def getPixmap():
"""
Open an image file and return the filename and the data.
Return ``None, None`` in case of failure.
"""
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 fileList:
return None, None
fname = fileList[0]
if filterUsed.split()[0] == "Picture":
qimage = qt.QImage(fname)
if qimage.isNull():
msg = qt.QMessageBox()
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Cannot read file %s as an image" % fname)
msg.exec()
return None, None
return os.path.basename(fname), convertQImageToArray(qimage)
if filterUsed.split()[0] in ["EDF", "ADSC"]:
edf = EdfFile.EdfFile(fname)
data = edf.GetData(0)
return os.path.basename(fname), data
return None, None
def getChimeraStack():
"""
Open an chimera file and return the filename and the data.
Return ``None, None`` in case the user cancelled the file dialog.
:raise IOError: If the data is not a 3D stack
"""
fileTypeList = ['Chimera Stack (*cmp)',
'Chimera Stack (*)']
old = PyMcaFileDialogs.PyMcaDirs.nativeFileDialogs * 1
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 fileList:
return None, None
filename = fileList[0]
with h5py.File(filename, mode='r') as f:
stack = f['Image/data'][...]
if not isinstance(stack, numpy.ndarray) or stack.ndim != 3:
raise IOError("Problem reading stack.")
return os.path.basename(filename), stack
def getMesh():
"""
Read an image data file (EDF, ADSC), return the data and image name.
This is then used to display the image as a height map.
Returns *None, None* if the file dialog is cancelled or loaing fails.
:return: legend, data
"""
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 fileList:
return None, None
filename = fileList[0]
edf = EdfFile.EdfFile(filename, access='rb')
data = edf.GetData(0).astype(numpy.float32)
return os.path.basename(filename), data
def _savesignal(self):
if self.lastInputDir is None:
self.lastInputDir = PyMcaDirs.outputDir
if self.lastInputDir is not None:
if not os.path.exists(self.lastInputDir):
self.lastInputDir = None
self.lastInputFilter = "Calibration files (*.calib)\n"
windir = self.lastInputDir
if windir is None:
windir = ""
filelist, filefilter = PyMcaFileDialogs.getFileList(
self,
filetypelist=["Calibration files (*.calib)"],
message="Save a new calibration file",
currentdir=windir,
mode="SAVE",
single=True,
getfilter=True,
currentfilter=self.lastInputFilter)
if not len(filelist):
return
filename = qt.safe_str(filelist[0])
if len(filename) < 6:
filename = filename + ".calib"
elif filename[-6:] != ".calib":
filename = filename + ".calib"
self.lastInputDir = os.path.dirname(filename)
PyMcaDirs.outputDir = os.path.dirname(filename)
comboitem, combotext = self.calbox.getCurrent()
self._emitpysignal(button="CalibrationSave",
box=[comboitem, combotext],
line_edit=filename,
event='clicked')
def getInputFilename(self):
if self._dir is None:
inidir = PyMcaDirs.inputDir
else:
inidir = self._dir
if not os.path.exists(inidir):
inidir = os.getcwd()
fileList = PyMcaFileDialogs.getFileList(parent=self,
filetypelist=["ini files (*.ini)"],
message="Select a .ini file",
currentdir=inidir,
mode="OPEN",
getfilter=False)
if len(fileList):
ret = fileList[0]
else:
ret = ""
if len(ret):
self._dir = os.path.dirname(ret)
PyMcaDirs.inputDir = os.path.dirname(ret)
return ret
def importFunctions(self, functionsfile=None):
if functionsfile is None:
filetypelist = ['Python files (*.py)', 'All Files (*)']
fileList = PyMcaFileDialogs.getFileList(self,
filetypelist=filetypelist,
message="Select input functions file",
currentdir=None,
mode="OPEN",
getfilter=None,
single=True,
currentfilter=filetypelist[0],
native=None)
if len(fileList):
functionsfile= qt.safe_str(fileList[0])
else:
functionsfile = ""
if not len(functionsfile):
return
try:
self.fitModule.importFunctions(functionsfile)
except:
if _logger.getEffectiveLevel() == logging.DEBUG:
raise
msg = qt.QMessageBox()
msg.setWindowTitle("SimpleFitGui error")
msg.setIcon(qt.QMessageBox.Critical)
msg.setInformativeText("Function not imported %s" % \
str(sys.exc_info()[1]))
msg.setDetailedText(traceback.format_exc())
msg.exec()
config = self.fitModule.getConfiguration()
self.topWidget.setFunctions(config['fit']['functions'])
def getPixmap():
"""
Open an image file and return the filename and the data.
