def __init__(self, credo, title='Sample-to-detector distance calibration'):
ToolDialog.__init__(self, credo, title=title, buttons=('OK', Gtk.ResponseType.OK, 'Apply', Gtk.ResponseType.APPLY, 'Cancel', Gtk.ResponseType.CANCEL))
vb = self.get_content_area()
f = Gtk.Expander(label='Exposure')
vb.pack_start(f, False, False, 0)
es = ExposureSelector(credo)
es.connect('open', self.do_load_exposure)
f.add(es)
f.set_expanded(True)
hb = Gtk.Box(orientation=Gtk.Orientation.HORIZONTAL)
vb.pack_start(hb, True, True, 0)
vb1 = Gtk.Box(orientation=Gtk.Orientation.VERTICAL)
hb.pack_start(vb1, False, False, 0)
hb1 = Gtk.Box(orientation=Gtk.Orientation.HORIZONTAL)
vb1.pack_start(hb1, True, True, 0)
self._treemodel = Gtk.ListStore(GObject.TYPE_PYOBJECT, # ErrorValue of uncalibrated data (pixel/radius)
GObject.TYPE_PYOBJECT, # ErrorValue of calibrated data (q)
GObject.TYPE_STRING, # String representation of uncalibrated data
GObject.TYPE_STRING) # String representation of calibrated data
self._treeview = Gtk.TreeView(self._treemodel)
sw = Gtk.ScrolledWindow()
sw.set_policy(Gtk.PolicyType.NEVER, Gtk.PolicyType.AUTOMATIC)
hb1.pack_start(sw, True, True, 0)
sw.add(self._treeview)
self._treeview.append_column(Gtk.TreeViewColumn('Pixel', Gtk.CellRendererText(), text=2))
self._treeview.append_column(Gtk.TreeViewColumn('q', Gtk.CellRendererText(), text=3))
self._treeview.set_rules_hint(True)
self._treeview.set_headers_visible(True)
self._treeview.get_selection().set_mode(Gtk.SelectionMode.MULTIPLE)
self._treeview.set_size_request(150, -1)
tv_buttonbox = Gtk.ButtonBox(orientation=Gtk.Orientation.VERTICAL)
tv_buttonbox.set_layout(Gtk.ButtonBoxStyle.START)
hb1.pack_start(tv_buttonbox, False, False, 0)
b = Gtk.Button(label='Add', image=Gtk.Image.new_from_icon_name('list-add', Gtk.IconSize.BUTTON))
tv_buttonbox.add(b)
b.connect('clicked', self._treeview_add)
b = Gtk.Button(label='Remove', image=Gtk.Image.new_from_icon_name('list-remove', Gtk.IconSize.BUTTON))
tv_buttonbox.add(b)
b.connect('clicked', self._treeview_remove)
b = Gtk.Button(label='Clear', image=Gtk.Image.new_from_icon_name('edit-clear', Gtk.IconSize.BUTTON))
tv_buttonbox.add(b)
b.connect('clicked', self._treeview_clear)
b = Gtk.Button(label='Save As', image=Gtk.Image.new_from_icon_name('document-save-as', Gtk.IconSize.BUTTON))
tv_buttonbox.add(b)
b.connect('clicked', self._treeview_saveas)
b = Gtk.Button(label='Open', image=Gtk.Image.new_from_icon_name('document-open', Gtk.IconSize.BUTTON))
tv_buttonbox.add(b)
b.connect('clicked', self._treeview_open)
b = Gtk.Button(label='Refresh', image=Gtk.Image.new_from_icon_name('view-refresh', Gtk.IconSize.BUTTON))
tv_buttonbox.add(b)
b.connect('clicked', self._treeview_refresh)
self._findpeakbutton = Gtk.Button(label='Find peaks',
image=Gtk.Image.new_from_icon_name('edit-find', Gtk.IconSize.BUTTON))
tv_buttonbox.add(self._findpeakbutton)
self._findpeakbutton.connect('clicked', self._treeview_findpeak)
self._findpeakbutton.set_sensitive(False)
b = Gtk.Button(label='Export to HTML')
tv_buttonbox.add(b)
b.connect('clicked', self._treeview_export_html)
vb2 = Gtk.Box(orientation=Gtk.Orientation.VERTICAL)
hb.pack_start(vb2, True, True, 0)
self._fig = Figure()
self._canvas = FigureCanvasGTK3Agg(self._fig)
self._canvas.set_size_request(400, 300)
vb2.pack_start(self._canvas, True, True, 0)
self._figtoolbar = NavigationToolbar2GTK3(self._canvas, None)
vb2.pack_start(self._figtoolbar, False, False, 0)
grid = Gtk.Grid()
vb.pack_start(grid, False, False, 0)
l = Gtk.Label(label='Wavelength:');
