def __showScanInfo(self, idx = None):
if idx is None:
if QTVERSION > '4.0.0':
idx = self.menu_idx
if DEBUG:
print("Scan information:")
try:
info = self.data.getDataObject(self.scans[idx]).info
except:
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
text = "Error: %s\n accessing scan information." % (sys.exc_info()[1])
msg.setText(text)
if QTVERSION < '4.0.0':
msg.exec_loop()
else:
msg.exec_()
if DEBUG:
raise
return
dataInfoWidget= SpecFileDataInfo.SpecFileDataInfo(info)
if "Header" in info:
if info['Header'] is not None:
if QTVERSION > '4.0.0':
dataInfoWidget.setWindowTitle(info['Header'][0])
else:
dataInfoWidget.setCaption(info['Header'][0])
dataInfoWidget.show()
wid = id(dataInfoWidget)
self.dataInfoWidgetDict[wid] = dataInfoWidget
if QTVERSION < '4.0.0':
self.connect(dataInfoWidget,
qt.PYSIGNAL('SpecFileDataInfoSignal'),
self._dataInfoClosed)
else:
dataInfoWidget.notifyCloseEventToWidget(self)
def _energySlot(self):
qstring = self.energy.text()
try:
value = float(str(qstring))
self.energyvalue = value
self.myslot(event='coeff')
self.energy.setPaletteBackgroundColor(qt.Qt.white)
if QTVERSION > '4.0.0':
cursor = self.__browsertext.textCursor()
cursor.movePosition(qt.QTextCursor.Start)
self.__browsertext.setTextCursor(cursor)
self.threshold.setFocus()
except:
msg = qt.QMessageBox(self.energy)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Invalid Float")
if QTVERSION < '4.0.0':
msg.exec_loop()
else:
msg.setWindowTitle("Invalid entry")
msg.exec_()
self.energy.setFocus()
return
def estimate(self):
self.setStatus("Estimate started")
self.statusWidget.chi2Line.setText("")
try:
x = self.fitModule._x
y = self.fitModule._y
if hasattr(self.graph, "addCurve"):
self.graph.addCurve(x, y, 'Data')
elif hasattr(self.graph, "newCurve"):
self.graph.newCurve('Data', x, y)
self.graph.removeCurve("Fit")
self.graph.removeCurve("Background", replot=True)
self.fitModule.estimate()
self.setStatus()
self.parametersTable.fillTableFromFit(self.fitModule.paramlist)
except:
if DEBUG:
raise
text = "%s:%s" % (sys.exc_info()[0], sys.exc_info()[1])
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText(text)
msg.exec_()
self.setStatus("Ready (after estimate error)")
def _energySlot(self):
string = str(self.energy.text())
if len(string):
try:
value = float(string)
except:
msg = qt.QMessageBox(self.energy)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Invalid Float")
msg.exec_loop()
self.energy.setFocus()
return
if self.energyValue is not None:
if value != self.energyValue:
self.energyValue = value
Elements.updateDict(energy=value)
else:
self.energyValue = value
Elements.updateDict(energy=value)
self.energy.setPaletteBackgroundColor(qt.QColor('white'))
self.infoWidget.setFocus()
else:
self.energyValue = None
self.energy.setText("")
def __mySlot(self):
qstring = self.text()
text = str(qstring)
try:
if len(text):
value = float(str(qstring))
ddict = {}
ddict['event'] = 'returnPressed'
ddict['value'] = value
ddict['text'] = text
ddict['qstring'] = qstring
if QTVERSION < '4.0.0':
self.emit(qt.PYSIGNAL('MyQLineEditSignal'), (ddict, ))
else:
self.emit(qt.SIGNAL('MyQLineEditSignal'), ddict)
except:
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Invalid Float")
if QTVERSION < '4.0.0':
msg.exec_loop()
else:
msg.exec_()
self.setFocus()
def showMessage(self, text):
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Information)
msg.setText(text)
msg.exec_()
def returnZonesForEqualize(zones,data):
if len(zones) == 1:
x1 = zones[-1][0]
x2 = zones[-1][3]
y1 = zones[-1][1]
y2 = zones[-1][4]
z1 = zones[-1][2]
z2 = zones[-1][5]
elif len(zones) > 1:
x1 = zones[-2][0]
x2 = zones[-2][3]
y1 = zones[-2][1]
y2 = zones[-2][4]
z1 = zones[-2][2]
z2 = zones[-2][5]
if z2<z1:
zs= z1
z1 = z2
z2 = zs
if y2<y1:
ys= y1
y1 = y2
y2 = ys
if x2<x1:
xs= x1
x1 = x2
x2 = xs
if z1< 0:
z1 = 0
elif z1> data.shape[0]:
msgBox = qt.QMessageBox()
msgBox.setText('Out of Volume')
msgBox.exec_()
if z2 < 0:
msgBox = qt.QMessageBox()
msgBox.setText('Out of Volume')
msgBox.exec_()
elif z2 > data.shape[0]:
z2 = data.shape[0] -1
if y1< 0:
y1 = 0
elif y1> data.shape[1]:
msgBox = qt.QMessageBox()
msgBox.setText('Out of Volume')
msgBox.exec_()
if y2 < 0:
msgBox = qt.QMessageBox()
msgBox.setText('Out of Volume')
msgBox.exec_()
elif y2 > data.shape[1]:
y2 = data.shape[1] -1
if x1< 0:
x1 = 0
elif x1> data.shape[2]:
msgBox = qt.QMessageBox()
msgBox.setText('Out of Volume')
msgBox.exec_()
if x2 < 0:
msgBox = qt.QMessageBox()
msgBox.setText('Out of Volume')
msgBox.exec_()
elif x2 > data.shape[2]:
x2 = data.shape[2] -1
if len(zones) == 1:
zones_in = [[z1,y1,x1,z2,y2,x2]]
elif len(zones) > 1:
x12 = zones[-1][0]
x22 = zones[-1][3]
y12 = zones[-1][1]
y22 = zones[-1][4]
z12 = zones[-1][2]
z22 = zones[-1][5]
if z22<z12:
zs= z12
z12 = z22
z22 = zs
if y22<y12:
ys= y12
y12 = y22
y22 = ys
if x22<x12:
xs= x12
x12 = x22
x22 = xs
if z12< 0:
z12 = 0
elif z12> data.shape[0]:
msgBox = qt.QMessageBox()
msgBox.setText('Out of Volume')
msgBox.exec_()
if z22 < 0:
msgBox = qt.QMessageBox()
msgBox.setText('Out of Volume')
msgBox.exec_()
elif z22 > data.shape[0]:
z22 = data.shape[0] -1
if y12< 0:
y12 = 0
elif y12> data.shape[1]:
msgBox = qt.QMessageBox()
msgBox.setText('Out of Volume')
msgBox.exec_()
if y22 < 0:
msgBox = qt.QMessageBox()
msgBox.setText('Out of Volume')
