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BioXTAS RAW Changelog

What's new in BioXTAS RAW 2.1.1

May 5, 2021
  • Overview:
  • The RAW team is pleased to announce the release of RAW version 2.1.1. The major change in this version is:
  • Fixed a serious bug that would cause RAW to crash on Ubuntu.
  • There are also several other small bug fixes and new features.
  • All changes:
  • Fixed a serious bug that would cause RAW to crash on Ubuntu (and possibly other OSes).
  • Fixed a bug where closing the Guinier window before autorg finished would result in an error.
  • Fixed a bug that could cause an error if the auto_dmax function failed to return a result.
  • Fixed a bug where using simple concentration regularizers would fail.
  • Fixed a bug where caching of certain compiled functions wasn’t working, leading to them having to be compiled every time RAW was opened.
  • Tweaked when functions are compiled to try to speed up the user experience, particularly when opening the Guinier window, and either IFT window.
  • Improved the speed of BIFT on Linux and Windows.
  • Fixed an issue where RAW wouldn’t work with matplotlib>=3.4.1.
  • Fixed an issue where available fonts weren’t properly displayed in the prebuilt versions.
  • In the RAW API, BIFT now defaults to single processor (should be faster), and you can specify the number of processors to use if you use it in multiprocessor mode.

New in BioXTAS RAW 2.1.0 (Apr 21, 2021)

  • Fixed a bug that was causing pyFAI to recreate the azimuthal integrator each time, slowing down radial averaging.
  • Fixed a BioCAT specific bug where concentration would end up in the profile info when it wasn’t actually known for that profile.
  • Fixed a bug where series files couldn’t be loaded or saved in python 3.8.
  • Fixed a bug where if you declined to load a config when you started RAW, the ATSAS install location wouldn’t be automatically found.
  • Fixed a bug where matplotlib 3.3 would mess up the plot toolbars.
  • Fixed a bug where you would see an error message if RAW failed to find a valid sample region in the LC series plot.
  • Fixed a bug where doing EFA on a series that had the q range of the subtracted profiles truncated relative to the unsubtracted profiles would fail.
  • Added the ability to generate PDF reports of analysis.
  • Fixed a bug where the profile and ift line options dialogs couldn’t be opened with matplotlib 3.3.
  • Significant improvements to auto_guinier function for both the GUI and API, including better accuracy, better handling of low quality data, and better handling of poorly formatted data.
  • Fixed a bug where if previous EFA ranges were available they wouldn’t be properly set when the EFA window was opened.
  • The RAW DENSS results .csv file now indicates if a refinement was run.
  • Fixed a bug where RAW could fail to load a .out file.
  • Fixed a bug where aborting in the middle of a DENSS average could cause an error.
  • Fixed a bug where opening the GNOM window if the profile had a non-integer Dmax value caused an error.
  • Added the REGALS technique.
  • Added an enhanced way to automatically find Dmax when using GNOM.
  • Fixed a bug where running GNOM when RAW was run with python 3.8 could fail.
  • Added ability to read in a fourth dQ column in .dat files, preserve the dQ values through analysis and saving. Note that merging and interpolating do not preserve the dQ values at this time.
  • Added ability to read in CRYSOL 3 .int files.
  • Fixed an off by one bug that could affect SVD/EFA/REGALS
  • Fixed a bug where settings could fail to save or load on Windows if they included non-ascii characters
  • Fixed a bug where calculating the corrected Porod volume MW could return an error
  • EFA now remembers the force positive settings for concentration.
  • Fixed a bug where if an EFA range was listed high to low it would cause an error.
  • Fixed a bug where scaling q by 10x or 0.1x only worked once (i.e. you could scale to 0.1x or 10x, but not 100x, and couldn’t go back to 1x after applying a scale).
  • Fixed a bug where the linear baseline wasn’t getting a good start value.
  • GNOM window now ‘truncates for dammif/n’, which truncates to the smaller of 8/Rg or 0.3.
  • Guinier window now opens faster.
  • Updated DENSS to version 1.6.3, which includes the possibility of doing DENSS on a GPU (requires RAW to be built from source).
  • Fixed a bug where multiple DENSS windows couldn’t be used at the same time.
  • Fixed a bug where subtracted and baseline corrected profiles from the LC Series Analysis window would have the prefix of the individual profiles in the series, rather than the series itself.
  • Fixed some possible memory leaks related to dialog creation/destruction.
  • Added a number of new tests.
  • Added compatibility with new string handing in h5py version 3.
  • Full compatibility with MacOS 11, which fixes several graphics glitches in 10.15 and 11. This required dropping support in the prebuilt version for MacOS 10.10 and earlier.
  • Fixed a bug with the API where loading multiple images from a single file wasn’t working properly.
  • Added the ability to abort DAMMIF/N and related functions and DENSS runs in the API.
  • Made SECM and RAWSettings objects pickalable, so they can be passed through a multiprocessing queue.
  • Fixed an API bug where saving a series would fail if you didn’t set a filename.
  • Fixed an API bug where saving the GNOM results to a profile was saving the wrong qmax value.
  • Fixed a bug in the API where Dmin and Dmax zero conditions weren’t getting set correctly for GNOM.
  • Added a feature to the API to truncate an IFT for dammif using either 8/rg or 0.3, whichever is smaller.
  • Fixed a bug in the API that could cause GNOM to fail to run.
  • The DENSS function in the API now returns chi squared, rg, and support volume as a function of iteration so you can check convergence.
  • Fixed a bug in the API where running EFA would change the associated ranges.
  • Fixed a bug in the API that could cause BIFT to fail.
  • Fixed a bug in the API that could cause the auto_guinier function to fail.
  • Fixed a bug in the mw_vp API function.

New in BioXTAS RAW 2.0.3 (Aug 11, 2020)

  • The RAW team is pleased to announce the release of RAW version 2.0.3. While this is only a point release, we are releasing a major new feature for RAW. There are only minor modifications to the RAW GUI, but we are releasing an entirely new RAW API. This means that RAW can now be imported as a python package and you can call RAW functions in your own scripts. The API is fully documented, and the documentation plus install instructions and some examples are available on the RAW website.