Return ``None, None`` in case of failure.
"""
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 fileList:
return None, None
fname = fileList[0]
if filterUsed.split()[0] == "Picture":
qimage = qt.QImage(fname)
if qimage.isNull():
msg = qt.QMessageBox()
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Cannot read file %s as an image" % fname)
msg.exec_()
return None, None
return os.path.basename(fname), convertQImageToArray(qimage)
if filterUsed.split()[0] in ["EDF", "ADSC"]:
edf = EdfFile.EdfFile(fname)
data = edf.GetData(0)
return os.path.basename(fname), data
return None, None
def getMesh():
"""
Read an image data file (EDF, ADSC), return the data and image name.
This is then used to display the image as a height map.
Returns *None, None* if the file dialog is cancelled or loaing fails.
:return: legend, data
"""
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 fileList:
return None, None
filename = fileList[0]
edf = EdfFile.EdfFile(filename, access='rb')
data = edf.GetData(0).astype(numpy.float32)
return os.path.basename(filename), data
def getChimeraStack():
"""
Open an chimera file and return the filename and the data.
Return ``None, None`` in case the user cancelled the file dialog.
:raise IOError: If the data is not a 3D stack
"""
fileTypeList = ['Chimera Stack (*cmp)',
'Chimera Stack (*)']
old = PyMcaFileDialogs.PyMcaDirs.nativeFileDialogs * 1
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 fileList:
return None, None
filename = fileList[0]
with h5py.File(filename) as f:
stack = f['Image/data'][...]
if not isinstance(stack, numpy.ndarray) or stack.ndim != 3:
raise IOError("Problem reading stack.")
return os.path.basename(filename), stack
def saveAllSpectra(self):
fltrs = ['Raw ASCII *.txt',
'","-separated CSV *.csv',
'";"-separated CSV *.csv',
'"tab"-separated CSV *.csv',
'OMNIC CSV *.csv']
message = "Enter file name to be used as root"
fileList, fileFilter = PyMcaFileDialogs.getFileList(parent=self,
filetypelist=fltrs,
message=message,
currentdir=None,
mode="SAVE",
getfilter=True,
single=True,
currentfilter=None,
native=None)
if not len(fileList):
return
fileroot = fileList[0]
dirname = os.path.dirname(fileroot)
root, ext = os.path.splitext(os.path.basename(fileroot))
if ext not in [".txt", ".csv"]:
root = root + ext
ext = ""
# get appropriate extensions and separators
filterused = fileFilter.split()
if filterused[0].startswith("Raw"):
csv = False
ext = "txt"
csvseparator = " "
elif filterused[0].startswith("OMNIC"):
# extension is csv but saved as ASCII
csv = False
ext = "csv"
csvseparator = ","
else:
csv = True
ext = "csv"
if "," in filterused[0]:
csvseparator = ","
elif ";" in filterused[0]:
csvseparator = ";"
elif "OMNIC" in filterused[0]:
csvseparator = ","
else:
csvseparator = "\t"
nSpectra = len(self.spectrumList)
n = int(numpy.log10(nSpectra)) + 1
fmt = "_%" + "0%dd" % n + ".%s"
for index in range(nSpectra):
legend = self.spectrumNames[index]
x = self.xValues[index]
