Changeset 35ac8df in sasview

Timestamp:

Aug 21, 2018 9:20:27 AM (6 years ago)

Author:

krzywon

Branches:

master, magnetic_scatt, release-4.2.2, ticket-1009, ticket-1094-headless, ticket-1242-2d-resolution, ticket-1243, ticket-1249, unittest-saveload

Children:

c2525bf

Parents:

96d06a4 (diff), ec52ea1 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'master' into ticket-1111

Files:

• docs/sphinx-docs/source/conf.py (modified) (2 diffs)
• docs/sphinx-docs/source/user/environment.rst (added)
• docs/sphinx-docs/source/user/working.rst (modified) (1 diff)
• installers/README-next-release.txt (modified) (1 diff)
• installers/README.txt (modified) (1 diff)
• src/sas/sascalc/dataloader/readers/abs_reader.py (modified) (1 diff)
• src/sas/sascalc/fit/pagestate.py (modified) (2 diffs)
• src/sas/sasgui/guiframe/local_perspectives/plotting/parameters_panel_slicer.py (modified) (2 diffs)
• src/sas/sasgui/guiframe/media/graph_help.rst (modified) (3 diffs)
• src/sas/sasgui/perspectives/calculator/pyconsole.py (modified) (2 diffs)
• src/sas/sasgui/perspectives/calculator/slit_length_calculator_panel.py (modified) (1 diff)
• src/sas/sasgui/perspectives/fitting/basepage.py (modified) (1 diff)
• src/sas/sasgui/perspectives/fitting/fitpage.py (modified) (3 diffs)
• src/sas/sasview/__init__.py (modified) (1 diff)
• test/sasdataloader/test/utest_abs_reader.py (modified) (1 diff)
• src/sas/sascalc/data_util/nxsunit.py (modified) (2 diffs)
• src/sas/sascalc/dataloader/file_reader_base_class.py (modified) (6 diffs)
• src/sas/sascalc/dataloader/readers/ascii_reader.py (modified) (1 diff)
• src/sas/sascalc/dataloader/readers/cansas_reader.py (modified) (1 diff)
• src/sas/sascalc/dataloader/readers/cansas_reader_HDF5.py (modified) (15 diffs)
• src/sas/sascalc/dataloader/readers/danse_reader.py (modified) (1 diff)
• src/sas/sascalc/dataloader/readers/red2d_reader.py (modified) (1 diff)
• src/sas/sascalc/file_converter/nxcansas_writer.py (modified) (5 diffs)
• src/sas/sasgui/guiframe/gui_manager.py (modified) (6 diffs)
• src/sas/sasgui/guiframe/local_perspectives/data_loader/data_loader.py (modified) (1 diff)
• src/sas/sasview/test/1d_data/33837rear_1D_1.75_16.5_NXcanSAS.h5 (deleted)
• src/sas/sasview/test/2d_data/33837rear_2D_1.75_16.5_NXcanSAS.h5 (deleted)
• test/sasdataloader/test/cansas_1Dand2D_multiplesasentry_multiplesasdata.h5 (deleted)
• test/sasdataloader/test/cansas_1Dand2D_samedatafile.h5 (deleted)
• test/sasdataloader/test/cansas_1Dand2D_samesasentry.h5 (deleted)
• test/sasdataloader/test/test_data/MAR07232_rest.h5 (moved) (moved from test/sasdataloader/test/MAR07232_rest.h5)
• test/sasdataloader/test/test_data/avg_testdata.txt (moved) (moved from test/sasdataloader/test/avg_testdata.txt) (1 diff)
• test/sasdataloader/test/test_data/nxcansas_1Dand2D_multisasdata.h5 (added)
• test/sasdataloader/test/test_data/nxcansas_1Dand2D_multisasentry.h5 (added)
• test/sasdataloader/test/test_data/nxcansas_1Dand2D_multisasentry_multisasdata.h5 (added)
• test/sasdataloader/test/test_data/ring_testdata.txt (moved) (moved from test/sasdataloader/test/ring_testdata.txt) (1 diff)
• test/sasdataloader/test/test_data/sectorphi_testdata.txt (moved) (moved from test/sasdataloader/test/sectorphi_testdata.txt) (1 diff)
• test/sasdataloader/test/test_data/sectorq_testdata.txt (moved) (moved from test/sasdataloader/test/sectorq_testdata.txt) (1 diff)
• test/sasdataloader/test/test_data/slabx_testdata.txt (moved) (moved from test/sasdataloader/test/slabx_testdata.txt) (1 diff)
• test/sasdataloader/test/test_data/slaby_testdata.txt (moved) (moved from test/sasdataloader/test/slaby_testdata.txt) (1 diff)
• test/sasdataloader/test/utest_averaging.py (modified) (10 diffs)
• test/sasdataloader/test/utest_cansas.py (modified) (6 diffs)
• test/sasdataloader/test/utest_red2d_reader.py (modified) (1 diff)

docs/sphinx-docs/source/conf.py

@@ -71 +71 @@
 # General information about the project.
 project = u'SasView'
-copyright = u'2017, The SasView Project'
+copyright = u'2018, The SasView Project'
 
 # The version info for the project you're documenting, acts as replacement for
@@ -80 +80 @@
 version = '4.2'
 # The full version, including alpha/beta/rc tags.
-release = '4.2.0'
+release = '4.2.0-beta'
 
