The RAW team is pleased to announce the release of RAW version 1.5.1. This version contains several small bug fixes. Normally we might wait to release these until more major changes had happened, but there is a workshop using RAW soon and we wanted these bugs fixed before then. Significant issues that have been eliminated:
- An issue where the electron density output from DENSS could fail to load into pymol correctly because the default scaling was too small (still loaded into Chimera fine). Strictly speaking I think this is a workaround for a bug in pymol …
- Several bugs with running GNOM, including using data with minimal sampling (<100 points).
- Fixed a bug where the .app package for Mac wasn’t displaying natively on retina displays, so the text was fuzzy.
You can see the full set of changes below.
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’
The RAW team is pleased to announce the release of RAW version 1.5.0. This version focused on several significant updates that will be invisible to most users. Namely:
- RAW is now compatible with wxpython4
- RAW no longer uses weave, which has been essentially unsupported for years, to compile code. It now uses the numba just-in-time compiler.
This will make it much easier for us to support RAW, and should make it easier for users to install RAW from source on any platform. It also prepares us for the inevitable transition to Python 3 that has to happen in the next several years.
In addition to a range of bug fixes and small enhancements detailed below, RAW also now incorporates the new DENSS alignment code. This is all done in python, in RAW. This removes the dependency on EMAN2, and means that all parts of density reconstructions work on Windows!
Finally, RAW is now saving configuration files in JSON format. This is human readable, and makes the RAW configuration files more open and accessible for other programs to use. However, this does mean that earlier versions of RAW will not be able to open configuration files created with version 1.5.0 or later. However, configuration files created in earlier versions of RAW ARE compatible with version 1.5.0.
- Fixed a bug where if atsas is in the path but not installed RAW will still find the directory from the path.
- ATSAS filepaths and filenames should be able to deal with spaces.
- Fixed various strange threadsafe bugs on debian 8.
- Weighted average now checks for similarity
- Fixed a bug where the dammif results window wouldn’t work when you did only one dammif run and had damaver checked.
- Fixed a bug where dammin in normal mode wouldn’t work on windows.
- Fixed a bug where dammif/n wouldn’t abort on windows.
- Added in new expected shape parameter for dammif in custom mode.
- Fabio, hdf5plugin, and pyfai are now required dependencies, rather than optional dependencies
- Mode all previously compiled code into using the numba just-in-time compiler. This is important because the previous code was compiled with weave, which has been unsupported for years.
- Fixed a bug where users could give dammif/n file prefixes that were too long for damaver.
- Fixed a bug where canceling out of the color change dialog didn’t cancel the color change.
- Made the plot options box resizable (important for computers with large font size).
- Fixed a bug where the sec plot right axis framestyle wouldn’t properly restore if you canceled out of the plot options dialog.
- Significant code restructuring and cleanup.
- EFA calculations are now in a thread, so it might not freeze the whole GUI.
- Circle and rectangle masks are now resizable.
- Added ability to automatically mask pixels at/above/below a given threshold.
- Added ability to automatically mask images based on known detector panel gaps.
- Added ability to create predefined size/location circle and rectangle masks.
- Added ability to control detector image left-right flip and up-down flip.
- Fixed a bug where RAW could crash under certain conditions when exporting analysis info.
- Fixed a bug where the Guinier window would give an error under certain circumstances.
- GNOM and BIFT windows now show scattering profiles on log-lin axes.
- RAW is now wxpython4 compatible.
- Added alpha as an available setting in the GNOM window.
- Fixed several bugs in the GNOM window that caused RAW to unnecessarily calculate the P(r) function, slowing down the program.
- Added drag and drop file loading for both the plot and control panels.
- Settings are now saved in JSON format, which is human readable, to increase compatibility and ease of use by other programs. This means that settings saved from RAW 1.5.0 are not compatible with previous versions of RAW. Settings saved from previous version of RAW ARE compatible with RAW 1.5.0.
- DENSS now uses custom python code for aligning and averaging density. This removes the requirement on EMAN2, which means all parts of DENNS will work on Windows.
