ImageD11.peakmerge | index /sware/exp/fable/standalone/redhate4-a64/lib/python2.5/site-packages/ImageD11/peakmerge.py

`Class for reading peaksearch files, merging peaks on adjacent frames
and writing out the result...
This is mostly replaced with the 3D blobsearcher - this algorithm uses a lot
of memory`

Modules
`` |  |
numpy.oldnumeric fabio | logging sys | time |

Classes
`` |  | 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`

Functions
`` |  | roundfloat(x, tol) `Return the float nearest to x stepsize tol`