class CalibrateDialog(NXDialog):
def __init__(self, parent=None):
super().__init__(parent)
self.plotview = None
self.data = None
self.counts = None
self.points = []
self.pattern_geometry = None
self.cake_geometry = None
self.polarization = None
self.is_calibrated = False
self.phi_max = -np.pi
cstr = str(ALL_CALIBRANTS)
calibrants = sorted(cstr[cstr.index(':')+2:].split(', '))
self.parameters = GridParameters()
self.parameters.add('calibrant', calibrants, 'Calibrant')
self.parameters['calibrant'].value = 'CeO2'
self.parameters.add('wavelength', 0.5, 'Wavelength (Ang)', False)
self.parameters.add('distance', 100.0, 'Detector Distance (mm)', True)
self.parameters.add('xc', 512, 'Beam Center - x', True)
self.parameters.add('yc', 512, 'Beam Center - y', True)
self.parameters.add('yaw', 0.0, 'Yaw (degrees)', True)
self.parameters.add('pitch', 0.0, 'Pitch (degrees)', True)
self.parameters.add('roll', 0.0, 'Roll (degrees)', True)
self.parameters.add('search_size', 10, 'Search Size (pixels)')
self.rings_box = self.select_box([f'Ring{i}' for i in range(1, 21)])
self.set_layout(self.select_entry(self.choose_entry),
self.progress_layout(close=True))
self.set_title('Calibrating Powder')
def choose_file(self):
super().choose_file()
powder_file = self.get_filename()
if powder_file:
self.data = load_image(powder_file)
self.counts = self.data.nxsignal.nxvalue
self.plot_data()
def choose_entry(self):
if self.layout.count() == 2:
self.insert_layout(
1, self.filebox('Choose Powder Calibration File'))
self.insert_layout(2, self.parameters.grid(header=False))
self.insert_layout(
3, self.action_buttons(('Select Points', self.select),
('Autogenerate Rings', self.auto),
('Clear Points', self.clear_points)))
self.insert_layout(4, self.make_layout(self.rings_box))
self.insert_layout(
5, self.action_buttons(('Calibrate', self.calibrate),
('Plot Cake', self.plot_cake),
('Restore', self.restore_parameters),
('Save', self.save_parameters)))
self.parameters['wavelength'].value = (
self.entry['instrument/monochromator/wavelength'])
detector = self.entry['instrument/detector']
self.parameters['distance'].value = detector['distance']
self.parameters['yaw'].value = detector['yaw']
self.parameters['pitch'].value = detector['pitch']
self.parameters['roll'].value = detector['roll']
if 'beam_center_x' in detector:
self.parameters['xc'].value = detector['beam_center_x']
if 'beam_center_y' in detector:
self.parameters['yc'].value = detector['beam_center_y']
self.pixel_size = (
self.entry['instrument/detector/pixel_size'].nxvalue * 1e-3)
self.pixel_mask = self.entry['instrument/detector/pixel_mask'].nxvalue
self.ring = self.selected_ring
if 'calibration' in self.entry['instrument']:
self.data = self.entry['instrument/calibration']
self.counts = self.data.nxsignal.nxvalue
self.plot_data()
else:
self.close_plots()
@property
def search_size(self):
return int(self.parameters['search_size'].value)
@property
def selected_ring(self):
return int(self.rings_box.currentText()[4:]) - 1
@property
def ring_color(self):
colors = ['r', 'b', 'g', 'c', 'm'] * 4
return colors[self.ring]
def plot_data(self):
if self.plotview is None:
if 'Powder Calibration' in plotviews:
self.plotview = plotviews['Powder Calibration']
else:
self.plotview = NXPlotView('Powder Calibration')
self.plotview.plot(self.data, log=True)
self.plotview.aspect = 'equal'
self.plotview.ytab.flipped = True
self.clear_points()
def on_button_press(self, event):
self.plotview.make_active()
if event.inaxes:
self.xp, self.yp = event.x, event.y
else:
self.xp, self.yp = 0, 0
def on_button_release(self, event):
self.ring = self.selected_ring
if event.inaxes:
if abs(event.x - self.xp) > 5 or abs(event.y - self.yp) > 5:
return
x, y = self.plotview.inverse_transform(event.xdata, event.ydata)
for i, point in enumerate(self.points):
circle = point[0]
if circle.shape.contains_point(
self.plotview.ax.transData.transform((x, y))):
circle.remove()
for circle in point[2]:
circle.remove()