New in BioXTAS RAW 2.0.2 (Jul 9, 2020)

  • Can now load .dat files from WAXSiS, .dat files that are comma separated.
  • Fixed a bug where the Vc integrated intensity plot was blank if the scattering profile had saved M.W. results.
  • Improved rebinning functions, particularly the log binning function.
  • Fixed a bug where error wasn't interpolated properly when interpolating a profile.
  • Fixed a bug where pixel size from header bindings was in the wrong units.
  • Fixed a bug where series type could get lost in certain operations.
  • Fixed a bug where centering and enantiomorph selection options were ignored in the DENSS alignment panel.
  • Fixed a bug where series buffer range finding was scaling profiles before testing for similarity.
  • Fixed a bug where SAXSLAB images failed to load with pillow version 7.
  • Fixed a bug where SAXSLAB images failed to radially average.
  • Fixed a bug where images wouldn't load if there was no beamstop mask.
  • Fixed a bug that could result in calculated data not displaying on the series plot.
  • Fixed a bug where series saved as .hdf5 with EFA analysis would fail to open the EFA window when reloaded.
  • Fixed a bug where datgnom couldn't be run on truncated profiles.
  • Fixed a bug where opening the advanced settings window from the GNOM window didn't properly update changed settings in the GNOM window.
  • Fixed a bug where .hdf5 files couldn't be plotted by dragging and dropping or using the 'Plot Series' button.
  • Fixed a bug where running a dammin refine with too long a filename would fail (previously thought to be fixed in 2.0.0).
  • Fixed a bug that could prevent DENSS from starting on Windows and Linux.
  • Fixed a bug that could prevent auto determination of number of components in EFA.

New in BioXTAS RAW 2.0.1 (Jun 1, 2020)

  • This version fixes several serious bugs in the previous version, including:
  • A bug where some of the M.W. calculations failed for profiles with a maximum q value greater than 0.5.
  • A bug where the standalone DENSS alignment window failed to run on Windows and Linux.
  • A bug where killing the prebuilt version of RAW on Linux would fail to delete temporary files, which could lead to the /tmp partition filling up.
  • There are also several other small bug fixes and new features.
  • All changes:
  • Fixed a bug where the 'More Info' button didn't work for DATCLASS M.W.
  • Fixed a bug where Bayes and DATCLASS M.W. weren't saved when saving all analysis info.
  • Fixed a bug wehre RAW woud fail to load in .out files if they were missing values for any of the perceptual criteria.
  • Fixed a bug where an error message was shown whenever a profile with qmax > 0.5 was opened in the M.W. window.
  • Fixed a bug where the Vp M.W. extrapolation range warning could be shown even if the qmax selected was inside the extrapolation range.
  • Added zero lines to DAMMIF, DENSS residual plots.
  • Fixed a bug where running DENSS without averaging could result in an error message.
  • Fixed a bug where running DENSS without averaging or alignment would result in an error message.
  • Fixed a bug where when there was more than one profile in the normalized Kratky plot the dashed lines to guide the eye were not removed when switching from dimensionless Rg to other plots, which would throw off the scale of the plot.
  • Fixed a bug on Windows where the standalone DENSS alignment window didn't work.
  • Fixed bugs where the advanced options couldn't be shown in the SUPCOMB or DENSS alignement standalone windows on Windows.
  • RAW now catches SIGINT and SIGTERM and tries to exit gracefully. This mostly fixes an issue with the prebuilt .deb installer where the temp files created when starting RAW don't get deleted.

New in BioXTAS RAW 2.0.0 (May 7, 2020)

  • Python 3 compatibility!
  • Conversion to pyFAI for radial integration
  • A .deb prebuilt installer for Debian/Ubuntu
  • A new series save format, .hdf5, that can be easily read by other programs. This new format is also ~50-70% smaller than the previous format.
  • New information windows above the control panel to display all your analysis
  • Ability to align DENSS and DAMMIF/N outputs to PDB files
  • Works with ATSAS 3 on all platforms
  • New Series adjustment panel that lets you adjust the scale, offset, and q range for all profiles in a series easily

New in BioXTAS RAW 1.6.4 (Mar 10, 2020)

  • Fixed a bug where negative values for error would cause points to not be read from .dat files.
  • Fixed a bug where the BIFT window wouldn't open if the profile and n min or n max for the q vector set to other than 0 and the length of the q vector.
  • Fixed a bug where looking for bind list keywords that don't exist in the RAW settings would prevent a file from loading.
  • Fixed a bug where damaver didn't run with symmetry even if dammif did.
  • Added a name to the dock/menu bar icon.
  • Fixed a bug with moving masks.
  • Added CHESS EIGER 4M to counter file reader options.
  • Fixed type-casting issues for max/min in polygonmasking that caused errors on some older systems.

New in BioXTAS RAW 1.6.3 (Nov 1, 2019)

  • Fixed a bug where if you averaged, subtracted, or merged two items with analysis done on them, you could end up with partial analysis info in the resulting file that would cause errors opening analysis windows.
  • Fixed a critical bug where when averaging detected different files, regardless of user choice it would always average all files (selecting just similar files didn't work).
  • Fixed a bug where the MW window wouldn't open if the Guinier fit hadn't been done.

New in BioXTAS RAW 1.6.2 (Nov 1, 2019)

  • The RAW team is pleased to announce the release of RAW version 1.6.2. This version fixes several critical bugs that could prevent DENSS from running. There are no other changes.