l.set_halign(Gtk.Align.START); l.set_valign(Gtk.Align.CENTER)
grid.attach(l, 0, 0, 1, 1)
self._wavelength_entry = Gtk.SpinButton(
adjustment=Gtk.Adjustment(value=0.15418, lower=0, upper=100, step_increment=0.01, page_increment=0.1, page_size=0.1),
digits=5)
self._wavelength_entry.set_value(0.15418)
grid.attach(self._wavelength_entry, 1, 0, 1, 1)
l = Gtk.Label(label='Pixel size:');
l.set_halign(Gtk.Align.START); l.set_valign(Gtk.Align.CENTER)
grid.attach(l, 2, 0, 1, 1)
self._pixelsize_entry = Gtk.SpinButton(
adjustment=Gtk.Adjustment(value=0.172, lower=0, upper=100, step_increment=0.01, page_increment=0.1),
digits=3)
self._pixelsize_entry.set_value(0.172)
grid.attach(self._pixelsize_entry, 3, 0, 1, 1)
l = Gtk.Label(label='Coefficient of determination (R2) of the fit:');
l.set_halign(Gtk.Align.START); l.set_valign(Gtk.Align.CENTER)
grid.attach(l, 0, 1, 1, 1)
self._r2_label = Gtk.Label(label='N/A')
grid.attach(self._r2_label, 1, 1, 1, 1)
l = Gtk.Label(label='Reduced Chi2 of the fit:')
l.set_halign(Gtk.Align.START); l.set_valign(Gtk.Align.CENTER)
grid.attach(l, 2, 1, 1, 1)
self._chi2_label = Gtk.Label(label='N/A')
grid.attach(self._chi2_label, 3, 1, 1, 1)
l = Gtk.Label(label='Sample-to-detector distance:');
l.set_halign(Gtk.Align.START); l.set_valign(Gtk.Align.CENTER)
grid.attach(l, 0, 2, 1, 1)
self._sddist_label = Gtk.Label(label='N/A')
grid.attach(self._sddist_label, 1, 2, 1, 1)
class DistCalibrationDialog(ToolDialog):
__gtype_name__ = 'SAXSCtrl_DistCalibrationDialog'
def __init__(self, credo, title='Sample-to-detector distance calibration'):
ToolDialog.__init__(self, credo, title=title, buttons=('OK', Gtk.ResponseType.OK, 'Apply', Gtk.ResponseType.APPLY, 'Cancel', Gtk.ResponseType.CANCEL))
vb = self.get_content_area()
f = Gtk.Expander(label='Exposure')
vb.pack_start(f, False, False, 0)
es = ExposureSelector(credo)
es.connect('open', self.do_load_exposure)
f.add(es)
f.set_expanded(True)
hb = Gtk.Box(orientation=Gtk.Orientation.HORIZONTAL)
vb.pack_start(hb, True, True, 0)
vb1 = Gtk.Box(orientation=Gtk.Orientation.VERTICAL)
hb.pack_start(vb1, False, False, 0)
hb1 = Gtk.Box(orientation=Gtk.Orientation.HORIZONTAL)
vb1.pack_start(hb1, True, True, 0)
self._treemodel = Gtk.ListStore(GObject.TYPE_PYOBJECT, # ErrorValue of uncalibrated data (pixel/radius)
GObject.TYPE_PYOBJECT, # ErrorValue of calibrated data (q)
GObject.TYPE_STRING, # String representation of uncalibrated data
GObject.TYPE_STRING) # String representation of calibrated data
self._treeview = Gtk.TreeView(self._treemodel)
sw = Gtk.ScrolledWindow()
sw.set_policy(Gtk.PolicyType.NEVER, Gtk.PolicyType.AUTOMATIC)
hb1.pack_start(sw, True, True, 0)
sw.add(self._treeview)
self._treeview.append_column(Gtk.TreeViewColumn('Pixel', Gtk.CellRendererText(), text=2))
self._treeview.append_column(Gtk.TreeViewColumn('q', Gtk.CellRendererText(), text=3))
self._treeview.set_rules_hint(True)
self._treeview.set_headers_visible(True)
self._treeview.get_selection().set_mode(Gtk.SelectionMode.MULTIPLE)
self._treeview.set_size_request(150, -1)
tv_buttonbox = Gtk.ButtonBox(orientation=Gtk.Orientation.VERTICAL)
tv_buttonbox.set_layout(Gtk.ButtonBoxStyle.START)
hb1.pack_start(tv_buttonbox, False, False, 0)
b = Gtk.Button(label='Add', image=Gtk.Image.new_from_icon_name('list-add', Gtk.IconSize.BUTTON))
tv_buttonbox.add(b)
b.connect('clicked', self._treeview_add)
b = Gtk.Button(label='Remove', image=Gtk.Image.new_from_icon_name('list-remove', Gtk.IconSize.BUTTON))
tv_buttonbox.add(b)
b.connect('clicked', self._treeview_remove)