del self.points[i]
return
self.add_points(x, y)
def circle(self, idx, idy, alpha=1.0):
return self.plotview.circle(idx, idy, self.search_size,
facecolor=self.ring_color, edgecolor='k',
alpha=alpha)
def select(self):
self.plotview.cidpress = self.plotview.mpl_connect(
'button_press_event', self.on_button_press)
self.plotview.cidrelease = self.plotview.mpl_connect(
'button_release_event', self.on_button_release)
def auto(self):
xc, yc = self.parameters['xc'].value, self.parameters['yc'].value
wavelength = self.parameters['wavelength'].value
distance = self.parameters['distance'].value * 1e-3
self.start_progress((0, self.selected_ring+1))
for ring in range(self.selected_ring+1):
self.update_progress(ring)
if len([p for p in self.points if p[3] == ring]) > 0:
continue
self.ring = ring
theta = 2 * np.arcsin(wavelength /
(2*self.calibrant.dSpacing[ring]))
r = distance * np.tan(theta) / self.pixel_size
phi = self.phi_max = -np.pi
while phi < np.pi:
x, y = np.int(xc + r*np.cos(phi)), np.int(yc + r*np.sin(phi))
if ((x > 0 and x < self.data.x.max()) and
(y > 0 and y < self.data.y.max()) and
not self.pixel_mask[y, x]):
self.add_points(x, y, phi)
phi = self.phi_max + 0.2
else:
phi = phi + 0.2
self.stop_progress()
def add_points(self, x, y, phi=0.0):
xc, yc = self.parameters['xc'].value, self.parameters['yc'].value
idx, idy = self.find_peak(x, y)
points = [(idy, idx)]
circles = []
massif = Massif(self.counts)
extra_points = massif.find_peaks((idy, idx))
for point in extra_points:
points.append(point)
circles.append(self.circle(point[1], point[0], alpha=0.3))
phis = np.array([np.arctan2(p[0]-yc, p[1]-xc) for p in points])
if phi < -0.5*np.pi:
phis[np.where(phis > 0.0)] -= 2 * np.pi
self.phi_max = max(*phis, self.phi_max)
self.points.append([self.circle(idx, idy), points, circles, self.ring])
def find_peak(self, x, y):
s = self.search_size
left = int(np.round(x - s * 0.5))
if left < 0:
left = 0
top = int(np.round(y - s * 0.5))
if top < 0:
top = 0
region = self.counts[top:(top+s), left:(left+s)]
idy, idx = np.where(region == region.max())
idx = left + idx[0]
idy = top + idy[0]
return idx, idy
def clear_points(self):
for i, point in enumerate(self.points):
circle = point[0]
circle.remove()
for circle in point[2]:
circle.remove()
self.points = []
@property
def calibrant(self):
return ALL_CALIBRANTS[self.parameters['calibrant'].value]
@property
def point_array(self):
points = []
for point in self.points:
for p in point[1]:
points.append((p[0], p[1], point[3]))
return np.array(points)
def prepare_parameters(self):
self.parameters.set_parameters()
self.wavelength = self.parameters['wavelength'].value * 1e-10
self.distance = self.parameters['distance'].value * 1e-3
self.yaw = np.radians(self.parameters['yaw'].value)
self.pitch = np.radians(self.parameters['pitch'].value)
self.roll = np.radians(self.parameters['roll'].value)
self.xc = self.parameters['xc'].value
self.yc = self.parameters['yc'].value
def calibrate(self):
self.prepare_parameters()
self.orig_pixel1 = self.pixel_size
self.orig_pixel2 = self.pixel_size
self.pattern_geometry = GeometryRefinement(self.point_array,
dist=self.distance,
wavelength=self.wavelength,
pixel1=self.pixel_size,
pixel2=self.pixel_size,
calibrant=self.calibrant)
self.refine()
self.create_cake_geometry()
self.pattern_geometry.reset()
def refine(self):
self.pattern_geometry.data = self.point_array
if self.parameters['wavelength'].vary:
self.pattern_geometry.refine2()
fix = []
else:
fix = ['wavelength']
if not self.parameters['distance'].vary:
fix.append('dist')
self.pattern_geometry.refine2_wavelength(fix=fix)
self.read_parameters()
self.is_calibrated = True
self.create_cake_geometry()
self.pattern_geometry.reset()
def create_cake_geometry(self):
self.cake_geometry = AzimuthalIntegrator()
pyFAI_parameter = self.pattern_geometry.getPyFAI()
pyFAI_parameter['wavelength'] = self.pattern_geometry.wavelength
self.cake_geometry.setPyFAI(dist=pyFAI_parameter['dist'],