New in BioXTAS RAW 1.6.1 (Oct 22, 2019)

  • All changes:
  • Fixed a bug where opening the Ambimeter panel could fail if ATSAS was installed in a directory with a space in the path name.
  • Fixed a bug where if RAW didn't load a settings file when opened it wouldn't automatically find the ATSAS directory on startup.
  • Fixed a possible bug where using the LC Series Analysis panel on series data being loaded in online mode could fail.
  • Added intensity type selector for the series panel when sending data to the main plot.
  • Fixed a bug where automatic integral baseline start/end region determination could set the wrong control limits.
  • Fixed a bug where zero lines on various plots (like the GNOM P(r)) plot weren't getting redrawn when necessary.
  • Fixed a bug with autoscaling in the LC Series Analysis plots when changing the data type displayed.
  • Fixed a bug where sample and buffer region comparison in the LC Series Analysis panel could return the wrong indices for dissimilar profiles.
  • Fixed a bug where profile comparison in LC Series Analysis would skip the first profile.
  • Fixed a bug where a very short series (<22 frames) could cause errors when opening the LC Series Analysis panel.
  • Improved automatic buffer search in the absence of major peaks.
  • Improved automatic buffer search to search on the right side of the main peak if it doesn't find a good buffer region on the left side.
  • Removed a bias to the left side of the peak in the automated sample region search.
  • Removed actual baseline correction values from being saved in file history, as history could get very long (>100000 lines).
  • Added a cutoff for header length, at which point RAW will stop saving file history. This avoids saving extremely large text files.
  • Added compatibility for pyFAI 0.18 (note: on linux and python 2.7 pyFAI 0.18 seems to be broken, stick with 0.17).
  • Added a new way of loading HDF5 files with definitions done in external files.
  • Added ability to load HDF5 files from LiX.
  • Fixed a bug where identical selected regions in the LC Series Analysis window didn't count as overlapping.
  • Fixed a couple of typos in messages.
  • Fixed a bug where Ambimeter and GNOM couldn't run if the current working directory was read only.
  • Improved how ATSAS programs are called, and added use of temporary file names and directories.
  • Fixed a bug where when dragging the image plot with the masking showing you could sometimes get an unexpected error.
  • Added the name of the series to the LC Series Analysis panel.
  • Fixed a bug where baseline subtracted profiles were improperly being skipped when calculating Rg etc in the LC Series Analysis panel.
  • Fixed a bug where if a series was loaded with a baseline already calculated, changing buffer range or other parameters wouldn't properly recalculate baseline corrected values.
  • Fixed a bug where if you set a baseline, then set it back to none, when exiting the LC Series Analysis window the baseline calculated values would be saved instead of the regular subtracted values.
  • Fixed a bug where if you loaded in a series curve with baseline correction, then turned off baseline correction, it wouldn't have any calculated values.
  • Fixed a bug where the LC Series Analysis panel would resize itself when any of the collapsible panes were collapsed or expanded.
  • Fixed a bug in the LC Series Analysis panel where if you had a range that was one frame long, when you closed and reopened the analysis window you couldn't adjust the range.
  • Fixed a bug in the LC Series Analysis panel where if you had a one frame long range you could get a reported correlation in the range.
  • Fixed some issues with window height where windows weren't opening large Fixed some issues with window size where windows could open up bigger than the screen.
  • Fixed a bug where in certain circumstances opening the SVD and EFA windows could fail.
  • Added compatibility with numba >= 0.44

New in BioXTAS RAW 1.6.0 (Jun 8, 2019)

  • Updated DENSS to have the latest features, including refining averaged structures, symmetry constraints, and the 'Membrane' protein mode.
  • Completely redid BIFT code from the ground up. This fixes several bugs, and now includes Monte Carlo estimation of errors.
  • Completely redid series analysis for SEC-SAXS data. Now includes automated buffer and sample region determination and baseline correction.
  • Added residual plots to GNOM, BIFT, and DAMMIF/N results.
  • Fixed several bugs related to setting error bar line styles.
  • Added ability to add arbitrary metadata to a file header when an image is processed by RAW
  • Updated the adjusted Porod volume MW method to match the newly published MoW2 approach.
  • Fixed a bug where info panel data could get improperly set
  • All appropriate fields in MW panel now editable.
  • You can now open any analysis window more than once (previously only one instance of each window was allowed).
  • Fixed a bug where in the GNOM window changing q_min or q_max didn’t update the IFT results.
  • RAW now loads the last used config (saved or loaded) by default rather than the last saved.
  • RAW now preserves all shared header values when averaging, subtracting, or merging datasets.
  • Added visual guidelines to the dimensionless Kratky plot.
  • Added option to display normalized residuals, now on by default.
  • Added Rigaku HiPix to known images (requires Fabio 0.9.0)
  • Guinier panel can now export Guinier fit data so users can make the Guinier plots in their plotting software of choice.
  • RAW’s file list no longer displays hidden files.
  • Can now read in time of each data point for BioCAT data.
  • Fixed a bug where closing the BIFT window with BIFT running would crash RAW.
  • Better formatting for numbers displayed in the status bar.
  • Fixed a bug where windows could be too large on low resolution displays.
  • Fixed a bug where series plot calculated data were not highlighted by the locater button.
  • Fixed a bug where markers were not highlighted by the locater button for any plot.
  • Fixed a bug where when selecting a line by clicking on it the plot markers were not highlighted.
  • Fixed a bug where selecting a line on the IFT plot didn’t work.
  • Can now display unsubtracted, subtracted, or baseline corrected intensity in the main series plot.
  • Fixed a bug where series data could be truncated when exporting.
  • Fixed a bug where the SVD window wasn’t doing the SVD on non-error-normalized curves.
  • Moved cormap to cython for speed, increased by at least 5x.
  • Modified layout of the repository to standardize.
  • Autorg now uses numba for just-in-time compiling. Speed increase of 2 orders of magnitude.
  • Fixed bugs that would occur when quick reduce, plot, plot series, or show images were used on folders, ‘..’, or with no files selected.
  • Added ability to plot intensity over a q range for series plots.
  • All-new icons that work with retina displays, including a new ‘eye’ for show/hide instead of a check box (hopefully more intuitive).
  • Fixed a few bugs in the DAMMIF/N GUI.