- The image plot now maintains the same zoom when you change images. Previously it would zoom back out to the full image whenever you showed a new image.
- Fixed a bug where the SVD would sometimes not open correctly.
- Fixed a bug where if there was one pixel in the q bin during integration the error would be set to 0 instead of the square root of the value
- Fixed a bug where nans or infinities in the SVD matrix would break SVD/EFA without an appropriate error message.
The RAW team is pleased to announce the release of RAW version 1.4.0. This is a major feature release for us! The big new feature is that RAW can now use the DENSS method to calculate electron density from SAXS scattering! You can read more about this at http://denss.org/.
To fully use this new feature (for density averaging and enantiomer filtering) you have to install EMAN2 (http://blake.bcm.edu/emanwiki/EMAN2/Install) which, sadly, doesn’t work on Windows. Windows users can still generate densities, but they won’t be able to average them. A new tutorial on DENSS in RAW is now available in the documentation (https://bioxtas-raw.readthedocs.io/en/latest/tutorial/s2_denss.html).
The other feature many folks will be interested in is the new error calculation for Guinier fits, which is a much requested feature. This is now available whenever you open the Guinier panel, and saves and exports with the rest of the analysis information as expected.
We’ve also done the usual set of bug fixes and tweaks. You can find a full list of changes below.
- 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 panel.
- 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 opened.
- 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 documentation.
- Removed the RAW-Windows-Source-Install-Essentials file from the downloads.
The RAW team is pleased to announce the release of RAW version 1.3.1. This is a very minor release. Several small bugs have been fixed, and we have updated the citations in the program to reflect the release of the new RAW paper. Most of the major work in this release went into updating the documentation, which we have already released on the new website: http://bioxtas-raw.readthedocs.io/
- Made RAW compatible with pyFAI 0.14 (not back compatible with 0.13)
- Improved the multiwire loading function
- Updated some citations and error messages in the program
- Revamped and updated all of the documentation and tutorials. It is now in sphinx format, in the RAW SVN for better tracking.
- Updated the RAW citation to reflect the newly released RAW paper.
- Updated the .app build on mac.
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!
- 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 t 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 re-release)
- Fixed a bug that could cause intensity integration to fail in the sec plot. (actually fixed in 1.2.3 re-release)
- 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.
The RAW team is pleased to announce the release of RAW version 1.2.3. The release again mostly focuses on bug fixes, speed improvements, and other small improvements to the user experience. There is one bit of exciting news: we are releasing a prebuilt version for Mac! Users can now download a .dmg with a RAW.app in it. This can be installed via drag-and-drop, like other app files, and run just like any other app. We hope this will make installation much easier for mac users. If you want to try this, the download is available in the usual area, and the mac install instructions have been updated.
In addition to the new prebuilt version, we’ve also made errors more obvious, now if there is an unhandled error in the program, rather than failing silently it will pop up a dialog box to let you know. We’re hoping this is seen as an improvement!
- 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 embedded 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.
The RAW team is pleased to announce the release of RAW version 1.2.2. This release mostly focuses on bug fixes, speed improvements, and other small improvements to the user experience. However, there are several changes/new features we think many of our users may want to know about:
- RAW now has the ability to do weighted averages of scattering profiles (accessible by the right click menu in the main control panel)
- RAW is now compatible with ATSAS version 2.8.0.
- You can now run DAMMIN from RAW (previously on DAMMIF was available). This includes using DAMMIN to refine the damstart.pdb file output from DAMAVER, which is now the default option.
- RAW can now handle files with multiple images in them, such as Eiger hdf5 files. This is an ongoing project, so some features, such as image viewing and SEC plotting do not yet handle these types of files perfectly.
- We have changed how the show/hide and collapse/expand buttons work. Previously they affected all items. Now if no items are selected they affect all items, otherwise they affect the selected items. We hope that once users are accustomed to this change they will find it useful.
- RAW has a new header type available, P12 Eiger header files.
