Diffraction Image: a new CCP4 library

• Rigaku for supplying demonstration code for Raxis IV images.
• Many different suppliers of example images of various detectors.
• Paul J. Ellis and Herbert J. Bernstein authors of the CBF library on which this library relies to support CBF format.

Appendix: Library API

• DiffractionImage
  
  

  Method	Description
  DiffractionImage()	Default constructor of a Diffraction Image.
  DiffractionImage(string filename)	Create and load everything available from the image file called "filename".
  int getWidth()	Return the width of image in pixels.
  int getHeight()	Return the height of image in pixels.
  float getBeamX()	Return the x position of the beam center in millimeters.
  float getBeamY()	Return the y position of the beam center in millimeters.
  float getWavelength()	Return the wavelength of X-Ray source in Angstroms.
  float getDistance()	Return the crystal to detector distance in millimeters.
  float getTwoTheta()	Return the two-theta angle used in data collection
  float getPhiStart()	Return the phi-angle at the beginning of the oscillation
  float getPhiEnd()	Return the phi-angle at the end of the oscillation
  float getPixelX()	Return the width of a pixel in millimeters.
  float getPixelY()	Return the height of a pixel in millimeters.
  float getExposureTime()	Return the exposure time in seconds.
  char* getFormat()	Return "mar", "adsc", "raxis", etc... according to the image format.
  char* getDate()	Return the date of the image collection using a formatted string (dd-mm-YYYY).
  char* getSerialNo()	Return the detector serial number if available.
  unsigned short * getImage()	Return a pointer to the image.
  void setBeamX(float x)	Sets the x-position of the beam center in millimeters.
  void setBeamY(float y)	Sets the y-position of the beam center in millimeters.
  void setWavelength(float wave)	Sets the wavelength in Angstroms.
  void setDistance(float dist)	Sets the crystal to detector distance in millimeters.
  void setTwoTheta(float twotheta)	Sets the two-theta angle used in data collection.
  void setPhiStart(float phistart)	Sets the phi-angle at the beginning of the oscillation
  void setPhiEnd(float phiend)	Sets the phi-angle at the end of the oscillation
  void setPixelX(float pixelwidth)	Sets the pixel size in millimeters
  void setPixelY(float pixelheight)	Sets the pixel size in millimeters
  void setExposureTime(float time)	Sets the exposure time in milliseconds
  void load(string fileName)	Load in an image from the file "filename".
  void loadHeader(string fileName)	Load header information only from the file "filename".
  float* assymetry(void)	Give an estimate of how much symmetry there is in the image background.
  float* radial(int bins)	Generate a radial profile of the image
  int corner(void)	Determine whether the image goes to the corner or whether it is an inscribed circle.
  int* histogram(void)	Calculate a contrast histogram.
  float gain(void)	Calculate an estimation of the gain (yet to be implemented).

  
  
• PeakList
  
  

  Method	Description
  PeakList()	Default constructor of a empty PeakList.
  PeakList(DiffractionImage* diffractionimage)	Construct a PeakList from the given DiffractionImage object.
  int length()	Gives the length of the list.
  void clear()	Clears the list.
  void add(float x, float y, float intensity)	Add a peak the image coordinates (x,y) and with the specified intensity.
  void remove(int offset)	Remove the Peak at the specified position in the list.
  void add(Peak peak)	Add the specified peak to the list.
  void find(DiffractionImage* diffractionimage)	Search for the peaks in the specified DiffractionImage object.
  void find(DiffractionImage* diffractionimage,                int maxPeaks)	Search for the peaks in the specified DiffractionImage object with a maximum of maxPeaks results.
  void find(DiffractionImage* diffractionimage,                int maxPeaks,                float intensityThreshold)	Search for the peaks in the specified DiffractionImage object with a maximum of maxPeaks results having an intensity of at least intensityTreshold.
  void reciprocal(float dist, float wave)	Convert the peak coordinates from dectetor coordinates to reciprocal space coordinates.
  void detector(float dist, float wave)	Convert the peak coordinates from reciprocal space coordinates to detector coordinates.
  Peak pop(int offset)	Gets the peak from the specified position and removes it from the list.
  Peak * getPeaks()	Return the content of the PeakList as a vector of Peak.
  int circle(int iter, float width,               float& x, float& y, float& r)	Find a circle in the spot using a stochastic process and return the most promising candidate. Width determines how close to the arc a spot must be to be accepted. Iter is the number of attemps in fitting a circle.
  int remove(float width, float x, float y, float r)	Removes the spots that were found to be on the circle fitted with the circle() method described above.

  
  
• Peak is a structure having the following 7 fields,
  • float x : x coordinate of the peak on the image
  • float y : y coordinate of the peak on the image
  • float theta : Theta value for the image where the spot is found 
  • float phi : phi value for the image where the spot is found 
  • float kappa : kappa value for the image where the spot is found 
  • float[3] p : Array containing the reciprocal spaces coordinates of the Peak
  • float intensity : Intensity of the Peak