| 505b47c | Keitaro Yamashita | 28 January 2016, 08:02:14 UTC | Update README.md | 28 January 2016, 08:02:14 UTC |
| 5e45205 | Keitaro Yamashita | 28 January 2016, 07:45:57 UTC | Add README.md | 28 January 2016, 07:48:25 UTC |
| aa4dc5a | bkpoon | 27 January 2016, 01:13:45 UTC | Ensemble Refinement GUI: bug fix for displaying dihedrals when some atoms for dihedral calculation are missing git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23649 3c1a6239-ac2c-0410-bc49-92500e444112 | 27 January 2016, 01:13:45 UTC |
| b4cdf78 | phyy-nx | 26 January 2016, 23:59:21 UTC | Eiger corner cases: Handle detector position at 0,0,0 Handle oscillation of 0 git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23648 3c1a6239-ac2c-0410-bc49-92500e444112 | 26 January 2016, 23:59:21 UTC |
| 5617533 | afonine | 26 January 2016, 23:42:30 UTC | New command to mask out a region in map for Fo-Fc git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23647 3c1a6239-ac2c-0410-bc49-92500e444112 | 26 January 2016, 23:42:30 UTC |
| f89be64 | nwmoriarty | 26 January 2016, 23:38:50 UTC | changed the version of Rosetta and started adding AFITT git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23646 3c1a6239-ac2c-0410-bc49-92500e444112 | 26 January 2016, 23:38:50 UTC |
| 766399b | tterwill | 26 January 2016, 20:33:15 UTC | clean clutter git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23645 3c1a6239-ac2c-0410-bc49-92500e444112 | 26 January 2016, 20:33:15 UTC |
| 1a2abd6 | tterwill | 26 January 2016, 20:26:50 UTC | Minor changes to keep sequences in sorting models and sequences git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23644 3c1a6239-ac2c-0410-bc49-92500e444112 | 26 January 2016, 20:26:50 UTC |
| bee7f38 | olegsobolev | 26 January 2016, 19:12:18 UTC | bugfix with test. git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23643 3c1a6239-ac2c-0410-bc49-92500e444112 | 26 January 2016, 19:12:18 UTC |
| bcecf15 | olegsobolev | 26 January 2016, 18:07:52 UTC | Suppress calls to unnecessary functions. git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23642 3c1a6239-ac2c-0410-bc49-92500e444112 | 26 January 2016, 18:07:52 UTC |
| 031ef42 | luc_j_bourhis | 26 January 2016, 16:40:26 UTC | Make test on twin refinement less strict git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23641 3c1a6239-ac2c-0410-bc49-92500e444112 | 26 January 2016, 16:40:26 UTC |
| 568dc76 | luc_j_bourhis | 26 January 2016, 16:37:00 UTC | Fix overzealous edit in rev 23639 git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23640 3c1a6239-ac2c-0410-bc49-92500e444112 | 26 January 2016, 16:37:00 UTC |
| d020797 | luc_j_bourhis | 26 January 2016, 16:27:44 UTC | Remove dead code from SConscript git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23639 3c1a6239-ac2c-0410-bc49-92500e444112 | 26 January 2016, 16:27:44 UTC |
| f6f10be | luc_j_bourhis | 26 January 2016, 14:07:41 UTC | Add a public typedef for rank-n update template parameter git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23638 3c1a6239-ac2c-0410-bc49-92500e444112 | 26 January 2016, 14:07:41 UTC |
| 81e9d8e | luc_j_bourhis | 26 January 2016, 14:07:33 UTC | Make normal equation building and Cholesky truly generic on float type git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23637 3c1a6239-ac2c-0410-bc49-92500e444112 | 26 January 2016, 14:07:33 UTC |
| 31e4804 | luc_j_bourhis | 26 January 2016, 14:07:23 UTC | Comment on class sum_of_symmetric_rank_1_updates git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23636 3c1a6239-ac2c-0410-bc49-92500e444112 | 26 January 2016, 14:07:23 UTC |
| cdaeeb7 | luc_j_bourhis | 26 January 2016, 13:50:49 UTC | Command-line smtbx.refine allows Q-peaks amidst atoms git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23635 3c1a6239-ac2c-0410-bc49-92500e444112 | 26 January 2016, 13:50:49 UTC |
| dfeebdd | luc_j_bourhis | 26 January 2016, 13:50:40 UTC | Construction of smtbx model from .res file with Q peaks amidst atoms git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23634 3c1a6239-ac2c-0410-bc49-92500e444112 | 26 January 2016, 13:50:40 UTC |