 # The language for content autogenerated by Sphinx. Refer to documentation

docs/sphinx-docs/source/user/working.rst

@@ -19 +19 @@
    Writing a Plugin Model <sasgui/perspectives/fitting/plugin>
 
+   Environment Variables <environment>
+
    Model marketplace <marketplace>

installers/README-next-release.txt

@@ -1 @@
-   - New in Version 3.?.?
+Release Notes
+=============
+    
+1- Features
+===========
+    - New in Version 4.2.0
+      --------------------
+      This point release heralds many improvements and a host of bug fixes. But there are also some significant changes from previous versions.
+      
+      - Changes
+         - The infrastucture for calculating 2D patterns from 3D orientated objects has been totally re-factored. It is now more accurate and consistent across models.
+         - The way that SasView defines the orientation of anisometric and aligned objects has been completely overhauled. It now differs from previous versions.
+         - Plugin models, including sum/multiply models, have completely migrated to the new infrastructure. ???DO WE NEED TO SAY SOMETHING ABOUT BACKWARD COMPATIBILITY OR LEGACY SUPPORT HERE???
+         - The NeXus loader has been removed (as it is superseded by the NXcanSAS loader).
+      - Improvements
+         - The accuracy/speed of some numerical integrations have been improved. ???CHECK WITH PAULK???
+         - An orientation viewer tool has been introduced (to assist in understanding the new orientation framework).
+         - Problems with the computation of magnetic scattering from some objects have been rectified.
+         - The known issue with the core_shell_parallelepiped model is now fixed.
+         - A number of issues and inconsistencies with the creation of sum|product models have been rectified (and more work is in progress).
+         - A Boltzmann distribution has been added for polydispersity/orientational distributions.
+         - Some batch slicing options have been introduced.
+         - Correlation function analysis now computes both the 1D and 3D functions.
+         - There are several data loading improvements.
+         - There are several improvements to Save/Load Project (with more to come).
+         - There have been numerous other bug fixes.
+      - Documentation
+         Several sections of the help documentation have undergone significant checking and updating, particularly those relating to orientation, magnetic scattering, and polydispersity distributions.
+      - Other work
+         - A Third-Party initiative has recently succeeded in getting SasView to run on Debian. More details at http://trac.sasview.org/wiki/DevNotes/Projects/Debian
+         - With this release we have started to prepare for the inevitable move to Python 3.
+         - SasView 5.0 is already in development. The two most significant features of this version will be (i) a move away from the present WxPython GUIs to new Qt5 GUIs, and (ii) implementation of the Beta-approximation for S(Q). Subject to resources, the latter functionality may be released (in a non-GUI form) in an interim SasView 4.3.0.
+      - Bug Fixes
+         Fixes #  14: Loading a saved project is really really slow  
+         Fixes # 260: Box integration does not update when entering values in dialog  
+         Fixes # 379: Need to make the BUMPS output page more more obvious  
+         Fixes # 446: Saving plot as PGF (not PDF!) format throws error  
+         Fixes # 467: Extend batch functionality to slicer  
+         Fixes # 489: ABS reader (NIST 1D) does not handle negative dx properly (USANS slit smearing)  
+         Fixes # 499: create sin(x)/x, 2*J1(x)/x and 3*j1(x)/x functions  
+         Fixes # 510: Build PDF documentation along with HTML  
+         Fixes # 525: Add GUI category defaults to models in sasmodels  
+         Fixes # 579: clean up sasview directory  
+         Fixes # 597: Need to document Combine Batch Fit  
+         Fixes # 645: GUI logic problem in Batch vs single fit mode  
+         Fixes # 648: Need to allow user input background value in Pr perspective  
+         Fixes # 685: Fix data upload to marketplace  
+         Fixes # 695: linear slope in onion model  
+         Fixes # 735: Review new Corfunc documentation  
+         Fixes # 741: Recalculate P(Q) and S(Q) components on model update.  
+         Fixes # 767: Sum/Product Models don't do what they should  
+         Fixes # 776: angular dispersity  
+         Fixes # 784: Add 3D integral to Correlation Function analysis  
+         Fixes # 786: core_shell_parallelepiped 1-D model is incorrect  
+         Fixes # 818: “report button” followed by “save” makes an empty pdf file???  
+         Fixes # 830: Check compliance of loader against NXcanSAS-1.0 release  
+         Fixes # 838: Fix model download from marketplace  
+         Fixes # 848: can't save analysis when only one fit page  
+         Fixes # 849: Load Folder should ignore files starting with .  
+         Fixes # 852: More unit tests, especially for oriented or 2d models  
+         Fixes # 854: remove unnecessary sleep() in fitting perspective  
+         Fixes # 856: Reading SAS_OPENCL from custom_config sometimes raises an ERROR  
+         Fixes # 861: cannot defined a structure factor plugin  
+         Fixes # 864: New Model Editor (simple plugin editor) error parsing parameter line  
+         Fixes # 865: Plugin live discovery issues  
+         Fixes # 866: inform user when NaN is returned from compute  
+         Fixes # 869: fit page computation thread cleanup  
+         Fixes # 875: Possible weirdness with 1D NXcanSAS data  
+         Fixes # 876: Add check for HDF5 format in dataloader  
+         Fixes # 887: reorganize tree, separating the installed source from the build source  
+         Fixes # 889: Refactor dataloader error handling infrastructure  
+         Fixes # 890: use new orientation definition for asymmetric shapes  
+         Fixes # 891: update docs for oriented shapes with new orientation definition  
+         Fixes # 896: equations in core shell parallelepiped docs do not match code  
+         Fixes # 898: Image Viewer Tool file selector issue  
+         Fixes # 899: Igor Reader q calculation  
+         Fixes # 902: IgorReader Q calculation needs fixing/improving  
+         Fixes # 903: sasview - all non-gui tests should be converted to run in Python 3  
+         Fixes # 906: polydispersity not showing up in tabulated results  
+         Fixes # 912: About box points to misleading contributors page on Github  
+         Fixes # 913: Need to add Diamond developer and logo in relevant places  
+         Fixes # 915: load project issues  
+         Fixes # 916: Proper Logging  
+         Fixes # 920: Logarithmic binning option in the slice viewer  
+         Fixes # 921: Improve developer communication methods  
+         Fixes # 922: Remove support for all data formats that are not in q space  
+         Fixes # 923: Add CI and trac integrations to Slack  
+         Fixes # 930: fitting help says chisq is normalized to number of points  
+         Fixes # 931: Allow admins to edit all models and upload data etc on marketplace  
+         Fixes # 932: Need to fix upload of data files to marketplace  
+         Fixes # 934: Slurp tutorial repo for tutorials  
+         Fixes # 935: Build new tutorials as PDF  
+         Fixes # 943: Deep copy error on setting model after data is selected  
+         Fixes # 950: Most of the readers don't close files properly.  
+         Fixes # 954: cross check dll/opencl/python polydispersity and orientation results  
+         Fixes # 956: Possible problem with new doc build process  
+         Fixes # 961: sasmodels tests should fail if the parameter name does not exist  
+         Fixes # 962: star polymer typo in docs  
+         Fixes # 966: Inconsistent chi2 reporting  
+         Fixes # 967: no uncertainties errors on fitting parameters  
+         Fixes # 969: About Box not picking up dls_logo.png  
+         Fixes # 970: ASCII loader doesn't handle ISIS 2D ASCII  
+         Fixes # 974: blacklist Intel HD 620/630 for double precision  
+         Fixes # 978: load project fails for pages which have not been defined  
+         Fixes # 980: Inconsistent results between Igor & SasView using Fractal Core-Shell model  
+         Fixes # 983: Remove Nexus Loader  
+         Fixes # 984: PDF reports are not being properly generated on Windows  
+         Fixes # 985: Saving Project Fails  
+         Fixes # 986: Send to fitting overwrites theory page even if blank FitPage has focus  
+         Fixes # 990: utest_sasview.py giving different results than run_one.py  
+         Fixes # 993: Windows x64 versions not installing to correct folder  
+         Fixes # 994: Error changing fit engine  
+         Fixes # 995: OpenCL required on Linux even if turned off in GUI  
+         Fixes #1006: multiplicity models don't work with SQ  
+         Fixes #1007: spherical_sld model freezes SasView  
+         Fixes #1008: plugin model scaling not working? S 
+         Fixes #1010: Win64 build script not creating working executable  
+         Fixes #1011: sld_test failing on ubuntu  
+         Fixes #1012: ESS GUI not updating after fitting  
+         Fixes #1013: FileReaderBaseClass output[] not reset - same file loaded multiple times  
+         Fixes #1018: add Boltzmann distribution  
+         Fixes #1021: add PDF documentation to website and document in wiki release process  
+         Fixes #1024: Update version numbers in master  
+         Fixes #1025: Sum/multiply editor hangs  
+         Fixes #1032: convert C++ modules to C  
+         Fixes #1035: Order of combining P(Q) and S(Q) in Plugins seems to matter  
+         Fixes #1037: data loader crop not working? & all fits crashing  
+         Fixes #1043: problem compiling marketplace models  
+         Fixes #1050: fix appveyor test for sasmodels win 64 python 3  
+         Fixes #1052: Can't use a user-created plugin model in a plugin model  
+         Fixes #1054: Check plugin & orientation descriptions in full docs once SasModels PR #57 is merged  
+         Fixes #1057: phi rotation issue for elliptical cylinder  
+         Fixes #1060: incorrect default for rectangle dispersion  
+         Fixes #1062: win32 build not installing correctly  
+         Fixes #1064: Fitting did not converge!!! error with a Sum|Multi plugin model  
+         Fixes #1068: 2d data (from NG7) not loadiing - strange format?  
+         Fixes #1069: GUI problem when using polydispersity/orientation distributions  
+         Fixes #1070: Parameter error boxes should not be editable  
+         Fixes #1072: Orientation distributions seem to depend on initial angle  
+         Fixes #1079: Remove save button in report dialog on Mac  
+         Fixes #1081: GUI problem with new orientation distribution  
+         Fixes #1083: Magnetic models not being computed  
+         Fixes #1099: Erratic behaviour of Sum|Multi model in 4.1.2  
+         Fixes #1101: Batch results page not displaying polydispersity values  
+         Fixes #1103: Problem with plugin models on mac when using ER  
+         Fixes #1134: sum/multi scale factor in 4.2 seems incorrect?  
+         Fixes #1139: Missing Docs and Help for new Batch Slicing  
+         Fixes #1145: Update models in model marketplace to 4.2 when 4.2 is released.  
+         Fixes #1146: Need to add Release notes for 4.2 
+      - Current Known Issues
+         Listed here are known issues that users should be aware of. A full list of known bugs and feature requests is available at http://trac.sasview.org/report/3
+      - Blocker
+         Ticket #1131: OpencCl dialog does not open                                              assigned wojciech defect blocker
+         Ticket #1132: Slit Size Calculator Tool not working                                     assigned krzywon defect blocker
+         Ticket #1133: Reference in Acknowledging SasView box will need updating for release     assigned ajj task blocker
+         Ticket #1142: Plugin framework is broken                                                reopened pkienzle defect blocker
+      - Critical
+         Ticket #1148: Documentation for S(Q) models need updating SasView 4.2.0                 assigned butler defect critical
+      - Other Significant
+         Ticket #1046: convert non builtin models in the marketplace to new API                  assigned butler task major
+         Ticket #1128: AutoPlot generation for model documentation does not include background   assigned pkienzle defect major
+         Ticket #1140: Batch Slicer requires plotting of all 2D data sets to use in batch        assigned krzywon enhancement major
+         Ticket #1141: Intro to scripting.rst needs improvement                                  new pkienzle enhancement major
+         Ticket #1143: Validate new orientation distribution                                     assigned butler task major
+         Ticket #1144: Redundant MultiplicationModel class                                       new pkienzle defect major
+      - Model Issues
+         Corrections will be posted to Marketplace as available (and fixed in following release)
+         Ticket #1044: Unable to upload c file to marketplace                                    assigned tim defect major
+
+      It is recommended that all users upgrade to this version, but your attention is drawn to the Changes section above.
+
+
+    - New in Version 4.1.2
+      --------------------
+      This point release is a bug-fix release addressing:
+
+       - Fixes #984: PDF Reports Generate Empty PDFs
+       - Fixes a path typo
+       - 64 bit and 32 bit Windows executables now available
+
+      It is recommended that all users upgrade to this version
+
+
+    - New in Version 4.1.1
+      --------------------
+      This point release is a bug-fix release addressing:
+
+       - Fixes #948: Mathjax CDN is going away
+       - Fixes #938: Cannot read canSAS1D file output by SasView
+       - Fixes #960: Save project throws error if empty fit page
+       - Fixes #929: Problem deleting data in first fit page
+       - Fixes #918: Test folders not bundled with release
+       - Fixes an issue with the live discovery of plugin models
+       - Fixes an issue with the NXcanSAS data loader
+       - Updated tutorials for SasView 4.x.y
+
+
+    - New in Version 4.1.0
+      ------------------
+      This incremental release brings a series of new features and improvements,
+      and a host of bug fixes. Of particular note are:
+      
+      - Correlation Function Analysis (Corfunc)
+        This performs a correlation function analysis of one-dimensional SAXS/SANS data, 
+            or generates a model-independent volume fraction profile from the SANS from an 
+            adsorbed polymer/surfactant layer.
+
+            A correlation function may be interpreted in terms of an imaginary rod moving 
+            through the structure of the material. Γ1D(R) is the probability that a rod of 
+            length R moving through the material has equal electron/neutron scattering 
+            length density at either end. Hence a frequently occurring spacing within a 
+            structure manifests itself as a peak.
+
+            A volume fraction profile \Phi(z) describes how the density of polymer 
+            segments/surfactant molecules varies with distance from an (assumed locally flat)
+            interface.
+
+      - Fitting of SESANS Data
+        Data from Spin-Echo SANS measurements can now be loaded and fitted. The data will 
+            be plotted against the correct axes and models will automatically perform a Hankel 
+            transform in order to calculate SESANS from a SANS model.
+
+      - Documentation
+        The documentation has undergone significant checking and updating.
+
+      - Improvements
+        - Correlation function (corfunc) analysis of 1D SAS data added from CCP13
+        - File converter tool for multi-file single column data sets
+        - SESANS data loading and direct fitting using the Hankel transformation
+        - Saving and loading of simultaneous and constrained fits now supported
+        - Save states from SasView v3.x.y now loaded using sasmodel model names
+        - Saving and loading of projects with 2D fits now supported
+        - Loading a project removes all existing data, fits, and plots
+        - Structure factor and form factor can be plotted independently
+        - OpenCL is disabled by default and can be enabled through a fit menu
+        - Data and theory fields are now independently expandable
+      - Bug Fixes
+        - Fixes #667: Models computed multiple times on parameters changes
+        - Fixes #673: Custom models override built in models of same name
+        - Fixes #678: Hard crash when running complex models on GPU
+        - Fixes $774: Old style plugin models unloadable
+        - Fixes #789: stacked disk scale doesn't match cylinder model
+        - Fixes #792: core_shell_fractal uses wrong effective radius
+        - Fixes #800: Plot range reset on plot redraws
+        - Fixes #811 and #825: 2D smearing broken
+        - Fixes #815: Integer model parameter handling
+        - Fixes #824: Cannot apply sector averaging when no detector data present
+        - Fixes #830: Cansas HDF5 reader fully compliant with NXCanSAS v1.0 format
+        - Fixes #835: Fractal model breaks with negative Q values
+        - Fixes #843: Multilayer vesicle does not define effective radius
+        - Fixes #858: Hayter MSA S(Q) returns errors
+        - Numerous grammatical and contexual errors in documention
+
+
+    - New in Version 4.0.1
+      ------------------
+      This release fixes the critical bug #750 in P(Q)*S(Q).  Most damaging
+      it appears that the background term was being added to S(Q) prior to
+      multiplication by P(Q).
+
+
+    - New in Version 4.0
+      ------------------
+      This release fixes the various bugs found during the alpha and beta testing
+      - Improvements
+        - Support for reading data files from Anton Paar Saxess instruments
+        - Adds documentation on how to write custom models in the new framework
+      - Bug Fixes
+        - Fixes bug #604 Pringle model questions
+        - Fixes bug #472 Reparameterize Teubner-Strey
+        - Fixes bug #530 Numerical instabilities in Teubner Strey model
+        - Fixes bug #658 ASCII reader very broken
+
+
+    - New in Version 4.0 beta 1
+      --------------------
+      This beta adds support for the magnetic and multilevel models of 3.1.2
+      and along with a host of bug fixes found in the alpha.
+
+      - Model package changes and improvements
+         - All 3.1.2 models now available in new interface
+         - Old custom models should now still work
+            - '''NOTE:''' These will be deprecated in a future version. Old
+            custom models should be converted to the new model format which
+            is now the same as the built in models and offers much better
+            support.
+         - Custom model editor now creates new style models
+         - Custom model editor supports better error checking
+      - Documentation improvements
+        - Continued general cleanup
+      - Other improvements/additions
+         - Support for new canSAS 2D data files added
+         - Plot axes range can now be set manually as well as by zooming
+         - Plot annotations can now be moved around after being placed on plot.
+         - The active optimizer is now listed on the top of the fit panel.
+         - Linear fits now update qmin and max when the x scale limits are
+         changed.  Also the plot range no longer resets after a fit.
+      - Bug fixes
+         - Fixes bug #511 Errors in linearized fits and clean up of interface
+         including Kratky representation
+         - Fixes bug #186 Data operation Tool now executes when something is
+         entered in the text box and does not wait for the user to hit enter
+         - Fixes bug #459 plot context menu bug
+         - Fixes bug #559 copy to clipboard in graph menu broken
+         - Fixes bug #466 cannot remove a linear fit from graph
+         - Numerous bugs introduced in the alpha
+
+
+    - New in Version 4.0.0-alpha
+      --------------------
+      This alpha release brings a major overhaul of the model system. The new model
+      package allows rapid integration of custom models and access to polydispersity
+      without requiring a compiler.
+
+      - Model package changes and improvements
+         - Model interface moved to independent sasmodels package.
+         - Most models converted to new interface.
+         - Allows rapid integration of user-written models.
+         - OpenCL GPU utilization for faster fitting.
+         - Improved numerical integration of Bessel functions.
+      - SESANS integration and implementation
+         - Scripting interface added for analysis of SESANS data.
+         - Hankel transformation now accepts finite acceptance angles.
+         - 2D cosine transformation added for TOF SESANS analysis.
+      - Documentation improvements
+         - The documentation tree was restructured for a better end user experience.
+         - The documentation for each model was revamped and verified by at least
+           two people following the conversion of the model.
+         - Theoretical 1D (and 2D if applicable) scattering curves are auto-generated
+           and added to the model documentation for each model.
+      - Separation of GUI and calculations for future GUI enhancements
+      - Bug fixes
+         - Fixes bug #411 No stop button on simultaneous fit page
+         - Fixes bug #410 Error with raspberry model
+         - Fixes bug #364 Possible inconsistency in Poly_GausCoil model
+         - Fixes bug #439 Hayter Penfold MSA code needs checking
+         - Fixes bug #484 lammellerPC is precision limited
+         - Fixes bug #498 $HOME/.matplotlib conflicts
+         - Fixes bug #348 Control order in which fit parameters appear in the gui
+         - Fixes bug #456 Provide DREAM Results Panel with something to identify
+           data and age of results
+         - Fixes bug #556 Build script improvements for developers
+
+
+   - New in Version 3.1.2
      --------------------
-
+     This release is a major stability improvement, having fixed a serious bug
+     that came to light since release 3.1.1. All users should upgrade.
+
+     - Fixes bug #468 broken remove constraint buttons in
+       simultaneous/constrained fitting panel
+     - Fixes bug #474 resulting from changes in 3.1.1 that had
+       introduced an error in the high-Q of slit-smeared models.
+     - Fixes bug #478 which would cause wx to run out of IDs and result
+       in SasView crashing even if left alone.
+     - Fixes bug #479 missing help button on simultaneous/constrained fit page
+     - Fixes bug #480 GUI resizing issues on simultaneous fit page
+     - Fixes bug #486 broken Report Results