msgBox.exec_()
elif y22 > data.shape[1]:
y22 = data.shape[1] -1
if x12< 0:
x12 = 0
elif x12> data.shape[2]:
msgBox = qt.QMessageBox()
msgBox.setText('Out of Volume')
msgBox.exec_()
if x22 < 0:
msgBox = qt.QMessageBox()
msgBox.setText('Out of Volume')
msgBox.exec_()
elif x22 > data.shape[2]:
x22 = data.shape[2] -1
zones_in = [[z1,y1,z1,z2,y2,x2],[z12,y12,z12,z22,y22,x22]]
return zones_in
def _mySignal(self, qstring0):
qstring = qstring0
text = str(qstring0)
if text == '-':
return
(result, index) = self.ownValidator.validate(qstring, 0)
if result != self.ownValidator.Valid:
qstring = self.ownValidator.fixup(qstring)
(result, index) = self.ownValidator.validate(qstring, 0)
if result != self.ownValidator.Valid:
text = str(qstring)
if text.endswith(" "):
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Invalid Material Name '%s'\n" % text + \
"It ends with a space character.\n")
msg.exec_()
msg = qt.QMessageBox.No
else:
try:
# this test is needed even if pyflakes complains
float(text)
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Invalid Material Name %s\n" % text + \
"You cannot use a number as material name.\n" +\
"Hint: You can use _%s_" % text)
if QTVERSION < '4.0.0':
msg.exec_loop()
else:
msg.exec_()
msg = qt.QMessageBox.No
except:
msg=qt.QMessageBox.information( self, "Invalid Material %s" % str(qstring),
"The material %s is not a valid Formula " \
"nor a valid Material.\n" \
"Do you want to define the material %s\n" % \
(str(qstring), str(qstring)),
qt.QMessageBox.Yes,qt.QMessageBox.No)
if msg == qt.QMessageBox.No:
if QTVERSION < '4.0.0':
self.setCurrentItem(0)
else:
self.setCurrentIndex(0)
for i in range(self.count()):
if QTVERSION < '4.0.0':
selftext = self.text(i)
else:
selftext = self.itemText(i)
if selftext == qstring0:
self.removeItem(i)
return
else:
qstring = qstring0
text = str(qstring)
if Elements.isValidFormula(text):
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Invalid Material Name %s\n" % text + \
"The material is a valid Formula.\n " \
"There is no need to define it.")
if QTVERSION < '4.0.0':
msg.exec_loop()
else:
msg.exec_()
if QTVERSION < '4.0.0':
self.setCurrentItem(0)
else:
self.setCurrentIndex(0)
for i in range(self.count()):
if QTVERSION < '4.0.0':
selftext = self.text(i)
else:
selftext = self.itemText(i)
if selftext == qstring0:
self.removeItem(i)
break
return
self.setCurrentText(text)
dict = {}
dict['event'] = 'activated'
dict['row'] = self.row
dict['col'] = self.col
dict['text'] = text
if qstring0 != qstring:
self.removeItem(self.count() - 1)
insert = True
for i in range(self.count()):
if QTVERSION < '4.0.0':
selftext = self.text(i)
else:
selftext = self.itemText(i)
if qstring == selftext:
insert = False
if insert:
if QTVERSION < '4.0.0':
self.insertItem(qstring, -1)
else:
self.insertItem(self.count(), qstring)
if self.lineEdit() is not None:
if QTVERSION < '4.0.0':
self.lineEdit().setPaletteBackgroundColor(qt.QColor("white"))
if QTVERSION < '4.0.0':
self.emit(qt.PYSIGNAL('MaterialComboBoxSignal'), (dict, ))
else:
self.emit(qt.SIGNAL('MaterialComboBoxSignal'), (dict))
def __tableSlot2(self, row, col):
if self.__fillingValues: return
if self.__lastRow is None:
self.__lastRow = row
if self.__lastColumn is None:
self.__lastColumn = col
if QTVERSION < '4.0.0':
qstring = self.__table.text(self.__lastRow, self.__lastColumn)
else:
item = self.__table.item(self.__lastRow, self.__lastColumn)
if item is None:
item = qt.QTableWidgetItem("", qt.QTableWidgetItem.Type)
self.__table.setItem(self.__lastRow, self.__lastColumn, item)
qstring = item.text()
if self.__lastColumn == 0:
compound = str(qstring)
if Elements.isValidFormula(compound):
pass
else:
matkey = Elements.getMaterialKey(compound)
if matkey is not None:
if QTVERSION < '4.0.0':
self.__table.setText(self.__lastRow, self.__lastColumn,
matkey)
else:
item = self.__table.item(self.__lastRow,
self.__lastColumn)
if item is None:
item = qt.QTableWidgetItem(
matkey, qt.QTableWidgetItem.Type)
self.__table.setItem(self.__lastRow,
self.__lastColumn, item)
else:
item.setText(matkey)
else:
msg = qt.QMessageBox(self.__table)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Invalid Formula %s" % compound)
if QTVERSION < '4.0.0':
msg.exec_loop()
else:
msg.exec_()
self.__table.setCurrentCell(self.__lastRow,
self.__lastColumn)
return
else:
try:
float(str(qstring))
except:
msg = qt.QMessageBox(self.__table)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Invalid Float")
if QTVERSION < '4.0.0':
msg.exec_loop()
else:
msg.exec_()
self.__table.setCurrentCell(self.__lastRow, self.__lastColumn)
return
self._updateCurrent()
def _addSelectionSlot(self, sel_list, event=None):
if DEBUG:
print("_addSelectionSlot")
print("sel_list = ", sel_list)
if event is None: event = "addSelection"
for sel in sel_list:
#The dispatcher should be a singleton to work properly
#implement a patch
targetwidgetid = sel.get('targetwidgetid', None)
if targetwidgetid not in [None, id(self)]:
continue
#find the source
sourcelist = sel['SourceName']
for source in self.sourceList:
if source.sourceName == sourcelist:
ddict = {}
ddict.update(sel)
ddict["event"] = event
#we have found the source
#this recovers the data and the info
if True:
#this creates a data object that is passed to everybody so
#there is only one read out.
