VIEW: Difference between revisions
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VIEW is the visualisation program of the XDS suite. | VIEW is the (obsolete) visualisation program of the XDS suite (the current one is [[XDS-Viewer]]). It is very useful for [[obtaining ORGX ORGY]] (needed for indexing), and for checking the final frame of the dataset with its superimposed predicted spot positions (FRAME.pck). | ||
All .pck files written by XDS or XSCALE can be viewed with VIEW (e.g. ABS.pck, BKGINIT.pck, MODPIX.pck). VIEW | VIEW -h gives a short help output with options, VIEW -hv shows a short manual. The mouse buttons, when used in the image area, have the following meaning: left - writes x,y to upper left corner; middle - zoom in; right - zoom out. | ||
All .pck files written by XDS or XSCALE can be viewed with VIEW (e.g. ABS.pck, BKGINIT.pck, MODPIX.pck). E.g., | |||
VIEW BKGINIT.pck | |||
could be run to look at the smoothed background image obtained from the INIT step. | |||
The most important file to look at is FRAME.pck (written by the [[INTEGRATE]] processing step). The Logo of this wiki (upper left) shows part of FRAME.pck as visualized with VIEW. Here we see the "pixel labelling method" of [[XDS]] at work: the thin lines around the reflections demarcate the limits of the integration area (which is used to calculate the intensity of the reflection). The size of the integration area is calculated from BEAM_DIVERGENCE, but in case two such integration areas overlap, then each pixel in the overlap region is assigned to the nearest reflection in reciprocal space. | The most important file to look at is FRAME.pck (written by the [[INTEGRATE]] processing step). The Logo of this wiki (upper left) shows part of FRAME.pck as visualized with VIEW. Here we see the "pixel labelling method" of [[XDS]] at work: the thin lines around the reflections demarcate the limits of the integration area (which is used to calculate the intensity of the reflection). The size of the integration area is calculated from BEAM_DIVERGENCE, but in case two such integration areas overlap, then each pixel in the overlap region is assigned to the nearest reflection in reciprocal space. | ||
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* reflections without integration area are partial reflections, whose center is on an adjacent frame | * reflections without integration area are partial reflections, whose center is on an adjacent frame | ||
VIEW can also be used to look at data frames (with a header). In that case, the user is prompted for the required information. Usually the numbers NX and NY are the answers to the first two questions, and the header size is given by the formula | |||
<framesize in bytes> - 2 * NX * NY . | |||
VIEW - | Note for experts: the pixel numbering in VIEW goes from 0 to NX-1 (similar for y), whereas XDS using a numbering of 1 to NX (NY). Thus, if you find out a position on the detector (e.g. the direct beam) by using VIEW, you should in principle add 1 in both x and y if you want to put the numbers into [[XDS.INP]]. In practice, the 1-pixel-offset does not matter. | ||
Latest revision as of 13:46, 27 October 2009
VIEW is the (obsolete) visualisation program of the XDS suite (the current one is XDS-Viewer). It is very useful for obtaining ORGX ORGY (needed for indexing), and for checking the final frame of the dataset with its superimposed predicted spot positions (FRAME.pck).
VIEW -h gives a short help output with options, VIEW -hv shows a short manual. The mouse buttons, when used in the image area, have the following meaning: left - writes x,y to upper left corner; middle - zoom in; right - zoom out.
All .pck files written by XDS or XSCALE can be viewed with VIEW (e.g. ABS.pck, BKGINIT.pck, MODPIX.pck). E.g.,
VIEW BKGINIT.pck
could be run to look at the smoothed background image obtained from the INIT step.
The most important file to look at is FRAME.pck (written by the INTEGRATE processing step). The Logo of this wiki (upper left) shows part of FRAME.pck as visualized with VIEW. Here we see the "pixel labelling method" of XDS at work: the thin lines around the reflections demarcate the limits of the integration area (which is used to calculate the intensity of the reflection). The size of the integration area is calculated from BEAM_DIVERGENCE, but in case two such integration areas overlap, then each pixel in the overlap region is assigned to the nearest reflection in reciprocal space.
If the integration has worked as it should, the following should be true for FRAME.pck:
- most (if not all) observed reflections are encircled by thin lines (corresponding to integration areas)
- empty integration areas belong to weak reflections
- reflections without integration area are partial reflections, whose center is on an adjacent frame
VIEW can also be used to look at data frames (with a header). In that case, the user is prompted for the required information. Usually the numbers NX and NY are the answers to the first two questions, and the header size is given by the formula <framesize in bytes> - 2 * NX * NY .
Note for experts: the pixel numbering in VIEW goes from 0 to NX-1 (similar for y), whereas XDS using a numbering of 1 to NX (NY). Thus, if you find out a position on the detector (e.g. the direct beam) by using VIEW, you should in principle add 1 in both x and y if you want to put the numbers into XDS.INP. In practice, the 1-pixel-offset does not matter.