+     - Fixes bug #488 redraw issues in fit page
+
+
+   - New in Version 3.1.1
+     --------------------
+     - Fixes bug #457 that prevented SasView from starting if the user was not
+       connected to the internet, or was behind a proxy server.
+
+
+   - New in Version 3.1.0
+     --------------------
+     - The documentation/help has had a complete overhaul including:
+       - A completely new presentation interface (Sphinx).
+       - Proof reading!
+       - Updating for latest features.
+       - A Help (or sometimes ?) button has been added to every panel, and some
+         sub panels if appropriate, linking to the appropriate section in the
+         documentation.
+       - The model help has been split so that the Details button now brings up
+         a very short pop-up giving the equation being used while HELP goes to
+         the section in the full documentation describing the model.
+       - Extensive help has also been added for the new optimizer engine (see
+         below) including rules of thumb on how and when to choose a given
+         optimizer and what the parameters do.
+     - The optimizer engine has been completely replaced. The new optimizer
+       still defaults to the standard Levenberg-Marquardt algorithm. However 4
+       other optimizers are now also available. Each starts with a set of default
+       parameters which can be tuned. The DREAM optimizer takes the longest but
+       is the most powerful and yields rich information including full parameter
+       correlation and uncertainty plots. A results panel has been added to
+       accommodate this.
+       - The five new optimizers are:
+         - A Levenberg-Marquardt optimizer
+         - A Quasi-Newton BFGS optimizer
+         - A Nelder-Mead Simplex optimizer
+         - A Differential Evolution optimizer
+         - A Monte Carlo optimizer (DREAM)
      - New models were added:
-       - LamellarPolLz
-
+         - MicelleSphCoreModel (currently residing in the Uncategorized category)
      - Existing models were updated:
-       - LamellarPS and LamellarPSHG have been changed to LamellarCaille and 
-         LamellarCailleHG
-       
+         - LamellarPS (bug in polydispersity integration fixed)
+         - RectangularPrismModel
+         - RectangularHollowPrismModel
+         - RectangularHollowPrismInfThinWallsModel
+     - Infrastructure to allow SESANS data to be fit with models was added. This
+       will become available in a future release but can currently be used from
+       the command line with some caveats.
+     - A number of bugs were fixed including a thread crashing issue and an
+       incorrect slit smearing resolution calculation.
+     - Implemented much more robust error logging to enable much easier
+       debugging in general but particularly the debugging of issues reported by
+       SasView users.
+     - A number of infrastructure tasks under the hood to enhance maintainability
+     - Upgrade from Wx 2.8 to Wx 3.0.2 which allows several new features but
+       required significant additional rework as well.
+     - Fully implemented Sphinx to the build process to produce both better
+       user documentation and developer documentation.
+     - Restructuring of the code base to more unified nomenclature and structure
+       so that the source installation tree more closely matches the installer
+       version tree.
+     - Code cleanup (an ongoing task) .
+     - Migration of the repository to github simplifying contributions from
+       non-project personnel through pull requests.
+
+
+   - New in Version 3.0.0
+     --------------------
+     - The GUI look and feel has been refactored to be more familiar for
+       Windows users by using MDI frames. Graph windows are also now free-
+       floating.
+     - Five new models have been added: PringlesModel, CoreShellEllipsoidXTModel,
+       RectangularPrismModel, RectangularHollowPrismModel and
+       RectangularHollowPrismInfThinWallsModel.
+     - The data loader now supports ILL DAT data files and reads the full meta
+       information from canSAS file formats.
+     - Redefined convention for specifying angular parameters for anisotropic
+       models.
+     - A number of minor features have been added such as permitting a log
+       distribution of points when using a model to simulate data, and the
+       addition of a Kratky plot option to the linear plots.
+     - A number of bugs have also been fixed.
+     - Save Project and Save Analysis now work more reliably.
+     - BETA: Magnetic contrast supporting full polarization analysis has been
+       implemented for some spherical and cylindrical models.
+     - BETA: Two new tools have been added:
+       - A generic scattering calculator which takes an atomic, magnetic or
+         SLD distribution in space and generates the appropriate 2D
+         scattering pattern. In some cases the orientationally averaged
+         (powder) 1D scattering can also be computed. Supported formats
+         include: SLD or text, PDB, and OMF magnetic moment distribution
+         file.
+       - An image viewer/converter for data in image format; this reads in
+         an image file and will attempt to convert the image pixels to
+         data. Supported formats include: TIFF, TIF, PNG, BMP, JPG.
+
+
+   - New in Version 2.2.1
+     --------------------
+     - Minor patch to support CanSAS XML v1.1 file format
+     - Added DataInfo for data in the DataExplorer and plots
+     - Added Maximize/Restore button in the title bar of the graphs
+     - Added a hide button in the toolbar of the graph panel
+     - The 'x' button now deletes a graph
+     - Edit SUM Model from the menubar can now generate and save more than one sum model
+     - Reports can now be saved in pdf format on WIN and MAC
+     - Made significant improvements to the batch/grid panel and fixed several bugs
+     - Fixed a number of other minor bugs
+
+
+   - New in Version 2.2.0
+     --------------------
+     - Application name changed to SasView
+     - New fully customizable Category Manager added for better management of
+       increasing number of models
+     - Improved the Grid Window functionality in the batch fitting mode
+     - Added a simpler Graph/Plot modification interface
+     - Added a new 'Data Operation' tool for addition, subtraction, multiplication,
+       division, of two data sets.
+     - The 'Sum Model' editor was extended and renamed 'Summation and Multiplication'
+       editor
+     - Added more plot symbols options for 1d plots
+     - Added improved trapping of compiling errors to the 'New model editor'
+     - Added some intelligent outputs (e.g., Rg, background, or rod diameter
+       depending on the choice of axis scale of the plot) to the linear fits
+     - Added more models
+
+   - Feature set from previous versions
+     -----------------------------------
+     - Perspectives Available
+       - Invariant calculator: Calculates the invariant, volume fraction, and
+         specific surface area.
+       - P(r) inversion calculator: Indirect Fourier transformation method.
+       - Fitting: the tool used for modeling and fitting 1D and 2D data to
+         analytical model functions
+       - Tools: provides a number of useful supplementary tools such as SLD
+         calculation
+
+     - Fitting
+       - Includes a large number of model functions, both form factors and structure factors.
+       - Support P(Q)*S(Q) for form factors that flag they can be so multiplied.
+       - Supports Gaussian, lognormal, Shulz, rectangular and custom distribution
+         functions for models that need to include polydispersity or for orientational
+         distributions if appropriate.
+       - Anisotropic shapes and magnetic moment modeling in 2D allow for a non-uniform
+         distribution of orientations of a given axis leading to modeling and fitting
+         capabilities of non azimuthaly symmetric data.
+       - User can choose to weight fits or not. If using weights, the user can choose
+         the error bar on each point if provided in the file, the square root
+         of the intensity or the intensity itself.
+       - Instrumental resolution smearing of model or fits is provided with several
+         options: read the resolution/point fromt he file. Input a pinhole resolution
+         or a slit resolution.
+       - Users can define the Qrange (Qmin and Qmax) for both 1D and 2D data for
+         fitting and modeling, but not graphically.  The range can be reset to the
+         defaults (limits of q in data set for a fit) with the reset button.
+       - A mask can be applied to 2D calculation and fitting.
+       - Normalized residual plots are provided with every fit.
+       - Model function help available through detail button or from the fitting panel.
+       - Simultaneous/(advanced)constrained fitting allows for fitting a single
+         data set or several different sets simultaneously with the application
+         of advanced constraints relating fit parameters to functions of other
+         parameters (including from a different set). For example thickness of
+         shell = sin(30) times the length.
+       - Models that are the sum of two other models can be easily generated through the
+         SUM Model menubar item.
+       - New Python models can be added on the fly by creating an appropriate Python
+         file in the model plugin directory. Two tools are provided to help:
+         An easy to use custom model editor allows the quick generation of new Python
+         models by supplying only the parameters and their default value (box 1)
+         and the mathematical function of the model (box 2) and generating the
+         necessary *.py file.  A separate advanced model editor provides a full Python
+         file editor.  Either way once saved the model becomes immediately available
+         to the application.
+       - A batch fitting capability allows for the analysis of a series of data sets to
+         a single model and provides the results in a tabular form suitable for saving
+         or plotting the evolution of the fit parameters with error bars (from within
+         the application).
+
+     - Tools
+       - A scattering length density calculator,including some X-ray information
+         is provided.
+       - A density to vol. fraction converter is provided
+       - In application access to a Python shell/editor (PyCrust) is provided
+       - An instrument resolution calculator, including possible gravitational and
+         TOF effects is provided
+       - A slit size calculator optimized for Anton Paar Saxess is provided.
+       - A kiessig fringe thickness calculator is provided
+
+     - Plots and plot management
+       - A 3D graphing option (for 2d data/results) is provided with the view
+         controlled by the mouse
+       - 2D plots are shown with an intensity color bar. 2D Color map can be user
+         adjusted.
+       - Supports output of plot to a variety of graphic formats. Supported formats
+         include: png, eps, emf, jpg/jpeg, pdf, ps, tif/tiff, rawRGBbitmap(raw, rgba),
+         and scalable vector graphic (svg/svgz)
+       - Supports ouput of data in plot (1 or 2D) to limited data formats
+       - Multiple data sets can be loaded into a single graph for viewing (but a fit
+         plot can currently only have a single plot).
+       - Extensive context sensitive plot/fitting/manipulation options are available
+         through a right mouse click pop-up menu on plots.
+
+     - Data management
+       - Supports 2 + column 1D ASCII data, NIST 1D and 2D data, and canSAS data
+         via plug-in mechanism which can easily allow other readers as appropriate.
+       - 2D data is expected in Q space but for historical reasons accepts the
+         NIST 2D raw pixel format and will do conversion internally.
+       - The full data and metadata available to SasView is viewable in ASCII via
+         right clicking on a data set and choosing Data Info in the DataExplorer
+         or on the plots
+       - Supports loading a single file, multiple files, or a whole folder
+       - An optional Data Explorer is provided (default) which simplifies managing,
+         plotting, deleting, or setup for computation. Most functions however do
+         not require access to the explorer/manager and can be accessed through
+         right click menus and the toolbar.  The data explorer can be re-started
+         from the menu bar.
+
+     - Data manipulation
+       - Support various 2D averaging methods : Circular, sectors, annular,
+         boxsum, boxQx and boxQy.
+       - A 2D data maks editor is provided
+       - 2D mask can be applied to the circular averaging.
+
+     - Miscellaneous features
+       - limited reports can be generated in pdf format
+       - Provides multiprocessor support(Windows only)
+       - Limited startup customization currently includes default startup
+         data folder and choice of default starting with data manager
+       - Limited support for saving(opening) a SasView project or a SasView analysis
+         (subproject) is provided.
+       - SasView can be launched and loaded with a file of interesty by double-clicking
+         on that file (recognized extension)
+       - A data file or data folder can be passed to SasView when launched from
+         the command line.
+       - Limited bookmarking capability to later recall the results of a fit calculation
+         is provided.
+       - Extensive help is provided through context sensitive mouse roll-over,
+         information bar (at the bottom of the panel), the console menu, and
+         access to the help files in several different ways.
+
+
+2- Downloading and Installing
+=============================
+
+   *** Note 1:  Much more information is available at www.sasview.org under links.
+                    Look in the 'For Developers' section and particularly the wiki at
+                www.sasview.org/trac/wiki.
+   *** Note 2:  If you have EXE or ZIP SasView installer, you won't need any of
+                the following.  However it is highly recommended that any
+                previous versions be un-installed prior to installing the
+                new version.
+
+   2.1- System Requirements
+        - Python version >= 2.5 and < 3.0 should be running on the system
+        - We currently use Python 2.7
+
+   2.2- Installing from source
+        - Get the source code
+          - to follow the current development version from source control use
+              git clone https://github.com/SasView/sasview.git
+              git clone https://github.com/bumps/bumps.git
+          - to install a specific version
+
+        - Build, install and run a specific release
+          - make sure the requirements below are already installed
+          - retrieve the source from https://github.com/SasView/sasview/releases
+          - open a command line window in the 'sasview-x.x.x' directory
+          - run 'python setup.py install'
+          - run 'python sasview.py' under the 'sasview' folder.
+
+        - Build, install and run the current development version
+          - clone the source from git; also clone bumps, which is developed in parallel
+              git clone https://github.com/SasView/sasview.git
+              git clone https://github.com/bumps/bumps.git
+          - open a command line window in the 'sasview' directory
+          - run 'python setup.py build'
+          - run 'python run.py'; this runs from the source directories, so you
+            don't have to rebuild every time you make a change, unless you are
+            changing the C++ model files
+
+        - The following modules are required (version numbers are what are used
+          in the windows release build):
+
+          - Common Packages
+            - reportlab 3.1.44
+            - lxml 3.4.4.0 (MAC 3.4.2.0)
+            - PIL 1.1.7
+            - xhtml2pdf 3.0.33 (MAC = not installed on build server)
+            - unittest-xml-reporting 1.12.0 (MAC 1.10.0)
+            - matplotlib Version Installed: 1.4.3 (MAC 1.1.1)
+            - bumps Version Installed: 0.7.5.9
+            - scipy Version Installed: 0.16.0b2 (MAC 0.11.0)
+            - periodictable Version Installed: 1.4.1
+            - setuptools Version Installed: 7.0 (MAC 12.0.5)
+            - sphinx Version Installed: 1.3.1 (MAC 1.3b2)
+            - pyparsing Version Installed: 2.0.3
+            - numpy Version Installed: 1.9.2 (MAC 1.6.2)
+            - html5lib Version Installed: 0.99999
+            - wx Version Installed: 3.0.2.0
+
+          - Windows Specific Packages
+            - pywin 219
+            - py2exe 0.6.9
+            - comtypes 1.1.1
+            - MinGW w/ gcc version 4.6.1 (WIN)
+            - vcredist_x86.exe (version 9.0.21022.8  -microsoft visual C 2008
+              re-distributable)
+            - Innosetup (WIN - isetup 5.4.2-unicode) - used to create distributable
+
+            *** Note: Windows build dependencies can be set up using anaconda. Instructions
+                can be found at http://trac.sasview.org/wiki/AnacondaSetup
+
+          - MAC Specifc Packages
+            - py2app 0.7.1
+
+
+3- Known Issues
+===============
+
+   4.1- All systems:
+      The conversion to sasmodels infrastructure is ongoing and should be
+      completed in the next release. In the meantime this leads to a few known
+      issues:
+        - The way that orientation is defined is being refactored to address
+        long standing issues and comments.  In release 4.1 however only models
+        with symmetry (e.g. a=b) have been converted to the new definitions.
+        The rest (a <> b <> c - e.g. parellelepiped) maintain the same
+        definition as before and will be converted in 4.2.  Note that
+        orientational distribution also makes much more sense in the new
+        framework.  The documentation should indicate which definition is being
+        used for a given model.
+        - The infrastructure currently handles internal conversion of old style
+        models so that user created models in previous versions should continue
+        to work for now. At some point in the future such support will go away.
+        Everyone is encouraged to convert to the new structure which should be
+        relatively straight forward and provides a number of benefits. 
+        - In that vein, the distributed models and those generated by the new
+        plugin model editor are in the new format, however those generated by
+        sum|multiply models are the old style sum|multiply models. This should
+        also disappear in the near future 
+        - The on the fly discovery of plugin models and changes thereto behave
+        inconsistently.  If a change to a plugin model does not seem to
+        register, the Load Plugin Models (under fitting -> Plugin Model
+        Operations) can be used.  However, after calling Load Plugin Models, the
+        active plugin will no longer be loaded (even though the GUI looks like
+        it is) unless it is a sum|multiply model which works properly.  All
+        others will need to be recalled from the model dropdown menu to reload
+        the model into the calculation engine.  While it might be annoying it
+        does not appear to prevent SasView from working..
+        - The model code and documentation review is ongoing. At this time the
+        core shell parellelepiped is known to have the C shell effectively fixed
+        at 0 (noted in documentation) while the triaxial ellipsoid does not seem
+        to reproduce the limit of the oblate or prolate ellipsoid. If errors are
+        found and corrected, corrected versions will be uploaded to the
+        marketplace. 
+   
+   3.1- All systems:
+        - The documentation window may take a few seconds to load the first time
+          it is called. Also, an internet connection is required before
+          equations will render properly. Until then they will show in their
+          original TeX format.
+        - If the documentation window remains stubbornly blank, try installing a
+          different browser and set that as your default browser. Issues have
+          been noted with Internet Explorer 11.
+        - Check for Updates may fail (with the status bar message ' Cannot
+          connect to the application server') if your internet connection uses
+          a proxy server. Tested resolutions for this are described on the
+          website FAQ.
+        - The copy and paste functions (^C, ^V) in the batch mode results grid
+          require two clicks: one to select the cell and a second to select the
+          contents of the cell.
+        - The tutorial has not yet been updated and is somewhat out of date
+        - Very old computers may struggle to run the 3.x and later releases
+        - Polydispersity on multiple parameters included in a simultaneous/
+          constrained fit will likely not be correct
+        - Constrained/simultaneous fit page does not have a stop button
+        - Constrained/simultaneous fit do not accept min/max limits
+        - Save project does not store the state of all the windows
+        - Loading projects can be very slow
+        - Save Project only works once a data set has been associated with
+          a model.  Error is reported on status bar.
+        - There is a numerical precision problem with the multishell model when
+          the iner radius gets large enough (ticket #288)
+        - The angular distribution angles are not clearly defined and may in
+          some cases lead to incorrect calculations(ticket #332)
+
+   3.2- Windows:
+        - If installed to same directory as old version without first removing
+          the old version, the old desktop icon will remain but point to the
+          new exe version. Likewise all the start menu folders and items will
+          have the old name even though pointing to the new version.  Usually
+          safest to uninstall old version prior to installing new version anyway.
+
+   3.3- MAC:
+        - Application normally starts up hidden. Click icon in Dock to view/use
+          application.
+        - Multiprocessing does not currently work on MAC OS
+
+   3.4- Linux:
+        - Not well tested
+
+
+4- SasView website
+==================
+
+   - www.sasview.org.  This main project site is the gateway to all
+     information about the sasview project.  It includes information
+     about the project, a FAQ page and links to all developer and user
+     information, tools and resources.
+
+
+5- Frequently Asked Questions
+=============================
+
+   - www.sasview.org/faq.html
+
+
+6- Installer download website
+=============================
+
+   - Latest release Version
+     - https://github.com/SasView/sasview/releases
+   - Latest developer builds
+     - https://jenkins.esss.dk/sasview/view/Master-Builds/