New in BioXTAS RAW 1.5.1 (Nov 2, 2018)

  • All changes:
  • Fixed a bug where automatic loading of BioCAT SEC data wouldn’t work if there was more than one underscore in the filename.
  • Fixed a bug where automatic loading of BioCAT SEC data wouldn’t work if there existed another file with the same name but different extension as one of the image files.
  • Added parsing of damsup.log file for bead models, which allows highlighting of the representative model in the dammif summary.
  • Dammif results summary now saved by default.
  • DENSS results summary now saved by default.
  • Fixed several bugs in the GNOM interface that could cause it to fail.
  • Fixed a bug that prevented some .fit files from being loaded.
  • Fixed a bug where the Rg for BIFT was being calculated incorrectly.
  • Fixed a bug where temporary files (with a .tmp prefix) would mess up SEC autoupdates.
  • Fixed an issue where you couldn’t run DENSS twice without closing the panel between each run.
  • Fixed an issue where the default scaling for DENSS was too small, and caused issues loading the electron densities into pymol.
  • Fixed a bug text in some items and list controls would display ‘fuzzy’ on high dpi monitors. This is still an issue for the plot labels.
  • Added the ability to run damaver and damclust on the same set of reconstructions.
  • Fixed a bug where the .app package for Mac wasn’t displaying natively on retina displays, so the text was fuzzy. Note that in order to fix this, even after you install the new version you may have to do the following:
  • Enter the following commands in your terminal:
  • /System/Library/Frameworks/CoreServices.framework/Frameworks/LaunchServices.framework/Support/lsregister -f /Applications/RAW.app
  • /System/Library/Frameworks/CoreServices.framework/Frameworks/LaunchServices.framework/Support/lsregister -kill -seed
  • /System/Library/Frameworks/CoreServices.framework/Frameworks/LaunchServices.framework/Support/lsregister -f /Applications -all local,user
  • You may then have to right click on RAW.app, select ‘Get Info’ and uncheck the box ‘Open in low resolution mode’

New in BioXTAS RAW 1.4.0 (Mar 20, 2018)

  • Added DENSS method for calculating electron density from SAXS profiles
  • Added support for EMAN2 averaging and enantiomer testing of DENSS results
  • Fixed a bug where the GNOM window could fail to exit and save the .out file to the IFT tab
  • Changed the default DAMMIF mode to slow.
  • Changed when the 'please wait' message appears when loading SEC-SAXS files in autoupdate mode. Now it only shows up if more than 5 files are loaded at once.
  • Fixed a bug where advanced options for GNOM and DAMMIF couldn't be set while the respective analysis windows were open.
  • Fixed a bug where the spectral color map couldn't be displayed, breaking the image control planel.
  • Fixed a bug where ambimeter would try to run in the DAMMIF window even if ambimeter wasn't available.
  • Fixed a bug where if files were averaged or subtracted and had analysis history, that analysis would get transfered to the new file.
  • Fixed a bug where Guinier fit limits would be improperly displayed on the plot when the Guinier window was first oepned.
  • Fixed a bug where calls to set up the DAMMIF results window could be non thread safe.
  • Added estimate of the parameter (Rg and I0) errors for a Guinier fit.
  • Reformatted the MW display to make it more compact.
  • Changed how numbers are displayed in all of the analysis windows, to better handle very large or very small values.
  • GNOM, Ambimeter, DAMMIF windows now open much faster.
  • Added support for BioCAT header files (new style).
  • Added support for autoloading of BioCAT Series curves.
  • Added GNOM P(r) parameters (Rg, I0) errors to the GNOM window, and the estimated Guinier errors.
  • Guinier parameter errors and GNOM P(r) parameter errors are now saved with profiles, and with analysis info spreadsheets.
  • Fixed bugs where spin controls could raises errors if a user entered a blank value.
  • Values from analysis windows are now saved with more precision.
  • Rearranged the manipulation item right click menu to make it more compact, put some less-used items on sub-menus.
  • Changed 'SEC' labels to 'Series' labels.
  • Fixed an off by one error in SEC autoupdate that could occur for certain file names.
  • Renamed and rearranged some menu items in the IFT item right click menu.
  • Added universal newline support when loading in scattering data.
  • Fixed a bug where averaging could fail if all the averaged files were different form the first file.
  • Fixed a bug where similarity testing could fail with an overflow error if there were too many points in the scattering profile.
  • Minor improvements to plotting speed with large numbers of files.
  • Fixed a bug where having no positive values in a curve displayed on a log-y axis would cause an error.
  • Updated the documentation to include a DENSS tutorial. Updated various other parts of the documentation, including the images, to reflect other new features.
  • Updated all of the installation documenation.
  • Removed the RAW-Windows-Source-Install-Essentials file from the downloads.

New in BioXTAS RAW 1.3.0 (Aug 10, 2017)

