| |
- peak
- peakmerger
- pkimage
class peak |
|
Represents a peak |
|
Methods defined here:
- __cmp__(self, other)
- For sorting - depreciated by DSU
- __eq__(self, other)
- For deciding if peaks overlap
- __init__(self, line, omega, threshold, num, tolerance)
- line = line in the outputfile from peaksearch
omega = omega rotation angle
threshold = the threshold level when the peak was found
tolerance = the distance (pixels) between peak centres for merging
- __repr__(self)
- Not sure that this is used, again, for printing
- __str__(self)
- for printing something
- combine(self, other)
- Combine this peak with another peak (eg merge!)
#
# If the thresholds are different, we see the same peaks
# twice. We will just pick the one with the lower threshold
#
# Otherwise we try to average them
#
|
class peakmerger |
|
The useful class - called by the gui to process peaksearch output
into spots |
|
Methods defined here:
- __init__(self, quiet='No')
- object to read in peaksearch output file and merge the peaks
quiet arg decides if we spray stdout
- filter(self)
- Does nothing really, just makes a self.finalpeaks array
TODO: pass functions to filter/compress finalpeaks
- getheaderinfo(self, key)
- try to find "key" in the headers and return it
- getheaderkeys(self)
- things in the headers
- harvestpeaks(self, numlim=None, omlim=None, thresholds=None)
- Harvests the peaks from the images within a range of
imagenumbers and/or omega
eg: it actually reads the numbers now
- mergepeaks(self)
- Merges peaks together - if they overlap and are on adjacent frames
More complex than initially planned
- readpeaks(self, filename, startom=0.0, omstep=1.0)
- Read in the output from the peaksearching script
Filename is the output file
optionally startom and omstep fill in omega ONLY if missing in file
- savepeaks(self, filename)
- # Write out minimal information
# list of xcorr,ycorr,omega, try to keep intensity now
- setpixeltolerance(self, tolerance=2)
- TODO ah... if only
|
class pkimage |
|
Contains the header information from an image
Also pointers to positions of lines in peaksearch output file |
|
Methods defined here:
- __init__(self, name)
- name is the filename
- addtoheader(self, headerline)
- save header info in dict
headerline is line starting with # in peaksearch output
- otherheaderstuff(self, headerline)
- Hard to parse header info - called by addtoheader
| |