Additionally, RAW users should be aware that we have added an additional dependency, the weave package (to replace scipy.weave, which was removed in scipy version 0.19), and that RAW is not yet compatible with matplotlib version 2.0 (released January 2017). We are working on updated install instructions to reflect these changes, and those will be available (hopefully) next week.
As always, we appreciate user feedback, as that is how we improve the program. If you have questions, need help, or want to report a bug, please contact us!
- Added ability to do a weighted average in RAW, using either error based weighting per q point or weighted by a counter value.
- Many small changes to the code to streamline how plotting works, which should results in modest speed improvements, particularly when working with large numbers of plotted files.
- If autoscaling is on for plots, plots should now autoscale in all appropriate instances (previously they didn’t autoscale when moving items between plots, rescaling the q range, and a few other instances)
- Trimmed out many dead functions to make the code easier to maintain.
- Changed how the visibility check box for control panel items works, which improved show/hide speed for a single item when lots of files were loaded by a factor of 2.
- Improved speed for certain actions that resulted in marking lots of items as modified.
- Fixed a bug in autorg where error for the rg value could fail to be calculated
- Fixed a bug in running GNOM for ATSAS <2.8 where certain advanced settings couldn’t be used.
- Fixed a bug where flatfielding would fail when using pyFAI to integrate images (not yet publicly available)
- Fixed a bug where using the roi_counter would fail when using pyFAI to integrate images (not yet publicly available)
- Fixed a bug where dezingering would fail using python for integration (instead of the compiled c++ modules)
- Removed the SASIft.py file that was unused.
- Fixed a bug where having nothing entered for limits in the plot options panel (such as when typing a new limit) would print an error message in the console.
- Fixed a bug where loading a roi_counter header value with no image header would give an error.
- Fixed a bug where legend position wasn’t maintained when all items were removed or hidden on a plot.
- Fixed a bug where the legend wouldn’t go away if all items on the SEC plot were hidden and there had previously been a legend.
- Updated how legend settings are handled in plot options to improve speed and maintainability.
- Fixed a bug where plot titles and axes labels didn’t reset appropriately when using the clear all button.
- Fixed a bug where the plot options font selector boxes didn’t work.
- Fixed a bug where not all settings were restored to previous values when canceling out of the plot options dialog.
- Fixed a bug where the Porod volume calculation was not getting properly interpolated to q=0.
- Fixed a bug where hitting the next/previous image buttons in the RAW Image plot would throw an error and crash RAW if the image currently displayed wasn’t in the current working directory of the Files panel.
- Fixed a bug where saving items wasn’t threadsafe on scientific linux 6.
- Fixed a bug in how the error bars for log(I) were calculated in the autorg function.
- Switched the autorg to calculate the Guinier fit without error weighting, to match how it is done in the Guinier panel.
- Fixed a bug where the how to cite button in the dammif frame wasn’t getting properly placed in wxpython < 3.0.
- Addeed the ability to run dammin from the DAMMIF (now DAMMIF/N) window.
- Added the ability to use dammin to refine damstart files from dammin/f in the DAMMIF window.
- Fixed a bug where autoMW, autoRG did not respect the limits set for the scattering profile in the manipulation controls.
- Changed how the show/hide and collapse/expand buttons work. Previously they affected all items. Now if no items are selected they affect all items, otherwise they affect the selected items.
- Added compatibility for gnom5 from ATSAS 2.8.
- Counters available for normalization now show up in the combo box in the normalization list panel.
- Made some progress fixing a windows specific bug having to do with hitting enter after clicking a button in another panel.
- Fixed some bugs on windows where the mouse would get captured and not released by txtctrl boxes.
- Fixed a bug where the rename option wasn’t working in the file overwrite dialog.
- Moved the version number into the RAWGlobals.py file.
- Improved speed of saving items from RAW, by a factor of ~160x for a large number of files on my test machine.
- Fixed a bug in the Guinier panel where the maximum point shown in the plot and used for the fit was one less than the maximum point shown in the spin control.
- Tweaked the autorg function to allow some intervals with qmaxRg > 1.3 (up to 1.35) to improve fitting.
