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authorThomas White <taw@physics.org>2023-02-15 12:04:18 +0100
committerThomas White <taw@physics.org>2023-02-15 15:03:21 +0100
commit78a7355a506859a4133c34fe9fef5516cf283314 (patch)
treed32429e1a8841aeacfd71e905c35ba79244d4c50
parent044560941c0aa28e1e809f148ce553e985b4e868 (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.rst24
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: