http://viper.lbl.gov:8080/cctbx.xfel/index.php?title=Data_viewer&feed=atom&action=history
Data viewer - Revision history
2024-03-29T13:07:12Z
Revision history for this page on the wiki
MediaWiki 1.23.1
http://viper.lbl.gov:8080/cctbx.xfel/index.php?title=Data_viewer&diff=1292&oldid=prev
Aaron at 16:16, 19 October 2016
2016-10-19T16:16:10Z
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<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 16:16, 19 October 2016</td>
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<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The command "<del class="diffchange diffchange-inline">cci</del>.pyana" can be configured to display the diffraction images streamed from an XTC file.</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The command "<ins class="diffchange diffchange-inline">cxi</ins>.pyana" can be configured to display the diffraction images streamed from an XTC file.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>== Configuring the viewer ==</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>== Configuring the viewer ==</div></td></tr>
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Aaron
http://viper.lbl.gov:8080/cctbx.xfel/index.php?title=Data_viewer&diff=453&oldid=prev
Sauter at 22:10, 5 May 2014
2014-05-05T22:10:33Z
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<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 22:10, 5 May 2014</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 28:</td>
<td colspan="2" class="diff-lineno">Line 28:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* <code>n_update</code>: GUI will only display every Nth event (every 120th image, in this example).</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* <code>n_update</code>: GUI will only display every Nth event (every 120th image, in this example).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* <code>n_collate</code>: GUI will display an average image over the last N events (last 60 events, in this example).</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* <code>n_collate</code>: GUI will display an average image over the last N events (last 60 events, in this example).</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Critical step:</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">'''</ins>Critical step:<ins class="diffchange diffchange-inline">'''</ins></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Please press the Run/Pause (green) button in the GUI to make the action start.</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">'''</ins>Please press the Run/Pause (green) button in the GUI to make the action start.<ins class="diffchange diffchange-inline">'''</ins></div></td></tr>
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Sauter
http://viper.lbl.gov:8080/cctbx.xfel/index.php?title=Data_viewer&diff=452&oldid=prev
Sauter at 22:08, 5 May 2014
2014-05-05T22:08:50Z
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<td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 22:08, 5 May 2014</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div></pre></div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div></pre></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>The command will marshal together all events from streams 0-4 in run 7 of experiment 346.  Those events with the CXI imaging detector with the given <code>address</code> will be sent to the <code>mod_view</code> module that displays images in a GUI.  Dark subtraction is done with the files <code>dark_path</code> and <code>dark_stddev</code> that are described on the [[Preparatory steps]] wiki page.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>The command will marshal together all events from streams 0-4 in run 7 of experiment 346.  Those events with the CXI imaging detector with the given <code>address</code> will be sent to the <code>mod_view</code> module that displays images in a GUI.  Dark subtraction is done with the files <code>dark_path</code> and <code>dark_stddev</code> that are described on the [[Preparatory steps]] wiki page.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">Critical </del>parameters are:</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">Important </ins>parameters are:</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* <code>n_update</code>: GUI will only display every Nth event (every 120th image, in this example).</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* <code>n_update</code>: GUI will only display every Nth event (every 120th image, in this example).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* <code>n_collate</code>: GUI will display an average image over the last N events (last 60 events, in this example).</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* <code>n_collate</code>: GUI will display an average image over the last N events (last 60 events, in this example).</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Critical step:</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Please press the Run/Pause (green) button in the GUI to make the action start.</ins></div></td></tr>
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Sauter
http://viper.lbl.gov:8080/cctbx.xfel/index.php?title=Data_viewer&diff=451&oldid=prev
Sauter at 22:05, 5 May 2014
2014-05-05T22:05:54Z
