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October 2017

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[git/dials_scratch] master: Command line script to allow running of scale_against_target. (da4fddd)	DIALS Scratch commit	Tue, 31 Oct 2017 16:40:54 +0000	567 lines
[git/dials_scratch] master: Method added to scale refelctions against a target Ih. (d1d13b9)	DIALS Scratch commit	Tue, 31 Oct 2017 16:39:55 +0000	573 lines
[git/dials] tag 'v1.8.0' created	DIALS commit	Tue, 31 Oct 2017 15:02:57 +0000	28 lines
[git/dials_scratch] master: Small temporary bugfix. (4d01972)	DIALS Scratch commit	Tue, 31 Oct 2017 14:11:51 +0000	93 lines
[git/dials_scratch] master: Development towards scaling against fixed Ih. (a182f19)	DIALS Scratch commit	Tue, 31 Oct 2017 14:04:37 +0000	442 lines
[git/dials_scratch] master: Reworking/cleaning of code and aimless constraint bugfix. (136fdec)	DIALS Scratch commit	Tue, 31 Oct 2017 11:20:01 +0000	86 lines
[git/dials_scratch] master: Code added to combine prf/sum intensities in similar manner to aimless. (14eecb8)	DIALS Scratch Commit via DLS Jenkins	Mon, 30 Oct 2017 16:30:26 +0000	453 lines
[git/dials] master: socket object reuse doesn't work on mac (e0ddc7d4)	DIALS Commit via DLS Jenkins	Mon, 30 Oct 2017 14:41:47 +0000	81 lines
[git/dials] master: relax timing restraint (4134f8b7)	DIALS Commit via DLS Jenkins	Mon, 30 Oct 2017 14:13:05 +0000	201 lines
[git/dials_scratch] master: Cleaning data manager clutter. (58b252a)	DIALS Scratch Commit via DLS Jenkins	Mon, 30 Oct 2017 13:51:21 +0000	298 lines
[git/dials_scratch] master: Improved plotting of absorption factors for aimless_scaling.py (30549cf)	DIALS Scratch Commit via DLS Jenkins	Mon, 30 Oct 2017 10:54:16 +0000	259 lines
[git/dials] master: Bugfixs for stills indexer for multiple lattice images (8c30f0ac)	DIALS Commit via DLS Jenkins	Sun, 29 Oct 2017 15:40:03 -0700	168 lines
[git/dials] master: Bug fix for stills indexer and multiple lattices. (5742984e)	DIALS Commit via DLS Jenkins	Fri, 27 Oct 2017 11:09:00 -0700	93 lines
[git/dials_scratch] master: Added plotting of absorption scale factors for aimless_scaling. (7611f11)	DIALS Scratch Commit via DLS Jenkins	Fri, 27 Oct 2017 17:22:52 +0100	273 lines
[git/dials_scratch] master: Absorption correction added to aimless_scaling.py code. (d78e9a9)	DIALS Scratch Commit via DLS Jenkins	Fri, 27 Oct 2017 16:30:46 +0100	1014 lines
[git/dials_scratch] master: Multicrystal option (two scans) added to aimless_scaling.py (dd79079)	DIALS Scratch Commit via DLS Jenkins	Fri, 27 Oct 2017 09:51:57 +0100	519 lines
[git/dials_scratch] master: Multicrystal option moved into main xds_scaling.py code (f7890f0)	DIALS Scratch Commit via DLS Jenkins	Thu, 26 Oct 2017 16:30:26 +0100	637 lines
[git/dials_scratch] master: Correcting plotting of absorption surfaces and naming of output files (a6d234b)	DIALS Scratch Commit via DLS Jenkins	Thu, 26 Oct 2017 15:49:17 +0100	331 lines
[git/dials] master: update list of developers (4cea9bf1)	DIALS Commit via DLS Jenkins	Thu, 26 Oct 2017 15:36:25 +0100	84 lines
