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Subject	From	Date	Size
[git/dials] master: correct formatting of a table (e5ee62a)	DIALS Commit via DLS Jenkins	Thu, 31 Mar 2016 09:55:37 +0100	87 lines
[git/dials] master: Bugfixes found by a dials.stills_process user. (d720d86)	DIALS Commit via DLS Jenkins	Wed, 30 Mar 2016 12:36:32 -0700	139 lines
[git/dials] master: fix typos etc. (f37b82e)	DIALS Commit via DLS Jenkins	Wed, 30 Mar 2016 16:58:57 +0100	304 lines
[git/dials] master: prefer math formatting for hkl (60d8fd9)	DIALS Commit via DLS Jenkins	Wed, 30 Mar 2016 16:39:49 +0100	94 lines
[git/dials] master: Text and figures for the correcting poor initial geometry tutorial (36b7102)	DIALS Commit via DLS Jenkins	Wed, 30 Mar 2016 16:38:15 +0100	1400 lines
[git/dials] master: add new tutorial to index (5338469)	DIALS Commit via DLS Jenkins	Wed, 30 Mar 2016 16:38:15 +0100	71 lines
[git/dials] master: Move procrunner from dials_regression and i19 module to dials (581cc32)	DIALS Commit via DLS Jenkins	Wed, 30 Mar 2016 15:13:12 +0100	667 lines
[git/dials] master: cleanup (22846ca)	DIALS Commit via DLS Jenkins	Wed, 30 Mar 2016 14:13:16 +0100	835 lines
[git/dials] master: Trap rays scattered into blind region (e2db6d0)	DIALS Commit via DLS Jenkins	Wed, 30 Mar 2016 10:09:10 +0100	154 lines
[git/dials] master: identified prediction order; added test for this (e5905ac)	DIALS Commit via DLS Jenkins	Wed, 30 Mar 2016 08:43:14 +0100	248 lines
[git/dials] master: FIXME for efficient usage; not obvious right now (143317c)	DIALS Commit via DLS Jenkins	Tue, 29 Mar 2016 19:19:26 +0100	78 lines
[git/dials] master: beginnings of a misindexing tutorial (aa40a13)	DIALS Commit via DLS Jenkins	Tue, 29 Mar 2016 17:15:24 +0100	411 lines
[git/dials] master: Clean up, add id_start, id_end to look at sequence of profiles (449685b)	DIALS Commit via DLS Jenkins	Tue, 29 Mar 2016 10:11:16 +0100	170 lines
[git/dials] master: Added debug mode; found crash (angle modulo 2pi problem; debugged / fixed (4ab6004)	DIALS Commit via DLS Jenkins	Mon, 28 Mar 2016 13:02:36 +0100	203 lines
[git/dials] master: Print Isum; start analysis (a852845)	DIALS Commit via DLS Jenkins	Mon, 28 Mar 2016 08:51:05 +0100	79 lines
[git/dials] master: Define min_isum parameter => filter out weakest reflections (not used by default) (1a1a305)	DIALS Commit via DLS Jenkins	Mon, 28 Mar 2016 08:49:03 +0100	102 lines
[git/dials] master: show=true parameter (f61c330)	DIALS Commit via DLS Jenkins	Mon, 28 Mar 2016 08:45:16 +0100	172 lines
[git/dials] master: Fix typo (7fb95ac)	DIALS Commit via DLS Jenkins	Mon, 28 Mar 2016 08:42:13 +0100	75 lines
[git/dials] master: Introduce profile CC calculation; seems sensible (72cd8fd)	DIALS Commit via DLS Jenkins	Mon, 28 Mar 2016 08:41:13 +0100	121 lines
[git/dials] master: Introduce scale as parameter i.e. #rays / count; FIXME on detector physics modelling (3632643)	DIALS Commit via DLS Jenkins	Mon, 28 Mar 2016 08:40:50 +0100	149 lines
[git/dials] master: Add rs_node_size parameter - defines 3D Gaussian in RS... (837a212)	DIALS Commit via DLS Jenkins	Mon, 28 Mar 2016 07:36:48 +0100	367 lines
[git/dials] master: First cut at raytracing, it is not fast or clever, but should give an illustration. Usage: dev.dials.duelling_profiles integrated_experiments.json integrated_shoeboxes.pickle.gz method=rt0 id=19363 output: Removed 5621 invalid reflections, 21825 remain Observed reflection (flattened in Z): (52a46a8)	DIALS Commit via DLS Jenkins	Mon, 28 Mar 2016 07:20:25 +0100	456 lines
[git/dials] master: Better random cone implementation, should be unbiased (e6f1a27)	DIALS Commit via DLS Jenkins	Mon, 28 Mar 2016 07:20:25 +0100	109 lines
[git/dials] master: Prediction code from Kabsch for arbitrary RS point (c5b8c8a)	DIALS Commit via DLS Jenkins	Mon, 28 Mar 2016 07:20:25 +0100	198 lines
[git/dials] master: Allow selection of reflections on command line via id=#; first use of git add -p; like (b047f1c)	DIALS Commit via DLS Jenkins	Mon, 28 Mar 2016 07:20:25 +0100	140 lines
[git/dials_scratch] master: Moved to main branch as cspad.detector_shifts. (1297cd5)	DIALS Scratch Commit via DLS Jenkins	Fri, 25 Mar 2016 17:30:50 -0700	677 lines
[git/dials_scratch] master: Tidying. Autodetermine max_hierarchy_level. (6b48d04)	DIALS Scratch Commit via DLS Jenkins	Fri, 25 Mar 2016 17:25:10 -0700	176 lines
[git/dials_scratch] master: Detector_shifts.py changes (b1bd0f6)	DIALS Scratch Commit via DLS Jenkins	Fri, 25 Mar 2016 17:10:37 -0700	531 lines
[git/dials_scratch] master: detector_shift.py: reformat as table, add X, Y and delta XY shifts. (63d7832)	DIALS Scratch Commit via DLS Jenkins	Fri, 25 Mar 2016 11:44:22 -0700	231 lines
[git/dials] master: larger spherical polar plots, aspect=1 and better title (12b0f7f)	DIALS Commit via DLS Jenkins	Thu, 24 Mar 2016 16:32:01 +0000	99 lines