y = self.spectrumList[index]
filename = os.path.join(dirname, root + fmt % (index, ext))
ArraySave.saveXY(x, y, filename, ylabel=legend,
csv=csv, csvseparator=csvseparator)
def browseConfigurationFile(self):
f = PyMcaFileDialogs.getFileList(parent=self,
filetypelist=["Configuration files (*.ini)",
"Configuration files (*.cfg)"],
message="Open a XAS configuration file",
mode="OPEN",
single=True)
if len(f):
self._configLine.setText(f[0])
def _getOutputFileNameAndFilter(self, format_list=None):
"""
returns outputfile, file type and filter used
"""
# get outputfile
self.outputDir = PyMcaDirs.outputDir
if self.outputDir is None:
self.outputDir = os.getcwd()
wdir = os.getcwd()
elif os.path.exists(self.outputDir):
wdir = self.outputDir
else:
self.outputDir = os.getcwd()
wdir = self.outputDir
if format_list is None:
format_list = ['Specfile MCA *.mca', 'Specfile Scan *.dat']
if self._plotType != "MCA":
format_list += ['Specfile MultiScan *.dat']
format_list += [
'Raw ASCII *.txt', '","-separated CSV *.csv',
'";"-separated CSV *.csv', '"tab"-separated CSV *.csv',
'OMNIC CSV *.csv', 'Widget PNG *.png', 'Widget JPG *.jpg',
'Graphics PNG *.png', 'Graphics EPS *.eps',
'Graphics SVG *.svg'
]
if self.outputFilter is None:
self.outputFilter = format_list[0]
fileList, fileFilter = PyMcaFileDialogs.getFileList(
self,
filetypelist=format_list,
message="Output File Selection",
currentdir=wdir,
single=True,
mode="SAVE",
getfilter=True,
currentfilter=self.outputFilter)
if not len(fileList):
return
self.outputFilter = fileFilter
filterused = self.outputFilter.split()
filetype = filterused[1]
extension = filterused[2]
outdir = qt.safe_str(fileList[0])
try:
self.outputDir = os.path.dirname(outdir)
PyMcaDirs.outputDir = os.path.dirname(outdir)
except:
self.outputDir = "."
try:
outputFile = os.path.basename(outdir)
except:
outputFile = outdir
if len(outputFile) < 5:
outputFile = outputFile + extension[-4:]
elif outputFile[-4:] != extension[-4:]:
outputFile = outputFile + extension[-4:]
return os.path.join(self.outputDir, outputFile), fileFilter
def __addFiles(self):
files = PyMcaFileDialogs.getFileList(self,
filetypelist=["Edf Files (*.edf)",
"All Files (*)"],
message="Add XIA Edf Files",
getfilter=False,
mode="OPEN",
single=False)
for name in files:
self.__addInFileList("file", name)
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 _getFilenameDialog(parent=None):
"""Open a dialog to select a file in a filesystem tree view.
Return the selected filename."""
from PyMca5.PyMcaGui.io import PyMcaFileDialogs
fileTypeList = ['HDF5 Files (*.h5 *.nxs *.hdf)',
'HDF5 Files (*)']
message = "Open HDF5 file"
filenamelist, ffilter = PyMcaFileDialogs.getFileList(parent=parent,
filetypelist=fileTypeList,
message=message,
getfilter=True,
single=True,
currentfilter=None)
if len(filenamelist) < 1:
return None
return filenamelist[0]
def _getFilenameDialog(parent=None):
"""Open a dialog to select a file in a filesystem tree view.
