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June 2016

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Subject	From	Date	Size
[git/dials] master: FIXME for single image integration (6e40dc6)	DIALS Commit via DLS Jenkins	Thu, 30 Jun 2016 15:46:23 +0100	109 lines
[git/dials] master: option to generate plot of background intensity vs resolution (c7a3315)	DIALS Commit via DLS Jenkins	Thu, 30 Jun 2016 11:29:13 +0100	176 lines
[git/dials] master: dials.stills_process: accept json files, not just raw images. Allows using dials.import with overrides like mosflm_beam_center. (68a5094)	DIALS Commit via DLS Jenkins	Wed, 29 Jun 2016 07:51:23 -0700	134 lines
[git/dials] master: Follow on from 6d7cd98, also use C++ helper class in scan-varying parameterisations for small but significant time savings (c53f070)	DIALS Commit via DLS Jenkins	Wed, 29 Jun 2016 12:28:16 +0100	192 lines
[git/dials] master: Further to #166: Only update view if any value has changed. Means you can still tab/click through the parameters without freezing (5ca25c9)	DIALS Commit via DLS Jenkins	Wed, 29 Jun 2016 10:44:08 +0100	101 lines
[git/dials] master: fixes #166 (bug probably introduced by 039b3c679fd5a7c5e5c78fdacc3e9a805cb6d65c) (a04434d)	DIALS Commit via DLS Jenkins	Wed, 29 Jun 2016 10:35:42 +0100	133 lines
[git/dials] master: Expose hard-coded parameters for stills indexing: (3f9c49d)	DIALS Commit via DLS Jenkins	Tue, 28 Jun 2016 22:12:48 -0700	148 lines
[git/dials] master: Potential workaround for group frames that have zero distance. @rjgildea Does this work now? (6fcb0cb)	DIALS Commit via DLS Jenkins	Tue, 28 Jun 2016 19:02:55 +0100	106 lines
[git/dials] master: Setting reflections_per_degree may be beneficial for large scan-varying refinement jobs to reduce memory use. However, until now there has been a memory spike at the end of the job when prediction is performed for all indexed reflections. This is now reduced somewhat by not caching derivatives in the reflection table in this case, as we only need them during refinement anyway. (b826caa)	DIALS Commit via DLS Jenkins	Tue, 28 Jun 2016 15:56:58 +0100	636 lines
[git/dials] master: cache frame number for scan-varying paramterisations to avoid composing more than once (5bfdaa6)	DIALS Commit via DLS Jenkins	Tue, 28 Jun 2016 14:21:43 +0100	144 lines
[git/dials] master: Also changed moslfm to plane here (1d1cdfa)	DIALS Commit via DLS Jenkins	Tue, 28 Jun 2016 13:16:11 +0100	118 lines
[git/dials] master: Changed outlier name from mosflm to plane as suggested by reviewer (f3aab5b)	DIALS Commit via DLS Jenkins	Tue, 28 Jun 2016 13:16:11 +0100	132 lines
[git/dials] master: Improved error message: although dmin is the variable name, d_min is what the user sees via phil (a7945b3)	DIALS Commit via DLS Jenkins	Tue, 28 Jun 2016 11:05:37 +0100	81 lines
[git/dials] master: Sanity check: closes #165 (15936e1)	DIALS Commit via DLS Jenkins	Tue, 28 Jun 2016 11:03:39 +0100	100 lines
[git/dials] master: Fail test if dials.import fails (d59f9ff)	DIALS Commit via DLS Jenkins	Mon, 27 Jun 2016 16:57:17 +0100	139 lines
[git/dials] master: Fixed test (d5670f6)	DIALS Commit via DLS Jenkins	Mon, 27 Jun 2016 16:56:06 +0100	98 lines