[git/dials] master: As well as plots of shifts using local panel coordinate frames, also plot shifts in the laboratory frame. This is useful for the CS-PAD, where fast and slow directions differ by 90 degrees between groups of panels. It is less useful for the P12M, where we prefer to 'unwrap the barrel'. For completeness, just produce both types of plots in any case. (b4930d9)	DIALS Commit via DLS Jenkins	Thu, 24 Mar 2016 16:22:38 +0000	236 lines
[git/dials] master: Implement grid_size, guess for known detectors, bug fix for scale of colour bars for panel_grid plots (34740a0)	DIALS Commit via DLS Jenkins	Thu, 24 Mar 2016 16:22:38 +0000	628 lines
[git/dials] master: Tool for Sm / F model (1c41d82)	DIALS Commit via DLS Jenkins	Thu, 24 Mar 2016 15:38:14 +0000	84 lines
[git/dials] master: Make reflections flat; useful for 2D mode (62ac1cc)	DIALS Commit via DLS Jenkins	Thu, 24 Mar 2016 06:25:39 +0000	101 lines
[git/dials_scratch] master: Moved to main xfel branch as cspad.detector_congruence (dbf6aea)	DIALS Scratch Commit via DLS Jenkins	Wed, 23 Mar 2016 14:36:40 -0700	1797 lines
[git/dials_scratch] master: Tidying (bc25630)	DIALS Scratch Commit via DLS Jenkins	Wed, 23 Mar 2016 13:05:10 -0700	319 lines
[git/dials] master: Add tag parameter for controlling output file names (47f1f37)	DIALS Commit via DLS Jenkins	Wed, 23 Mar 2016 12:44:35 -0700	264 lines
[git/dials] master: changes to support different types of plot (e13e229)	DIALS Commit via DLS Jenkins	Wed, 23 Mar 2016 16:01:26 +0000	422 lines
[git/dials] master: new spherical_polar plot option that should work for any detector (b3bbd0d)	DIALS Commit via DLS Jenkins	Wed, 23 Mar 2016 16:01:26 +0000	354 lines
[git/dials] master: don't use goniometer axis here, otherwise get opposite offset to intended if axis = (-1, 0, 0) (b63a433)	DIALS Commit via DLS Jenkins	Wed, 23 Mar 2016 15:36:41 +0000	115 lines
[git/dials] master: Added median background algorithm. Probably shouldn't be used (especially for low background) but useful for comparison of robustness. (d2be030)	DIALS Commit via DLS Jenkins	Wed, 23 Mar 2016 14:27:48 +0000	740 lines
[git/dials] master: bug fix (cf57210)	DIALS Commit via DLS Jenkins	Wed, 23 Mar 2016 13:58:26 +0000	74 lines
[git/dials] master: map_to_asu=True (b3b5112)	DIALS Commit via DLS Jenkins	Wed, 23 Mar 2016 13:58:18 +0000	78 lines
[git/dials] master: incorporate misindexing grid search into dials.index (859a689)	DIALS Commit via DLS Jenkins	Wed, 23 Mar 2016 11:19:23 +0000	566 lines
[git/dials] master: refactor using function call plot_stack_of_panels (d02ae62)	DIALS Commit via DLS Jenkins	Wed, 23 Mar 2016 09:38:38 +0000	337 lines
[git/dials] master: Set real aspect ratio (b3f7f19)	DIALS Commit via DLS Jenkins	Wed, 23 Mar 2016 09:38:38 +0000	159 lines
[git/dials] master: minor fixes for tutorials (e7283e5)	DIALS Commit via DLS Jenkins	Wed, 23 Mar 2016 09:38:38 +0000	115 lines
[git/dials] master: Make nicer by use of OptionParser, help string etc. (ef34c74)	DIALS Commit via DLS Jenkins	Wed, 23 Mar 2016 09:38:37 +0000	551 lines
[git/dials] master: enable compression of reflection pickle files on writing (3e5a45b)	DIALS Commit via DLS Jenkins	Wed, 23 Mar 2016 09:08:28 +0000	80 lines
[git/dials] master: Replace local magic code with libtbx.smart_open.for_reading; thanks @Richard for pointer (56ea6b6)	DIALS Commit via DLS Jenkins	Wed, 23 Mar 2016 08:04:12 +0000	122 lines
[git/dials_scratch] master: Change to only look at Z shift in local frame (71885cb)	DIALS Scratch Commit via DLS Jenkins	Tue, 22 Mar 2016 21:49:54 -0700	156 lines
[git/dials_scratch] master: Detector congruence: improve table output. Detector shifts: bugfix. (0e7ba04)	DIALS Scratch Commit via DLS Jenkins	Tue, 22 Mar 2016 16:13:01 -0700	365 lines
[git/dials] master: Can add multiple methods for model_reflection => do not tread on toes; use method=example to call model_reflection_example etc; uses witchcraft to call right method (be21da1)	DIALS Commit via DLS Jenkins	Tue, 22 Mar 2016 21:58:10 +0000	157 lines
[git/dials] master: Some changes, realise everything about the experiment is needed to predict one reflection including the general impact; also dug out some code to predict the Poissonian background for given mean (cbc5e43)	DIALS Commit via DLS Jenkins	Tue, 22 Mar 2016 19:52:01 +0000	160 lines
[git/dials] master: Mostly there, I think the models which are needed are broadly available, though clearly some bits are missing (i.e. beam etc.) your mileage may vary but can start from here. (c6de8b0)	DIALS Commit via DLS Jenkins	Tue, 22 Mar 2016 19:39:36 +0000	207 lines
[git/dials] master: magic_open: transparent opening of gzip'd pickles, can add bzip2 optionally (trivial); only on read at the moment can be a big help (67ff34e)	DIALS Commit via DLS Jenkins	Tue, 22 Mar 2016 16:41:53 +0000	119 lines
[git/dials] master: Start of stubs for dev.dials.dp (f6b634b)	DIALS Commit via DLS Jenkins	Tue, 22 Mar 2016 16:41:53 +0000	164 lines
[git/dials] master: improvements to tutorial text (f8db042)	DIALS Commit via DLS Jenkins	Tue, 22 Mar 2016 14:31:53 +0000	217 lines
