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This removes the big potential for confusion, which has happened several
times (see e.g. 095cbebaf6). It also fixes in-tree builds with CMake
(but seriously, always use out-of-tree builds).
Fixes #2.
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This isn't necessary after all, for the same reason that im-sandbox
doesn't need escaping: it can count off the fields where spaces aren't
allowed, and anything left is the filename. I was over-thinking things.
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Unfortunately, PinkIndexer needs the real camera length for its centre
refinement. Giving a fake value and scaling the resulting shift does
not work - the indexing rate drops with even a small error.
Ideally, this would work in the same way as --wavelength-estimate, by
using a static value from the geometry file if it's given. However,
this is rather complicated to implement because of the way all the units
stuff is implemented. Therefore, this is left as an improvement for the
future.
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The FIXMEs have both already been fixed.
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There is presumably an MPSD that also needs to be added.
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Significant change: the solution file must now come with the lattice
type, centering and (if applicable) unique axis information at the end
of each line, e.g. 'cI' (cubic I), 'mAb' (monoclinic A, unique axis b).
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This give FromFile its own private command-lien option processing, like
the other indexers. It removes the ability to auto-generate the
solution filename, but I don't think there's a way to do that without
breaking abstractions.
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It's only used for some error messages, and it doesn't compile anyway.
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Everything should use the per-crystal detector shift now.
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Also adds to meson.build
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This is a more general replacement for --pinkIndexer-thread-count.
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There doesn't seem to be any point in allocating them earlier, except to
make space for some nice bugs.
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This will return later in a more centralised form, if we decide to work
further on wide bandwidth.
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... and calculate the real value afterwards, checking that the detector
is really flat enough for it to work.
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These conflict badly with CrystFEL's own checks, creating a horrible
user and developer experience.
Later, if we want to handle wide bandwidth beams, we will improve the
central CrystFEL checks to support it.
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This allows the refined detector position to be used in a lot of places.
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This brings it up to date after e7cf3911104f.
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There is absolutely nothing useful that an indexing algorithm can do
with the opaque DataTemplate object.
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This is a more sensible non-indexer-specific and non-Xray-specific
replacement for --pinkIndexer-override-photon-energy
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This tells Mosflm not to try to load environ.def and defaults.def. We
don't need either.
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These needed to be kept up to date with a call to map_all_peaks every
time anything changed - wavelength, detector position etc. Not doing so
has already led to bugs in another branch, and probably already causes
problems on this branch.
This patch eliminates the rx,ry,rz completely. Anyone who needs
reciprocal space coordinates for a peak is now responsible for calling
detgeom_transform_coords themselves.
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This gives a huge speed improvement, without sacrificing very much in
indexing rate.
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Commented out debug message is no longer relevant
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Fixes CRYS-240
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This allows the indexing method private options structures to be set up
easily.
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Overall detector offsets can now be done via the geometry file, and this
is labelled as a hack. It doesn't actually do very much anyway, because the
"updated" detector is thrown away for the next pattern. The updated detector
is used only for subsequent indexing attempts on the same pattern.
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