| 1 | Release Notes |
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| 2 | ============= |
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| 3 | |
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| 4 | 1- Features |
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| 5 | =========== |
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| 6 | - New in Version 4.2.0 |
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| 7 | -------------------- |
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| 8 | This release heralds many improvements and a host of bug fixes, along with |
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| 9 | some significant changes from previous versions. Further, as promised, it |
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| 10 | marks the end of support for 32 bit operating systems and is only |
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| 11 | available for 64 bit operating systems. |
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| 12 | |
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| 13 | With this version the change to the new model API and plugins infrastructure |
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| 14 | begun with 4.0 is essentially complete (though extensions are in the works |
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| 15 | and more are likely they should remain backwardly compatible with previous |
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| 16 | versions of SasView). |
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| 17 | |
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| 18 | NOTE: Old-style plugin models, including old sum|multiply models will continue |
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| 19 | to be supported (i.e. SasView will be able to run them) in 4.x. However, |
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| 20 | the expectation is that such support will be removed in 5.0 and everyone |
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| 21 | is strongly encouraged to convert their custom models to the new API. |
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| 22 | |
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| 23 | Finally, the changes to orientation angles and orientational distribution |
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| 24 | definitions are now also complete. |
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| 25 | |
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| 26 | - Changes |
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| 27 | - The infrastucture for calculating 2D patterns from 3D orientated objects |
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| 28 | has been totally re-factored. It is now more accurate and consistent |
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| 29 | across models. |
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| 30 | - The way that SasView defines the orientation of anisometric and |
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| 31 | aligned objects has been completely overhauled. It now differs from |
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| 32 | previous versions. |
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| 33 | - Plugin models, including sum|multiply models, have completely migrated |
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| 34 | to the new infrastructure. NOTE that 3.x type models as well as early, |
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| 35 | intermediate 4.x type models, including those generated by sum|multiply |
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| 36 | will continue to be supported in 4.x but will likely no longer be |
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| 37 | supported after the move to 5.0. Users are strongly encouraged to |
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| 38 | migrate any custom models. |
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| 39 | - The NeXus loader has been removed as it is superseded by the NXcanSAS |
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| 40 | standard loader and SasView does not support the treatment of raw |
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| 41 | data. |
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| 42 | - Improvements |
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| 43 | - The accuracy/speed of some numerical integrations have been improved. |
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| 44 | - An orientation viewer tool has been introduced to assist in |
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| 45 | understanding the new orientation framework. |
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| 46 | - Problems with the computation of magnetic scattering from some |
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| 47 | objects have been rectified. Some questions remain however. |
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| 48 | - The known issue with the core_shell_parallelepiped model is now fixed. |
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| 49 | - A number of issues and inconsistencies with the creation of |
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| 50 | sum|multiply models have been rectified. |
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| 51 | - A Boltzmann distribution has been added for polydispersity/orientational |
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| 52 | distributions. |
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| 53 | - Some batch slicing options have been introduced. |
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| 54 | - Correlation function analysis now computes both the 1D and 3D functions. |
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| 55 | - There are several data loading improvements. |
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| 56 | - There are several improvements to Save/Load Project. |
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| 57 | - There have been numerous other bug fixes. |
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| 58 | - Documentation |
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| 59 | Several sections of the help documentation have undergone significant |
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| 60 | checking and updating, particularly those relating to orientation, |
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| 61 | magnetic scattering, and polydispersity distributions. Detailed |
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| 62 | advanced instructions for plugin writing and some scripting |
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| 63 | instructions have been added. |
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| 64 | - Other work |
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| 65 | - A Third-Party initiative has recently succeeded in getting SasView to |
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| 66 | run on Debian. More details at |
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| 67 | http://trac.sasview.org/wiki/DevNotes/Projects/Debian |
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| 68 | - With this release we have started to prepare for the inevitable move |
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| 69 | to Python 3, which will occur with the release of 5.0 |
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| 70 | - SasView 5.0 is currently in development. The two most significant |
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| 71 | features of this version will be (i) a move away from the present |
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| 72 | WxPython GUIs to new, completely rewritten, Qt5 GUIs, and |
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| 73 | (ii)implementation of the Beta-approximation for S(Q). Subject to |
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| 74 | resources, some limited access to the latter functionality may be |
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| 75 | available in a future SasView 4.x release. |
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| 76 | - Bug Fixes |
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| 77 | Fixes # 260: Box integration does not update when entering values in dialog |
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| 78 | Fixes # 446: Saving plot as PGF (not PDF!) format throws error |
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| 79 | Fixes # 467: Extend batch functionality to slicer |
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| 80 | Fixes # 489: ABS reader (NIST 1D) does not handle negative dx properly |
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| 81 | (USANS slit smearing) |
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| 82 | Fixes # 499: create sin(x)/x, 2*J1(x)/x and 3*j1(x)/x functions |
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| 83 | Fixes # 510: Build PDF documentation along with HTML |
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| 84 | Fixes # 525: Add GUI category defaults to models in sasmodels |
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| 85 | Fixes # 579: clean up sasview directory |
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| 86 | Fixes # 597: Need to document Combine Batch Fit |
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| 87 | Fixes # 645: GUI logic problem in Batch vs single fit mode |
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| 88 | Fixes # 648: Need to allow user input background value in Pr perspective |
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| 89 | Fixes # 685: Fix data upload to marketplace |
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| 90 | Fixes # 695: linear slope in onion model |
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| 91 | Fixes # 735: Review new Corfunc documentation |
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| 92 | Fixes # 741: Recalculate P(Q) and S(Q) components on model update. |
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| 93 | Fixes # 767: Sum/Product Models don't do what they should |
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| 94 | Fixes # 776: angular dispersity |
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| 95 | Fixes # 784: Add 3D integral to Correlation Function analysis |
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| 96 | Fixes # 786: core_shell_parallelepiped 1-D model is incorrect |
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| 97 | Fixes # 818: "report button" followed by "save" makes an empty pdf file |
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| 98 | Fixes # 838: Fix model download from marketplace |
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| 99 | Fixes # 848: can't save analysis when only one fit page |
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| 100 | Fixes # 849: Load Folder should ignore files starting with "." |
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| 101 | Fixes # 852: More unit tests, especially for oriented or 2d models |
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| 102 | Fixes # 854: remove unnecessary sleep() in fitting perspective |
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| 103 | Fixes # 856: Reading SAS_OPENCL from custom_config sometimes raises an ERROR |
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| 104 | Fixes # 861: cannot defined a structure factor plugin |
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| 105 | Fixes # 864: New Model Editor (simple plugin editor) error parsing |
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| 106 | parameter line |
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| 107 | Fixes # 865: Plugin live discovery issues |
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| 108 | Fixes # 866: inform user when NaN is returned from compute |
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| 109 | Fixes # 869: fit page computation thread cleanup |
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| 110 | Fixes # 875: Possible weirdness with 1D NXcanSAS data |
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| 111 | Fixes # 876: Add check for HDF5 format in dataloader |
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| 112 | Fixes # 887: reorganize tree, separating the installed source from the |
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| 113 | build source |
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| 114 | Fixes # 889: Refactor dataloader error handling infrastructure |
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| 115 | Fixes # 890: use new orientation definition for asymmetric shapes |
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| 116 | Fixes # 891: update docs for oriented shapes with new orientation definition |
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| 117 | Fixes # 896: equations in core shell parallelepiped docs do not match code |
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| 118 | Fixes # 898: Image Viewer Tool file selector issue |
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| 119 | Fixes # 899: Igor Reader q calculation |
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| 120 | Fixes # 902: IgorReader Q calculation needs fixing/improving |
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| 121 | Fixes # 903: sasview - all non-gui tests should be converted to run in Python 3 |
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| 122 | Fixes # 906: polydispersity not showing up in tabulated results |
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| 123 | Fixes # 912: About box points to misleading contributors page on Github |
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| 124 | Fixes # 915: load project issues |
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| 125 | Fixes # 916: Proper Logging |
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| 126 | Fixes # 920: Logarithmic binning option in the slice viewer |
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| 127 | Fixes # 921: Improve developer communication methods |
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| 128 | Fixes # 922: Remove support for all data formats that are not in q space |
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| 129 | Fixes # 923: Add CI and trac integrations to Slack |
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| 130 | Fixes # 930: fitting help says chisq is normalized to number of points |
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| 131 | Fixes # 931: Allow admins to edit all models and upload data etc on |
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| 132 | marketplace |
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| 133 | Fixes # 932: Need to fix upload of data files to marketplace |
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| 134 | Fixes # 934: Slurp tutorial repo for tutorials |
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| 135 | Fixes # 935: Build new tutorials as PDF |
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| 136 | Fixes # 943: Deep copy error on setting model after data is selected |
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| 137 | Fixes # 950: Most of the readers don't close files properly. |
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| 138 | Fixes # 954: cross check dll/opencl/python polydispersity and |
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| 139 | orientation results |
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| 140 | Fixes # 956: Possible problem with new doc build process |
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| 141 | Fixes # 961: sasmodels tests should fail if the parameter name does not exist |
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| 142 | Fixes # 962: star polymer typo in docs |
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| 143 | Fixes # 967: no uncertainties errors on fitting parameters |
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| 144 | Fixes # 969: About Box not picking up dls_logo.png |
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| 145 | Fixes # 970: ASCII loader doesn't handle ISIS 2D ASCII |
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| 146 | Fixes # 974: blacklist Intel HD 620/630 for double precision |
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| 147 | Fixes # 978: load project fails for pages which have not been defined |
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| 148 | Fixes # 983: Remove Nexus Loader |
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| 149 | Fixes # 984: PDF reports are not being properly generated on Windows |
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| 150 | Fixes # 985: Saving Project Fails |
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| 151 | Fixes # 986: Send to fitting overwrites theory page even if blank |
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| 152 | FitPage has focus |
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| 153 | Fixes # 990: utest_sasview.py giving different results than run_one.py |
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| 154 | Fixes # 993: Windows x64 versions not installing to correct folder |
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| 155 | Fixes # 994: Error changing fit engine |
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| 156 | Fixes # 995: OpenCL required on Linux even if turned off in GUI |
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| 157 | Fixes #1006: multiplicity models don't work with SQ |
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| 158 | Fixes #1007: spherical_sld model freezes SasView |
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| 159 | Fixes #1008: plugin model scaling not working? S |
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| 160 | Fixes #1010: Win64 build script not creating working executable |
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| 161 | Fixes #1011: sld_test failing on ubuntu |
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| 162 | Fixes #1013: FileReaderBaseClass output[] not reset - same file loaded |
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| 163 | multiple times |
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| 164 | Fixes #1018: add Boltzmann distribution |
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| 165 | Fixes #1021: add PDF documentation to website and document in wiki |
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| 166 | release process |
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| 167 | Fixes #1024: Update version numbers in master |
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| 168 | Fixes #1025: Sum/multiply editor hangs |
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| 169 | Fixes #1032: convert C++ modules to C |
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| 170 | Fixes #1035: Order of combining P(Q) and S(Q) in Plugins seems to matter |
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| 171 | Fixes #1037: data loader crop not working? & all fits crashing |
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| 172 | Fixes #1043: problem compiling marketplace models |
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| 173 | Fixes #1050: fix appveyor test for sasmodels win 64 python 3 |
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| 174 | Fixes #1052: Can't use a user-created plugin model in a plugin model |
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| 175 | Fixes #1057: phi rotation issue for elliptical cylinder |
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| 176 | Fixes #1060: incorrect default for rectangle dispersion |
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| 177 | Fixes #1062: win32 build not installing correctly |
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| 178 | Fixes #1064: Fitting did not converge!!! error with a Sum|Multi plugin model |
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| 179 | Fixes #1069: GUI problem when using polydispersity/orientation distributions |
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| 180 | Fixes #1070: Parameter error boxes should not be editable |
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| 181 | Fixes #1079: Remove save button in report dialog on Mac |
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| 182 | Fixes #1081: GUI problem with new orientation distribution |
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| 183 | Fixes #1083: Magnetic models not being computed |
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| 184 | Fixes #1099: Erratic behaviour of Sum|Multi model in 4.1.2 |
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| 185 | Fixes #1101: Batch results page not displaying polydispersity values |
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| 186 | Fixes #1131: OpencCl dialog does not open |
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| 187 | Fixes #1132: Slit Size Calculator Tool not working |
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| 188 | Fixes #1139: Missing Docs and Help for new Batch Slicing |
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| 189 | Fixes #1141: Intro to scripting.rst needs improvement |
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| 190 | Fixes #1142: Plugin framework is broken |
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| 191 | Fixes #1044: Unable to upload c file to marketplace |
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| 192 | Fixes #1145: Update models in model marketplace to 4.2 when 4.2 is released. |
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| 193 | Fixes #1148: Documentation for S(Q) models need updating |
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| 194 | Fixes #1128: AutoPlot generation for model documentation does not |
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| 195 | include background |
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| 196 | |
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| 197 | It is recommended that all users upgrade to this version, but your |
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| 198 | attention is drawn to the Changes section above. |
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| 199 | |
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| 200 | |
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| 201 | - New in Version 4.2.0-Beta |
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| 202 | ------------------------- |
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| 203 | This is a beta pre-release version of 4.2.0. A number of fixes and changes |
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| 204 | have been made in the year since the previous release. Full release notes |
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| 205 | will be compiled prior to the full release 4.2.0. |
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| 206 | |
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| 207 | Highlights are: |
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| 208 | - Infrastucture for calculating 2D patterns from 3D orientated objects |
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| 209 | has now been totally refactored |
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| 210 | - Plugins have completely migrated to the new infrastructure now, |
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| 211 | including sum/multiply models |
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| 212 | - Some batch slicing options have been introduced |
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| 213 | - The known issue with the core_shell_parallelepiped is now fixed |
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| 214 | - Several data loading improvements |
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| 215 | - Several save Project improvements (though there are more to come) |
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| 216 | - Numerous bug fixes |
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| 217 | - Lots of documentation enhancement |
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| 218 | |
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| 219 | In the meantime please report any bugs or issues found while using this beta |
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| 220 | |
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| 221 | |
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| 222 | - New in Version 4.1.2 |
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| 223 | -------------------- |
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| 224 | This point release is a bug-fix release addressing: |
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| 225 | |
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| 226 | - Fixes #984: PDF Reports Generate Empty PDFs |
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| 227 | - Fixes a path typo |
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| 228 | - 64 bit and 32 bit Windows executables now available |
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| 229 | |
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| 230 | It is recommended that all users upgrade to this version |
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| 231 | |
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| 232 | |
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| 233 | - New in Version 4.1.1 |
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| 234 | -------------------- |
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| 235 | This point release is a bug-fix release addressing: |
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| 236 | |
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| 237 | - Fixes #948: Mathjax CDN is going away |
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| 238 | - Fixes #938: Cannot read canSAS1D file output by SasView |
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| 239 | - Fixes #960: Save project throws error if empty fit page |
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| 240 | - Fixes #929: Problem deleting data in first fit page |
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| 241 | - Fixes #918: Test folders not bundled with release |
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| 242 | - Fixes an issue with the live discovery of plugin models |
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| 243 | - Fixes an issue with the NXcanSAS data loader |
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| 244 | - Updated tutorials for SasView 4.x.y |
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| 245 | |
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| 246 | |
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| 247 | - New in Version 4.1.0 |
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| 248 | ------------------ |
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| 249 | This incremental release brings a series of new features and improvements, |
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| 250 | and a host of bug fixes. Of particular note are: |
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| 251 | |
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| 252 | - Correlation Function Analysis (Corfunc) |
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| 253 | This performs a correlation function analysis of one-dimensional SAXS/SANS data, |
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| 254 | or generates a model-independent volume fraction profile from the SANS from an |
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| 255 | adsorbed polymer/surfactant layer. |
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| 256 | |
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| 257 | A correlation function may be interpreted in terms of an imaginary rod moving |
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| 258 | through the structure of the material. G1(R) is the probability that a rod of |
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| 259 | length R moving through the material has equal electron/neutron scattering |
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| 260 | length density at either end. Hence a frequently occurring spacing within a |
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| 261 | structure manifests itself as a peak. |
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| 262 | |
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| 263 | A volume fraction profile \Phi(z) describes how the density of polymer |
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| 264 | segments/surfactant molecules varies with distance from an (assumed locally flat) |
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| 265 | interface. |
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| 266 | |
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| 267 | - Fitting of SESANS Data |
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| 268 | Data from Spin-Echo SANS measurements can now be loaded and fitted. The data will |
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| 269 | be plotted against the correct axes and models will automatically perform a Hankel |
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| 270 | transform in order to calculate SESANS from a SANS model. |
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| 271 | |
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| 272 | - Documentation |
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| 273 | The documentation has undergone significant checking and updating. |
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| 274 | |
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| 275 | - Improvements |
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| 276 | - Correlation function (corfunc) analysis of 1D SAS data added from CCP13 |
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| 277 | - File converter tool for multi-file single column data sets |
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| 278 | - SESANS data loading and direct fitting using the Hankel transformation |
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| 279 | - Saving and loading of simultaneous and constrained fits now supported |
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| 280 | - Save states from SasView v3.x.y now loaded using sasmodel model names |
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| 281 | - Saving and loading of projects with 2D fits now supported |
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| 282 | - Loading a project removes all existing data, fits, and plots |
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| 283 | - Structure factor and form factor can be plotted independently |
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| 284 | - OpenCL is disabled by default and can be enabled through a fit menu |
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| 285 | - Data and theory fields are now independently expandable |
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| 286 | - Bug Fixes |
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| 287 | - Fixes #667: Models computed multiple times on parameters changes |
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| 288 | - Fixes #673: Custom models override built in models of same name |
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| 289 | - Fixes #678: Hard crash when running complex models on GPU |
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| 290 | - Fixes $774: Old style plugin models unloadable |
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| 291 | - Fixes #789: stacked disk scale doesn't match cylinder model |
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| 292 | - Fixes #792: core_shell_fractal uses wrong effective radius |
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| 293 | - Fixes #800: Plot range reset on plot redraws |
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| 294 | - Fixes #811 and #825: 2D smearing broken |
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| 295 | - Fixes #815: Integer model parameter handling |
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| 296 | - Fixes #824: Cannot apply sector averaging when no detector data present |
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| 297 | - Fixes #830: Cansas HDF5 reader fully compliant with NXCanSAS v1.0 format |
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| 298 | - Fixes #835: Fractal model breaks with negative Q values |
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| 299 | - Fixes #843: Multilayer vesicle does not define effective radius |
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| 300 | - Fixes #858: Hayter MSA S(Q) returns errors |
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| 301 | - Numerous grammatical and contexual errors in documention |
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| 302 | |
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| 303 | |
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| 304 | - New in Version 4.0.1 |
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| 305 | ------------------ |
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| 306 | This release fixes the critical bug #750 in P(Q)*S(Q). Most damaging |
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| 307 | it appears that the background term was being added to S(Q) prior to |
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| 308 | multiplication by P(Q). |
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| 309 | |
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| 310 | |
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| 311 | - New in Version 4.0 |
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| 312 | ------------------ |
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| 313 | This release fixes the various bugs found during the alpha and beta testing |
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| 314 | - Improvements |
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| 315 | - Support for reading data files from Anton Paar Saxess instruments |
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| 316 | - Adds documentation on how to write custom models in the new framework |
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| 317 | - Bug Fixes |
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| 318 | - Fixes bug #604 Pringle model questions |
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| 319 | - Fixes bug #472 Reparameterize Teubner-Strey |
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| 320 | - Fixes bug #530 Numerical instabilities in Teubner Strey model |
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| 321 | - Fixes bug #658 ASCII reader very broken |
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| 322 | |
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| 323 | |
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| 324 | - New in Version 4.0 beta 1 |
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| 325 | -------------------- |
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| 326 | This beta adds support for the magnetic and multilevel models of 3.1.2 |
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| 327 | and along with a host of bug fixes found in the alpha. |
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| 328 | |
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| 329 | - Model package changes and improvements |
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| 330 | - All 3.1.2 models now available in new interface |
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| 331 | - Old custom models should now still work |
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| 332 | - '''NOTE:''' These will be deprecated in a future version. Old |
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| 333 | custom models should be converted to the new model format which |
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| 334 | is now the same as the built in models and offers much better |
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| 335 | support. |
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| 336 | - Custom model editor now creates new style models |
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| 337 | - Custom model editor supports better error checking |
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| 338 | - Documentation improvements |
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| 339 | - Continued general cleanup |
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| 340 | - Other improvements/additions |
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| 341 | - Support for new canSAS 2D data files added |
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| 342 | - Plot axes range can now be set manually as well as by zooming |
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| 343 | - Plot annotations can now be moved around after being placed on plot. |
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| 344 | - The active optimizer is now listed on the top of the fit panel. |
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| 345 | - Linear fits now update qmin and max when the x scale limits are |
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| 346 | changed. Also the plot range no longer resets after a fit. |
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| 347 | - Bug fixes |
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| 348 | - Fixes bug #511 Errors in linearized fits and clean up of interface |
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| 349 | including Kratky representation |
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| 350 | - Fixes bug #186 Data operation Tool now executes when something is |
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| 351 | entered in the text box and does not wait for the user to hit enter |
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| 352 | - Fixes bug #459 plot context menu bug |
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| 353 | - Fixes bug #559 copy to clipboard in graph menu broken |
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| 354 | - Fixes bug #466 cannot remove a linear fit from graph |
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| 355 | - Numerous bugs introduced in the alpha |
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| 356 | |
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| 357 | |
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| 358 | |
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| 359 | - New in Version 4.0.0-alpha |
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| 360 | -------------------- |
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| 361 | This alpha release brings a major overhaul of the model system. The new model |
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| 362 | package allows rapid integration of custom models and access to polydispersity |
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| 363 | without requiring a compiler. |
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| 364 | |
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| 365 | - Model package changes and improvements |
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| 366 | - Model interface moved to independent sasmodels package. |
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| 367 | - Most models converted to new interface. |
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| 368 | - Allows rapid integration of user-written models. |
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| 369 | - OpenCL GPU utilization for faster fitting. |
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| 370 | - Improved numerical integration of Bessel functions. |
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| 371 | - SESANS integration and implementation |
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| 372 | - Scripting interface added for analysis of SESANS data. |
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| 373 | - Hankel transformation now accepts finite acceptance angles. |
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| 374 | - 2D cosine transformation added for TOF SESANS analysis. |
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| 375 | - Documentation improvements |
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| 376 | - The documentation tree was restructured for a better end user experience. |
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| 377 | - The documentation for each model was revamped and verified by at least |
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| 378 | two people following the conversion of the model. |
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| 379 | - Theoretical 1D (and 2D if applicable) scattering curves are auto-generated |
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| 380 | and added to the model documentation for each model. |
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| 381 | - Separation of GUI and calculations for future GUI enhancements |
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| 382 | - Bug fixes |
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| 383 | - Fixes bug #411 No stop button on simultaneous fit page |
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| 384 | - Fixes bug #410 Error with raspberry model |
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| 385 | - Fixes bug #364 Possible inconsistency in Poly_GausCoil model |
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| 386 | - Fixes bug #439 Hayter Penfold MSA code needs checking |
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| 387 | - Fixes bug #484 lammellerPC is precision limited |
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| 388 | - Fixes bug #498 $HOME/.matplotlib conflicts |
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| 389 | - Fixes bug #348 Control order in which fit parameters appear in the gui |
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| 390 | - Fixes bug #456 Provide DREAM Results Panel with something to identify |
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| 391 | data and age of results |
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| 392 | - Fixes bug #556 Build script improvements for developers |
|---|
| 393 | |
|---|
| 394 | |
|---|
| 395 | |
|---|
| 396 | - New in Version 3.1.2 |
|---|
| 397 | -------------------- |
|---|
| 398 | This release is a major stability improvement, having fixed a serious bug |
|---|
| 399 | that came to light since release 3.1.1. All users should upgrade. |
|---|
| 400 | |
|---|
| 401 | - Fixes bug #468 broken remove constraint buttons in |
|---|
| 402 | simultaneous/constrained fitting panel |
|---|
| 403 | - Fixes bug #474 resulting from changes in 3.1.1 that had |
|---|
| 404 | introduced an error in the high-Q of slit-smeared models. |
|---|
| 405 | - Fixes bug #478 which would cause wx to run out of IDs and result |
|---|
| 406 | in SasView crashing even if left alone. |
|---|
| 407 | - Fixes bug #479 missing help button on simultaneous/constrained fit page |
|---|
| 408 | - Fixes bug #480 GUI resizing issues on simultaneous fit page |
|---|
| 409 | - Fixes bug #486 broken Report Results |
|---|
| 410 | - Fixes bug #488 redraw issues in fit page |
|---|
| 411 | |
|---|
| 412 | |
|---|
| 413 | |
|---|
| 414 | - New in Version 3.1.1 |
|---|
| 415 | -------------------- |
|---|
| 416 | - Fixes bug #457 that prevented SasView from starting if the user was not |
|---|
| 417 | connected to the internet, or was behind a proxy server. |
|---|
| 418 | |
|---|
| 419 | - New in Version 3.1.0 |
|---|
| 420 | -------------------- |
|---|
| 421 | - The documentation/help has had a complete overhaul including: |
|---|
| 422 | - A completely new presentation interface (Sphinx). |
|---|
| 423 | - Proof reading! |
|---|
| 424 | - Updating for latest features. |
|---|
| 425 | - A Help (or sometimes ?) button has been added to every panel, and some |
|---|
| 426 | sub panels if appropriate, linking to the appropriate section in the |
|---|
| 427 | documentation. |
|---|
| 428 | - The model help has been split so that the Details button now brings up |
|---|
| 429 | a very short pop-up giving the equation being used while HELP goes to |
|---|
| 430 | the section in the full documentation describing the model. |
|---|
| 431 | - Extensive help has also been added for the new optimizer engine (see |
|---|
| 432 | below) including rules of thumb on how and when to choose a given |
|---|
| 433 | optimizer and what the parameters do. |
|---|
| 434 | - The optimizer engine has been completely replaced. The new optimizer |
|---|
| 435 | still defaults to the standard Levenberg-Marquardt algorithm. However 4 |
|---|
| 436 | other optimizers are now also available. Each starts with a set of default |
|---|
| 437 | parameters which can be tuned. The DREAM optimizer takes the longest but |
|---|
| 438 | is the most powerful and yields rich information including full parameter |
|---|
| 439 | correlation and uncertainty plots. A results panel has been added to |
|---|
| 440 | accommodate this. |
|---|
| 441 | - The five new optimizers are: |
|---|
| 442 | - A Levenberg-Marquardt optimizer |
|---|
| 443 | - A Quasi-Newton BFGS optimizer |
|---|
| 444 | - A Nelder-Mead Simplex optimizer |
|---|
| 445 | - A Differential Evolution optimizer |
|---|
| 446 | - A Monte Carlo optimizer (DREAM) |
|---|
| 447 | - New models were added: |
|---|
| 448 | - MicelleSphCoreModel (currently residing in the Uncategorized category) |
|---|
| 449 | - Existing models were updated: |
|---|
| 450 | - LamellarPS (bug in polydispersity integration fixed) |
|---|
| 451 | - RectangularPrismModel |
|---|
| 452 | - RectangularHollowPrismModel |
|---|
| 453 | - RectangularHollowPrismInfThinWallsModel |
|---|
| 454 | - Infrastructure to allow SESANS data to be fit with models was added. This |
|---|
| 455 | will become available in a future release but can currently be used from |
|---|
| 456 | the command line with some caveats. |
|---|
| 457 | - A number of bugs were fixed including a thread crashing issue and an |
|---|
| 458 | incorrect slit smearing resolution calculation. |
|---|
| 459 | - Implemented much more robust error logging to enable much easier |
|---|
| 460 | debugging in general but particularly the debugging of issues reported by |
|---|
| 461 | SasView users. |
|---|
| 462 | - A number of infrastructure tasks under the hood to enhance maintainability |
|---|
| 463 | - Upgrade from Wx 2.8 to Wx 3.0.2 which allows several new features but |
|---|
| 464 | required significant additional rework as well. |
|---|
| 465 | - Fully implemented Sphinx to the build process to produce both better |
|---|
| 466 | user documentation and developer documentation. |
|---|
| 467 | - Restructuring of the code base to more unified nomenclature and structure |
|---|
| 468 | so that the source installation tree more closely matches the installer |
|---|
| 469 | version tree. |
|---|
| 470 | - Code cleanup (an ongoing task) . |
|---|
| 471 | - Migration of the repository to github simplifying contributions from |
|---|
| 472 | non-project personnel through pull requests. |
|---|
| 473 | |
|---|
| 474 | - New in Version 3.0.0 |
|---|
| 475 | -------------------- |
|---|
| 476 | - The GUI look and feel has been refactored to be more familiar for |
|---|
| 477 | Windows users by using MDI frames. Graph windows are also now free- |
|---|
| 478 | floating. |
|---|
| 479 | - Five new models have been added: PringlesModel, CoreShellEllipsoidXTModel, |
|---|
| 480 | RectangularPrismModel, RectangularHollowPrismModel and |
|---|
| 481 | RectangularHollowPrismInfThinWallsModel. |
|---|
| 482 | - The data loader now supports ILL DAT data files and reads the full meta |
|---|
| 483 | information from canSAS file formats. |
|---|
| 484 | - Redefined convention for specifying angular parameters for anisotropic |
|---|
| 485 | models. |
|---|
| 486 | - A number of minor features have been added such as permitting a log |
|---|
| 487 | distribution of points when using a model to simulate data, and the |
|---|
| 488 | addition of a Kratky plot option to the linear plots. |
|---|
| 489 | - A number of bugs have also been fixed. |
|---|
| 490 | - Save Project and Save Analysis now work more reliably. |
|---|
| 491 | - BETA: Magnetic contrast supporting full polarization analysis has been |
|---|
| 492 | implemented for some spherical and cylindrical models. |
|---|
| 493 | - BETA: Two new tools have been added: |
|---|
| 494 | - A generic scattering calculator which takes an atomic, magnetic or |
|---|
| 495 | SLD distribution in space and generates the appropriate 2D |
|---|
| 496 | scattering pattern. In some cases the orientationally averaged |
|---|
| 497 | (powder) 1D scattering can also be computed. Supported formats |
|---|
| 498 | include: SLD or text, PDB, and OMF magnetic moment distribution |
|---|
| 499 | file. |
|---|
| 500 | - An image viewer/converter for data in image format; this reads in |
|---|
| 501 | an image file and will attempt to convert the image pixels to |
|---|
| 502 | data. Supported formats include: TIFF, TIF, PNG, BMP, JPG. |
|---|
| 503 | |
|---|
| 504 | - New in Version 2.2.1 |
|---|
| 505 | -------------------- |
|---|
| 506 | - Minor patch to support CanSAS XML v1.1 file format |
|---|
| 507 | - Added DataInfo for data in the DataExplorer and plots |
|---|
| 508 | - Added Maximize/Restore button in the title bar of the graphs |
|---|
| 509 | - Added a hide button in the toolbar of the graph panel |
|---|
| 510 | - The 'x' button now deletes a graph |
|---|
| 511 | - Edit SUM Model from the menubar can now generate and save more than one sum model |
|---|
| 512 | - Reports can now be saved in pdf format on WIN and MAC |
|---|
| 513 | - Made significant improvements to the batch/grid panel and fixed several bugs |
|---|
| 514 | - Fixed a number of other minor bugs |
|---|
| 515 | |
|---|
| 516 | - New in Version 2.2.0 |
|---|
| 517 | -------------------- |
|---|
| 518 | - Application name changed to SasView |
|---|
| 519 | - New fully customizable Category Manager added for better management of |
|---|
| 520 | increasing number of models |
|---|
| 521 | - Improved the Grid Window functionality in the batch fitting mode |
|---|
| 522 | - Added a simpler Graph/Plot modification interface |
|---|
| 523 | - Added a new 'Data Operation' tool for addition, subtraction, multiplication, |
|---|
| 524 | division, of two data sets. |
|---|
| 525 | - The 'Sum Model' editor was extended and renamed 'Summation and Multiplication' |
|---|
| 526 | editor |
|---|
| 527 | - Added more plot symbols options for 1d plots |
|---|
| 528 | - Added improved trapping of compiling errors to the 'New model editor' |
|---|
| 529 | - Added some intelligent outputs (e.g., Rg, background, or rod diameter |
|---|
| 530 | depending on the choice of axis scale of the plot) to the linear fits |
|---|
| 531 | - Added more models |
|---|
| 532 | |
|---|
| 533 | - Feature set from previous versions |
|---|
| 534 | ----------------------------------- |
|---|
| 535 | - Perspectives Available |
|---|
| 536 | - Invariant calculator: Calculates the invariant, volume fraction, and |
|---|
| 537 | specific surface area. |
|---|
| 538 | - P(r) inversion calculator: Indirect Fourier transformation method. |
|---|
| 539 | - Fitting: the tool used for modeling and fitting 1D and 2D data to |
|---|
| 540 | analytical model functions |
|---|
| 541 | - Tools: provides a number of useful supplementary tools such as SLD |
|---|
| 542 | calculation |
|---|
| 543 | |
|---|
| 544 | - Fitting |
|---|
| 545 | - Includes a large number of model functions, both form factors and structure factors. |
|---|
| 546 | - Support P(Q)*S(Q) for form factors that flag they can be so multiplied. |
|---|
| 547 | - Supports Gaussian, lognormal, Shulz, rectangular and custom distribution |
|---|
| 548 | functions for models that need to include polydispersity or for orientational |
|---|
| 549 | distributions if appropriate. |
|---|
| 550 | - Anisotropic shapes and magnetic moment modeling in 2D allow for a non-uniform |
|---|
| 551 | distribution of orientations of a given axis leading to modeling and fitting |
|---|
| 552 | capabilities of non azimuthaly symmetric data. |
|---|
| 553 | - User can choose to weight fits or not. If using weights, the user can choose |
|---|
| 554 | the error bar on each point if provided in the file, the square root |
|---|
| 555 | of the intensity or the intensity itself. |
|---|
| 556 | - Instrumental resolution smearing of model or fits is provided with several |
|---|
| 557 | options: read the resolution/point fromt he file. Input a pinhole resolution |
|---|
| 558 | or a slit resolution. |
|---|
| 559 | - Users can define the Qrange (Qmin and Qmax) for both 1D and 2D data for |
|---|
| 560 | fitting and modeling, but not graphically. The range can be reset to the |
|---|
| 561 | defaults (limits of q in data set for a fit) with the reset button. |
|---|
| 562 | - A mask can be applied to 2D calculation and fitting. |
|---|
| 563 | - Normalized residual plots are provided with every fit. |
|---|
| 564 | - Model function help available through detail button or from the fitting panel. |
|---|
| 565 | - Simultaneous/(advanced)constrained fitting allows for fitting a single |
|---|
| 566 | data set or several different sets simultaneously with the application |
|---|
| 567 | of advanced constraints relating fit parameters to functions of other |
|---|
| 568 | parameters (including from a different set). For example thickness of |
|---|
| 569 | shell = sin(30) times the length. |
|---|
| 570 | - Models that are the sum of two other models can be easily generated through the |
|---|
| 571 | SUM Model menubar item. |
|---|
| 572 | - New Python models can be added on the fly by creating an appropriate Python |
|---|
| 573 | file in the model plugin directory. Two tools are provided to help: |
|---|
| 574 | An easy to use custom model editor allows the quick generation of new Python |
|---|
| 575 | models by supplying only the parameters and their default value (box 1) |
|---|
| 576 | and the mathematical function of the model (box 2) and generating the |
|---|
| 577 | necessary *.py file. A separate advanced model editor provides a full Python |
|---|
| 578 | file editor. Either way once saved the model becomes immediately available |
|---|
| 579 | to the application. |
|---|
| 580 | - A batch fitting capability allows for the analysis of a series of data sets to |
|---|
| 581 | a single model and provides the results in a tabular form suitable for saving |
|---|
| 582 | or plotting the evolution of the fit parameters with error bars (from within |
|---|
| 583 | the application). |
|---|
| 584 | |
|---|
| 585 | - Tools |
|---|
| 586 | - A scattering length density calculator,including some X-ray information |
|---|
| 587 | is provided. |
|---|
| 588 | - A density to vol. fraction converter is provided |
|---|
| 589 | - In application access to a Python shell/editor (PyCrust) is provided |
|---|
| 590 | - An instrument resolution calculator, including possible gravitational and |
|---|
| 591 | TOF effects is provided |
|---|
| 592 | - A slit size calculator optimized for Anton Paar Saxess is provided. |
|---|
| 593 | - A kiessig fringe thickness calculator is provided |
|---|
| 594 | |
|---|
| 595 | - Plots and plot management |
|---|
| 596 | - A 3D graphing option (for 2d data/results) is provided with the view |
|---|
| 597 | controlled by the mouse |
|---|
| 598 | - 2D plots are shown with an intensity color bar. 2D Color map can be user |
|---|
| 599 | adjusted. |
|---|
| 600 | - Supports output of plot to a variety of graphic formats. Supported formats |
|---|
| 601 | include: png, eps, emf, jpg/jpeg, pdf, ps, tif/tiff, rawRGBbitmap(raw, rgba), |
|---|
| 602 | and scalable vector graphic (svg/svgz) |
|---|
| 603 | - Supports ouput of data in plot (1 or 2D) to limited data formats |
|---|
| 604 | - Multiple data sets can be loaded into a single graph for viewing (but a fit |
|---|
| 605 | plot can currently only have a single plot). |
|---|
| 606 | - Extensive context sensitive plot/fitting/manipulation options are available |
|---|
| 607 | through a right mouse click pop-up menu on plots. |
|---|
| 608 | |
|---|
| 609 | - Data management |
|---|
| 610 | - Supports 2 + column 1D ASCII data, NIST 1D and 2D data, and canSAS data |
|---|
| 611 | via plug-in mechanism which can easily allow other readers as appropriate. |
|---|
| 612 | - 2D data is expected in Q space but for historical reasons accepts the |
|---|
| 613 | NIST 2D raw pixel format and will do conversion internally. |
|---|
| 614 | - The full data and metadata available to SasView is viewable in ASCII via |
|---|
| 615 | right clicking on a data set and choosing Data Info in the DataExplorer |
|---|
| 616 | or on the plots |
|---|
| 617 | - Supports loading a single file, multiple files, or a whole folder |
|---|
| 618 | - An optional Data Explorer is provided (default) which simplifies managing, |
|---|
| 619 | plotting, deleting, or setup for computation. Most functions however do |
|---|
| 620 | not require access to the explorer/manager and can be accessed through |
|---|
| 621 | right click menus and the toolbar. The data explorer can be re-started |
|---|
| 622 | from the menu bar. |
|---|
| 623 | |
|---|
| 624 | - Data manipulation |
|---|
| 625 | - Support various 2D averaging methods : Circular, sectors, annular, |
|---|
| 626 | boxsum, boxQx and boxQy. |
|---|
| 627 | - A 2D data maks editor is provided |
|---|
| 628 | - 2D mask can be applied to the circular averaging. |
|---|
| 629 | |
|---|
| 630 | - Miscellaneous features |
|---|
| 631 | - limited reports can be generated in pdf format |
|---|
| 632 | - Provides multiprocessor support(Windows only) |
|---|
| 633 | - Limited startup customization currently includes default startup |
|---|
| 634 | data folder and choice of default starting with data manager |
|---|
| 635 | - Limited support for saving(opening) a SasView project or a SasView analysis |
|---|
| 636 | (subproject) is provided. |
|---|
| 637 | - SasView can be launched and loaded with a file of interesty by double-clicking |
|---|
| 638 | on that file (recognized extension) |
|---|
| 639 | - A data file or data folder can be passed to SasView when launched from |
|---|
| 640 | the command line. |
|---|
| 641 | - Limited bookmarking capability to later recall the results of a fit calculation |
|---|
| 642 | is provided. |
|---|
| 643 | - Extensive help is provided through context sensitive mouse roll-over, |
|---|
| 644 | information bar (at the bottom of the panel), the console menu, and |
|---|
| 645 | access to the help files in several different ways. |
|---|
| 646 | |
|---|
| 647 | |
|---|
| 648 | 2- Downloading and Installing |
|---|
| 649 | ============================= |
|---|
| 650 | |
|---|
| 651 | *** Note 1: If you have a SasView installer (.EXE or .MSI), you do not need to |
|---|
| 652 | worry about any of the following. However, it is highly recommended |
|---|
| 653 | that any previous versions of SasView are uninstalled prior to |
|---|
| 654 | installing the new version UNLESS you are installing SasView to |
|---|
| 655 | versioned folders. |
|---|
| 656 | |
|---|
| 657 | *** Note 2: The easiest approach to setting up the proper environment to |
|---|
| 658 | build from source is to use Conda. Instructions for setting up |
|---|
| 659 | and using Conda can be found at: |
|---|
| 660 | http://trac.sasview.org/wiki/DevNotes/CondaDevSetup |
|---|
| 661 | |
|---|
| 662 | *** Note 3: Much more information is available at www.sasview.org under |
|---|
| 663 | links/downloads. In particular, look in the 'For Developers' section. |
|---|
| 664 | Also have a look at http://trac.sasview.org/. |
|---|
| 665 | |
|---|
| 666 | 2.1- System Requirements |
|---|
| 667 | - Python version >= 2.5 and < 3.0 should be running on the system |
|---|
| 668 | - We currently use Python 2.7 |
|---|
| 669 | |
|---|
| 670 | 2.2- Package Dependencies |
|---|
| 671 | - Ensure the required dependencies are installed |
|---|
| 672 | - For the latest list of dependencies see the appropriate yml file in |
|---|
| 673 | the SasView repo at sasview/build_tools/conda/ymls |
|---|
| 674 | |
|---|
| 675 | 2.3- Installing from Source |
|---|
| 676 | - Get the source code |
|---|
| 677 | - create a folder to contain the source code; if working with |
|---|
| 678 | multiple versions you might want to use versioned folder names |
|---|
| 679 | like 'sasview-x.x.x' |
|---|
| 680 | - open a command line window in the source code folder |
|---|
| 681 | - to get the CURRENT DEVELOPMENT VERSION from source control use |
|---|
| 682 | git clone https://github.com/SasView/sasview.git sasview |
|---|
| 683 | git clone https://github.com/Sasview/sasmodels.git sasmodels |
|---|
| 684 | git clone https://github.com/bumps/bumps.git bumps |
|---|
| 685 | - to get a SPECIFIC RELEASE VERSION from source control go to |
|---|
| 686 | https://github.com/SasView/sasview/releases |
|---|
| 687 | and download the required zip or tar.gz file. Unzip/untar it |
|---|
| 688 | to the source code folder. |
|---|
| 689 | |
|---|
| 690 | 2.4- Building and Installing |
|---|
| 691 | - use 'python setup.py build' |
|---|
| 692 | - use 'python setup.py install' |
|---|
| 693 | To build the documentation |
|---|
| 694 | - use'python setup.py docs' |
|---|
| 695 | |
|---|
| 696 | 2.5- Running SasView |
|---|
| 697 | - use 'python run.py'; this runs from the source directories, so you |
|---|
| 698 | don't have to rebuild every time you make a change, unless you are |
|---|
| 699 | changing the C model files. |
|---|
| 700 | - if using Conda the above command will also build SasView, but you |
|---|
| 701 | must issue 'activate sasview' first. |
|---|
