def _getFileList(self, fileTypeList, message=None, getfilter=None):
if message is None:
message = "Please select a file"
if getfilter is None:
getfilter = False
wdir = PyMcaDirs.inputDir
filterused = None
if getfilter:
filelist, filterused = PyMcaFileDialogs.getFileList(self.parent,
filetypelist=fileTypeList,
mode="OPEN",
message=message,
currentdir=wdir,
getfilter=True,
single=False,
native=True)
else:
filelist = PyMcaFileDialogs.getFileList(self.parent,
filetypelist=fileTypeList,
mode="OPEN",
message=message,
currentdir=wdir,
getfilter=False,
single=False,
native=True)
if not(len(filelist)):
return []
PyMcaDirs.inputDir = os.path.dirname(filelist[0])
if PyMcaDirs.outputDir is None:
PyMcaDirs.outputDir = os.path.dirname(filelist[0])
if getfilter:
return filelist, filterused
else:
return filelist
def browseFitConfiguration(self):
if self._inputDir is None:
self._inputDir = PyMcaDirs.inputDir
elif os.path.exists(self._inputDir):
PyMcaDirs.inputDir = self._inputDir
filetypes = ["Configuration Files (*.cfg)"]
if self._inputDir is None:
self._inputDir = PyMcaDirs.inputDir
elif os.path.exists(self._inputDir):
PyMcaDirs.inputDir = self._inputDir
message = "Select a Simple Fit Configuration File"
mode = "OPEN"
getfilter = False
currentfilter = None #self._lastInputFileFilter
fileList = PyMcaFileDialogs.getFileList(self,
filetypelist=filetypes,
message=message,
mode=mode,
getfilter=getfilter,
single=True,
currentfilter=currentfilter)
if not len(fileList):
return
self._inputDir = os.path.dirname(fileList[0])
self.setFitConfigurationFile(fileList[0])
self.raise_()
def _getOutputTiffFilename(self):
fileTypes = "TIFF Files (*.tif *.tiff *.TIF *.TIFF)"
message = "Enter output filename"
wdir = PyMcaDirs.outputDir
filename = PyMcaFileDialogs.getFileList(self,
message=message,
mode="SAVE",
currentdir=wdir,
filetypelist=[fileTypes],
getfilter=False,
single=True)
if len(filename):
filename = filename[0]
if len(filename):
try:
fname = qt.safe_str(filename)
if fname.endswith('.tif') or\
fname.endswith('.tiff') or\
fname.endswith('.TIF') or\
fname.endswith('.TIFF'):
return fname
else:
return fname + ".tif"
except UnicodeEncodeError:
msg = qt.QMessageBox(self)
msg.setWindowTitle("Encoding error")
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Please use ASCII characters in file name and path")
msg.exec_()
return ""
def _getOutputTiffFilename(self):
fileTypes = "TIFF Files (*.tif *.tiff *.TIF *.TIFF)"
message = "Enter output filename"
wdir = PyMcaDirs.outputDir
filename = PyMcaFileDialogs.getFileList(self,
message=message,
mode="SAVE",
currentdir=wdir,
filetypelist=[fileTypes],
getfilter=False,
single=True)
if len(filename):
filename = filename[0]
if len(filename):
try:
fname = qt.safe_str(filename)
if fname.endswith('.tif') or\
fname.endswith('.tiff') or\
fname.endswith('.TIF') or\
fname.endswith('.TIFF'):
return fname
else:
return fname + ".tif"
except UnicodeEncodeError:
msg = qt.QMessageBox(self)
msg.setWindowTitle("Encoding error")
msg.setIcon(qt.QMessageBox.Critical)
msg.setText(
"Please use ASCII characters in file name and path")
msg.exec_()
return ""
def _loadSlot(self):
if self.inputDir is None:
if self.inputDir is not None:
self.inputDir = self.outputDir
else:
self.inputDir = PyMcaDirs.inputDir
wdir = self.inputDir
if not os.path.exists(wdir):
wdir = os.getcwd()
filename = PyMcaFileDialogs.getFileList(self,
filetypelist=["Transmission table files (*.csv)",
"Transmission table files (*)"],
mode="OPEN",
message="Choose 2-column transmission table file",
currentdir=wdir,
single=True)
if len(filename):
filename = qt.safe_str(filename[0])
if len(filename):
try:
self.loadTransmissionTable(filename)
self.inputDir = os.path.dirname(filename)
PyMcaDirs.inputDir = self.inputDir
except:
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Error transmission table: %s" % (sys.exc_info()[1]))
msg.exec()
return
def loadButtonClicked(self):
if self.inputDir is None:
if self.inputDir is not None:
self.inputDir = self.outputDir
else:
self.inputDir = PyMcaDirs.inputDir
wdir = self.inputDir
if not os.path.exists(wdir):
wdir = os.getcwd()
filename = PyMcaFileDialogs.getFileList(
self,
filetypelist=["Energy table files (*.csv)"],
mode="OPEN",
message="Choose energy table file",
currentdir=wdir,
single=True)
if len(filename):
filename = qt.safe_str(filename[0])
if len(filename):
try:
self.loadEnergyTableParameters(filename)
self.inputDir = os.path.dirname(filename)
PyMcaDirs.inputDir = self.inputDir
except:
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Error loading energy table: %s" %
(sys.exc_info()[1]))
msg.exec_()
def loadButtonClicked(self):
if self.inputDir is None:
if self.inputDir is not None:
self.inputDir = self.outputDir
else:
self.inputDir = PyMcaDirs.inputDir
wdir = self.inputDir
if not os.path.exists(wdir):
wdir = os.getcwd()
filename = PyMcaFileDialogs.getFileList(self,
filetypelist=["Energy table files (*.csv)"],
mode="OPEN",
message="Choose energy table file",
currentdir=wdir,
single=True)
if len(filename):
filename = qt.safe_str(filename[0])
if len(filename):
try:
self.loadEnergyTableParameters(filename)
self.inputDir = os.path.dirname(filename)
PyMcaDirs.inputDir = self.inputDir
except:
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Error loading energy table: %s" % (sys.exc_info()[1]))
msg.exec_()
def browseFitConfiguration(self):
if self._inputDir is None:
self._inputDir = PyMcaDirs.inputDir