#I should create a weakref to it in order to be informed
#about its deletion.
if source.sourceType != "SPS":
if DEBUG:
dataObject = source.getDataObject(
sel['Key'], selection=sel['selection'])
else:
try:
dataObject = source.getDataObject(
sel['Key'], selection=sel['selection'])
except:
error = sys.exc_info()
text = "Failed to read data source.\n"
text += "Source: %s\n" % source.sourceName
text += "Key: %s\n" % sel['Key']
text += "Error: %s" % error[1]
if QTVERSION < '4.0.0':
qt.QMessageBox.critical(
self, "%s" % error[0], text)
else:
msg = qt.QMessageBox(self)
msg.setWindowTitle('Source Error')
msg.setIcon(qt.QMessageBox.Critical)
msg.setInformativeText(text)
msg.setDetailedText(\
traceback.format_exc())
continue
else:
dataObject = source.getDataObject(
sel['Key'],
selection=sel['selection'],
poll=False)
if dataObject is not None:
dataObject.info['legend'] = sel['legend']
dataObject.info[
'targetwidgetid'] = targetwidgetid
source.addToPoller(dataObject)
else:
#this may happen on deletion??
return
ddict['dataobject'] = dataObject
if QTVERSION < '4.0.0':
self.emit(qt.PYSIGNAL(event), (ddict, ))
else:
self.emit(qt.SIGNAL(event), ddict)
else:
#this creates a weak reference to the source object
#the clients will be able to retrieve the data
#the problem is that 10 clients will requiere
#10 read outs
ddict["sourcereference"] = weakref.ref(source)
if QTVERSION < '4.0.0':
self.emit(qt.PYSIGNAL(event), (ddict, ))
else:
self.emit(qt.SIGNAL(event), ddict)
def applyShifts(self):
'''
Generic shift method. The method shifts curves
according to the shift stored in self.shiftDict
and executes the method stored in self.shiftMethod.
Curves are sorted with respect to their legend,
the values of self.shiftDict are sorted with
respect to their key.
'''
if len(self.shiftDict) == 0:
msg = qt.QMessageBox(None)
msg.setWindowTitle('Alignment Error')
msg.setText('No shift data present.')
msg.setStandardButtons(qt.QMessageBox.Ok)
msg.exec_()
return False
# Check if interpolation is needed
if self.shiftMethod == self.fftShift:
curves = self.interpolate()
else:
curves = self.getAllCurves()
if len(self.shiftList) != len(curves):
msg = qt.QMessageBox(None)
msg.setWindowTitle('Alignment Error')
msg.setText(
'''Number of shifts does not match the number of curves.
Do you want to continue anyway?''')
msg.setStandardButtons(qt.QMessageBox.Ok)
msg.setStandardButtons(qt.QMessageBox.Ok | qt.QMessageBox.Cancel)
msg.setDefaultButton(qt.QMessageBox.Ok)
if msg.exec_() != qt.QMessageBox.Ok:
return False
if DEBUG:
print('applyShifts -- Shifting ...')