poni1=pyFAI_parameter['poni1'],
poni2=pyFAI_parameter['poni2'],
rot1=pyFAI_parameter['rot1'],
rot2=pyFAI_parameter['rot2'],
rot3=pyFAI_parameter['rot3'],
pixel1=pyFAI_parameter['pixel1'],
pixel2=pyFAI_parameter['pixel2'])
self.cake_geometry.wavelength = pyFAI_parameter['wavelength']
def plot_cake(self):
if 'Cake Plot' in plotviews:
plotview = plotviews['Cake Plot']
else:
plotview = NXPlotView('Cake Plot')
if not self.is_calibrated:
raise NeXusError('No refinement performed')
res = self.cake_geometry.integrate2d(self.counts,
1024, 1024,
method='csr',
unit='2th_deg',
correctSolidAngle=True)
self.cake_data = NXdata(res[0],
(NXfield(res[2], name='azimumthal_angle'),
NXfield(res[1], name='polar_angle')))
self.cake_data['title'] = 'Cake Plot'
plotview.plot(self.cake_data, log=True)
wavelength = self.parameters['wavelength'].value
polar_angles = [2 * np.degrees(np.arcsin(wavelength/(2*d)))
for d in self.calibrant.dSpacing]
plotview.vlines([polar_angle for polar_angle in polar_angles
if polar_angle < plotview.xaxis.max],
linestyle=':', color='r')
def read_parameters(self):
pyFAI = self.pattern_geometry.getPyFAI()
fit2d = self.pattern_geometry.getFit2D()
self.parameters['wavelength'].value = (
self.pattern_geometry.wavelength * 1e10)
self.parameters['distance'].value = pyFAI['dist'] * 1e3
self.parameters['yaw'].value = np.degrees(pyFAI['rot1'])
self.parameters['pitch'].value = np.degrees(pyFAI['rot2'])
self.parameters['roll'].value = np.degrees(pyFAI['rot3'])
self.parameters['xc'].value = fit2d['centerX']
self.parameters['yc'].value = fit2d['centerY']
def restore_parameters(self):
self.parameters.restore_parameters()
def save_parameters(self):
if not self.is_calibrated:
raise NeXusError('No refinement performed')
elif 'calibration' in self.entry['instrument']:
if confirm_action(
"Do you want to overwrite existing calibration data?"):
del self.entry['instrument/calibration']
else:
return
self.entry['instrument/calibration'] = self.data
if 'refinement' in self.entry['instrument/calibration']:
if confirm_action('Overwrite previous refinement?'):
del self.entry['instrument/calibration/refinement']
else:
return
self.entry['instrument/calibration/calibrant'] = (
self.parameters['calibrant'].value)
process = NXprocess()
process.program = 'pyFAI'
process.version = pyFAI.version
process.parameters = NXcollection()
process.parameters['Detector'] = (
self.entry['instrument/detector/description'])
pyFAI_parameter = self.pattern_geometry.getPyFAI()
process.parameters['PixelSize1'] = pyFAI_parameter['pixel1']
process.parameters['PixelSize2'] = pyFAI_parameter['pixel2']
process.parameters['Distance'] = pyFAI_parameter['dist']
process.parameters['Poni1'] = pyFAI_parameter['poni1']
process.parameters['Poni2'] = pyFAI_parameter['poni2']
process.parameters['Rot1'] = pyFAI_parameter['rot1']
process.parameters['Rot2'] = pyFAI_parameter['rot2']
process.parameters['Rot3'] = pyFAI_parameter['rot3']
process.parameters['Wavelength'] = pyFAI_parameter['wavelength']
self.entry['instrument/calibration/refinement'] = process
self.entry['instrument/monochromator/wavelength'] = (
self.parameters['wavelength'].value)
self.entry['instrument/monochromator/energy'] = (
12.398419739640717 / self.parameters['wavelength'].value)
detector = self.entry['instrument/detector']
detector['distance'] = self.parameters['distance'].value
detector['yaw'] = self.parameters['yaw'].value
detector['pitch'] = self.parameters['pitch'].value
detector['roll'] = self.parameters['roll'].value
detector['beam_center_x'] = self.parameters['xc'].value
detector['beam_center_y'] = self.parameters['yc'].value
try:
detector['polarization'] = self.pattern_geometry.polarization(
factor=0.99, shape=detector['mask'].shape)
except Exception:
pass
def close_plots(self):
if 'Powder Calibration' in plotviews:
plotviews['Powder Calibration'].close()
if 'Cake Plot' in plotviews:
plotviews['Cake Plot'].close()
def closeEvent(self, event):
self.close_plots()
event.accept()