| b4e4d92 | luc_j_bourhis | 26 January 2016, 13:29:52 UTC | Windows support for tbxx::time_accu git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23633 3c1a6239-ac2c-0410-bc49-92500e444112 | 26 January 2016, 13:29:52 UTC |
| de913b6 | luc_j_bourhis | 26 January 2016, 13:01:12 UTC | French cl.exe prints "version", not "Version"!! git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23632 3c1a6239-ac2c-0410-bc49-92500e444112 | 26 January 2016, 13:01:12 UTC |
| 5ba7fba | luc_j_bourhis | 26 January 2016, 13:01:04 UTC | Fix test of exercise_retrieve_unless_exists on Windows git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23631 3c1a6239-ac2c-0410-bc49-92500e444112 | 26 January 2016, 13:01:04 UTC |
| e66ee2c | olegsobolev | 26 January 2016, 00:59:28 UTC | In NCS find procedure: quotes around chain_id. Stop renaming empty chain ids! Updated tests. git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23630 3c1a6239-ac2c-0410-bc49-92500e444112 | 26 January 2016, 00:59:28 UTC |
| 81ee115 | phyy-nx | 25 January 2016, 23:50:57 UTC | Clean up and bug fixes for xfel image averaging. CSPAD CBFs can average without a psana config file now. git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23629 3c1a6239-ac2c-0410-bc49-92500e444112 | 25 January 2016, 23:50:57 UTC |
| 6274f95 | nksauter | 25 January 2016, 05:03:41 UTC | Guarantee that the supposed sparse::matrix data actually contributes no zero values, thus protecting against memory error caused if the triplet list gets too big. git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23628 3c1a6239-ac2c-0410-bc49-92500e444112 | 25 January 2016, 05:03:41 UTC |
| e73a6a9 | nksauter | 23 January 2016, 01:19:36 UTC | Convert characters in web form input to HTML-safe sequences. git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23627 3c1a6239-ac2c-0410-bc49-92500e444112 | 23 January 2016, 01:19:36 UTC |
| 67028fa | bkpoon | 22 January 2016, 21:07:56 UTC | Ensemble Refinement: bug fix for displaying chain selection containing a blank chain id git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23626 3c1a6239-ac2c-0410-bc49-92500e444112 | 22 January 2016, 21:07:56 UTC |
| ae92ff5 | bkpoon | 22 January 2016, 17:55:32 UTC | Ensemble Refinement GUI: improved clustering of dihedral distributions around mean git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23625 3c1a6239-ac2c-0410-bc49-92500e444112 | 22 January 2016, 17:55:32 UTC |
| f171b52 | mgerstel | 22 January 2016, 13:23:39 UTC | remove unused import git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23624 3c1a6239-ac2c-0410-bc49-92500e444112 | 22 January 2016, 13:23:39 UTC |
| 1835c5c | mgerstel | 22 January 2016, 13:09:47 UTC | Refactor dxtbx format classes to lazily create cbf_handles. Internally use self._get_cbf_handle() instead of self._cbf_handle to access the handle. It will then be initialized if necessary. This saves time in those cases where the handle itself is not actually required, eg. in the first pass of dials.import. git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23623 3c1a6239-ac2c-0410-bc49-92500e444112 | 22 January 2016, 13:09:47 UTC |
| 92822b6 | mgerstel | 22 January 2016, 12:44:44 UTC | notation fixes git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23622 3c1a6239-ac2c-0410-bc49-92500e444112 | 22 January 2016, 12:44:44 UTC |
| 57612fe | mgerstel | 22 January 2016, 12:43:00 UTC | _cbf_handle is already set in the superclass git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23621 3c1a6239-ac2c-0410-bc49-92500e444112 | 22 January 2016, 12:43:00 UTC |
| f212afe | monarin | 22 January 2016, 02:30:52 UTC | Optimizing computing time and coding (should see 4-5 folds improvement in computing time). git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23620 3c1a6239-ac2c-0410-bc49-92500e444112 | 22 January 2016, 02:30:52 UTC |
| 47edc7c | bkpoon | 22 January 2016, 00:45:26 UTC | Ensemble Refinement GUI: Added button to save output statistics git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23619 3c1a6239-ac2c-0410-bc49-92500e444112 | 22 January 2016, 00:45:26 UTC |
| fc791d1 | phyy-nx | 22 January 2016, 00:35:55 UTC | Add dxtbx tests to the cctbx nightly regression git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23618 3c1a6239-ac2c-0410-bc49-92500e444112 | 22 January 2016, 00:35:55 UTC |