for idx, (x,y,legend,info) in enumerate(curves):
shift = self.shiftDict[legend]
if shift is None:
if DEBUG:
print('\tCurve \'%s\' not found in shiftDict\n%s'\
%(legend,str(self.shiftDict)))
continue
if shift == float('NaN'):
if DEBUG:
print('\tCurve \'%s\' has NaN shift'%legend)
continue
# Limit shift to zoomed in area
xmin, xmax = self.getGraphXLimits()
mask = numpy.nonzero((xmin<=x) & (x<=xmax))[0]
# Execute method stored in self.shiftMethod
xShifted, yShifted = self.shiftMethod(shift, x[mask], y[mask])
if idx == 0:
replace, replot = True, False
elif idx == (len(curves)-1):
replace, replot = False, True
else:
replace, replot = False, False
# Check if scan number is adopted by new curve
if DEBUG:
print('\'%s\' -- shifts -> \'%s\' by %f'%(self.shiftList[idx], legend, shift))
selectionlegend = info.get('selectionlegend',legend)
self.addCurve(xShifted, yShifted,
(selectionlegend + ' SHIFT'),
info,
replace, replot)
return True
def _loadImageFiles(self):
if self.getStackDataObject() is None:
return
getfilter = True
fileTypeList = [
"PNG Files (*png)", "JPEG Files (*jpg *jpeg)", "IMAGE Files (*)",
"EDF Files (*edf)", "EDF Files (*ccd)", "EDF Files (*)"
]
message = "Open image file"
filenamelist, filefilter = PyMcaFileDialogs.getFileList(
parent=None,
filetypelist=fileTypeList,
message=message,
getfilter=getfilter,
single=False,
currentfilter=None)
if len(filenamelist) < 1:
return
imagelist = []
imagenames = []
mask = self.getStackSelectionMask()
if mask is None:
r, n = self.getStackROIImagesAndNames()
shape = r[0].shape
else:
shape = mask.shape
if filefilter.split()[0] in ["EDF"]:
for filename in filenamelist:
#read the edf file
edf = EDFStack.EdfFileDataSource.EdfFileDataSource(filename)
#the list of images
keylist = edf.getSourceInfo()['KeyList']
if len(keylist) < 1:
msg = qt.QMessageBox(None)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Cannot read image from file")
msg.exec_()
return
for key in keylist:
#get the data
dataObject = edf.getDataObject(key)
data = dataObject.data
if data.shape[0] not in shape:
continue
if data.shape[1] not in shape:
continue
imagename = dataObject.info.get('Title', "")
if imagename != "":
imagename += " "
imagename += os.path.basename(filename) + " " + key
imagelist.append(data)
imagenames.append(imagename)
if len(imagelist) == 0:
msg = qt.QMessageBox(None)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Cannot read a valid image from the file")
msg.exec_()
return
crop = False
self.widget = StackPluginResultsWindow.StackPluginResultsWindow(
parent=None, usetab=False)
self.widget.buildAndConnectImageButtonBox()
qt.QObject.connect(self.widget, qt.SIGNAL('MaskImageWidgetSignal'),
self.mySlot)
self.widget.setStackPluginResults(imagelist,
image_names=imagenames)
self._showWidget()
return
else:
#Try pure Image formats
for filename in filenamelist:
image = qt.QImage(filename)
if image.isNull():
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Cannot read file %s as an image" % filename)
msg.exec_()
return
imagelist.append(image)
imagenames.append(os.path.basename(filename))
if len(imagelist) == 0:
msg = qt.QMessageBox(None)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Cannot read a valid image from the file")
msg.exec_()
return
self.widget = ExternalImagesWindow.ExternalImagesWindow(
parent=None,
rgbwidget=None,
selection=True,
colormap=True,
imageicons=True,
standalonesave=True)
self.widget.buildAndConnectImageButtonBox()
qt.QObject.connect(self.widget, qt.SIGNAL('MaskImageWidgetSignal'),
self.mySlot)
self.widget.setImageData(None)
self.widget.setQImageList(imagelist,
shape[1],
shape[0],
clearmask=False,
data=None,
imagenames=imagenames)
#data=self.__stackImageData)
self._showWidget()
return
def _pluginClicked(self):
actionList = []
menu = qt.QMenu(self)
text = qt.QString("Reload")
menu.addAction(text)
actionList.append(text)
menu.addSeparator()
callableKeys = ["Dummy"]
for m in self.pluginList:
if m == "PyMcaPlugins.Plugin1DBase":
continue
module = sys.modules[m]
if hasattr(module, 'MENU_TEXT'):
text = qt.QString(module.MENU_TEXT)
else:
text = os.path.basename(module.__file__)
if text.endswith('.pyc'):
text = text[:-4]
elif text.endswith('.py'):
text = text[:-3]
text = qt.QString(text)
methods = self.pluginInstanceDict[m].getMethods(plottype="SCAN")
if not len(methods):
continue
menu.addAction(text)
actionList.append(text)
callableKeys.append(m)
a = menu.exec_(qt.QCursor.pos())
if a is None:
return None
idx = actionList.index(a.text())
if idx == 0:
n = self.getPlugins()
if n < 1:
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Information)
msg.setText("Problem loading plugins")
msg.exec_()
return
key = callableKeys[idx]
methods = self.pluginInstanceDict[key].getMethods(plottype="SCAN")
if len(methods) == 1:
idx = 0
else:
actionList = []
methods.sort()
menu = qt.QMenu(self)
for method in methods:
text = qt.QString(method)
pixmap = self.pluginInstanceDict[key].getMethodPixmap(method)
tip = qt.QString(
self.pluginInstanceDict[key].getMethodToolTip(method))
if pixmap is not None:
action = qt.QAction(qt.QIcon(qt.QPixmap(pixmap)), text,
self)
else:
action = qt.QAction(text, self)
if tip is not None:
action.setToolTip(tip)
menu.addAction(action)
actionList.append((text, pixmap, tip, action))
qt.QObject.connect(menu, qt.SIGNAL("hovered(QAction *)"),
self._actionHovered)
a = menu.exec_(qt.QCursor.pos())
