSeparator(len(self.experimentsDict))
topLayout = qt.QHBoxLayout()
topLayout.addWidget(buttonUpdate)
topLayout.addWidget(buttonOptions)
topLayout.addWidget(buttonInfo)
topLayout.addWidget(qt.HorizontalSpacer(self))
topLayout.addWidget(self.expCBox)
leftLayout = qt.QGridLayout()
leftLayout.setContentsMargins(1, 1, 1, 1)
leftLayout.setSpacing(2)
leftLayout.addLayout(topLayout, 0, 0)
leftLayout.addWidget(self.list, 1, 0)
leftWidget = qt.QWidget(self)
leftWidget.setLayout(leftLayout)
self.analysisWindow.setSizePolicy(qt.QSizePolicy.Minimum, qt.QSizePolicy.Minimum)
#self.splitter = qt.QSplitter(qt.Qt.Horizontal, self)
self.splitter = qt.QSplitter(qt.Qt.Vertical, self)
self.splitter.addWidget(leftWidget)
self.splitter.addWidget(self.analysisWindow)
stretch = int(leftWidget.width())
# If window size changes, only the scan window size changes
self.splitter.setStretchFactor(
self.splitter.indexOf(self.analysisWindow),1)
mainLayout = qt.QVBoxLayout()
mainLayout.setContentsMargins(0,0,0,0)
mainLayout.addWidget(self.splitter)
self.setLayout(mainLayout)
# Connects
self.expCBox.currentIndexChanged['QString'].connect(self.updateTree)
self.expCBox.currentIndexChanged['QString'].connect(self.selectExperiment)
self.list.selectionModifiedSignal.connect(self.updateSelectionDict)
self.setSelectionSignal.connect(self.analysisWindow.processSelection)
self.analysisWindow.saveOptionsSignal.connect(self.optsWindow.saveOptions)
self.optsWindow.accepted[()].connect(self.updateTree)
buttonUpdate.clicked.connect(self.updatePlots)
buttonOptions.clicked.connect(self.showOptionsWindow)
buttonInfo.clicked.connect(self.showInfoWindow)
self.updateTree()
self.list.sortByColumn(1, qt.Qt.AscendingOrder)
def sizeHint(self):
return self.list.sizeHint() + self.analysisWindow.sizeHint()
def addExperiment(self):
exp, chk = qt.QInputDialog.\
getText(self,
'Configure new experiment',
'Enter experiment title',
qt.QLineEdit.Normal,
'ID00: <Title>')
if chk and (not exp.isEmpty()):
exp = str(exp)
opts = XMCDOptions(self, self.motorNamesList, False)
if opts.exec_():
self.experimentsDict[exp] = opts.getOptions()
cBox = self.expCBox
new = [cBox.itemText(i) for i in range(cBox.count())][0:-2]
new += [exp]
new.append('Add new configuration')
cBox.clear()
cBox.addItems(new)
cBox.insertSeparator(len(new)-1)
idx = cBox.findText([exp][0])
if idx < 0:
cBox.setCurrentIndex(0)
else:
cBox.setCurrentIndex(idx)
opts.destroy()
idx = self.expCBox.findText(exp)
if idx < 0:
idx = 0
self.expCBox.setCurrentIndex(idx)
def showOptionsWindow(self):
if self.optsWindow.exec_():
options = self.optsWindow.getOptions()
self.analysisWindow.processOptions(options)
def showInfoWindow(self):
if self.helpFileBrowser is None:
msg = qt.QMessageBox()
msg.setWindowTitle('XLD/XMCD Error')
msg.setText('No help file found.')
msg.exec_()
return
else:
self.helpFileBrowser.show()
self.helpFileBrowser.raise_()
# Implement new assignment routines here BEGIN
def selectExperiment(self, exp):
exp = str(exp)
if exp == 'Add new configuration':
self.addExperiment()
self.updateTree()
elif exp in self.experimentsDict:
try:
# Sets motors 0 to 4 in optsWindow
self.optsWindow.setOptions(self.experimentsDict[exp])
except ValueError:
self.optsWindow.setOptions(
self.experimentsDict['Generic Dichorism'])
return
# Get motor values from tree
self.updateTree()
values0 = numpy.array(
self.list.getColumn(4, convertType=float))
values1 = numpy.array(
self.list.getColumn(5, convertType=float))
values2 = numpy.array(
self.list.getColumn(6, convertType=float))
values3 = numpy.array(
self.list.getColumn(7, convertType=float))
values4 = numpy.array(
self.list.getColumn(8, convertType=float))
# Determine p/m selection
if exp.startswith('ID08: XLD'):
values = values0
mask = numpy.where(numpy.isfinite(values))[0]
minmax = values.take(mask)
if len(minmax):
vmin = minmax.min()
vmax = minmax.max()
vpivot = .5 * (vmax + vmin)
else:
vpivot = 0.