elif os.path.exists(self._inputDir):
PyMcaDirs.inputDir = self._inputDir
filetypes = ["Configuration Files (*.cfg)"]
if self._inputDir is None:
self._inputDir = PyMcaDirs.inputDir
elif os.path.exists(self._inputDir):
PyMcaDirs.inputDir = self._inputDir
message = "Select a Simple Fit Configuration File"
mode = "OPEN"
getfilter = False
currentfilter = None #self._lastInputFileFilter
fileList = PyMcaFileDialogs.getFileList(self,
filetypelist=filetypes,
message=message,
mode=mode,
getfilter=getfilter,
single=True,
currentfilter=currentfilter)
if not len(fileList):
return
self._inputDir = os.path.dirname(fileList[0])
self.setFitConfigurationFile(fileList[0])
self.raise_()
def saveSignal(self):
fileList = PyMcaFileDialogs.getFileList(self,
filetypelist=['cfg file (*.cfg)'],
mode="SAVE",
single=True,
getfilter=False)
if len(fileList):
self.saveConfiguration(fileList[0])
def browseConfigurationFile(self):
f = PyMcaFileDialogs.getFileList(parent=self,
filetypelist=["Configuration files (*.cfg)"],
message="Open a fit configuration file",
mode="OPEN",
single=True)
if len(f):
self._configLine.setText(f[0])
def browseConfigurationFile(self):
f = PyMcaFileDialogs.getFileList(parent=self,
filetypelist=["Configuration files (*.cfg)"],
message="Open a fit configuration file",
mode="OPEN",
single=True)
if len(f):
self._configLine.setText(f[0])
def saveSignal(self):
fileList = PyMcaFileDialogs.getFileList(self,
filetypelist=['cfg file (*.cfg)'],
mode="SAVE",
single=True,
getfilter=False)
if len(fileList):
self.saveConfiguration(fileList[0])
def saveImage(self):
filelist = PyMcaFileDialogs.getFileList(
parent=self,
filetypelist=["Image files (*.png)"],
message="Please give output file name",
mode="SAVE",
getfilter=False)
if len(filelist):
self.glWidget.saveImage(filelist[0])
def saveImage(self):
filelist = PyMcaFileDialogs.getFileList(
parent=self,
filetypelist=["Image files (*.png)"],
message="Please give output file name",
mode="SAVE",
getfilter=False)
if len(filelist):
self.glWidget.saveImage(filelist[0])
def _saveSlot(self):
if self.outputDir is None:
if self.inputDir is not None:
self.outputDir = self.inputDir
else:
self.outputDir = PyMcaDirs.outputDir
wdir = self.outputDir
format_list = ['";"-separated CSV *.csv',
'","-separated CSV *.csv',
'"tab"-separated CSV *.csv']
if self.outputFilter is None:
self.outputFilter = format_list[0]
outfile, filterused = PyMcaFileDialogs.getFileList(self,
filetypelist=format_list,
mode="SAVE",
message="Output File Selection",
currentdir=wdir,
currentfilter=self.outputFilter,
getfilter=True,
single=True)
if len(outfile):
outputFile = qt.safe_str(outfile[0])
else:
return
self.outputFilter = qt.safe_str(filterused)
filterused = self.outputFilter.split()
try:
self.outputDir = os.path.dirname(outputFile)
PyMcaDirs.outputDir = os.path.dirname(outputFile)
except:
self.outputDir = "."
if not outputFile.endswith('.csv'):
outputFile += '.csv'
#always overwrite
if "," in filterused[0]:
csv = ","
elif ";" in filterused[0]:
csv = ";"
else:
csv = "\t"
ddict = self.getTransmissionTable()
x = ddict["energy"]
y = ddict["transmission"]
try:
ArraySave.saveXY(x, y, outputFile,
xlabel="Energy", ylabel="Transmission",
csv=True, csvseparator=csv)
except IOError:
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Input Output Error: %s" % (sys.exc_info()[1]))
msg.exec()
return
def load(self):
fileList = PyMcaFileDialogs.getFileList(parent=self,
filetypelist=["Fit files (*.cfg)"],
message="Select a fit configuration file",
mode="OPEN",
getfilter=False,
single=True)
if len(fileList):
d = ConfigDict.ConfigDict()
d.read(fileList[0])
self.setParameters(d)
def load(self):
fileList = PyMcaFileDialogs.getFileList(parent=self,
filetypelist=["Fit files (*.cfg)"],
message="Select a fit configuration file",
mode="OPEN",
getfilter=False,
single=True)
if len(fileList):
d = ConfigDict.ConfigDict()
d.read(fileList[0])
self.setParameters(d)
def browseFile(self):
filelist = PyMcaFileDialogs.getFileList(self,
filetypelist=['HDF5 files (*.h5)'],
message="Please enter output file",
mode="SAVE",
single=True)
if len(filelist):
name = filelist[0]
if not name.endswith('.h5'):
name = name + ".h5"
self.fileName.setText(name)
def browseFile(self):
filelist = PyMcaFileDialogs.getFileList(self,
filetypelist=['HDF5 files (*.h5)'],
message="Please enter output file",
mode="SAVE",
single=True)
if len(filelist):
name = filelist[0]
if not name.endswith('.h5'):
name = name + ".h5"
self.fileName.setText(name)
def getObject3DInstance(config=None):
#for the time being a former configuration
#for serializing purposes is not implemented
#I do the import here for the case PyMca is not installed
#because the modules could be instanstiated without using
#this method
try:
from PyMca5.PyMcaIO import EDFStack
from PyMca5.PyMcaIO import TiffStack
except ImportError:
import EDFStack
import TiffStack
fileTypeList = [
'EDF Z Stack (*edf *ccd)', 'EDF X Stack (*edf *ccd)',
'TIFF Stack (*tif *tiff)'
]
old = PyMcaFileDialogs.PyMcaDirs.nativeFileDialogs * 1
PyMcaFileDialogs.PyMcaDirs.nativeFileDialogs = False
fileList, filterUsed = PyMcaFileDialogs.getFileList(
parent=None,
filetypelist=fileTypeList,
message="Please select the object file(s)",
mode="OPEN",
getfilter=True)
PyMcaFileDialogs.PyMcaDirs.nativeFileDialogs = old
if not len(fileList):
return None
if filterUsed == fileTypeList[0]:
fileindex = 2
else:
fileindex = 1
#file index is irrelevant in case of an actual 3D stack.