[git/dials] master: More sensible caching and return of derivatives for multi-state parameterisations; also clean up dead code (7b3d9ac)	DIALS Commit via DLS Jenkins	Mon, 27 Jun 2016 16:40:22 +0100	1901 lines
[git/dials] master: fix some sphinx warnings (3db12e0)	DIALS Commit via DLS Jenkins	Mon, 27 Jun 2016 12:42:15 +0100	288 lines
[git/dials] master: fix documentation (ff5cb2e)	DIALS Commit via DLS Jenkins	Mon, 27 Jun 2016 12:11:34 +0100	81 lines
[git/dials] master: missing print >> out (549568d)	DIALS Commit via DLS Jenkins	Mon, 27 Jun 2016 12:11:34 +0100	125 lines
[git/dials] master: remove unused parameter (58279c2)	DIALS Commit via DLS Jenkins	Mon, 27 Jun 2016 12:11:34 +0100	74 lines
[git/dials] master: Update parallax correction if geometry is updated. Fixes #163 (c098a69)	DIALS Commit via DLS Jenkins	Mon, 27 Jun 2016 11:58:29 +0100	176 lines
[git/dials] master: Fix for #155 view predictions in RLV (e8dfddb)	DIALS Commit via DLS Jenkins	Mon, 27 Jun 2016 11:37:56 +0100	271 lines
[git/dials] master: Fixed bug (7aab8e2)	DIALS Commit via DLS Jenkins	Mon, 27 Jun 2016 11:21:13 +0100	78 lines
[git/dials] master: Fix documnentation (a4a89ec)	DIALS Commit via DLS Jenkins	Mon, 27 Jun 2016 11:02:54 +0100	75 lines
[git/dials] master: Check make exit codes and stop on error (6d0366d)	DIALS Commit via DLS Jenkins	Mon, 27 Jun 2016 10:31:27 +0100	116 lines
[git/dials] master: dials.export: change default output name hklout -> integrated (52041f9)	DIALS Commit via DLS Jenkins	Fri, 24 Jun 2016 16:08:24 -0500	193 lines
[git/dials] master: consistent use of EOF vs eof in heredocs in documentation (02edfc4)	DIALS Commit via DLS Jenkins	Fri, 24 Jun 2016 15:30:31 -0500	205 lines
[git/dials] master: support for viewing files imported from xds in reciprocal lattice viewer (786c3a7)	DIALS Commit via DLS Jenkins	Fri, 24 Jun 2016 10:18:03 -0500	139 lines
[git/dials] master: P1 is a special case (8fce7f0)	DIALS Commit via DLS Jenkins	Fri, 24 Jun 2016 06:50:14 -0500	94 lines
[git/dials] master: Say what we are using (08176a5)	DIALS Commit via DLS Jenkins	Fri, 24 Jun 2016 12:23:31 +0100	74 lines
[git/dials] master: Fix ice ring filtering for blank images (f44b64c)	DIALS Commit via DLS Jenkins	Fri, 24 Jun 2016 09:31:10 +0100	126 lines
[git/dials] master: update multi-lattice tutorial to reflect current best usage (3949ef0)	DIALS Commit via DLS Jenkins	Thu, 23 Jun 2016 22:55:39 -0500	169 lines
[git/dials] master: print table of bravais lattice to space groups in dials.refine_bravais_settings (0c6f8e7)	DIALS Commit via DLS Jenkins	Thu, 23 Jun 2016 22:51:51 -0500	146 lines
[git/dials] master: no need to recalculate bin tt values as already calculated by histogram code (27623bd)	DIALS Commit via DLS Jenkins	Thu, 23 Jun 2016 11:56:39 -0500	100 lines
[git/dials] master: fix dials.background (411daeb)	DIALS Commit via DLS Jenkins	Thu, 23 Jun 2016 11:44:37 -0500	97 lines
[git/dials] master: more debug output for find_max_cell (d37da74)	DIALS Commit via DLS Jenkins	Thu, 23 Jun 2016 14:39:56 +0100	98 lines
[git/dials] master: bug fix for display of unindexed reflections from integrated.pickle (8c39ec3)	DIALS Commit via DLS Jenkins	Tue, 21 Jun 2016 15:05:42 -0500	95 lines
