Age | Commit message (Collapse) | Author |
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This doesn't do anything. The very next lines override all the
settings.
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Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/64
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If there are lots of error messages (e.g. a missing mask file), looking
at the last 4k of the log file is not always enough. Now it will go
back to 16k, in steps of 4k. It will stop early if it finds the start
of the file, and it will complain if it still doesn't find what it's
looking for.
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Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/61
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This checks that indexamajig correctly recognises when no files could be
processed.
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No other code path under image_expand_frames() actually opens the file,
because HDF5s are currently the only format supporting multiple frames.
The aim of the existence check is to give a better error message
(compared to the HDF5 backtrace splurge), but it doesn't need to be done
so early. In fact, checking so early had the side-effect of breaking
indexamajig --wait-for-file.
Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/65
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This tests that indexamajig --wait-for-file works
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Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/59
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Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/58
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correct a simple typo
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This makes it explicit that the Meson and Ninja steps should be run from
the CrystFEL folder, not (e.g.) the Meson folder.
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This is no longer needed after 48c02e71e5bf. Simply set the correct
PATH before starting the GUI, and it will be propagated to the SLURM
jobs.
Astute readers will notice that the feature has been silently broken
since last March (65a1afdce2da5cd), anyway. Whoops.
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Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/56
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Unfortunately, several environments rely on "magic" environment
variables to make things work. These need to be propagated.
The path to the GUI will no longer be added to the PATH. This was
intended to help when the indexing executables (mosflm, dirax etc) were
found alongside the CrystFEL executables. However, it's highly likely
that the path to the CrystFEL executables will be in PATH anyway.
This way, running the SLURM jobs in the same environment as the GUI
itself, also seems more compliant with the "principle of least
surprise".
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When running online, there's no input file handle to close.
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This avoids the process getting killed while waiting e.g. between runs
in an online context.
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Usually, one will want this option enabled. However, sometimes it
speeds things up a lot to disable it.
Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/54
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Otherwise, setting the defaults won't work properly.
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Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/51
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There's already some confusion between "loading a stream into the GUI"
and "adding a stream as a result". This should help resolve it, as well
as simplifying multi-stream results (coming up).
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Requires that the array of crystals isn't allocated on the stack.
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The csplit format is ambiguous when the filenames contain spaces. To
make things a bit clearer, the file now requires the fields to be
separated by exactly one space rather than any number of tabs/spaces.
Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/55
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The reciprocal space distance limit has been set as one third of the
smallest inter-Bragg spacing.
Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/38
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refinement
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Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/1
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Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/27
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Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/17
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This got missed out by accident in the conversion to DataTemplate, but
absolutely no-one noticed. In the meantime, my views on how the
geometry files should work have changed somewhat. I don't want to
maintain the extra complexity here when it isn't even clear that it will
eliminate the need to re-refine geometry for each camera length.
This commit just takes the rail direction stuff out of the documentation
and the geometry file parser.
Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/50
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Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/18
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Previously, the combination of reflection_new and add_refl_to_list gave
a way to side-step the usual check that the indices were not larger
than 512. This causes corruption of the RefList, so much be avoided.
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Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/52
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