[git/dials] master: It's a copy, not a move (a3ef5e4)	DIALS Commit via DLS Jenkins	Tue, 22 Mar 2016 14:29:24 +0000	70 lines
[git/dials] master: update dev.dials.generate_tutorial_text, update logs it produces (a9b9a80)	DIALS Commit via DLS Jenkins	Tue, 22 Mar 2016 14:00:37 +0000	75 lines
[git/dials] master: updates to processing in detail tutorial (8c1986a)	DIALS Commit via DLS Jenkins	Tue, 22 Mar 2016 12:19:23 +0000	841 lines
[git/dials] master: Changes to update the getting started tutorial (9cfeeb4)	DIALS Commit via DLS Jenkins	Tue, 22 Mar 2016 11:52:01 +0000	346 lines
[git/dials] master: figure for tutorial (3aeed78)	DIALS Commit via DLS Jenkins	Tue, 22 Mar 2016 11:52:01 +0000	340 lines
[git/dials] master: grammar (9f958ce)	DIALS Commit via DLS Jenkins	Tue, 22 Mar 2016 11:52:01 +0000	78 lines
[git/dials] master: Using reflections_per_degree=100 in refine_bravais_settings reduces wall clock time on the I04 BAG training data by an order of magnitude (4066235)	DIALS Commit via DLS Jenkins	Tue, 22 Mar 2016 11:52:01 +0000	90 lines
[git/dials_scratch] master: Detector_congruence features Add draw_normal_arrows: useful for visualizing tilt Add z offsets plot Fix cases where panel groups have no reflections Don't project panels and arrows into the lab space z plane, instead show them relative to the detector face, regardless of its tilt. (e4332bf)	DIALS Scratch Commit via DLS Jenkins	Mon, 21 Mar 2016 14:16:24 -0700	361 lines
[git/dials_scratch] master: Plot 'extents' of each panel group instead of individual panels, respecting the hierarchy_level parameter (3f17769)	DIALS Scratch Commit via DLS Jenkins	Mon, 21 Mar 2016 12:43:46 -0700	439 lines
[git/dials_scratch] master: Bugfix for detector_congruence.py (f2398c9)	DIALS Scratch Commit via DLS Jenkins	Mon, 21 Mar 2016 11:18:14 -0700	155 lines
[git/dials_scratch] master: Show unit cell distribution in printout (fd68849)	DIALS Scratch Commit via DLS Jenkins	Mon, 21 Mar 2016 10:40:29 -0700	129 lines
[git/dials] master: Fixed test (e3daae2)	DIALS Commit via DLS Jenkins	Mon, 21 Mar 2016 17:39:47 +0000	75 lines
[git/dials] master: Added parameter to use input profile parameters (964f04f)	DIALS Commit via DLS Jenkins	Mon, 21 Mar 2016 17:00:54 +0000	110 lines
[git/dials_scratch] master: Script to look at delta Z changes from a reference to a moving detector at 3 hierarchy levels. (f257b73)	DIALS Scratch Commit via DLS Jenkins	Sun, 20 Mar 2016 21:56:05 -0700	363 lines
[git/dials_scratch] master: set local frame instead of global frame (ad0ee69)	DIALS Scratch Commit via DLS Jenkins	Sun, 20 Mar 2016 19:32:13 +0000	90 lines
[git/dials_scratch] master: script to plot multiple reflection profile cc vs resolution plots (93f9e6d)	DIALS Scratch Commit via DLS Jenkins	Sun, 20 Mar 2016 19:32:13 +0000	120 lines
[git/dials] master: add plot of profile correlations vs resolution to dials.report; fix json output (need to add test) (21aff41)	DIALS Commit via DLS Jenkins	Sun, 20 Mar 2016 19:30:17 +0000	268 lines
[git/dials] master: hardcoded layout for I23 detector grid sizes (e2f3d7b)	DIALS Commit via DLS Jenkins	Sun, 20 Mar 2016 19:30:16 +0000	145 lines
[git/dials_scratch] master: Detector congruence update (dac6a07)	DIALS Scratch Commit via DLS Jenkins	Sat, 19 Mar 2016 17:20:40 -0700	397 lines
[git/dials] master: minor change to RMSD by panel table (f515729)	DIALS Commit via DLS Jenkins	Sat, 19 Mar 2016 00:36:26 +0000	80 lines
[git/dials] master: updated test: (3b1b072)	DIALS Commit via DLS Jenkins	Fri, 18 Mar 2016 17:45:11 +0000	100 lines
[git/dials] master: Add check for centroid outliers (8d3c243)	DIALS Commit via DLS Jenkins	Fri, 18 Mar 2016 17:27:07 +0000	83 lines
[git/dials] master: Added background value and variance to mtz file output (d681c0e)	DIALS Commit via DLS Jenkins	Fri, 18 Mar 2016 17:27:07 +0000	557 lines
[git/dials] master: Fixed bug for exporting stills looking for fixed_rotation (1fcebe1)	DIALS Commit via DLS Jenkins	Fri, 18 Mar 2016 17:27:07 +0000	83 lines
[git/dials] master: Move core of the run method to _run_core, shared by LevMar and SparseLevMar (78ce96d)	DIALS Commit via DLS Jenkins	Fri, 18 Mar 2016 15:28:48 +0000	398 lines
[git/dials] master: move SparseLevMar's progress report into a method which is just a placeholder for LevMar so the run methods are unified (5245f0c)	DIALS Commit via DLS Jenkins	Fri, 18 Mar 2016 15:17:11 +0000	172 lines
[git/dials] master: tidying (0bac4da)	DIALS Commit via DLS Jenkins	Fri, 18 Mar 2016 15:03:14 +0000	77 lines
[git/dials] master: abstraction of calls relying on the LSTBX dense matrix interface to two methods, setup_mu and add_constant_to_diagonal, which are overridden by SparseLevenbergMarquardtIterations, which uses the sparse matrix Eigen wrapper (5866763)	DIALS Commit via DLS Jenkins	Fri, 18 Mar 2016 14:59:47 +0000	238 lines
[git/dials] master: Use a set_cholesky_factor method generally, which is overridden by SparseLevMar (79d9344)	DIALS Commit via DLS Jenkins	Fri, 18 Mar 2016 12:55:15 +0000	270 lines
