Utility routines for peak searching/matching.
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Functions
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detlim2
integrate
refill
set2
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detlim2
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detlim2 ( peaks )
Given a list of peaks, estimate the accuracy that set2 should use
for merging Friedel opposites. For internal use in set2 |
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integrate
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integrate (
pnt,
data,
sz=config.initialpeaksize,
allowshift=1.0,
gain=1.6,
)
Integrate a peak at pixel coordinates pnt from the frame at data.
parameters:
- pnt
a 2-tuple of the (horizontal, vertical) pixel coordinates
where the peak is expected.
- data
a 2D array containing the frame data, with the vertical
coordinate from top to bottom as the first coordinate,
and the horizontal coordinate from left to right as
the second coordinate (top-left is 0,0)
optional parameters:
- sz
starting size of the integration area. This is automatically
refined by the procedure.
- allowshift
distance in pixels that the final peak position is
allowed to differ from the given pnt.
- gain
approximate gain of the detector, used for determination of
the standard deviation.
return value:
A projtls.Record() instance, with the following attributes:
- ihmax
horizontal pixel coordinate of pixel with highest value
- ivmax
vertical pixel coordinate of pixel with highest value
- ih
horizontal pixel coordinate of final center of integration
- iv
vertical pixel coordinate of final center of integration
- bg1
first guess at background level
- int1
first guess at peak intensity
- bg
final background level
- int
final intensity
- rh
horizontal coordinate of the center of gravity of the peak
- rv
vertical coordinate of the center of gravity of the peak
- rad
single-sigma peak radius of the peak
- sigma
standard deviation of the intensity
- pixel
the highest pixel value in the peak
- numbgpix
number of pixels used for background estimation
- numpkpix
number of pixels integrated for peak intensity
- size
final refined size of the area used for integration
- h10
horizontal full width at 10% maximum
- v10
vertical full width at 10% maximum
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refill
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refill (
oldpk,
filename,
dis,
peaksclass=Peaks,
header=None,
)
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set2
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set2 (
peaks,
suppresssingles=0,
lim1=None,
lim2=None,
)
Given a list of peaks, merge Friedel opposites.
arguments:
- peaks
peak list containing .c attributes with the
diffraction angle corresponding to the peak.
- suppressingles
if set to 1, will not return any reflections
that do not occur as Friedel pair.
- lim1
a merging criterion, if not given set to sqrt(lim2)
- lim2
another merging criterion. If not given, estimated
using detlim2
return value: another peak list. |
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Classes
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| DistortionError | Exception raised when no distortion correction is available when it is required. | | IntensityFilter | Peak filter that removes peaks weaker than a given intensity | | NoDatabasePeakSearcher | Class that can turn image files into 'peak lists | | PeakSearcher | PeakSearcher class that will read/write the peak database if allowed | | Peaks | Extends the SimplePeaks records with the following attributes | | SigmaFilter | Peak filter that removes peaks weaker than a given number of sigmas | | SimplePeaks | Stand-alone peak storage class. | | ThetaFilter | Peak filter that removes peaks outside given theta limits | | ZetaFilter | Peak Filter that removes peaks that are above a chi limit. |
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