[git/dials_scratch] master: Updated file parsing in my scaling scripts to take multiple files. (72dba0e)	DIALS Scratch Commit via DLS Jenkins	Thu, 26 Oct 2017 13:48:31 +0100	904 lines
[git/dials_scratch] master: Small change to print statement in datamanager (3d0deb1)	DIALS Scratch Commit via DLS Jenkins	Thu, 26 Oct 2017 13:48:31 +0100	80 lines
[git/dials_scratch] master: Add test to make sure common space group between json files. (798fdfb)	DIALS Scratch Commit via DLS Jenkins	Thu, 26 Oct 2017 13:48:31 +0100	93 lines
[git/dials_scratch] master: Updated code to use a default rotation bin interval of 15 degrees (d9a8aee)	DIALS Scratch Commit via DLS Jenkins	Thu, 26 Oct 2017 13:48:31 +0100	712 lines
[git/dials_scratch] master: Strip out Uij==0 for H; compute B for H & not-H (6977528)	DIALS Scratch Commit via DLS Jenkins	Thu, 26 Oct 2017 12:22:50 +0100	128 lines
[git/dials_scratch] master: Cleaned clutter (668841d)	DIALS Scratch Commit via DLS Jenkins	Wed, 25 Oct 2017 15:56:07 +0100	160 lines
[git/dials_scratch] master: Code refactoring to allow (basic) combined scaling of two datasets. (bb21df5)	DIALS Scratch Commit via DLS Jenkins	Wed, 25 Oct 2017 15:51:05 +0100	1425 lines
[git/dials_scratch] master: Rewriting of multicrystal datamanager. (da711d8)	DIALS Scratch Commit via DLS Jenkins	Wed, 25 Oct 2017 15:51:05 +0100	631 lines
[git/dials_scratch] master: Looks like some files have no modules; guess that is what makes them 'nearly' nexus ... (d1d8830)	DIALS Scratch Commit via DLS Jenkins	Wed, 25 Oct 2017 15:46:00 +0100	115 lines
[git/dials_scratch] master: Now derive the beam centre from first principles; i.e. from transformation stack (38cb8c7)	DIALS Scratch Commit via DLS Jenkins	Wed, 25 Oct 2017 15:41:58 +0100	250 lines
[git/dials_scratch] master: Cleaning clutter (e749360)	DIALS Scratch Commit via DLS Jenkins	Wed, 25 Oct 2017 15:04:23 +0100	50 lines
[git/dials_scratch] master: HDF5 / NXmx practical truthful validator (c0f8ace)	DIALS Scratch Commit via DLS Jenkins	Wed, 25 Oct 2017 15:04:06 +0100	346 lines
[git/dials_scratch] master: Jiffy to determine mean isotropic B factor from a CIF file (3df458c)	DIALS Scratch Commit via DLS Jenkins	Wed, 25 Oct 2017 11:51:45 +0100	122 lines
[git/dials] master: add docstrings for 'pytest --fixtures' output (5abea4bd)	DIALS Commit via DLS Jenkins	Wed, 25 Oct 2017 11:12:19 +0100	108 lines
[git/dials] master: more refactoring (999984aa)	DIALS Commit via DLS Jenkins	Wed, 25 Oct 2017 09:07:39 +0100	419 lines
[git/dials] master: Add parameter min_reflections_per_experiment to dials.combine_experiments. (6ee77b91)	DIALS Commit via DLS Jenkins	Tue, 24 Oct 2017 12:41:27 -0700	174 lines
[git/dials] master: Stills integration refactoring (7fe6e13a)	DIALS Commit via DLS Jenkins	Tue, 24 Oct 2017 12:41:27 -0700	396 lines
[git/dials] master: slight refactoring of the indexing test (204441de)	DIALS Commit via DLS Jenkins	Tue, 24 Oct 2017 16:12:42 +0100	742 lines
[git/dials] master: add pytest fixtures (9fd204fb)	DIALS Commit via DLS Jenkins	Tue, 24 Oct 2017 16:02:05 +0100	174 lines
[git/dials_scratch] master: Datamanager constructed for join minimisation of two datasets. (2fda5d3)	DIALS Scratch Commit via DLS Jenkins	Tue, 24 Oct 2017 14:16:38 +0100	442 lines
