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phase_match/__init__

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FoSpy.plotting.diffraction.phase_match

X_LABEL module-attribute 

X_LABEL = cfg.diffraction.x_label

cfg module-attribute 

cfg = None

PhaseMatcher

Source code in FoSpy/plotting/diffraction/phase_match/__init__.py 
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class PhaseMatcher:
    def __init__(self, exp_2theta, exp_int, cif_dict):

        self.baseline_cfg = cfg.get("diffraction.baseline")
        self.find_cfg = cfg.get("diffraction.find_peaks")

        frames = {'exp':DataFrame({X_LABEL:exp_2theta, "int":exp_int}).set_index(X_LABEL)}
        # x_min=min(exp_2theta)
        # x_max=max(exp_2theta)
        for name, cif in cif_dict.items():
            engine = cif.new_engine(engine_name='pymatgen')
            frames[name] = engine.get_pattern().set_index(X_LABEL)
        self.cifs = cif_dict
        self.frames = frames

    def match_peaks(self):
        import numpy as np
        from ._utils import match_peaks
        from ._utils import rows_to_2th

        exp_frame = self.frames['exp']/self.frames['exp'].max()
        exp_data = exp_frame['int']
        exp_index = exp_frame.index

        matchsets = {}

        for name, cif in self.cifs.items():
            peak_list = cif.get_peaks()

            peak_idx = np.searchsorted(exp_index, [x for (x, y) in peak_list])

            matches = match_peaks(exp_data, peak_idx)

            matches = rows_to_2th(exp_index,matches)

            matchsets[name] = matches

        return matchsets

    def find_peaks(self, interactive=False, ui=None,**interactive_kwargs):
        self.find_baseline(interactive=interactive, ui=ui)
        interactive = check_for_interactive(interactive, "find_peaks")

        exp_corrected = self.frames['exp']['corrected'].to_numpy()

        from ._utils import unpack_peaks


        find_cfg = self.find_cfg
        if not interactive:
            return unpack_peaks(exp_corrected, "widths",**find_cfg)

        from ..ui.peaks import PeakFinder

        interactive_kwargs.setdefault('title', "Baseline-Corrected Peak Finder")
        if interactive_kwargs['title'].startswith("+"):
            suffix = interactive_kwargs['title'][1:]
            interactive_kwargs['title'] = f"Baseline-Corrected Peak Finder\n{suffix}"

        peak_finder = PeakFinder(exp_corrected, self.frames['exp'].index, cfg=find_cfg, ui=ui, **interactive_kwargs)
        return peak_finder.main_loop()





    def plot_matches(self, cif_name, ax=None, show=False):
        import numpy as np
        from matplotlib import pyplot as plt
        from ._utils import plot_stick_at_x

        matchset = self.match_peaks()[cif_name]
        peak_list = self.cifs[cif_name].get_peaks()

        peaks_x = np.array([x for (x, y) in peak_list])
        peaks_y = np.array([y for (x, y) in peak_list])

        if ax is None:
            fig, ax = plt.gcf(), plt.gca()
        else:
            fig = ax.get_figure()

        self.frames['exp'].plot(ax=ax)

        for _, x_matches in matchset['matches']:
            for x in x_matches:
                plot_stick_at_x(x, peaks_x, peaks_y, ax=ax, color='g')

        for missing in matchset['missing']:
            plot_stick_at_x(missing, peaks_x, peaks_y, ax=ax, color='r')

        if show:
            plt.show()

        return fig, ax

    def find_baseline(self, interactive=False, ui=None):
        interactive = check_for_interactive(interactive, "baseline")

        from pybaselines import Baseline

        exp_frame = self.frames['exp']
        fitter = Baseline()

        baseline_args = convert_baseline_cfg(self.baseline_cfg)
        exp_int = exp_frame['int'].to_numpy()


        baseline, _ = fitter.arpls(
            exp_int,
            **baseline_args
        )
        exp_frame['baseline'] = baseline
        exp_frame['corrected'] = exp_int - baseline

        if not interactive:
            return

        from ..ui.baseline import BaselineFinder

        exp_2th = exp_frame.index.to_numpy()
        finder = BaselineFinder(exp_int, exp_2th, cfg=self.baseline_cfg, ui=ui)

        baseline, corrected = finder.main_loop()

        exp_frame['baseline'] = baseline
        exp_frame['corrected'] = corrected

baseline_cfg instance-attribute 

baseline_cfg = cfg.get('diffraction.baseline')

cifs instance-attribute 

cifs = cif_dict

find_cfg instance-attribute 

find_cfg = cfg.get('diffraction.find_peaks')

frames instance-attribute 

frames = frames

__init__ 

__init__(exp_2theta, exp_int, cif_dict)
Source code in FoSpy/plotting/diffraction/phase_match/__init__.py 
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def __init__(self, exp_2theta, exp_int, cif_dict):

    self.baseline_cfg = cfg.get("diffraction.baseline")
    self.find_cfg = cfg.get("diffraction.find_peaks")