installers/README.txt

@@ -1 +1 @@
 Release Notes
 =============
-
+    This is a beta pre-release version of 4.2.0.  A number of fixes and changes
+    have been made in the year since the previous release.  
+    Full release notes will be compiled prior to the full release 4.2.0.
+    
+    Highlights are:
+        - Infrastucture for calculating 2D patterns from 3D orientated objects
+          has now been totally refactored
+        - Plugins have completely migrated to the new infrastructure now, 
+          including sum/multiply models
+        - Some batch slicing options have been introduced
+        - The known issue with the core_shell_parallelepiped is now fixed
+        - Several data loading improvements
+        - Several save Project improvements (though there are more to come)
+        - Numerous bug fixes
+        - Lots of documentation enhancement
+    
+    In the meantime please report any bugs or issues found while using this beta
+    
 1- Features
 ===========

src/sas/sascalc/dataloader/readers/abs_reader.py

@@ -171 +171 @@
 
                 try:
-                    _x = float(toks[0])
+                    _x = float(toks[4])
                     _y = float(toks[1])
                     _dy = float(toks[2])

src/sas/sascalc/fit/pagestate.py

@@ -13 +13 @@
 ################################################################################
 import time
+import re
 import os
 import sys
@@ -962 +963 @@
         if node.get('version'):
             # Get the version for model conversion purposes
-            self.version = tuple(int(e) for e in
-                                 str.split(node.get('version'), "."))
+            x = re.sub('[^\d.]', '', node.get('version'))
+            self.version = tuple(int(e) for e in str.split(x, "."))
             # The tuple must be at least 3 items long
             while len(self.version) < 3:

src/sas/sasgui/guiframe/local_perspectives/plotting/parameters_panel_slicer.py

@@ -251 +251 @@
             self.bck.Add(self.batch_slicer_button, (iy, ix), (1, 1),
                          wx.LEFT | wx.EXPAND | wx.ADJUST_MINSIZE, 15)
+            # Help button
+
+            self.bt_help = wx.Button(self, wx.NewId(), "HELP")
+            self.bt_help.SetToolTipString(
+                "Help for the slicer parameters and batch slicing.")
+            self.bck.Add(self.bt_help, (iy, 1), (1, 1),
+                         wx.ALIGN_RIGHT | wx.ADJUST_MINSIZE, 15)
+            wx.EVT_BUTTON(self, self.bt_help.GetId(), self.on_help)
+
             iy += 1
             self.bck.Add((5, 5), (iy, ix), (1, 1),
                          wx.LEFT | wx.EXPAND | wx.ADJUST_MINSIZE, 5)
+
         self.bck.Layout()
         self.bck.Fit(self)
@@ -535 +545 @@
             self.default_value += "_{0}".format(key).split(" [")[0]
             self.default_value += "-{:.2f}".format(params[key])
+
+    def on_help(self, event=None):
+        """
+        Opens a help window for the slicer parameters/batch slicing window
+        :param event:
+        :return:
+        """
+        from sas.sasgui.guiframe.documentation_window import DocumentationWindow
+
+        _TreeLocation = "user/sasgui/guiframe/graph_help.html"
+        _doc_viewer = DocumentationWindow(self, wx.ID_ANY, _TreeLocation,
+                                          "#d-data-averaging",
+                                          "Data Explorer Help")

src/sas/sasgui/guiframe/media/graph_help.rst

@@ -266 +266 @@
 
 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+.. _d_data_averaging:
 
 2D data averaging
@@ -301 +302 @@
 Alternatively, once a 'slicer' is active you can also select the region to
 average by bringing back the *Dataset Menu* and selecting *Edit Slicer
-Parameters*. A dialog window will appear in which you can enter values to
-define a region or select the number of points to plot (*nbins*).
+Parameters and Batch Fitting*. A dialog window will appear in which you can
+enter values to define a region, select the number of points to plot (*nbins*),
+or apply the slicer to any or all other 2D data plots.
 
 A separate plot window will also have appeared, displaying the requested
@@ -315 +317 @@
 
 To remove a 'slicer', bring back the *Dataset menu* and select *Clear Slicer*.
+
+Batch Slicing
+^^^^^^^^^^^^^
+
+A slicer can be applied to any or all existing 2D data plots using the 'Slicer
+Parameters' window. To open the window, select *Edit Slicer Parameters and Batch
+Fitting* in the *Dataset Menu* (see Invoking_the_dataset_menu_). Batch slicing
+options are available at the bottom of the window.
+
+Select the 2D plots you want to apply the slicer to. All 2D plots are selected
+by default. The resulting 1D data for all slicers can be saved as a text file
+and then sent to fitting by selecting the *Auto save generated 1D* check box.
+Sending data to the fitting perspective requires the data be saved.
+
+Once the auto save check box is selected, you can select where the files are
+saved. The file name for the saved data is the slicer name plus the file name
+of the original data set, plus what is in the *Append to file name* field. The
+default value in the append to field includes the names and values for all of
+the slicer parameters.
+
+The batch of slices can be sent to fitting if desired, with three options
+available. The first is to not fit the data, the second is to send the
+slices to individual fit pages, and the third is to send all sliced data to a
+single batch fit window.
+
+Clicking *Apply Slicer to Selected Plots* will create a slicer for each selected
+plot with the parameters entered in the 'Slicer Parameters' window. Depending on
+the options selected the data may then be saved, loaded as separate data sets in
+the data manager panel, and finally sent to fitting.
 
 Unmasked circular average

src/sas/sasgui/perspectives/calculator/pyconsole.py

@@ -28 +28 @@
     Check that the model on the path can run.
     """
+    # TODO: fix model caching
+    # model_test.run_one() is directly forcing a reload of the module, but
+    # sasview_model is caching models that have already been loaded.
+    # If the sasview load happens before the test, then the module is
+    # reloaded out from under it, which causes the global variables in
+    # the model function definitions to be cleared (at least in python 2.7).
+    # To fix the proximal problem of models failing on test, perform the
+    # run_one() tests first.  To fix the deeper problem we should either
+    # remove caching from sasmodels.sasview_model.load_custom_model() or
+    # add caching to sasmodels.custom.load_custom_kernel_module().  Another
+    # option is to add a runTests method to SasviewModel which runs the
+    # test suite directly from the model info structure.  Probably some
+    # combination of options:
+    #    (1) have this function (check_model) operate on a loaded model
+    #    so that caching isn't needed in sasview_models.load_custom_model
+    #    (2) add the runTests method to SasviewModel so that tests can
+    #    be run on a loaded module.
+    #
+    # Also, note that the model test suite runs the equivalent of the
+    # "try running the model" block below, and doesn't need to be run
+    # twice.  The reason for duplicating the block here is to generate
+    # an exception that show_model_output can catch.  Need to write the
+    # runTests method so that it returns success flag as well as output
+    # string so that the extra test is not necessary.
+
+    # check the model's unit tests run
+    from sasmodels.model_test import run_one
+    result = run_one(path)
+
+    # remove cached version of the model, if any
+    from sasmodels import sasview_model
+    sasview_model.MODEL_BY_PATH.pop(path, None)
+
     # try running the model
-    from sasmodels.sasview_model import load_custom_model
-    Model = load_custom_model(path)
+    Model = sasview_model.load_custom_model(path)
     model = Model()
     q =  np.array([0.01, 0.1])
@@ -36 +68 @@
     qx, qy =  np.array([0.01, 0.01]), np.array([0.1, 0.1])
     Iqxy = model.evalDistribution([qx, qy])
-
-    # check the model's unit tests run
-    from sasmodels.model_test import run_one
-    result = run_one(path)
 
     return result

src/sas/sasgui/perspectives/calculator/slit_length_calculator_panel.py

@@ -248 +248 @@
             Complete the loading and compute the slit size
         """
+        if isinstance(data, list):
+            data = data[0]
         if data is None or data.__class__.__name__ == 'Data2D':
             if self.parent.parent is None:

src/sas/sasgui/perspectives/fitting/basepage.py

@@ -2552 +2552 @@
             # draw
             self._draw_model()
+            self.Layout()
             self.Refresh()
         except Exception:

src/sas/sasgui/perspectives/fitting/fitpage.py

@@ -706 +706 @@
 
                         ix = 3
-                        ctl2 = wx.TextCtrl(self, wx.ID_ANY,
-                                           size=(_BOX_WIDTH / 1.3, 20),
-                                           style=0)
+                        ctl2 = BGTextCtrl(self, wx.ID_ANY,
+                                           size=(_BOX_WIDTH / 1.3, 20))
 
                         self.sizer4_4.Add(ctl2, (iy, ix), (1, 1),
@@ -1998 +1997 @@
         self.on_smear_helper()
         self.on_set_focus(None)
+        self.Layout()
         self.Refresh()
         # update model plot with new data information
@@ -2892 +2892 @@
                         text2.Hide()
                     ix += 1
-                    ctl2 = wx.TextCtrl(self, wx.ID_ANY,
-                                       size=(_BOX_WIDTH / 1.2, 20), style=0)
+                    ctl2 = BGTextCtrl(self, wx.ID_ANY,
+                                       size=(_BOX_WIDTH / 1.2, 20))
                     sizer.Add(ctl2, (iy, ix), (1, 1),
                               wx.EXPAND | wx.ADJUST_MINSIZE, 0)

src/sas/sasview/__init__.py

@@ -1 @@
-__version__ = "4.2.0"
+__version__ = "4.2.0-beta"
 __build__ = "GIT_COMMIT"

test/sasdataloader/test/utest_abs_reader.py

@@ -53 +53 @@
 
         self.assertEqual(self.data.y_unit, 'cm^{-1}')
-        self.assertEqual(self.data.x[0], 0.002618)
-        self.assertEqual(self.data.x[1], 0.007854)
-        self.assertEqual(self.data.x[2], 0.01309)
+        self.assertEqual(self.data.x[0], 0.008082)
+        self.assertEqual(self.data.x[1], 0.0275)
+        self.assertEqual(self.data.x[2], 0.02762)
         self.assertEqual(self.data.x[126], 0.5828)
 

src/sas/sascalc/data_util/nxsunit.py

@@ -136 +136 @@
     sld = { '10^-6 Angstrom^-2': 1e-6, 'Angstrom^-2': 1 }
     Q = { 'invA': 1, 'invAng': 1, 'invAngstroms': 1, '1/A': 1,
+          '1/Angstrom': 1, '1/angstrom': 1, 'A^{-1}': 1, 'cm^{-1}': 1e-8,
           '10^-3 Angstrom^-1': 1e-3, '1/cm': 1e-8, '1/m': 1e-10,
-          'nm^-1': 0.1, '1/nm': 0.1, 'n_m^-1': 0.1 }
+          'nm^{-1}': 1, 'nm^-1': 0.1, '1/nm': 0.1, 'n_m^-1': 0.1 }
 
     _caret_optional(sld)
@@ -157 +158 @@
     # units for that particular dimension.
     # Note: don't have support for dimensionless units.
-    unknown = {None:1, '???':1, '': 1, 'a.u.': 1}
+    unknown = {None:1, '???':1, '': 1, 'a.u.': 1, 'Counts': 1, 'counts': 1}
 
     def __init__(self, name):

src/sas/sascalc/dataloader/file_reader_base_class.py

@@ -16 +16 @@
 from .data_info import Data1D, Data2D, DataInfo, plottable_1D, plottable_2D,\
     combine_data_info_with_plottable
+from sas.sascalc.data_util.nxsunit import Converter
 
 logger = logging.getLogger(__name__)
@@ -98 +99 @@
                     if len(self.output) > 0:
                         # Sort the data that's been loaded
-                        self.sort_one_d_data()
-                        self.sort_two_d_data()
+                        self.convert_data_units()
+                        self.sort_data()
         else:
             msg = "Unable to find file at: {}\n".format(filepath)
@@ -166 +167 @@
         self.output.append(data_obj)
 
-    def sort_one_d_data(self):
+    def sort_data(self):
         """
         Sort 1D data along the X axis for consistency
@@ -174 +175 @@
                 # Normalize the units for
                 data.x_unit = self.format_unit(data.x_unit)
+                data._xunit = data.x_unit
                 data.y_unit = self.format_unit(data.y_unit)
+                data._yunit = data.y_unit
                 # Sort data by increasing x and remove 1st point
                 ind = np.lexsort((data.y, data.x))
@@ -203 +206 @@
                     data.ymin = np.min(data.y)
                     data.ymax = np.max(data.y)
+            elif isinstance(data, Data2D):
+                # Normalize the units for
+                data.Q_unit = self.format_unit(data.Q_unit)
+                data.I_unit = self.format_unit(data.I_unit)
+                data._xunit = data.Q_unit
+                data._yunit = data.Q_unit
+                data._zunit = data.I_unit
+                data.data = data.data.astype(np.float64)
+                data.qx_data = data.qx_data.astype(np.float64)
+                data.xmin = np.min(data.qx_data)
+                data.xmax = np.max(data.qx_data)
+                data.qy_data = data.qy_data.astype(np.float64)
+                data.ymin = np.min(data.qy_data)
+                data.ymax = np.max(data.qy_data)
+                data.q_data = np.sqrt(data.qx_data * data.qx_data
+                                         + data.qy_data * data.qy_data)
+                if data.err_data is not None:
+                    data.err_data = data.err_data.astype(np.float64)
+                if data.dqx_data is not None:
+                    data.dqx_data = data.dqx_data.astype(np.float64)
+                if data.dqy_data is not None:
+                    data.dqy_data = data.dqy_data.astype(np.float64)
+                if data.mask is not None:
+                    data.mask = data.mask.astype(dtype=bool)
+
+                if len(data.data.shape) == 2:
+                    n_rows, n_cols = data.data.shape
+                    data.y_bins = data.qy_data[0::int(n_cols)]
+                    data.x_bins = data.qx_data[:int(n_cols)]
+                    data.data = data.data.flatten()
+                    data = self._remove_nans_in_data(data)
+                if len(data.data) > 0:
+                    data.xmin = np.min(data.qx_data)
+                    data.xmax = np.max(data.qx_data)
+                    data.ymin = np.min(data.qy_data)
+                    data.ymax = np.max(data.qx_data)
 
