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August 2016

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Subject	From	Date	Size
[git/dials] master: dials.geometry_viewer: add option to change detector distance (56eca57)	DIALS Commit via DLS Jenkins	Wed, 31 Aug 2016 14:44:21 +0100	260 lines
[git/dials] master: speed up shadow mask generation by optimising flex -> numpy array conversions (5b0b27b)	DIALS Commit via DLS Jenkins	Wed, 31 Aug 2016 13:39:07 +0100	180 lines
[git/dials] master: Add command line option to generate mmCIF output. (b3cdf4a)	DIALS Commit via DLS Jenkins	Wed, 31 Aug 2016 12:09:33 +0100	255 lines
[git/dials_scratch] master: Add more units (f33a697)	DIALS Scratch Commit via DLS Jenkins	Tue, 30 Aug 2016 15:16:14 -0700	239 lines
[git/dials_scratch] master: Several improvements for detector_residuals plots: (4993c5b)	DIALS Scratch Commit via DLS Jenkins	Tue, 30 Aug 2016 14:42:14 -0700	604 lines
[git/dials_scratch] master: Compute RMSD only for bright reflections (IE I/sigI >= cutoff provided) (e275f6d)	DIALS Scratch Commit via DLS Jenkins	Tue, 30 Aug 2016 14:42:13 -0700	168 lines
[git/dials] master: Bugfix (c2003c5)	DIALS Commit via DLS Jenkins	Tue, 30 Aug 2016 14:20:34 -0700	94 lines
[git/dials] master: don't interpret max_cell so strictly in fft3d (9cabe65)	DIALS Commit via DLS Jenkins	Tue, 30 Aug 2016 14:37:26 +0100	306 lines
[git/dials] master: More bugfixes. (6aa26e2)	DIALS Commit via DLS Jenkins	Mon, 29 Aug 2016 16:07:19 -0700	116 lines
[git/dials] master: Bugfix (69cf706)	DIALS Commit via DLS Jenkins	Mon, 29 Aug 2016 14:34:19 -0700	79 lines
[git/dials] master: Add parameter reference_geometry to dials.stills_process. Use to reprocess data after refining detector parameters. (1733c45)	DIALS Commit via DLS Jenkins	Mon, 29 Aug 2016 14:30:17 -0700	225 lines
[git/dials] master: For stills, when removing the scan/gonio prior to indexing in indexer.py, save _models. This preserves any changes done to the imageset prior to indexing. (9b1a87f)	DIALS Commit via DLS Jenkins	Mon, 29 Aug 2016 14:27:33 -0700	89 lines
[git/dials] master: insert origin to list of goniometer points (ad5bd5e)	DIALS Commit via DLS Jenkins	Fri, 26 Aug 2016 16:07:06 +0100	77 lines
[git/dials] master: bug fix (396b037)	DIALS Commit via DLS Jenkins	Fri, 26 Aug 2016 09:56:39 +0100	140 lines
[git/dials] master: Bugfix (1a6b6bf)	DIALS Commit via DLS Jenkins	Thu, 25 Aug 2016 09:33:48 -0700	80 lines
[git/dials] master: new dials.geometry_viewer (5446684)	DIALS Commit via DLS Jenkins	Thu, 25 Aug 2016 16:36:19 +0100	999 lines
[git/dials_scratch] master: moved to dials proper (25751a1)	DIALS Scratch Commit via DLS Jenkins	Thu, 25 Aug 2016 16:16:55 +0100	988 lines
[git/dials] master: show_mask2 option: much faster than show_mask for larger masked regions, but only sets raw data to -2 instead of drawing red overlay (6f4ea75)	DIALS Commit via DLS Jenkins	Thu, 25 Aug 2016 16:14:49 +0100	144 lines
[git/dials] master: convex hull algorithm for finding full outline of shadow on each panel (26a2ff6)	DIALS Commit via DLS Jenkins	Thu, 25 Aug 2016 16:14:49 +0100	305 lines
[git/dials] master: bug fix (9920fba)	DIALS Commit via DLS Jenkins	Thu, 25 Aug 2016 16:14:49 +0100	120 lines
[git/dials] master: Added extra check (bad8334)	DIALS Commit via DLS Jenkins	Thu, 25 Aug 2016 11:19:57 +0100	77 lines
