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Module: kcdheader filetype/kcdheader.py

Handle KCD image headers

It should never be necessary to use these functions/classes. Rather use the general interfaces in imagereader and imagewriter to access general image and header data.

KCD header data.

Besides the "obligatory" header information that is present in any image header (and described elsewhere ) the KappaCCD header can contain many more fields:

repeats

The number of times the image was "repeated". i.e. the total number of frames in the image is one higher than the number of repeats. See also "numimg".

numimg

The total number of frames in the image. 1 higher than the number of repeats. See also "repeats"

adcspeed

The speed of the AD convertor in kHz.

shutter

0 if the image was taken with the X-ray shutter closed, 1 if it was taken with the shutter opened. This is a later addition to the KappaCCD header. For older headers a guess is made based on the generator settings present in the header, but if a generator without remote addressing was used, this will fail, and give the wrong shutter value. It is, however, the best you can do.

p0 and p1

the position of the goniostat at the beginning and end of the scan. These are goniometer.Position() objects. Some motor values inside these positions may be None!

phiinterval, omegainterval, kappainterval, dxinterval, thetainterval

The difference between motor positions in p0 and p1 might differ from the scan interval requested to the hardware especially for extremely slow and/or extremely fast scans. The originally requested values are available as "*interval". All angle values are given in radians.

scanangle

If from the 5 "range" attributes only the "omegarange" value is nonzero, the "scanangle" attribute will be set to the string "Omega". Likewise, it will be set to "Phi" for pure phi scans.

scanrange

Set to the maximum absolute value of the 5 individual motor "range" attributes.

expectedfilesize

Set to the size the file should have on disk, measured in bytes.

expectedfilesizeerror

Set to the maximum allowed difference of the file size.

voltage

The generator voltage, in kV.

current

The generator current, in mA. This may be a floating point value less than 1.0 for MicroSource generators.

alpha1

The wavelength of alpha1 radiation. In Angstrom.

alpha2

The wavelength of alpha2 radiation. In Angstrom.

wavelengthratio

The ratio of intensities alpha1/alpha2.

wavelength

The weighted average wavelength. In Angstrom.

monochromator

A string, either "PERPENDICULAR", "ANTIPARALLEL", "PARALLEL", "OSMIC" or "NONE", specifying type of monochromator and (if applicable) the orientation of the graphite monochromator in the beam.

kappasupportangle

The angle of the kappa support (also called "alpha" in some other documentation) in the goniostat. In radians. Will be approximately 50 degrees for the Mach3 goniostat.

precessionmatrix

Only present for synthetic precession images. The Numeric 3x3 matrix that produces the column vector (x pixel,y pixel,Z[HKL]) from a column C-vector. The actual pixel number is then produced by adding half of the image dimensions to the x-pixel and y-pixel values.

precessionrange

Only present for synthetic precession images. A 2-tuple (Z-min,Z-max) of the minimum and maximum accepted Z value (see also "precessionmatrix".

date

A string representing the "Windows" date/time that the image was collected. This can be in a range of different formats, please do not use!

gonid

Serial number of the goniostat.

exposuretime

The time the shutter has been open (per frame). In seconds.

integrationtime

The time the detector has been enabled (per frame). In seconds.

targetmaterial

The chemical symbol for the type of radiation used. All capitals.

added and scale

If an image is written for which not all data fit within the 0...65536 range, it will be scaled/shifted to fit. The parameters for this are stored in these two attributes. Since the ImageReader() will automatically scale-back the image to the original data, you should not need these attributes yourself.

corrected

For images after processing, this attempts to give a summary of the corrections that were applied. If you write your own ImageSink() that requires some corrections to be applied first, that can be checked here (see the description of the imageheader class for special access methods).

scinttype and scintload

A description code for the type and amount of scintillator used on the detector. This can be used for correcting image sensitivity.

Functions   
Build
Default
Read
Scan
adcid
  Build 
Build ( x )

Convert a header record h to a binary string suitable as KCD file header

  Default 
Default ()

Make a dummy KCD header.

  Read 
Read ( filename )

Read the header from the named KCD image file.

Exceptions   
IOError( 2, "File does not exist" )
  Scan 
Scan ( s )

Parse the binary data in string s as a KCD header, returning a projtls.Record() loaded with the header data

Exceptions   
ValueError( "Found %d byte image. This doesn't fit any detector" % sz )
ValueError( "Incomplete header" )
  adcid 
adcid ( n )

Convert an ADC frequency to an ADC id

Classes   
Header

KCD header class


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This document was automatically generated on Tue Nov 25 12:18:58 2008 by HappyDoc version WORKING