[git/dials] master: tidying (7179318)	DIALS Commit via DLS Jenkins	Fri, 18 Mar 2016 12:19:26 +0000	120 lines
[git/dials] master: Use a mixin DisableMPmixin to disable setting of nproc for engines where this is not allowed (73c46d0)	DIALS Commit via DLS Jenkins	Fri, 18 Mar 2016 12:12:22 +0000	263 lines
[git/dials] master: log the SparseLevMar objective vs mu table, control with verbosity. Note it is harder to log the eigen summary as this is sent to stdout via printf in wrapped C++ code (f14bc2e)	DIALS Commit via DLS Jenkins	Fri, 18 Mar 2016 12:12:21 +0000	132 lines
[git/dials_scratch] master: Moved to cctbx_project/xfel/command_line (0b21f0f)	DIALS Scratch Commit via DLS Jenkins	Thu, 17 Mar 2016 10:58:32 -0700	130 lines
[git/dials] master: Bugfix for multiple files. (deee49c)	DIALS Commit via DLS Jenkins	Thu, 17 Mar 2016 10:28:57 -0700	78 lines
[git/dials_scratch] master: reformulate as inverse scale factor; use unscaled unmerged intensities in calculation of residuals: numbers = better (2731303)	DIALS Scratch Commit via DLS Jenkins	Thu, 17 Mar 2016 11:54:59 +0000	181 lines
[git/dials] master: dev.dials.diffraction_geometry_viewer (ecfd260)	DIALS Commit via DLS Jenkins	Thu, 17 Mar 2016 11:11:54 +0000	267 lines
[git/dials_scratch] master: simple toy batch scaling script (c3f273a)	DIALS Scratch Commit via DLS Jenkins	Thu, 17 Mar 2016 10:50:01 +0000	359 lines
[git/dials_scratch] master: Change panel group center computation (76bfa7c)	DIALS Scratch Commit via DLS Jenkins	Wed, 16 Mar 2016 17:52:29 -0700	247 lines
[git/dials_scratch] master: Squashed commit of the following: (8e09ada)	DIALS Scratch Commit via DLS Jenkins	Wed, 16 Mar 2016 15:00:48 -0700	989 lines
[git/dials] master: Fixed bug when using gain with spot finding (067288c)	DIALS Commit via DLS Jenkins	Wed, 16 Mar 2016 19:06:06 +0000	117 lines
[git/dials] master: fix tests that used scan.get_oscillation incorrectly (467a764)	DIALS Commit via DLS Jenkins	Wed, 16 Mar 2016 16:30:49 +0000	368 lines
[git/dials_scratch] master: fix ylabel (9fb0d4f)	DIALS Scratch Commit via DLS Jenkins	Wed, 16 Mar 2016 14:44:43 +0000	73 lines
[git/dials_scratch] master: add (what I believe to be) chi^2 plot against resolution (5fff56f)	DIALS Scratch Commit via DLS Jenkins	Wed, 16 Mar 2016 14:42:14 +0000	121 lines
[git/dials] master: Fixed test (ab7934d)	DIALS Commit via DLS Jenkins	Wed, 16 Mar 2016 09:12:39 +0000	74 lines
[git/dials_scratch] master: Bugfix, for hierarchy_level=0 (5cdddc0)	DIALS Scratch Commit via DLS Jenkins	Tue, 15 Mar 2016 13:40:00 -0700	248 lines
[git/dials_scratch] master: Bugfix. (1de7c22)	DIALS Scratch Commit via DLS Jenkins	Tue, 15 Mar 2016 13:34:18 -0700	80 lines
[git/dials_scratch] master: Units in each column header (99acf71)	DIALS Scratch Commit via DLS Jenkins	Tue, 15 Mar 2016 13:19:27 -0700	175 lines
[git/dials] master: Different strategy for C++ library includes, compatible with older C++ compilers. (b5ad8c1)	DIALS Commit via DLS Jenkins	Tue, 15 Mar 2016 12:28:06 -0700	74 lines
[git/dials] master: Support standard C++ library includes. (11c5031)	DIALS Commit via DLS Jenkins	Tue, 15 Mar 2016 12:16:47 -0700	72 lines
[git/dials_scratch] master: Add z offsets of each panel group along the detector normal. (4f34090)	DIALS Scratch Commit via DLS Jenkins	Tue, 15 Mar 2016 11:22:34 -0700	313 lines
[git/dials] master: Merge branch 'faster_dp' (3d1813b)	DIALS Commit via DLS Jenkins	Tue, 15 Mar 2016 18:04:12 +0000	138 lines
[git/dials_scratch] master: Sort detector_congruence tables by resolution (acad3bd)	DIALS Scratch Commit via DLS Jenkins	Tue, 15 Mar 2016 10:40:27 -0700	404 lines
[git/dials] master: Fixed bug (427a203)	DIALS Commit via DLS Jenkins	Tue, 15 Mar 2016 17:31:08 +0000	74 lines
[git/dials] master: Do centroid on image volune (cad40ee)	DIALS Commit via DLS Jenkins	Tue, 15 Mar 2016 11:22:55 +0000	629 lines
[git/dials] master: Added some extra info (7201475)	DIALS Commit via DLS Jenkins	Tue, 15 Mar 2016 11:22:55 +0000	442 lines
[git/dials] master: Fixed a couple of bugs (3f08dc6)	DIALS Commit via DLS Jenkins	Tue, 15 Mar 2016 11:22:55 +0000	136 lines
[git/dials] master: Do background with image volume (bec6712)	DIALS Commit via DLS Jenkins	Tue, 15 Mar 2016 11:22:55 +0000	1326 lines
[git/dials] master: Added support in simple background algorithm (eda1093)	DIALS Commit via DLS Jenkins	Tue, 15 Mar 2016 11:22:55 +0000	744 lines
[git/dials] master: Fixed bug. Use pixel fraction to detect where shoebox is over edge of panel (68de26d)	DIALS Commit via DLS Jenkins	Tue, 15 Mar 2016 11:22:55 +0000	696 lines
[git/dials] master: Do summation from image volume (6ffb90b)	DIALS Commit via DLS Jenkins	Tue, 15 Mar 2016 11:22:55 +0000	728 lines
[git/dials] master: Fixed and added check for single imageset (7f2bebe)	DIALS Commit via DLS Jenkins	Tue, 15 Mar 2016 11:22:55 +0000	189 lines