     @staticmethod
@@ -242 +281 @@
         return data
 
-    def sort_two_d_data(self):
-        for dataset in self.output:
-            if isinstance(dataset, Data2D):
-                # Normalize the units for
-                dataset.x_unit = self.format_unit(dataset.Q_unit)
-                dataset.y_unit = self.format_unit(dataset.I_unit)
-                dataset.data = dataset.data.astype(np.float64)
-                dataset.qx_data = dataset.qx_data.astype(np.float64)
-                dataset.xmin = np.min(dataset.qx_data)
-                dataset.xmax = np.max(dataset.qx_data)
-                dataset.qy_data = dataset.qy_data.astype(np.float64)
-                dataset.ymin = np.min(dataset.qy_data)
-                dataset.ymax = np.max(dataset.qy_data)
-                dataset.q_data = np.sqrt(dataset.qx_data * dataset.qx_data
-                                         + dataset.qy_data * dataset.qy_data)
-                if dataset.err_data is not None:
-                    dataset.err_data = dataset.err_data.astype(np.float64)
-                if dataset.dqx_data is not None:
-                    dataset.dqx_data = dataset.dqx_data.astype(np.float64)
-                if dataset.dqy_data is not None:
-                    dataset.dqy_data = dataset.dqy_data.astype(np.float64)
-                if dataset.mask is not None:
-                    dataset.mask = dataset.mask.astype(dtype=bool)
-
-                if len(dataset.data.shape) == 2:
-                    n_rows, n_cols = dataset.data.shape
-                    dataset.y_bins = dataset.qy_data[0::int(n_cols)]
-                    dataset.x_bins = dataset.qx_data[:int(n_cols)]
-                dataset.data = dataset.data.flatten()
-                dataset = self._remove_nans_in_data(dataset)
-                if len(dataset.data) > 0:
-                    dataset.xmin = np.min(dataset.qx_data)
-                    dataset.xmax = np.max(dataset.qx_data)
-                    dataset.ymin = np.min(dataset.qy_data)
-                    dataset.ymax = np.max(dataset.qx_data)
+    @staticmethod
+    def set_default_1d_units(data):
+        """
+        Set the x and y axes to the default 1D units
+        :param data: 1D data set
+        :return:
+        """
+        data.xaxis("\\rm{Q}", '1/A')
+        data.yaxis("\\rm{Intensity}", "1/cm")
+        return data
+
+    @staticmethod
+    def set_default_2d_units(data):
+        """
+        Set the x and y axes to the default 2D units
+        :param data: 2D data set
+        :return:
+        """
+        data.xaxis("\\rm{Q_{x}}", '1/A')
+        data.yaxis("\\rm{Q_{y}}", '1/A')
+        data.zaxis("\\rm{Intensity}", "1/cm")
+        return data
+
+    def convert_data_units(self, default_q_unit="1/A", default_i_unit="1/cm"):
+        """
+        Converts al; data to the sasview default of units of A^{-1} for Q and
+        cm^{-1} for I.
+        :param default_x_unit: The default x unit used by Sasview
+        :param default_y_unit: The default y unit used by Sasview
+        """
+        new_output = []
+        for data in self.output:
+            if data.isSesans:
+                new_output.append(data)
+                continue
+            file_x_unit = data._xunit
+            data_conv_x = Converter(file_x_unit)
+            file_y_unit = data._yunit
+            data_conv_y = Converter(file_y_unit)
+            if isinstance(data, Data1D):
+                try:
+                    data.x = data_conv_x(data.x, units=default_q_unit)
+                    data._xunit = default_q_unit
+                    data.x_unit = default_q_unit
+                    if data.dx is not None:
+                        data.dx = data_conv_x(data.dx, units=default_q_unit)
+                    if data.dxl is not None:
+                        data.dxl = data_conv_x(data.dxl, units=default_q_unit)
+                    if data.dxw is not None:
+                        data.dxw = data_conv_x(data.dxw, units=default_q_unit)
+                except KeyError:
+                    message = "Unable to convert Q units from {0} to 1/A."
+                    message.format(default_q_unit)
+                    data.errors.append(message)
+                try:
+                    data.y = data_conv_y(data.y, units=default_i_unit)
+                    data._yunit = default_i_unit
+                    data.y_unit = default_i_unit
+                    if data.dy is not None:
+                        data.dy = data_conv_y(data.dy, units=default_i_unit)
+                except KeyError:
+                    message = "Unable to convert I units from {0} to 1/cm."
+                    message.format(default_q_unit)
+                    data.errors.append(message)
+            elif isinstance(data, Data2D):
+                try:
+                    data.qx_data = data_conv_x(data.qx_data, units=default_q_unit)
+                    if data.dqx_data is not None:
+                        data.dqx_data = data_conv_x(data.dqx_data, units=default_q_unit)
+                    data.qy_data = data_conv_y(data.qy_data, units=default_q_unit)
+                    if data.dqy_data is not None:
+                        data.dqy_data = data_conv_y(data.dqy_data, units=default_q_unit)
+                except KeyError:
+                    message = "Unable to convert Q units from {0} to 1/A."
+                    message.format(default_q_unit)
+                    data.errors.append(message)
+                try:
+                    file_z_unit = data._zunit
+                    data_conv_z = Converter(file_z_unit)
+                    data.data = data_conv_z(data.data, units=default_i_unit)
+                    if data.err_data is not None:
+                        data.err_data = data_conv_z(data.err_data, units=default_i_unit)
+                except KeyError:
+                    message = "Unable to convert I units from {0} to 1/cm."
+                    message.format(default_q_unit)
+                    data.errors.append(message)
+            else:
+                # TODO: Throw error of some sort...
+                pass
+            new_output.append(data)
+        self.output = new_output
 
     def format_unit(self, unit=None):

src/sas/sascalc/dataloader/readers/ascii_reader.py

@@ -157 +157 @@
 
         self.remove_empty_q_values()
-        self.current_dataset.xaxis("\\rm{Q}", 'A^{-1}')
-        self.current_dataset.yaxis("\\rm{Intensity}", "cm^{-1}")
+        self.current_dataset = self.set_default_1d_units(self.current_dataset)
 
         # Store loading process information

src/sas/sascalc/dataloader/readers/cansas_reader.py

@@ -812 +812 @@
             node.append(point)
             self.write_node(point, "Q", datainfo.x[i],
-                            {'unit': datainfo.x_unit})
+                            {'unit': datainfo._xunit})
             if len(datainfo.y) >= i:
                 self.write_node(point, "I", datainfo.y[i],
-                                {'unit': datainfo.y_unit})
+                                {'unit': datainfo._yunit})
             if datainfo.dy is not None and len(datainfo.dy) > i:
                 self.write_node(point, "Idev", datainfo.dy[i],
-                                {'unit': datainfo.y_unit})
+                                {'unit': datainfo._yunit})
             if datainfo.dx is not None and len(datainfo.dx) > i:
                 self.write_node(point, "Qdev", datainfo.dx[i],
-                                {'unit': datainfo.x_unit})
+                                {'unit': datainfo._xunit})
             if datainfo.dxw is not None and len(datainfo.dxw) > i:
                 self.write_node(point, "dQw", datainfo.dxw[i],
-                                {'unit': datainfo.x_unit})
+                                {'unit': datainfo._xunit})
             if datainfo.dxl is not None and len(datainfo.dxl) > i:
                 self.write_node(point, "dQl", datainfo.dxl[i],
-                                {'unit': datainfo.x_unit})
+                                {'unit': datainfo._xunit})
         if datainfo.isSesans:
             sesans_attrib = {'x_axis': datainfo._xaxis,

src/sas/sascalc/dataloader/readers/cansas_reader_HDF5.py

@@ -38 +38 @@
     # CanSAS version
     cansas_version = 2.0
-    # Logged warnings or messages
-    logging = None
-    # List of errors for the current data set
-    errors = None
-    # Raw file contents to be processed
-    raw_data = None
-    # List of plottable1D objects that should be linked to the current_datainfo
-    data1d = None
-    # List of plottable2D objects that should be linked to the current_datainfo
-    data2d = None
     # Data type name
-    type_name = "CanSAS 2.0"
+    type_name = "NXcanSAS"
     # Wildcards
-    type = ["CanSAS 2.0 HDF5 Files (*.h5)|*.h5"]
+    type = ["NXcanSAS HDF5 Files (*.h5)|*.h5|"]
     # List of allowed extensions
     ext = ['.h5', '.H5']
@@ -81 +71 @@
                 except Exception as e:
                     if extension not in self.ext:
-                        msg = "CanSAS2.0 HDF5 Reader could not load file {}".format(basename + extension)
+                        msg = "NXcanSAS HDF5 Reader could not load file {}".format(basename + extension)
                         raise DefaultReaderException(msg)
                     raise FileContentsException(e.message)
@@ -111 +101 @@
         self.errors = set()
         self.logging = []
+        self.q_name = []
+        self.mask_name = u''
+        self.i_name = u''
+        self.i_node = u''
+        self.q_uncertainties = []
+        self.q_resolutions = []
+        self.i_uncertainties = u''
         self.parent_class = u''
         self.detector = Detector()
@@ -140 +137 @@
             if isinstance(value, h5py.Group):
                 # Set parent class before recursion
+                last_parent_class = self.parent_class
                 self.parent_class = class_name
                 parent_list.append(key)
@@ -147 +145 @@
                     self.add_data_set(key)
                 elif class_prog.match(u'SASdata'):
-                    self._initialize_new_data_set(parent_list)
+                    self._initialize_new_data_set(value)
+                    self._find_data_attributes(value)
                 # Recursion step to access data within the group
                 self.read_children(value, parent_list)
+                self.add_intermediate()
                 # Reset parent class when returning from recursive method
-                self.parent_class = class_name
-                self.add_intermediate()
+                self.parent_class = last_parent_class
                 parent_list.remove(key)
 
@@ -159 +158 @@
                 data_set = data[key][:]
                 unit = self._get_unit(value)
-
-                # I and Q Data
-                if key == u'I':
-                    if isinstance(self.current_dataset, plottable_2D):
-                        self.current_dataset.data = data_set
-                        self.current_dataset.zaxis("Intensity", unit)
-                    else:
-                        self.current_dataset.y = data_set.flatten()
-                        self.current_dataset.yaxis("Intensity", unit)
-                    continue
-                elif key == u'Idev':
-                    if isinstance(self.current_dataset, plottable_2D):
-                        self.current_dataset.err_data = data_set.flatten()
-                    else:
-                        self.current_dataset.dy = data_set.flatten()
-                    continue
-                elif key == u'Q':
-                    self.current_dataset.xaxis("Q", unit)
-                    if isinstance(self.current_dataset, plottable_2D):
-                        self.current_dataset.q = data_set.flatten()
-                    else:
-                        self.current_dataset.x = data_set.flatten()
-                    continue
-                elif key == u'Qdev':
-                    self.current_dataset.dx = data_set.flatten()
-                    continue
-                elif key == u'dQw':
-                    self.current_dataset.dxw = data_set.flatten()
-                    continue
-                elif key == u'dQl':
-                    self.current_dataset.dxl = data_set.flatten()
-                    continue
-                elif key == u'Qy':
-                    self.current_dataset.yaxis("Q_y", unit)
-                    self.current_dataset.qy_data = data_set.flatten()
-                    continue
-                elif key == u'Qydev':
-                    self.current_dataset.dqy_data = data_set.flatten()
-                    continue
-                elif key == u'Qx':
-                    self.current_dataset.xaxis("Q_x", unit)
-                    self.current_dataset.qx_data = data_set.flatten()
-                    continue
-                elif key == u'Qxdev':
-                    self.current_dataset.dqx_data = data_set.flatten()
-                    continue
-                elif key == u'Mask':
-                    self.current_dataset.mask = data_set.flatten()
-                    continue
-                # Transmission Spectrum
-                elif (key == u'T'
-                      and self.parent_class == u'SAStransmission_spectrum'):
-                    self.trans_spectrum.transmission = data_set.flatten()
-                    continue
-                elif (key == u'Tdev'
-                      and self.parent_class == u'SAStransmission_spectrum'):
-                    self.trans_spectrum.transmission_deviation = \
-                        data_set.flatten()
-                    continue
-                elif (key == u'lambda'
-                      and self.parent_class == u'SAStransmission_spectrum'):
-                    self.trans_spectrum.wavelength = data_set.flatten()
-                    continue
 