values = numpy.array(
[float('NaN')]*len(self.legendList))
elif exp.startswith('ID08: XMCD'):
mask = numpy.where(numpy.isfinite(values0))[0]
polarization = values0.take(mask)
values1 = values1.take(mask)
signMagnets = numpy.sign(values1)
if len(polarization)==0:
vpivot = 0.
values = numpy.array(
[float('NaN')]*len(self.legendList))
elif numpy.all(signMagnets>=0.) or\
numpy.all(signMagnets<=0.) or\
numpy.all(signMagnets==0.):
vmin = polarization.min()
vmax = polarization.max()
vpivot = .5 * (vmax + vmin)
values = polarization
else:
vpivot = 0.
values = polarization * signMagnets
elif exp.startswith('ID12: XLD (quater wave plate)'):
# Extract counters from third column
counters = self.list.getColumn(3, convertType=str)
polarization = []
for counter in counters:
# Relevant counters Ihor, Iver resp. Ihor0, Iver0, etc.
if 'hor' in counter:
pol = -1.
elif 'ver' in counter:
pol = 1.
else:
pol = float('nan')
polarization += [pol]
values = numpy.asarray(polarization, dtype=float)
vpivot = 0.
elif exp.startswith('ID12: XMCD (Flipper)'):
# Extract counters from third column
counters = self.list.getColumn(1, convertType=str)
polarization = []
for counter in counters:
# Relevant counters: Fminus/Fplus resp. Rminus/Rplus
if 'minus' in counter:
pol = 1.
elif 'plus' in counter:
pol = -1.
else:
pol = float('nan')
polarization += [pol]
magnets = values0 + values1 + values2
values = numpy.asarray(polarization, dtype=float)*\
magnets
vpivot = 0.
elif exp.startswith('ID12: XMCD'):
# Sum over phases..
polarization = values0 + values1
# ..and magnets
magnets = values2 + values3 + values4
signMagnets = numpy.sign(magnets)
if numpy.all(signMagnets==0.):
values = polarization
else:
values = numpy.sign(polarization)*\
numpy.sign(magnets)
vpivot = 0.
else:
values = numpy.array([float('NaN')]*len(self.legendList))
vpivot = 0.
# Sequence is generate according to values and vpivot
seq = ''
for x in values:
if str(x) == 'nan':
seq += 'D'
elif x<vpivot:
# Minus group
seq += 'A'
else:
# Plus group
seq += 'B'
self.list.setSelectionToSequence(seq)
# Implement new assignment routines here END
def triggerXMCD(self):
groupA = self.selectionDict['A']
groupB = self.selectionDict['B']
self.analysisWindow.processSelection(groupA, groupB)
def removeCurve_(self):
sel = self.list.getColumn(1,
selectedOnly=True,
convertType=str)
for legend in sel:
self.plotWindow.removeCurve(legend)
for selection in self.selectionDict.values():
if legend in selection:
selection.remove(legend)
# Remove from XMCDScanWindow.curvesDict
if legend in self.analysisWindow.curvesDict.keys():
del(self.analysisWindow.curvesDict[legend])
# Remove from XMCDScanWindow.selectionDict
for selection in self.analysisWindow.selectionDict.values():
if legend in selection:
selection.remove(legend)
self.updatePlots()
def updateSelectionDict(self):
# Get selDict from self.list. It consists of tree items:
# {GROUP0: LIST_OF_LEGENDS_IN_GROUP0,
# GROUP1: LIST_OF_LEGENDS_IN_GROUP1,
# GROUP2: LIST_OF_LEGENDS_IN_GROUP2}
selDict = self.list.getSelection()
