From e8c9b0f221f4a389f338aff9adefe277b44829fd Mon Sep 17 00:00:00 2001 From: Thomas White Date: Mon, 17 May 2021 14:16:47 +0200 Subject: Fix RST backticks --- doc/articles/electrons.rst | 43 ++++++++++++++++++++++--------------------- 1 file changed, 22 insertions(+), 21 deletions(-) (limited to 'doc') diff --git a/doc/articles/electrons.rst b/doc/articles/electrons.rst index c1a7ab2c..00d326a8 100644 --- a/doc/articles/electrons.rst +++ b/doc/articles/electrons.rst @@ -25,9 +25,10 @@ give the wavelength directly:: wavelength 2.51e-12 m -You can also use `V` instead of `kV` and `A` (Angstroms) instead of `m`. +You can also use ``V`` instead of ``kV`` and ``A`` (Angstroms) instead of +``m``. -Obviously, do not use `photon_energy` - that's only for electromagnetic +Obviously, do not use ``photon_energy`` - that's only for electromagnetic radiation. @@ -43,22 +44,22 @@ location of the shifts in the geometry file, for example:: detector_shift_x = /%/shots/shift_x_mm mm detector_shift_y = /%/shots/shift_y_mm mm -The location (`/%/shots/shift_x_mm`) will, of course, depend on your -pre-processing. These are the correct locations for data from `diffractem`. +The location (``/%/shots/shift_x_mm``) will, of course, depend on your +pre-processing. These are the correct locations for data from ``diffractem``. Note that the coordinates are shifts of the *detector* (not the *beam*) in the -*laboratory coordinate system* (see `man crystfel_geometry`). Shifts in -"detector coordinates" (i.e. `detector_shift_fs`) would only make sense for +*laboratory coordinate system* (see ``man crystfel_geometry``). Shifts in +"detector coordinates" (i.e. ``detector_shift_fs``) would only make sense for single-panel detectors and are therefore not implemented. Correcting elliptical distortions of the projector lens can be done quite well -by setting the panel direction vectors (see `man crystfel_geometry` again) to be +by setting the panel direction vectors (see ``man crystfel_geometry`` again) to be non-orthogonal. For example:: p0/fs = +0.9934x -0.0092y p0/ss = -0.0092x +1.0067y -This is also covered by `diffractem`. +This is also covered by ``diffractem``. Indexing patterns @@ -66,9 +67,9 @@ Indexing patterns The only indexing method suitable for electrons is PinkIndexer, but more methods might be added in the future. As well as selecting the indexing method -using `--indexing=pinkindexer`, you will need to configure PinkIndexer's +using ``--indexing=pinkindexer``, you will need to configure PinkIndexer's assumption about the size of a reflection in reciprocal space using -`--pinkIndexer-reflection-radius=0.003`:: +``--pinkIndexer-reflection-radius=0.003``:: indexamajig -g sample.geom -i input-files.lst -o sample.stream \ --indexing=pinkindexer --pinkIndexer-reflection-radius=0.003 \ @@ -80,20 +81,20 @@ diffraction data. The default parameters give quick and reasonably good indexing. You can get more accurate results by increasing the granularity of refinement within -Pinkindexer using `--pinkIndexer-refinement-type=N`, with `N` from 0 (least +Pinkindexer using ``--pinkIndexer-refinement-type=N``, with ``N`` from 0 (least precise and fastest) to 5 (most precise and slowest). The default value is 1. -For speed, you might want to add `--max-indexer-threads=N`, where `N` is the +For speed, you might want to add ``--max-indexer-threads=N``, where ``N`` is the number of threads that PinkIndexer should use within itself. You should also -use `-j M` to specify the number of frames that `indexamajig` should process in -parallel. The sum of `N` and `M` should be roughly the number of available CPU -cores. It's also useful to try indexing each pattern only once (`--no-retry`). +use ``-j M`` to specify the number of frames that ``indexamajig`` should process in +parallel. The sum of ``N`` and ``M`` should be roughly the number of available CPU +cores. It's also useful to try indexing each pattern only once (``--no-retry``). If the camera length is specified in the geometry file by referencing values from image file headers, then you will also need to give an estimate of the -camera length using `--camera-length-estimate`. The same applies if the +camera length using ``--camera-length-estimate``. The same applies if the wavelength is specified indirectly, in which case you will need -`--wavelength-estimate`. Neither of these are usually necessary for electron +``--wavelength-estimate``. Neither of these are usually necessary for electron diffraction data. @@ -102,21 +103,21 @@ Saving and re-loading indexing results Indexing patterns with PinkIndexer can take a long time, which makes it painful to try (for example) different integration parameters. To mitigate this, you -can store the results from one run of `indexamajig` and re-run the process +can store the results from one run of ``indexamajig`` and re-run the process using the previous indexing results instead of repeating the PinkIndexer step. -First, create a *solution file* from the stream using the `stream2sol.py` +First, create a *solution file* from the stream using the ``stream2sol.py`` program from the CrystFEL scripts folder:: stream2sol.py -i sample.stream -o sample.sol -Then, run `indexamajig` using `--indexing=file` and giving the filename:: +Then, run ``indexamajig`` using ``--indexing=file`` and giving the filename:: indexamajig -g sample.geom -i input-files.lst -o output.stream \ --indexing=file --fromfile-input-file=sample.sol \ --no-refine --no-check-peaks --no-retry \ --int-radius=10,12,14 -Note the options `--no-refine --no-check-peaks --no-retry` are added to skip +Note the options ``--no-refine --no-check-peaks --no-retry`` are added to skip the checks and refinement stages normally performed after indexing - these are not necessary when replaying solutions like this. -- cgit v1.2.3