[git/dials] master: move workshops page to the correct place; add more links and contact information (b4e6001)	DIALS Commit via DLS Jenkins	Tue, 21 Jun 2016 12:08:21 +0100	167 lines
[git/dials] master: Feedback from DESY: make workshop proceedings more visible by putting them in their own page, not 'Links'. Move Framework Report to Publications (01bb483)	DIALS Commit via DLS Jenkins	Tue, 21 Jun 2016 11:35:30 +0100	296 lines
[git/dials] master: Missing Sorry() imports lead to hilarious tracebacks. (6cc2028)	DIALS Commit via DLS Jenkins	Tue, 21 Jun 2016 09:22:16 +0100	104 lines
[git/dials] master: Tool to generate histogram of #spots in resolution shells, scaled as 1/d**2 (6a3e174)	DIALS Commit via DLS Jenkins	Fri, 17 Jun 2016 13:51:11 +0100	251 lines
[git/dials] master: Fix indentation of comments (d792fa0)	DIALS Commit via DLS Jenkins	Fri, 17 Jun 2016 13:44:57 +0100	88 lines
[git/dials] master: Did clean cluter (c4a53af)	DIALS Commit via DLS Jenkins	Fri, 17 Jun 2016 13:39:52 +0100	48 lines
[git/dials] master: Added gain to spot finding (e6e2c52)	DIALS Commit via DLS Jenkins	Fri, 17 Jun 2016 13:26:25 +0100	192 lines
[git/dials] master: fix for #156 (62dbb4a)	DIALS Commit via DLS Jenkins	Fri, 17 Jun 2016 10:13:49 +0100	84 lines
[git/dials] master: Allow indexing for data imported from XDS SPOT.XDS (f484810)	DIALS Commit via DLS Jenkins	Wed, 15 Jun 2016 10:11:08 +0100	112 lines
[git/dials] master: Catch no reflection in input and raise Sorry (fda54e6)	DIALS Commit via DLS Jenkins	Tue, 14 Jun 2016 12:05:39 +0100	87 lines
[git/dials] master: Use new flex.weighted_histogram; gives identical results :)@ (dfabf94)	DIALS Commit via DLS Jenkins	Tue, 14 Jun 2016 09:20:16 +0100	155 lines
[git/dials] master: Allow setting frames; helps with datablock.json (540acf4)	DIALS Commit via DLS Jenkins	Tue, 14 Jun 2016 08:15:40 +0100	102 lines
[git/dials] master: Add isoform refinement to the stills indexer. (fff3ca5)	DIALS Commit via DLS Jenkins	Mon, 13 Jun 2016 15:56:49 -0700	379 lines
[git/dials] master: For stills integration, remove reflections with at least one bad foreground pixel. (e73416d)	DIALS Commit via DLS Jenkins	Mon, 13 Jun 2016 11:39:58 -0700	91 lines
[git/dials] master: Clean code some; add summary information; FIXME should re-use resolution array (bf14998)	DIALS Commit via DLS Jenkins	Mon, 13 Jun 2016 15:52:03 +0100	242 lines
[git/dials] master: Move background to dials.background; philling (71005cf)	DIALS Commit via DLS Jenkins	Mon, 13 Jun 2016 15:22:56 +0100	349 lines
[git/dials] master: Documentation for the distl/dials apache spotfinder server. (13963a7)	DIALS Commit via DLS Jenkins	Fri, 10 Jun 2016 09:25:54 -0700	289 lines
[git/dials] master: FIXME; I think yes (7c4ebcd)	DIALS Commit via DLS Jenkins	Fri, 10 Jun 2016 16:08:04 +0100	189 lines
[git/dials] master: Add option to only show integration shoeboxes (b09455e)	DIALS Commit via DLS Jenkins	Fri, 10 Jun 2016 13:30:52 +0100	190 lines
[git/dials] master: Add option to only display integrated reflections (630e22c)	DIALS Commit via DLS Jenkins	Fri, 10 Jun 2016 10:57:08 +0100	157 lines
[git/dials] master: Fixes for plotting integrated experiments and reflections when using multi-panel detector e.g. I23 (518d136)	DIALS Commit via DLS Jenkins	Fri, 10 Jun 2016 09:30:33 +0100	146 lines
