def _readImageListSpec(self, filenamelist):
# 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])
if not imagenames:
self._criticalError('No valid data provided')
return imagenames, imagelist
def convert_image(scan_no, frame_no, detector_info):
_spec = specfilewrapper.Specfile(spec_path + 'ma2254_sixcvertical.spec')
scan = _spec.select('{0}.1'.format(scan_no))
UB = np.array(scan.header('G')[2].split(' ')[-9:], dtype=np.float)
wavelength = float(scan.header('G')[1].split(' ')[-1])
scanparams = wavelength, UB
pointparams = get_point_params(
scan, frame_no) # 2D array of diffractometer angles + mon + transm
img_loader = edf_image.edf_image_loader(spec_path +
'ma2254_sixcvertical.spec')
img = img_loader.load_frame(edf_path,
scan_no,
frame_no,
gz_compressed=True,
normalize=True,
monitor_names=['transm', 'mon'])
proc_img, img_params = process_image(scanparams, pointparams, img,
detector_info)
wavelength, UB, gamma, delta, theta, mu, chi, phi = img_params
HKL = project(wavelength, UB, gamma, delta, theta, mu, chi, phi)
return HKL, proc_img
def _loadExternalData(self):
getfilter = True
fileTypeList = ["EDF Files (*edf *ccd *tif)"]
if HDF5:
fileTypeList.append('HDF5 Files (*.h5 *.nxs *.hdf)')
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.getDatasetDialog(
filename,
value=True,
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
print("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 test():
a = qt.QApplication(sys.argv)
a.lastWindowClosed.connect(a.quit)
w = ParametersTab()
w.show()
from PyMca5.PyMca import specfilewrapper as specfile
from PyMca5.PyMca import Specfit
from PyMca5 import PyMcaDataDir
import numpy
sf = specfile.Specfile(
os.path.join(PyMcaDataDir.PYMCA_DATA_DIR, "XRFSpectrum.mca"))
scan = sf.select('2.1')
mcadata = scan.mca(1)
y = numpy.array(mcadata)
#x=numpy.arange(len(y))
x = numpy.arange(len(y)) * 0.0502883 - 0.492773
fit = Specfit.Specfit()
fit.setdata(x=x, y=y)
fit.importfun(
os.path.join(os.path.dirname(Specfit.__file__), "SpecfitFunctions.py"))
fit.settheory('Hypermet')
fit.configure(Yscaling=1.,
WeightFlag=1,
PosFwhmFlag=1,
HeightAreaFlag=1,
FwhmPoints=16,
PositionFlag=1,
HypermetTails=1)
fit.setbackground('Linear')
if 1:
mcaresult = fit.mcafit(x=x, xmin=x[300], xmax=x[1000])
w.fillfrommca(mcaresult)
else:
fit.estimate()
fit.startfit()
w.fillfromfit(fit.paramlist, current='Fit')
w.removeview(view='Region 1')
a.exec_()
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 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