                 for data_point in data_set:
@@ -232 +168 @@
                     if key == u'definition':
                         self.current_datainfo.meta_data['reader'] = data_point
+                    # Run
                     elif key == u'run':
                         self.current_datainfo.run.append(data_point)
@@ -240 +177 @@
                         except Exception:
                             pass
+                    # Title
                     elif key == u'title':
                         self.current_datainfo.title = data_point
+                    # Note
                     elif key == u'SASnote':
                         self.current_datainfo.notes.append(data_point)
-
                     # Sample Information
-                    # CanSAS 2.0 format
-                    elif key == u'Title' and self.parent_class == u'SASsample':
-                        self.current_datainfo.sample.name = data_point
-                    # NXcanSAS format
-                    elif key == u'name' and self.parent_class == u'SASsample':
-                        self.current_datainfo.sample.name = data_point
-                    # NXcanSAS format
-                    elif key == u'ID' and self.parent_class == u'SASsample':
-                        self.current_datainfo.sample.name = data_point
-                    elif (key == u'thickness'
-                          and self.parent_class == u'SASsample'):
-                        self.current_datainfo.sample.thickness = data_point
-                    elif (key == u'temperature'
-                          and self.parent_class == u'SASsample'):
-                        self.current_datainfo.sample.temperature = data_point
-                    elif (key == u'transmission'
-                          and self.parent_class == u'SASsample'):
-                        self.current_datainfo.sample.transmission = data_point
-                    elif (key == u'x_position'
-                          and self.parent_class == u'SASsample'):
-                        self.current_datainfo.sample.position.x = data_point
-                    elif (key == u'y_position'
-                          and self.parent_class == u'SASsample'):
-                        self.current_datainfo.sample.position.y = data_point
-                    elif key == u'pitch' and self.parent_class == u'SASsample':
-                        self.current_datainfo.sample.orientation.x = data_point
-                    elif key == u'yaw' and self.parent_class == u'SASsample':
-                        self.current_datainfo.sample.orientation.y = data_point
-                    elif key == u'roll' and self.parent_class == u'SASsample':
-                        self.current_datainfo.sample.orientation.z = data_point
-                    elif (key == u'details'
-                          and self.parent_class == u'SASsample'):
-                        self.current_datainfo.sample.details.append(data_point)
-
+                    elif self.parent_class == u'SASsample':
+                        self.process_sample(data_point, key)
                     # Instrumental Information
                     elif (key == u'name'
                           and self.parent_class == u'SASinstrument'):
                         self.current_datainfo.instrument = data_point
-                    elif key == u'name' and self.parent_class == u'SASdetector':
-                        self.detector.name = data_point
-                    elif key == u'SDD' and self.parent_class == u'SASdetector':
-                        self.detector.distance = float(data_point)
-                        self.detector.distance_unit = unit
-                    elif (key == u'slit_length'
-                          and self.parent_class == u'SASdetector'):
-                        self.detector.slit_length = float(data_point)
-                        self.detector.slit_length_unit = unit
-                    elif (key == u'x_position'
-                          and self.parent_class == u'SASdetector'):
-                        self.detector.offset.x = float(data_point)
-                        self.detector.offset_unit = unit
-                    elif (key == u'y_position'
-                          and self.parent_class == u'SASdetector'):
-                        self.detector.offset.y = float(data_point)
-                        self.detector.offset_unit = unit
-                    elif (key == u'pitch'
-                          and self.parent_class == u'SASdetector'):
-                        self.detector.orientation.x = float(data_point)
-                        self.detector.orientation_unit = unit
-                    elif key == u'roll' and self.parent_class == u'SASdetector':
-                        self.detector.orientation.z = float(data_point)
-                        self.detector.orientation_unit = unit
-                    elif key == u'yaw' and self.parent_class == u'SASdetector':
-                        self.detector.orientation.y = float(data_point)
-                        self.detector.orientation_unit = unit
-                    elif (key == u'beam_center_x'
-                          and self.parent_class == u'SASdetector'):
-                        self.detector.beam_center.x = float(data_point)
-                        self.detector.beam_center_unit = unit
-                    elif (key == u'beam_center_y'
-                          and self.parent_class == u'SASdetector'):
-                        self.detector.beam_center.y = float(data_point)
-                        self.detector.beam_center_unit = unit
-                    elif (key == u'x_pixel_size'
-                          and self.parent_class == u'SASdetector'):
-                        self.detector.pixel_size.x = float(data_point)
-                        self.detector.pixel_size_unit = unit
-                    elif (key == u'y_pixel_size'
-                          and self.parent_class == u'SASdetector'):
-                        self.detector.pixel_size.y = float(data_point)
-                        self.detector.pixel_size_unit = unit
-                    elif (key == u'distance'
-                          and self.parent_class == u'SAScollimation'):
-                        self.collimation.length = data_point
-                        self.collimation.length_unit = unit
-                    elif (key == u'name'
-                          and self.parent_class == u'SAScollimation'):
-                        self.collimation.name = data_point
-                    elif (key == u'shape'
-                          and self.parent_class == u'SASaperture'):
-                        self.aperture.shape = data_point
-                    elif (key == u'x_gap'
-                          and self.parent_class == u'SASaperture'):
-                        self.aperture.size.x = data_point
-                    elif (key == u'y_gap'
-                          and self.parent_class == u'SASaperture'):
-                        self.aperture.size.y = data_point
-
+                    # Detector
+                    elif self.parent_class == u'SASdetector':
+                        self.process_detector(data_point, key, unit)
+                    # Collimation
+                    elif self.parent_class == u'SAScollimation':
+                        self.process_collimation(data_point, key, unit)
+                    # Aperture
+                    elif self.parent_class == u'SASaperture':
+                        self.process_aperture(data_point, key)
                     # Process Information
-                    elif (key == u'Title'
-                          and self.parent_class == u'SASprocess'): # CanSAS 2.0
-                        self.process.name = data_point
-                    elif (key == u'name'
-                          and self.parent_class == u'SASprocess'): # NXcanSAS
-                        self.process.name = data_point
-                    elif (key == u'description'
-                          and self.parent_class == u'SASprocess'):
-                        self.process.description = data_point
-                    elif key == u'date' and self.parent_class == u'SASprocess':
-                        self.process.date = data_point
-                    elif key == u'term' and self.parent_class == u'SASprocess':
-                        self.process.term = data_point
-                    elif self.parent_class == u'SASprocess':
-                        self.process.notes.append(data_point)
-
+                    elif self.parent_class == u'SASprocess': # CanSAS 2.0
+                        self.process_process(data_point, key)
                     # Source
-                    elif (key == u'wavelength'
-                          and self.parent_class == u'SASdata'):
-                        self.current_datainfo.source.wavelength = data_point
-                        self.current_datainfo.source.wavelength_unit = unit
-                    elif (key == u'incident_wavelength'
-                          and self.parent_class == 'SASsource'):
-                        self.current_datainfo.source.wavelength = data_point
-                        self.current_datainfo.source.wavelength_unit = unit
-                    elif (key == u'wavelength_max'
-                          and self.parent_class == u'SASsource'):
-                        self.current_datainfo.source.wavelength_max = data_point
-                        self.current_datainfo.source.wavelength_max_unit = unit
-                    elif (key == u'wavelength_min'
-                          and self.parent_class == u'SASsource'):
-                        self.current_datainfo.source.wavelength_min = data_point
-                        self.current_datainfo.source.wavelength_min_unit = unit
-                    elif (key == u'incident_wavelength_spread'
-                          and self.parent_class == u'SASsource'):
-                        self.current_datainfo.source.wavelength_spread = \
-                            data_point
-                        self.current_datainfo.source.wavelength_spread_unit = \
-                            unit
-                    elif (key == u'beam_size_x'
-                          and self.parent_class == u'SASsource'):
-                        self.current_datainfo.source.beam_size.x = data_point
-                        self.current_datainfo.source.beam_size_unit = unit
-                    elif (key == u'beam_size_y'
-                          and self.parent_class == u'SASsource'):
-                        self.current_datainfo.source.beam_size.y = data_point
-                        self.current_datainfo.source.beam_size_unit = unit
-                    elif (key == u'beam_shape'
-                          and self.parent_class == u'SASsource'):
-                        self.current_datainfo.source.beam_shape = data_point
-                    elif (key == u'radiation'
-                          and self.parent_class == u'SASsource'):
-                        self.current_datainfo.source.radiation = data_point
-                    elif (key == u'transmission'
-                          and self.parent_class == u'SASdata'):
-                        self.current_datainfo.sample.transmission = data_point
-
+                    elif self.parent_class == u'SASsource':
+                        self.process_source(data_point, key, unit)
                     # Everything else goes in meta_data
+                    elif self.parent_class == u'SASdata':
+                        if isinstance(self.current_dataset, plottable_2D):
+                            self.process_2d_data_object(data_set, key, unit)
+                        else:
+                            self.process_1d_data_object(data_set, key, unit)
+
+                        break
+                    elif self.parent_class == u'SAStransmission_spectrum':
+                        self.process_trans_spectrum(data_set, key)
+                        break
                     else:
                         new_key = self._create_unique_key(
@@ -411 +224 @@
                 # I don't know if this reachable code
                 self.errors.add("ShouldNeverHappenException")
+
+    def process_1d_data_object(self, data_set, key, unit):
+        """
+        SASdata processor method for 1d data items
+        :param data_set: data from HDF5 file
+        :param key: canSAS_class attribute
+        :param unit: unit attribute
+        """
+        if key == self.i_name:
+            self.current_dataset.y = data_set.flatten()
+            self.current_dataset.yaxis("Intensity", unit)
+        elif key == self.i_uncertainties:
+            self.current_dataset.dy = data_set.flatten()
+        elif key in self.q_name:
+            self.current_dataset.xaxis("Q", unit)
+            self.current_dataset.x = data_set.flatten()
+        elif key in self.q_uncertainties or key in self.q_resolutions:
+            if (len(self.q_resolutions) > 1
+                    and np.where(self.q_resolutions == key)[0] == 0):
+                self.current_dataset.dxw = data_set.flatten()
+            elif (len(self.q_resolutions) > 1
+                  and np.where(self.q_resolutions == key)[0] == 1):
+                self.current_dataset.dxl = data_set.flatten()
+            else:
+                self.current_dataset.dx = data_set.flatten()
+        elif key == self.mask_name:
+            self.current_dataset.mask = data_set.flatten()
+        elif key == u'wavelength':
+            self.current_datainfo.source.wavelength = data_set[0]
+            self.current_datainfo.source.wavelength_unit = unit
+
+    def process_2d_data_object(self, data_set, key, unit):
+        if key == self.i_name:
+            self.current_dataset.data = data_set
+            self.current_dataset.zaxis("Intensity", unit)
+        elif key == self.i_uncertainties:
+            self.current_dataset.err_data = data_set.flatten()
+        elif key in self.q_name:
+            self.current_dataset.xaxis("Q", unit)
+            self.current_dataset.yaxis("Q", unit)
+            #FIXME: This is broken - need to properly handle 2D data
+            # TODO: Check shape of array (2d - cash money, homey!)
+            # TODO: 3D - check dims, etc.
+            # TODO: Put data where it belongs
+            pass
+        elif key in self.q_uncertainties or key in self.q_resolutions:
+            # FIXME: This isn't right either.
+            # TODO: find resolution/uncertainty specific to q_name
+            pass
+        elif key == u'Qy':
+            self.current_dataset.yaxis("Q_y", unit)
+            self.current_dataset.qy_data = data_set.flatten()
+        elif key == u'Qydev':
+            self.current_dataset.dqy_data = data_set.flatten()
+        elif key == u'Qx':
+            self.current_dataset.xaxis("Q_x", unit)
+            self.current_dataset.qx_data = data_set.flatten()
+        elif key == u'Qxdev':
+            self.current_dataset.dqx_data = data_set.flatten()
+
+    def process_trans_spectrum(self, data_set, key):
+        """
+        SAStransmission_spectrum processor
+        :param data_set: data from HDF5 file
+        :param key: canSAS_class attribute
+        """
+        if key == u'T':
+            self.trans_spectrum.transmission = data_set.flatten()
+        elif key == u'Tdev':
+            self.trans_spectrum.transmission_deviation = data_set.flatten()
+        elif key == u'lambda':
+            self.trans_spectrum.wavelength = data_set.flatten()
+
+    def process_sample(self, data_point, key):
+        """
+        SASsample processor
+        :param data_point: Single point from an HDF5 data file
+        :param key: class name data_point was taken from
+        """
+        if key == u'Title':
+            self.current_datainfo.sample.name = data_point
+        elif key == u'name':
+            self.current_datainfo.sample.name = data_point
+        elif key == u'ID':
+            self.current_datainfo.sample.name = data_point
+        elif key == u'thickness':
+            self.current_datainfo.sample.thickness = data_point
+        elif key == u'temperature':
+            self.current_datainfo.sample.temperature = data_point
+        elif key == u'transmission':
+            self.current_datainfo.sample.transmission = data_point
+        elif key == u'x_position':
+            self.current_datainfo.sample.position.x = data_point
+        elif key == u'y_position':
+            self.current_datainfo.sample.position.y = data_point
+        elif key == u'pitch':
+            self.current_datainfo.sample.orientation.x = data_point
+        elif key == u'yaw':
+            self.current_datainfo.sample.orientation.y = data_point
+        elif key == u'roll':
+            self.current_datainfo.sample.orientation.z = data_point
+        elif key == u'details':
+            self.current_datainfo.sample.details.append(data_point)
+
+    def process_detector(self, data_point, key, unit):
+        """
+        SASdetector processor
+        :param data_point: Single point from an HDF5 data file
+        :param key: class name data_point was taken from
+        :param unit: unit attribute from data set
+        """
+        if key == u'name':
+            self.detector.name = data_point
+        elif key == u'SDD':
+            self.detector.distance = float(data_point)
+            self.detector.distance_unit = unit
+        elif key == u'slit_length':
+            self.detector.slit_length = float(data_point)
+            self.detector.slit_length_unit = unit
+        elif key == u'x_position':
+            self.detector.offset.x = float(data_point)
+            self.detector.offset_unit = unit
+        elif key == u'y_position':
+            self.detector.offset.y = float(data_point)
+            self.detector.offset_unit = unit
+        elif key == u'pitch':
+            self.detector.orientation.x = float(data_point)
+            self.detector.orientation_unit = unit
+        elif key == u'roll':
+            self.detector.orientation.z = float(data_point)
+            self.detector.orientation_unit = unit
+        elif key == u'yaw':
+            self.detector.orientation.y = float(data_point)
+            self.detector.orientation_unit = unit
+        elif key == u'beam_center_x':
+            self.detector.beam_center.x = float(data_point)
+            self.detector.beam_center_unit = unit
+        elif key == u'beam_center_y':
+            self.detector.beam_center.y = float(data_point)
+            self.detector.beam_center_unit = unit
+        elif key == u'x_pixel_size':
+            self.detector.pixel_size.x = float(data_point)
+            self.detector.pixel_size_unit = unit
+        elif key == u'y_pixel_size':
+            self.detector.pixel_size.y = float(data_point)
+            self.detector.pixel_size_unit = unit
+
+    def process_collimation(self, data_point, key, unit):
+        """
+        SAScollimation processor
+        :param data_point: Single point from an HDF5 data file
+        :param key: class name data_point was taken from
+        :param unit: unit attribute from data set
+        """
+        if key == u'distance':
+            self.collimation.length = data_point
+            self.collimation.length_unit = unit
+        elif key == u'name':
+            self.collimation.name = data_point
+
+    def process_aperture(self, data_point, key):
+        """
+        SASaperture processor
+        :param data_point: Single point from an HDF5 data file
+        :param key: class name data_point was taken from
+        """
+        if key == u'shape':
+            self.aperture.shape = data_point
+        elif key == u'x_gap':
+            self.aperture.size.x = data_point
+        elif key == u'y_gap':
+            self.aperture.size.y = data_point
+
+    def process_source(self, data_point, key, unit):
+        """
+        SASsource processor
+        :param data_point: Single point from an HDF5 data file
+        :param key: class name data_point was taken from
+        :param unit: unit attribute from data set
+        """
+        if key == u'incident_wavelength':
+            self.current_datainfo.source.wavelength = data_point
+            self.current_datainfo.source.wavelength_unit = unit
+        elif key == u'wavelength_max':
+            self.current_datainfo.source.wavelength_max = data_point
+            self.current_datainfo.source.wavelength_max_unit = unit
+        elif key == u'wavelength_min':
+            self.current_datainfo.source.wavelength_min = data_point
+            self.current_datainfo.source.wavelength_min_unit = unit
+        elif key == u'incident_wavelength_spread':
+            self.current_datainfo.source.wavelength_spread = data_point
+            self.current_datainfo.source.wavelength_spread_unit = unit
+        elif key == u'beam_size_x':
+            self.current_datainfo.source.beam_size.x = data_point
+            self.current_datainfo.source.beam_size_unit = unit
+        elif key == u'beam_size_y':
+            self.current_datainfo.source.beam_size.y = data_point
+            self.current_datainfo.source.beam_size_unit = unit
+        elif key == u'beam_shape':
+            self.current_datainfo.source.beam_shape = data_point
+        elif key == u'radiation':
+            self.current_datainfo.source.radiation = data_point
+
+    def process_process(self, data_point, key):
+        """
+        SASprocess processor
+        :param data_point: Single point from an HDF5 data file
+        :param key: class name data_point was taken from
+        """
+        term_match = re.compile(u'^term[0-9]+$')
+        if key == u'Title':  # CanSAS 2.0
+            self.process.name = data_point
+        elif key == u'name':  # NXcanSAS
+            self.process.name = data_point
+        elif key == u'description':
+            self.process.description = data_point
+        elif key == u'date':
+            self.process.date = data_point
+        elif term_match.match(key):
+            self.process.term.append(data_point)
+        else:
+            self.process.notes.append(data_point)
 
     def add_intermediate(self):
@@ -452 +487 @@
             spectrum_list = []
             for spectrum in self.current_datainfo.trans_spectrum:
-                spectrum.transmission = np.delete(spectrum.transmission, [0])
                 spectrum.transmission = spectrum.transmission.astype(np.float64)
-                spectrum.transmission_deviation = np.delete(
-                    spectrum.transmission_deviation, [0])
                 spectrum.transmission_deviation = \
                     spectrum.transmission_deviation.astype(np.float64)
-                spectrum.wavelength = np.delete(spectrum.wavelength, [0])
                 spectrum.wavelength = spectrum.wavelength.astype(np.float64)
                 if len(spectrum.transmission) > 0:
@@ -491 +522 @@
                 (n_rows, n_cols) = dataset.data.shape
                 dataset.y_bins = dataset.qy_data[0::n_cols]
-                dataset.x_bins = dataset.qx_data[:n_cols]
+                dataset.x_bins = dataset.qx_data[0::n_rows]
                 dataset.data = dataset.data.flatten()
             self.current_dataset = dataset
@@ -515 +546 @@
         self.current_datainfo = DataInfo()
 