if a is None:
return None
idx = -1
for action in actionList:
if a.text() == action[0]:
idx = actionList.index(action)
try:
self.pluginInstanceDict[key].applyMethod(methods[idx])
except:
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
if QTVERSION < '4.0.0':
msg.setText("%s" % sys.exc_info()[1])
else:
msg.setWindowTitle("Plugin error")
msg.setText("An error has occured while executing the plugin:")
msg.setInformativeText(str(sys.exc_info()[1]))
msg.setDetailedText(traceback.format_exc())
msg.exec_()
def _calculateSlot(self):
if self._data is None:
msg = qt.QMessageBox(self)
msg.setWindowTitle("No data")
msg.setIcon(qt.QMessageBox.Information)
msg.setText("No data to perform calculation")
msg.exec_()
return
if self.nnmaParametersDialog is None:
self.nnmaParametersDialog = NNMAWindow.NNMAParametersDialog(self)
self.nnmaParametersDialog.nPC.setMaximum(self._spectrumLength)
self.nnmaParametersDialog.nPC.setValue(
min(10, self._spectrumLength))
ddict = {
'options': self._binningOptions,
'binning': 1,
'method': 0
}
self.nnmaParametersDialog.setParameters(ddict)
ret = self.nnmaParametersDialog.exec_()
if ret:
if DEBUG:
t0 = time.time()
nnmaParameters = self.nnmaParametersDialog.getParameters()
self.nnmaParametersDialog.close()
function = nnmaParameters['function']
binning = nnmaParameters['binning']
npc = nnmaParameters['npc']
kw = nnmaParameters['kw']
data = self._data
old_shape = self._data.shape
if DEBUG:
images, eigenvalues, eigenvectors = function(data,
npc,
binning=binning,
**kw)
else:
try:
threadResult = self._submitThread(function,
data,
npc,
binning=binning,
**kw)
if type(threadResult) == type((1, )):
if len(threadResult):
if threadResult[0] == "Exception":
raise Exception(threadResult[1],
threadResult[2])
images, eigenvalues, eigenvectors = threadResult
except:
if isinstance(data, numpy.ndarray):
self._data.shape = old_shape
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("%s" % sys.exc_info()[1])
msg.exec_()
return
if isinstance(self._data, numpy.ndarray):
self._data.shape = old_shape
if DEBUG:
print("NNMA Elapsed = ", time.time() - t0)
self.nnmaWindow.setPCAData(images, eigenvalues, eigenvectors)
self.nnmaWindow.show()
self.nnmaWindow.raise_()
def __printps(self, text):
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Sorry, Qt4 printing not implemented yet")
msg.exec_()
def estimate(self):
if self.specfit.fitconfig['McaMode']:
try:
mcaresult=self.specfit.mcafit()
except:
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Error on mcafit")
if QTVERSION < '4.0.0':msg.exec_loop()
else: msg.exec_()
ddict={}
ddict['event'] = 'FitError'
if QTVERSION < '4.0.0':
self.emit(qt.PYSIGNAL('SpecfitGUISignal'),(ddict,))
else:
self.emit(qt.SIGNAL('SpecfitGUISignal'), ddict)
if DEBUG:
raise
return
self.guiparameters.fillfrommca(mcaresult)
ddict={}
ddict['event'] = 'McaFitFinished'
ddict['data'] = mcaresult
if QTVERSION < '4.0.0':
self.emit(qt.PYSIGNAL('SpecfitGUISignal'),(ddict,))
else:
self.emit(qt.SIGNAL('SpecfitGUISignal'), ddict)
#self.guiparameters.removeallviews(keep='Region 1')
else:
try:
if self.specfit.theorydict[self.specfit.fitconfig['fittheory']][2] is not None:
self.specfit.estimate()
else:
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Information)
text = "Function does not define a way to estimate\n"
text += "the initial parameters. Please, fill them\n"
text += "yourself in the table and press Start Fit\n"
msg.setText(text)
if QTVERSION < '4.0.0':
msg.exec_loop()
else:
msg.setWindowTitle('SpecfitGUI Message')
msg.exec_()
return
except:
if DEBUG:
raise
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Error on estimate: %s" % sys.exc_info()[1])
if QTVERSION < '4.0.0':
msg.exec_loop()
else:
msg.exec_()
return
self.guiparameters.fillfromfit(self.specfit.paramlist,current='Fit')
self.guiparameters.removeallviews(keep='Fit')
ddict={}
ddict['event'] = 'EstimateFinished'
ddict['data'] = self.specfit.paramlist
if QTVERSION < '4.0.0':
self.emit(qt.PYSIGNAL('SpecfitGUISignal'),(ddict,))
else:
self.emit(qt.SIGNAL('SpecfitGUISignal'), ddict)
return
def getStack(self, filelist=None, imagestack=None):
if filelist in [None, []]:
filelist, filefilter = self._getStackOfFiles(getfilter=True)
else:
filefilter = ""
if not len(filelist):
return None
if filefilter == "":
if HDF5:
if h5py.is_hdf5(filelist[0]):
filefilter = "HDF5"
fileindex = 0
begin = None
end = None
aifirafile = False
if len(filelist):
PyMcaDirs.inputDir = os.path.dirname(filelist[0])
#if we are dealing with HDF5, no more tests needed
if not filefilter.upper().startswith('HDF5'):
f = open(filelist[0], 'rb')
#read 10 characters
if sys.version < '3.0':
line = f.read(10)
else:
line = str(f.read(10).decode())
f.close()
omnicfile = False
if filefilter.upper().startswith('HDF5'):
stack = QHDF5Stack1D.QHDF5Stack1D(filelist)
omnicfile = True
elif filefilter.upper().startswith('OPUS-DPT'):
stack = OpusDPTMap.OpusDPTMap(filelist[0])
omnicfile = True
elif filefilter.upper().startswith("AIFIRA"):
stack = AifiraMap.AifiraMap(filelist[0])
omnicfile = True
aifirafile = True
elif filefilter.upper().startswith("SUPAVISIO"):
stack = SupaVisioMap.SupaVisioMap(filelist[0])
omnicfile = True
elif filefilter.upper().startswith("TEXTIMAGE"):
imagestack = True
fileindex = 0
stack = TextImageStack.TextImageStack(imagestack=True)
elif filefilter.upper().startswith("IMAGE") and\