def accept(self):
super().accept()
self.close_plots()
def reject(self):
super().reject()
self.close_plots()
class CalibrateDialog(BaseDialog):
def __init__(self, parent=None):
super(CalibrateDialog, self).__init__(parent)
self.plotview = None
self.data = None
self.counts = None
self.points = []
self.pattern_geometry = None
self.cake_geometry = None
self.is_calibrated = False
cstr = str(ALL_CALIBRANTS)
calibrants = sorted(cstr[cstr.index(':') + 2:].split(', '))
self.parameters = GridParameters()
self.parameters.add('calibrant', calibrants, 'Calibrant')
self.parameters['calibrant'].value = 'CeO2'
self.parameters.add('wavelength', 0.5, 'Wavelength (Ang)', False)
self.parameters.add('distance', 100.0, 'Detector Distance (mm)', True)
self.parameters.add('xc', 512, 'Beam Center - x', True)
self.parameters.add('yc', 512, 'Beam Center - y', True)
self.parameters.add('yaw', 0.0, 'Yaw (degrees)', True)
self.parameters.add('pitch', 0.0, 'Pitch (degrees)', True)
self.parameters.add('roll', 0.0, 'Roll (degrees)', True)
self.parameters.add('search_size', 10, 'Search Size (pixels)')
rings = ['Ring1', 'Ring2', 'Ring3', 'Ring4', 'Ring5']
self.rings_box = self.select_box(rings)
self.set_layout(
self.select_entry(self.choose_entry),
self.action_buttons(('Plot Calibration', self.plot_data)),
self.parameters.grid(header=False),
self.make_layout(
self.action_buttons(('Select Points', self.select)),
self.rings_box),
self.action_buttons(('Calibrate', self.calibrate),
('Plot Cake', self.plot_cake),
('Restore', self.restore_parameters),
('Save', self.save_parameters)),
self.close_buttons(close=True))
self.set_title('Calibrating Powder')
def choose_entry(self):
if 'calibration' not in self.entry['instrument']:
raise NeXusError('Please load calibration data to this entry')
self.update_parameters()
self.plot_data()
def update_parameters(self):
self.parameters['wavelength'].value = self.entry[
'instrument/monochromator/wavelength']
detector = self.entry['instrument/detector']
self.parameters['distance'].value = detector['distance']
self.parameters['yaw'].value = detector['yaw']
self.parameters['pitch'].value = detector['pitch']
self.parameters['roll'].value = detector['roll']
if 'beam_center_x' in detector:
self.parameters['xc'].value = detector['beam_center_x']
if 'beam_center_y' in detector:
self.parameters['yc'].value = detector['beam_center_y']
self.data = self.entry['instrument/calibration']
self.counts = self.data.nxsignal.nxvalue
@property
def search_size(self):
return int(self.parameters['search_size'].value)
@property
def ring(self):
return int(self.rings_box.currentText()[-1]) - 1
@property
def ring_color(self):
colors = ['r', 'b', 'g', 'c', 'm']
return colors[self.ring]
def plot_data(self):
if self.plotview is None:
if 'Powder Calibration' in plotviews:
self.plotview = plotviews['Powder Calibration']
else:
self.plotview = NXPlotView('Powder Calibration')
self.plotview.plot(self.data, log=True)
self.plotview.aspect = 'equal'
self.plotview.ytab.flipped = True
self.clear_peaks()
def on_button_press(self, event):
self.plotview.make_active()
if event.inaxes:
self.xp, self.yp = event.x, event.y
else:
self.xp, self.yp = 0, 0
def on_button_release(self, event):
if event.inaxes:
if abs(event.x - self.xp) > 5 or abs(event.y - self.yp) > 5:
return
x, y = self.plotview.inverse_transform(event.xdata, event.ydata)
for i, point in enumerate(self.points):
circle = point[0]
if circle.contains_point(
self.plotview.ax.transData.transform((x, y))):
circle.remove()
for circle in point[2]:
circle.remove()
del self.points[i]
return
idx, idy = self.find_peak(x, y)
points = [(idy, idx)]
circles = []
massif = Massif(self.counts)
extra_points = massif.find_peaks((idy, idx))
for point in extra_points:
points.append(point)
circles.append(self.circle(point[1], point[0], alpha=0.3))
self.points.append(
[self.circle(idx, idy), points, circles, self.ring])
def circle(self, idx, idy, alpha=1.0):
return self.plotview.circle(idx,
idy,
