-
Notifications
You must be signed in to change notification settings - Fork 9
Release notes
Jan Ilavsky edited this page Dec 30, 2021
·
36 revisions
Igor 8.04 and 9.x compatible.
- Fix All tools using the new Multi-GUI (MultiPlot, Simple Fits, bioSAXS...) to handle data with liberal names, apparently that was forgotten.
- New tools:
- System Specific models - this is replacement of Analytical models with new GUI. Mostly working. Needs testing and may be add more functionality.
- Analyze Results - new tool with new GUI for analysis of results Irena produces. For now, Size distributions. Replaced Analyze Size Distribution tool. Can be extended as needed.
- Data Manipulation III - WIP, not finished yet. Multi sample selection tool and ability to modify data. Can delete data (finished).
- Simple Fits & Analysis tool - added 1D correlation model.
- All - changed wrong spelling Ploting into correct Plotting. This may leave some windows opened on restart.
- Fixed all fixed length wave names (hopefully). Now should use long names if user chooses so in Configuration for all waves and folders.
- Merge data tool - fix use of long folder names. It was not following user choice on use of long names. Add merging parameters into the wave note.
- Merge data tool - Added Optimization method: "Optimize Overlap, trim Data1" when data122 are trimmed at the very start of overlap, removing noise at overlap.
- Unified fit - fixed fitting problem when "Link B to G/Rg/P?" was selected, code was not refreshing calculated B during fitting. Caused misfits.
- Unified fit - set automatically k as P varies, this reduces clutter on GUI and behaves more reasonable.
- Multi data plotting tool - added Contour plot and Waterfall plot.
- Export data tool - add option to export SAXS/WAXS data against Q, d, or Two theta.
- Form factor - add disk form factor with thickness as dimension.
- Structure factor - added Distorted crystal SF.
- ASCII export - fix export of USAXS data to ASCII which failed to export correct Q values.
- Igor 9 compatible.
- Fixed all fixed length wave names (hopefully). Now should use long names if user chooses so in Configuration for all waves and folders.
- Fixed edf importer which developed bugs over time due to changes in detector software.
- Add new Eiger detector dimensions to Pilatus detector options.
- Fixed all fixed length wave names (hopefully). Now should use long names if user chooses so in Configuration for all waves and folders.
- Sample Survey tool - multiple row selection enabled, Clipboard now handles multiple rows. Manual updated. Added ability to import image from jpg/tiff/gif... files
- Minor changes to various setting to make user life easier.
- Step scanning in BlueSky (uses Nexus file) now fully supported and well tested.
- Fractals - added optional use of Unified Fit Sphere form factor. This removes high-q Bessel function oscillations which are nto reasonable for most cases.
- Added Multi Data Plot tool, new tool to plot quickly many data sets. New ipf file...
- Added Metadata Browser tool, enables relatively easy extraction of values from metadata in wave notes.
- Added Basic fits tool, new tool and new capabilities. Guinier, Porod, Sphere and Spheroid, more to come as needed
- Added group of bioSAS tools - specialized simple import, data averaging and buffer subtraction, etc. Linked to menu also some existing tools for other functions bioSAS needs Import ASCII, Average/Subtract/Scale tool, PDDF + Molecular weight calculator (uses ATSAS to get PDDF), and Concentration series extrapolation tool.
- DataBrowser in Igor 8 : added Buttons to display w1 vs w2 and extract info from USAXS Folder name strings. Same tools are in Igor 9 right click.
- Added for every graph right click option to export as jpg and pxp. Also to duplicate graph (which Igor does on ctrl/cmd-D) but with duplicate of all data in the graph. 1D graphs only.
- WAXS - changed how JCPDS cards are named (using chemical name or formula+PDF number) + enabled long name support for Igor 8 and when user chooses. Added "Distance correction" for sticks. Tweaks calculated 2Theta angle using distance ratio correction.