# self.selectionDict -> Uses ScanNumbers instead of legends...
newDict = {}
for (idx, selList) in selDict.items():
if idx not in newDict.keys():
newDict[idx] = []
for legend in selList:
newDict[idx] += [legend]
self.selectionDict = newDict
self.setSelectionSignal.emit(self.selectionDict['A'],
self.selectionDict['B'])
def updatePlots(self,
newLegends = None,
newMotorValues = None):
# Check if curves in plotWindow changed..
curves = self.plotWindow.getAllCurves(just_legend=True)
if curves == self.legendList:
# ..if not, just replot to account for zoom
self.triggerXMCD()
return
self._setLists()
self.motorNamesList = [''] + self._getAllMotorNames()
self.motorNamesList.sort()
self.optsWindow.updateMotorList(self.motorNamesList)
self.updateTree()
experiment = str(self.expCBox.currentText())
if experiment != 'Generic Dichorism':
self.selectExperiment(experiment)
return
def updateTree(self):
mList = self.optsWindow.getMotors()
labels = ["Group",'Legend','S#','Counter'] + mList
items = []
for i in range(len(self.legendList)):
# Loop through rows
# Each row is represented by QStringList
legend = self.legendList[i]
values = self.motorsList[i]
info = self.infoList[i]
selection = ''
# Determine Group from selectionDict
for (idx, v) in self.selectionDict.items():
if (legend in v) and (idx != 'D'):
selection = idx
break
# Add filename, scanNo, counter
#sourceName = info.get('SourceName','')
#if isinstance(sourceName,list):
# filename = basename(sourceName[0])
#else:
# filename = basename(sourceName)
filename = legend
scanNo = info.get('Key','')
counter = info.get('ylabel',None)
if counter is None:
selDict = info.get('selection',{})
if len(selDict) == 0:
counter = ''
else:
# When do multiple selections occur?
try:
yIdx = selDict['y'][0]
cntList = selDict['cnt_list']
counter = cntList[yIdx]
except Exception:
counter = ''
tmp = QStringList([selection, filename, scanNo, counter])
# Determine value for each motor
for m in mList:
if len(m) == 0:
tmp.append('')
else:
tmp.append(str(values.get(m, '---')))
items.append(tmp)
self.list.build(items, labels)
for idx in range(self.list.columnCount()):
self.list.resizeColumnToContents(idx)
def setAsA(self):
self.list.setSelectionAs('A')
def setAsB(self):
self.list.setSelectionAs('B')
def _getAllMotorNames(self):
names = []
for dic in self.motorsList:
for key in dic.keys():
if key not in names:
names.append(key)
names.sort()
return names
def _convertInfoDictionary(self, infosList):
ret = []
for info in infosList :
motorNames = info.get('MotorNames', None)
if motorNames is not None:
if type(motorNames) == str:
namesList = motorNames.split()
elif type(motorNames) == list:
namesList = motorNames
else:
namesList = []
else:
namesList = []
motorValues = info.get('MotorValues', None)
if motorNames is not None:
if type(motorValues) == str:
valuesList = motorValues.split()
elif type(motorValues) == list:
valuesList = motorValues
else:
valuesList = []
else:
valuesList = []
if len(namesList) == len(valuesList):
ret.append(dict(zip(namesList, valuesList)))
else:
print("Number of motors and values does not match!")
return ret
def _setLists(self):
'''
Curves retrieved from the main plot window using the
Plugin1DBase getActiveCurve() resp. getAllCurves()
member functions are tuple resp. a list of tuples
containing x-data, y-data, legend and the info dictionary.