Return the selected filename."""
from PyMca5.PyMcaGui.io import PyMcaFileDialogs
fileTypeList = ['HDF5 Files (*.h5 *.nxs *.hdf)', 'HDF5 Files (*)']
message = "Open HDF5 file"
filenamelist, ffilter = PyMcaFileDialogs.getFileList(
parent=parent,
filetypelist=fileTypeList,
message=message,
getfilter=True,
single=True,
currentfilter=None)
if len(filenamelist) < 1:
return None
return filenamelist[0]
def get4DStack():
"""
Open a stack of image files in EDF or TIFF format, and return
the data with metadata.
:returns: legend, data, xScale, yScale, fileindex
Legend and data are both ``None`` in case of failure.
Scales are 2-tuples (originX, deltaX).
fileindex indicates the dimension/axis in the data corresponding to
the Z-axis.
:raise IOError: If the data could not be read
"""
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 fileList:
return None, None
if filterUsed.startswith('EDF Z'):
fileindex = 2
else:
fileindex = 1
filename = fileList[0]
legend = os.path.basename(filename)
if filterUsed.startswith('TIFF'):
stack = TiffStack.TiffStack(dtype=numpy.float32, imagestack=False)
stack.loadFileList(fileList, fileindex=1)
else:
stack = EDFStack.EDFStack(dtype=numpy.float32, imagestack=False)
if len(fileList) == 1:
stack.loadIndexedStack(filename, fileindex=fileindex)
else:
stack.loadFileList(fileList, fileindex=fileindex)
if stack is None:
raise IOError("Problem reading stack.")
xScale = stack.info.get("xScale")
yScale = stack.info.get("yScale")
return legend, stack.data, xScale, yScale, fileindex
def get4DStack():
"""
Open a stack of image files in EDF or TIFF format, and return
the data with metadata.
:returns: legend, data, xScale, yScale, fileindex
Legend and data are both ``None`` in case of failure.
Scales are 2-tuples (originX, deltaX).
fileindex indicates the dimension/axis in the data corresponding to
the Z-axis.
:raise IOError: If the data could not be read
"""
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 fileList:
return None, None
if filterUsed.startswith('EDF Z'):
fileindex = 2
else:
fileindex = 1
filename = fileList[0]
legend = os.path.basename(filename)
if filterUsed.startswith('TIFF'):
stack = TiffStack.TiffStack(dtype=numpy.float32, imagestack=False)
stack.loadFileList(fileList, fileindex=1)
else:
stack = EDFStack.EDFStack(dtype=numpy.float32, imagestack=False)
if len(fileList) == 1:
stack.loadIndexedStack(filename, fileindex=fileindex)
else:
stack.loadFileList(fileList, fileindex=fileindex)
if stack is None:
raise IOError("Problem reading stack.")
xScale = stack.info.get("xScale")
yScale = stack.info.get("yScale")
return legend, stack.data, xScale, yScale, fileindex
def save(self):
if self.initDir is None:
self.initDir = PyMcaDirs.outputDir
filetypelist = ["Fit configuration files (*.cfg)"]
message = "Enter ouput fit configuration file"
initdir = self.initDir
fileList = PyMcaFileDialogs.getFileList(parent=self,
filetypelist=filetypelist, message=message,
currentdir=initdir,
mode="SAVE",
getfilter=False,
single=True,
currentfilter=None,
native=None)
if len(fileList):
filename = fileList[0]
self.saveConfiguration(filename)
self.initDir = os.path.dirname(filename)
return
def load(self):
filetypelist = ["Fit configuration files (*.cfg)"]
message = "Choose fit configuration file"
initdir = os.path.curdir
if self.initDir is not None:
if os.path.isdir(self.initDir):
initdir = self.initDir
fileList = PyMcaFileDialogs.getFileList(parent=self,
filetypelist=filetypelist, message=message,
currentdir=initdir,
mode="OPEN",
getfilter=False,
single=True,
currentfilter=None,
native=None)
if len(fileList):
filename = fileList[0]