filename = fileList[0]
legend = os.path.basename(filename)
if filterUsed == fileTypeList[2]:
#TIFF
stack = TiffStack.TiffStack(dtype=numpy.float32, imagestack=False)
stack.loadFileList(fileList, fileindex=1)
elif len(fileList) == 1:
stack = EDFStack.EDFStack(dtype=numpy.float32, imagestack=False)
stack.loadIndexedStack(filename, fileindex=fileindex)
else:
stack = EDFStack.EDFStack(dtype=numpy.float32, imagestack=False)
stack.loadFileList(fileList, fileindex=fileindex)
if stack is None:
raise IOError("Problem reading stack.")
object3D = Object3DStack(name=legend)
object3D.setStack(stack)
return object3D
def _loadImageFiles(self):
fileTypeList = ["PNG Files (*png)",
"JPEG Files (*jpg *jpeg)",
"IMAGE Files (*)",
"DAT Files (*dat)",
"CSV Files (*csv)",
"EDF Files (*edf)",
"EDF Files (*ccd)",
"EDF Files (*)",
'HDF5 Files (*.h5 *.nxs *.hdf *.hdf5)']
filenamelist, filefilter = PyMcaFileDialogs.getFileList(parent=None,
filetypelist=fileTypeList,
message="Open image file",
getfilter=True,
single=False,
currentfilter=None)
if not filenamelist:
return
filefilter = filefilter.split()[0].lower()
extension = qt.safe_str(os.path.splitext(filenamelist[0])[1]).lower()
if (filefilter in ["edf"]) or \
(extension in [".edf", ".tif"]):
imagenames, imagelist = self._readImageListEdf(filenamelist)
if imagenames:
try:
self._createStackPluginWindowEdf(imagenames, imagelist)
except AttributeError:
self._createStackPluginWindow(imagenames, imagelist)
elif (filefilter in ["hdf5"]) or \
(extension in [".h5", ".nxs", ".hdf", ".hdf5"]):
imagenames, imagelist = self._readImageListHdf5(filenamelist)
if imagenames:
try:
self._createStackPluginWindowHdf5(imagenames, imagelist)
except AttributeError:
self._createStackPluginWindow(imagenames, imagelist)
elif extension in [".csv", ".dat"]:
imagenames, imagelist = self._readImageListSpec(filenamelist)
if imagenames:
try:
self._createStackPluginWindowSpec(imagenames, imagelist)
except AttributeError:
self._createStackPluginWindow(imagenames, imagelist)
else:
imagenames, imagelist = self._readImageListQImageReadable(filenamelist)
if imagenames:
try:
self._createStackPluginWindowQImage(imagenames, imagelist)
except AttributeError:
self._createStackPluginWindow(imagenames, imagelist)
def getObject3DInstance(config=None):
#for the time being a former configuration
#for serializing purposes is not implemented
#I do the import here for the case PyMca is not installed
#because the modules could be instanstiated without using
#this method
try:
from PyMca5.PyMcaIO import EDFStack
from PyMca5.PyMcaIO import TiffStack
except ImportError:
import EDFStack
import TiffStack
fileTypeList = ['EDF Z Stack (*edf *ccd)',
'EDF X Stack (*edf *ccd)',
'TIFF Stack (*tif *tiff)']
old = PyMcaFileDialogs.PyMcaDirs.nativeFileDialogs * 1
PyMcaFileDialogs.PyMcaDirs.nativeFileDialogs = False
fileList, filterUsed = PyMcaFileDialogs.getFileList(
parent=None,
filetypelist=fileTypeList,
message="Please select the object file(s)",
mode="OPEN",
getfilter=True)
PyMcaFileDialogs.PyMcaDirs.nativeFileDialogs = old
if not len(fileList):
return None
if filterUsed == fileTypeList[0]:
fileindex = 2
else:
fileindex = 1
#file index is irrelevant in case of an actual 3D stack.
filename = fileList[0]
legend = os.path.basename(filename)
if filterUsed == fileTypeList[2]:
#TIFF
stack = TiffStack.TiffStack(dtype=numpy.float32, imagestack=False)
stack.loadFileList(fileList, fileindex=1)
elif len(fileList) == 1:
stack = EDFStack.EDFStack(dtype=numpy.float32, imagestack=False)
stack.loadIndexedStack(filename, fileindex=fileindex)
else:
stack = EDFStack.EDFStack(dtype=numpy.float32, imagestack=False)
stack.loadFileList(fileList, fileindex=fileindex)
if stack is None:
raise IOError("Problem reading stack.")