[git/dials] master: Did a clean clutter (7a46a94)	DIALS Commit via DLS Jenkins	Thu, 25 Aug 2016 11:16:22 +0100	93 lines
[git/dials] master: Added import (6277d60)	DIALS Commit via DLS Jenkins	Thu, 25 Aug 2016 11:12:38 +0100	72 lines
[git/dials] master: Expose dispersion thershold class (d2e5705)	DIALS Commit via DLS Jenkins	Thu, 25 Aug 2016 11:07:40 +0100	101 lines
[git/dials] master: Added a modeller class (02d43b8)	DIALS Commit via DLS Jenkins	Thu, 25 Aug 2016 11:03:45 +0100	357 lines
[git/dials] master: Added pixel filter and gap filling stuff (895569f)	DIALS Commit via DLS Jenkins	Thu, 25 Aug 2016 10:56:49 +0100	2504 lines
[git/dials] master: Added background modeller code (a0c05de)	DIALS Commit via DLS Jenkins	Thu, 25 Aug 2016 10:49:24 +0100	881 lines
[git/dials] master: Added command line program to model background (7121071)	DIALS Commit via DLS Jenkins	Thu, 25 Aug 2016 10:45:25 +0100	348 lines
[git/dials] master: Added some tests (2482c37)	DIALS Commit via DLS Jenkins	Thu, 25 Aug 2016 10:27:36 +0100	303 lines
[git/dials] master: Added some stuff to fill holes (acaa5ca)	DIALS Commit via DLS Jenkins	Thu, 25 Aug 2016 10:24:46 +0100	440 lines
[git/dials] master: Added some filtering stuff (7286e1b)	DIALS Commit via DLS Jenkins	Thu, 25 Aug 2016 10:21:06 +0100	931 lines
[git/dials] master: fix bug introduced by 89e0a64ab297d35f713ae479089b85ff1513ede5 (fa75942)	DIALS Commit via DLS Jenkins	Thu, 25 Aug 2016 09:10:13 +0100	81 lines
[git/dials] master: print help if no input (18fb766)	DIALS Commit via DLS Jenkins	Thu, 25 Aug 2016 09:10:13 +0100	78 lines
[git/dials] master: Better RMSD output after integration (b594e9f)	DIALS Commit via DLS Jenkins	Wed, 24 Aug 2016 10:58:38 -0700	122 lines
[git/dials] master: Added test to run_tests script (ef16bee)	DIALS Commit via DLS Jenkins	Wed, 24 Aug 2016 15:41:28 +0100	71 lines
[git/dials] master: Added background algorithm that takes a background model and does fitting of the background in both a simple and robust way. Also added a test. (637fa09)	DIALS Commit via DLS Jenkins	Wed, 24 Aug 2016 15:40:32 +0100	1855 lines
[git/dials_scratch] master: draw all goniometer axes; allow all goniometer angles to be changed in GUI (4edd0e9)	DIALS Scratch Commit via DLS Jenkins	Tue, 23 Aug 2016 11:10:53 +0100	613 lines
[git/dials] master: Fixes for using mouse to make masks. (f4cf8bb)	DIALS Commit via DLS Jenkins	Mon, 22 Aug 2016 15:32:12 -0700	116 lines
[git/dials] master: Added a check for integration flags (c7cdb9d)	DIALS Commit via DLS Jenkins	Mon, 22 Aug 2016 17:39:12 +0100	96 lines
[git/dials_scratch] master: utility to visualise goniometer shadowing (e2c3cc7)	DIALS Scratch Commit via DLS Jenkins	Mon, 22 Aug 2016 17:31:50 +0100	1159 lines
[git/dials] master: mask_untrusted_polygon will fail fewer than 4 points provided (c254019)	DIALS Commit via DLS Jenkins	Fri, 19 Aug 2016 20:08:44 +0100	75 lines
[git/dials_scratch] master: code moved to dials/util/masking.py (55e8930)	DIALS Scratch Commit via DLS Jenkins	Fri, 19 Aug 2016 16:08:49 +0100	240 lines
[git/dials] master: add GoniometerShadowMaskGenerator code (a6d2310)	DIALS Commit via DLS Jenkins	Fri, 19 Aug 2016 16:05:35 +0100	221 lines
[git/dials] master: new dials.image_viewer option show_mask(=False) (0628170)	DIALS Commit via DLS Jenkins	Fri, 19 Aug 2016 16:05:16 +0100	147 lines
[git/dials] master: use LightweightDrawPointLayer2 for displaying masked pixels for performance reasons (2181133)	DIALS Commit via DLS Jenkins	Fri, 19 Aug 2016 13:58:33 +0100	78 lines