self.search_size,
facecolor=self.ring_color,
edgecolor='k',
alpha=alpha)
def select(self):
self.plotview.cidpress = self.plotview.mpl_connect(
'button_press_event', self.on_button_press)
self.plotview.cidrelease = self.plotview.mpl_connect(
'button_release_event', self.on_button_release)
def find_peak(self, x, y):
s = self.search_size
left = int(np.round(x - s * 0.5))
if left < 0:
left = 0
top = int(np.round(y - s * 0.5))
if top < 0:
top = 0
region = self.counts[top:(top + s), left:(left + s)]
idy, idx = np.where(region == region.max())
idx = left + idx[0]
idy = top + idy[0]
return idx, idy
def clear_peaks(self):
self.points = []
@property
def calibrant(self):
return ALL_CALIBRANTS[self.parameters['calibrant'].value]
@property
def point_array(self):
points = []
for point in self.points:
for p in point[1]:
points.append((p[0], p[1], point[3]))
return np.array(points)
def prepare_parameters(self):
self.parameters.set_parameters()
self.wavelength = self.parameters['wavelength'].value * 1e-10
self.distance = self.parameters['distance'].value * 1e-3
self.yaw = np.radians(self.parameters['yaw'].value)
self.pitch = np.radians(self.parameters['pitch'].value)
self.roll = np.radians(self.parameters['roll'].value)
self.pixel_size = self.entry[
'instrument/detector/pixel_size'].nxvalue * 1e-3
self.xc = self.parameters['xc'].value
self.yc = self.parameters['yc'].value
def calibrate(self):
self.prepare_parameters()
self.orig_pixel1 = self.pixel_size
self.orig_pixel2 = self.pixel_size
self.pattern_geometry = GeometryRefinement(self.point_array,
dist=self.distance,
wavelength=self.wavelength,
pixel1=self.pixel_size,
pixel2=self.pixel_size,
calibrant=self.calibrant)
self.refine()
self.create_cake_geometry()
self.pattern_geometry.reset()
def refine(self):
self.pattern_geometry.data = self.point_array
if self.parameters['wavelength'].vary:
self.pattern_geometry.refine2()
fix = []
else:
fix = ['wavelength']
if not self.parameters['distance'].vary:
fix.append('dist')
self.pattern_geometry.refine2_wavelength(fix=fix)
self.read_parameters()
self.is_calibrated = True
self.create_cake_geometry()
self.pattern_geometry.reset()
def create_cake_geometry(self):
self.cake_geometry = AzimuthalIntegrator()
pyFAI_parameter = self.pattern_geometry.getPyFAI()
pyFAI_parameter['wavelength'] = self.pattern_geometry.wavelength
self.cake_geometry.setPyFAI(dist=pyFAI_parameter['dist'],
poni1=pyFAI_parameter['poni1'],
poni2=pyFAI_parameter['poni2'],
rot1=pyFAI_parameter['rot1'],
rot2=pyFAI_parameter['rot2'],
rot3=pyFAI_parameter['rot3'],
pixel1=pyFAI_parameter['pixel1'],
pixel2=pyFAI_parameter['pixel2'])
self.cake_geometry.wavelength = pyFAI_parameter['wavelength']
def plot_cake(self):
if 'Cake Plot' in plotviews:
plotview = plotviews['Cake Plot']
else:
plotview = NXPlotView('Cake Plot')
if not self.is_calibrated:
raise NeXusError('No refinement performed')
res = self.cake_geometry.integrate2d(self.counts,
1024,
1024,
method='csr',
unit='2th_deg',
correctSolidAngle=True)
self.cake_data = NXdata(res[0],
(NXfield(res[2], name='azimumthal_angle'),
NXfield(res[1], name='polar_angle')))
self.cake_data['title'] = self.entry['instrument/calibration/title']
plotview.plot(self.cake_data, log=True)
wavelength = self.parameters['wavelength'].value
polar_angles = [
2 * np.degrees(np.arcsin(wavelength / (2 * d)))
for d in self.calibrant.dSpacing
]
plotview.vlines([
polar_angle
for polar_angle in polar_angles if polar_angle < plotview.xaxis.max
],
linestyle=':',
color='r')
def read_parameters(self):
pyFAI = self.pattern_geometry.getPyFAI()
fit2d = self.pattern_geometry.getFit2D()
self.parameters[
'wavelength'].value = self.pattern_geometry.wavelength * 1e10
self.parameters['distance'].value = pyFAI['dist'] * 1e3
self.parameters['yaw'].value = np.degrees(pyFAI['rot1'])
self.parameters['pitch'].value = np.degrees(pyFAI['rot2'])
self.parameters['roll'].value = np.degrees(pyFAI['rot3'])
self.parameters['xc'].value = fit2d['centerX']