- Main panel - change sorting option "_001". This will now look from the end of name for first number. This is to help with NSLS samples names MyName_00001_waxs.ext etc. Will work for normal files Myname_0001.ext also.
- Attempt to fix NXcanSAS data importer. WIP, fixed just two basic types for now, waiting for test data.
- Fixed problem with Sector graph sometimes looking weird - apparently ImageLineProfile sometimes makes different point numbers and this needs to be accounted for.
- Add Sector graph which accounts for tilts, pre request.
- Fixed/modified Calibrated 2D data canSAS/nexus input, needed by SMI instrument from NSLS-II.
- DataBrowser in Igor 8 : added Buttons to display w1 vs w2 and extract info from USAXS Folder name strings. Same tools are in Igor 9 right click.
- Added for every graph right click option to export as jpg and pxp. Also to duplicate graph (which Igor does on ctrl/cmd-D) but with duplicate of all data in the graph. 1D graphs only.
- Added "Smart select Blank" for selection of Blank measured BEFORE the sample measurements.
- DataBrowser in Igor 8 : added Buttons to display w1 vs w2 and extract info from USAXS Folder name strings. Same tools are in Igor 9 right click.
- Added for every graph right click option to export as jpg and pxp. Also to duplicate graph (which Igor does on ctrl/cmd-D) but with duplicate of all data in the graph. 1D graphs only.
- Added new samplePlate tool for users to prepare command files.
- Changed code compiler instruction to rtGLobals=3. This is less forgiving compile which prevents more accidental bugs, but may generate new errors in old code. Debugging took a long time.
- 3D models - added new set of tools : 3DAggregate,
- Due to verification issues, SAXSMorph code in release version of Irena is disabled. Use Master version if you want to test the code.
- Scripting tool - added save individual Populations data when running from Scripting tool.
- Added new group of Anisotropy characterization tools, first one is HOP - Hermans Orientation Parameter.
- Unified fit added info about k value on the panel.
- Data manipulation II - fixed issues with liberal names and actually very long names. Now should create long names, if Igor 8 and user enabled it.
- Guinier-Porod - fixed fitting of structure factor parameters. Was not working at all (forgot to include that).
- Data picker - fixed use of root folder for data (BAD IDEA), use of weird characters in names (like [], etc=bad idea) and use of QIS data (not tested very well, do not have much test data).
- Create QRS folder structure should now handle also QIS data.
- Main code - added Batch processing - this prevents display of images and all graphing updates. Speeds up code by 2-3x in my testing. Added info window when in use and comments in History since else it looks like Nika hangs.
- APS 12ID support fix. Added ability to read all many options how mask can be defined for goldaverage program.
- Changed Nika GSAS export file type to xye (was using old GSA).
- Modified to accept in Empty/Dark, Mask, Flood, etc. that tiff and tif files are the same.
- Allow for Azimuthal line angle negative values. NOTE: if AzAngle<0 ->>> internally equivalent to AzAngle = 180+ AzAngle.
- Added ability of Flyscanning data reduction to guess minimum useable q for data reduction. Based on intensity ratio between sample and blank - note, it is q dependent ratio. Black magic.
- Changed default number of USAXS points to 500, seems reasonable now.
- Igor 8 OSX XOPs now available. Version 2.0 of 64-bit xops.
- Fix mailman links, remove non functioning menu items to open pdf manual and other tstuff which does not exist anymore.
- Control procedures - increases speed about twice of generating the menu strings.
- ASCII SAS data import - improve importing of slit smeared data.
- Unified fit - add left axis units which match units inside the Intensity wave note.
- Size distribution, Guinier-Porod, Analytical models, SASDiffraction - add left axis units which match units inside the Intensity wave note.
- Size distribution - add new parameters introduced in version 2.67 to wave note and arrange their saving and recovery. Somehow this was forgotten during the original work.
- Plotting - remove CanSAS data type. Not used...