b = Gtk.Button(label='Clear', image=Gtk.Image.new_from_icon_name('edit-clear', Gtk.IconSize.BUTTON))
tv_buttonbox.add(b)
b.connect('clicked', self._treeview_clear)
b = Gtk.Button(label='Save As', image=Gtk.Image.new_from_icon_name('document-save-as', Gtk.IconSize.BUTTON))
tv_buttonbox.add(b)
b.connect('clicked', self._treeview_saveas)
b = Gtk.Button(label='Open', image=Gtk.Image.new_from_icon_name('document-open', Gtk.IconSize.BUTTON))
tv_buttonbox.add(b)
b.connect('clicked', self._treeview_open)
b = Gtk.Button(label='Refresh', image=Gtk.Image.new_from_icon_name('view-refresh', Gtk.IconSize.BUTTON))
tv_buttonbox.add(b)
b.connect('clicked', self._treeview_refresh)
self._findpeakbutton = Gtk.Button(label='Find peaks',
image=Gtk.Image.new_from_icon_name('edit-find', Gtk.IconSize.BUTTON))
tv_buttonbox.add(self._findpeakbutton)
self._findpeakbutton.connect('clicked', self._treeview_findpeak)
self._findpeakbutton.set_sensitive(False)
b = Gtk.Button(label='Export to HTML')
tv_buttonbox.add(b)
b.connect('clicked', self._treeview_export_html)
vb2 = Gtk.Box(orientation=Gtk.Orientation.VERTICAL)
hb.pack_start(vb2, True, True, 0)
self._fig = Figure()
self._canvas = FigureCanvasGTK3Agg(self._fig)
self._canvas.set_size_request(400, 300)
vb2.pack_start(self._canvas, True, True, 0)
self._figtoolbar = NavigationToolbar2GTK3(self._canvas, None)
vb2.pack_start(self._figtoolbar, False, False, 0)
grid = Gtk.Grid()
vb.pack_start(grid, False, False, 0)
l = Gtk.Label(label='Wavelength:');
l.set_halign(Gtk.Align.START); l.set_valign(Gtk.Align.CENTER)
grid.attach(l, 0, 0, 1, 1)
self._wavelength_entry = Gtk.SpinButton(
adjustment=Gtk.Adjustment(value=0.15418, lower=0, upper=100, step_increment=0.01, page_increment=0.1, page_size=0.1),
digits=5)
self._wavelength_entry.set_value(0.15418)
grid.attach(self._wavelength_entry, 1, 0, 1, 1)
l = Gtk.Label(label='Pixel size:');
l.set_halign(Gtk.Align.START); l.set_valign(Gtk.Align.CENTER)
grid.attach(l, 2, 0, 1, 1)
self._pixelsize_entry = Gtk.SpinButton(
adjustment=Gtk.Adjustment(value=0.172, lower=0, upper=100, step_increment=0.01, page_increment=0.1),
digits=3)
self._pixelsize_entry.set_value(0.172)
grid.attach(self._pixelsize_entry, 3, 0, 1, 1)
l = Gtk.Label(label='Coefficient of determination (R2) of the fit:');
l.set_halign(Gtk.Align.START); l.set_valign(Gtk.Align.CENTER)
grid.attach(l, 0, 1, 1, 1)
self._r2_label = Gtk.Label(label='N/A')
grid.attach(self._r2_label, 1, 1, 1, 1)
l = Gtk.Label(label='Reduced Chi2 of the fit:')
l.set_halign(Gtk.Align.START); l.set_valign(Gtk.Align.CENTER)
grid.attach(l, 2, 1, 1, 1)
self._chi2_label = Gtk.Label(label='N/A')
grid.attach(self._chi2_label, 3, 1, 1, 1)
l = Gtk.Label(label='Sample-to-detector distance:');
l.set_halign(Gtk.Align.START); l.set_valign(Gtk.Align.CENTER)
grid.attach(l, 0, 2, 1, 1)
self._sddist_label = Gtk.Label(label='N/A')
grid.attach(self._sddist_label, 1, 2, 1, 1)
def do_response(self, respid):
if respid in (Gtk.ResponseType.OK, Gtk.ResponseType.APPLY) and hasattr(self, '_dist'):
self.credo.dist = self._dist.val
self.credo.dist_error = self._dist.err
if respid in (Gtk.ResponseType.OK, Gtk.ResponseType.CANCEL):
ToolDialog.do_response(self, respid)
return
def do_load_exposure(self, exposureselector, exposure):
try:
self._rad = exposure.radial_average(pixel=True)
del exposure
self._findpeakbutton.set_sensitive(True)
except sastool.classes.SASExposureException:
md = Gtk.MessageDialog(self.get_toplevel(), Gtk.DialogFlags.DESTROY_WITH_PARENT | Gtk.DialogFlags.MODAL,
Gtk.MessageType.ERROR, Gtk.ButtonsType.OK, 'Please load a mask!')