object3D = Object3DStack(name=legend)
object3D.setStack(stack)
return object3D
def _getFileList(self, fileTypeList, message=None, getfilter=None):
if message is None:
message = "Please select a file"
if getfilter is None:
getfilter = False
wdir = PyMcaDirs.inputDir
filterused = None
if getfilter:
filelist, filterused = PyMcaFileDialogs.getFileList(
self.parent,
filetypelist=fileTypeList,
mode="OPEN",
message=message,
currentdir=wdir,
getfilter=True,
single=False,
native=True)
else:
filelist = PyMcaFileDialogs.getFileList(self.parent,
filetypelist=fileTypeList,
mode="OPEN",
message=message,
currentdir=wdir,
getfilter=False,
single=False,
native=True)
if not (len(filelist)):
return []
PyMcaDirs.inputDir = os.path.dirname(filelist[0])
if PyMcaDirs.outputDir is None:
PyMcaDirs.outputDir = os.path.dirname(filelist[0])
if getfilter:
return filelist, filterused
else:
return filelist
def saveParameters(self, fname=None):
if fname is None:
fname = PyMcaFileDialogs.getFileList(self,
filetypelist=["Configuration (*.ini)",
"Configuration (*.cfg)"],
message="Please enter output file name",
mode="SAVE",
getfilter=False,
single=True)
if len(fname):
fname = fname[0]
else:
return
ddict = ConfigDict.ConfigDict()
ddict["XASParameters"] = self.getParameters()
ddict.write(fname)
def saveParameters(self, fname=None):
if fname is None:
fname = PyMcaFileDialogs.getFileList(self,
filetypelist=["Configuration (*.ini)",
"Configuration (*.cfg)"],
message="Please enter output file name",
mode="SAVE",
getfilter=False,
single=True)
if len(fname):
fname = fname[0]
else:
return
ddict = ConfigDict.ConfigDict()
ddict["XASParameters"] = self.getParameters()
ddict.write(fname)
def loadParameters(self, fname=None):
if fname is None:
fname = PyMcaFileDialogs.getFileList(self,
filetypelist=["Configuration (*.ini)",
"Configuration (*.cfg)",
"All files (*)"],
message="Please set input file name",
mode="OPEN",
getfilter=False,
single=True)
if len(fname):
fname = fname[0]
else:
return
d = ConfigDict.ConfigDict()
d.read(fname)
self.setParameters(d["XASParameters"])
def browseOutputDirectory(self):
if self._outputDir is None:
self._outputDir = PyMcaDirs.outputDir
elif os.path.exists(self._outputDir):
PyMcaDirs.inputDir = self._outputDir
message = "Select a Simple Fit Configuration File"
mode = "OPEN"
fileList = PyMcaFileDialogs.getExistingDirectory(self,
message=message,
mode=mode)
if not len(fileList):
return
if type(fileList) != type([]):
fileList = [fileList]
self._outputDir = os.path.dirname(fileList[0])
self.setOutputDirectory(fileList[0])
self.raise_()
def browseOutputDirectory(self):
if self._outputDir is None:
self._outputDir = PyMcaDirs.outputDir
elif os.path.exists(self._outputDir):
PyMcaDirs.inputDir = self._outputDir
message = "Select a Simple Fit Configuration File"
mode = "OPEN"
fileList = PyMcaFileDialogs.getExistingDirectory(self,
message=message,
mode=mode)
if not len(fileList):
return
if type(fileList) != type([]):
fileList = [fileList]
self._outputDir = os.path.dirname(fileList[0])
self.setOutputDirectory(fileList[0])
self.raise_()
def loadParameters(self, fname=None):
if fname is None:
fname = PyMcaFileDialogs.getFileList(self,
filetypelist=["Configuration (*.ini)",
"Configuration (*.cfg)",
"All files (*)"],
message="Please set input file name",
mode="OPEN",
getfilter=False,
single=True)
if len(fname):
fname = fname[0]
else:
return
d = ConfigDict.ConfigDict()
d.read(fname)
self.setParameters(d["XASParameters"])
def funevent(self, item):
item = str(item)
if item in self.specfit.theorylist:
self.specfit.settheory(item)
else:
filelist = PyMcaFileDialogs.getFileList(
self,
message="Select python module with your function(s)",
filetypelist=["Python Files (*.py)", "All Files (*)"],
mode="OPEN",
single=True,
getfilter=False)
if not len(filelist):
functionsfile = ""
else:
functionsfile = filelist[0]
if len(functionsfile):
try:
if self.specfit.importfun(functionsfile):
qt.QMessageBox.critical(self, "ERROR",
"Function not imported")
return
else:
#empty the ComboBox
n = self.guiconfig.FunComBox.count()
while (self.guiconfig.FunComBox.count() > 1):
self.guiconfig.FunComBox.removeItem(1)
#and fill it again
for key in self.specfit.theorylist:
if QTVERSION < '4.0.0':
self.guiconfig.FunComBox.insertItem(str(key))
else:
self.guiconfig.FunComBox.addItem(str(key))
except:
qt.QMessageBox.critical(self, "ERROR",
"Function not imported")
i = 1 + self.specfit.theorylist.index(
self.specfit.fitconfig['fittheory'])
if QTVERSION < '4.0.0':
self.guiconfig.FunComBox.setCurrentItem(i)
else:
self.guiconfig.FunComBox.setCurrentIndex(i)
self.__initialparameters()
return
def getObject3DInstance(config=None):
fileTypeList = [
'Picture Files (*jpg *jpeg *tif *tiff *png)', 'EDF Files (*edf)',
'EDF Files (*ccd)', 'ADSC Files (*img)', 'EDF Files (*)'
]
fileList, filterUsed = PyMcaFileDialogs.getFileList(
parent=None,
filetypelist=fileTypeList,
message="Please select one object data file",
mode="OPEN",
getfilter=True)
if not len(fileList):
return
fname = fileList[0]
if filterUsed.split()[0] == "Picture":
qimage = qt.QImage(fname)
if qimage.isNull():
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Cannot read file %s as an image" % fname)
msg.exec_()
return
object3D = Object3DPixmap(os.path.basename(fname))
object3D.setQImage(qimage)
return object3D
if filterUsed.split()[0] in ["EDF", "ADSC"]:
edf = EdfFile.EdfFile(fname)
data = edf.GetData(0)
if True:
object3D = Object3DPixmap(os.path.basename(fname))
object3D.setImageData(data)
else:
(image, size, minmax) = spslut.transform(data, (1, 0),
(spslut.LINEAR, 3.0),
"RGBX", spslut.TEMP, 1,
(0, 1), (0, 255), 1)
object3D = Object3DPixmap(os.path.basename(fname))
object3D.setPixmap(image,
size[0],
size[1],
xmirror=False,
ymirror=False)
return object3D
return None
def browseList(self):
if self._inputDir is None:
self._inputDir = PyMcaDirs.inputDir
elif os.path.exists(self._inputDir):
PyMcaDirs.inputDir = self._inputDir
filetypes = ["Mca Files (*.mca)", "Edf Files (*.edf)"]
if HDF5SUPPORT:
filetypes.append("HDF5 Files(*.nxs *.h5 *.hdf)")
filetypes.append("SPEC Files (*.spec)")
filetypes.append("SPEC Files (*.dat)")
filetypes.append("All files (*)")
message = "Open a set of files"
mode = "OPEN"
getfilter = True
currentfilter = self._lastInputFileFilter
fileList, fileFilter = PyMcaFileDialogs.getFileList(
self,
filetypelist=filetypes,
message=message,
mode=mode,
getfilter=getfilter,
single=False,
currentfilter=currentfilter)
if not len(fileList):
return
else:
self._lastInputFileFilter = fileFilter
self._inputDir = os.path.dirname(fileList[0])
if (QTVERSION < '4.2.0') or (not len(self._fileList)):
self.setFileList(fileList)
self.raise_()
return
msg = qt.QMessageBox()
msg.setWindowTitle("Append or replace")
msg.setIcon(qt.QMessageBox.Information)
msg.setText("Do you want to delete current file list?")
msg.setStandardButtons(qt.QMessageBox.Yes | qt.QMessageBox.No)
answer = msg.exec()
if answer == qt.QMessageBox.Yes:
append = False
else:
append = True
self.setFileList(fileList, append=append)
self.raise_()
def funevent(self,item):
item=str(item)
if item in self.specfit.theorylist:
self.specfit.settheory(item)
else:
filelist = PyMcaFileDialogs.getFileList(self,
message="Select python module with your function(s)",
filetypelist=["Python Files (*.py)",
"All Files (*)"],
mode="OPEN",
single=True,
getfilter=False)
if not len(filelist):
functionsfile = ""
else:
functionsfile = filelist[0]
if len(functionsfile):
try:
if self.specfit.importfun(functionsfile):
qt.QMessageBox.critical(self, "ERROR",
"Function not imported")
return
else:
#empty the ComboBox
n=self.guiconfig.FunComBox.count()
while(self.guiconfig.FunComBox.count()>1):
self.guiconfig.FunComBox.removeItem(1)
#and fill it again
for key in self.specfit.theorylist:
if QTVERSION < '4.0.0':
self.guiconfig.FunComBox.insertItem(str(key))
else:
self.guiconfig.FunComBox.addItem(str(key))
except:
qt.QMessageBox.critical(self, "ERROR",
"Function not imported")
i=1+self.specfit.theorylist.index(self.specfit.fitconfig['fittheory'])
if QTVERSION < '4.0.0':
self.guiconfig.FunComBox.setCurrentItem(i)
else:
self.guiconfig.FunComBox.setCurrentIndex(i)
self.__initialparameters()
return
def browseList(self):
if self._inputDir is None:
self._inputDir = PyMcaDirs.inputDir
elif os.path.exists(self._inputDir):
PyMcaDirs.inputDir = self._inputDir
filetypes = ["Mca Files (*.mca)",
"Edf Files (*.edf)"]
if HDF5SUPPORT:
filetypes.append("HDF5 Files(*.nxs *.h5 *.hdf)")
filetypes.append("SPEC Files (*.spec)")
filetypes.append("SPEC Files (*.dat)")
filetypes.append("All files (*)")
message = "Open a set of files"
mode = "OPEN"
getfilter = True
currentfilter = self._lastInputFileFilter
fileList, fileFilter = PyMcaFileDialogs.getFileList(self,
filetypelist=filetypes,
message=message,
mode=mode,
getfilter=getfilter,
single=False,
currentfilter=currentfilter)
if not len(fileList):
return
else:
self._lastInputFileFilter = fileFilter
self._inputDir = os.path.dirname(fileList[0])
if (QTVERSION < '4.2.0') or (not len(self._fileList)):
self.setFileList(fileList)
self.raise_()
return
msg = qt.QMessageBox()
msg.setWindowTitle("Append or replace")
msg.setIcon(qt.QMessageBox.Information)
msg.setText("Do you want to delete current file list?")