[git/dials] master: Tidied up import a bit - was previously difficult to see what was going on. Added some code to transform stills to sweeps if oscillation is given. (e6510c8)	DIALS Commit via DLS Jenkins	Thu, 9 Jun 2016 17:09:18 +0100	2163 lines
[git/dials] master: Add refinement paper to publications.html (910155c)	DIALS Commit via DLS Jenkins	Thu, 9 Jun 2016 15:34:32 +0100	69 lines
[git/dials] master: Exclude further directories from installer (b7ad223)	DIALS Commit via DLS Jenkins	Thu, 9 Jun 2016 11:17:33 +0100	89 lines
[git/dials] master: 1.2.5 released (d3ef762)	DIALS Commit via DLS Jenkins	Thu, 9 Jun 2016 08:47:49 +0100	130 lines
[git/dials] master: fix README (1606df6)	DIALS Commit via DLS Jenkins	Wed, 8 Jun 2016 17:23:38 +0100	76 lines
[git/dials] master: correction for revision e584ac9 - the method exists in Pillow, it just raises Exception (ed46252)	DIALS Commit via DLS Jenkins	Wed, 8 Jun 2016 15:20:47 +0100	128 lines
[git/dials] master: Moved import of scipy so that it's always before any cctbx modues (90d437a)	DIALS Commit via DLS Jenkins	Wed, 8 Jun 2016 15:17:07 +0100	117 lines
[git/dials] master: More warnings that should probably be debug (5a4a1fd)	DIALS Commit via DLS Jenkins	Wed, 8 Jun 2016 14:46:21 +0100	145 lines
[git/dials] master: Bug fix (4a24459)	DIALS Commit via DLS Jenkins	Wed, 8 Jun 2016 14:37:10 +0100	99 lines
[git/dials] master: Putative fix for #107; involves not showing masks if sum_images != 1 (89e0a64)	DIALS Commit via DLS Jenkins	Wed, 8 Jun 2016 14:31:47 +0100	180 lines
[git/dials] master: Send to debug instead to suppress excessive number of these warnings appearing in the user log (c29c10e)	DIALS Commit via DLS Jenkins	Wed, 8 Jun 2016 13:58:44 +0100	92 lines
[git/dials] master: Allow z-min z-max in rlv; fixes #145 (bbe3278)	DIALS Commit via DLS Jenkins	Wed, 8 Jun 2016 11:32:52 +0100	268 lines
[git/dials] master: Move sim_mx data to dials_regression. Update tests. Suggested change for #149 (e012b64)	DIALS Commit via DLS Jenkins	Wed, 8 Jun 2016 11:25:22 +0100	80 lines
[git/dials] master: Is this a bug? (4b993a2)	DIALS Commit via DLS Jenkins	Wed, 8 Jun 2016 11:12:34 +0100	81 lines
[git/dials] master: defluff installer, fixes #149 (937a231)	DIALS Commit via DLS Jenkins	Wed, 8 Jun 2016 10:55:11 +0100	193 lines
[git/dials] master: print out auto value of mp_chunksize (c6df3b6)	DIALS Commit via DLS Jenkins	Wed, 8 Jun 2016 10:28:56 +0100	75 lines
[git/dials] master: Key control of view; use up/down/left/right for big moves; shift+same for finer control (0.1*scale); fixes #142 (1b1b82b)	DIALS Commit via DLS Jenkins	Wed, 8 Jun 2016 10:27:14 +0100	227 lines
[git/dials] master: simpler to use libtbx.python -m pip install (71311a5)	DIALS Commit via DLS Jenkins	Wed, 8 Jun 2016 09:46:14 +0100	103 lines
[git/dials] master: Set chunksize to auto; fixes #150 (5cbe9ac)	DIALS Commit via DLS Jenkins	Wed, 8 Jun 2016 08:27:38 +0100	113 lines
[git/dials] master: Add mask=filename to dials.image_viewer for easy viewing of dials mask files. (9828fc8)	DIALS Commit via DLS Jenkins	Tue, 7 Jun 2016 16:32:43 -0700	248 lines