[git/dials] master: sprinkle ()s (f0d2c44f)	DIALS Commit via DLS Jenkins	Tue, 24 Oct 2017 08:56:47 +0100	220 lines
[git/dials] master: need newer pytest (ff7f7e2a)	DIALS Commit via DLS Jenkins	Tue, 24 Oct 2017 08:23:58 +0100	72 lines
[git/dials] master: Rearrange how to keep integration shoeboxes around temporarily. (07f4f4b9)	DIALS Commit via DLS Jenkins	Mon, 23 Oct 2017 14:15:15 -0700	253 lines
[git/dials] master: Bugfix: don't fail everything when stddev of a single item fails. (a659244b)	DIALS Commit via DLS Jenkins	Mon, 23 Oct 2017 14:12:29 -0700	100 lines
[git/dials_scratch] master: Ih_table object written for multi(two) crystal analysis, untested. (aa45f3b)	DIALS Scratch Commit via DLS Jenkins	Mon, 23 Oct 2017 14:05:41 +0100	674 lines
[git/dials_scratch] master: Bugfix to fix non-updating of scale factors in update_for_min method. (00e67d4)	DIALS Scratch Commit via DLS Jenkins	Mon, 23 Oct 2017 10:40:54 +0100	166 lines
[git/dials_scratch] master: Development of Ih_table object to explore multi-scan analysis. (71d9334)	DIALS Scratch Commit via DLS Jenkins	Mon, 23 Oct 2017 10:33:27 +0100	746 lines
[git/dials_scratch] master: Bugfix for binning in aimless_data_manager. (d973fba)	DIALS Scratch Commit via DLS Jenkins	Fri, 20 Oct 2017 16:04:36 +0100	102 lines
[git/dials_scratch] master: xds_scaling code updated to include full smoothing of all parameters. (baa5885)	DIALS Scratch Commit via DLS Jenkins	Fri, 20 Oct 2017 15:56:16 +0100	732 lines
[git/dials] master: update DBEM test (efe31007)	DIALS Commit via DLS Jenkins	Fri, 20 Oct 2017 15:27:41 +0100	116 lines
[git/dials] master: dials.modify_geometry: bug fix, and enable output of modified datablock (901dd806)	DIALS Commit via DLS Jenkins	Fri, 20 Oct 2017 14:47:20 +0100	111 lines
[git/dials] master: update find_spots_client test for changes to ice-ring filtering (58ae79af)	DIALS Commit via DLS Jenkins	Fri, 20 Oct 2017 14:29:11 +0100	115 lines
[git/dials] master: bug fix for filter_reflections if no datablock or experiments provided (3dad8b84)	DIALS Commit via DLS Jenkins	Fri, 20 Oct 2017 14:08:19 +0100	95 lines
[git/dials_scratch] master: Code cleaned-up and minimisers unified for aimless/xds methods. (d9dbb1d)	DIALS Scratch Commit via DLS Jenkins	Fri, 20 Oct 2017 13:39:51 +0100	1824 lines
[git/dials] master: update default value from d to 1/d^2 (e4283996)	DIALS Commit via DLS Jenkins	Fri, 20 Oct 2017 13:35:04 +0100	83 lines
[git/dials] master: In ice-ring filtering of spot lists use ice-ring width based on 1/d^2 instead of d to ensure more uniform width with resolution (a510c1a3)	DIALS Commit via DLS Jenkins	Fri, 20 Oct 2017 13:35:03 +0100	307 lines
[git/dials] master: add optional ice-ring filtering to filter_reflections tool (4fa7559c)	DIALS Commit via DLS Jenkins	Fri, 20 Oct 2017 13:35:03 +0100	280 lines
[git/dials] master: Change Python2 exception syntax to Python3. Some effort towards #459 (0b354cbb)	DIALS Commit via DLS Jenkins	Fri, 20 Oct 2017 10:45:00 +0100	380 lines
[git/dials] master: python3 preparation (c357ed01)	DIALS Commit via DLS Jenkins	Thu, 19 Oct 2017 21:38:41 +0100	76 lines
