def choose_file(self):
"""
Opens a file dialog and sets the file text box to the chosen path
"""
from pyspec.spec import SpecDataFile
filename, _ = QtGui.QFileDialog.getOpenFileName(self, 'Open file',
os.path.expanduser('~'))
self.filename.setText(str(filename))
self.SPECfile = SpecDataFile(self.get_filename())
self.spectra = self.SPECfile.findex.keys()
self.scanmin.setText(str(self.spectra[0]))
self.scanmax.setText(str(self.spectra[-1]))
def compute(self):
spec_params = self.get_input("spec_file_params")
spec_file_root = spec_params.spec_file_root
data_folder_path = spec_params.data_folder_path
scan_no = spec_params.scan_number
print spec_file_root
print data_folder_path
sf = SpecDataFile(spec_file_root, ccdpath=data_folder_path)
scan = sf[scan_no]
fp = FileProcessor(spec=scan)
fp.process()
arr_2d_stack = fp.getImage()
self.set_output("spec_img_stack", arr_2d_stack)
self.set_output("spec_file", self)
self.fp = fp
self.sf = sf
self.scan = scan
class ImportDialog(BaseImportDialog):
"""Dialog to import SPEC Scans"""
def __init__(self, parent=None):
super(ImportDialog, self).__init__(parent)
self.layout = QtGui.QVBoxLayout()
self.layout.addLayout(self.filebox())
self.layout.addLayout(self.scanbox())
self.layout.addWidget(self.buttonbox())
self.setLayout(self.layout)
self.setWindowTitle("Import "+str(filetype))
def scanbox(self):
scanbox = QtGui.QHBoxLayout()
scanminlabel = QtGui.QLabel("Min. Scan")
self.scanmin = QtGui.QLineEdit()
self.scanmin.setFixedWidth(100)
self.scanmin.setAlignment(QtCore.Qt.AlignRight)
scanmaxlabel = QtGui.QLabel("Max. Scan")
self.scanmax = QtGui.QLineEdit()
self.scanmax.setFixedWidth(100)
self.scanmax.setAlignment(QtCore.Qt.AlignRight)
scanbox.addWidget(scanminlabel)
scanbox.addWidget(self.scanmin)
scanbox.addWidget(scanmaxlabel)
scanbox.addWidget(self.scanmax)
return scanbox
def choose_file(self):
"""
Opens a file dialog and sets the file text box to the chosen path
"""
from pyspec.spec import SpecDataFile
filename, _ = QtGui.QFileDialog.getOpenFileName(self, 'Open file',
os.path.expanduser('~'))
self.filename.setText(str(filename))
self.SPECfile = SpecDataFile(self.get_filename())
self.spectra = self.SPECfile.findex.keys()
self.scanmin.setText(str(self.spectra[0]))
self.scanmax.setText(str(self.spectra[-1]))
def get_spectra(self):
try:
specrange = sorted([int(self.scanmin.text()), int(self.scanmax.text())])
specmin = self.spectra.index(specrange[0])
specmax = self.spectra.index(specrange[1]) + 1
return specmin, specmax
except ValueError(error_message):
QtGui.QMessageBox.critical(
self, "Invalid spectra", str(error_message),
QtGui.QMessageBox.Ok, QtGui.QMessageBox.NoButton)
def get_data(self):
root = NXroot()
specmin, specmax = self.get_spectra()
for i in self.spectra[0:specmax]:
scan = self.SPECfile.getScan(i)
if i < self.spectra[specmin]:
continue
title, entry, scan_type, cols, axis = self.parse_scan(scan)
root[entry] = NXentry()
root[entry].title = title
root[entry].comments = scan.comments
root[entry].data = NXdata()
if isinstance(axis,list):
scan_shape = (axis[1][1].size, axis[0][1].size)
scan_size = np.prod(scan_shape)
j = 0
for col in cols:
root[entry].data[col] = NXfield(reshape_data(scan.data[:,j],
scan_shape))
j += 1
else:
j = 0
for col in cols:
root[entry].data[col] = NXfield(scan.data[:,j])
j += 1
root[entry].data.nxsignal = root[entry].data[cols[-1]]
root[entry].data.errors = NXfield(np.sqrt(root[entry].data.nxsignal))
if isinstance(axis,list):
root[entry].data[axis[0][0]] = axis[0][1]
root[entry].data[axis[1][0]] = axis[1][1]
root[entry].data.nxaxes = [root[entry].data[axis[1][0]],
root[entry].data[axis[0][0]]]
else:
root[entry].data.nxaxes = root[entry].data[axis]
return root
def parse_scan(self, scan):
title = scan.header.splitlines()[0]
words = title.split()
scan_number = 's%s' % words[1]
scan_type = words[2]
cols = [lower(col.replace(' ', '_')) for col in scan.cols]
axis = cols[0]
try:
if scan_type == "hscan":
axis = 'H'
elif scan_type == "kscan":
axis = 'K'
elif scan_type == "lscan":
axis = 'L'
elif scan_type == "hklscan":
Hstart, Hend, Kstart, Kend, Lstart, Lend = words[3:8]
if Hstart <> Hend:
axis = 'H'
elif Kstart <> Kend:
axis = 'K'
else:
axis = 'L'
elif scan_type == "hklmesh":
Q0, Q0start, Q0end, NQ0 = words[3], float(words[4]), float(words[5]), int(words[6])+1
Q1, Q1start, Q1end, NQ1 = words[7], float(words[8]), float(words[9]), int(words[10])+1
axis = [(Q0, np.linspace(Q0start, Q0end, NQ0)),
(Q1, np.linspace(Q1end, Q1start, NQ1))]
else:
if words[3] in motors.keys():
axis = motors[words[3]]
finally:
return title, scan_number, scan_type, cols, axis