_setLists splits these tuples into lists, thus setting
the attributes
self.legendList
self.infoList
self.motorsList
'''
if self.plotWindow is not None:
curves = self.plotWindow.getAllCurves()
else:
if DEBUG:
print('_setLists -- Set self.plotWindow before calling self._setLists')
return
# nCurves = len(curves)
self.legendList = [leg for (xvals, yvals, leg, info) in curves]
self.infoList = [info for (xvals, yvals, leg, info) in curves]
# Try to recover the scan number from the legend, if not set
# Requires additional import:
#from re import search as regexpSearch
#for ddict in self.infoList:
# key = ddict.get('Key','')
# if len(key)== 0:
# selectionlegend = ddict['selectionlegend']
# match = regexpSearch(r'(?<= )\d{1,5}\.\d{1}',selectionlegend)
# if match:
# scanNo = match.group(0)
# ddict['Key'] = scanNo
self.motorsList = self._convertInfoDictionary(self.infoList)
class XMCDFileDialog(qt.QFileDialog):
def __init__(self, parent, caption, directory, filter):
qt.QFileDialog.__init__(self, parent, caption, directory, filter)
saveOptsGB = qt.QGroupBox('Save options', self)
self.appendBox = qt.QCheckBox('Append to existing file', self)
self.commentBox = qt.QTextEdit('Enter comment', self)
mainLayout = self.layout()
optsLayout = qt.QGridLayout()
optsLayout.addWidget(self.appendBox, 0, 0)
optsLayout.addWidget(self.commentBox, 1, 0)
saveOptsGB.setLayout(optsLayout)
mainLayout.addWidget(saveOptsGB, 4, 0, 1, 3)
self.appendBox.stateChanged.connect(self.appendChecked)
def appendChecked(self, state):
if state == qt.Qt.Unchecked:
self.setConfirmOverwrite(True)
self.setFileMode(qt.QFileDialog.AnyFile)
else:
self.setConfirmOverwrite(False)
self.setFileMode(qt.QFileDialog.ExistingFile)
def getSaveFileName(parent, caption, directory, filter):
dial = XMCDFileDialog(parent, caption, directory, filter)
dial.setAcceptMode(qt.QFileDialog.AcceptSave)
append = None
comment = None
files = []
if dial.exec_():
append = dial.appendBox.isChecked()
comment = str(dial.commentBox.toPlainText())
if comment == 'Enter comment':
comment = ''
files = [qt.safe_str(fn) for fn in dial.selectedFiles()]
return (files, append, comment)
def main():
app = qt.QApplication([])
# Create dummy ScanWindow
swin = sw.ScanWindow()
info0 = {'xlabel': 'foo',
'ylabel': 'arb',
'MotorNames': 'oxPS PhaseA Phase BRUKER CRYO OXFORD',
'MotorValues': '1 -6.27247094 -3.11222732 6.34150808 -34.75892563 21.99607165'}
info1 = {'MotorNames': 'PhaseD oxPS PhaseA Phase BRUKER CRYO OXFORD',
'MotorValues': '0.470746882688 0.25876374531 -0.18515967 -28.31216591 18.54513221 -28.09735532 -26.78833172'}
info2 = {'MotorNames': 'PhaseD oxPS PhaseA Phase BRUKER CRYO OXFORD',
'MotorValues': '-9.45353059 -25.37448851 24.37665651 18.88048044 -0.26018745 2 0.901968648111 '}
x = numpy.arange(100.,1100.)
y0 = 10*x + 10000.*numpy.exp(-0.5*(x-500)**2/400) + 1500*numpy.random.random(1000.)
y1 = 10*x + 10000.*numpy.exp(-0.5*(x-600)**2/400) + 1500*numpy.random.random(1000.)
y2 = 10*x + 10000.*numpy.exp(-0.5*(x-400)**2/400) + 1500*numpy.random.random(1000.)
swin.newCurve(x, y2, legend="Curve2", xlabel='ene_st2', ylabel='Ihor', info=info2, replot=False, replace=False)
swin.newCurve(x, y0, legend="Curve0", xlabel='ene_st0', ylabel='Iver', info=info0, replot=False, replace=False)
swin.newCurve(x, y1, legend="Curve1", xlabel='ene_st1', ylabel='Ihor', info=info1, replot=False, replace=False)
# info['Key'] is overwritten when using newCurve
swin.dataObjectsDict['Curve2 Ihor'].info['Key'] = '1.1'
swin.dataObjectsDict['Curve0 Iver'].info['Key'] = '34.1'
swin.dataObjectsDict['Curve1 Ihor'].info['Key'] = '123.1'
w = XMCDWidget(None, swin, 'ID08', nSelectors = 5)
w.show()
# helpFileBrowser = qt.QTextBrowser()
# helpFileBrowser.setLineWrapMode(qt.QTextEdit.FixedPixelWidth)
# helpFileBrowser.setLineWrapColumnOrWidth(500)
# helpFileBrowser.resize(520,400)
# helpFileHandle = open('/home/truter/lab/XMCD_infotext.html')
# helpFileHTML = helpFileHandle.read()
# helpFileHandle.close()
# helpFileBrowser.setHtml(helpFileHTML)
# helpFileBrowser.show()
app.exec_()
if __name__ == '__main__':
main()
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