def _threadFinished(self):
result = self.thread.result
self.thread = None
if type(result) == type((1, )):
#if we receive a tuple there was an error
if len(result):
if result[0] == "Exception":
# somehow this exception is not caught
raise Exception(result[1], result[2]) #, result[3])
return
# Show results
with result.bufferContext(update=True):
imageNames = result.labels('roisum', labeltype='title')
images = result['roisum']
self._widget = StackPluginResultsWindow.StackPluginResultsWindow(\
usetab=False)
self._widget.buildAndConnectImageButtonBox(replace=True,
multiple=True)
qt = StackPluginResultsWindow.qt
self._widget.sigMaskImageWidgetSignal.connect(self.mySlot)
self._widget.setStackPluginResults(images, image_names=imageNames)
self._showWidget()
# Save results
result.save()
def _threadFinished(self):
result = self.thread.result
self.thread = None
if type(result) == type((1, )):
#if we receive a tuple there was an error
if len(result):
if result[0] == "Exception":
# somehow this exception is not caught
raise Exception(result[1], result[2]) #, result[3])
return
# Show results
if 'massfractions' in result:
imageNames = result.parameter_names + result.massfraction_names
images = numpy.concatenate(
(result['parameters'], result['massfractions']), axis=0)
else:
imageNames = result.parameter_names
images = result['parameters']
nImages = images.shape[0]
self._widget = StackPluginResultsWindow.StackPluginResultsWindow(\
usetab=False)
self._widget.buildAndConnectImageButtonBox(replace=True, multiple=True)
qt = StackPluginResultsWindow.qt
self._widget.sigMaskImageWidgetSignal.connect(self.mySlot)
self._widget.setStackPluginResults(images, image_names=imageNames)
self._showWidget()
# Save results
result.save()
def threadFinished(self):
if DEBUG:
print("NNMAStackPlugin threadFinished")
result = self.thread.result
self.thread = None
if type(result) == type((1,)):
#if we receive a tuple there was an error
if len(result):
if type(result[0]) == type("Exception"):
if result[0] == "Exception":
self._status.setText("Ready after calculation error")
self.configurationWidget.setEnabled(True)
raise Exception(result[1], result[2])
return
self._status.setText("Ready")
curve = self.configurationWidget.getSpectrum(binned=True)
if curve not in [None, []]:
xValues = curve[0]
else:
xValues = None
self.configurationWidget.setEnabled(True)
self.configurationWidget.close()
images, eigenValues, eigenVectors = result
imageNames = None
vectorNames = None
nimages = images.shape[0]
imageNames = []
vectorNames = []
vectorTitles = []
for i in range(nimages):
imageNames.append("NNMA Image %02d" % i)
vectorNames.append("NNMA Component %02d" % i)
vectorTitles.append("%g %% explained intensity" %\
eigenValues[i])
if DEBUG:
print("NNMAStackPlugin threadFinished. Create widget")
self.widget = StackPluginResultsWindow.StackPluginResultsWindow(\
usetab=True)
if DEBUG:
print("NNMAStackPlugin threadFinished. Widget created")
self.widget.buildAndConnectImageButtonBox(replace=True,
multiple=True)
qt = StackPluginResultsWindow.qt
self.widget.sigMaskImageWidgetSignal.connect(self.mySlot)
if xValues is not None:
xValues = [xValues] * nimages
self.widget.setStackPluginResults(images,
spectra=eigenVectors,
image_names=imageNames,
xvalues=xValues,
spectra_names=vectorNames,
spectra_titles=vectorTitles)
self._showWidget()
def threadFinished(self):
result = self.thread.getResult()
self.thread = None
if type(result) == type((1, )):
#if we receive a tuple there was an error
if len(result):
if result[0] == "Exception":
self._status.setText("Ready after calculation error")
self.configurationWidget.setEnabled(True)
raise Exception(result[1], result[2])
return
self._status.setText("Ready")
curve = self.configurationWidget.getSpectrum(binned=True)
if curve not in [None, []]:
xValues = curve[0]
else:
xValues = None
self.configurationWidget.setEnabled(True)
self.configurationWidget.close()
images, eigenValues, eigenVectors = result
methodlabel = self.__methodlabel
imageNames = None
vectorNames = None
