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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 code hasn't been looked at for a very long time, and can be made a
bit faster by iterating in a more cache-friendly way.
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The unique filename is needed by the GUI for looking up results in a
stream. Otherwise, the filename is "(null)" for everything and the
lookup just returns the first chunk in the stream.
The filename is generated based on the unique serial number for each
chunk, and is therefore unique across one run of indexamajig regardless
of the number of worker processes (-j). This might have to change in future
to accommodate jobs run across multiple nodes, if there is any demand
for looking at results in one big concatenated stream.
This also changes the condition for deciding when to look for a 'real'
file, to take into account that there is always a non-NULL filename.
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The changes in b22f6f524 were incorrect. config.h should never be
included from libcrystfel headers, because that will include the main
CrystFEL program config.h instead.
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This moves the entry point for loading MsgPack data to a new function,
image_read_data_block. Inside image.c, the image structure can be
created using exactly the same functions as for data files.
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For data formats other than HDF5, the location can be anything.
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Indexamajig uses only ZMQ, to receive streaming data, while libcrystfel
uses only msgpack to implement another type of image format.
The two of these are eventually tied together in process_image, which
does this: if ( have_zmq_data ) interpret_zmq_data_as_msgpack;
- however, they would be easy to split up if we wanted to do something
else (CBF data over ZMQ, anyone?).
This commit also switches the ZMQ connector to use a pub/sub socket
instead of a request/reply one. This matches changes in OnDA.
At the moment, the MessagePack image reader simply dumps the object to
disk.
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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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This simultaneously implements --copy-header/--copy-hdf5-field and gives
access to metadata (e.g. detector position or wavelength) when loading
from a stream with header-specified values.
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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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This makes the behaviour consistent with the prediction itself, and
removes another bit of mutable state.
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Previously, this was handled by updating the detector, but this could
easily lead to strange double accounting.
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See c876486b for rationale.
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This allows, for example, masks which have fewer % signs in their HDF5
locations than the main data.
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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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