| 702 | |
|---|
| 703 | |
|---|
| 704 | 3- Known Issues |
|---|
| 705 | =============== |
|---|
| 706 | |
|---|
| 707 | 4.2.0 - All systems |
|---|
| 708 | There are currently no major known issues. A full list of known bugs and |
|---|
| 709 | feature requests by release version that users may wish to be aware of |
|---|
| 710 | can be viewed at http://trac.sasview.org/report/3 |
|---|
| 711 | NOTE: Any corrections to models that may become known/available will be |
|---|
| 712 | posted to Marketplace as available (and fixed in the following release) |
|---|
| 713 | |
|---|
| 714 | 4.1- All systems: |
|---|
| 715 | The conversion to sasmodels infrastructure is ongoing and should be |
|---|
| 716 | completed in the next release. In the meantime this leads to a few known |
|---|
| 717 | issues: |
|---|
| 718 | - The way that orientation is defined is being refactored to address |
|---|
| 719 | long standing issues and comments. In release 4.1 however only models |
|---|
| 720 | with symmetry (e.g. a=b) have been converted to the new definitions. |
|---|
| 721 | The rest (a <> b <> c - e.g. parellelepiped) maintain the same |
|---|
| 722 | definition as before and will be converted in 4.2. Note that |
|---|
| 723 | orientational distribution also makes much more sense in the new |
|---|
| 724 | framework. The documentation should indicate which definition is being |
|---|
| 725 | used for a given model. |
|---|
| 726 | - The infrastructure currently handles internal conversion of old style |
|---|
| 727 | models so that user created models in previous versions should continue |
|---|
| 728 | to work for now. At some point in the future such support will go away. |
|---|
| 729 | Everyone is encouraged to convert to the new structure which should be |
|---|
| 730 | relatively straight forward and provides a number of benefits. |
|---|
| 731 | - In that vein, the distributed models and those generated by the new |
|---|
| 732 | plugin model editor are in the new format, however those generated by |
|---|
| 733 | sum|multiply models are the old style sum|multiply models. This should |
|---|
| 734 | also disappear in the near future |
|---|
| 735 | - The on the fly discovery of plugin models and changes thereto behave |
|---|
| 736 | inconsistently. If a change to a plugin model does not seem to |
|---|
| 737 | register, the Load Plugin Models (under fitting -> Plugin Model |
|---|
| 738 | Operations) can be used. However, after calling Load Plugin Models, the |
|---|
| 739 | active plugin will no longer be loaded (even though the GUI looks like |
|---|
| 740 | it is) unless it is a sum|multiply model which works properly. All |
|---|
| 741 | others will need to be recalled from the model dropdown menu to reload |
|---|
| 742 | the model into the calculation engine. While it might be annoying it |
|---|
| 743 | does not appear to prevent SasView from working.. |
|---|
| 744 | - The model code and documentation review is ongoing. At this time the |
|---|
| 745 | core shell parellelepiped is known to have the C shell effectively fixed |
|---|
| 746 | at 0 (noted in documentation) while the triaxial ellipsoid does not seem |
|---|
| 747 | to reproduce the limit of the oblate or prolate ellipsoid. If errors are |
|---|
| 748 | found and corrected, corrected versions will be uploaded to the |
|---|
| 749 | marketplace. |
|---|
| 750 | |
|---|
| 751 | 3.1- All systems: |
|---|
| 752 | - The documentation window may take a few seconds to load the first time |
|---|
| 753 | it is called. Also, an internet connection is required before |
|---|
| 754 | equations will render properly. Until then they will show in their |
|---|
| 755 | original TeX format. |
|---|
| 756 | - If the documentation window remains stubbornly blank, try installing a |
|---|
| 757 | different browser and set that as your default browser. Issues have |
|---|
| 758 | been noted with Internet Explorer 11. |
|---|
| 759 | - Check for Updates may fail (with the status bar message ' Cannot |
|---|
| 760 | connect to the application server') if your internet connection uses |
|---|
| 761 | a proxy server. Tested resolutions for this are described on the |
|---|
| 762 | website FAQ. |
|---|
| 763 | - The copy and paste functions (^C, ^V) in the batch mode results grid |
|---|
| 764 | require two clicks: one to select the cell and a second to select the |
|---|
| 765 | contents of the cell. |
|---|
| 766 | - The tutorial has not yet been updated and is somewhat out of date |
|---|
| 767 | - Very old computers may struggle to run the 3.x and later releases |
|---|
| 768 | - Polydispersity on multiple parameters included in a simultaneous/ |
|---|
| 769 | constrained fit will likely not be correct |
|---|
| 770 | - Constrained/simultaneous fit page does not have a stop button |
|---|
| 771 | - Constrained/simultaneous fit do not accept min/max limits |
|---|
| 772 | - Save project does not store the state of all the windows |
|---|
| 773 | - Loading projects can be very slow |
|---|
| 774 | - Save Project only works once a data set has been associated with |
|---|
| 775 | a model. Error is reported on status bar. |
|---|
| 776 | - There is a numerical precision problem with the multishell model when |
|---|
| 777 | the iner radius gets large enough (ticket #288) |
|---|
| 778 | - The angular distribution angles are not clearly defined and may in |
|---|
| 779 | some cases lead to incorrect calculations(ticket #332) |
|---|
| 780 | |
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| 781 | 3.2- Windows: |
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| 782 | - If installed to same directory as old version without first removing |
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| 783 | the old version, the old desktop icon will remain but point to the |
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| 784 | new exe version. Likewise all the start menu folders and items will |
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| 785 | have the old name even though pointing to the new version. Usually |
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| 786 | safest to uninstall old version prior to installing new version anyway. |
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| 787 | |
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| 788 | 3.3- MAC: |
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| 789 | - Application normally starts up hidden. Click icon in Dock to view/use |
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| 790 | application. |
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| 791 | - Multiprocessing does not currently work on MAC OS |
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| 792 | |
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| 793 | 3.4- Linux: |
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| 794 | - Not well tested |
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| 795 | |
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| 796 | |
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| 797 | 4- SasView website |
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| 798 | ================== |
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| 799 | |
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| 800 | - www.sasview.org. This main project site is the gateway to all |
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| 801 | information about the sasview project. It includes information |
|---|
| 802 | about the project, a FAQ page and links to all developer and user |
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| 803 | information, tools and resources. |
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| 804 | |
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| 805 | |
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| 806 | 5- Frequently Asked Questions |
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| 807 | ============================= |
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| 808 | |
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| 809 | - www.sasview.org/faq.html |
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| 810 | |
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| 811 | |
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| 812 | 6- Installer download website |
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| 813 | ============================= |
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| 814 | |
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| 815 | - Latest release Version |
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| 816 | - https://github.com/SasView/sasview/releases |
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| 817 | - Latest developer builds |
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| 818 | - https://jenkins.esss.dk/sasview/view/Master-Builds/ |
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