Scancheck

• Introduction
  
• How it works
  
• Invocation
  
• Input/Output files
  

Introduction

How it works

1. scancheck reads the images, and stores/calculates the following fields, if available:

   name	units	description
   Time	seconds	Time difference (wallclock) since first image
   dTim	seconds	Elapsed time (wallclock) since previous image
   ExpTim	seconds	Exposure time
   Rot1	degrees	Rotation angle start
   Rot2	degrees	Rotation angle end
   Gonio1	degrees	First goniometer angle (usually omega)
   Gonio2	degrees	Second goniometer angle (usually chi)
   Gonio3	degrees	Third goniometer angle (usually phi)
   Dist	mm	detector distance in mm
   Swing	degrees	Detector swing angle
   Lambda	Ångström	wavelength
   Cryo	Kelvin	crystal temperature
   Dettemp	Celsius	Detector temperature
   Bg20	pixel intensity	The intensities of (a subset of) all pixels are sorted. Bg20 is the 20% percentile value
   Bg10	pixel intensity	The intensities of (a subset of) all pixels are sorted. Bg10 is the 10% percentile value
   Gain		The lowest gain (sigma*sigma/mean) of the four corners (10% of image dimensions)
   Ave	pixel intensity	The average pixel intensity of the whole image
   DD		Day of month
   MM		Month
   YY		Year
   Rep		number of repeats
   FullTime	HH:MM:SS.mmm	Wallclock time
   Name		Image name

2. If a field is changing unexpectedly, a warning is printed.
   • The walltime difference between two succeeding images varies more than 10 seconds.
   • The exposure time varies more than 0.008 seconds.
   • The wavelength varies more than 0.01 Å,
   • Rotstart differs more than 0.0001 radians from RotEnd of the previous image.
   • Bg20 varies more than 10%
   • Gonio1, Gonio2 or Gonio3 differ more than 0.01 degree
   • Swing differs more thanan 0.01 degree
   • Dist differs more dan 0.01 mm
3. Two tables are written.
   • To the screen. This table contains fields with varying values. So fields with a constant value for all images are not printed. The last column in this table may contain a warning.
   • To a logfile. The complete table with all information.

Invocation

Input/Output files

Input Files

Output files