[git/dials] master: Find overlaps (06cd8f2)	DIALS Commit via DLS Jenkins	Tue, 15 Mar 2016 11:22:55 +0000	988 lines
[git/dials] master: Fixed a bit (a727a23)	DIALS Commit via DLS Jenkins	Tue, 15 Mar 2016 11:22:55 +0000	169 lines
[git/dials] master: Made class templated on float type (826bbe6)	DIALS Commit via DLS Jenkins	Tue, 15 Mar 2016 11:22:55 +0000	1231 lines
[git/dials] master: Fixed some bits and added into image integrator (d07a161)	DIALS Commit via DLS Jenkins	Tue, 15 Mar 2016 11:22:54 +0000	409 lines
[git/dials] master: Splitting reflections into partials (f79bafc)	DIALS Commit via DLS Jenkins	Tue, 15 Mar 2016 11:22:54 +0000	615 lines
[git/dials] master: Initial commit of faster dp integrator (16f9cb2)	DIALS Commit via DLS Jenkins	Tue, 15 Mar 2016 11:22:54 +0000	806 lines
[git/dials] master: Do mask calculation on image volume array directly (fe761d8)	DIALS Commit via DLS Jenkins	Tue, 15 Mar 2016 11:22:54 +0000	723 lines
[git/dials] master: Added some more book-keeping for new integrator (ab60ab6)	DIALS Commit via DLS Jenkins	Tue, 15 Mar 2016 11:22:54 +0000	1013 lines
[git/dials] master: Added consistency check and 2d masking (67ccb07)	DIALS Commit via DLS Jenkins	Tue, 15 Mar 2016 11:22:54 +0000	356 lines
[git/dials] master: Added some more book-keeping for fast integrator (fd98886)	DIALS Commit via DLS Jenkins	Tue, 15 Mar 2016 11:22:54 +0000	465 lines
[git/dials] master: Added class to represent image volume (940821f)	DIALS Commit via DLS Jenkins	Tue, 15 Mar 2016 11:22:54 +0000	766 lines
[git/dials_scratch] master: Add rot z to detector_congruence (49ce37d)	DIALS Scratch Commit via DLS Jenkins	Mon, 14 Mar 2016 16:54:39 -0700	286 lines
[git/dials_scratch] master: Add new table to detector congruence (3f0d959)	DIALS Scratch Commit via DLS Jenkins	Mon, 14 Mar 2016 15:56:19 -0700	477 lines
[git/dials] master: Fixed a bit (988b1ec)	DIALS Commit via DLS Jenkins	Mon, 14 Mar 2016 17:51:35 +0000	169 lines
[git/dials] master: Fixed bug. Use pixel fraction to detect where shoebox is over edge of panel (02ff6b9)	DIALS Commit via DLS Jenkins	Mon, 14 Mar 2016 17:08:07 +0000	696 lines
[git/dials] master: Find overlaps (250c6a3)	DIALS Commit via DLS Jenkins	Mon, 14 Mar 2016 16:00:43 +0000	988 lines
[git/dials] master: dials.reindex: allow use of reference to transform experiments.json only (cbaaf83)	DIALS Commit via DLS Jenkins	Mon, 14 Mar 2016 14:22:08 +0000	246 lines
[git/dials] master: fix dials.image_viewer sum_images option (broken by cctbx commit r24000): closes #105 (1ac673a)	DIALS Commit via DLS Jenkins	Mon, 14 Mar 2016 09:40:26 +0000	78 lines
[git/dials_scratch] master: Add radial/transverse RMSDs to table output and change to weighted means/stddevs. (df03f9d)	DIALS Scratch Commit via DLS Jenkins	Sun, 13 Mar 2016 15:00:36 -0700	229 lines
[git/dials_scratch] master: Refactor, moving all plotting code under the show_plots if statement. (6f8042d)	DIALS Scratch Commit via DLS Jenkins	Sun, 13 Mar 2016 14:16:19 -0700	414 lines
[git/dials_scratch] master: Typo (5b11c5e)	DIALS Scratch Commit via DLS Jenkins	Sat, 12 Mar 2016 17:24:18 -0800	87 lines
[git/dials_scratch] master: Add weighted standard deviations (1358aae)	DIALS Scratch Commit via DLS Jenkins	Sat, 12 Mar 2016 17:09:52 -0800	170 lines
[git/dials_scratch] master: Tidy up, removing unused code and a bad plot. (6f054a3)	DIALS Scratch Commit via DLS Jenkins	Sat, 12 Mar 2016 16:38:22 -0800	427 lines
[git/dials_scratch] master: Bit 'o documentation (06251b8)	DIALS Scratch Commit via DLS Jenkins	Sat, 12 Mar 2016 16:04:51 -0800	91 lines
[git/dials_scratch] master: Updates for detctor_congruence (9008ab7)	DIALS Scratch Commit via DLS Jenkins	Sat, 12 Mar 2016 15:30:45 -0800	256 lines
[git/dials] master: Add xfel as a dials dependency as a temporary fix for stills_process (c1f4e47)	DIALS Commit via DLS Jenkins	Sat, 12 Mar 2016 14:16:31 -0800	81 lines
[git/dials_scratch] master: Bug fix (e11d89e)	DIALS Scratch Commit via DLS Jenkins	Sat, 12 Mar 2016 14:01:35 -0800	109 lines
[git/dials_scratch] master: Add deltapsi vs. delta 2 theta plots. (09fda4a)	DIALS Scratch Commit via DLS Jenkins	Sat, 12 Mar 2016 12:59:16 -0800	365 lines
[git/dials] master: Link to 1.1 release. Page will probably need some more polishing. (d48745a)	DIALS Commit via DLS Jenkins	Fri, 11 Mar 2016 22:39:50 +0000	123 lines
[git/dials] master: update developer instructions (027e3b9)	DIALS Commit via DLS Jenkins	Fri, 11 Mar 2016 22:39:47 +0000	148 lines
[git/dials] master: Missing __init__.py file (f78ff00)	DIALS Commit via DLS Jenkins	Fri, 11 Mar 2016 12:30:15 -0800	56 lines
[git/dials] master: Allow to treat merges as a single commit for version number purposes. This is mostly relevant for stable release branches (4b6f815)	DIALS Commit via DLS Jenkins	Fri, 11 Mar 2016 14:25:49 +0000	230 lines
[git/dials_scratch] master: set_frame not set_local_frame (e11cfab)	DIALS Scratch Commit via DLS Jenkins	Fri, 11 Mar 2016 14:19:20 +0000	75 lines
