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XDSGUI: Difference between revisions
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== How to use XDSGUI == | == How to use XDSGUI == | ||
The program may be used to analyze graphically any existing directory with files earlier written by XDS, or may be used to create these files. It should be started in a terminal window, which will later show the output of the programs that are run (XDS, pointless, XDSCONV, ...). | The program may be used to analyze graphically any existing directory with files earlier written by XDS, or may be used to create these files. '''It should be started in a terminal window''', which will later show the output of the programs that are run (XDS, pointless, XDSCONV, ...). | ||
The user is supposed to use the tabs on the top, from left to right. | The user is supposed to use the tabs on the top, from left to right. | ||
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* ctrl-+ (control-plus) and ctrl-- (control-minus) enlarge or decrease the font size of characters. | * ctrl-+ (control-plus) and ctrl-- (control-minus) enlarge or decrease the font size of characters. | ||
* flexibility of operation: all commands in the ''tools'' tab may be modified by the user, simply by modifying the (bash) code in the text field below the button. The user-changed command is automagically and permanently stored in ~/.xds-gui . The user may also change what is written on a button, by editing ~/.xds-gui. It should be obvious what to change. | * flexibility of operation: all commands in the ''tools'' tab may be modified by the user, simply by modifying the (bash) code in the text field below the button. The user-changed command is automagically and permanently stored in ~/.xds-gui . The user may also change what is written on a button, by editing ~/.xds-gui. It should be obvious what to change. | ||
* Menu / Settings is used for | * Menu / Settings is used for specifying, in "Library", the name of a "generic library" (e.g. /usr/local/lib64/dectris-neggia.so) for reading HDF5 files, the "Paths" for binaries (xds_par, xscale_par, shelxc/d/e, ...), and the "Appearance" (font size and default plot height). The Settings menu can be opened on the Mac by clicking upper-left on "xdsgui", then "Preferences ...", or pressing the "Command" (⌘) key and the "," key. Changed settings are automatically stored in ~/.xdsgui . | ||
== Tabs == | == Tabs == | ||
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=== Frame === | === Frame === | ||
to display existing 2-dimensional data frames, or to start XDS data processing by displaying a raw data frame. In the latter case, the "generate XDS.INP" button runs the [[generate_XDS.INP]] script to create a first XDS.INP from the header of the raw data frame that is being displayed. (Note: this button needs to be used only once per dataset; all later changes to XDS.INP are done by different means - manually or scripted) The blue circle(s) delineate(s) the area(s) of the detector within TRUSTED_REGION; the green circles correspond to INCLUDE_RESOLUTION_RANGE, and the red hatched regions correspond to EXCLUDE_RESOLUTION_RANGEs. The locations of the circles are not as accurate as those that XDS uses internally, because a simplified formula (and only values from XDS.INP, not the refined ones from XPARM.XDS) is used to calculate the resolution; this e.g. does not take care of detector swingout or otherwise skew geometry. | to display existing 2-dimensional data frames, or to start XDS data processing by displaying a raw data frame. In the latter case, the "generate XDS.INP" button runs the [[generate_XDS.INP]] script to create a first XDS.INP from the header of the raw data frame that is being displayed. (Note: this button needs to be used only once per dataset; all later changes to XDS.INP are done by different means - manually or scripted) The blue circle(s) delineate(s) the area(s) of the detector within TRUSTED_REGION; the green circles correspond to INCLUDE_RESOLUTION_RANGE, and the red [[XDSGUI#Technical aspects of XDSGUI usage|hatched]] regions correspond to EXCLUDE_RESOLUTION_RANGEs. The locations of the circles are not as accurate as those that XDS uses internally, because a simplified formula (and only values from XDS.INP, not the refined ones from XPARM.XDS) is used to calculate the resolution; this e.g. does not take care of detector swingout or otherwise skew geometry. | ||