(filelist[0].upper().endswith("TIF") or\
filelist[0].upper().endswith("TIFF")):
stack = TiffStack.TiffStack(imagestack=True)
elif filefilter == "" and\
(filelist[0].upper().endswith("TIF") or\
filelist[0].upper().endswith("TIFF")):
stack = TiffStack.TiffStack(imagestack=True)
elif filefilter.upper().startswith("IMAGE"):
if imagestack is None:
imagestack = True
fileindex = 0
stack = QStack(imagestack=imagestack)
elif line[0] == "{":
if filelist[0].upper().endswith("RAW"):
if imagestack is None:
imagestack = True
stack = QStack(imagestack=imagestack)
elif line[0:2] in ["II", "MM"]:
if imagestack is None:
imagestack = True
stack = QStack(imagestack=imagestack)
elif line.startswith('Spectral'):
stack = OmnicMap.OmnicMap(filelist[0])
omnicfile = True
elif line.startswith('#\tDate'):
stack = LuciaMap.LuciaMap(filelist[0])
omnicfile = True
elif filelist[0].upper().endswith("RAW.GZ")or\
filelist[0].upper().endswith("EDF.GZ")or\
filelist[0].upper().endswith("CCD.GZ")or\
filelist[0].upper().endswith("RAW.BZ2")or\
filelist[0].upper().endswith("EDF.BZ2")or\
filelist[0].upper().endswith("CCD.BZ2"):
if imagestack is None:
imagestack = True
stack = QStack(imagestack=imagestack)
elif filelist[0][-4:].upper() in ["PIGE", "PIGE"]:
stack = SupaVisioMap.SupaVisioMap(filelist[0])
omnicfile = True
elif filelist[0][-3:].upper() in ["RBS"]:
stack = SupaVisioMap.SupaVisioMap(filelist[0])
omnicfile = True
elif filelist[0][-3:].upper() in ["SPE"] and\
(line[0] not in ['$', '#']):
#Roper Scientific format
#handle it as MarCCD stack
stack = QStack(imagestack=True)
else:
stack = QSpecFileStack()
if len(filelist) == 1:
if not omnicfile:
try:
stack.loadIndexedStack(filelist[0],
begin,
end,
fileindex=fileindex)
except:
msg = qt.QMessageBox()
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("%s" % sys.exc_info()[1])
if QTVERSION < '4.0.0':
msg.exec_loop()
else:
msg.exec_()
if DEBUG:
raise
elif len(filelist):
if not omnicfile:
try:
stack.loadFileList(filelist, fileindex=fileindex)
except:
msg = qt.QMessageBox()
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("%s" % sys.exc_info()[1])
if QTVERSION < '4.0.0':
msg.exec_loop()
else:
msg.exec_()
if DEBUG:
raise
if aifirafile:
masterStack = DataObject.DataObject()
masterStack.info = copy.deepcopy(stack.info)
masterStack.data = stack.data[:, :, 0:1024]
masterStack.info['Dim_2'] = int(masterStack.info['Dim_2'] / 2)
slaveStack = DataObject.DataObject()
slaveStack.info = copy.deepcopy(stack.info)
slaveStack.data = stack.data[:, :, 1024:]
slaveStack.info['Dim_2'] = int(slaveStack.info['Dim_2'] / 2)
return [masterStack, slaveStack]
else:
return stack
def __init__(self, parent = None, printer = None, name = "PyMcaPrintPreview", \
modal = 0, fl = 0):
qt.QDialog.__init__(self, parent)
self.setWindowTitle(name)
self.setModal(modal)
self.resize(400, 500)
self.printDialog = None
if printer is None:
printer = qt.QPrinter(qt.QPrinter.HighResolution)
printer.setPageSize(qt.QPrinter.A4)
printerName = "%s" % printer.printerName()
if printerName in ['id24b2u']:
#id24 printer very slow in color mode
printer.setColorMode(qt.QPrinter.GrayScale)
printer.setFullPage(True)
if (printer.width() <= 0) or (printer.height() <= 0):
if QTVERSION < '4.2.0': #this is impossible (no QGraphicsView)
filename = "PyMCA_print.pdf"
else:
filename = "PyMCA_print.ps"
if sys.platform == 'win32':
home = os.getenv('USERPROFILE')
try:
l = len(home)
directory = os.path.join(home, "My Documents")
except:
home = '\\'
directory = '\\'
if os.path.isdir('%s' % directory):
directory = os.path.join(directory, "PyMca")
else:
directory = os.path.join(home, "PyMca")
if not os.path.exists('%s' % directory):
os.mkdir('%s' % directory)
finalfile = os.path.join(directory, filename)
else:
home = os.getenv('HOME')
directory = os.path.join(home, "PyMca")
if not os.path.exists('%s' % directory):
os.mkdir('%s' % directory)
finalfile = os.path.join(directory, filename)
printer.setOutputFileName(finalfile)
printer.setColorMode(qt.QPrinter.Color)
if (printer.width() <= 0) or (printer.height() <= 0):
self.message = qt.QMessageBox(self)
self.message.setIcon(qt.QMessageBox.Critical)
self.message.setText(
"Unknown library error \non printer initialization")
self.message.setWindowTitle("Library Error")
self.message.setModal(0)
self.badNews = True
self.printer = None
return
else:
self.badNews = False
self.printer = printer
self.mainLayout = qt.QVBoxLayout(self)
self.mainLayout.setMargin(0)
self.mainLayout.setSpacing(0)
self._buildToolbar()
self.scene = qt.QGraphicsScene()
self.scene.setBackgroundBrush(qt.QColor(qt.Qt.lightGray))
self.page = qt.QGraphicsRectItem(0, 0, printer.width(),
printer.height())
self.page.setBrush(qt.QColor(qt.Qt.white))
self.scene.setSceneRect(
qt.QRectF(0, 0, printer.width(), printer.height()))
self.scene.addItem(self.page)
self.view = qt.QGraphicsView(self.scene)
self.mainLayout.addWidget(self.view)
self._buildStatusBar()
self.view.fitInView(self.page.rect(), qt.Qt.KeepAspectRatio)
self._viewScale = 1.00
def calculateShiftsFit(self, derivative=False, thr=30):
retDict = {}
retList = []
curves = self.getAllCurves()
nCurves = len(curves)
if nCurves < 2:
raise ValueError("At least 2 curves needed")
return
# Check if scan window is zoomed in
xmin, xmax = self.getGraphXLimits()
# Determine largest overlap between curves
xmin0, xmax0 = self.getXLimits(x for (x,y,leg,info) in curves)