[git/dials] master: use jinja2 templates to create html reports (b7ed590)	DIALS Commit via DLS Jenkins	Fri, 3 Jun 2016 17:06:05 +0100	1077 lines
[git/dials] master: image_viewer optimisations when no spots to display (28a845f)	DIALS Commit via DLS Jenkins	Fri, 3 Jun 2016 16:41:35 +0100	160 lines
[git/dials] master: avoid double call of _get_flex_image() on loading of new image (039b3c6)	DIALS Commit via DLS Jenkins	Fri, 3 Jun 2016 16:28:24 +0100	285 lines
[git/dials_scratch] master: fix for interface change (178bcca)	DIALS Scratch Commit via DLS Jenkins	Fri, 3 Jun 2016 15:50:06 +0100	91 lines
[git/dials] master: Use sparse storage in Gaussian smoother, where many elts are expected to be 0.0 (51d0733)	DIALS Commit via DLS Jenkins	Fri, 3 Jun 2016 15:26:48 +0100	299 lines
[git/dials] master: refactoring to improve code reusability (a6acda9)	DIALS Commit via DLS Jenkins	Fri, 3 Jun 2016 15:26:48 +0100	2702 lines
[git/dials] master: more refactoring (07cba11)	DIALS Commit via DLS Jenkins	Fri, 3 Jun 2016 15:26:48 +0100	1689 lines
[git/dials] master: with a little more generic variable naming the loops over parameterisations can be shared between scans and stills type parameterisations and hence moved to the shared base (5cc562f)	DIALS Commit via DLS Jenkins	Fri, 3 Jun 2016 15:26:48 +0100	1392 lines
[git/dials] master: move a shared method to a base class (6e0d1e4)	DIALS Commit via DLS Jenkins	Fri, 3 Jun 2016 15:26:48 +0100	272 lines
[git/dials] master: tidying up, improving docstrings etc. after refactoring (d1ff8c2)	DIALS Commit via DLS Jenkins	Fri, 3 Jun 2016 15:26:48 +0100	1364 lines
[git/dials] master: more refactoring (14e1c16)	DIALS Commit via DLS Jenkins	Fri, 3 Jun 2016 15:26:48 +0100	1083 lines
[git/dials] master: Now _get_gradients_core is the same in all derived classes, so move it to the base class get_gradients method (84a99bf)	DIALS Commit via DLS Jenkins	Fri, 3 Jun 2016 15:26:48 +0100	460 lines
[git/dials] master: Use None to signify null derivatives and short circuit calculations involving these (9590380)	DIALS Commit via DLS Jenkins	Fri, 3 Jun 2016 15:26:48 +0100	1438 lines
[git/dials] master: Fixed for HDF5 files in multiple jobs and processes. Need to make sure file is closed because of fork behaviour in python multiprocessing. Fixes #144 (b19510e)	DIALS Commit via DLS Jenkins	Thu, 2 Jun 2016 15:50:04 +0100	153 lines
[git/dials] master: Propagate stdout/stderr so that GUI can intercept. Also make running command asynchronous, with mutex locks to ensure that nothing gets messed up. (3930e61)	DIALS Commit via DLS Jenkins	Thu, 2 Jun 2016 13:41:28 +0100	1408 lines
[git/dials] master: Removed absolute paths in state file. (1d9dee7)	DIALS Commit via DLS Jenkins	Wed, 1 Jun 2016 14:11:17 +0100	435 lines
[git/dials] master: removing commented and no longer needed test print (e392d98)	DIALS Commit via DLS Jenkins	Wed, 1 Jun 2016 13:50:31 +0100	80 lines
[git/dials] master: Moved controller part of idials to util/idials so it can be incorporated into GUI (c0ea570)	DIALS Commit via DLS Jenkins	Wed, 1 Jun 2016 13:15:55 +0100	63 lines
[git/dials] master: Fixed a bug in idials (c0bd4e5)	DIALS Commit via DLS Jenkins	Wed, 1 Jun 2016 10:14:08 +0100	266 lines

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