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<td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 22:05, 5 May 2014</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 24:</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>cxi.pyana -c myconfig_file.cfg /path/to/xtc/streams/e346-r0007-s0[0-4]-c00.xtc</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>cxi.pyana -c myconfig_file.cfg /path/to/xtc/streams/e346-r0007-s0[0-4]-c00.xtc</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div></pre></div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div></pre></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The command will marshal together all events from streams 0-4 in run 7 of experiment 346.  Those events with the CXI imaging detector with the given <code>address</code> will be sent to the <code>mod_view</code> that displays images in a GUI.  Dark subtraction is done with the files <code>dark_path</code> and <code>dark_stddev</code> that are described on the [[Preparatory steps]] wiki page.</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The command will marshal together all events from streams 0-4 in run 7 of experiment 346.  Those events with the CXI imaging detector with the given <code>address</code> will be sent to the <code>mod_view</code> <ins class="diffchange diffchange-inline">module </ins>that displays images in a GUI.  Dark subtraction is done with the files <code>dark_path</code> and <code>dark_stddev</code> that are described on the [[Preparatory steps]] wiki page.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Critical parameters are:</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Critical parameters are:</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* <code>n_update</code>: GUI will only display every Nth event (every 120th image, in this example).</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* <code>n_update</code>: GUI will only display every Nth event (every 120th image, in this example).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* <code>n_collate</code>: GUI will display an average image over the last N events (last 60 events, in this example).</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* <code>n_collate</code>: GUI will display an average image over the last N events (last 60 events, in this example).</div></td></tr>
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Sauter
http://viper.lbl.gov:8080/cctbx.xfel/index.php?title=Data_viewer&diff=450&oldid=prev
Sauter at 22:04, 5 May 2014
2014-05-05T22:04:43Z
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<table class='diff diff-contentalign-left'>
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<td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 22:04, 5 May 2014</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 1:</td>
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<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The command "cci.pyana<del class="diffchange diffchange-inline">'' </del>can be configured to display the diffraction images streamed from an XTC file.</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The command "cci.pyana<ins class="diffchange diffchange-inline">" </ins>can be configured to display the diffraction images streamed from an XTC file.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>== Configuring the viewer ==</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>== Configuring the viewer ==</div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 10:</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>[my_ana_pkg.mod_view]</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>[my_ana_pkg.mod_view]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>address    = CxiDs1-0|Cspad-0</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>address    = CxiDs1-0|Cspad-0</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>calib_dir  = /reg/<del class="diffchange diffchange-inline">neh</del>/<del class="diffchange diffchange-inline">home3</del>/<del class="diffchange diffchange-inline">nksauter/phenix/src</del>/cctbx_project/xfel/metrology/CSPad/run4/CxiDs1.0_Cspad.0</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>calib_dir  = /reg/<ins class="diffchange diffchange-inline">g</ins>/<ins class="diffchange diffchange-inline">cctbx</ins>/<ins class="diffchange diffchange-inline">sources</ins>/cctbx_project/xfel/metrology/CSPad/run4/CxiDs1.0_Cspad.0</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>dark_path      = /reg/d/psdm/cxi/cxib9713/res/darks/r0001-Ds1-avg.pickle</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>dark_path      = /reg/d/psdm/cxi/cxib9713/res/darks/r0001-Ds1-avg.pickle</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>dark_stddev    = /reg/d/psdm/cxi/cxib9713/res/darks/r0001-Ds1-stddev.pickle</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>dark_stddev    = /reg/d/psdm/cxi/cxib9713/res/darks/r0001-Ds1-stddev.pickle</div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 20:</td>
<td colspan="2" class="diff-lineno">Line 20:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div></pre></div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div></pre></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">These three parameters turn on and configure database-backed logging of hitfinding results</del>:</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">The command is run as follows</ins>:</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">* trial_id: we find it useful to organize processing in numbered trials</del>. <del class="diffchange diffchange-inline"> Whenever we go back and change the parameters of our processing, adjusting the target cell or spotfinder parameters for example, we re</del>-<del class="diffchange diffchange-inline">process under a different trial ID</del>. <del class="diffchange diffchange-inline"> When you submit your processing job using cxi</del>.<del class="diffchange diffchange-inline">lsf, you can specify the trial ID on the </del>command <del class="diffchange diffchange-inline">line with –t.  What you specify </del>will <del class="diffchange diffchange-inline">overwrite what is listed here </del>in <del class="diffchange diffchange-inline">the cfg file</del>.  <del class="diffchange diffchange-inline">If you use bsub, then what is in </del>the <del class="diffchange diffchange-inline">cfg file is what’s used.  Note, it isn’t a good idea to re-use </del>the <del class="diffchange diffchange-inline">trial_id when re-prossing the data if database logging is being used, simply because the hits </del>will be <del class="diffchange diffchange-inline">logged twice which will clutter future analysis.  