msg.setStandardButtons(qt.QMessageBox.Yes|qt.QMessageBox.No)
answer=msg.exec_()
if answer == qt.QMessageBox.Yes:
append = False
else:
append = True
self.setFileList(fileList, append=append)
self.raise_()
def getObject3DInstance(config=None):
fileTypeList = ['Picture Files (*jpg *jpeg *tif *tiff *png)',
'EDF Files (*edf)',
'EDF Files (*ccd)',
'ADSC Files (*img)',
'EDF Files (*)']
fileList, filterUsed = PyMcaFileDialogs.getFileList(
parent=None,
filetypelist=fileTypeList,
message="Please select one object data file",
mode="OPEN",
getfilter=True)
if not len(fileList):
return
fname = fileList[0]
if filterUsed.split()[0] == "Picture":
qimage = qt.QImage(fname)
if qimage.isNull():
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Cannot read file %s as an image" % fname)
msg.exec_()
return
object3D = Object3DPixmap(os.path.basename(fname))
object3D.setQImage(qimage)
return object3D
if filterUsed.split()[0] in ["EDF", "ADSC"]:
edf = EdfFile.EdfFile(fname)
data = edf.GetData(0)
if True:
object3D = Object3DPixmap(os.path.basename(fname))
object3D.setImageData(data)
else:
(image,size,minmax)= spslut.transform(data, (1,0),
(spslut.LINEAR,3.0),
"RGBX", spslut.TEMP,
1,
(0, 1),
(0, 255), 1)
object3D = Object3DPixmap(os.path.basename(fname))
object3D.setPixmap(image, size[0], size[1], xmirror = False, ymirror = False)
return object3D
return None
def _getStackOfFiles(self):
wdir = PyMcaDirs.inputDir
fileTypeList = [
"Batch Result Files (*dat)", "EDF Files (*edf)",
"EDF Files (*ccd)", "TIFF Files (*tif *tiff *TIF *TIFF)",
"Image Files (* jpg *jpeg *tif *tiff *png)", "All Files (*)"
]
message = "Open ONE Batch result file or SEVERAL EDF files"
filelist = PyMcaFileDialogs.getFileList(parent=self,
filetypelist=fileTypeList,
message=message,
currentdir=wdir,
mode="OPEN",
single=False)
if filelist:
PyMcaDirs.inputDir = os.path.dirname(filelist[0])
return filelist
else:
return []
def _getStackOfFiles(self):
wdir = PyMcaDirs.inputDir
fileTypeList = ["Batch Result Files (*dat)",
"EDF Files (*edf)",
"EDF Files (*ccd)",
"TIFF Files (*tif *tiff *TIF *TIFF)",
"Image Files (* jpg *jpeg *tif *tiff *png)",
"All Files (*)"]
message = "Open ONE Batch result file or SEVERAL EDF files"
filelist = PyMcaFileDialogs.getFileList(parent=self,
filetypelist=fileTypeList,
message=message,
currentdir=wdir,
mode="OPEN",
single=False)
if not len(filelist):
return []
PyMcaDirs.inputDir = os.path.dirname(filelist[0])
return filelist
def replace1DAxisWithASCII(self):
stack = self.getStackDataObject()
mcaIndex = stack.info.get('McaIndex', -1)
nPoints = stack.data.shape[mcaIndex]
fileList = PyMcaFileDialogs.getFileList(None,
filetypelist=["ASCII files (*)"],
message="Select ASCII file",
mode="OPEN",
getfilter=False,
single=True)
if not len(fileList):
return
filename = fileList[0]
data = numpy.loadtxt(filename)
data.shape = -1
if data.size != nPoints:
raise ValueError("Number of read values not equal to %d" % nPoints)
else:
stack.x = [data]
self.setStack(stack, mcaindex=mcaIndex)
def getObject3DInstance(config=None):
#for the time being a former configuration
#for serializing purposes is not implemented
#I do the import here for the case PyMca is not installed
#because the modules could be instanstiated without using
#this method
try:
from PyMca5.PyMcaIO import EdfFile
except ImportError:
import EdfFile
fileTypeList = ['EDF Files (*edf)',
'EDF Files (*ccd)',
'ADSC Files (*img)',
'All Files (*)']
old = PyMcaFileDialogs.PyMcaDirs.nativeFileDialogs * 1
PyMcaFileDialogs.PyMcaDirs.nativeFileDialogs = False
fileList, filterUsed = PyMcaFileDialogs.getFileList(
parent=None,
filetypelist=fileTypeList,
message="Please select one object data file",
mode="OPEN",
getfilter=True)
PyMcaFileDialogs.PyMcaDirs.nativeFileDialogs = old
if not len(fileList):
return None
if filterUsed == fileTypeList[0]:
fileindex = 2
else:
fileindex = 1
#file index is irrelevant in case of an actual 3D stack.
filename = fileList[0]
legend = os.path.basename(filename)
edf = EdfFile.EdfFile(filename, access='rb')
data = edf.GetData(0).astype(numpy.float32)
object3D = Object3DMesh(os.path.basename(filename))
object3D.setData(data, z=data[:])
return object3D
def getObject3DInstance(config=None):
#for the time being a former configuration
#for serializing purposes is not implemented
#I do the import here for the case PyMca is not installed
#because the modules could be instanstiated without using
#this method
try:
from PyMca5.PyMcaIO import EDFStack
except ImportError:
import EDFStack
fileTypeList = ['Chimera Stack (*cmp)',
'Chimera Stack (*)']
old = PyMcaFileDialogs.PyMcaDirs.nativeFileDialogs * 1
#PyMcaFileDialogs.PyMcaDirs.nativeFileDialogs = False
fileList, filterUsed = PyMcaFileDialogs.getFileList(
parent=None,
filetypelist=fileTypeList,
message="Please select the object file(s)",
mode="OPEN",
getfilter=True)
PyMcaFileDialogs.PyMcaDirs.nativeFileDialogs = old
if not len(fileList):
return None
if filterUsed == fileTypeList[0]:
fileindex = 2
else:
fileindex = 1
#file index is irrelevant in case of an actual 3D stack.
filename = fileList[0]
legend = os.path.basename(filename)
f = h5py.File(filename)
stack = f['Image']['data'].value
f = None
if stack is None:
raise IOError("Problem reading stack.")
object3D = ChimeraStack(name=legend)
object3D.setStack(stack)
return object3D
def getObject3DInstance(config=None):
#for the time being a former configuration
#for serializing purposes is not implemented
#I do the import here for the case PyMca is not installed
#because the modules could be instanstiated without using
#this method
try:
from PyMca5.PyMcaIO import EdfFile
except ImportError:
import EdfFile
fileTypeList = ['EDF Files (*edf)',
'EDF Files (*ccd)',
'ADSC Files (*img)',
'All Files (*)']
old = PyMcaFileDialogs.PyMcaDirs.nativeFileDialogs * 1
PyMcaFileDialogs.PyMcaDirs.nativeFileDialogs = False
fileList, filterUsed = PyMcaFileDialogs.getFileList(
parent=None,
filetypelist=fileTypeList,
message="Please select one object data file",
mode="OPEN",
getfilter=True)
PyMcaFileDialogs.PyMcaDirs.nativeFileDialogs = old
if not len(fileList):
return None
if filterUsed == fileTypeList[0]:
fileindex = 2
else:
fileindex = 1
#file index is irrelevant in case of an actual 3D stack.