  • The RAW team is pleased to announce the release of RAW version 1.3.0. This release is a major feature release, and we're very excited that you get to use all of the fun new stuff we’ve added in!
  • The major new features are:
  • Similarity testing for scattering profiles using the CorMap test. This allows statistical testing of whether or not profiles are similar. This is done automatically when averaging profiles or picking a buffer region of a SEC curve, and is also available in the right click menu for profiles, IFTs, and sec files. In the automatic check, if it detects files that may be different, you’ll see a message asking you how you want to proceed.
  • Normalized Kratky plots can now be made, and are accessible through the right click menu.
  • We’ve added a results summary panel for dammif/n reconstructions that shows the NSD, resolution (if SASRES is installed), and statistics about the individual reconstructions including chi squared, rg, dmax, excluded volume, and molecular weight. There is also a new dammif results viewer panel that lets you get a basic look at the reconstructions (this panel is still very simple).
  • Absolute scaling can now be done using the NIST glassy carbon standard SRM 3600.
  • In addition to all of these major changes, we’ve made the usual range of small tweaks, bug fixes, and enhancements. See the full list of changes below.
  • Finally, we’re happy to announce that we’re also releasing a new tutorial, that has been updated to include tutorials for all of the new features mentioned above!
  • Changes:
  • Fixed a bug where switching between linear and log scale in the image display could change the overall scaling of the image without changing the displayed limits in the dialog.
  • Added a new dammif/n results summary panel.
  • Added a new dammif/n results viewer panel.
  • Added a new normalized kratky plot panel
  • Changed how multiple images in a single file are deal with when loaded as a sec curve (now each is loaded as an individual point on the curve).
  • Added a new check for statistical similarity between profiles (or IFTs or SEC curves).
  • Now on average, RAW automatically checks whether the profiles are statistically similar.
  • Fixed a bug where the first image loaded from a file with multiple images in it was flipped left-to-right relative to the rest.
  • Fixed a bug where if a configuration file is loaded and doesn’t contain certain setting keys (a configuration made with a previous version where those settings don’t exist, for example), those settings are now set to default, rather than left as whatever is loaded in RAW.
  • Added ability to view all images in a single file if the file contains more than one image.
  • Added ability to use glassy carbon (NIST SRM 3600) to calibrate absolute scale.
  • Fixed a bug in subtraction that could result in the q and i vectors being rounded.
  • Fixed a bug where if the beam center was in the masked region of the image it could be assigned a non-zero value.
  • Fixed a bug where a RAW setting for a choice type with default value of None could cause an error when trying to set the field in the Advanced Options window.
  • Added a check for syncing items to make sure that an item is starred and an item is selected.
  • Added ability to reset all settings to default values from the advanced options panel.
  • Marker face, marker edge, and error bar colors are now saved when you save a workspace.
  • Error bars now show up correctly for Guinier, Kratky, and Porod axes in the Main Plots.
  • Added ability to use error weighting in fits, and ability for user to toggle that on and off in the advanced options panel. Fitting is now by default done with error weighting.
  • RAW can now load .txt files.
  • Fixed a bug where on a single core machine there would be no default selection for the number of simultaneous runs in the dammif/n window.
  • Font list now includes matplotlib fonts
  • Changed LaTeX symbols to default to regular instead of italics.
  • Fixed a bug where line size on a plot would change when opening/closing the line properties window without making any changes to the line size in the window.
  • Added ability to use fractional line sizes.
  • Fixed a typo in the readme
  • Removed a message asking if you’re sure you want to load the workspace.
  • RAW now checks whether or not you’re saving something when it quits. If it is saving something, it warns you that you might now want to quit.
  • Legend labels are now saved with a workspace.
  • Fixed a bug where the legend label for IFT items would get changed from the default when you opened the line properties window.
  • Fixed a bug where the calculated markers for a SEC item would show when loading a workspace even if the item wasn’t supposed to be visible.
  • Added sync and superimpose to the right click menu, tools menu.
  • Added the program version to integrated dat files history.
  • Added integration method and calibration parameters to the integrated dat files history.
  • Fixed a bug where a dammin refine would try to run even if damaver didn’t run.
  • Fixed a bug where superimpose could break for different q vectors.
  • Fixed a bug where the slider and custom color boxes in the color dialogs didn’t change line/marker colors.
  • Fixed a bug where in autoupdate mode the SEC plot could fail to switch between rg, mw, i0 on the right axis.
  • Fixed a bug where you couldn’t resize custom question dialogs.
  • Fixed a bug where SVD/EFA wouldn’t work with some sec data loaded in autoupdate mode.
  • Fixed a bug where when updating the SEC data in autoupdate mode, an improper q value could be used when getting the intensity at a given q.
  • Fixed a bug where if improper values were entered in the buffer range or window size and the set/update parameter button was pressed, if autoupdate mode was on it would stop.
  • Removed the error printing on startup that backup.ini file could not be found.
  • Fixed a bug where carrying out EFA to panel 3, then going back to panel 1 and changing the frame range used, then carrying out EFA again could cause an error in the rotation.
  • Fixed a bug where for unsubtracted profiles from images, EFA would use the full profile rather than the appropriately truncated profile.
  • Fixed a bug where the options panel couldn’t be opened twice in windows.
  • Added a check to prevent errors with missing lines when changing plot type in the main plots.
  • Added a check to prevent index errors when setting the q range of a sasm.
  • Fixed a bug where online mode would show an error if the directory being watched was removed.
  • Added a choice in the GNOM panel to force dmax to zero or not.
  • Added ability to use superimpose to find scale, offset, or scale and offset.
  • Fixed a bug where EFA results wouldn’t export due to getting the wrong q values from the scattering profiles.
  • Fixed a bug with new versions of numpy not integrating images correctly. (actually fixed in 1.2.3 rerelease)
  • Changed the generic error message. (actually fixed in 1.2.3 rerelease)
  • Fixed a bug where temporary files that vanish in the online directory could raise an error. (actually fixed in 1.2.3 rerelease)
  • Fixed a bug that could cause intensity integration to fail in the sec plot. (actually fixed in 1.2.3 rerelease)
  • Fixed a bug where calculating the scale constant of water could cause the main thread to lock up if it had an error.
  • Verified compatibility with ATSAS 2.8.2.
  • Fixed a bug where in the prebuilt windows version any plots not in the main window (for example, guinier plots) couldn’t be saved.
  • Fixed a bug where line colors didn’t reset properly when canceling out of any of the line properties dialogs.
  • Fixed a bug where the SVD window could have no default selection for type of profile to use.
  • Fixed a bug where the advanced options window didn’t open properly centered on the parent window.
  • Minor speed improvements from code streamlining.

New in BioXTAS RAW 1.2.3 (May 9, 2017)