- Fixed a bug where interpolate did not work on multiple selected scattering profiles.
- Fixed a bug where interpolate was giving the interpolated file the wrong name.
- Fixed a bug where writing the header could cause RAW to crash due to improper json serialization.
- Changed how normalization deals with zero values. Instead of raising an error it prints a warning.
- Added the GNU disclaimer at the top of all .py files that didn’t have it.
- Added a header type for P12 Eiger, Petra III
- Updated image loading and all associated functions to handle multiple images in a single file, for example eiger files.
- Added filtering of headers so that () and  characters are removed, as header names with these characters could not be used for normalization.
- Fixed a bug where image and other headers were getting filtered differently.
- Added some new file types to the TestData folder.
- Added error catching for json formatting of file headers upon save. If the header can’t be serialized properly, the files saves without a header (used to cause a crash).
- Fixed a bug where ambimeter could fail if there were spaces in the filename.
- Fixed a bug where with older versions of wxpython and matplotlib, failure to find points in the autocentering mode could cause RAW to freeze.
- Fixed a bug where quick reduce would crash if it couldn’t find the header.
- Replaced the dependency on scipy.weave with the weave package (which is a fork of scipy.weave), as scipy.weave is removed in scipy 0.19.
The RAW team is happy to announce the release of RAW version 1.2.1. This version focuses on bug fixes and small improvements to the user experience. There were a few significant changes:
- In addition to numerous bug fixes, the EFA technique can now be used with explicit, iterative, or hybrid methods for computing the concentration profiles of the components. Previously, only the iterative approach was available.
- We added a new automated centering and calibration routine using the pyFAI library, for better determination of beam center and sample-detector distance.
In addition to a new version of RAW, we have also released new installation instructions for all platforms.
As always, we appreciate user feedback, as that is how we improve the program. If you have questions, need help, or want to report a bug, please contact us!
- 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.
The RAW team is very pleased to announce the release of version 1.2.0. We’ve added two major new features, the first of which is the ability to perform SVD on a set of scattering profiles, IFTs, or a SEC-SAXS curve. We’ve also implemented the exciting new evolving factor analysis (EFA) method for deconvolving overlapping data. This is primarily intended to be applied to SEC-SAXS data, but it is implemented so that it can be applied to any set of scattering profiles or IFTs. We want to note that while EFA is an exciting new technique, it is still in ongoing development. We intend continuing development on the stability and utility of the algorithm.
We will release an updated tutorial document and dataset which includes examples of doing SVD and EFA soon.
As always, we appreciate feedback from users, either positive or negative.
The RAW Team
 Steve P. Meisburger, Alexander B. Taylor, Crystal A. Khan, Shengnan Zhang, Paul F. Fitzpatrick, and Nozomi Ando. Journal of the American Chemical Society 2016 138 (20), 6506-6516.
- 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 has 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.
The RAW team is happy to announce the release of version 1.1.0. While there are several significant new features, the major milestone that pushed us into version 1.1 is the integration (after almost a year) of the RAW code that has been available on this website and the RAW code improvements made by Soren Skou for use with the SAXSLAB homesource machines. All of RAW is now unified, and we intend to have only one development trunk for the foreseeable future (though we may have temporary branches for major feature development).
We have also added in a solid angle correction for integrating images into scattering profiles. This correction accounts for the change in solid angle of a pixel as you change q. We have tested it against the solid angle correction implemented in pyFAI, and found that the results are identical. This effect will get stronger at higher q, and cause an overall increase in intensity of integrated profiles. On a Pilatus detector, the solid angle correction has a ~0.5% effect on integrated intensity at q=0.25 A^-1 and ~4% effect at q=0.75 A^-1.