[git/dials_scratch] master: class to generate goniometer mask; optionally generate mp4 animation of shadow mask (83b1c27)	DIALS Scratch Commit via DLS Jenkins	Fri, 19 Aug 2016 13:15:33 +0100	554 lines
[git/dials_scratch] master: script for simulating shadow from simple cone model of goniometer onto detector surface (ba00777)	DIALS Scratch Commit via DLS Jenkins	Thu, 18 Aug 2016 11:52:38 +0100	342 lines
[git/dials] master: get axis names from goniometer; option to write xoalign config file (f19598c)	DIALS Commit via DLS Jenkins	Wed, 17 Aug 2016 15:48:55 +0100	258 lines
[git/dials] master: tidying up a bit (f6655ca)	DIALS Commit via DLS Jenkins	Tue, 16 Aug 2016 17:43:48 +0100	250 lines
[git/dials] master: making bitmap even faster by removing one memory allocation (da5daaa)	DIALS Commit via DLS Jenkins	Tue, 16 Aug 2016 17:26:30 +0100	715 lines
[git/dials] master: print axes and angles in ImgCIF and MOSFLM conventions (10799a0)	DIALS Commit via DLS Jenkins	Tue, 16 Aug 2016 14:54:40 +0100	147 lines
[git/dials] master: new dials.goniometer_calibration tool (19a3f60)	DIALS Commit via DLS Jenkins	Tue, 16 Aug 2016 11:28:37 +0100	258 lines
[git/dials] master: making bitmap generator 5 times faster by swapping the order of some loops (de5f385)	DIALS Commit via DLS Jenkins	Mon, 15 Aug 2016 13:22:07 +0100	169 lines
[git/dials] master: Merge pull request #192 from dials/dials-191 (e64f4ea)	DIALS Commit via DLS Jenkins	Thu, 11 Aug 2016 15:43:33 +0100	79 lines
[git/dials] master: add test case where setting matrix != I3 (724c0ee)	DIALS Commit via DLS Jenkins	Thu, 11 Aug 2016 14:59:38 +0100	189 lines
[git/dials] master: remove debugging code (19e72eb)	DIALS Commit via DLS Jenkins	Thu, 11 Aug 2016 14:25:32 +0100	119 lines
[git/dials] master: fix calculate_entering_flags() to take into account goniometer setting rotation (see also 1743efe) (79408bd)	DIALS Commit via DLS Jenkins	Thu, 11 Aug 2016 14:16:14 +0100	82 lines
[git/dials] master: fix indexer_base.calculate_entering_flags() to take into account goniometer setting rotation (1743efe)	DIALS Commit via DLS Jenkins	Thu, 11 Aug 2016 13:55:20 +0100	85 lines
[git/dials] master: Check email update on branch for YT only (98e5740)	DIALS Commit via DLS Jenkins	Thu, 11 Aug 2016 12:49:25 +0100	71 lines
[git/dials] master: debugging code to assert that angle between observed and calculated s1 vectors is small (2de39a5)	DIALS Commit via DLS Jenkins	Thu, 11 Aug 2016 12:05:43 +0100	122 lines
[git/dials] master: Bugfixes (1d3f5a5)	DIALS Commit via DLS Jenkins	Wed, 10 Aug 2016 14:00:50 -0700	171 lines
[git/dials_scratch] master: Script for estimating diffraction resolution cutoff from a pile of dials integration results, then finding the top 20. (2b25163)	DIALS Scratch Commit via DLS Jenkins	Wed, 10 Aug 2016 12:05:34 -0700	445 lines
[git/dials] master: Changed some bits due to update in detector model. (464bf9d)	DIALS Commit via DLS Jenkins	Wed, 10 Aug 2016 19:29:19 +0100	269 lines
[git/dials] master: possibly this needed here too? (c20a2ba)	DIALS Commit via DLS Jenkins	Wed, 10 Aug 2016 17:23:42 +0100	90 lines
[git/dials] master: Trying to work out why setting matrix not working; moveto branch dials-191; looks like this is made more compex by assumptions of incoming axis in refinement parameterization code (e31a87b)	DIALS Commit via DLS Jenkins	Wed, 10 Aug 2016 14:14:30 +0100	295 lines