self.parameters['yc'].value = fit2d['centerY']
def restore_parameters(self):
self.parameters.restore_parameters()
def save_parameters(self):
if not self.is_calibrated:
raise NeXusError('No refinement performed')
elif 'refinement' in self.entry['instrument/calibration']:
if confirm_action('Overwrite previous refinement?'):
del self.entry['instrument/calibration/refinement']
else:
return
self.entry['instrument/calibration/calibrant'] = self.parameters[
'calibrant'].value
process = NXprocess()
process.program = 'pyFAI'
process.version = pyFAI.version
process.parameters = NXcollection()
process.parameters['Detector'] = self.entry[
'instrument/detector/description']
pyFAI_parameter = self.pattern_geometry.getPyFAI()
process.parameters['PixelSize1'] = pyFAI_parameter['pixel1']
process.parameters['PixelSize2'] = pyFAI_parameter['pixel2']
process.parameters['Distance'] = pyFAI_parameter['dist']
process.parameters['Poni1'] = pyFAI_parameter['poni1']
process.parameters['Poni2'] = pyFAI_parameter['poni2']
process.parameters['Rot1'] = pyFAI_parameter['rot1']
process.parameters['Rot2'] = pyFAI_parameter['rot2']
process.parameters['Rot3'] = pyFAI_parameter['rot3']
process.parameters['Wavelength'] = pyFAI_parameter['wavelength']
self.entry['instrument/calibration/refinement'] = process
self.entry['instrument/monochromator/wavelength'] = self.parameters[
'wavelength'].value
self.entry[
'instrument/monochromator/energy'] = 12.398419739640717 / self.parameters[
'wavelength'].value
detector = self.entry['instrument/detector']
detector['distance'] = self.parameters['distance'].value
detector['yaw'] = self.parameters['yaw'].value
detector['pitch'] = self.parameters['pitch'].value
detector['roll'] = self.parameters['roll'].value
detector['beam_center_x'] = self.parameters['xc'].value
detector['beam_center_y'] = self.parameters['yc'].value
def reject(self):
super(CalibrateDialog, self).reject()
if 'Powder Calibration' in plotviews:
plotviews['Powder Calibration'].close_view()
if 'Cake Plot' in plotviews:
plotviews['Cake Plot'].close_view()
class CalibrateDialog(BaseDialog):
def __init__(self, parent=None):
super(CalibrateDialog, self).__init__(parent)
self.plotview = None
self.data = None
self.counts = None
self.points = []
self.pattern_geometry = None
self.cake_geometry = None
self.is_calibrated = False
cstr = str(ALL_CALIBRANTS)
calibrants = sorted(cstr[cstr.index(':')+2:].split(', '))
self.parameters = GridParameters()
self.parameters.add('calibrant', calibrants, 'Calibrant')
self.parameters['calibrant'].value = 'CeO2'
self.parameters.add('wavelength', 0.5, 'Wavelength (Ang)', False)
self.parameters.add('distance', 100.0, 'Detector Distance (mm)', True)
self.parameters.add('xc', 512, 'Beam Center - x', True)
self.parameters.add('yc', 512, 'Beam Center - y', True)
self.parameters.add('yaw', 0.0, 'Yaw (degrees)', True)
self.parameters.add('pitch', 0.0, 'Pitch (degrees)', True)
self.parameters.add('roll', 0.0, 'Roll (degrees)', True)
self.parameters.add('search_size', 10, 'Search Size (pixels)')
rings = ['Ring%s' % i for i in range(1,21)]
self.rings_box = self.select_box(rings)
self.set_layout(self.select_entry(self.choose_entry),
self.action_buttons(('Plot Calibration', self.plot_data)),
self.parameters.grid(header=False),
self.make_layout(
self.action_buttons(('Select Points', self.select)),
self.rings_box),
self.action_buttons(('Calibrate', self.calibrate),
('Plot Cake', self.plot_cake),
('Restore', self.restore_parameters),
('Save', self.save_parameters)),
self.close_buttons(close=True))
self.set_title('Calibrating Powder')
def choose_entry(self):
if 'calibration' not in self.entry['instrument']:
raise NeXusError('Please load calibration data to this entry')
self.update_parameters()
self.plot_data()
def update_parameters(self):
self.parameters['wavelength'].value = self.entry['instrument/monochromator/wavelength']
detector = self.entry['instrument/detector']
self.parameters['distance'].value = detector['distance']