    frames = {'exp':DataFrame({X_LABEL:exp_2theta, "int":exp_int}).set_index(X_LABEL)}
    # x_min=min(exp_2theta)
    # x_max=max(exp_2theta)
    for name, cif in cif_dict.items():
        engine = cif.new_engine(engine_name='pymatgen')
        frames[name] = engine.get_pattern().set_index(X_LABEL)
    self.cifs = cif_dict
    self.frames = frames

find_baseline 

find_baseline(interactive=False, ui=None)
Source code in FoSpy/plotting/diffraction/phase_match/__init__.py 
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def find_baseline(self, interactive=False, ui=None):
    interactive = check_for_interactive(interactive, "baseline")

    from pybaselines import Baseline

    exp_frame = self.frames['exp']
    fitter = Baseline()

    baseline_args = convert_baseline_cfg(self.baseline_cfg)
    exp_int = exp_frame['int'].to_numpy()


    baseline, _ = fitter.arpls(
        exp_int,
        **baseline_args
    )
    exp_frame['baseline'] = baseline
    exp_frame['corrected'] = exp_int - baseline

    if not interactive:
        return

    from ..ui.baseline import BaselineFinder

    exp_2th = exp_frame.index.to_numpy()
    finder = BaselineFinder(exp_int, exp_2th, cfg=self.baseline_cfg, ui=ui)

    baseline, corrected = finder.main_loop()

    exp_frame['baseline'] = baseline
    exp_frame['corrected'] = corrected

find_peaks 

find_peaks(
    interactive=False, ui=None, **interactive_kwargs
)
Source code in FoSpy/plotting/diffraction/phase_match/__init__.py 
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def find_peaks(self, interactive=False, ui=None,**interactive_kwargs):
    self.find_baseline(interactive=interactive, ui=ui)
    interactive = check_for_interactive(interactive, "find_peaks")

    exp_corrected = self.frames['exp']['corrected'].to_numpy()

    from ._utils import unpack_peaks


    find_cfg = self.find_cfg
    if not interactive:
        return unpack_peaks(exp_corrected, "widths",**find_cfg)

    from ..ui.peaks import PeakFinder

    interactive_kwargs.setdefault('title', "Baseline-Corrected Peak Finder")
    if interactive_kwargs['title'].startswith("+"):
        suffix = interactive_kwargs['title'][1:]
        interactive_kwargs['title'] = f"Baseline-Corrected Peak Finder\n{suffix}"

    peak_finder = PeakFinder(exp_corrected, self.frames['exp'].index, cfg=find_cfg, ui=ui, **interactive_kwargs)
    return peak_finder.main_loop()

match_peaks 

match_peaks()
Source code in FoSpy/plotting/diffraction/phase_match/__init__.py 
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def match_peaks(self):
    import numpy as np
    from ._utils import match_peaks
    from ._utils import rows_to_2th

    exp_frame = self.frames['exp']/self.frames['exp'].max()
    exp_data = exp_frame['int']
    exp_index = exp_frame.index

    matchsets = {}

    for name, cif in self.cifs.items():
        peak_list = cif.get_peaks()

        peak_idx = np.searchsorted(exp_index, [x for (x, y) in peak_list])

        matches = match_peaks(exp_data, peak_idx)

        matches = rows_to_2th(exp_index,matches)

        matchsets[name] = matches

    return matchsets

plot_matches 

plot_matches(cif_name, ax=None, show=False)
Source code in FoSpy/plotting/diffraction/phase_match/__init__.py 
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def plot_matches(self, cif_name, ax=None, show=False):
    import numpy as np
    from matplotlib import pyplot as plt
    from ._utils import plot_stick_at_x

    matchset = self.match_peaks()[cif_name]
    peak_list = self.cifs[cif_name].get_peaks()

    peaks_x = np.array([x for (x, y) in peak_list])
    peaks_y = np.array([y for (x, y) in peak_list])

    if ax is None:
        fig, ax = plt.gcf(), plt.gca()
    else:
        fig = ax.get_figure()

    self.frames['exp'].plot(ax=ax)

    for _, x_matches in matchset['matches']:
        for x in x_matches:
            plot_stick_at_x(x, peaks_x, peaks_y, ax=ax, color='g')

    for missing in matchset['missing']:
        plot_stick_at_x(missing, peaks_x, peaks_y, ax=ax, color='r')

    if show:
        plt.show()

    return fig, ax

check_for_interactive 

check_for_interactive(interactive, kw)
Source code in FoSpy/plotting/diffraction/phase_match/_utils.py 
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def check_for_interactive(interactive, kw):
    if isinstance(interactive, bool):
        return interactive
    elif isinstance(interactive, str):
        return interactive == kw
    elif isinstance(interactive, list):
        return kw in interactive

convert_baseline_cfg 

convert_baseline_cfg(baseline_cfg)
Source code in FoSpy/plotting/diffraction/phase_match/_utils.py 
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def convert_baseline_cfg(baseline_cfg):
    out = baseline_cfg.copy()

    out['lam'] = 10**out['lam']

    for int_cfg in ("max_iter", "diff_order"):
        out[int_cfg] = int(out[int_cfg])

    return out