Untrusted areas can be specified by the user, using two (UNTRUSTED_ELLIPSE; UNTRUSTED_RECTANGLE) or four (UNTRUSTED QUADRILATERAL) right mouse clicks. The resulting areas are shown with red outline, and the keyword/parameter pairs are | Untrusted areas can be specified by the user, using two (UNTRUSTED_ELLIPSE; UNTRUSTED_RECTANGLE) or four (UNTRUSTED QUADRILATERAL) right mouse clicks. The resulting areas are shown with red outline, and the keyword/parameter pairs are placed in the XDS.INP tab. Step-by-step: | ||
* "Load" a | * "Load" a data file (e.g. FRAME.cbf) or, in case of Eiger HDF5 data, a frame based on a *master.h5 file to have it displayed. The pane can be "dragged" with the left mouse button; the mouse wheel zooms. The parameters in the XDS.INP tab are taken for resolution calculations (i.e. the frame header is not being interpreted in any way). For HDF5 data, the *master.h5 file must be loaded; this will automatically show its first frame (note that for this to work, the path to the correct [[XDSGUI#Technical aspects of XDSGUI usage|"generic library"]] must be specified in Menu/Settings). The frame number can be chosen with the selection box on the right, or the up-down arrows. | ||
* if XDS.INP does not yet exist, click "generate XDS.INP" (this ''will'' read the header). Check the XDS.INP tab afterwards but then go back to the Frame tab. Note that the current [[generate_XDS.INP]] works well for Pilatus, ADSC, Mar, [[Eiger]] and some Rigaku detectors; for other kinds of detectors the values marked XXX in XDS.INP have to be filled in manually. | * if XDS.INP does not yet exist, click "generate XDS.INP" (this ''will'' read the header). Check the XDS.INP tab afterwards but then go back to the Frame tab. Note that the current [[generate_XDS.INP]] works well for Pilatus, ADSC, Mar, [[Eiger]] and some Rigaku detectors; for other kinds of detectors the values marked XXX in XDS.INP have to be filled in manually. | ||
* left-click on "Untrusted areas" -> a pulldown menu appears | * left-click on "Untrusted areas" -> a pulldown menu appears | ||
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=== Installation === | === Installation === | ||
The program can be downloaded, by academic users, as Qt5 binary for Linux [https://{{SERVERNAME}}/pub/linux_bin/xdsgui 64bit] (compiled on | The program can be downloaded, by academic users, as Qt5 binary for Linux [https://{{SERVERNAME}}/pub/linux_bin/xdsgui 64bit] (compiled on RHEL7) and as Qt4 binary for [https://{{SERVERNAME}}/pub/mac_bin/xdsgui_qt4.dmg Mac] (works on OSX 10.6 and up). | ||
A Qt4 version for [https://{{SERVERNAME}}/pub/linux_bin/xdsgui.qt4 old Linux distributions], and a Qt5 version (attention: needs Qt5 installation!) for [https://{{SERVERNAME}}/pub/mac_bin/xdsgui_qt5.dmg latest MacOS] is also available. | |||
Industrial users: pls contact me directly. | Industrial users: pls contact me directly. | ||
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# ''Problem description: On the Mac, after loading frames, by clicking “generate XDS.INP”, the program gives some strange symbol “Ô in XDS.INP. And the more you click “save” button, the more “Ô appeared. This looks like <br>SPACE_GROUP_NUMBER=0 à ! 0 if unknown <br>UNIT_CELL_CONSTANTS= 70 80 90 90 90 90 à .''<br> The problem is due to the “Rich text” format in TextEdit when saving "generate_XDS.INP". It is solved by re-downloading the script, and changing format to Plain - everything is working now. | # ''Problem description: On the Mac, after loading frames, by clicking “generate XDS.INP”, the program gives some strange symbol “Ô in XDS.INP. And the more you click “save” button, the more “Ô appeared. This looks like <br>SPACE_GROUP_NUMBER=0 à ! 0 if unknown <br>UNIT_CELL_CONSTANTS= 70 80 90 90 90 90 à .''<br> The problem is due to the “Rich text” format in TextEdit when saving "generate_XDS.INP". It is solved by re-downloading the script, and changing format to Plain - everything is working now. | ||