self.parameters['yaw'].value = detector['yaw']
self.parameters['pitch'].value = detector['pitch']
self.parameters['roll'].value = detector['roll']
if 'beam_center_x' in detector:
self.parameters['xc'].value = detector['beam_center_x']
if 'beam_center_y' in detector:
self.parameters['yc'].value = detector['beam_center_y']
self.data = self.entry['instrument/calibration']
self.counts = self.data.nxsignal.nxvalue
@property
def search_size(self):
return int(self.parameters['search_size'].value)
@property
def ring(self):
return int(self.rings_box.currentText()[4:]) - 1
@property
def ring_color(self):
colors = ['r', 'b', 'g', 'c', 'm'] * 4
return colors[self.ring]
def plot_data(self):
if self.plotview is None:
if 'Powder Calibration' in plotviews:
self.plotview = plotviews['Powder Calibration']
else:
self.plotview = NXPlotView('Powder Calibration')
self.plotview.plot(self.data, log=True)
self.plotview.aspect='equal'
self.plotview.ytab.flipped = True
self.clear_peaks()
def on_button_press(self, event):
self.plotview.make_active()
if event.inaxes:
self.xp, self.yp = event.x, event.y
else:
self.xp, self.yp = 0, 0
def on_button_release(self, event):
if event.inaxes:
if abs(event.x - self.xp) > 5 or abs(event.y - self.yp) > 5:
return
x, y = self.plotview.inverse_transform(event.xdata, event.ydata)
for i, point in enumerate(self.points):
circle = point[0]
if circle.contains_point(self.plotview.ax.transData.transform((x,y))):
circle.remove()
for circle in point[2]:
circle.remove()
del self.points[i]
return
idx, idy = self.find_peak(x, y)
points = [(idy, idx)]
circles = []
massif = Massif(self.counts)
extra_points = massif.find_peaks((idy, idx))
for point in extra_points:
points.append(point)
circles.append(self.circle(point[1], point[0], alpha=0.3))
self.points.append([self.circle(idx, idy), points, circles, self.ring])
def circle(self, idx, idy, alpha=1.0):
return self.plotview.circle(idx, idy, self.search_size,
facecolor=self.ring_color, edgecolor='k',
alpha=alpha)
def select(self):
self.plotview.cidpress = self.plotview.mpl_connect(
'button_press_event', self.on_button_press)
self.plotview.cidrelease = self.plotview.mpl_connect(
'button_release_event', self.on_button_release)
def find_peak(self, x, y):
s = self.search_size
left = int(np.round(x - s * 0.5))
if left < 0:
left = 0
top = int(np.round(y - s * 0.5))
if top < 0:
top = 0
region = self.counts[top:(top+s),left:(left+s)]
idy, idx = np.where(region == region.max())
idx = left + idx[0]
idy = top + idy[0]
return idx, idy
def clear_peaks(self):
self.points = []
@property
def calibrant(self):
return ALL_CALIBRANTS[self.parameters['calibrant'].value]
@property
def point_array(self):
points = []
for point in self.points:
for p in point[1]:
points.append((p[0], p[1], point[3]))
return np.array(points)
def prepare_parameters(self):
self.parameters.set_parameters()
self.wavelength = self.parameters['wavelength'].value * 1e-10
self.distance = self.parameters['distance'].value * 1e-3
self.yaw = np.radians(self.parameters['yaw'].value)
self.pitch = np.radians(self.parameters['pitch'].value)
self.roll = np.radians(self.parameters['roll'].value)
self.pixel_size = self.entry['instrument/detector/pixel_size'].nxvalue * 1e-3
self.xc = self.parameters['xc'].value
self.yc = self.parameters['yc'].value
def calibrate(self):
self.prepare_parameters()
self.orig_pixel1 = self.pixel_size
self.orig_pixel2 = self.pixel_size
self.pattern_geometry = GeometryRefinement(self.point_array,
dist=self.distance,
wavelength=self.wavelength,
pixel1=self.pixel_size,
pixel2=self.pixel_size,
calibrant=self.calibrant)
self.refine()
self.create_cake_geometry()
self.pattern_geometry.reset()
def refine(self):
self.pattern_geometry.data = self.point_array
if self.parameters['wavelength'].vary:
self.pattern_geometry.refine2()
fix = []
else:
fix = ['wavelength']
if not self.parameters['distance'].vary:
fix.append('dist')
self.pattern_geometry.refine2_wavelength(fix=fix)