- Plotting tool - changed the mirror size axis to show 2pi/Q and modified label to "Diameter/dimension 2pi/q [A]"
- Modified "Configure GUI..." menu name and added warning on name shortening. Should generate dialog when names are too long and users are not using Igor 8 with long names enabled. Only once per Igor experiment.
- Evaluate Size distributions - fixed failure with data from Modeling (II) when user used Pop1 as non-size distribution and used Size distribution in higher Pops. GUI and parameter readout failed at that situation. Checked (and fixed) for data from Modeling package - using Number of Volume distribution and using Radius or Diameter. Previously problem was with Number density of particles and Specific surface area = all worked well only for Diameters. Needed to add hooks for Radius conversion as needed...
- Nexus export - fixed Nexus export to output files compatible with SasView (beta version for now). Should work with both desmeared and slit smeared data now.
- Merge data - added more functionality, ability to shift in Q data 1 as well as 2, and modified graph for WAXS and SAXS display. Completely reworked optimization routines to make all more robust and easier to fix. Removed lots of ugly repetitive code.
- Added circles on drawing which are in Q steps. Currently 12 log-spaced circles will be added, red color, with labels of Q values.
- Modified "Configure GUI..." menu name and added warning on name shortening. Should generate dialog when names are too long and users are not using Igor 8 with long names enabled. Only once per Igor experiment.
- Fixed GUI bug which was causing hang of Main Panel on Igor 8. Igor 8 bug, but due to coding bad practice.
- Fixed solid angle correction bug. It was multiplying by the solid angle instead of dividing by it.
- Modified 9ID data reduction to include solid angle correction.
- Added support for 12ID-C.
- Fixed DND-CAT support to use current output model.
- Modified "Configure GUI..." menu name and added warning on name shortening. Should generate dialog when names are too long and users are not using Igor 8 with long names enabled. Only once per Igor experiment.
- Added checkbox to use for calibration FWHM of sample and not Blank. Variability of Blanks adds to uncertainty of the absolute intensity calibration. Usually sample FHWM is better measure of Solid angle. Will be overwritten if sample FWHM is too large (Multiple scattering).
- Improved on negative background subtractions...
- Added ability to overwrite Flyscan amplifier dead times.
- Fixed problem with color scale for amplifiers not showing correctly.
- Igor 8.0 tested. Updated Installer to version 1.07, prior version works, but throws error at users.
- Converted all procedure files to UTF8 to prevent text encoding issues.
- Nexus exporter - changed to use 1/angstrom for Q as sasView below 4.1.2 (probably below 4.3 at least) cannot convert Q units on import. Other necessary fixes also.
- Nexus Importer - fixed and modified to be able to import NXcanSAS files from DAWN and Mantid.
- Checked that - with reduced functionality - code will work without Github distributed xops. Needed as Igor 8 . requires recompiled xops on OSX and these are NOT available yet.
- Size distribution - added power law slope to Background so one can subtract also low-q power law slope. Added buttons to perform power law fit and background fit. Added option to fit the parameters when data are added to the tool.
- Unified fit - modified how the limits and steps are handled when user set value to 0. Fixed Uncertainty analysis in Unified fit which seems to have failed on Igor 8.
- Created depository for user contributed form factors on Github: https://github.com/jilavsky/SAXS_IgorCode/tree/master/User%20form%20factors%20for%20Irena
- Fixed Case spelling of USAXS Error data to SMR_Error and DSM_Error
- Plotting tool I - added control which enforces maximum number of items in legend (default=30). If more waves are in graph, legend gets decimated by necessary integer(2, 3, 4,...). First and last are always included. This presents selection of data names when too many data sets are used.
- MergeData - added ability to fit-extrapolate data 1 at high q end and added possibility to fit arbitrary combination of merging parameters. Lots of changes. More capable and more complicated.
- Unified Fit - added button "Copy/Swap level" which will move content of existing level to another level.
