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Merge pull request #1872 from jlaehne/FindPeaks_Docstring
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Improved docstrings for find_peaks_ohaver and find_peaks1D_ohaver
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@ericpre
ericpre committed Mar 20, 2018
2 parents e6bb38d + 70ecf6b commit 1710e0d
Showing 1 changed file with 53 additions and 44 deletions.
97 changes: 53 additions & 44 deletions hyperspy/_signals/signal1d.py
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Original file line number Diff line number Diff line change
Expand Up @@ -62,44 +62,53 @@ def find_peaks_ohaver(y, x=None, slope_thresh=0., amp_thresh=None,
medfilt_radius=5, maxpeakn=30000, peakgroup=10,
subchannel=True,):
"""Find peaks along a 1D line.
Function to locate the positive peaks in a noisy x-y data set.
Detects peaks by looking for downward zero-crossings in the first
derivative that exceed 'slope_thresh'.
Returns an array containing position, height, and width of each peak.
Sorted by position.
'slope_thresh' and 'amp_thresh', control sensitivity: higher values will
neglect smaller features.
'slope_thresh' and 'amp_thresh', control sensitivity: higher values
will neglect wider peaks (slope) and smaller features (amp),
respectively.
Parameters
---------
----------
y : array
1D input array, e.g. a spectrum
x : array (optional)
1D array describing the calibration of y (must have same shape as y)
slope_thresh : float (optional)
1st derivative threshold to count the peak
default is set to 0.5
higher values will neglect smaller features.
1st derivative threshold to count the peak;
higher values will neglect broader features;
default is set to 0.
amp_thresh : float (optional)
intensity threshold above which
default is set to 10% of max(y)
higher values will neglect smaller features.
intensity threshold below which peaks are ignored;
higher values will neglect smaller features;
default is set to 10% of max(y).
medfilt_radius : int (optional)
median filter window to apply to smooth the data
(see scipy.signal.medfilt)
if 0, no filter will be applied.
default is set to 5
(see scipy.signal.medfilt);
if 0, no filter will be applied;
default is set to 5.
peakgroup : int (optional)
number of points around the "top part" of the peak
default is set to 10
number of points around the "top part" of the peak that
are taken to estimate the peak height; for spikes or
very narrow peaks, keep PeakGroup=1 or 2; for broad or
noisy peaks, make PeakGroup larger to reduce the effect
of noise;
default is set to 10.
maxpeakn : int (optional)
number of maximum detectable peaks
default is set to 30000
number of maximum detectable peaks;
default is set to 30000.
subchannel : bool (optional)
default is set to True
default is set to True.
Returns
-------
P : structured array of shape (npeaks) and fields: position, width, height
contains position, height, and width of each peak
P : structured array of shape (npeaks)
contains fields: 'position', 'width', and 'height' for each peak.
Examples
--------
>>> x = np.arange(0,50,0.01)
Expand Down Expand Up @@ -1244,53 +1253,53 @@ def find_peaks1D_ohaver(self, xdim=None, slope_thresh=0, amp_thresh=None,
peak.
'slope_thresh' and 'amp_thresh', control sensitivity: higher
values will
neglect smaller features.
values will neglect broad peaks (slope) and smaller features (amp),
respectively.
peakgroup is the number of points around the top peak to search
around
peakgroup is the number of points around the top of the peak
that are taken to estimate the peak height. For spikes or very
narrow peaks, keep PeakGroup=1 or 2; for broad or noisy peaks,
make PeakGroup larger to reduce the effect of noise.
Parameters
---------
----------
slope_thresh : float (optional)
1st derivative threshold to count the peak
default is set to 0.5
higher values will neglect smaller features.
1st derivative threshold to count the peak;
higher values will neglect broader features;
default is set to 0.
amp_thresh : float (optional)
intensity threshold above which
default is set to 10% of max(y)
higher values will neglect smaller features.
intensity threshold below which peaks are ignored;
higher values will neglect smaller features;
default is set to 10% of max(y).
medfilt_radius : int (optional)
median filter window to apply to smooth the data
(see scipy.signal.medfilt)
if 0, no filter will be applied.
default is set to 5
(see scipy.signal.medfilt);
if 0, no filter will be applied;
default is set to 5.
peakgroup : int (optional)
number of points around the "top part" of the peak
number of points around the "top part" of the peak
that are taken to estimate the peak height;
default is set to 10
maxpeakn : int (optional)
number of maximum detectable peaks
default is set to 5000
number of maximum detectable peaks;
default is set to 5000.
subpix : bool (optional)
default is set to True
subchannel : bool (optional)
default is set to True.
parallel : {None, bool}
Perform the operation in a threaded (parallel) manner.
Returns
-------
peaks : structured array of shape _navigation_shape_in_array in which
each cell contains an array that contains as many structured arrays as
peaks where found at that location and which fields: position, height,
width, contains position, height, and width of each peak.
peaks : structured array of shape (npeaks)
contains fields: 'position', 'width', and 'height' for each peak.
Raises
------
Expand Down

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