if xmin0 > xmin:
xmin = xmin0
if xmax0 < xmax:
xmax = xmax0
if DEBUG:
print('calculateShiftsFit -- xmin = %.3f, xmax = %.3f'%(xmin, xmax))
# Get active curve
activeCurve = self.getActiveCurve()
if activeCurve is None:
# If active curve is not set, continue with first curve
activeCurve = curves[0]
else:
activeLegend = activeCurve[2]
idx = list.index([curve[2] for curve in curves],
activeLegend)
activeCurve = curves[idx]
x0, y0 = activeCurve[0], activeCurve[1]
idx = numpy.nonzero((xmin <= x0) & (x0 <= xmax))[0]
x0 = numpy.take(x0, idx)
y0 = numpy.take(y0, idx)
if derivative:
# Take first derivative
y0 = numpy.diff(y0)/numpy.diff(x0)
x0 = .5 * (x0[1:] + x0[:-1])
peak0 = self.findPeaks(x0, y0, .80, derivative)
if peak0:
xp0, yp0, fwhm0, fitrange0 = peak0
else:
raise ValueError("No peak identified in '%s'"%activeCurve[2])
fitp0, chisq0, sigma0 = LSF(gauss,
numpy.asarray([yp0, xp0, fwhm0]),
xdata=x0[fitrange0],
ydata=y0[fitrange0])
if DEBUG:
if derivative:
print('calculateShiftsFit -- Results (Leg, PeakPos, Shift):')
else:
print('calculateShiftsFitDerivative -- Results (Leg, PeakPos, Shift):')
for x,y,legend,info in curves:
idx = numpy.nonzero((xmin <= x) & (x <= xmax))[0]
x = numpy.take(x, idx)
y = numpy.take(y, idx)
if derivative:
# Take first derivative
y = numpy.diff(y)/numpy.diff(x)
x = .5 * (x[1:] + x[:-1])
peak = self.findPeaks(x, y, .80, derivative)
if peak:
xp, yp, fwhm, fitrange = peak
else:
raise ValueError("No peak identified in '%s'"%activeCurve[2])
try:
fitp, chisq, sigma = LSF(gauss,
numpy.asarray([yp, xp, fwhm]),
xdata=x[fitrange],
ydata=y[fitrange])
# Shift is difference in peak's x position
shift = fitp0[1] - fitp[1]
except numpy.linalg.linalg.LinAlgError:
msg = qt.QMessageBox(None)
msg.setWindowTitle('Alignment Error')
msg.setText('Singular matrix encountered during least squares fit.')
msg.setStandardButtons(qt.QMessageBox.Ok)
msg.exec_()
shift = float('NaN')
key = legend
retList.append(key)
retDict[key] = shift
if DEBUG:
print( '\t%s\t%.3f\t%.3f'%(legend, fitp[1], shift))
return retList, retDict
def updateGraph(self, ddict):
self.__lastDict = ddict
edgeEnergy = ddict['edge_energy']
preRegions = ddict['pre_edge']['regions']
postRegions = ddict['post_edge']['regions']
event = ddict.get('event', None)
if event == "AutoEdgeEnergyClicked":
try:
# recalculate edge energy following region limits
xmin = edgeEnergy + preRegions[0][0]
xmax = edgeEnergy + postRegions[0][1]
idx = numpy.nonzero((self.energy >= xmin) &\
(self.energy <= xmax))[0]
x = numpy.take(self.energy, idx)
y = numpy.take(self.spectrum, idx)
edgeEnergy = XASNormalization.estimateXANESEdge(y,
energy=x,
full=False)
self.parametersWidget.setEdgeEnergy(edgeEnergy,
emin=self.energy.min(),
emax=self.energy.max())
self.__lastDict['edge_energy'] = edgeEnergy
except:
pass
parameters = {}
parameters['pre_edge_order'] = ddict['pre_edge']['polynomial']
parameters['post_edge_order'] = ddict['post_edge']['polynomial']
algorithm = 'polynomial'
if self.__markerHandling:
self.updateMarkers(edgeEnergy,
preRegions,
postRegions,
edge_auto=ddict['auto_edge'])
else:
self.graph.addCurve(
[edgeEnergy, edgeEnergy],
[self.spectrum.min(), self.spectrum.max()],
legend="Edge Position",
replace=False)
try:
normalizationResult = XASNormalization.XASNormalization(
self.spectrum,
self.energy,
edge=edgeEnergy,
pre_edge_regions=preRegions,
post_edge_regions=postRegions,
algorithm=algorithm,
algorithm_parameters=parameters)
except:
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setWindowTitle("Normalization Error")
msg.setText("An error has occured while normalizing the data")
msg.setInformativeText(str(sys.exc_info()[1]))
msg.setDetailedText(traceback.format_exc())
msg.exec_()
return
nEnergy, nSpectrum, usedEdge, jump = normalizationResult[0:4]
preEdgeFunction, preEdgeParameters = normalizationResult[4:6]
postEdgeFunction, postEdgeParameters = normalizationResult[6:8]
idx = self.energy > (usedEdge + preRegions[0][0])
x = self.energy[idx]
yPre = preEdgeFunction(preEdgeParameters, x)
yPost = postEdgeFunction(postEdgeParameters, x)
self.graph.addCurve(x,
yPre,
legend="Pre-edge Polynomial",
replace=False)
self.graph.addCurve(x,
yPost + yPre,
legend="Post-edge Polynomial",
replace=False,
replot=True)
def saveClicked(self):
outfile = qt.QFileDialog(self)
outfile.setModal(1)
if self.lastOutputDir is None:
self.lastOutputDir = PyMcaDirs.outputDir
outfile.setWindowTitle("Output File Selection")
if hasattr(qt, "QStringList"):
strlist = qt.QStringList()
else:
strlist = []
format_list = []
format_list.append('Graphics PNG *.png')
format_list.append('Graphics EPS *.eps')
format_list.append('Graphics SVG *.svg')
for f in format_list:
strlist.append(f)
outfile.setFilters(strlist)
outfile.setFileMode(outfile.AnyFile)
outfile.setAcceptMode(qt.QFileDialog.AcceptSave)
outfile.setDirectory(self.lastOutputDir)
ret = outfile.exec_()
if ret:
filterused = qt.safe_str(outfile.selectedFilter()).split()
filedescription = filterused[0]
filetype = filterused[1]
extension = filterused[2]
try:
outstr = qt.safe_str(outfile.selectedFiles()[0])
except:
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Error saving image: %s" % sys.exc_info()[1])
msg.setWindowTitle('Matplotlib Save Image')
msg.exec_()
try:
outputDir = os.path.dirname(outstr)
self.lastOutputDir = outputDir
PyMcaDirs.outputDir = outputDir
except:
outputDir = "."