md.run()
md.destroy()
del md
def _treeview_add(self, button=None):
self._treemodel.append((sastool.ErrorValue(0, 0), sastool.ErrorValue(0, 0), '0', '0'))
def _treeview_remove(self, button=None):
model, selection = self._treeview.get_selection().get_selected_rows()
for row in reversed(selection):
model.remove(self._treemodel.get_iter(row))
self._treeview_refresh()
def _treeview_clear(self, button=None):
self._treemodel.clear()
def _treeview_saveas(self, button=None):
pass
def _treeview_open(self, button=None):
pass
def _treeview_export_html(self, button=None):
htmlout = '<table border="1" cellpadding="1" cellspacing="1" style="width:500px">\n'
htmlout = htmlout + ' <tr>\n'
htmlout = htmlout + ' <th>Uncalibrated values (pixel)</th>\n'
htmlout = htmlout + ' <th>Calibrated values (1/nm)</th>\n'
htmlout = htmlout + ' <th>Determined from (calibration sample, peak nr.)</th>\n'
htmlout = htmlout + ' </tr>\n'
for uncal, cal, struncal, strcal in self._treemodel:
htmlout = htmlout + ' <tr>\n'
htmlout = htmlout + ' <td>%s</td>\n <td>%s</td>\n <td>...</td>\n' % (uncal.tostring(extra_digits=1), cal.tostring(extra_digits=1))
htmlout = htmlout + ' </tr>\n'
htmlout = htmlout + '</table>\n'
Gtk.Clipboard.get(Gdk.SELECTION_CLIPBOARD).set_text(htmlout, -1)
def _treeview_refresh(self, button=None):
self._fig.clear()
axes = self._fig.add_subplot(1, 1, 1)
x = np.array([r[0].val for r in self._treemodel])
y = np.array([r[1].val for r in self._treemodel])
dx = np.array([r[0].err for r in self._treemodel])
dy = np.array([r[1].err for r in self._treemodel])
axes.errorbar(x, y, dx, dy, 'bo', label='Calibration points')
def qfrompix(pix, pixelsize, wavelength, dist):
return 4 * np.pi * np.sin(0.5 * np.arctan(pixelsize * pix / dist)) / wavelength
if len(x) > 1:
dist, stat = sastool.easylsq.nonlinear_leastsquares(x, y, dy, qfrompix,
[sastool.FixedParameter(self._pixelsize_entry.get_value()),
sastool.FixedParameter(self._wavelength_entry.get_value()),
100.
])[2:]
pixscale = np.linspace(x.min(), x.max(), 100)
self._r2_label.set_label(str(stat['R2']))
self._chi2_label.set_label(str(stat['Chi2_reduced']))
else:
q = sastool.ErrorValue(y[0], dy[0])
pix = sastool.ErrorValue(x[0], dx[0])
dist = self._pixelsize_entry.get_value() * pix / np.tan(np.arcsin(q * self._wavelength_entry.get_value() / (4 * np.pi)) * 2)
pixscale = np.linspace(0, float(pix), 100)
self._r2_label.set_label('N/A')
self._chi2_label.set_label('N/A')
self._sddist_label.set_label(dist.tostring(extra_digits=3))
self._dist = dist
axes.plot(pixscale, qfrompix(pixscale, self._pixelsize_entry.get_value(), self._wavelength_entry.get_value(), dist), 'r-', label='Calibration curve from LSQ fit')
axes.set_xlabel('Pixels')
axes.set_ylabel('q')
axes.legend(loc='best')
self._fig.canvas.draw()
def _treeview_findpeak(self, button=None):
pf = PeakFinder(self._rad)
res = Gtk.ResponseType.APPLY
conn = pf.connect('peak-found', self._on_peak_found)
try:
res = pf.run()
finally:
pf.disconnect(conn)
pf.destroy()
def _on_peak_found(self, peakfinder, a, x0, sigma, y0, stat, cal):
if not isinstance(cal, sastool.ErrorValue):
uncal = sastool.ErrorValue(cal)
self._treemodel.append((x0, cal, unicode(x0), unicode(cal)))
self._treeview_refresh()