| a3b9100 | phyy-nx | 21 January 2016, 22:51:12 UTC | Bugfix for CSPAD CBF. Change section column name. Thanks to Herbert Bernstein for pointing it out. git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23617 3c1a6239-ac2c-0410-bc49-92500e444112 | 21 January 2016, 22:51:12 UTC |
| bcb78b8 | phyy-nx | 21 January 2016, 22:41:42 UTC | Add underload for CSPAD CBFs git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23616 3c1a6239-ac2c-0410-bc49-92500e444112 | 21 January 2016, 22:41:42 UTC |
| 06900dd | luc_j_bourhis | 21 January 2016, 22:30:40 UTC | Retrieve file from URL unless already done, based on digest comparison git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23615 3c1a6239-ac2c-0410-bc49-92500e444112 | 21 January 2016, 22:30:40 UTC |
| 98e0d1d | luc_j_bourhis | 21 January 2016, 22:30:32 UTC | Use tempfile to create a temporary dir instead of polluting current dir git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23614 3c1a6239-ac2c-0410-bc49-92500e444112 | 21 January 2016, 22:30:32 UTC |
| f00dfb6 | bkpoon | 21 January 2016, 18:41:28 UTC | Ensemble Refinement: added panel for looking at dihedral angle distributions in ensemble of models git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23613 3c1a6239-ac2c-0410-bc49-92500e444112 | 21 January 2016, 18:41:28 UTC |
| 0e5d11c | bkpoon | 21 January 2016, 18:37:17 UTC | Added options for setting x and y limits to histogram plots git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23612 3c1a6239-ac2c-0410-bc49-92500e444112 | 21 January 2016, 18:37:17 UTC |
| 851d093 | phyy-nx | 21 January 2016, 18:12:23 UTC | Refactor to use dxtbx. Code only used in dials_regression to test iotbx and dxtbx and in iotbx/command_line/detector_image_as_png.py. The latter could be refactored to use dxtbx and this code could be moved to dials_regression in the future. git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23611 3c1a6239-ac2c-0410-bc49-92500e444112 | 21 January 2016, 18:12:23 UTC |
| b5f99cb | phyy-nx | 21 January 2016, 02:09:15 UTC | Refactor of dxtbx to clean up behavior of get_raw_data(). Summary: For certain dxtbx Format classes, the get_raw_data() method can sometimes take an optional index parameter, but its meaning wasn't consistent. For multi-panel images this parameter was being used to refer to panel number, and multi-file images, such as HDF5, index was being used to refer to image number within the file. Here, all instances of the former are removed. get_raw_data() now has the following behavior: -Single panel: return a flex array. -Multi panel: return a tuple of flex arrays. -Single image: no index parameter allowed (will raise an exception). -Multi image: index parameter accepted. Generally, if the user uses the dxtbx ImageSet class, they will get a reader that will handle these cases for them. Details: 1) Change the behavior of get_raw_data for 5 format classes: - Remove index=None from the get_raw_data method signature - Always return a tuple of asics Classes affected: FormatCBFMiniPilatusDLS12M, FormatCBFMiniPilatusDLS6MSN100, FormatCBFMultiTile, FormatCBFMultiTileHierarchy, and FormatPYmultitile. 2) Change some read and iterate functions of imageset.py to not assemble arrays of multipanel data. Let the format class do this. 3) Fixes throughout the sources to remove instance where the code was assembling arrays of multipanel data. Affects the image viewer and some xfel and dxtbx command line scripts. git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23610 3c1a6239-ac2c-0410-bc49-92500e444112 | 21 January 2016, 02:09:15 UTC |
| a518193 | mgerstel | 20 January 2016, 15:20:46 UTC | fix test git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23609 3c1a6239-ac2c-0410-bc49-92500e444112 | 20 January 2016, 15:20:46 UTC |
| ce64e9d | jmp85 | 20 January 2016, 14:43:30 UTC | Changed detector == to use geometry info git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23608 3c1a6239-ac2c-0410-bc49-92500e444112 | 20 January 2016, 14:43:30 UTC |
| 61c6cfd | mgerstel | 20 January 2016, 13:24:37 UTC | Just in case also test for equality of detector objects git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23607 3c1a6239-ac2c-0410-bc49-92500e444112 | 20 January 2016, 13:24:37 UTC |
| 35ceca8 | mgerstel | 20 January 2016, 12:56:14 UTC | fix dials test git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23606 3c1a6239-ac2c-0410-bc49-92500e444112 | 20 January 2016, 12:56:14 UTC |
| 902205d | mgerstel | 20 January 2016, 11:52:27 UTC | Workaround for ill-defined equality operators for detector objects. git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23605 3c1a6239-ac2c-0410-bc49-92500e444112 | 20 January 2016, 11:52:27 UTC |
| e05317d | mgerstel | 20 January 2016, 11:48:47 UTC | Equality operator on detector objects is ill-defined. Currently it picks up differences in name, but not in setting. Add test to demonstrate this. git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23604 3c1a6239-ac2c-0410-bc49-92500e444112 | 20 January 2016, 11:48:47 UTC |
| f6a81f0 | jmp85 | 20 January 2016, 11:35:59 UTC | Fixed bug in h5py string length git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23603 3c1a6239-ac2c-0410-bc49-92500e444112 | 20 January 2016, 11:35:59 UTC |
| fa88a2f | phyy-nx | 20 January 2016, 07:06:03 UTC | Updates for xfel_process: Remove explicit refinement step as it done during stills indexing Add writing cxi.merge style integration pickles during integration Remove mtz step git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23602 3c1a6239-ac2c-0410-bc49-92500e444112 | 20 January 2016, 07:06:03 UTC |
| c79ceee | olegsobolev | 20 January 2016, 03:55:30 UTC | Bugfixes in iselection->string procedure with tests. git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23601 3c1a6239-ac2c-0410-bc49-92500e444112 | 20 January 2016, 03:55:30 UTC |
| 3407964 | chrisjwilliams | 19 January 2016, 20:54:08 UTC | variable-naming bugfix to cablam oneline output git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23600 3c1a6239-ac2c-0410-bc49-92500e444112 | 19 January 2016, 20:54:08 UTC |
| 05505ef | jmp85 | 19 January 2016, 18:38:10 UTC | Fixed libtbx_find_unused_impoort git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23599 3c1a6239-ac2c-0410-bc49-92500e444112 | 19 January 2016, 18:38:10 UTC |
| 82e164b | jmp85 | 19 January 2016, 18:32:45 UTC | Added a format class for eiger "nearly nexus" files. NOTE that this format is a bit hacky. A temp file is made in /tmp which is the fixed nexus file. This is then read back in. I could probably make this better but it means that I can otherwise reuse the Nexus code. git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23598 3c1a6239-ac2c-0410-bc49-92500e444112 | 19 January 2016, 18:32:45 UTC |
| 710918e | jmp85 | 19 January 2016, 15:41:49 UTC | Add method to make format instance null in single file reader. Hack to fix paralleism for HDF5 files which doesn't work due to the use of os.fork. git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23597 3c1a6239-ac2c-0410-bc49-92500e444112 | 19 January 2016, 15:41:49 UTC |
| 41d634f | mgerstel | 19 January 2016, 08:52:34 UTC | Do not build with --download-only parameter given git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23596 3c1a6239-ac2c-0410-bc49-92500e444112 | 19 January 2016, 08:52:34 UTC |
| 93ab981 | gaborb | 18 January 2016, 10:04:18 UTC | Allow spaces in names for CLUSTAL alignments git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23595 3c1a6239-ac2c-0410-bc49-92500e444112 | 18 January 2016, 10:04:18 UTC |
| b80143c | idyoung | 16 January 2016, 01:29:50 UTC | Example plugin. Drop "_hidden" from the filename to get it to be picked up by cctbx.image_viewer. git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23594 3c1a6239-ac2c-0410-bc49-92500e444112 | 16 January 2016, 01:29:50 UTC |
| e7b38f7 | graeme_winter | 15 January 2016, 16:31:10 UTC | Comment about application of this format git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23593 3c1a6239-ac2c-0410-bc49-92500e444112 | 15 January 2016, 16:31:10 UTC |
| 87471e4 | phyy-nx | 14 January 2016, 18:55:59 UTC | Cross-platform fixes for Dectris HDF5 LZ4/bitshuffle plugin. Remove -march=native, remove reference to homebrew/macports and remove openmp. git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23592 3c1a6239-ac2c-0410-bc49-92500e444112 | 14 January 2016, 18:55:59 UTC |
| a4ad6da | jmp85 | 14 January 2016, 15:29:53 UTC | Added pixel mask to Nexus format stuff git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23591 3c1a6239-ac2c-0410-bc49-92500e444112 | 14 January 2016, 15:29:53 UTC |
| 7a52d77 | phyy-nx | 14 January 2016, 05:03:01 UTC | For Nexus files, add support for LZ4 and LZ4 bitshuffle compression using a plugin. The environment variable HDF5_PLUGIN_PATH is set here before any module-level imports are done as the path is needed at load time for the hdf5 plugin. Suggestions for cleaner ways to do this are welcome :) git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23590 3c1a6239-ac2c-0410-bc49-92500e444112 | 14 January 2016, 05:03:01 UTC |
| 9a281a8 | phyy-nx | 14 January 2016, 05:00:04 UTC | Add LZ4 and LZ4 bitshuffle compression support from Dectris for Dectris HDF5 files. git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23589 3c1a6239-ac2c-0410-bc49-92500e444112 | 14 January 2016, 05:00:04 UTC |
| e9bd174 | idyoung | 14 January 2016, 01:16:46 UTC | Set up to allow additional, custom overlays in cctbx.image_viewer. Anything ending in _frame_plugin.py in the same directory will be found and imported. Plugins must have a PluginHelper class that has class attributes _plugin_title, _plugin_hide_text, _plugin_show_text, and _plugin_settings_frame. git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23588 3c1a6239-ac2c-0410-bc49-92500e444112 | 14 January 2016, 01:16:46 UTC |
| ecefd46 | graeme_winter | 13 January 2016, 12:03:40 UTC | Remove debug git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23587 3c1a6239-ac2c-0410-bc49-92500e444112 | 13 January 2016, 12:03:40 UTC |
| 6d6831f | graeme_winter | 13 January 2016, 08:57:36 UTC | Putative support for Rigaku Eiger 1M and Pilatus 300K detectors; Eiger needs more testing (beam centre not read right?) git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23586 3c1a6239-ac2c-0410-bc49-92500e444112 | 13 January 2016, 08:57:36 UTC |
| 5245994 | olegsobolev | 12 January 2016, 23:04:30 UTC | Rewritten procedure for conversion from iselection to string selection. Updated tests. git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23585 3c1a6239-ac2c-0410-bc49-92500e444112 | 12 January 2016, 23:04:30 UTC |
| 5caa6ce | olegsobolev | 12 January 2016, 23:01:35 UTC | Some comments. git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23584 3c1a6239-ac2c-0410-bc49-92500e444112 | 12 January 2016, 23:01:35 UTC |
| a4e27a4 | mgerstel | 12 January 2016, 09:09:34 UTC | Use --rebase instead of --ff-only to update a git repository, as this can deal with rewritten revision histories. Add a note on what to do if this build step fails. git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23583 3c1a6239-ac2c-0410-bc49-92500e444112 | 12 January 2016, 09:09:34 UTC |
| 27f8936 | olegsobolev | 11 January 2016, 19:54:07 UTC | clean clutter git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23582 3c1a6239-ac2c-0410-bc49-92500e444112 | 11 January 2016, 19:54:07 UTC |
| 7b82667 | olegsobolev | 11 January 2016, 19:47:28 UTC | New core procedure for grouping NCS chains. No more attempts to group several chains in one selection. Number of improvements in related fuctions, e.g. iselections to string conversion. A lot of debugging print outs are left (commented) to facilitate further debugging. May be cleared later. git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23581 3c1a6239-ac2c-0410-bc49-92500e444112 | 11 January 2016, 19:47:28 UTC |
| e4f6f6f | mgerstel | 11 January 2016, 17:00:57 UTC | Do not use 'new' python syntax here. Code will be run by system python. git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23580 3c1a6239-ac2c-0410-bc49-92500e444112 | 11 January 2016, 17:00:57 UTC |
| 56e05d3 | nksauter | 09 January 2016, 21:59:10 UTC | Implement an add_equations() function within the non-linear least squares Eigen wrapper. Function signature accepts a CCTBX-sparse type Jacobian matrix. Intended use is within the SparseLevMar refinement algorithm of the DIALS refinery. git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23579 3c1a6239-ac2c-0410-bc49-92500e444112 | 09 January 2016, 21:59:10 UTC |
| eed7ce2 | nksauter | 09 January 2016, 00:20:05 UTC | Bugfix commit to avoid a divide by zero when reference intensities don't cover the entire resolution range. git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23578 3c1a6239-ac2c-0410-bc49-92500e444112 | 09 January 2016, 00:20:05 UTC |
| 56c1a5c | luc_j_bourhis | 09 January 2016, 00:10:37 UTC | Optional modules configured only if explicitly requested on cmd line git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23577 3c1a6239-ac2c-0410-bc49-92500e444112 | 09 January 2016, 00:10:37 UTC |
| 62b1587 | luc_j_bourhis | 09 January 2016, 00:10:30 UTC | Record the modules explicitly specified on the command-line git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23576 3c1a6239-ac2c-0410-bc49-92500e444112 | 09 January 2016, 00:10:30 UTC |
| 7c14329 | luc_j_bourhis | 09 January 2016, 00:10:20 UTC | Efficient computation of MD5 digest for potentially very large files git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23575 3c1a6239-ac2c-0410-bc49-92500e444112 | 09 January 2016, 00:10:20 UTC |
| e2e1b13 | phyy-nx | 08 January 2016, 21:36:05 UTC | Script to find high resolution shots from XFEL data Example usage: cxi.find_highres_shots data=r000[6-9]/001/integration data=r001[1-4]/001/integration min_good_reflections=100 min_IsigI=10 This looks at each integration pickle and selects the strong reflections (I/sigI >= 10). Then, we throw out all images with less than 100 strong reflections. For the images that are left, we find the 10 images whose strong reflections diffract to the highest resolution. The command prints out a cctbx.image_viewer command you can directly run to see these images. git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23574 3c1a6239-ac2c-0410-bc49-92500e444112 | 08 January 2016, 21:36:05 UTC |
| 5bba2a2 | tmmclark | 08 January 2016, 20:15:01 UTC | changed process_reference function and indexed variable to match the DIALS updated process_reference function and return tuple git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23573 3c1a6239-ac2c-0410-bc49-92500e444112 | 08 January 2016, 20:15:01 UTC |
| 9ca09e0 | jmp85 | 08 January 2016, 16:39:31 UTC | Added checks in print_header and made Format class return None for beam/detctor/goniometer etc by default git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23572 3c1a6239-ac2c-0410-bc49-92500e444112 | 08 January 2016, 16:39:31 UTC |
| 3fa4519 | rjgildea | 08 January 2016, 14:38:45 UTC | humans generally like to start counting from 1 git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23571 3c1a6239-ac2c-0410-bc49-92500e444112 | 08 January 2016, 14:38:45 UTC |
| 55735d9 | jmp85 | 08 January 2016, 11:03:03 UTC | Fixed bug by chaning __cmp__ to __eq__. git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23570 3c1a6239-ac2c-0410-bc49-92500e444112 | 08 January 2016, 11:03:03 UTC |
| acd9e0d | rjgildea | 07 January 2016, 09:50:29 UTC | fix compatible with wxPython 2.8 and 3.0.1 git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23569 3c1a6239-ac2c-0410-bc49-92500e444112 | 07 January 2016, 09:50:29 UTC |
| a6490ff | alyubimov | 07 January 2016, 02:10:48 UTC | IOTA v2.24; cleaned clutter (One trailing space. One.) git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23568 3c1a6239-ac2c-0410-bc49-92500e444112 | 07 January 2016, 02:10:48 UTC |
| 65d0f8c | alyubimov | 07 January 2016, 02:01:59 UTC | IOTA v2.24, bug fixes and minor adjustments Bug fixes: 1. Smart search no longer returns zeroes for spotfinding params in some cases. 2. Heatmap automatically turned off when no grid search is selected (would cause exceptions before) New Features: 1. image_conversion.distance option to override crystal to detector distance 2. new cctbx.xfel settings now included in the target file 3. new grid search settings ("None", "brute_force" and "smart") git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23567 3c1a6239-ac2c-0410-bc49-92500e444112 | 07 January 2016, 02:01:59 UTC |
| b8264f4 | bkpoon | 06 January 2016, 22:29:28 UTC | Comprehensive Validation GUI: fixed display for RNA pucker outlier results git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23566 3c1a6239-ac2c-0410-bc49-92500e444112 | 06 January 2016, 22:29:28 UTC |
| 06e5791 | rjgildea | 06 January 2016, 15:29:52 UTC | apparent fix for opengl viewer resizing bug with wxpython 3.0.2 on mac and linux git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23565 3c1a6239-ac2c-0410-bc49-92500e444112 | 06 January 2016, 15:29:52 UTC |
| 060a4c3 | bkpoon | 06 January 2016, 00:46:56 UTC | Comprehensive Validation GUI: updated to show RNA results git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23564 3c1a6239-ac2c-0410-bc49-92500e444112 | 06 January 2016, 00:46:56 UTC |
| a24b16a | rjgildea | 05 January 2016, 10:19:12 UTC | fix bug introduced by r23501 git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23563 3c1a6239-ac2c-0410-bc49-92500e444112 | 05 January 2016, 10:19:12 UTC |
| a3c1ef3 | graeme_winter | 05 January 2016, 10:06:29 UTC | Right now; just ignore missing mask... git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23562 3c1a6239-ac2c-0410-bc49-92500e444112 | 05 January 2016, 10:06:29 UTC |
| 247ec9c | nksauter | 04 January 2016, 05:50:58 UTC | Guest code to retrieve the modified orientations after rotational fitting. git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23561 3c1a6239-ac2c-0410-bc49-92500e444112 | 04 January 2016, 05:50:58 UTC |
| 34dce9e | nksauter | 03 January 2016, 20:59:56 UTC | Unpacking code now handles general paramter tags. Code added to show histogram of rotational increments. git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23560 3c1a6239-ac2c-0410-bc49-92500e444112 | 03 January 2016, 20:59:56 UTC |
| bb3f587 | nksauter | 03 January 2016, 19:07:40 UTC | bugfix git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23559 3c1a6239-ac2c-0410-bc49-92500e444112 | 03 January 2016, 19:07:40 UTC |
| 81a7500 | nksauter | 03 January 2016, 19:05:07 UTC | If file names are available, base the half-data selection on the last digit in the filename. This way, CC 1/2 is reproducible, even though the files are joined in randomized order as a result of multiprocessing. git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23558 3c1a6239-ac2c-0410-bc49-92500e444112 | 03 January 2016, 19:05:07 UTC |
| 106d5ba | nksauter | 03 January 2016, 05:50:19 UTC | postrefine Rxy git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23557 3c1a6239-ac2c-0410-bc49-92500e444112 | 03 January 2016, 05:50:19 UTC |
| f27ba2c | nksauter | 03 January 2016, 02:10:25 UTC | Define the outer (or tensor) product between two vectors. Not sure why this hasn't come up before...developers please let me know if this is duplicated functionality. git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23556 3c1a6239-ac2c-0410-bc49-92500e444112 | 03 January 2016, 02:10:25 UTC |
| b121405 | nksauter | 03 January 2016, 00:00:04 UTC | Python level can select a specialized helper class for parameter-specific postrefinement. git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23555 3c1a6239-ac2c-0410-bc49-92500e444112 | 03 January 2016, 00:00:04 UTC |
| c3203d2 | nksauter | 01 January 2016, 20:59:24 UTC | Choose which parameters to refine with a phil choice at the python level, and a bitflag enum at the C++ level. Correctly apply reindexing op to the orientation model. Implement mosaic domain size partiality model. git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23554 3c1a6239-ac2c-0410-bc49-92500e444112 | 01 January 2016, 20:59:24 UTC |
| ed21eef | nksauter | 01 January 2016, 01:29:22 UTC | Read the experiment info and original HKL needed to model partiality, down into the C++ data structure. git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23553 3c1a6239-ac2c-0410-bc49-92500e444112 | 01 January 2016, 01:29:22 UTC |
| c6e0def | nksauter | 31 December 2015, 20:20:01 UTC | Methods to write the original HKL and xtal parameters to pickle database. git-svn-id: http://svn.code.sf.net/p/cctbx/code/trunk@23552 3c1a6239-ac2c-0410-bc49-92500e444112 | 31 December 2015, 20:20:01 UTC |