Finally, if you want </del>to <del class="diffchange diffchange-inline">see which trials you have used for which runs, execute '''cxi.list_db_metadata'''</del></div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"><pre></ins></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">* db_logging: Switch for turning on and off logging</del></div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">cxi</ins>.<ins class="diffchange diffchange-inline">pyana </ins>-<ins class="diffchange diffchange-inline">c myconfig_file</ins>.<ins class="diffchange diffchange-inline">cfg /path/to/xtc/streams/e346-r0007-s0[0-4]-c00</ins>.<ins class="diffchange diffchange-inline">xtc</ins></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">* sql_buffer_size: </del>a <del class="diffchange diffchange-inline">queue size for regulating how often to add data to the database</del>.  <del class="diffchange diffchange-inline">In our experience, 5 has been just fine.</del></div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"></pre></ins></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">The </ins>command will <ins class="diffchange diffchange-inline">marshal together all events from streams 0-4 </ins>in <ins class="diffchange diffchange-inline">run 7 of experiment 346</ins>.  <ins class="diffchange diffchange-inline">Those events with </ins>the <ins class="diffchange diffchange-inline">CXI imaging detector with </ins>the <ins class="diffchange diffchange-inline">given <code>address</code> </ins>will be <ins class="diffchange diffchange-inline">sent </ins>to <ins class="diffchange diffchange-inline">the <code>mod_view</code> that displays images in </ins>a <ins class="diffchange diffchange-inline">GUI</ins>.  <ins class="diffchange diffchange-inline">Dark subtraction is done </ins>with <ins class="diffchange diffchange-inline">the files </ins><<ins class="diffchange diffchange-inline">code>dark_path</code</ins>> and <ins class="diffchange diffchange-inline"><code>dark_stddev</code> that </ins>are <ins class="diffchange diffchange-inline">described on </ins>the <ins class="diffchange diffchange-inline">[[Preparatory steps]] wiki page</ins>.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">== Monitoring hit finding in real time ==</del></div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">Critical parameters are</ins>:</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">After submitting a job </del>with <del class="diffchange diffchange-inline">db logging enabled, use cxi.monitor_trials </del><<del class="diffchange diffchange-inline">trial number</del>> <del class="diffchange diffchange-inline">to display the hit rate during processing.  Other command line options </del>and <del class="diffchange diffchange-inline">their defaults </del>are <del class="diffchange diffchange-inline">listed below, including </del>the <del class="diffchange diffchange-inline">ability to display multiple runs at once.  The default is to display the 5 latest runs by timestamp</del>.</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* <ins class="diffchange diffchange-inline"><code>n_update</code></ins>: <ins class="diffchange diffchange-inline">GUI </ins>will <ins class="diffchange diffchange-inline">only </ins>display <ins class="diffchange diffchange-inline">every Nth event (every 120th image, in this example)</ins>.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">* t_wait = 8000</del>: <del class="diffchange diffchange-inline">amount of time in ms between queries to the database</del></div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* <ins class="diffchange diffchange-inline"><code>n_collate</code></ins>: <ins class="diffchange diffchange-inline">GUI will </ins>display <ins class="diffchange diffchange-inline">an average image over </ins>the <ins class="diffchange diffchange-inline">last N events </ins>(<ins class="diffchange diffchange-inline">last 60 events, in this example</ins>).</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* <del class="diffchange diffchange-inline">hit_cutoff = 16</del>: <del class="diffchange diffchange-inline">the number of bragg spots before a frame is considered a hit.  If this is different than what’s in your config file, then the monitor </del>will <del class="diffchange diffchange-inline">be using a different cutoff to </del>display <del class="diffchange diffchange-inline">which frames are hits</del>.</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* <del class="diffchange diffchange-inline">average_window = 1000</del>: <del class="diffchange diffchange-inline">how many frames are in the sliding averaging window shown in the hit % graph</del></div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">* n_points = 1000: how many total points to </del>display <del class="diffchange diffchange-inline">on </del>the <del class="diffchange diffchange-inline">graph.  Set it to 0 to display all the data points </del>(<del class="diffchange diffchange-inline">can be computationally intensive</del>).</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">* display_time = 1800: number of seconds of experiment time to display.  Displays this number of seconds unless that would add up to more than 5 runs.</del></div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">* run_num = display only this run</del></div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">* run_min = start at this run</del></div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">* run_max = end with this run</del></div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div></div></td></tr>
</table>
Sauter
http://viper.lbl.gov:8080/cctbx.xfel/index.php?title=Data_viewer&diff=449&oldid=prev
Sauter: Created page with "The command "cci.pyana'' can be configured to display the diffraction images streamed from an XTC file. == Configuring the viewer == Add to the mod_view section of your pyana..."