  • Made numerous changes to fix strange behavior in frozen version on mac
  • Created instructions for building a frozen version on mac
  • RAW icon now shows up in the dock instead of the top bar on mac
  • Fixed how RAWWorkDir is used in the program, and how it gets set. It now gets set appropriately for each type of OS
  • Switched to using an embeded version of the BioXTAS logo, for easier packaging
  • Changed the default directory for RAW if there is no previous directory. It now uses the documents directory
  • Fixed a bug in the Porod volume calculation that in some cases could extrapolate to q<0
  • Added Guinier extrapolation to the volume of correlation molecular weight calculation
  • Changed how Guinier extrapolation is done for the adjusted porod volume method
  • Updated some of the text in the More Info buttons of the MW panel
  • Fixed a bug where changing the q vector of a scattering profile would print an error in the console
  • Updated the A and B coefficients for the adjusted porod volume method to perfectly match those used in the paper
  • Updated GNOM and BIFT windows to both report reduced chi squared values
  • Fixed a bug where having an ROI mask set could prevent loading image headers in the calibration section of the advanced settings
  • Tweaked the MW, GNOM, and BIFT GUIs
  • Fixed a bug where GNOM wouldn't run on SL6 with ATSAS 2.7.2
  • Fixed a bug where rescaling profiles wouldn't work on a kratky plot
  • Fixed a bug where IFT data plot could display the wrong scale for Guinier and Porod plots
  • Changed how Guinier plots are displayed from I vs. q2 on a loglin scale to log(I) vs. q2 on a linlin scale, to match with labels shown on the plot
  • Fixed a bug that could cause autorg to crash
  • Changed the circle masking tool to draw more quickly/smoothly
  • Improved responsiveness of dragging masks on an image
  • Fixed a bug where the beam center wouldn't turn off if the masking panel was closed
  • Improved responsiveness of updating positions of calibrant rings and beam center when working in the centering panel
  • Fixed some bugs that could happen when switching between calibration and masking windows without hitting the okay or cancel buttons first
  • Fixed a bug where VC integration was highly unstable in some cases, required switching from simpsons method to trapezoid method for numerical integration
  • Attempted to fix a not reproducible bug where clicking the clear all button could cause a segfault on linux
  • Fixed a bug so that the info panel is only cleared if the user actually decides to clear all items when clicking the clear all button
  • Fixed a bug where loading FoXS files with fits would not load the fit
  • Fixed a bug where PIL.Image couldn't load files (prevented loading of SAXSLAB300 images)
  • Fixed a bug where if an image load returned no header, RAW could crash
  • Did some futureproofing in the code
  • Fixed a possible memory leak when loading certain image types
  • Attempted to fix an irreproducible bug where masking would fail because pixel positions were floats instead of ints
  • Error bars, if shown, now move properly with the line on scale and offset
  • Fixed a bug where the Guinier window didn't respect the q limits set on the manipulation panel
  • Set the default plot type to log-lin instead of lin-lin
  • Fixed a bug where using the next/previous image buttons would cause the image to flicker if a fixed range were set for the color scale
  • Fixed a bug where scaling q didn't mark the item as modified
  • Fixed a bug where online mode loading more than one image didn't update the image plot
  • Changed the green for the average file name text from green to forest green, which may be easier to read
  • Fixed a bug where the centering panel being displayed without an image loaded could cause an error.
  • Fixed a bug where the ATSAS 2.8.0 GNOM wouldn’t run if an Rg for the profile had not been calculated.
  • Fixed a bug where DAMCLUST wouldn’t run.
  • Added a global error handler to pop up a dialog for unhandled errors.
  • Attempted to fix a bug where the program could run out of control ids on mac, causing a crash.
  • Fixed a bug where damclust and dammin refine could both be selected in the advanced options window.
  • Fixed a bug where dammin refine could be selected without damaver being selected in the advanced options window
  • Fixed a bug where setting a flatfield image could fail if there wasn’t an absolute scale normalization factor set
  • Fixed a bug where GNOM and BIFT autosaving could be turned on without directories selected.
  • Fixed a bug where switching from linear to log scale or vice versa with limits locked in the image display would set the slider bar maximum value incorrectly.
  • Removed tifffile.py (no longer used).
  • Fixed a bug where automated centering wouldn’t work with the newest pyFAI
  • Fixed a bug where typing an incomplete LaTeX expression in the plot label could cause an error.
  • Added some error checking to running GNOM/DATGNOM in case it fails for some reason.

New in BioXTAS RAW 1.2.2 (Mar 22, 2017)

  • Fixed bugs with new matplotlib 2.0 version so that most of RAW works fine.
  • Fixed a bug where zooming or paning on the guinier or gnom window plots would break autoupdating of the limits.
  • Changed imports to allow RAW to use scipy.weave or weave, depending on which is installed (weave preferred)
  • Updated pyinstaller hook file for pyfai.calibrant so that the windows installer builds properly.

New in BioXTAS RAW 1.2.1 (Feb 1, 2017)

  • Updated online mode so RAW only plots files if there are files to plot. This prevents some flickering when files enter the directory but are not plotted for any reason (such as not being suitable images).
  • Updated online mode so that the “Processing incoming file…” status doesn’t linger forever after an image is processed, but goes away suitably quickly.
  • Fixed a bug that prevented EFA from running on scattering profiles that don’t use the full range of their q vector.
  • Fixed a bug where concentration wasn’t saved when the ‘save all analysis info’ option was used.
  • Fixed a bug where changing SEC plot axes while SEC live update is going could cause a crash
  • Fixed a bug where Normalization information got saved in the scattering profile processing parameters twice, once with a capital N, once with a lowercase n.
  • Fixed a bug where the wrong upper limit was getting set for the end of range controls in the third EFA control panel.
  • Fixed a bug where if no normalizations were set in the normalization list, the solid angle correction would not be saved in the normalization history list for the scattering profile.
  • Made a change where if EFA has a converged solution, if the ranges are changed it uses that solution as a starting point. This leads to faster convergence to the new solution.
  • Added ability to display calibration rings from any calibrant in the pyFAI library.
  • Fixed a bug where plotting certain scattering profiles on a Kratky plot would cause RAW to crash
  • Fixed a bug where having the SEC plot set to display the intensity at a particular q value would prevent structural parameters from being calculated, and in some cases could prevent new SEC items from being plotted.
  • Fixed a bug where the plot legend wasn’t updated if the plot was turned on, then off, and then items were removed from the plot.
  • Added an energy box in the centering and calibration window, so that if energy is entered, wavelength is automatically calibrated, and vice versa.
  • Fixed a bug where changing centering values with no centering values selected could crash RAW.
  • Added ability to explicit calculation of concentrations for EFA, as opposed to currently iterative method.
  • Added ability to use a hybrid method for calculation EFA, using the explicit calculation as a starting point, then refining iteratively.
  • Added ability to chose rotation method for EFA in the third EFA control panel.
  • Fixed a bug where the range plot in the third EFA panel was not refreshing properly when the number of significant values was changed.
  • Fixed a bug where the info panel was not updated when a scattering profile was selected by clicking on it on the main plot.
  • Updated build commands for making a windows installer, including adding some explicit hooks for pyFAI and pyinstaller.
  • Added the optional use of the hdf5plugin to RAW to support eiger images.
  • Fixed a bug in the image display where the dialog box could fail to open because the maximum value in the image was greater than 2^31-1 (the maximum value a wx slider can handle).
  • Added a feature for automatic centering and fitting of the beam center and sample to detector distance. Requires pyFAI to be installed.
  • Added a header reader for g1 eiger files, which have the spec header file one level up from the image files.
  • Fixed a bug where the RAW ROI could not consistently be used for normalization.