self.loadConfiguration(filename)
self.initDir = os.path.dirname(filename)
return
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 _loadExternalData(self):
getfilter = True
fileTypeList = ["EDF Files (*edf *ccd *tif)"]
if HDF5:
fileTypeList.append('HDF5 Files (*.h5 *.nxs *.hdf *.hdf5)')
fileTypeList.append('ASCII Files (*)')
fileTypeList.append("EDF Files (*)")
message = "Open data file"
filenamelist, ffilter = PyMcaFileDialogs.getFileList(
parent=None,
filetypelist=fileTypeList,
message=message,
getfilter=getfilter,
single=True,
currentfilter=None)
if len(filenamelist) < 1:
return
filename = filenamelist[0]
if ffilter.startswith('HDF5'):
data = HDF5Widget.getDatasetValueDialog(
filename=filename,
message='Select your data set by a double click')
elif ffilter.startswith("EDF"):
edf = EdfFile.EdfFile(filename, "rb")
if edf.GetNumImages() > 1:
# TODO: A dialog showing the different images
# based on the external images browser needed
_logger.warning("WARNING: Taking first image")
data = edf.GetData(0)
edf = None
elif ffilter.startswith("ASCII"):
#data=numpy.loadtxt(filename)
sf = specfilewrapper.Specfile(filename)
targetScan = sf[0]
data = numpy.array(targetScan.data().T, copy=True)
targetScan = None
sf = None
return data
def getConfigurationFilePath(parent=None, filetypelist=None, message=None,
currentdir=None, mode="OPEN", getfilter=None,
single=True, currentfilter=None, native=None):
if filetypelist is None:
filetypelist = ["Configuration from .ini files (*.ini)"]
if HAS_H5PY:
filetypelist.append(
"Configuration from HDF5 file (*%s)" % " *".join(_HDF5_EXTENSIONS))
filetypelist.append("All files (*)")
if message is None:
message = "Choose configuration file"
fileList = PyMcaFileDialogs.getFileList(parent=parent,
filetypelist=filetypelist, message=message,
currentdir=currentdir,
mode="OPEN", # input ignored
getfilter=getfilter,
single=single,
currentfilter=currentfilter,
native=native)
if getfilter:
fileList, usedfilter = fileList
if HAS_H5PY:
newList = []
for filename in fileList:
if is_hdf5(filename):
# we have to select a dataset
msg = 'Select the configuration dataset by a double click'
uri = getDatasetUri(parent=parent, filename=filename, message=msg)
if uri:
newList.append(uri)
else:
newList.append(filename)
fileList = newList
if getfilter:
return fileList, usedfilter
else:
return fileList
def openFile(self, filename=None, justloaded=None, specsession=False):
_logger.debug("openfile = %s", filename)
staticDialog = False
if specsession == "bliss":
specsession = False
session = filename
node = RedisTools.get_node(session)
if not node:
txt = "No REDIS information retrieved from session %s" % \
session
raise IOError(txt)
filename = RedisTools.get_session_filename(node)
if not len(filename):
txt = "Cannot retrieve last output filename from session %s" % \
session
raise IOError(txt)
if not os.path.exists(filename):
txt = "Last output file <%s> does not exist" % filename
raise IOError(txt)
filename = [filename]
key = os.path.basename(filename[0])
try:
self._emitSourceSelectedOrReloaded(filename, key)
except:
_logger.error("Problem opening %s" % filename[0])
key = "%s" % session
self._emitSourceSelectedOrReloaded([session], key)
return
if not specsession:
if justloaded is None:
justloaded = True
if filename is None:
if self.lastInputDir is not None:
if not os.path.exists(self.lastInputDir):
self.lastInputDir = None
wdir = self.lastInputDir
filelist, fileFilter = PyMcaFileDialogs.getFileList(
self,
filetypelist=self.fileTypeList,
message="Open a new source file",
currentdir=wdir,
mode="OPEN",
getfilter=True,
single=False,
currentfilter=self.lastFileFilter)