2014-05-05T21:50:23Z
<p>Created page with "The command "cci.pyana'' can be configured to display the diffraction images streamed from an XTC file. == Configuring the viewer == Add to the mod_view section of your pyana..."</p>
<p><b>New page</b></p><div>The command "cci.pyana'' can be configured to display the diffraction images streamed from an XTC file.<br />
<br />
== Configuring the viewer ==<br />
Add to the mod_view section of your pyana config file as follows:<br />
<pre><br />
[pyana]<br />
modules = my_ana_pkg.mod_view<br />
num-cpu = 1<br />
<br />
[my_ana_pkg.mod_view]<br />
address = CxiDs1-0|Cspad-0<br />
calib_dir = /reg/neh/home3/nksauter/phenix/src/cctbx_project/xfel/metrology/CSPad/run4/CxiDs1.0_Cspad.0<br />
dark_path = /reg/d/psdm/cxi/cxib9713/res/darks/r0001-Ds1-avg.pickle<br />
dark_stddev = /reg/d/psdm/cxi/cxib9713/res/darks/r0001-Ds1-stddev.pickle<br />
detz_offset = 555<br />
<br />
# Suitable values depend on the repetition rate of the instrument.<br />
n_update = 120<br />
n_collate = 60<br />
</pre><br />
<br />
These three parameters turn on and configure database-backed logging of hitfinding results:<br />
* trial_id: we find it useful to organize processing in numbered trials. Whenever we go back and change the parameters of our processing, adjusting the target cell or spotfinder parameters for example, we re-process under a different trial ID. When you submit your processing job using cxi.lsf, you can specify the trial ID on the command line with –t. What you specify will overwrite what is listed here in the cfg file. If you use bsub, then what is in the cfg file is what’s used. Note, it isn’t a good idea to re-use the trial_id when re-prossing the data if database logging is being used, simply because the hits will be logged twice which will clutter future analysis. Finally, if you want to see which trials you have used for which runs, execute '''cxi.list_db_metadata'''<br />
* db_logging: Switch for turning on and off logging<br />
* sql_buffer_size: a queue size for regulating how often to add data to the database. In our experience, 5 has been just fine.<br />
<br />
== Monitoring hit finding in real time ==<br />
After submitting a job with db logging enabled, use cxi.monitor_trials <trial number> to display the hit rate during processing. Other command line options and their defaults are listed below, including the ability to display multiple runs at once. The default is to display the 5 latest runs by timestamp.<br />
* t_wait = 8000: amount of time in ms between queries to the database<br />
* hit_cutoff = 16: the number of bragg spots before a frame is considered a hit. If this is different than what’s in your config file, then the monitor will be using a different cutoff to display which frames are hits.<br />
* average_window = 1000: how many frames are in the sliding averaging window shown in the hit % graph<br />
* n_points = 1000: how many total points to display on the graph. Set it to 0 to display all the data points (can be computationally intensive).<br />
* display_time = 1800: number of seconds of experiment time to display. Displays this number of seconds unless that would add up to more than 5 runs.<br />
* run_num = display only this run<br />
* run_min = start at this run<br />
* run_max = end with this run</div>
Sauter