cwgaldino / brixs Goto Github PK

def inspect(self):
    """Plots data in a inspection window.

    If the mouse pointer hovers over a datapoint, the index of this datapoint is showed.
    """
    raise NotImplementedError('This is not implemented yet.')


def metadata(self):
    """Opens a windows with all user defined variables for inspection.
    """
    raise NotImplementedError('This is not implemented yet.')

%matplotlib widget
# %% ------------------------- Standard Imports --------------------------- %% #
from RIXSMacros import *

# matplotlib
br.set_cycler(n='tab10', ls=2)

# %% ------------------------- Initial definitions ------------------------ %% #
TOP  = Path(r'.')
RIXS = TOP/'RIXS'
XAS  = TOP/'XAS'
# out  = Path(r'S:\')

prefix = 'Cr_'

# %% step-by-step (FELIPE)
if True:
    pe = br.ADRESS.read(RIXS/'Cr_0038_d1.h5', type_='pe')
    pe.binning(nbins=(6000, 20))

    # 
    br.figure()
    pe.plot(color='black')
    pe.reduced.plot()

    # 
    br.figure()
    pe.plot(color='black')
    pe.reduced.vlines(color='red')

    # 
    br.figure()
    _ = pe.reduced.columns.plot()

    # 
    pe.calculate_shifts()
    popt, model, R2 = pe.calculated_shifts.polyfit()

    x = np.linspace(min(pe.x), max(pe.x), 100)
    fit = br.Spectrum(x=x, y=model(x))

    # 
    br.figure()
    pe.calculated_shifts.plot(marker='o')
    fit.plot()


    # 
    br.figure()
    pe.plot(color='black')

    offset = pe.reduced.columns[0].x[np.argmax(pe.reduced.columns[0].y)]
    plt.plot(fit.x, -fit.y+offset, color='red')

    # 
    pe.set_shifts(p=popt)

    # 
    br.figure()
    pe.plot(color='black')

     _ = pe.reduced.columns.plot()
     # 
---> pe.calculate_shifts()
     popt, model, R2 = pe.calculated_shifts.polyfit()
     x = np.linspace(min(pe.x), max(pe.x), 100)

File brixs/brixs.py:2199, in PhotonEvents.calculate_shifts(self, axis)
   2196 mode = 'cc'
   2197 assert self.reduced is not None, 'Image was not binned yet.\nPlease, use PhotonEvents.binning()'
-> 2199 self.reduced.calculate_shifts(axis=axis, mode=mode)
   2201 if mode in cc:
   2202     if axis == 0:

File brixs/brixs.py:1417, in Image.calculate_shifts(self, axis, mode, limit_size)
   1415 if mode in cc:
   1416     self._calculated_shifts = ss.calculated_shifts
-> 1417     self.calculated_shifts.factor = ss.step
   1418 else:
   1419     self._calculated_shifts = ss.calculated_shifts

File brixs/brixs.py:2768, in Spectrum.factor(self, value)
   2766 @factor.setter
   2767 def factor(self, value):
-> 2768     self.set_factor(value)

File brixs/brixs.py:3345, in Spectrum.set_factor(self, value, type_)
   3342     self._factor = value
   3344 # special
-> 3345 self.peaks.set_factors(value=value, type_=type_)

File brixs/peaks.py:826, in Peaks.set_factors(self, value, type_)
    824     self['area'].value = self['area'].value * self.factor**-1
    825 if value != 1:
--> 826     self['amp'].value  = self['amp'].value * value
    827     self['area'].value = self['area'].value * value
    828 self._factor = value

File brixs/peaks.py:149, in Peaks.__getitem__(self, name)
    147         name = name + f'_{index}'
    148     else:
--> 149         raise ValueError(f'This list has multiple peaks, please, identify the peak number')
    150 if name in self:
    151     return super().__getitem__(name)

ValueError: This list has multiple peaks, please, identify the peak number