[git/dials_scratch] master: simple script to copy detector metrology, not particularly clever yet (7438896)	DIALS Scratch Commit via DLS Jenkins	Fri, 11 Mar 2016 11:13:51 +0000	234 lines
[git/dials] master: allow dials.split_experiments to work on experiments.json alone (db6b7f2)	DIALS Commit via DLS Jenkins	Fri, 11 Mar 2016 11:10:05 +0000	228 lines
[git/dials] master: Fixed a couple of bugs (880c0b6)	DIALS Commit via DLS Jenkins	Thu, 10 Mar 2016 16:59:59 +0000	136 lines
[git/dials] master: Fixed and added check for single imageset (363cac3)	DIALS Commit via DLS Jenkins	Thu, 10 Mar 2016 16:16:16 +0000	189 lines
[git/dials] master: Made class templated on float type (ffe6734)	DIALS Commit via DLS Jenkins	Thu, 10 Mar 2016 15:58:02 +0000	1231 lines
[git/dials] master: New verbosity levels: 0 - silent, 1 - inexpensive essentials (avoids sorting reflection lists for stats), 2 - standard output for dials.refine, 3 - output of extra (potentially expensive) analysis (6bc9e1b)	DIALS Commit via DLS Jenkins	Thu, 10 Mar 2016 14:21:33 +0000	275 lines
[git/dials] master: Added some extra info (c93d1f9)	DIALS Commit via DLS Jenkins	Thu, 10 Mar 2016 14:19:05 +0000	442 lines
[git/dials] master: Added support in simple background algorithm (8e1a03f)	DIALS Commit via DLS Jenkins	Thu, 10 Mar 2016 13:21:35 +0000	744 lines
[git/dials] master: remove old FIXMEs (c858fbc)	DIALS Commit via DLS Jenkins	Thu, 10 Mar 2016 13:15:24 +0000	100 lines
[git/dials] master: Set Refiner's default verbosity to 0 (silent). dials.refine overrides this to 1 (65fa898)	DIALS Commit via DLS Jenkins	Thu, 10 Mar 2016 13:13:27 +0000	956 lines
[git/dials] master: Do background with image volume (fcb5900)	DIALS Commit via DLS Jenkins	Thu, 10 Mar 2016 12:04:26 +0000	1326 lines
[git/dials_scratch] master: print column type (b7c511d)	DIALS Scratch Commit via DLS Jenkins	Thu, 10 Mar 2016 11:57:24 +0000	72 lines
[git/dials_scratch] master: script to time pickling/unpickling of reflections files and individual columns (3316788)	DIALS Scratch Commit via DLS Jenkins	Thu, 10 Mar 2016 11:43:33 +0000	122 lines
[git/dials] master: call reflections.as_pickle instead of using easy_pickle (6cf383d)	DIALS Commit via DLS Jenkins	Thu, 10 Mar 2016 11:04:22 +0000	79 lines
[git/dials] master: use verbosity to control calculation of the table of top 20 worst reflections. This is expensive and not generally interesting, so calculate and display only if verbosity >= 2 (923f88b)	DIALS Commit via DLS Jenkins	Thu, 10 Mar 2016 10:55:33 +0000	125 lines
[git/dials] master: Do not calculate unit cell errors here. At this point the crystal knows the covariance of its B matrix, so unit cell errors can be calculated as required (0b6c5c5)	DIALS Commit via DLS Jenkins	Thu, 10 Mar 2016 10:55:33 +0000	111 lines
[git/dials] master: don't calculate (or print) stats on matches if verbosity==0 (2d6098b)	DIALS Commit via DLS Jenkins	Thu, 10 Mar 2016 10:55:33 +0000	98 lines
[git/dials] master: lines not needed here now (9e9eaa7)	DIALS Commit via DLS Jenkins	Thu, 10 Mar 2016 10:55:33 +0000	78 lines
[git/dials] master: show up to 100 rows of RMSDs by experiments when verbosity <= 1 (304547e)	DIALS Commit via DLS Jenkins	Thu, 10 Mar 2016 10:55:33 +0000	77 lines
[git/dials] master: Do centroid on image volune (4d0ae41)	DIALS Commit via DLS Jenkins	Thu, 10 Mar 2016 10:51:07 +0000	629 lines
[git/dials] master: speed up some dials.index tests (f677fed)	DIALS Commit via DLS Jenkins	Thu, 10 Mar 2016 10:33:17 +0000	196 lines
[git/dials] master: no point in testing for ice rings beyond minimum d_spacing (wasting cpu cycles) (bb4c1fd)	DIALS Commit via DLS Jenkins	Thu, 10 Mar 2016 10:24:31 +0000	78 lines
[git/dials_scratch] master: Tidying (ebacf3e)	DIALS Scratch Commit via DLS Jenkins	Wed, 9 Mar 2016 15:06:43 -0800	114 lines
[git/dials_scratch] master: More improvements for detector_residuals (bedbeb1)	DIALS Scratch Commit via DLS Jenkins	Wed, 9 Mar 2016 15:02:44 -0800	426 lines
[git/dials] master: correct skipping message (f038a50)	DIALS Commit via DLS Jenkins	Wed, 9 Mar 2016 22:54:17 +0000	145 lines
[git/dials] master: Do summation from image volume (3c35357)	DIALS Commit via DLS Jenkins	Wed, 9 Mar 2016 21:33:12 +0000	728 lines
[git/dials] master: Added consistency check and 2d masking (ee3ce01)	DIALS Commit via DLS Jenkins	Wed, 9 Mar 2016 18:05:59 +0000	356 lines
[git/dials] master: Do mask calculation on image volume array directly (65c7d4e)	DIALS Commit via DLS Jenkins	Wed, 9 Mar 2016 17:58:35 +0000	723 lines
[git/dials] master: use flex.sort_permutation instead of hideously inefficient __builtin__.sorted (de77530)	DIALS Commit via DLS Jenkins	Wed, 9 Mar 2016 17:33:48 +0000	92 lines
[git/dials] master: Fixed some bits and added into image integrator (d85f7eb)	DIALS Commit via DLS Jenkins	Wed, 9 Mar 2016 16:49:05 +0000	409 lines
[git/dials] master: Added class to represent image volume (819cb1e)	DIALS Commit via DLS Jenkins	Wed, 9 Mar 2016 16:34:11 +0000	766 lines