if not len(filelist):
return
if not len(filelist[0]):
return
filename = []
for f in filelist:
filename.append(qt.safe_str(f))
if not len(filename):
return
if len(filename):
self.lastInputDir = os.path.dirname(filename[0])
PyMcaDirs.inputDir = os.path.dirname(filename[0])
self.lastFileFilter = fileFilter
justloaded = True
if justloaded:
if type(filename) != type([]):
filename = [filename]
if not os.path.exists(filename[0]):
if '%' not in filename[0]:
raise IOError("File %s does not exist" % filename[0])
#check if it is a stack
if len(filename) > 1:
key = "STACK from %s to %s" % (filename[0], filename[-1])
else:
key = os.path.basename(filename[0])
else:
key = filename
if key not in sps.getspeclist():
qt.QMessageBox.critical(
self, "SPS Error",
"No shared memory source named %s" % key)
return
self._emitSourceSelectedOrReloaded(filename, key)
def _getOutputFileNameAndFilter(self, format_list=None):
"""
returns outputfile, file type and filter used
"""
# get outputfile
self.outputDir = PyMcaDirs.outputDir
if self.outputDir is None:
self.outputDir = os.getcwd()
wdir = os.getcwd()
elif os.path.exists(self.outputDir):
wdir = self.outputDir
else:
self.outputDir = os.getcwd()
wdir = self.outputDir
if format_list is None:
format_list = ['Specfile MCA *.mca',
'Specfile Scan *.dat']
if self._plotType != "MCA":
format_list += ['Specfile MultiScan *.dat']
format_list += ['Raw ASCII *.txt',
'","-separated CSV *.csv',
'";"-separated CSV *.csv',
'"tab"-separated CSV *.csv',
'OMNIC CSV *.csv',
'Widget PNG *.png',
'Widget JPG *.jpg',
'Graphics PNG *.png',
'Graphics EPS *.eps',
'Graphics SVG *.svg']
if self.outputFilter is None:
self.outputFilter = format_list[0]
fileList, fileFilter = PyMcaFileDialogs.getFileList(
self,
filetypelist=format_list,
message="Output File Selection",
currentdir=wdir,
single=True,
mode="SAVE",
getfilter=True,
currentfilter=self.outputFilter)
if not len(fileList):
return
self.outputFilter = fileFilter
filterused = self.outputFilter.split()
filetype = filterused[1]
extension = filterused[2]
outdir = qt.safe_str(fileList[0])
try:
self.outputDir = os.path.dirname(outdir)
PyMcaDirs.outputDir = os.path.dirname(outdir)
except:
self.outputDir = "."
try:
outputFile = os.path.basename(outdir)
except:
outputFile = outdir
if len(outputFile) < 5:
outputFile = outputFile + extension[-4:]
elif outputFile[-4:] != extension[-4:]:
outputFile = outputFile + extension[-4:]
return os.path.join(self.outputDir, outputFile), fileFilter
def openFile(self, filename=None, justloaded=None, specsession = False):
_logger.debug("openfile = %s", filename)
staticDialog = False
if not specsession:
if justloaded is None:
justloaded = True
if filename is None:
if self.lastInputDir is not None:
if not os.path.exists(self.lastInputDir):
self.lastInputDir = None
wdir = self.lastInputDir
filelist, fileFilter = PyMcaFileDialogs.getFileList(self,
filetypelist=self.fileTypeList,
message="Open a new source file",
currentdir=wdir,
mode="OPEN",
getfilter=True,
single=False,
currentfilter=self.lastFileFilter)
if not len(filelist):
return
if not len(filelist[0]):
return
filename=[]
for f in filelist:
filename.append(qt.safe_str(f))
if not len(filename):
return
if len(filename):
self.lastInputDir = os.path.dirname(filename[0])
PyMcaDirs.inputDir = os.path.dirname(filename[0])
self.lastFileFilter = fileFilter
justloaded = True
if justloaded:
if type(filename) != type([]):
filename = [filename]
if not os.path.exists(filename[0]):
if '%' not in filename[0]:
raise IOError("File %s does not exist" % filename[0])
#check if it is a stack
if len(filename) > 1:
