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authorThomas White <taw@physics.org>2010-10-27 12:21:45 +0200
committerThomas White <taw@physics.org>2012-02-22 15:27:04 +0100
commitf47803a3d004131493b20f9a3a3b5d9cccdaaf2a (patch)
tree8d66bcbaa6d702adc90bffee652caa5dd049b65a /doc/geometry.txt
parent244c17e424b1d2e320d81c6aea2116c2b888b4b4 (diff)
Update docs
Diffstat (limited to 'doc/geometry.txt')
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1 files changed, 22 insertions, 4 deletions
diff --git a/doc/geometry.txt b/doc/geometry.txt
index 22e4ae3f..414ad634 100644
--- a/doc/geometry.txt
+++ b/doc/geometry.txt
@@ -13,10 +13,10 @@ coordinates are specified inclusively, meaning that a minimum of 0 and a maximum
of 9 results in ten items. Counting begins from zero. All pixels in the image
must be assigned to a panel.
-See "A note on data orientation" in the top level README file for important
-information about how CrystFEL defines the axes. All coordinates (including the
-centre coordinates for each panel) are measured according to these axes: there
-is no coordinate system local to a panel.
+See "A note on data orientation" below for important information about how
+CrystFEL defines the axes. All coordinates (including the centre coordinates
+for each panel) are measured according to these axes: there is no coordinate
+system local to a panel.
The syntax for a simple geometry might be as follows:
@@ -54,3 +54,21 @@ n_panels = 1
See the "examples" folder for some examples.
+
+
+A note on data orientation
+--------------------------
+
+In the image data extracted from the HDF5 file, CrystFEL defines "x" as the most
+quickly varying coordinate in the data, and "y" as the second most quickly
+varying coordinate in the data. It doesn't know what to do with any extra
+dimensions in the HDF5 dataset beyond the second.
+
+The origin, which is considered the lower left corner of the image, is defined
+by CrystFEL as the first element in the image data. Positive x points in a
+direction to the right, and positive y points upwards. CrystFEL considers the
+positive z direction to be the direction of the incident beam completing the
+right-handed set of axes.
+
+The detector surface is currently always assumed to be perpendicular to the
+incident beam.