def onProcessStackFinished(self):
_logger.debug("Stack proccessed")
self._status = "Stack Fitting finished"
if self.fixedLenghtOutput:
self._status = "Writing output files"
nParameters = len(self._parameters)
datalist = [None] * (2*len(self._sigmas.keys())+1)
labels = []
for i in range(nParameters):
parameter = self._parameters[i]
datalist[2*i] = self._images[parameter]
datalist[2*i + 1] = self._sigmas[parameter]
labels.append(parameter)
labels.append('s(%s)' % parameter)
datalist[-1] = self._images['chisq']
labels.append('chisq')
filenames = self.getOutputFileNames()
csvName = filenames['csv']
edfName = filenames['edf']
ArraySave.save2DArrayListAsASCII(datalist,
csvName,
labels=labels,
csv=True,
csvseparator=";")
ArraySave.save2DArrayListAsEDF(datalist,
edfName,
labels = labels,
dtype=numpy.float32)
def onProcessStackFinished(self):
_logger.debug("Stack proccessed")
self._status = "Stack Fitting finished"
if self.fixedLenghtOutput:
self._status = "Writing output files"
nParameters = len(self._parameters)
datalist = [None] * (2 * len(self._sigmas.keys()) + 1)
labels = []
for i in range(nParameters):
parameter = self._parameters[i]
datalist[2 * i] = self._images[parameter]
datalist[2 * i + 1] = self._sigmas[parameter]
labels.append(parameter)
labels.append('s(%s)' % parameter)
datalist[-1] = self._images['chisq']
labels.append('chisq')
filenames = self.getOutputFileNames()
csvName = filenames['csv']
edfName = filenames['edf']
ArraySave.save2DArrayListAsASCII(datalist,
csvName,
labels=labels,
csv=True,
csvseparator=";")
ArraySave.save2DArrayListAsEDF(datalist,
edfName,
labels=labels,
dtype=numpy.float32)
def _handleSaveIcon(self, event):
"""Handle save icon events.
Get current active image and save it as a file.
"""
if event['event'] == 'iconClicked' and event['key'] == 'save':
imageData = self.getActiveImage()
if imageData is None:
qt.QMessageBox.information(self, "No Data",
"No image to be saved")
return
data, legend, info, pixmap = imageData
imageList = [data]
labels = ['value']
# Copied from MaskImageWidget.saveImageList
filename = self.getOutputFileName()
if not len(filename):
return
# Add PNG and JPG adapted from PlotWindow.defaultSaveAction
if 'WIDGET' in self._saveFilter.upper():
fformat = self._saveFilter[-3:].upper()
pixmap = qt.QPixmap.grabWidget(self._imagePlot)
# Use the following instead to grab the image + histograms
# pixmap = qt.QPixmap.grabWidget(self)
if not pixmap.save(filename, fformat):
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setInformativeText(str(sys.exc_info()[1]))
msg.setDetailedText(traceback.format_exc())
msg.exec_()
return
if filename.lower().endswith(".edf"):
ArraySave.save2DArrayListAsEDF(imageList, filename, labels)
elif filename.lower().endswith(".csv"):
if "," in self._saveFilter:
csvseparator = ","
elif ";" in self._saveFilter:
csvseparator = ";"
else:
csvseparator = "\t"
ArraySave.save2DArrayListAsASCII(imageList, filename, labels,
csv=True,
csvseparator=csvseparator)
else:
ArraySave.save2DArrayListAsASCII(imageList, filename, labels,
csv=False)
def saveImageList(self, filename, imageList, labels, csvseparator=None):
if not imageList:
qt.QMessageBox.information(
self, "No Data", "Image list is empty.\nNothing to be saved")
return
if filename.lower().endswith(".edf"):
ArraySave.save2DArrayListAsEDF(imageList, filename, labels)
elif filename.lower().endswith(".csv"):
assert csvseparator is not None
ArraySave.save2DArrayListAsASCII(imageList,
filename,
labels,
csv=True,
csvseparator=csvseparator)
else:
ArraySave.save2DArrayListAsASCII(imageList,
filename,
labels,
csv=False)
def saveImageList(self, filename, imageList, labels,
csvseparator=None):
if not imageList:
qt.QMessageBox.information(
self,
"No Data",
"Image list is empty.\nNothing to be saved")
return
if filename.lower().endswith(".edf"):
ArraySave.save2DArrayListAsEDF(imageList, filename, labels)
elif filename.lower().endswith(".tif"):
ArraySave.save2DArrayListAsMonochromaticTiff(imageList,
filename,
labels)
elif filename.lower().endswith(".csv"):
assert csvseparator is not None
ArraySave.save2DArrayListAsASCII(imageList, filename, labels,
csv=True,
csvseparator=csvseparator)
else:
ArraySave.save2DArrayListAsASCII(imageList, filename, labels,
csv=False)
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 _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()
# 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)
fileImageNames = [None] * (nImages)
j = 0
for i in range(nImages):
name = imageNames[i].replace(" ","-")
fileImageNames[j] = name
imageList[j] = images[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]
mass_fraction = "_" + label
fileName = os.path.join(imagesDir,
fileRoot + mass_fraction + ".tif")
ArraySave.save2DArrayListAsMonochromaticTiff([imageList[i]],
fileName,
labels=[label],
dtype=numpy.float32)
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])
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()
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)