try:
outputFile = os.path.basename(outstr)
except:
outputFile = outstr
outfile.close()
del outfile
else:
outfile.close()
del outfile
return
#always overwrite for the time being
if len(outputFile) < len(extension[1:]):
outputFile += extension[1:]
elif outputFile[-4:] != extension[1:]:
outputFile += extension[1:]
finalFile = os.path.join(outputDir, outputFile)
if os.path.exists(finalFile):
try:
os.remove(finalFile)
except:
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Cannot overwrite file: %s" % sys.exc_info()[1])
msg.setWindowTitle('Matplotlib Save Image')
msg.exec_()
return
try:
self.imageWidget.print_figure(finalFile,
edgecolor='w',
facecolor='w',
format=finalFile[-3:],
dpi=self.imageWidget.config['outputdpi'])
except:
print("WARNING: trying to save using obsolete method")
config = self.imageWidget.getParameters()
try:
s=PyMcaMatplotlibSave.PyMcaMatplotlibSaveImage(self.imageWidget.imageData)
if self.imageWidget.pixmapImage is not None:
s.setPixmapImage(self.imageWidget.pixmapImage)
s.setParameters(config)
s.saveImage(finalFile)
except:
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Error saving file: %s" % sys.exc_info()[1])
msg.setWindowTitle('Matplotlib Save Image')
msg.exec_()
def _calculateSlot(self):
if self._data is None:
msg = qt.QMessageBox(self)
msg.setWindowTitle("No data")
msg.setIcon(qt.QMessageBox.Information)
msg.setText("No data to perform calculation")
msg.exec_()
return
if not self.pcaParametersDialogInitialized:
self.pcaParametersDialog.nPC.setMaximum(self._spectrumLength)
self.pcaParametersDialog.nPC.setValue(
min(10, self._spectrumLength))
ddict = {'options': self._binningOptions,
'binning': 1,
'method': 0}
self.pcaParametersDialog.setParameters(ddict)
self.pcaParametersDialogInitialized = True
ret = self.pcaParametersDialog.exec_()
if ret:
if DEBUG:
t0 = time.time()
pcaParameters = self.pcaParametersDialog.getParameters()
self.pcaParametersDialog.close()
function = pcaParameters['function']
binning = pcaParameters['binning']
npc = pcaParameters['npc']
mask = pcaParameters['mask']
kw = pcaParameters.get('kw', {})
data = self._data
old_shape = self._data.shape
if mask is not None:
if mask.sum() < npc:
msg = qt.QMessageBox(self)
msg.setWindowTitle("Not enough data")
msg.setIcon(qt.QMessageBox.Information)
msg.setText("Number of components too high")
msg.exec_()
return
if DEBUG:
images, eigenvalues, eigenvectors = function(data,
npc,
binning=binning,
mask=mask,
**kw)
else:
try:
threadResult = self._submitThread(function,
data,
npc,
binning=binning,
mask=mask,
**kw)
if type(threadResult) == type((1,)):
if len(threadResult):
if threadResult[0] == "Exception":
raise Exception(threadResult[1],
threadResult[2])
images, eigenvalues, eigenvectors = threadResult
except:
if isinstance(data, numpy.ndarray):
self._data.shape = old_shape
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("%s" % sys.exc_info()[1])
msg.exec_()
return
if isinstance(self._data, numpy.ndarray):
self._data.shape = old_shape
if DEBUG:
print("PCA Elapsed = ", time.time() - t0)
methodlabel = pcaParameters.get('methodlabel', "")
imagenames = None
vectornames = None
if " ICA " in methodlabel:
nimages = images.shape[0]
imagenames = []
vectornames = []
itmp = int(nimages / 2)
for i in range(itmp):
imagenames.append("ICAimage %02d" % i)
vectornames.append("ICAvector %02d" % i)
for i in range(itmp):
imagenames.append("Eigenimage %02d" % i)
vectornames.append("Eigenvector %02d" % i)
self.pcaWindow.setPCAData(images,
eigenvalues,
eigenvectors,
imagenames=imagenames,
vectornames=vectornames)
self.pcaWindow.show()
self.pcaWindow.raise_()