1.80 7/7/2018
- Removed range selection controls and moved Save data options to its own tab "Save"
- Added ImageStatistics and control for user for delay between series of images.
- Added font type and size control from configuration to be used for CCD image label.
- Added ability to fix negative intensities over subtraction. Checkbox on Empty tab and if checked, ~1.5*abs(V_min) is added to ALL points intensities.
- Modified main interface to have radio buttons and only one button for action. This makes cleaner interface as some controls can be hidden. Unluckily, panel is now higher by 20 points.
- Added support for ALS SRoXS soft energy beamline.
- Improved 9IDC USAXS support.
- Added more masking options into main panel listbox right click.
- Bug fix - changed ki/kout single precision waves to double precision. This caused issues under very small angles when data were unintentionally binned to less points what should have been produced. This is very old bug causing issues at very small Q vectors with short wavelengths and no beamstops.
- Modified behavior of Automatic blank selection in GUI.
- Fixed Case spelling of USAXS Error data to SMR_Error and DSM_Error.
- Added ability to smooth R_Int data - suitable mostly for Blank where it removes noise from the blank. Should reduce noise of the USAXS data.
- Added masking options into FLyscan panel Listbox.
- Web site for the manual: http://saxs-igorcodedocs.readthedocs.io/ is now the only maintained manual for Irena, Nika and in the future Indra. These manuals version 1.3.0 is version which belongs to November 2017 releases.
- Internal changes and improvements resulting in less and cleaner code.
- Promoted required minimum version to 7.05 due to bug in Igor prior of this version.
- Panels now restore prior size and position. This is set when you drag lower-right corner to scale them up. Data stored on the user computer and size is limited to 50% width and 90% height of current screen size. Hold down any modifier key and size will be reset to original default state.
- Added Update Message to CheckForUpdate code. If file is present in GH depository, it will display a message for users.
- Removed pdf manual from distribution. It was obsolete, use on-line version and if needed, download pdf from the on-line source.
- Merge two data sets - added option of sorting qrs names by xyz_string, needed for Nika. Added SMR and DSM data to USAXS.
- Modeling - added calculation of Rg for size distributions. Requested by Dale Schaefer.
- Unified fit - changes to two phase systems requested by Dale. Added ability to handle multiple levels at the same time where possible…
- Data merging tool - modified Optimize code to prevent failures, hopefully improved fitting capabilities.
- WAXS - Added option to import free AMS diffraction data (http://rruff.geo.arizona.edu/AMS/result.php) - this database contains d, hkl, intensities for minerals.
- ASCII exporter - added export of GSAS-II xye data file.
- Added ColorTable to preferences, Saved every time color table is changed and restored as needed. Should change the Panel GUI and colors of graph, if exists.
- Modified folder name length - now each segments (_C, sectors, etc) will use longest possible part of the input file name, previously was limited to 17 characters. This allows longest user input names, but different directions may have different length of name allowed as the strings are different length. _C is shortest, in this case the length of name is about 29 characters.
- Added ability to read multidimensional data from Nexus. Up to 4D data can be read, index 0 is first, index 2 second index, next two indexes are the image points. Standard. 3D data have only index1 (index0=0), 2D data have both indexes=0.
- 9ID support - will keep the _270_30 sector of SAXS data for use with desmeared USAXS data. Added UserSamplename string to each folder for long names.
- Changed and streamlined 9IDC support package to have less controls and be more robust. Reads parameters from each file.
- Added Desmearing to Data reduction as final step. Saves both SMR and DSM data. Contains much less choices as USAXS is reasonably stable and choices are known. May fail for border cases.
- Added UserSamplename string to each folder for long names.
Created new GH repo for manuals and created web site for the users: http://saxs-igorcodedocs.readthedocs.io/ . The site contains port of current manuals version - released version 1.1.0 of the web based manuals as stable and they now contain index and all prior information. This is now main location for these manuals.
- Made Igor 7 compatible ONLY. Thanks to GeneralProcedures changes will not work on Igor 6.