[git/dials_scratch] master: Code refactoring to clean up aimless data manager (7cba5ae)	DIALS Scratch Commit via DLS Jenkins	Thu, 19 Oct 2017 15:28:00 +0100	88 lines
[git/dials_scratch] master: Scaling code partly refactored, classes moved out of data_manager. (5d49341)	DIALS Scratch Commit via DLS Jenkins	Thu, 19 Oct 2017 15:27:58 +0100	2531 lines
[git/dials_scratch] master: updates to nearest neighbour plots (2a32c3d)	DIALS Scratch Commit via DLS Jenkins	Thu, 19 Oct 2017 13:26:44 +0100	305 lines
[git/dials_scratch] master: 2D Smoothing added to xds_scaling algorithm. (2019e9f)	DIALS Scratch Commit via DLS Jenkins	Wed, 18 Oct 2017 13:21:35 +0100	2122 lines
[git/dials_scratch] master: 2D smoothing implemented for decay correction in xds_scaling. (9e0ad9c)	DIALS Scratch Commit via DLS Jenkins	Tue, 17 Oct 2017 15:19:11 +0100	819 lines
[git/dials_scratch] master: Partially updated xds_scaling code for 2D smoothing. (7b15e74)	DIALS Scratch Commit via DLS Jenkins	Tue, 17 Oct 2017 14:34:13 +0100	742 lines
[git/dials_scratch] master: Scaling code refactored for implementation of aimless smoothing (0851509)	DIALS Scratch Commit via DLS Jenkins	Tue, 17 Oct 2017 10:17:15 +0100	1592 lines
[git/dials_scratch] master: Smoothing added to aimless (KB) type scaling. (ba74dea)	DIALS Scratch Commit via DLS Jenkins	Mon, 16 Oct 2017 16:45:41 +0100	671 lines
[git/dials_scratch] master: Smoothing functionality added to aimless scaling. (95eb72d)	DIALS Scratch Commit via DLS Jenkins	Mon, 16 Oct 2017 14:13:16 +0100	762 lines
[git/dials_scratch] master: Refactored scaling code to allow smooth scaling for scale factor (aimless) (a66881b)	DIALS Scratch Commit via DLS Jenkins	Mon, 16 Oct 2017 11:23:40 +0100	667 lines
[git/dials_scratch] master: script to compare partialities between full and sliced dataset (d882902)	DIALS Scratch Commit via DLS Jenkins	Fri, 13 Oct 2017 17:10:52 +0100	352 lines
[git/dials] master: reciprocal_lattice_viewer: add min/max partiality controls (c3447bb8)	DIALS Commit via DLS Jenkins	Fri, 13 Oct 2017 14:57:15 +0100	250 lines
[git/dials_scratch] master: Bugfix for radial absorption binning. (92a4219)	DIALS Scratch Commit via DLS Jenkins	Fri, 13 Oct 2017 11:12:44 +0100	1040 lines
[git/dials] master: per_image_analysis plot: separate #spots and resolution into subplots; add subplot of total intensity (a18cf409)	DIALS Commit via DLS Jenkins	Fri, 13 Oct 2017 09:55:54 +0100	274 lines
[git/dials_scratch] master: Bugfix for radial abosprtion binning. (e911598)	DIALS Scratch Commit via DLS Jenkins	Thu, 12 Oct 2017 14:28:23 +0100	204 lines
[git/dials] master: If apply_scales && inverse_scale_factor in table apply them in output so you can do this: (184911c1)	DIALS Commit via DLS Jenkins	Thu, 12 Oct 2017 11:43:35 +0100	262 lines
[git/dials] master: Clean clutter (f5e58540)	DIALS Commit via DLS Jenkins	Thu, 12 Oct 2017 11:42:42 +0100	48 lines
[git/dials_scratch] master: Debugging with @jbe (7fcbf96)	DIALS Scratch Commit via DLS Jenkins	Thu, 12 Oct 2017 11:23:37 +0100	85 lines
[git/dials_scratch] master: Clean histogram since we know the limits (6fbe2ca)	DIALS Scratch Commit via DLS Jenkins	Thu, 12 Oct 2017 09:03:02 +0100	74 lines
