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== How does INTEGRATE treat overlaps? ==
 
== How does INTEGRATE treat overlaps? ==
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The integration algorithm proceeds along the following lines:
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The integration algorithm (see [http://dx.doi.org/10.1107/S0021889888007903]) proceeds along the following lines:
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# the x,y,z, center of each pixel of the detector (z corresponds to phi, and the z pixelsize is delta-phi) is assigned to its nearest (predicted) reflection in reciprocal space ("pixel-labelling", see [http://dx.doi.org/10.1107/S0021889888007903]). As a consequence, ''each pixel of the detector is used for at most one reflection''.  
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# pixel-labelling: the x,y,z, center of each pixel of the detector (z corresponds to phi, and the z pixelsize is delta-phi) is assigned to its closest (predicted) reflection in reciprocal space. As a consequence, ''each pixel of the detector is used for at most one reflection''.  
# some of these pixels will mostly allow the background estimation, others will mostly contribute to the integration area (but as they are transformed into a local coordinate system [http://dx.doi.org/10.1107/S0021889888007903] there is not a 1:1 relationship).  
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# transformation to local coordinate system: some of these pixels will mostly allow the background estimation, others will mostly contribute to the integration area (but there is not a 1:1 relationship).  
# for each reflection, the background is estimated, and the 3D profile is assembled from the pixels contributing to it. Pixels which are mostly background but whose counts are higher than expected (e.g. due to overlap) are rejected.
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# average profile: the average profile is formed on a grid (using the 3D local coordinate system) from strong reflections. The signal part of the profile is defined by those gridpoints of the average profile that are above a threshold (called "CUT" in XDS.INP).
# the average profile is formed on a grid by superimposition of strong reflections found in step 3. The signal part of the profile is defined by those gridpoints of the average profile that are above a threshold (called "CUT" in XDS.INP).
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# estimating the intensity: for each reflection, the background is estimated, and the 3D profile is assembled from the pixels contributing to it. Pixels which are mostly background but whose counts are higher than expected (e.g. due to overlap) are rejected.
# not all pixels of a reflection, which would be required to assemble its full profile (whose shape is given by the average profile formed in step 4), may have been observed due to step 1. Therefore, in another pass, for each reflection, the observed fraction of its theoretical profile is calculated. If this fraction is less than a threshold (called "MINPK" in XDS.INP), this reflection will be discarded ("too much overlap"). If it is above MINPK, the observed intensity (from the incomplete profile) is scaled up with the inverse of the fraction.
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# handling overlap: not all pixels of a reflection, which would be required to assemble its full profile (whose shape is given by the average profile), may have been observed due to step 1. Therefore, in another pass, for each reflection, the observed fraction of its theoretical profile is calculated. If this fraction is less than a threshold (called "MINPK" in XDS.INP), this reflection will be discarded ("too much overlap"). If it is above MINPK, the observed intensity (from the incomplete profile) is scaled up with the inverse of the fraction.
    
Among other things, this means that:
 
Among other things, this means that:
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