New in BioXTAS RAW 1.2.0 (Oct 28, 2016)

  • Full list of new features:
  • Added the solid angle correction to the normalization parameters in the sasm history, so that if it is used, that use is recorded.
  • Fixed a bug where SAXSLAB images could not be loaded when using version 3.0 or newer of the pillow library.
  • Added in the ability to use a RAW defined beamstop mask in addition to a SAXSLAB beamstop mask for SAXSLAB data.
  • Fixed a bug (on OSX, wxpython 3.0) where clicking the OK button in the Masking Panel was returning the plot window to the IFT panel instead of the Main Panel.
  • Added in some dialog boxes letting users know they can't modify the SAXSLAB header mask in RAW. Previously, the Remove and Set buttons in the masking panel appeared to work for the SAXSLAB header beamstop mask, but in reality did nothing. Now they still do nothing, but pop up a dialog letting the user know that nothing has happened (and no longer appear to do anything).
  • Added a molecule type choice to the SEC calculate parameters panel, so that the user no longer ha to change the default molecule type in the mol weight options panel.
  • Fixed a bug where the Clear All button was not properly clearing some fields in the SEC control panel.
  • Added SVD capability.
  • Fixed a bug which prevented some .sec curves from being loaded.
  • Added overwrite checking to the .sec saving function.
  • Fixed a bug where the SEC item filename didn't change when the item was saved with a different name.
  • Made how SEC names are deal with consistent with how scattering profile names are dealt with.
  • Added overwrite checking to the Export data option for SEC curves.
  • The parameters on a SEC plot now default to markers, not lines.
  • Fixed a bug where in a 3 column data file with no non-data first line (empty or otherwise), the first data point would get cut off.
  • Added evolving factor analysis (EFA) capability
  • Added 'How To Cite' buttons for the RAW functions that incorporate other people's work, so that they can correctly cite the methods.
  • Added in backwards compatibility for loading .sec files from previous versions of RAW, and workspaces with saved .sec files from previous versions of RAW.
  • Saving/Loading a workspace now preserves the file order in the workspace.
  • Fixed a bug where selecting log axes would crash RAW if you tried to do so before loading any data.
  • Fixed a bug where the legend label for ift and sec items got set when it didn't need to be.

New in BioXTAS RAW 1.0.3 (Jul 28, 2016)

  • Changes:
  • Fixed a bug where saving a mask without an image loaded would cause an error.
  • Fixed a bug where attempting to show a SAXSLAB BS Mask without a SAXSLAB image loaded would cause an error.
  • Fixed a bug where autosaving for files (processed image files, averaged files, subtracted files) could be turned on without a valid save directory selected.
  • Added a feature so that when an autosave directory is cleared, autosave for that filetype is turned off.
  • Fixed a bug where the final lines of the damaver output were not being shown in the dammif window.
  • Added some extra information to the two most common error messages we get contacted about: inability to load an image type, and inability to load a header file.
  • Fixed an error where if an image header contained non-unicode characters, when a scattering profile generated from that image header was saved it would crash RAW. Fixed the same error if the header was shown.
  • Removed some unused settings values.
  • Removed the brightness bar in the image settings pop up window, as it was currently disabled. This may be re-enabled in the future.
  • Set the image settings pop up window to have the default upper value be the max pixel value, rather than 65535.
  • Fixed a bug where starting two dammif runs in the same window (running it again after either aborting or letting the current runs finish) did not clear the old log tabs.
  • Fixed a bug where entering a wavelength longer than ~115 A resulted in an error. Now a window pops up informing you of the error and you have to re-enter the wavelength value.
  • Fixed a bug where the quick reduce dialog was not displaying, and thus quick reduce could not be used.
  • Profiles reduced using quick reduce will now have a q range corresponding to the start/end skip points in RAW, consistent with items loaded into RAW and saved from there.
  • Fixed a bug where certain .fit files and FoXS .dat files with 4 columns would not plot properly.
  • Fixed a bug where the x and y axis values of the Guinier plot were not updating when the data range was changed
  • Relabeled the residual plot in the Guinier window with the correct axis labels.
  • Updated how GNOM, BIFT, an Guinier plots are refreshed for improved speed and to remove certain display glitches.
  • Changed the header display in the image panel to be read only (since changes there were not saved).
  • Removed the automation and SANS options panels, as they had no effect. These may be reenabled in the future.
  • Changed the default bin size in RAW for q spacing from 2 to 1.
  • Removed some extraneous print statements.
  • Cleaned up RAWAnalysis.py code and some code in SASFileIO.py
  • Added ability to load .fir files.
  • Fixed a bug where most of the new image types added in RAW 1.0.2 were not being recognized by RAW.

New in BioXTAS RAW 1.0.2 (Jul 28, 2016)

