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2021-03-05Mass update of copyright dates in source code commentsThomas White
2021-03-01data_template_new_from_string: Fail gracefully if fs/ss bad region lacks ↵Thomas White
panel name Fixes CRYS-245
2021-02-15Check that bad regions are actually within panel boundsThomas White
2021-02-09Add fom_is_comparison()Thomas White
2021-02-08Add fom_name()Thomas White
2021-02-08Expose fom_is_anomalous()Thomas White
2021-02-05Documentation for new FoM APIThomas White
2021-02-05Move fom_type_from_string out of APIThomas White
If it's needed, we'll replace it with a better piece of API (...which doesn't abort the program in the event of a typo!)
2021-02-05check_hkl: Remove standard deviation of intensityThomas White
It would've been difficult to calculate this in the new unified FoM API, and the figure is completely useless anyway. If you disagree with both of the above statements, please get in touch!
2021-02-05check_hkl: Move "single-list" FoMs into APIThomas White
Reasons for differences: 1. Resolution shells slightly different The binning calculation needs to take into account small rounding errors in the resolution calculation, when not using an explicit resolution range (--highres). The old version did this by taking a min/max resolution range slightly larger than the resolution of the data. The new version handles the rounding errors explicitly, so does not need this. 2. Number of reflections with infinite/invalid I/sigI values halved The number reported for this count was twice what it should have been, due to a bug in the old check_hkl. 3. Overall SNR is different When the above warning message applies, the old version still allowed the reflections with invalid I/sigI values to contribute to the denominator of the mean SNR calculation. The new version does not include them in the SNR calculation at all. Note that the reflections contribute to the other figures of merit unless otherwise stated. 4. Standard deviation of intensity is not calculated It would've been a lot of work to include this in the new version, and it's a totally useless number. If you disagree, please get in touch!
2021-01-28Stream: Use separate DataTemplate for reading and writingThomas White
This solves a tricky conceptual issue: Stream owns the DataTemplate when it's reading (because it came from the stream headers), but not when writing (when it's provided to us).
2021-01-27partialator/reflist: Propagate calloc NULL returnThomas White
This prevents an out-of-memory situation (due to ulimit) from manifesting as a segfault.
2021-01-27stream_close: Free the DataTemplateThomas White
2021-01-27image_free: Also free the spectrumThomas White
2021-01-27DataTemplate: fix some small memory leaksThomas White
2021-01-22compare_hkl: Remove --intensity-shellsThomas White
No-one uses it, it doubles the complexity of the code, and the manual even warns not to use it.
2021-01-22Remove selection of reflections for FoM to libcrystfelThomas White
2021-01-22Improve names for FoM APIThomas White
2021-01-22Move figure of merit calculation into libcrystfelThomas White
2021-01-15Correct P to R centeringThomas White
2021-01-15FormattingThomas White
2021-01-14Correct bad region coordinatesThomas White
Bad regions are specified (in the geometry file) in terms of the "file" coordinates, which might be different to the panel-relative ones.
2021-01-14Remove old debuggingThomas White
2021-01-14Avoid very slow loop over pixels to create bad pixel mapThomas White
Bad regions specified in terms of x/y still require an iteration over all pixels of the detector, but I don't see an easy way around that. Avoiding x/y bad regions will give best performance.
2021-01-14Stream: Remove in_chunkThomas White
It's not used any more - nowhere is it set to 1.
2021-01-14stream_open_for_read: Avoid using fseek()Thomas White
2021-01-14data_template_new_from_string: Fix error pathThomas White
2021-01-12FussinessThomas White
2021-01-11create_badmap: Break down into subroutinesThomas White
Also flips the order of iteration for (negligibly) better performance
2021-01-11resolution(): Use reciprocal representation instead of crystallographicThomas White
This avoids a load of trigonometric functions. In combination with the new UnitCell representation caching, this gives a significant speedup for cases where resolution() is called in a loop.
2021-01-11UnitCell: Store all representations once they're calculatedThomas White
Previously, the "getter" functions would re-calculate the requested representation every time they were called. This could mean doing a matrix inversion in the middle of a tight loop, wasting loads of time. Now, it stores the calculated values and returns them directly next time. Setting the parameters invalidates the values for all representations other than the one given. The cost of doing this is that the cell can no longer be "const" in the getter functions. This tracked through some other code, but nothing too severe.
2021-01-08detgeom_transform_coords: Avoid using trigonometric functionsThomas White
2021-01-08Update documentation about max_adu, and add a warningThomas White
2021-01-08Remove "Bragg proximity check" during integrationThomas White
This test is meant to avoid integrating overlapping spots. It does a very bad job of this, because it doesn't take into account whether the neighbouring reflection is actually excited, or even allowed by the lattice. It's even worse when we think about wide bandwidth.
2021-01-08locate_peak_on_panel: Check sign of 1/muThomas White
2021-01-07Formatting fussinessThomas White
2021-01-06partialator: Reject crystals with obviously too large profile radiiThomas White
The criterion for "too large" is 20% of the 1/d value for the lowest reflection which is not systematically absent according to the centering. A profile radius larger than the 1/d value for a reflection will crash the xsphere partiality model, and some visualisation shows that this is a clearly non-physical situation. The profile radius shouldn't be anywhere near the inter-Bragg spacing for reasonable data. However, feedback shows that this is happening quite often in real data, probably due to bad indexing.
2021-01-05Remove unused structure memberThomas White
2020-12-18Add peak_list_type in geometry fileThomas White
2020-12-16Add flag_{lessthan,morethan,equal} in geometry fileThomas White
This makes handling Pilatus/Eiger files, as well as many others, much easier.
2020-12-14Meson: Add GSL to libcrystfel's declare_dependency()Thomas White
2020-12-07Get rid of ImageFeature->rx,ry,rzThomas White
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.
2020-10-27Add a new StreamFlag for generating the detgeom structureThomas White
This is a hack, and should be replaced by something which gets the metadata from the stream rather than hitting the read image file every time.
2020-10-27image_set_zero_{data,mask}: Speed up creation of blank arraysThomas White
2020-10-27Fix a possibly overrun stringThomas White
2020-10-26Label all uses of cell tolerancesThomas White
I'm sick of fixing this same issue over and over again. New rule: any code handling unit cell tolerances MUST be labelled with details of units.
2020-10-22image_expand_frames: When files are not HDF5, just return null eventsThomas White
2020-10-22compare_cell_parameters: Accept R/P pair as equivalentThomas White
See 0f18ff76a3d1f5979db for some discussion.
2020-10-15Shuffle default order of indexing methodsThomas White
2020-10-15Add TakeTwo to the list of indexers automatically usedThomas White
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