[git/dials] master: bug fix (44450eb)	DIALS Commit via DLS Jenkins	Wed, 9 Mar 2016 15:43:02 +0000	74 lines
[git/dials] master: Splitting reflections into partials (6ddb064)	DIALS Commit via DLS Jenkins	Wed, 9 Mar 2016 13:15:29 +0000	615 lines
[git/dials] master: Added some more book-keeping for new integrator (eb7200d)	DIALS Commit via DLS Jenkins	Wed, 9 Mar 2016 11:51:46 +0000	1013 lines
[git/dials] master: Modified bits using imageset[ function to use get_raw_data to preserve behaviour after changing imageset (413d14b)	DIALS Commit via DLS Jenkins	Wed, 9 Mar 2016 10:20:26 +0000	270 lines
[git/dials_scratch] master: Add overall radial and transverse RMSDs, adjust units of printouts (9c32cef)	DIALS Scratch Commit via DLS Jenkins	Tue, 8 Mar 2016 16:58:09 -0800	182 lines
[git/dials_scratch] master: Refactor, putting the radial and transverse components for each reflection in the reflection table for further use (4890d01)	DIALS Scratch Commit via DLS Jenkins	Tue, 8 Mar 2016 16:46:49 -0800	177 lines
[git/dials_scratch] master: Detector_residuals improvements (55a09b6)	DIALS Scratch Commit via DLS Jenkins	Tue, 8 Mar 2016 13:36:23 -0800	498 lines
[git/dials] master: enable autospin (2f163f5)	DIALS Commit via DLS Jenkins	Tue, 8 Mar 2016 16:30:21 +0000	97 lines
[git/dials] master: Keep references to expose instantiated objects. Add load_image method to load an image by filename (4860145)	DIALS Commit via DLS Jenkins	Tue, 8 Mar 2016 16:20:08 +0000	194 lines
[git/dials] master: Add an event to load an image by file name from another thread (9d86856)	DIALS Commit via DLS Jenkins	Tue, 8 Mar 2016 16:19:30 +0000	184 lines
[git/dials] master: Added some more book-keeping for fast integrator (81cdd88)	DIALS Commit via DLS Jenkins	Tue, 8 Mar 2016 14:46:58 +0000	465 lines
[git/dials] master: Initial commit of faster dp integrator (9462480)	DIALS Commit via DLS Jenkins	Tue, 8 Mar 2016 14:33:37 +0000	806 lines
[git/dials] master: release numbers are now reserved for builds from release branches. Development builds get 1.dev. number (a73ba81)	DIALS Commit via DLS Jenkins	Mon, 7 Mar 2016 12:23:18 +0000	76 lines
[git/dials] tag 'v1.dev' created	DIALS Commit via DLS Jenkins	Mon, 7 Mar 2016 12:23:18 +0000	28 lines
[git/dials] tag 'v1.1.0' created	DIALS Commit via DLS Jenkins	Mon, 7 Mar 2016 11:34:44 +0000	28 lines
[git/dials] master: add MedianUnitCellTie option for cases where unit cells differ a great deal or there are outliers that would affect the mean (571b456)	DIALS Commit via DLS Jenkins	Mon, 7 Mar 2016 10:37:44 +0000	254 lines
[git/dials] master: Fixed test (dc37141)	DIALS Commit via DLS Jenkins	Mon, 7 Mar 2016 10:07:59 +0000	74 lines
[git/dials_scratch] master: Logical fix (5a29b9e)	DIALS Scratch Commit via DLS Jenkins	Mon, 7 Mar 2016 09:59:16 +0000	99 lines
[git/dials] master: Added inscribed resolution limit that works for multi panel detectors. (64370ee)	DIALS Commit via DLS Jenkins	Mon, 7 Mar 2016 09:49:41 +0000	87 lines
[git/dials_scratch] master: Add 2d histogram of pos vs. neg delta psi per image. Intention is to see how many images are biased with either more positive or negative delta psi values. (fe20447)	DIALS Scratch Commit via DLS Jenkins	Sun, 6 Mar 2016 16:39:22 -0800	133 lines
[git/dials] master: A low memory version of unit cell ties to their mean that ignores the gradients of the mean. Gradients are therefore slightly inaccurate, but the restraints Jacobian is much more sparse, so this can be used in big problems (3514bf6)	DIALS Commit via DLS Jenkins	Fri, 4 Mar 2016 23:52:09 +0000	222 lines
[git/dials_scratch] master: Error checking and tidying (927abe8)	DIALS Scratch Commit via DLS Jenkins	Fri, 4 Mar 2016 13:43:06 -0800	342 lines
[git/dials_scratch] master: script for looking at scaling errors (cc58e7c)	DIALS Scratch Commit via DLS Jenkins	Fri, 4 Mar 2016 17:32:27 +0000	283 lines
[git/dials] master: Reorder residuals in group restraints for more efficient block assignment in sparse Jacobian (a609f85)	DIALS Commit via DLS Jenkins	Fri, 4 Mar 2016 16:02:44 +0000	550 lines
[git/dials] master: dials.report: use katex instead of MathJax; new option output.external_dependencies=*remote local embed (5cfcfaf)	DIALS Commit via DLS Jenkins	Fri, 4 Mar 2016 14:41:31 +0000	439 lines
[git/dials] master: add external dependencies for dials.report (9f3e261)	DIALS Commit via DLS Jenkins	Fri, 4 Mar 2016 14:41:31 +0000	294 lines
[git/dials] master: Changed to have both min_spots.overall and min_spots.per_degree. Fixes #94 (2d782e6)	DIALS Commit via DLS Jenkins	Fri, 4 Mar 2016 13:04:14 +0000	216 lines
[git/dials] master: Modified test to ensure arguments are sorted (glob doesn't guarentee this). Also modify -s command line parameter to mean "don't sort" in dials.import. (a581132)	DIALS Commit via DLS Jenkins	Fri, 4 Mar 2016 09:56:27 +0000	126 lines
[git/dials_scratch] master: Add unit cells plot (f747838)	DIALS Scratch Commit via DLS Jenkins	Thu, 3 Mar 2016 15:36:53 -0800	169 lines