filename = fileList[0]
legend = os.path.basename(filename)
edf = EdfFile.EdfFile(filename, access='rb')
data = edf.GetData(0).astype(numpy.float32)
object3D = Object3DMesh(os.path.basename(filename))
object3D.setData(data, z=data[:])
return object3D
def getObject3DInstance(config=None):
#for the time being a former configuration
#for serializing purposes is not implemented
#I do the import here for the case PyMca is not installed
#because the modules could be instanstiated without using
#this method
try:
from PyMca5.PyMcaIO import EDFStack
except ImportError:
import EDFStack
fileTypeList = ['Chimera Stack (*cmp)', 'Chimera Stack (*)']
old = PyMcaFileDialogs.PyMcaDirs.nativeFileDialogs * 1
#PyMcaFileDialogs.PyMcaDirs.nativeFileDialogs = False
fileList, filterUsed = PyMcaFileDialogs.getFileList(
parent=None,
filetypelist=fileTypeList,
message="Please select the object file(s)",
mode="OPEN",
getfilter=True)
PyMcaFileDialogs.PyMcaDirs.nativeFileDialogs = old
if not len(fileList):
return None
if filterUsed == fileTypeList[0]:
fileindex = 2
else:
fileindex = 1
#file index is irrelevant in case of an actual 3D stack.
filename = fileList[0]
legend = os.path.basename(filename)
f = h5py.File(filename)
stack = f['Image']['data'].value
f = None
if stack is None:
raise IOError("Problem reading stack.")
object3D = ChimeraStack(name=legend)
object3D.setStack(stack)
return object3D
def browseOutputDir(self):
f = PyMcaFileDialogs.getExistingDirectory(
parent=self, message="Please select output directory", mode="OPEN")
if len(f):
self._outLine.setText(f)
def saveButtonClicked(self):
energylist, weightlist, flaglist, scatterlist = self.table.getParameters()
if self.outputDir is None:
if self.inputDir is not None:
self.outputDir = self.inputDir
else:
self.outputDir = PyMcaDirs.outputDir
wdir = self.outputDir
format_list = ['";"-separated CSV *.csv',
'","-separated CSV *.csv',
'"tab"-separated CSV *.csv']
if self.outputFilter is None:
self.outputFilter = format_list[0]
outfile, filterused = PyMcaFileDialogs.getFileList(self,
filetypelist=format_list,
mode="SAVE",
message="Output File Selection",
currentdir=wdir,
currentfilter=self.outputFilter,
getfilter=True,
single=True)
if len(outfile):
outputFile = qt.safe_str(outfile[0])
else:
return
self.outputFilter = qt.safe_str(filterused)
filterused = self.outputFilter.split()
try:
self.outputDir = os.path.dirname(outputFile)
PyMcaDirs.outputDir = os.path.dirname(outputFile)
except:
self.outputDir = "."
if not outputFile.endswith('.csv'):
outputFile += '.csv'
#always overwrite
if os.path.exists(outputFile):
os.remove(outputFile)
try:
if sys.version < "3.0.0":
ffile=open(outputFile,'wb')
else:
ffile=open(outputFile,'w')
except IOError:
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Input Output Error: %s" % (sys.exc_info()[1]))
msg.exec_()
return
if "," in filterused[0]:
csv = ","
elif ";" in filterused[0]:
csv = ";"
else:
csv = "\t"
ffile.write('"energy"%s"weight"%s"flag"%s"scatter"\n' % (csv, csv, csv))
#write the scatter lines in first instance
alreadysaved = []
for i in range(len(energylist)):
if (energylist[i] is not None) and \
(scatterlist[i] == 1):
ffile.write("%f%s%f%s%d%s%d\n" % \
(energylist[i], csv,
weightlist[i], csv,
flaglist[i], csv,
scatterlist[i]))
alreadysaved.append(i)
for i in range(len(energylist)):
if energylist[i] is not None:
if i not in alreadysaved:
ffile.write("%f%s%f%s%d%s%d\n" % \
(energylist[i], csv,
weightlist[i], csv,
flaglist[i], csv,
scatterlist[i]))
ffile.close()
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 _shiftFromFile(self):
stack = self.getStackDataObject()
if stack is None:
return
data = stack.data
mcaIndex = stack.info.get("McaIndex")
if not (mcaIndex in [0, -1, 2]):
raise IndexError("1D index must be 0, 2, or -1")
filefilter = ["HDF5 Files (*.h5 *.nxs *.hdf)", "CSV 2-column (*.csv)", "ASCII 2-column (*)"]
filename, ffilter = PyMcaFileDialogs.getFileList(
parent=None,
filetypelist=filefilter,
message="Load",
mode="OPEN",
single=True,
getfilter=True,
currentfilter=filefilter[0],
)
if len(filename):
if DEBUG:
print("file name = %s file filter = %s" % (filename, ffilter))
else:
if DEBUG:
print("nothing selected")
return
filename = filename[0]
if ffilter.startswith("HDF5"):
# browse
self.__hdf5Dialog = qt.QDialog()
self.__hdf5Dialog.setWindowTitle("Select your data set by a double click")
self.__hdf5Dialog.mainLayout = qt.QVBoxLayout(self.__hdf5Dialog)
self.__hdf5Dialog.mainLayout.setContentsMargins(0, 0, 0, 0)
self.__hdf5Dialog.mainLayout.setSpacing(0)
fileModel = HDF5Widget.FileModel()
fileView = HDF5Widget.HDF5Widget(fileModel)
hdf5File = fileModel.openFile(filename)
shiftsDataset = None
fileView.sigHDF5WidgetSignal.connect(self._hdf5WidgetSlot)
self.__hdf5Dialog.mainLayout.addWidget(fileView)
self.__hdf5Dialog.resize(400, 200)
ret = self.__hdf5Dialog.exec_()
if not ret:
return
shifts = hdf5File[self.__shitfsDataset].value
hdf5File.close()
