diff options
Diffstat (limited to 'doc')
| -rw-r--r-- | doc/geometry.txt | 26 | ||||
| -rw-r--r-- | doc/indexamajig.txt | 6 |
2 files changed, 25 insertions, 7 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. diff --git a/doc/indexamajig.txt b/doc/indexamajig.txt index 42f63771..71bd9991 100644 --- a/doc/indexamajig.txt +++ b/doc/indexamajig.txt @@ -1,7 +1,7 @@ -indexmajig - bulk indexing and data reduction program ------------------------------------------------------ +indexamajig - bulk indexing and data reduction program +------------------------------------------------------ -The indexamajig program takes as input a list of diffraction image files, +The "indexamajig" program takes as input a list of diffraction image files, currently in HDF5 format. For each image, it attempts to find peaks and then index the pattern. If successful, it will measure the intensities of the peaks at Bragg locations and produce a list in the form "h k l I", with some extra |