CrystFEL
  1. CrystFEL

CrystFEL

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AuthorCommitMessageCommit dateIssues
Thomas WhiteThomas White
54752e2ce0aread_peaks: Simplify logic
Thomas WhiteThomas White
dad7c029fdfFix slabbiness assumptionsThis adds a new routine, data_template_slabby_file_to_panel_coords, to be used (only!) in places where external forces require assumptions of slabbiness: pixel maps and MsgPack/HDF5 peak lists (including CXI-style). This also fixes the prototype of data_template_file_to_panel_coords to make the panel number strictly an input parameter. This was an oversight in the implementation of DataTempla...
Thomas WhiteThomas White
0b758e3ae3cstream_open_for_write: Fix documentation
Thomas WhiteThomas White
d86ac738071Drop compatibility with old stream format versionsCrystFEL hasn't written any version other than 2.3 since before 2015. Supporting the old versions is getting difficult because of slabbiness assumptions, so it's time to get rid of it.
Thomas WhiteThomas White
44ab14686dcUpdate merging tests to latest stream version
Thomas WhiteThomas White
59e8a7ef447Add tests/stream_roundtrip
Thomas WhiteThomas White
a40d7a356c3indexamajig: Don't back up image data if not filteringThis takes a non-negligible amount of time (40 ms per frame for 16M), so should be skipped if not needed.
Thomas WhiteThomas White
08f49ce8d56indexamajig: Use fine-grained profiling
Thomas WhiteThomas White
8f3fe09b4a0time_accounts_init: Add a warning if timer is not available
Thomas WhiteThomas White
aa6ac737854Add image_read_with_time_accounting for fine-grained data load profiling
Thomas WhiteThomas White
19b57c06602Move time-accounts to libcrystfel
Thomas WhiteThomas White
c062c1a7632Add new time accounts (preparation for finer-grained profiling)
Thomas WhiteThomas White
ed80ad943b4indexamajig: Remove pointless time account/last task/pingThis doesn't do anything. The very next lines override all the settings.
Thomas WhiteThomas White
1deed95e55cGUI: Fix stream rescan logicFixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/64
Thomas WhiteThomas White
634ac34f8ffGUI: Better handling of error-filled indexamajig logsIf 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.
Thomas WhiteThomas White
049d7fb351bGUI: Use fixed profile radius for indexing onceFixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/61
Thomas WhiteThomas White
f36b114e46eAdd tests/indexamajig-missing-fileThis checks that indexamajig correctly recognises when no files could be processed.
Thomas WhiteThomas White
b1d75cb3af1indexamajig: Return a specific error code (5) if no files could be processed
Thomas WhiteThomas White
5ca91a38d9dMove file_exists() check to right before opening the HDF5No 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://...
Thomas WhiteThomas White
1c797288d02Formatting and increased verbosity
Thomas WhiteThomas White
31f03d0a978Add tests/file-waitThis tests that indexamajig --wait-for-file works
Thomas WhiteThomas White
e882d83df17Add section about syminfo.lib to INSTALL.md
Thomas WhiteThomas White
4512983699dAdd scripts/install-indexers
Thomas WhiteThomas White
3619f7952b1Add new tutorial
Thomas WhiteThomas White
872935d9514cell_explorer: Handle smooth scrolling eventsFixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/59
Thomas WhiteThomas White
4c898a1f455CrystFELImageView: Handle smooth scrolling eventsFixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/58
Thomas WhiteThomas White
7840ff8f988Update dependencies for Fedora
Thomas WhiteThomas White
7ff63986038MMerge pull request #5 from kif/typocorrect a simple typo
Jerome KiefferJerome Kieffer
aeaeb73b03bcorrect a simple typo
Thomas WhiteThomas White
5566d02188fThis is CrystFEL 0.10.1
Thomas WhiteThomas White
2a966a1d7ccINSTALL.md: Add 'cd /home/user/downloads/crystfel'This makes it explicit that the Meson and Ninja steps should be run from the CrystFEL folder, not (e.g.) the Meson folder.
Thomas WhiteThomas White
11c80118ed5SLURM: Fix a silly mistake counting the environment entries
Thomas WhiteThomas White
c2eb263f916SLURM: Get rid of path_addThis 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.
Thomas WhiteThomas White
a50a84632beGUI: Try to get geometry from result (stream), if not explicitly providedFixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/56
Thomas WhiteThomas White
48c02e71e5bSLURM: Copy environment from parent processUnfortunately, 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 any...
Thomas WhiteThomas White
5f4d0976a89Meson: Switch to libccp4c from WrapDB
Thomas WhiteThomas White
2559e9f05e8indexamajig: Set file read time account for unpacking frame data
Thomas WhiteThomas White
3358c0312b3indexamajig: Avoid fclose(NULL)When running online, there's no input file handle to close.
Thomas WhiteThomas White
f17e7abda4aindexamajig: Send sandbox ping while waiting for next frameThis avoids the process getting killed while waiting e.g. between runs in an online context.
Thomas WhiteThomas White
0c5f4739df5indexamajig: Generate per-frame profiling numbers
Thomas WhiteThomas White
fe938a0ad2aindexamajig: Shut down cleanly on SIGUSR1
Thomas WhiteThomas White
681fbbe63fcGUI: Add a checkbox for automatically rescanning streamsUsually, 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
Thomas WhiteThomas White
70bf4744ce5GUI: Always set toggle actions at startupOtherwise, setting the defaults won't work properly.
Thomas WhiteThomas White
381931b8360GUI: Allow selection of multiple streamsFixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/51
Thomas WhiteThomas White
77bdea2d5e7Add GtkMultiFileChooserButton
Thomas WhiteThomas White
cc8b4303f42GUI: Don't store stream filename in projectThere'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).
Thomas WhiteThomas White
a509bb92bfepartialator: Use image_free() to avoid memory leaksRequires that the array of crystals isn't allocated on the stack.
Thomas WhiteThomas White
f5d198b468dpartialator: Handle spaces in custom split fileThe 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
Thomas WhiteThomas White
652872f38e4pair_peaks: Use reciprocal space distance instead of pixel distanceThe 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
Thomas WhiteThomas White
100ad72d704Ensure that crystal doesn't end up with invalid reflist after prediction refinement