  • Changes:
  • Removed tifffile warnings upon opening RAW
  • Improved the SEC-SAXS online mode based on user feedback to make it easier to work with.
  • Fixed an issue where active masks could be removed from memory when saving config files.
  • Fixed an issue where no warning was being displayed when config files failed to save properly.
  • Improved the speed of selecting large numbers of manipulation, IFT, and SEC items by at least 3 orders of magnitude.
  • Udated how loading and plotting works to improve speed by a factor of ~2.5 for both loading and subtracting large numbers of items.
  • Updated the Plot Sec button to improve the speed of file loading in certain cases.
  • Fixed a bug where FLICAM images could no longer be loaded due to changes in how tiffs are loaded in pillow >=3.0
  • Removed some possible issues with loading items where files were not getting closed correctly.
  • Fixed an error where rebinning an item under certain conditions could crash RAW.
  • Added a warning if a users tries to update or send frames from a hidden SEC curve (assumes that they forgot to change their selection)
  • Fixed a big where sending the same frames twice to the main plot from a SEC curve would cause various problems with RAW.
  • IFT items are now marked as modified when they are renamed.
  • Fixed an error caused by clicking on the top item of the advanced options configuration tree
  • Fixed an error in the Image tab where selecting the pan/zoom buttons wouldn't always properly toggle the button in the tolbar.
  • Fixed a bug where the popup menu for inverting the mask couldn't show.
  • Fixed a bug where panning or zooming when centering would turn off the silver behenate centering rings
  • Fixed a bug in OS X where holding down the centering arrows didn't continuously move the beam center position
  • Fixed a bug where the centering arrows wouldn't move the beam center in smaller than integer steps (when holding them down).
  • Updated the sync function to greatly increase speed when used with lots of items.
  • Updated the superimpose function to greatly increase the speed when used with ltos of items.
  • The file panel now automatically refereshes when you switch to the file tab.
  • Added the ability to use the common keyboard shortcut ctrl-A to select all items in the manipulation, IFT, and SEC lists.
  • Fixed an issue with the beam center indicator in the masking panel vanishing when it should not.
  • Fixed a bug where error bar color was not maintained when moving a line bewteen different plots.
  • Fixed a bug where the error bar color selector for the manipulation and IFT line properties displayed the wrong color in the line properties box.
  • Added the ability to change the calculated line name in the SEC line properties box.
  • Fixed an issue where, if the legend position had been changed, it reset to the default position when the legend was updated.
  • Fixed an issue where the legend shadow went away when legend was updated.
  • Added ability to load many more image types using the fabIO library.
  • Fixed a bug where the wrong legend label would sometimes be used for SEC curves in windows.

New in BioXTAS RAW 1.0.1 (Jul 28, 2016)

  • Changes:
  • Fixed a bug where online mode without an online filter would load files twice.
  • Fixed a bug which caused dammif to crash when run in a directory where the path contained a space.
  • Masking panel now defaults to the beamstop mask, not the ROI mask.
  • Fixed a bug where if OS X preview files became visible on another system, loading them would crash RAW.
  • Fixed an intermitant bug where in scientific linux 6 and wxpython 2.8, occasional calls to the File List would crash RAW.
  • Added in error catching, so attempting to load bad .cfg files (either corrupted, or non-RAW files with the same extension) doesn't crash RAW.
  • Added in automatic verification of saved .cfg files, to check they can be loaded back into RAW.
  • Scrolling with the third mouse button in the Image plot panel, but outside of an image, no longer produces errors in the console.
  • Moving manipulation items between plots now respects visibility of the manipulation items.
  • The plot axes now automatically refresh when the scale or offset of an item is changed if the axes are set to autoscale.
  • Tool tips now work in wxpython 3.0 on OS X
  • Selecting the "remove" option in a right click context menu in the Manipulation, IFT, or SEC control tabs no longer causes a seg fault in wxpython 3.0 and OS X.
  • Removed MM and conc from Guinier panel, to unify GUi so that MW information is only in the MW panel.
  • Added ability to change online mode directory without going offline and back online.
  • Added a sort to the online mode, so that files should load in order if multiple files are detected in a given online mode load sequence.
  • Added a size check to the online mode load, so that if a file fails to load because it hadn't finished writing/copying, it should load when it is finished.
  • Removed the Load button in the SEC control panel .SEC items are now loaded automatically once the file is selected.
  • Added an online mode for SEC-SAXS
  • Fixed a bug in how SEC-SAXS data was updated when no parameters were being calculated.
  • Added a feature so that RAW's online mode will not load in files that RAW saves in the online directory.
  • Fixed a bug occasionally preventing the ATSAS directory from being automatically detected.
  • Changing control tabs now automatically clears/loads the info window as appropriate.
  • Fixed a bug with running datgnom from inside RAW that caused it to fail in certain circumstances.

New in BioXTAS RAW 1.0.0 (Jul 28, 2016)

  • The major new features in this release:
  • Added support for running GNOM from RAW.
  • Added support for running DAMMIF from RAW.
  • Added support for running DAMAVER from RAW.
  • Added support for running AMBIMETER from RAW.
  • Major overhaul of the IFT panel, so it actually works, which involved changing how BIFT is run.
  • Minor changes/bug fixes:
  • Added support for reading in FoXS .dat files that have both experimental and model intensities in them.
  • Fixed a bug where after using the Clear SEC data button RAW could still think there were unsaved changes in the SEC panel.
  • After removing an item from a plot, the plot axes will automatically resize (unless automatic axes size is turned off in plot options).
  • Added a README file in the RAW directory with information on installation and getting help.
  • Fixed an issue with the porod volume MW calculator crashing if the scattering profile extended to q greater than 0.45 A^-1.
  • Fixed a bug where MW for RNA was not properly calculated in the SEC plot.
  • Added ability to save all integreated scattering profiles from a SEC curve as dats.
  • Fixed an issue where header for save analysis csv files was not using the correct delimiter.
  • Fixed an issue where beam center did not initially show up correctly in the centering/calibration panel.
  • Fixed a bug where changing font size for the plot title and axis labels had no effect.
  • Fixed an issue where the home button in the sec plot didn't work if the calc data existed but was not shown.
  • Added complied windows 8 exentions, updated compiled windows 7 extensions.
  • Various other small bug fixes.

New in BioXTAS RAW 1.0.0b (Jul 28, 2016)

  • New:
  • Easy processing of in-line SEC-SAXS data
  • New molecular weight panel for calculating mol. weight from the volume of correlation, adjusted porod volume, and absolute scaling.
  • AutoRG now available.
  • Uncompiled running, which allows RAW to run as long as the appropriate python packages are installed, even if the extension files cannot be compiled.
  • Files saved as .dats now automatically save all analysis information in the header, and reload it into RAW when loaded again.
  • Improvements:
  • Speeded up loading and plotting for large numbers of files on a test machine by a factor of ~30.
  • Speeded up subtraction of large numbers of scattering profiles by a factor of ~4.
  • Improved responsiveness when large numbers of scattering profiles are plotted.