else:
sf = specfilewrapper.Specfile(filename)
nScans = len(sf)
targetScan = None
for scan in sf:
if scan.lines() == data.shape[stack.info["McaIndex"]]:
targetScan = scan
break
if targetScan is None:
scan = None
sf = None
raise IOError("Number of read lines does not match stack shape")
shifts = targetScan.data()
targetScan = None
scan = None
sf = None
if shifts.shape[0] == 3 and shifts.shape[1] == data.shape[stack.info["McaIndex"]]:
# one column was added (point number)
shifts = shifts[1:].T
filename = None
if not isinstance(data, numpy.ndarray):
filefilter = ["HDF5 Files (*.h5)"]
filename = PyMcaFileDialogs.getFileList(
parent=None,
filetypelist=filefilter,
message="Select output file",
mode="SAVE",
single=True,
getfilter=False,
currentfilter=filefilter[0],
)
if len(filename):
filename = filename[0]
if DEBUG:
print("file name = %s" % filename)
else:
raise IOError("No output file selected")
if filename is not None:
self.__hdf5 = self.initializeHDF5File(filename)
crop = False
if DEBUG:
result = self.shiftStack(stack, shifts, crop=crop, filename=filename)
else:
result = self.__shiftStack(stack, shifts, crop=crop, filename=filename)
if result is not None:
# exception occurred
raise Exception(result[1], result[2], result[3])
if filename is not None:
hdf = self.__hdf5
alignmentGroup = hdf["/entry_000/Alignment"]
outputShifts = self.getHDF5BufferIntoGroup(
alignmentGroup, shape=(stack.data.shape[mcaIndex], 2), name="shifts", dtype=numpy.float32
)
outputShifts[:, :] = shifts
attributes = {"interpretation": "image"}
# fill the axes information
dataGroup = hdf["/entry_000/Data"]
if mcaIndex == 0:
reference_shape = data[0].shape
else:
reference_shape = data.shape[0], data.shape[1]
try:
activeCurve = self.getActiveCurve()
if activeCurve is None:
activeCurve = self.getAllCurves()[0]
x, y, legend, info = activeCurve
dataGroup[info["xlabel"]] = numpy.array(x, dtype=numpy.float32)
dataGroup[info["xlabel"]].attrs["axis"] = numpy.int32(1)
axesAttribute = "%s:dim_1:dim_2" % info["xlabel"]
except:
if DEBUG:
raise
dataGroup["dim_0"] = numpy.arange(stack.data.shape[mcaIndex]).astype(numpy.float32)
dataGroup["dim_0"].attrs["axis"] = numpy.int32(1)
axesAttribute = "dim_0:dim_1:dim_2"
dataGroup["dim_1"] = numpy.arange(reference_shape[0]).astype(numpy.float32)
dataGroup["dim_1"].attrs["axis"] = numpy.int32(2)
dataGroup["dim_2"] = numpy.arange(reference_shape[1]).astype(numpy.float32)
dataGroup["dim_2"].attrs["axis"] = numpy.int32(3)
dim2 = numpy.arange(reference_shape[1]).astype(numpy.float32)
dataGroup["data"].attrs["axes"] = axesAttribute
self.finishHDF5File(hdf)
else:
self.setStack(stack)
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
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 browseOutputDir(self):
fileList = PyMcaFileDialogs.getExistingDirectory(parent=self,
message="Please select output directory",
mode="OPEN")
if len(fileList):
self._outdirLine.setText(fileList)
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
def saveButtonClicked(self):
energylist, weightlist, flaglist, scatterlist = self.table.getParameters(
)
if self.outputDir is None:
if self.inputDir is not None:
self.outputDir = self.inputDir
else:
self.outputDir = PyMcaDirs.outputDir
wdir = self.outputDir
format_list = [
'";"-separated CSV *.csv', '","-separated CSV *.csv',
'"tab"-separated CSV *.csv'
]
if self.outputFilter is None:
self.outputFilter = format_list[0]
outfile, filterused = PyMcaFileDialogs.getFileList(
self,
filetypelist=format_list,
mode="SAVE",
message="Output File Selection",
currentdir=wdir,
currentfilter=self.outputFilter,
getfilter=True,
single=True)
if len(outfile):
outputFile = qt.safe_str(outfile[0])
else:
return
self.outputFilter = qt.safe_str(filterused)
filterused = self.outputFilter.split()
try:
self.outputDir = os.path.dirname(outputFile)
PyMcaDirs.outputDir = os.path.dirname(outputFile)
except:
self.outputDir = "."
if not outputFile.endswith('.csv'):
outputFile += '.csv'
#always overwrite
if os.path.exists(outputFile):
os.remove(outputFile)
try:
if sys.version < "3.0.0":
ffile = open(outputFile, 'wb')
else:
ffile = open(outputFile, 'w')
except IOError:
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Input Output Error: %s" % (sys.exc_info()[1]))
msg.exec_()
return
if "," in filterused[0]:
csv = ","
elif ";" in filterused[0]:
csv = ";"
else:
csv = "\t"
ffile.write('"energy"%s"weight"%s"flag"%s"scatter"\n' %
(csv, csv, csv))
#write the scatter lines in first instance
alreadysaved = []
for i in range(len(energylist)):
if (energylist[i] is not None) and \
(scatterlist[i] == 1):
ffile.write("%f%s%f%s%d%s%d\n" % \
(energylist[i], csv,
weightlist[i], csv,
flaglist[i], csv,
scatterlist[i]))
alreadysaved.append(i)
for i in range(len(energylist)):
if energylist[i] is not None:
if i not in alreadysaved:
ffile.write("%f%s%f%s%d%s%d\n" % \
(energylist[i], csv,
weightlist[i], csv,
flaglist[i], csv,
scatterlist[i]))
ffile.close()
