def find_peaks(self, min_peak_height=0.3, min_peak_distance=0.05, max_num_peaks=None, exclude_lt_edge=0.0, exclude_rt_edge=0.0):
"""Find the peaks (maximums) of the profile using a simple maximum value search.
Returns
-------
peak_vals : numpy.array, numpy.array
The peak values and the peak indices.
See Also
--------
common_functions.peak_detect : Further parameter info
"""
peak_vals, peak_idxs = peak_detect(self.y_values, self.x_values, min_peak_height, min_peak_distance,
max_num_peaks, exclude_lt_edge, exclude_rt_edge)
self.peaks = [Point(value=peak_val, idx=peak_idx) for peak_idx, peak_val in zip(peak_idxs, peak_vals)]
return self._return_extrema_val_as_list('peak'), self._return_extrema_idx_as_list('peak')
def find_valleys(self, min_peak_height=0.3, min_peak_distance=10, max_num_peaks=None, exclude_lt_edge=0.0, exclude_rt_edge=0.0):
"""Find the valleys (minimums) of the profile using a simple minimum value search.
Returns
-------
numpy.array, numpy.array
Two arrays are returned: The valley values and the valley indices.
See Also
--------
common_functions.peak_detect : Further parameter info
"""
valley_vals, valley_idxs = peak_detect(self.y_values, self.x_values, min_peak_height, min_peak_distance,
max_num_peaks, exclude_lt_edge, exclude_rt_edge, find_min_instead=True)
self.valleys = [Point(value=valley_val, idx=valley_idx) for valley_idx, valley_val in zip(valley_idxs, valley_vals)]
return self._return_extrema_val_as_list('valley'), self._return_extrema_idx_as_list('valley')
def _get_initial_peak(self, initial_peak, exclusion_region=0.1):
"""Determine an initial peak to use as a rough guideline.
Parameters
----------
exclusion_region : float
The ratio of the profile to exclude from either side of the profile when searching
for the initial peak. Must be between 0 and 1.
"""
# if not passed, get one by peak searching.
if initial_peak is None:
while True:
_, initial_peak_arr = peak_detect(self.y_values, self.x_values, max_num_peaks=1, exclude_lt_edge=exclusion_region,
exclude_rt_edge=exclusion_region)
try:
initial_peak = initial_peak_arr[0]
break
except IndexError:
exclusion_region -= 0.01
if exclusion_region < 0:
raise ValueError("A reasonable initial peak was not found in the profile. Ensure peak is not at profile edge")
# otherwise use the one passed.
else:
while True:
# ensure peak is within the x_data region and not near an edge
peak_near_left_edge = initial_peak < self.x_values[int(exclusion_region * len(self.x_values))]
peak_near_right_edge = initial_peak > self.x_values[int((1-exclusion_region) * len(self.x_values))]
if peak_near_left_edge or peak_near_right_edge:
exclusion_region -= 0.01
else:
break
if exclusion_region < 0:
raise IndexError("Initial peak that was passed was not reasonably within the profile x_data range")
initial_peak = np.where(self.x_values == initial_peak)[0]
return int(initial_peak)
