diff options
| author | Thomas White <taw@physics.org> | 2023-02-15 12:04:18 +0100 |
|---|---|---|
| committer | Thomas White <taw@physics.org> | 2023-02-15 15:03:21 +0100 |
| commit | 78a7355a506859a4133c34fe9fef5516cf283314 (patch) | |
| tree | d32429e1a8841aeacfd71e905c35ba79244d4c50 | |
| parent | 044560941c0aa28e1e809f148ce553e985b4e868 (diff) | |
Tutorial: update text about detector-shift and peakogram-stream
These are now installed (no more copy/chmod needed), and accessible from
the GUI.
| -rw-r--r-- | doc/articles/tutorial.rst | 24 |
1 files changed, 15 insertions, 9 deletions
diff --git a/doc/articles/tutorial.rst b/doc/articles/tutorial.rst index a6b7a4cf..15c23ae0 100644 --- a/doc/articles/tutorial.rst +++ b/doc/articles/tutorial.rst @@ -782,14 +782,17 @@ of section 8):: predict_refine/det_shift x = -0.016 y = -0.002 mm $ -A script provided with CrystFEL called detector-shift will plot these values. +A program provided with CrystFEL called detector-shift will plot these values. Simply run it on the stream:: - $ cp ~/crystfel/scripts/detector-shift . - $ chmod +x detector-shift - $ ./detector-shift index-all-cell-1/crystfel.stream + $ detector-shift index-all-cell-1/crystfel.stream Mean shifts: dx = 0.0062 mm, dy = -0.0097 mm +You can also run ``detector-shift`` conveniently from within the CrystFEL GUI: +Simply choose **Check detector shift** from the **Tools** menu. This will run +``detector-shift`` on whichever indexing result is currently selected (see the +start of section 7). + A window should open, which shows the detector shifts as a scatter plot: .. image:: tutorial-images/detector-shift.png @@ -809,10 +812,10 @@ Notice that the cluster of points is significantly displaced from the origin. This offset has already been taken into account by CrystFEL when calculating the position of Bragg peaks, but the results will be better overall if the geometry is correct from the start of the process. In this case, it would be a -good idea to update the geometry file. The detector-shift script can fix the +good idea to update the geometry file. The detector-shift program can fix the geometry file for you:: - $ ~/crystfel/scripts/detector-shift index-all-cell-1/crystfel.stream jf-swissfel-16M.geom + $ detector-shift index-all-cell-1/crystfel.stream jf-swissfel-16M.geom Mean shifts: dx = -0.14 mm, dy = -0.25 mm Applying corrections to jf-swissfel-16M.geom, output filename jf-swissfel-16M-predrefine.geom default res 9097.525473 @@ -836,9 +839,12 @@ small program distributed with CrystFEL, called ``peakogram-stream``, will help you judge the maximum intensity to allow for a reflection. Run it on your stream, like this:: - $ cp ~/crystfel/scripts/peakogram-stream . - $ chmod +x peakogram-stream - $ ./peakogram-stream -i index-all-cell-1/crystfel.stream + $ peakogram-stream -i index-all-cell-1/crystfel.stream + +You can also run ``peakogram-stream`` from the CrystFEL user interface by +selecting **Check detector saturation (peakogram)** from the **Tools** menu. +As with ``detector-shift``, this applies to the currently selected indexing +result. A graph like this should appear: |