self.read_parameters()
self.is_calibrated = True
self.create_cake_geometry()
self.pattern_geometry.reset()
def create_cake_geometry(self):
self.cake_geometry = AzimuthalIntegrator()
pyFAI_parameter = self.pattern_geometry.getPyFAI()
pyFAI_parameter['wavelength'] = self.pattern_geometry.wavelength
self.cake_geometry.setPyFAI(dist=pyFAI_parameter['dist'],
poni1=pyFAI_parameter['poni1'],
poni2=pyFAI_parameter['poni2'],
rot1=pyFAI_parameter['rot1'],
rot2=pyFAI_parameter['rot2'],
rot3=pyFAI_parameter['rot3'],
pixel1=pyFAI_parameter['pixel1'],
pixel2=pyFAI_parameter['pixel2'])
self.cake_geometry.wavelength = pyFAI_parameter['wavelength']
def plot_cake(self):
if 'Cake Plot' in plotviews:
plotview = plotviews['Cake Plot']
else:
plotview = NXPlotView('Cake Plot')
if not self.is_calibrated:
raise NeXusError('No refinement performed')
res = self.cake_geometry.integrate2d(self.counts,
1024, 1024,
method='csr',
unit='2th_deg',
correctSolidAngle=True)
self.cake_data = NXdata(res[0], (NXfield(res[2], name='azimumthal_angle'),
NXfield(res[1], name='polar_angle')))
self.cake_data['title'] = self.entry['instrument/calibration/title']
plotview.plot(self.cake_data, log=True)
wavelength = self.parameters['wavelength'].value
polar_angles = [2 * np.degrees(np.arcsin(wavelength/(2*d)))
for d in self.calibrant.dSpacing]
plotview.vlines([polar_angle for polar_angle in polar_angles
if polar_angle < plotview.xaxis.max],
linestyle=':', color='r')
def read_parameters(self):
pyFAI = self.pattern_geometry.getPyFAI()
fit2d = self.pattern_geometry.getFit2D()
self.parameters['wavelength'].value = self.pattern_geometry.wavelength * 1e10
self.parameters['distance'].value = pyFAI['dist'] * 1e3
self.parameters['yaw'].value = np.degrees(pyFAI['rot1'])
self.parameters['pitch'].value = np.degrees(pyFAI['rot2'])
self.parameters['roll'].value = np.degrees(pyFAI['rot3'])
self.parameters['xc'].value = fit2d['centerX']
self.parameters['yc'].value = fit2d['centerY']
def restore_parameters(self):
self.parameters.restore_parameters()
def save_parameters(self):
if not self.is_calibrated:
raise NeXusError('No refinement performed')
elif 'refinement' in self.entry['instrument/calibration']:
if confirm_action('Overwrite previous refinement?'):
del self.entry['instrument/calibration/refinement']
else:
return
self.entry['instrument/calibration/calibrant'] = self.parameters['calibrant'].value
process = NXprocess()
process.program = 'pyFAI'
process.version = pyFAI.version
process.parameters = NXcollection()
process.parameters['Detector'] = self.entry['instrument/detector/description']
pyFAI_parameter = self.pattern_geometry.getPyFAI()
process.parameters['PixelSize1'] = pyFAI_parameter['pixel1']
process.parameters['PixelSize2'] = pyFAI_parameter['pixel2']
process.parameters['Distance'] = pyFAI_parameter['dist']
process.parameters['Poni1'] = pyFAI_parameter['poni1']
process.parameters['Poni2'] = pyFAI_parameter['poni2']
process.parameters['Rot1'] = pyFAI_parameter['rot1']
process.parameters['Rot2'] = pyFAI_parameter['rot2']
process.parameters['Rot3'] = pyFAI_parameter['rot3']
process.parameters['Wavelength'] = pyFAI_parameter['wavelength']
self.entry['instrument/calibration/refinement'] = process
self.entry['instrument/monochromator/wavelength'] = self.parameters['wavelength'].value
self.entry['instrument/monochromator/energy'] = 12.398419739640717 / self.parameters['wavelength'].value
detector = self.entry['instrument/detector']
detector['distance'] = self.parameters['distance'].value
detector['yaw'] = self.parameters['yaw'].value
detector['pitch'] = self.parameters['pitch'].value
detector['roll'] = self.parameters['roll'].value
detector['beam_center_x'] = self.parameters['xc'].value
detector['beam_center_y'] = self.parameters['yc'].value
def reject(self):
super(CalibrateDialog, self).reject()
if 'Powder Calibration' in plotviews:
plotviews['Powder Calibration'].close_view()
if 'Cake Plot' in plotviews:
plotviews['Cake Plot'].close_view()