key = "STACK from %s to %s" % (filename[0], filename[-1])
else:
key = os.path.basename(filename[0])
else:
key = filename
if key not in sps.getspeclist():
qt.QMessageBox.critical(self,
"SPS Error",
"No shared memory source named %s" % key)
return
ddict = {}
ddict["event"] = "NewSourceSelected"
if key in self.mapCombo.keys():
if self.mapCombo[key] == filename:
#Reloaded event
ddict["event"] = "SourceReloaded"
else:
i = 0
while key in self.mapCombo.keys():
key += "_%d" % i
ddict["combokey"] = key
ddict["sourcelist"] = filename
self.mapCombo[key] = filename
if ddict["event"] =="NewSourceSelected":
nitems = self.fileCombo.count()
self.fileCombo.insertItem(nitems, key)
self.fileCombo.setCurrentIndex(nitems)
else:
if hasattr(qt, "QString"):
nitem = self.fileCombo.findText(qt.QString(key))
else:
nitem = self.fileCombo.findText(key)
self.fileCombo.setCurrentIndex(nitem)
self.sigSourceSelectorSignal.emit(ddict)
def __addDirectory(self):
directory = PyMcaFileDialogs.getExistingDirectory(self,
message="Add Full Directory",
mode="OPEN")
if directory not in [None, ""]:
self.__addInFileList("directory", directory)
def openFile(self, filename=None, justloaded=None, specsession=False):
if DEBUG:
print("openfile = ", filename)
staticDialog = False
if not specsession:
if justloaded is None:
justloaded = True
if filename is None:
if self.lastInputDir is not None:
if not os.path.exists(self.lastInputDir):
self.lastInputDir = None
wdir = self.lastInputDir
filelist, fileFilter = PyMcaFileDialogs.getFileList(
self,
filetypelist=self.fileTypeList,
message="Open a new source file",
currentdir=wdir,
mode="OPEN",
getfilter=True,
single=False,
currentfilter=self.lastFileFilter)
if not len(filelist):
return
if not len(filelist[0]):
return
filename = []
for f in filelist:
filename.append(qt.safe_str(f))
if not len(filename):
return
if len(filename):
self.lastInputDir = os.path.dirname(filename[0])
PyMcaDirs.inputDir = os.path.dirname(filename[0])
self.lastFileFilter = fileFilter
justloaded = True
if justloaded:
if type(filename) != type([]):
filename = [filename]
if not os.path.exists(filename[0]):
if '%' not in filename[0]:
raise IOError("File %s does not exist" % filename[0])
#check if it is a stack
if len(filename) > 1:
key = "STACK from %s to %s" % (filename[0], filename[-1])
else:
key = os.path.basename(filename[0])
else:
key = filename
if key not in sps.getspeclist():
qt.QMessageBox.critical(
self, "SPS Error",
"No shared memory source named %s" % key)
return
ddict = {}
ddict["event"] = "NewSourceSelected"
if key in self.mapCombo.keys():
if self.mapCombo[key] == filename:
#Reloaded event
ddict["event"] = "SourceReloaded"
else:
i = 0
while key in self.mapCombo.keys():
key += "_%d" % i
ddict["combokey"] = key
ddict["sourcelist"] = filename
self.mapCombo[key] = filename
if ddict["event"] == "NewSourceSelected":
nitems = self.fileCombo.count()
self.fileCombo.insertItem(nitems, key)
self.fileCombo.setCurrentIndex(nitems)
else:
if hasattr(qt, "QString"):
nitem = self.fileCombo.findText(qt.QString(key))
else:
nitem = self.fileCombo.findText(key)
self.fileCombo.setCurrentIndex(nitem)
self.sigSourceSelectorSignal.emit(ddict)
def browseOutputDir(self):
f = PyMcaFileDialogs.getExistingDirectory(parent=self,
message="Please select output directory",
mode="OPEN")
if len(f):
self._outdirLine.setText(f)
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 not filenamelist:
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.startswith("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 or data.shape[1] not in shape:
# print("Ignoring %s (inconsistent shape)" % key)
continue