[git/dials_scratch] master: Merge of my local branch to incorporate changes to aimless_scaling.py (c4dc77a)	DIALS Scratch Commit via DLS Jenkins	Thu, 12 Oct 2017 08:44:56 +0100	58 lines
[git/dials_scratch] master: Wilson test added to scaling code to reject large outliers. (a3f168f)	DIALS Scratch Commit via DLS Jenkins	Thu, 12 Oct 2017 08:40:31 +0100	787 lines
[git/dials_scratch] master: Clean clutter (85b565c)	DIALS Scratch Commit via DLS Jenkins	Thu, 12 Oct 2017 06:48:04 +0100	52 lines
[git/dials_scratch] master: Jiffy to split partials out for plotting; usage: dials_scratch.split_partials integrated.pickle out97.pickle 0.97 0.025820267 - 0.074528982: 1 0.074528982 - 0.1232377: 0 0.1232377 - 0.17194641: 0 0.17194641 - 0.22065513: 1 0.22065513 - 0.26936384: 0 0.26936384 - 0.31807256: 1 0.31807256 - 0.36678127: 0 0.36678127 - 0.41548999: 0 0.41548999 - 0.4641987: 0 0.4641987 - 0.51290742: 1 0.51290742 - 0.56161613: 1 0.56161613 - 0.61032485: 1 0.61032485 - 0.65903356: 0 0.65903356 - 0.70774228: 3 0.70774228 - 0.75645099: 2 0.75645099 - 0.80515971: 3 0.80515971 - 0.85386842: 5 0.85386842 - 0.90257713: 4 0.90257713 - 0.95128585: 3 0.95128585 - 0.99999456: 741 Wrote 32 reflections with partiality < 0.970 to out97.pickle (95db49a)	DIALS Scratch Commit via DLS Jenkins	Thu, 12 Oct 2017 06:47:46 +0100	157 lines
[git/dials] master: dials.report: set all=False when selecting integrated reflections (646a5af6)	DIALS Commit via DLS Jenkins	Wed, 11 Oct 2017 16:37:33 +0100	142 lines
[git/dials] master: dials.show: fix max_reflections option (84e7f6d6)	DIALS Commit via DLS Jenkins	Wed, 11 Oct 2017 15:27:17 +0100	90 lines
[git/dials] master: add partiality histogram to dials.report (672862cc)	DIALS Commit via DLS Jenkins	Wed, 11 Oct 2017 15:26:46 +0100	158 lines
[git/dials] master: add partiality.min, partiality.max options to dev.dials.filter_reflections (42b97da7)	DIALS Commit via DLS Jenkins	Wed, 11 Oct 2017 15:25:42 +0100	196 lines
[git/dials] master: fixes #458 - not entirely happy but appears to work for now (baf81255)	DIALS Commit via DLS Jenkins	Wed, 11 Oct 2017 09:45:21 +0100	77 lines
[git/dials] master: Add by_detector to dials.split_experiments, and update test (dbf05c5b)	DIALS Commit via DLS Jenkins	Tue, 10 Oct 2017 09:50:39 -0700	388 lines
[git/dials] master: dials.align_crystal: more informative output (specify rotation order of primary/secondary axes if applicable) (e83c9a85)	DIALS Commit via DLS Jenkins	Tue, 10 Oct 2017 14:18:49 +0100	342 lines
[git/dials_scratch] master: Scaling calculation performed only on nonzero weighted data. (debe6d2)	DIALS Scratch Commit via DLS Jenkins	Tue, 10 Oct 2017 11:30:53 +0100	2016 lines
[git/dials] master: Replace libtbx.property with @property (ac333bb9)	DIALS Commit via DLS Jenkins	Tue, 10 Oct 2017 10:39:33 +0100	96 lines
[git/dials] master: image viewer: add ice rings width control to masking tool (e28397d6)	DIALS Commit via DLS Jenkins	Mon, 9 Oct 2017 16:27:33 +0100	143 lines
[git/dials_scratch] master: Started to implement aimless-like scaling. (5178d8e)	DIALS Scratch Commit via DLS Jenkins	Mon, 9 Oct 2017 15:55:51 +0100	1737 lines