nimages = images.shape[0]
imageNames = []
vectorNames = []
itmp = nimages
if " ICA " in methodlabel:
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.widget = StackPluginResultsWindow.StackPluginResultsWindow(\
usetab=True)
self.widget.buildAndConnectImageButtonBox(replace=True, multiple=True)
qt = StackPluginResultsWindow.qt
self.widget.sigMaskImageWidgetSignal.connect(self.mySlot)
if xValues is not None:
xValues = [xValues] * nimages
self.widget.setStackPluginResults(images,
spectra=eigenVectors,
image_names=imageNames,
xvalues=xValues,
spectra_names=vectorNames)
self._showWidget()
def _threadFinished(self):
result = self.thread.result
self.thread = None
if type(result) == type((1, )):
#if we receive a tuple there was an error
if len(result):
if result[0] == "Exception":
# somehow this exception is not caught
raise Exception(result[1], result[2]) #, result[3])
return
imageNames = result['names']
images = result["images"]
nImages = images.shape[0]
self._widget = StackPluginResultsWindow.StackPluginResultsWindow(\
usetab=False)
self._widget.buildAndConnectImageButtonBox(replace=True, multiple=True)
qt = StackPluginResultsWindow.qt
self._widget.sigMaskImageWidgetSignal.connect(self.mySlot)
self._widget.setStackPluginResults(images, image_names=imageNames)
self._showWidget()
def _threadFinished(self):
result = self.thread.result
self.thread = None
if type(result) == type((1, )):
#if we receive a tuple there was an error
if len(result):
if result[0] == "Exception":
# somehow this exception is not caught
raise Exception(result[1], result[2]) #, result[3])
return
if 'concentrations' in result:
imageNames = result['names']
images = numpy.concatenate(
(result['parameters'], result['concentrations']), axis=0)
else:
images = result['parameters']
imageNames = result['names']
nImages = images.shape[0]
self._widget = StackPluginResultsWindow.StackPluginResultsWindow(\
usetab=False)
self._widget.buildAndConnectImageButtonBox(replace=True, multiple=True)
qt = StackPluginResultsWindow.qt
self._widget.sigMaskImageWidgetSignal.connect(self.mySlot)
self._widget.setStackPluginResults(images, image_names=imageNames)
self._showWidget()
# save to output directory
parameters = self.configurationWidget.getParameters()
outputDir = parameters["output_dir"]
if outputDir in [None, ""]:
if DEBUG:
print("Nothing to be saved")
return
if parameters["file_root"] is None:
fileRoot = ""
else:
fileRoot = parameters["file_root"].replace(" ", "")
if fileRoot in [None, ""]:
fileRoot = "images"
if not os.path.exists(outputDir):
os.mkdir(outputDir)
imagesDir = os.path.join(outputDir, "IMAGES")
if not os.path.exists(imagesDir):
os.mkdir(imagesDir)
imageList = [None] * (nImages + len(result['uncertainties']))
fileImageNames = [None] * (nImages + len(result['uncertainties']))
j = 0
for i in range(nImages):
name = imageNames[i].replace(" ", "-")
fileImageNames[j] = name
imageList[j] = images[i]
j += 1
if not imageNames[i].startswith("C("):
# fitted parameter
fileImageNames[j] = "s(%s)" % name
imageList[j] = result['uncertainties'][i]
j += 1
fileName = os.path.join(imagesDir, fileRoot + ".edf")
ArraySave.save2DArrayListAsEDF(imageList,
fileName,
labels=fileImageNames)
fileName = os.path.join(imagesDir, fileRoot + ".csv")
ArraySave.save2DArrayListAsASCII(imageList,
fileName,
csv=True,
labels=fileImageNames)
if parameters["tiff"]:
i = 0
for i in range(len(fileImageNames)):
label = fileImageNames[i]
if label.startswith("s("):
continue
elif label.startswith("C("):
mass_fraction = "_" + label[2:-1] + "_mass_fraction"
else:
mass_fraction = "_" + label
fileName = os.path.join(imagesDir,
fileRoot + mass_fraction + ".tif")
ArraySave.save2DArrayListAsMonochromaticTiff(
[imageList[i]],
fileName,
labels=[label],
dtype=numpy.float32)
def XASNormalize(self):
stack = self.getStackDataObject()
if not isinstance(stack.data, numpy.ndarray):
text = "This method does not work with dynamically loaded stacks"
raise TypeError(text)
activeCurve = self.getActiveCurve()
if activeCurve in [None, []]:
return
x, spectrum, legend, info = activeCurve
if self.widget is None:
self.widget = XASNormalizationWindow.XASNormalizationDialog(
None, spectrum, energy=x)
else:
oldParameters = self.widget.getParameters()
oldEnergy = self.widget.parametersWidget.energy
oldEMin = oldEnergy.min()
oldEMax = oldEnergy.max()
self.widget.setData(spectrum, energy=x)
if abs(oldEMin - x.min()) < 1:
if abs(oldEMax - x.max()) < 1:
self.widget.setParameters(oldParameters)
ret = self.widget.exec()
if ret:
parameters = self.widget.getParameters()
# TODO: this dictionary adaptation should be made
# by the configuration
if parameters['auto_edge']:
edge = None
else:
edge = parameters['edge_energy']
energy = x
pre_edge_regions = parameters['pre_edge']['regions']
post_edge_regions = parameters['post_edge']['regions']
algorithm = 'polynomial'
algorithm_parameters = {}
algorithm_parameters['pre_edge_order'] = parameters['pre_edge']\
['polynomial']
algorithm_parameters['post_edge_order'] = parameters['post_edge']\
['polynomial']
result = self.__replaceStackByXASNormalizedData(
stack,
energy=energy,
edge=edge,
pre_edge_regions=pre_edge_regions,
post_edge_regions=post_edge_regions,
algorithm=algorithm,
algorithm_parameters=algorithm_parameters)
if result[0] == 'Exception':
# exception occurred
raise Exception(result[1], result[2], result[3])
else:
edges, jumps, errors = result
images, names = self.getStackROIImagesAndNames()
edges.shape = images[0].shape
jumps.shape = images[0].shape
errors.shape = images[0].shape
self.setStack(stack)
if self.imageWidget is None:
self.imageWidget = StackPluginResultsWindow.StackPluginResultsWindow(\
usetab=False,profileselection=True)
self.imageWidget.buildAndConnectImageButtonBox()
qt = StackPluginResultsWindow.qt
self.imageWidget.sigMaskImageWidgetSignal.connect(self.mySlot)
self.methodDict["Show Images"] = [
self._showImageWidget,
"Show calculated jump and edge position images", None
]
self.__methodKeys.append("Show Images")
self.imageWidget.setStackPluginResults(
[jumps, errors, edges],
image_names=['Jump', 'Errors', 'Edge Position'])
self._showImageWidget()
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()
self.widget.sigMaskImageWidgetSignal.connect(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()
self.widget.sigMaskImageWidgetSignal.connect(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 _loadImageFiles(self):
if self.getStackDataObject() is None:
return
getfilter = True
fileTypeList = [
"PNG Files (*png)", "JPEG Files (*jpg *jpeg)", "IMAGE Files (*)",
"DAT Files (*dat)", "CSV Files (*csv)", "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
extension = qt.safe_str(os.path.splitext(filenamelist[0])[1])
if (filefilter.split()[0] in ["EDF"]) or \
(extension.upper() in [".EDF", ".TIF"]):
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()
self.widget.sigMaskImageWidgetSignal.connect(self.mySlot)
self.widget.setStackPluginResults(imagelist,
image_names=imagenames)
self._showWidget()
return
elif extension.lower() in [".csv", ".dat"]:
# what to do if more than one file selected ?
from PyMca5.PyMca import specfilewrapper as Specfile
sf = Specfile.Specfile(filenamelist[0])
scan = sf[0]
labels = scan.alllabels()
data = scan.data()
scan = None
sf = None
if "column" in labels:
offset = labels.index("column")
ncols = int(data[offset].max() + 1)
offset += 1
else:
raise IOError("Only images exported as csv supported")
imagelist = []
imagenames = []
for i in range(offset, len(labels)):
if labels[i].startswith("s("):
continue
tmpData = data[i]
tmpData.shape = -1, ncols
imagelist.append(tmpData)
imagenames.append(labels[i])
crop = False
self.widget = StackPluginResultsWindow.StackPluginResultsWindow(
parent=None, usetab=False)
self.widget.buildAndConnectImageButtonBox()
self.widget.sigMaskImageWidgetSignal.connect(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(None)
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()
self.widget.sigMaskImageWidgetSignal.connect(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