imagename = dataObject.info.get('Title', "")
if imagename != "":
imagename += " "
imagename += os.path.basename(filename) + " " + key
imagelist.append(data)
imagenames.append(imagename)
if not imagelist:
msg = qt.QMessageBox(None)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Cannot read a valid image from the file")
msg.exec_()
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])
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 not imagelist:
msg = qt.QMessageBox(None)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Cannot read a valid image from the file")
msg.exec_()
return
for i, image in enumerate(imagelist):
imagelist[i] = self.qImageToRgba(image)
image_shape = self._getStackImageShape()
origin, delta = self._getStackOriginDelta()
h = delta[1] * image_shape[0]
w = delta[0] * image_shape[1]
for bgimg, bglabel in zip(imagelist, imagenames):
if bglabel not in self.windows:
self.windows[
bglabel] = SilxExternalImagesWindow.SilxExternalImagesWindow(
)
self.windows[bglabel].sigMaskImageWidget.connect(
self.onWidgetSignal)
self.windows[bglabel].show()
# add the stack image for mask operation
self.windows[bglabel].setImages([self.getStackOriginalImage()],
labels=["stack data"],
origin=origin,
width=w,
height=h)
self.windows[bglabel].plot.getImage("current").setAlpha(0)
# add the external image
self.windows[bglabel].setBackgroundImages([bgimg],
labels=[bglabel],
origins=[origin],
widths=[w],
heights=[h])
self.windows[bglabel].plot.setGraphTitle(bglabel)
self._showWidget(bglabel)
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 not filenamelist:
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.startswith("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 or data.shape[1] not in shape:
# print("Ignoring %s (inconsistent shape)" % key)
continue
imagename = dataObject.info.get('Title', "")
if imagename != "":
imagename += " "
imagename += os.path.basename(filename) + " " + key
imagelist.append(data)
imagenames.append(imagename)
if not imagelist:
msg = qt.QMessageBox(None)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Cannot read a valid image from the file")
msg.exec_()
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])
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 not imagelist:
msg = qt.QMessageBox(None)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Cannot read a valid image from the file")
msg.exec_()
return
for i, image in enumerate(imagelist):
imagelist[i] = self.qImageToRgba(image)
image_shape = self._getStackImageShape()
origin, delta = self._getStackOriginDelta()
h = delta[1] * image_shape[0]
w = delta[0] * image_shape[1]
stack_images, stack_names = self.getStackROIImagesAndNames()
stack_info = self.getStackInfo()
if "bgimages" not in stack_info:
stack_info["bgimages"] = {}
for bgimg, bglabel in zip(imagelist, imagenames):
if bglabel not in self.windows:
self.windows[bglabel] = SilxExternalImagesWindow.SilxExternalImagesWindow()
self.windows[bglabel].sigMaskImageWidget.connect(
self.onWidgetSignal)
self.windows[bglabel].show()
# add the stack image for mask operation
self.windows[bglabel].setImages([stack_images[0]],
labels=[stack_names[0]],
origin=origin, width=w, height=h)
self.windows[bglabel].plot.getImage("current").setAlpha(0)
# add the external image
self.windows[bglabel].setBackgroundImages([bgimg],
labels=[bglabel],
origins=[origin],
widths=[w],
heights=[h])
self.windows[bglabel].plot.setGraphTitle(bglabel)
# also store bg images as a stack info attribute
stack_info["bgimages"][bglabel] = {"data": bgimg,
"origin": origin,
"width": w,
"height": h}
self._showWidget(bglabel)