[git/dials] master: Clean clutter (6e0a978)	DIALS Commit via DLS Jenkins	Wed, 10 Aug 2016 14:11:47 +0100	49 lines
[git/dials] master: set timeout=1 second for select command reading from stdin (3272c21)	DIALS Commit via DLS Jenkins	Wed, 10 Aug 2016 11:46:39 +0100	76 lines
[git/dials] master: Missed one in tests (f21e4c4)	DIALS Commit via DLS Jenkins	Wed, 10 Aug 2016 11:27:25 +0100	95 lines
[git/dials] master: automatically generate & update download links (bc0fcb8)	DIALS Commit via DLS Jenkins	Wed, 10 Aug 2016 11:26:46 +0100	354 lines
[git/dials] master: Fix tests (db10ff8)	DIALS Commit via DLS Jenkins	Wed, 10 Aug 2016 11:16:58 +0100	177 lines
[git/dials] master: Now need setting rotation (b3ecddd)	DIALS Commit via DLS Jenkins	Wed, 10 Aug 2016 11:03:57 +0100	74 lines
[git/dials] master: Space to use setting matrix in reflection prediction; now working on making it work; for #191 (f62fa8a)	DIALS Commit via DLS Jenkins	Wed, 10 Aug 2016 10:45:37 +0100	198 lines
[git/dials] master: Now have proper rotation axis i.e. assumes setting will be applied; see cctbx revision 25144 (f1ac49e)	DIALS Commit via DLS Jenkins	Wed, 10 Aug 2016 10:33:18 +0100	83 lines
[git/dials] master: Now have the setting matrix correctly applied as follows: setting matrix needs to be applied to S before rotation; rotation axis needs to be multiplied by setting.inverse() to give the right behavior; FIXME should rotation axis be multiplied by setting.inverse() in constructor rather than in here? Probably yes if we want to make (5402a09)	DIALS Commit via DLS Jenkins	Wed, 10 Aug 2016 09:46:48 +0100	116 lines
[git/dials] master: Correct definition for using setting rotation; before did nothing; still not sure it is correct; certainly does not work for indexing until we have the prediction equations fixed up for this; test case incoming (a9244ca)	DIALS Commit via DLS Jenkins	Wed, 10 Aug 2016 09:22:59 +0100	103 lines
[git/dials] master: somehow lost an e (30ebddd)	DIALS Commit via DLS Jenkins	Wed, 10 Aug 2016 09:03:22 +0100	80 lines
[git/dials] master: putative fixes for setting matrix (c29edd5)	DIALS Commit via DLS Jenkins	Wed, 10 Aug 2016 08:55:43 +0100	86 lines
[git/dials] master: Two fixes for stills (5c2d2fe)	DIALS Commit via DLS Jenkins	Tue, 9 Aug 2016 13:44:25 -0700	110 lines
[git/dials] master: Fixes for inverted rotation axis; NB GUI change (more sensible label) fixes #184 (65e7384)	DIALS Commit via DLS Jenkins	Mon, 8 Aug 2016 13:54:35 +0100	305 lines
[git/dials] master: Bugfix for dials.stills_process for NeXus files. Use tag to not overwrite integration pickles. (29ff309)	DIALS Commit via DLS Jenkins	Tue, 2 Aug 2016 09:47:34 -0700	186 lines
[git/dials] master: Determine python library paths dynamically. Different locations on MacOS X (0e6b936)	DIALS Commit via DLS Jenkins	Tue, 2 Aug 2016 09:06:49 +0100	136 lines
[git/dials] master: 1.3.1 download links (9288423)	DIALS Commit via DLS Jenkins	Mon, 1 Aug 2016 14:36:57 +0100	130 lines
[git/dials] master: Incorrect API usage, fixes core failure of #186 (f62fcf8)	DIALS Commit via DLS Jenkins	Mon, 1 Aug 2016 11:23:24 +0100	82 lines
[git/dials] master: Add mpi support to dials.stills_process. (86dc717)	DIALS Commit via DLS Jenkins	Sun, 31 Jul 2016 22:44:15 -0700	224 lines

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