[git/dials_scratch] master: Adds and cleans up a ton of plots. These are for the cspad but are generally useful for stills. Plot positional RMSDs, Rayleigh distribution of deltaXY vectors, deltaXY referenced to absolute position or relative to a common center, the same but also for delta psi, the Sauter/Poon 2010 cummulative distribution function, and N reflections. (e173627)	DIALS Scratch Commit via DLS Jenkins	Thu, 3 Mar 2016 14:46:52 -0800	1471 lines
[git/dials] master: Changed min_spots to min_spots_per_degree. Often fails for small wedges of data otherwise. (8ce08cb)	DIALS Commit via DLS Jenkins	Thu, 3 Mar 2016 13:45:20 +0000	165 lines
[git/dials] master: Added checks for multiporcessing on windows. Print a warning if nproc>1. Fixes #39 (4e34237)	DIALS Commit via DLS Jenkins	Thu, 3 Mar 2016 11:43:32 +0000	202 lines
[git/dials] master: change default output filename (21de26e)	DIALS Commit via DLS Jenkins	Thu, 3 Mar 2016 10:58:51 +0000	99 lines
[git/dials] master: new block_size option for slicing a single scan into blocks. Useful for testing static refinement in small blocks (like the other programs do) (ce4eec0)	DIALS Commit via DLS Jenkins	Thu, 3 Mar 2016 10:53:30 +0000	360 lines
[git/dials] master: move calculate_frame_numbers to refinement_helpers to share between refine and slice_sweep (042e6f7)	DIALS Commit via DLS Jenkins	Thu, 3 Mar 2016 10:53:30 +0000	360 lines
[git/dials] master: Fixed test (5b3564b)	DIALS Commit via DLS Jenkins	Thu, 3 Mar 2016 09:45:05 +0000	79 lines
[git/dials] master: Make worst 20 positional residuals into a simple_table for stills, like it is for scans (13bec1a)	DIALS Commit via DLS Jenkins	Wed, 2 Mar 2016 11:52:55 +0000	159 lines
[git/dials] master: Add table of number of outliers detected per experiment to debug log for multi-experiment refinements. Warn if more than 30% of reflections are detected as outliers for any experiment (51e36bb)	DIALS Commit via DLS Jenkins	Wed, 2 Mar 2016 11:52:55 +0000	177 lines
[git/dials] master: Added a parameter to throw an exception if multiple sweeps are found. In most cases, people will probably only want to import a single sweep at a time in any case. The problem is that often if multiple sweeps are imported, it means there is something wrong with the image headers. This usually results in an indexing failure and is one of the most common DIALS failures I've seen at CCP4 workshops. Having this check will hopefully mean that the reason for failure is clearer. The old behaviour can be selected by setting the parameter allow_multiple_sweeps=True (3aa231c)	DIALS Commit via DLS Jenkins	Wed, 2 Mar 2016 10:47:21 +0000	293 lines
[git/dials] master: Use the same logic for matching parameter names in col_select as for fix_list. Rename and move the function that does this to refinement_helpers (a8c06e5)	DIALS Commit via DLS Jenkins	Wed, 2 Mar 2016 10:15:01 +0000	458 lines
[git/dials] master: remove save_matrix option (it might as well always be true) (a142fd7)	DIALS Commit via DLS Jenkins	Wed, 2 Mar 2016 09:42:49 +0000	177 lines
[git/dials] master: more generic name (a984b9e)	DIALS Commit via DLS Jenkins	Wed, 2 Mar 2016 09:37:07 +0000	130 lines
[git/dials] master: move parameter_correlation_plot to refinement_helpers to support creation of correlation plots without a Refiner (e78a7a6)	DIALS Commit via DLS Jenkins	Wed, 2 Mar 2016 09:34:15 +0000	412 lines
[git/dials] master: remove dash from version numbers (4f1541c)	DIALS Commit via DLS Jenkins	Wed, 2 Mar 2016 09:10:00 +0000	83 lines
[git/dials] master: keep unindexed (id<0) points white (6d0cb2e)	DIALS Commit via DLS Jenkins	Wed, 2 Mar 2016 08:22:56 +0000	98 lines
[git/dials] master: I tried to merge a feature branch back into the master branch and managed to get my git repository in such a state that I had no idea how to recover. Therefore, I've done like the XKCD cartoon, copied my local changes, cloned a new repository and I'm applying all my changes now! For our resident XKCD fans: https://xkcd.com/1597/ (79acbc1)	DIALS Commit via DLS Jenkins	Tue, 1 Mar 2016 17:40:04 +0000	206 lines
[git/dials] master: Moved peak_finding to spot_finding (496cf49)	DIALS Commit via DLS Jenkins	Tue, 1 Mar 2016 17:40:03 +0000	146 lines
[git/dials] master: dials.show: calculate beam centre if possible (9966d2b)	DIALS Commit via DLS Jenkins	Tue, 1 Mar 2016 16:27:27 +0000	227 lines
[git/dials] master: split col_select if comma-separated, and don't crash if the selection is invalid (d7d851d)	DIALS Commit via DLS Jenkins	Tue, 1 Mar 2016 16:15:23 +0000	248 lines
[git/dials] master: remove limitation of 7 experiments/imagesets; instead recycle colours (ef24fd8)	DIALS Commit via DLS Jenkins	Tue, 1 Mar 2016 13:13:44 +0000	87 lines
[git/dials] master: move this outside of two for loops to avoid multiple warnings (2d13c9c)	DIALS Commit via DLS Jenkins	Tue, 1 Mar 2016 11:15:34 +0000	140 lines

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