- Added buttons with links to web based manual pages to each tool.
- Monthly version check - using Github IgorInstallerCofing.xml to read the latest release version info.
- Fixed more slow debugging calls, most tools should see improvement in speed, thanks to speedup of data selection functions used by practically every tool.
- Optimized slit smearing function, slit smearing the data should be up to 6x faster. All packages working with slit smeared data should be faster. Especially fitting of slit smeared data.
- Unified fit - removed requirement that modeled Qmax is larger than 3*slit length for slit smeared data. Qmax for modeling and fitting now can be anything reasonable. Data are silently extended, modeled, smeared, and truncated, same method as Modeling II.
- Size distribution - removed requirement that modeled Qmax is larger than 3*slit length for slit smeared data. Qmax for modeling now can be anything reasonable. Data are silently extended, modeled, smeared, and truncated, same method as Modeling II.
- Size distribution - Optimized speed (~2x improvement). Removed limitation that Qmax > 3*slit length for slit smeared data.
- Size distribution - fixed bug introduced in MaximumEntropy
- Data merging - added name modifier string and defaulted to new folder name even for QRS name systems.
- Completely removed Modeling I - about 2k lines of code. Moved code where needed and removed about 3 ipf files from loading.
- Made Igor 7 compatible ONLY. Thanks to GeneralProcedures changes will not work on Igor 6.
- Monthly version check - using Github IgorInstallerCofing.xml to read the latest release version info.
- Added buttons with links to web based manual pages to each tool.
- Igor 7 required now.
- Updated manual
- Modified Nexus support, added new library to use it.
- Moved some common functions to IN2G_GeneralProcedures
- Fix to QRS names which failed on names containing string “spec” in the name.
- Added checkbox for slit smeared/desmeared USAXS data in Merge 2 data sets tool.
- Small-angle diffraction - when user selects “oversample” the parameters for peaks (d, q, width) are now calculated at 5x higher resolution than measured Q points.
- Desmearing - propagate dQ and if does not exist, create dQ based on points distance.
- Pair Distance Distribution - changed Matrix solving method since the one used was deprecated by Igor 7.
- Plotting tool - added ability to add top 2pi/Q linked axis. Using Transform axis package from Igor Pro. Added few new styles and modified existing settings. Fixed Gizmo for Igor 7 which stopped working due to Gizmo function syntax changes.
- WAXS - removed LaueGo capability and added import of PDF-4+ xml files. Fixed help file.
- Modeling II - if you hold any modifier key (shift/ctrl/opt/alt…) while clicking on parameters change arrows, the step for next step is set 10x smaller. This enables making small changes to the values. Just keep holding the modifier key, first step is still large, subsequent are small.
- Size distribution - fixed Regularization for Igor 7, modified trust ranges which were using wrong logic. Now large size is estimated 2pi/Q while small size pi/Q.
- Fixed slow down caused by debugging messages function
- Fixed old bug where Sample Thickness was not converted to cm before use. This means that prior experiments with calibration constants need to have calibration constant also scaled by factor of 10 to compensate. Added warning to Panel version check.
- Modified Nexus support, added new library to use it. Major revision of Nexus import and export of data.
- Moved some common functions to IN2G_GeneralProcedures
- Removed Utility_JZT from distribution, not needed and causing conflict with JZT package.
- Updated manual.
- Fixed slow down caused by debugging messages function
- Modified Nexus support, added new library to use it.
- Removed Utility_JZT from distribution, not needed and causing conflict with JZT package. `
- Added OverRideSampleThickness where user can set new sample thickness for range of samples. Set to 0 to ignore.
- Added Live processing of data same as Nika has.
- Fixed internal bug which caused problems when dark current on UPD was measured too high.
- Added overwrite for Dark current 5
- Added overwrite for sample thickness
- Fixed slow down caused by debugging messages function.
- Fixed up readme and reorganized menu to make it easier to find important items.