# on a Mac, you may find a stream of the following error messages in the console window: <code>Jan 31 14:35:17 xdsgui[20939] <Error>: Error: this application, or a library it uses, has passed an invalid numeric value (NaN, or not-a-number) to CoreGraphics API and this value is being ignored. Please fix this problem. Jan 31 14:35:17 xdsgui[20939] <Error>: If you want to see the backtrace, please set CG_NUMERICS_SHOW_BACKTRACE environmental variable.</code> This sounds terrible, but is actually harmless. Since it is a message from Qt (which XDSGUI uses for graphics), ''it does not compromise the XDS data processing in any way''. If it bothers you, just suppress the printout of these messages, by <code>xdsgui 2>&1 | egrep -v 'CoreGraphics|CG_NUMERICS'</code> | # on a Mac, you may find a stream of the following error messages in the console window: <code>Jan 31 14:35:17 xdsgui[20939] <Error>: Error: this application, or a library it uses, has passed an invalid numeric value (NaN, or not-a-number) to CoreGraphics API and this value is being ignored. Please fix this problem. Jan 31 14:35:17 xdsgui[20939] <Error>: If you want to see the backtrace, please set CG_NUMERICS_SHOW_BACKTRACE environmental variable.</code> This sounds terrible, but is actually harmless. Since it is a message from Qt (which XDSGUI uses for graphics), ''it does not compromise the XDS data processing in any way''. If it bothers you, just suppress the printout of these messages, by <code>xdsgui 2>&1 | egrep -v 'CoreGraphics|CG_NUMERICS'</code> | ||
# | # Frames from HDF5-files (*master.h5) are not being displayed: the symptom is that the frames appear to be empty/blank. This means you have not specified the correct "generic library" - see [[XDSGUI#Technical aspects of XDSGUI usage|Technical aspects of XDSGUI usage]]. The fix is: go to (upper left) "Menu"->"Settings"->insert the string "/usr/local/lib64/dectris-neggia.so" as "generic library", or try "/usr/local/lib64/durin-plugin.so" for DIAMOND data. Ask the system administrator for the exact path! If none of these works, leave "generic library" empty and install <code>H5ToXds</code> or <code>hdf2mini-cbf</code> as explained above. | ||
If you find a bug, please send email to Kay dot Diederichs at uni-konstanz dot de , with enough information/data to reproduce the bug ("it does not work" is not enough!). | If you find a bug, please send email to Kay dot Diederichs at uni-konstanz dot de , with enough information/data to reproduce the bug ("it does not work" is not enough!). | ||
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* The display of large frames in the FRAME tab may be slow over the network. | * The display of large frames in the FRAME tab may be slow over the network. | ||
* The green INCLUDE_RESOLUTION and red semi-transparent EXCLUDE_RESOLUTION_RANGE circles in the Frame tab as well as all resolution values in the Frame and IDXREF tabs are calculated from values in XDS.INP (rather than from the refined values in XPARM.XDS, which XDS uses). For the (curved) Pilatus 12M, the calculations in XDSGUI do not give the correct results. | * The green INCLUDE_RESOLUTION and red semi-transparent EXCLUDE_RESOLUTION_RANGE circles in the Frame tab as well as all resolution values in the Frame and IDXREF tabs are calculated from values in XDS.INP (rather than from the refined values in XPARM.XDS, which XDS uses). For the (curved) Pilatus 12M, the calculations in XDSGUI do not give the correct results. | ||
* The path (e.g. /usr/local/lib64/dectris-neggia.so) to the <code>dectris-neggia</code> library (available from Dectris) or the <code>durin-plugin</code> library (download from Diamond Light Source, DLS) should be entered into the "generic frame library" entry, in Menu->Settings, to enable visualization of raw data from Eiger detectors, but this mechanism | * The path (e.g. /usr/local/lib64/dectris-neggia.so) to the <code>dectris-neggia</code> library (available from Dectris) or the <code>durin-plugin</code> library (download from Diamond Light Source, DLS) should be entered into the "generic frame library" entry, in Menu->Settings, to enable visualization of raw data from Eiger detectors, but this mechanism may not work properly. Therefore, <code>H5ToXds</code> or (better because maintained by GlobalPhasing)<code>hdf2mini-cbf</code> may be installed as explained above. | ||
== News == | == News == | ||