-
-    def _initialize_new_data_set(self, parent_list=None):
+    def _initialize_new_data_set(self, value=None):
         """
         A private class method to generate a new 1D or 2D data object based on
@@ -524 +554 @@
         :param parent_list: List of names of parent elements
         """
-
-        if parent_list is None:
-            parent_list = []
-        if self._find_intermediate(parent_list, "Qx"):
+        if self._is2d(value):
             self.current_dataset = plottable_2D()
         else:
@@ -534 +561 @@
             self.current_dataset = plottable_1D(x, y)
         self.current_datainfo.filename = self.raw_data.filename
-
-    def _find_intermediate(self, parent_list, basename=""):
-        """
-        A private class used to find an entry by either using a direct key or
-        knowing the approximate basename.
+        self.mask_name = ""
+        self.i_name = ""
+        self.i_node = ""
+        self.q_name = []
+        self.q_uncertainties = []
+        self.q_resolutions = []
+        self.i_uncertainties = ""
+
+    @staticmethod
+    def check_is_list_or_array(iterable):
+        try:
+            iter(iterable)
+            if (not isinstance(iterable, np.ndarray)) or (isinstance(iterable, str)
+                    or isinstance(iterable, unicode)):
+                raise TypeError
+        except TypeError:
+            iterable = iterable.split(",")
+        return iterable
+
+    def _find_data_attributes(self, value):
+        """
+        A class to find the indices for Q, the name of the Qdev and Idev, and
+        the name of the mask.
+        :param value: SASdata/NXdata HDF5 Group
+        """
+        attrs = value.attrs
+        signal = attrs.get("signal", "I")
+        i_axes = attrs.get("I_axes", ["Q"])
+        q_indices = attrs.get("Q_indices", [0])
+        q_indices = map(int, self.check_is_list_or_array(q_indices))
+        i_axes = self.check_is_list_or_array(i_axes)
+        keys = value.keys()
+        self.mask_name = attrs.get("mask")
+        for val in q_indices:
+            self.q_name.append(i_axes[val])
+        self.i_name = signal
+        self.i_node = value.get(self.i_name)
+        for item in self.q_name:
+            if item in keys:
+                q_vals = value.get(item)
+                if q_vals.attrs.get("uncertainties") is not None:
+                    self.q_uncertainties = q_vals.attrs.get("uncertainties")
+                elif q_vals.attrs.get("uncertainty") is not None:
+                    self.q_uncertainties = q_vals.attrs.get("uncertainty")
+                if isinstance(self.q_uncertainties, str) is not None:
+                    self.q_uncertainties = [self.q_uncertainties]
+                if q_vals.attrs.get("resolutions") is not None:
+                    self.q_resolutions = q_vals.attrs.get("resolutions")
+                if isinstance(self.q_resolutions, str):
+                    self.q_resolutions = self.q_resolutions.split(",")
+        if self.i_name in keys:
+            i_vals = value.get(self.i_name)
+            self.i_uncertainties = i_vals.attrs.get("uncertainties")
+            if self.i_uncertainties is None:
+                self.i_uncertainties = i_vals.attrs.get("uncertainty")
+
+    def _is2d(self, value, basename="I"):
+        """
+        A private class to determine if the data set is 1d or 2d.
 
         :param parent_list: List of parents nodes in the HDF5 file
         :param basename: Approximate name of an entry to search for
-        :return:
-        """
-
-        entry = False
-        key_prog = re.compile(basename)
-        top = self.raw_data
-        for parent in parent_list:
-            top = top.get(parent)
-        for key in top.keys():
-            if key_prog.match(key):
-                entry = True
-                break
-        return entry
+        :return: True if 2D, otherwise false
+        """
+
+        vals = value.get(basename)
+        return (vals is not None and vals.shape is not None
+                and len(vals.shape) != 1)
 
     def _create_unique_key(self, dictionary, name, numb=0):
@@ -583 +657 @@
         if unit is None:
             unit = h5attr(value, u'unit')
-        # Convert the unit formats
-        if unit == "1/A":
-            unit = "A^{-1}"
-        elif unit == "1/cm":
-            unit = "cm^{-1}"
         return unit

src/sas/sascalc/dataloader/readers/danse_reader.py

@@ -180 +180 @@
         detector.beam_center.y = center_y * pixel
 
-
-        self.current_dataset.xaxis("\\rm{Q_{x}}", 'A^{-1}')
-        self.current_dataset.yaxis("\\rm{Q_{y}}", 'A^{-1}')
-        self.current_dataset.zaxis("\\rm{Intensity}", "cm^{-1}")
-
+        self.current_dataset = self.set_default_2d_units(self.current_dataset)
         self.current_dataset.x_bins = x_vals
         self.current_dataset.y_bins = y_vals

src/sas/sascalc/dataloader/readers/red2d_reader.py

@@ -317 +317 @@
 
         # Units of axes
-        self.current_dataset.xaxis(r"\rm{Q_{x}}", 'A^{-1}')
-        self.current_dataset.yaxis(r"\rm{Q_{y}}", 'A^{-1}')
-        self.current_dataset.zaxis(r"\rm{Intensity}", "cm^{-1}")
+        self.current_dataset = self.set_default_2d_units(self.current_dataset)
 
         # Store loading process information

src/sas/sascalc/file_converter/nxcansas_writer.py

@@ -175 +175 @@
             names=['beam_size_x', 'beam_size_y'],
             units=data_info.source.beam_size_unit, write_fn=_write_h5_float)
-
 
         # Collimation metadata
@@ -232 +231 @@
             detector_entry.attrs['name'] = ''
 
+        # Process meta data
+        if len(data_info.process) > 0 and not data_info.process[0].is_empty():
+            i = 1
+            for process in data_info.process:
+                process_entry = sasentry.create_group(
+                    'sasprocess{0:0=2d}'.format(i))
+                process_entry.attrs['canSAS_class'] = 'SASprocess'
+                if process.name:
+                    name = _h5_string(process.name)
+                    process_entry.create_dataset('name', data=name)
+                if process.date:
+                    date = _h5_string(process.date)
+                    process_entry.create_dataset('date', data=date)
+                if process.description:
+                    desc = _h5_string(process.description)
+                    process_entry.create_dataset('description', data=desc)
+                j = 1
+                for term in process.term:
+                    if term:
+                        h5_term = _h5_string(term)
+                        process_entry.create_dataset('term{0:0=2d}'.format(j),
+                                                     data=h5_term)
+                    j += 1
+                j = 1
+                for note in process.notes:
+                    if note:
+                        h5_note = _h5_string(note)
+                        process_entry.create_dataset('note{0:0=2d}'.format(j),
+                                                     data=h5_note)
+                    j += 1
+                i += 1
+
+        # Transmission Spectrum
+        if len(data_info.trans_spectrum) > 0:
+            i = 1
+            for trans in data_info.trans_spectrum:
+                trans_entry = sasentry.create_group(
+                    'sastransmission_spectrum{0:0=2d}'.format(i))
+                trans_entry.attrs['canSAS_class'] = 'SAStransmission_spectrum'
+                trans_entry.attrs['signal'] = 'T'
+                trans_entry.attrs['T_axes'] = 'T'
+                trans_entry.attrs['name'] = trans.name
+                if trans.timestamp is not '':
+                    trans_entry.attrs['timestamp'] = trans.timestamp
+                transmission = trans_entry.create_dataset(
+                    'T', data=trans.transmission)
+                transmission.attrs['unertainties'] = 'Tdev'
+                trans_entry.create_dataset('Tdev',
+                                           data = trans.transmission_deviation)
+                trans_entry.create_dataset('lambda', data=trans.wavelength)
+
         note_entry = sasentry.create_group('sasnote'.format(i))
         note_entry.attrs['canSAS_class'] = 'SASnote'
@@ -254 +304 @@
         data_entry.attrs['signal'] = 'I'
         data_entry.attrs['I_axes'] = 'Q'
-        data_entry.attrs['I_uncertainties'] = 'Idev'
-        data_entry.attrs['Q_indicies'] = 0
-
-        dI = data_obj.dy
-        if dI is None:
-            dI = np.zeros((data_obj.y.shape))
-
-        data_entry.create_dataset('Q', data=data_obj.x)
-        data_entry.create_dataset('I', data=data_obj.y)
-        data_entry.create_dataset('Idev', data=dI)
+        data_entry.attrs['Q_indices'] = [0]
+        q_entry = data_entry.create_dataset('Q', data=data_obj.x)
+        q_entry.attrs['units'] = data_obj.x_unit
+        i_entry = data_entry.create_dataset('I', data=data_obj.y)
+        i_entry.attrs['units'] = data_obj.y_unit
+        if data_obj.dy is not None:
+            i_entry.attrs['uncertainties'] = 'Idev'
+            i_dev_entry = data_entry.create_dataset('Idev', data=data_obj.dy)
+            i_dev_entry.attrs['units'] = data_obj.y_unit
+        if data_obj.dx is not None:
+            q_entry.attrs['resolutions'] = 'dQ'
+            dq_entry = data_entry.create_dataset('dQ', data=data_obj.dx)
+            dq_entry.attrs['units'] = data_obj.x_unit
+        elif data_obj.dxl is not None:
+            q_entry.attrs['resolutions'] = ['dQl','dQw']
+            dql_entry = data_entry.create_dataset('dQl', data=data_obj.dxl)
+            dql_entry.attrs['units'] = data_obj.x_unit
+            dqw_entry = data_entry.create_dataset('dQw', data=data_obj.dxw)
+            dqw_entry.attrs['units'] = data_obj.x_unit
 
     def _write_2d_data(self, data, data_entry):
@@ -273 +332 @@
         """
         data_entry.attrs['signal'] = 'I'
-        data_entry.attrs['I_axes'] = 'Q,Q'
-        data_entry.attrs['I_uncertainties'] = 'Idev'
-        data_entry.attrs['Q_indicies'] = [0,1]
+        data_entry.attrs['I_axes'] = 'Qx,Qy'
+        data_entry.attrs['Q_indices'] = [0,1]
 
         (n_rows, n_cols) = (len(data.y_bins), len(data.x_bins))
@@ -288 +346 @@
                 raise ValueError("Unable to calculate dimensions of 2D data")
 
-        I = np.reshape(data.data, (n_rows, n_cols))
-        dI = np.zeros((n_rows, n_cols))
-        if not all(data.err_data == [None]):
-            dI = np.reshape(data.err_data, (n_rows, n_cols))
-        qx =  np.reshape(data.qx_data, (n_rows, n_cols))
+        intensity = np.reshape(data.data, (n_rows, n_cols))
+        qx = np.reshape(data.qx_data, (n_rows, n_cols))
         qy = np.reshape(data.qy_data, (n_rows, n_cols))
 
-        I_entry = data_entry.create_dataset('I', data=I)
-        I_entry.attrs['units'] = data.I_unit
-        Qx_entry = data_entry.create_dataset('Qx', data=qx)
-        Qx_entry.attrs['units'] = data.Q_unit
-        Qy_entry = data_entry.create_dataset('Qy', data=qy)
-        Qy_entry.attrs['units'] = data.Q_unit
-        Idev_entry = data_entry.create_dataset('Idev', data=dI)
-        Idev_entry.attrs['units'] = data.I_unit
+        i_entry = data_entry.create_dataset('I', data=intensity)
+        i_entry.attrs['units'] = data.I_unit
+        qx_entry = data_entry.create_dataset('Qx', data=qx)
+        qx_entry.attrs['units'] = data.Q_unit
+        qy_entry = data_entry.create_dataset('Qy', data=qy)
+        qy_entry.attrs['units'] = data.Q_unit
+        if data.err_data is not None and not all(data.err_data == [None]):
+            d_i = np.reshape(data.err_data, (n_rows, n_cols))
+            i_entry.attrs['uncertainties'] = 'Idev'
+            i_dev_entry = data_entry.create_dataset('Idev', data=d_i)
+            i_dev_entry.attrs['units'] = data.I_unit
+        if data.dqx_data is not None and not all(data.dqx_data == [None]):
+            qx_entry.attrs['resolutions'] = 'dQx'
+            dqx_entry = data_entry.create_dataset('dQx', data=data.dqx_data)
+            dqx_entry.attrs['units'] = data.Q_unit
+        if data.dqy_data is not None and not all(data.dqy_data == [None]):
+            qy_entry.attrs['resolutions'] = 'dQy'
+            dqy_entry = data_entry.create_dataset('dQy', data=data.dqy_data)
+            dqy_entry.attrs['units'] = data.Q_unit

src/sas/sasgui/guiframe/gui_manager.py

@@ -46 +46 @@
 from sas.sasgui.guiframe.CategoryManager import CategoryManager
 from sas.sascalc.dataloader.loader import Loader
+from sas.sascalc.file_converter.nxcansas_writer import NXcanSASWriter
 from sas.sasgui.guiframe.proxy import Connection
 