[git/dials] master: Remove extraneous raise in the integrate step. (4b598d01)	DIALS Commit via DLS Jenkins	Thu, 5 Oct 2017 13:24:10 -0700	77 lines
[git/dials_scratch] master: May as well include #pixels, better analysis clearly possible but this is an interesting start (b28f3b5)	DIALS Scratch Commit via DLS Jenkins	Thu, 5 Oct 2017 21:18:09 +0100	77 lines
[git/dials_scratch] master: Override defaults in signal determination (ccc7840)	DIALS Scratch Commit via DLS Jenkins	Thu, 5 Oct 2017 20:36:56 +0100	77 lines
[git/dials_scratch] master: Scratch code to show using signal mask to decide common pixels from image j to j+1 (d4c0ad9)	DIALS Scratch Commit via DLS Jenkins	Thu, 5 Oct 2017 20:36:56 +0100	205 lines
[git/dials_scratch] master: Added test_derivatives.py to test gradient calculation for scaling. (07819af)	DIALS Scratch Commit via DLS Jenkins	Thu, 5 Oct 2017 14:01:21 +0100	432 lines
[git/dials_scratch] master: Scaling code updated to fix error in gradient calculation. (0a6bc1c)	DIALS Scratch Commit via DLS Jenkins	Thu, 5 Oct 2017 11:10:59 +0100	1865 lines
[git/dials] master: Raise default max_iterations for LevMar engine in dials.refine to allow refinement to RMSD convergence for difficult cases, such as the flat Ewald sphere of electron diffraction geometry (5d0f9e92)	DIALS Commit via DLS Jenkins	Wed, 4 Oct 2017 12:46:25 +0100	82 lines
[git/dials_scratch] master: Added some progress towards parallel integrator (06cae08)	DIALS Scratch Commit via DLS Jenkins	Wed, 4 Oct 2017 10:56:45 +0100	80 lines
[git/dials_scratch] master: Add overlap handling in threading code (1cc8987)	DIALS Scratch Commit via DLS Jenkins	Wed, 4 Oct 2017 10:56:45 +0100	338 lines
[git/dials_scratch] master: Added a little script to convert cbf to a hdf5 file (eff8ac8)	DIALS Scratch Commit via DLS Jenkins	Wed, 4 Oct 2017 10:56:45 +0100	115 lines
[git/dials_scratch] master: Adding overlap handling to new integration code (80111d2)	DIALS Scratch Commit via DLS Jenkins	Wed, 4 Oct 2017 10:56:45 +0100	539 lines
[git/dials_scratch] master: Deconvoltion profile fitting also dont compile for others atm (0c314a3)	DIALS Scratch Commit via DLS Jenkins	Wed, 4 Oct 2017 10:56:45 +0100	1281 lines
[git/dials_scratch] master: Use dials thread pool (d1b5416)	DIALS Scratch Commit via DLS Jenkins	Wed, 4 Oct 2017 10:56:45 +0100	1064 lines
[git/dials_scratch] master: adhoc integration (84c9518)	DIALS Scratch Commit via DLS Jenkins	Wed, 4 Oct 2017 10:56:45 +0100	963 lines
[git/dials_scratch] master: Added multi panel support (a3538c0)	DIALS Scratch Commit via DLS Jenkins	Wed, 4 Oct 2017 10:56:45 +0100	2330 lines
[git/dials] master: Revert James' commits regarding the reflection class due to problems with the Windows build. (baadcc6b)	DIALS Commit via DLS Jenkins	Wed, 4 Oct 2017 10:33:22 +0100	1127 lines
[git/dials_scratch] master: Print out more info i.e. dataset if small, dimensions / shape if large, or if scalar say do (39aa18b)	DIALS Scratch Commit via DLS Jenkins	Wed, 4 Oct 2017 09:29:42 +0100	113 lines

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