@@ -2422 +2423 @@
         default_name = fname
         wildcard = "Text files (*.txt)|*.txt|"\
-                    "CanSAS 1D files(*.xml)|*.xml"
-        path = None
+                    "CanSAS 1D files (*.xml)|*.xml|"\
+                     "NXcanSAS files (*.h5)|*.h5|"
+        options = {0: ".txt",
+                   1: ".xml",
+                   2: ".h5"}
         dlg = wx.FileDialog(self, "Choose a file",
                             self._default_save_location,
@@ -2433 +2437 @@
             # This is MAC Fix
             ext_num = dlg.GetFilterIndex()
-            if ext_num == 0:
-                ext_format = '.txt'
-            else:
-                ext_format = '.xml'
+
+            ext_format = options[ext_num]
             path = os.path.splitext(path)[0] + ext_format
             mypath = os.path.basename(path)
-
-            # Instantiate a loader
-            loader = Loader()
-            ext_format = ".txt"
-            if os.path.splitext(mypath)[1].lower() == ext_format:
+            fName = os.path.splitext(path)[0] + ext_format
+
+            if os.path.splitext(mypath)[1].lower() == options[0]:
                 # Make sure the ext included in the file name
                 # especially on MAC
-                fName = os.path.splitext(path)[0] + ext_format
                 self._onsaveTXT(data, fName)
-            ext_format = ".xml"
-            if os.path.splitext(mypath)[1].lower() == ext_format:
+            elif os.path.splitext(mypath)[1].lower() == options[1]:
                 # Make sure the ext included in the file name
                 # especially on MAC
-                fName = os.path.splitext(path)[0] + ext_format
+                # Instantiate a loader
+                loader = Loader()
                 loader.save(fName, data, ext_format)
+            elif os.path.splitext(mypath)[1].lower() == options[2]:
+                nxcansaswriter = NXcanSASWriter()
+                nxcansaswriter.write([data], fName)
             try:
                 self._default_save_location = os.path.dirname(path)
@@ -2565 +2567 @@
         """
         default_name = fname
-        wildcard = "IGOR/DAT 2D file in Q_map (*.dat)|*.DAT"
+        wildcard = "IGOR/DAT 2D file in Q_map (*.dat)|*.DAT|"\
+                   "NXcanSAS files (*.h5)|*.h5|"
         dlg = wx.FileDialog(self, "Choose a file",
                             self._default_save_location,
@@ -2577 +2580 @@
             if ext_num == 0:
                 ext_format = '.dat'
+            elif ext_num == 1:
+                ext_format = '.h5'
             else:
                 ext_format = ''
@@ -2584 +2589 @@
             # Instantiate a loader
             loader = Loader()
-
-            ext_format = ".dat"
-            if os.path.splitext(mypath)[1].lower() == ext_format:
+            if os.path.splitext(mypath)[1].lower() == '.dat':
                 # Make sure the ext included in the file name
                 # especially on MAC
                 fileName = os.path.splitext(path)[0] + ext_format
                 loader.save(fileName, data, ext_format)
+            elif os.path.splitext(mypath)[1].lower() == '.h5':
+                # Make sure the ext included in the file name
+                # especially on MAC
+                fileName = os.path.splitext(path)[0] + ext_format
+                nxcansaswriter = NXcanSASWriter()
+                nxcansaswriter.write([data], fileName)
             try:
                 self._default_save_location = os.path.dirname(path)

src/sas/sasgui/guiframe/local_perspectives/data_loader/data_loader.py

@@ -239 +239 @@
             self.load_complete(output=output, message="Loading data complete!",
                                info="info")
-        else:
-            self.load_complete(output=None, message=error_message, info="error")
 
     def load_update(self, message="", info="warning"):

test/sasdataloader/test/test_data/avg_testdata.txt

@@ -1 +1 @@
 0.00019987186878 -0.01196215 0.148605728355
-0.000453772721237 0.02091606 0.0680283029334
-0.000750492390439 -0.01337855 0.0444902910757
-0.00103996394336 0.03062 0.0580312894528
-0.0013420198959 0.0811008333333 0.0540469289108
-0.001652061869 0.167022288372 0.0651891320031
-0.00196086470492 27.5554711176 0.735053300957
+0.000453772721237 0.02091606 0.23372601
+0.000750492390439 -0.01337855 0.17169562
+0.00103996394336 0.03062 0.13136407
+0.0013420198959 0.0811008333333 0.10681163
+0.001652061869 0.167022288372 0.10098903
+0.00196086470492 27.5554711176 0.7350533
 0.00226262401224 105.031578947 1.35744586624
 0.00256734439716 82.1791776119 1.10749938588

test/sasdataloader/test/test_data/ring_testdata.txt

@@ -4 +4 @@
 0.628318530718 0.964040908176 0.0790933208542
 0.942477796077 0.922142905769 0.0781616076625
-1.25663706144 1.02710537736 0.080875897538
+1.25663706144 1.02710537736 0.08136351514804
 1.57079632679 1.01448978075 0.0808313893873
 1.88495559215 1.04677136013 0.0828850195035

test/sasdataloader/test/test_data/sectorphi_testdata.txt

@@ -13 +13 @@
 0.981747704247 0.893411561538 0.151685984204
 1.06028752059 0.86231787 0.152618707077
-1.13882733693 1.0607364925 0.164276150316
+1.13882733693 1.0607364925 0.166167546658
 1.21736715327 1.0684421475 0.163649496829
-1.29590696961 1.09330437436 0.167871645263
+1.29590696961 1.09330437436 0.16981858402
 1.37444678595 0.88759347 0.150974201439
 1.45298660229 1.1352002 0.172191803977

test/sasdataloader/test/test_data/sectorq_testdata.txt

@@ -17 +17 @@
 0.00913119845523 0.405669568421 0.0705339106673
 0.00938052380065 0.331241946 0.061307573431
-0.00962825731078 0.237315993939 0.0578654769893
+0.00962825731078 0.237315993939 0.059602636160850493
 0.00987552050718 0.296916590385 0.0592796733987

test/sasdataloader/test/test_data/slabx_testdata.txt

@@ -21 +21 @@
 -0.00184475260646 2.40154 1.09579651396
 -0.00143541414791 0.065281 0.198049867458
--0.00102607559383 -0.04767235 0.154389685536
--0.000616736954402 -0.0090503 0.0960105462957
+-0.00102607559383 -0.04767235 0.52329358394690839
+-0.000616736954402 -0.0090503 0.36635778277525377
 -0.000207398273925 0.03109325 0.246629023029
-0.000201940423805 -0.027508775 0.082928847514
+0.000201940423805 -0.027508775 0.36314899662535211
 0.000611279108096 0.03251315 0.246951260373
-0.00102061774154 -0.00987975 0.144233534589
-0.00142995630705 0.075937 0.19485507435
+0.00102061774154 -0.00987975 0.38184199939241886
+0.00142995630705 0.075937 0.53662696540520582
 0.00183929475361 10.60918375 1.62858709853
 0.00224863307777 106.2485 7.2886384188

test/sasdataloader/test/test_data/slaby_testdata.txt

@@ -1 @@
--0.00981587154747 0.197046827778 0.0872226309261
+-0.00981587154747 0.197046827778 0.09153902
 -0.00940654133769 0.2466434 0.124972263589
 -0.0089972103454 0.218745969444 0.0838510368061
 -0.00858787875434 0.126093522222 0.107482002513
--0.00817854644886 0.310427366667 0.100945289852
+-0.00817854644886 0.310427366667 0.10469745
 -0.0077692135991 0.0843802722222 0.103942898914
 -0.00735988010303 0.246036369444 0.0916479235889

test/sasdataloader/test/utest_averaging.py

@@ -106 +106 @@
 
     def setUp(self):
-        filepath = find('MAR07232_rest.h5')
+        filepath = find('test_data//MAR07232_rest.h5')
         self.data_list = Loader().load(filepath)
         self.data = self.data_list[0]
@@ -121 +121 @@
 
         o = r(self.data)
-        filepath = find('ring_testdata.txt')
+        filepath = find('test_data//ring_testdata.txt')
         answer_list = Loader().load(filepath)
         answer = answer_list[0]
@@ -142 +142 @@
         o = r(self.data)
 
-        filepath = find('avg_testdata.txt')
+        filepath = find('test_data//avg_testdata.txt')
         answer = Loader().load(filepath)[0]
         for i in range(r.nbins_phi):
@@ -158 +158 @@
         s, ds, npoints = r(self.data)
         self.assertAlmostEqual(s, 34.278990899999997, 4)
-        self.assertAlmostEqual(ds, 7.8007981835194293, 4)
+        self.assertAlmostEqual(ds, 8.237259999538685, 4)
         self.assertAlmostEqual(npoints, 324.0000, 4)
 
@@ -164 +164 @@
         s, ds = r(self.data)
         self.assertAlmostEqual(s, 0.10579935462962962, 4)
-        self.assertAlmostEqual(ds, 0.024076537603455028, 4)
+        self.assertAlmostEqual(ds, 0.02542364197388483, 4)
 
     def test_slabX(self):
@@ -177 +177 @@
         o = r(self.data)
 
-        filepath = find('slabx_testdata.txt')
+        filepath = find('test_data//slabx_testdata.txt')
         answer = Loader().load(filepath)[0]
         for i in range(len(o.x)):
@@ -195 +195 @@
         o = r(self.data)
 
-        filepath = find('slaby_testdata.txt')
+        filepath = find('test_data//slaby_testdata.txt')
         answer = Loader().load(filepath)[0]
         for i in range(len(o.x)):
@@ -221 +221 @@
         o = r(self.data)
 
-        filepath = find('ring_testdata.txt')
+        filepath = find('test_data//ring_testdata.txt')
         answer = Loader().load(filepath)[0]
         for i in range(len(o.x)):
@@ -238 +238 @@
         o = r(self.data)
 
-        filepath = find('sectorphi_testdata.txt')
+        filepath = find('test_data//sectorphi_testdata.txt')
         answer = Loader().load(filepath)[0]
         for i in range(len(o.x)):
@@ -255 +255 @@
         o = r(self.data)
 
-        filepath = find('sectorq_testdata.txt')
+        filepath = find('test_data//sectorq_testdata.txt')
         answer = Loader().load(filepath)[0]
         for i in range(len(o.x)):

test/sasdataloader/test/utest_cansas.py

@@ -91 +91 @@
         reader = XMLreader(self.xml_valid, self.schema_1_0)
         valid = reader.validate_xml()
-        if valid:
-            self.assertTrue(valid)
-        else:
-            self.assertFalse(valid)
+        self.assertTrue(valid)
 
     def _check_data(self, data):
@@ -193 +190 @@
     def test_save_cansas_v1_0(self):
         xmlreader = XMLreader(self.isis_1_0, self.schema_1_0)
-        valid = xmlreader.validate_xml()
-        self.assertTrue(valid)
+        self.assertTrue(xmlreader.validate_xml())
         reader_generic = Loader()
         dataloader = reader_generic.load(self.isis_1_0)
@@ -207 +203 @@
             return_data = reader2.read(self.write_1_0_filename)
             written_data = return_data[0]
-            XMLreader(self.write_1_0_filename, self.schema_1_0)
-            valid = xmlreader.validate_xml()
-            self.assertTrue(valid)
+            xmlreader = XMLreader(self.write_1_0_filename, self.schema_1_0)
+            self.assertTrue(xmlreader.validate_xml())
             self._check_data(written_data)
         if os.path.isfile(self.write_1_0_filename):
@@ -260 +255 @@
         self.loader = Loader()
         self.datafile_basic = find("simpleexamplefile.h5")
-        self.datafile_multiplesasentry = find("cansas_1Dand2D_samedatafile.h5")
-        self.datafile_multiplesasdata = find("cansas_1Dand2D_samesasentry.h5")
-        self.datafile_multiplesasdata_multiplesasentry = find("cansas_1Dand2D_multiplesasentry_multiplesasdata.h5")
+        self.datafile_multiplesasentry = find(
+            "test_data//nxcansas_1Dand2D_multisasdata.h5")
+        self.datafile_multiplesasdata = find(
+            "test_data//nxcansas_1Dand2D_multisasentry.h5")
+        self.datafile_multiplesasdata_multiplesasentry = find(
+            "test_data//nxcansas_1Dand2D_multisasentry_multisasdata.h5")
 
     def test_real_data(self):
@@ -273 +271 @@
         self._check_multiple_data(self.data[0])
         self._check_multiple_data(self.data[1])
-        self._check_1d_data(self.data[0])
+        if isinstance(self.data[0], Data1D):
+            self._check_1d_data(self.data[0])
+            self._check_2d_data(self.data[1])
+        else:
+            self._check_1d_data(self.data[1])
+            self._check_2d_data(self.data[0])
 
     def _check_multiple_data(self, data):
@@ -281 +284 @@
         self.assertTrue(data.instrument == "SANS2D")
         self.assertTrue(data.source.radiation == "Spallation Neutron Source")
-        self.assertTrue(len(data.detector) == 1)
-        self.assertTrue(data.detector[0].name == "rear-detector")
-        self.assertTrue(data.detector[0].distance == 4.385281)
-        self.assertTrue(data.detector[0].distance_unit == 'm')
+        self.assertTrue(len(data.detector) == 2)
+        self.assertTrue(data.detector[0].name == "rear-detector"
+                        or data.detector[1].name == "rear-detector")
+        self.assertTrue(data.detector[0].name == "front-detector"
+                        or data.detector[1].name == "front-detector")
+        self.assertAlmostEqual(data.detector[0].distance +
+                               data.detector[1].distance, 7230.54, 2)
+        self.assertTrue(data.detector[0].distance_unit == 'mm')
         self.assertTrue(len(data.trans_spectrum) == 1)
 
     def _check_1d_data(self, data):
-        self.assertTrue(isinstance(data, Data1D))
         self.assertTrue(len(data.x) == 66)
         self.assertTrue(len(data.x) == len(data.y))
-        self.assertTrue(data.dy[10] == 0.20721350111248701)
-        self.assertTrue(data.y[10] == 24.193889608153476)
-        self.assertTrue(data.x[10] == 0.008981127988654792)
+        self.assertTrue(data.dy[10] == 0.207214)
+        self.assertTrue(data.y[10] == 24.1939)
+        self.assertTrue(data.x[10] == 0.00898113)
 
     def _check_2d_data(self, data):
         self.assertTrue(isinstance(data, Data2D))
-        self.assertTrue(len(data.x) == 66)
-        self.assertTrue(len(data.x) == len(data.y))
-        self.assertTrue(data.dy[10] == 0.20721350111248701)
-        self.assertTrue(data.y[10] == 24.193889608153476)
-        self.assertTrue(data.x[10] == 0.008981127988654792)
+        self.assertTrue(len(data.q_data) == 150*150)
+        self.assertTrue(len(data.q_data) == len(data.data))
+        print(data.err_data[10])
+        self.assertAlmostEqual(data.err_data[10], 0.186723989418)
+        self.assertAlmostEqual(data.data[10], 0.465181425808)
+        self.assertAlmostEqual(data.qx_data[10], -0.129)
+        self.assertAlmostEqual(data.qy_data[10], -0.149)
 
     def _check_example_data(self, data):

test/sasdataloader/test/utest_red2d_reader.py

@@ -31 +31 @@
         self.assertEqual(f.qx_data[0],-0.03573497)
         self.assertEqual(f.qx_data[36863],0.2908819)
-        self.assertEqual(f.Q_unit, '1/A')
-        self.assertEqual(f.I_unit, '1/cm')
+        self.assertEqual(f.Q_unit, 'A^{-1}')
+        self.assertEqual(f.I_unit, 'cm^{-1}')
 
         self.assertEqual(f.meta_data['loader'],"IGOR/DAT 2D Q_map")