Major new features include:
- The solid angle correction mentioned above
- Improved speed when calculating Rg, MW, and I(0) for SEC-SAXS curves (up to a factor of 7 faster in our limited testing)
- Ability to read in multiwire (.mpa) files
- Ability to read in headers from SAXS beamline BL19U2 at the Shanghai Synchrotron Radiation Facility
- Merging, rebinning, and interpolating now all save history information like averaging and subtracting have
- Scattering profile history (either: averaging, subtracting, merging, rebinning, and interpolating, or information about loading in and normalization) can now be viewed within RAW by right clicking and selecting ‘Show history’
- RAW is now (mostly) compatible with wxpython 3.0 on Linux
Beyond these changes, there are numerous small improvements, visual tweaks, and bug fixes. You can find a full list of those below.
Simultaneous with this release we are also releasing updated installation guides for all platforms. We are happy to say that we are confidant enough in our ability to produce prebuilt windows installers that we now recommend that windows users install from the .msi files unless they know that they need to compile from source.
As always, we appreciate any feedback (positive, or, especially, negative), bug reports, and suggestions for new features!
- Fixed a bug that prevented BIFT from running in uncomplied mode
- AutoRG now runs automatically when the Guinier window opens, assuming there is no previous Guinier analysis
- Fixed a bug where BIFT failing to find a solution caused RAW to crash
- If autosave is active, and a the folder vanishes, autosave now detects that, and is disabled, instead of crashing RAW
- When RAW settings are loaded, all folders and files in the settings (autosave directory, online directory, flatfield file) are checked. If they cannot be found, these settings are disabled, and the user is notified.
- Visual improvements of the BIFT window, DAMMIF window, and some options windows
- Fixed a bug where analysis windows would show up behind the main window, where you could move them by dragging the title bar without losing focus on the analysis windows, and where you could bring them to the front without first clicking on the main window
- Changed the layout in the SEC tab to be more descriptive, and to save space
- Changed welcome dialog info
- Fixed display problems of the Guinier and GNOM windows under wxpython 2.8 on Ubuntu
- Added the ability to start online mode at startup with a predefined directory
- Added the option of automatic saving of BIFT and GNOM results
- Updated save functions in RAW so that files that RAW saves are not automatically loaded back into RAW
- Added in option (on by default) to apply a solid angle correction to the integrated data to account for change in solid angle of the pixels with q
- Fixed several small bugs with the online mode: crashing when the online mode directory ceased to exist, online mode being able to start without selecting an online directory
- All counters and image header parameters now automatically have any spaces in the file name replaced with underscores, so that they do not crash the normalization
- DAMCLUST is now available as an alternative to DAMAVER after running DAMMIF
- Merging, rebinning, and interpolation now add to the file history in the same way that subtracting and averaging have
- Added a new feature to view the file manipulation history or load history within RAW (right click on a scattering profile in the manipulation list and select ‘Show history’)
- Added a sorting function to the .dat file saving so that file parameters should always appear in the same order in the saved file
- Fixed a bug where a tiff file with the wrong header getting read in as a Pilatus tiff file would cause RAW to hang up
- Added extra error catching to the file header load function
- Sped up calculation of SEC-SAXS Rg, MW, and I0 by adding a threshold function. The threshold checks the ratio of integrated sample intensity (or whatever intensity is being used for the SEC plot) of the average buffer to the average sample files. If the intensity is not above the set threshold (1.02 by default), it does not try to calculate the parameters. This means all of the buffer curves are automatically skipped, and calculation is much faster. It depends on the threshold and the data, but I saw speed increases of up to ~7x. This can be set by the user in the new SEC-SAXS panel in the Advanced Options window.
- Changed how normalization information is saved when a .dat file is saved. Now, normalization information is only saved when it is applied. The absolute scale factor applied is also now saved
- Added more files to the list of files that can be loaded in online mode
- Updated sync function so that files are only marked as modified when something is changed during the sync
- Modified how the centering arrows work to catch faster clicks, and to (mostly) prevent two moves with one click (noticed on a mac)
- Masks with zero area are no longer saved as masks
- Added the ability to load some multiwire detector files (.mpa files)
- Added the ability to read in the header for files from BL19U2 at the Shanghai Synchrotron Radiation Facility
- If the image or beamline header contains a concentration key word, that is now set as the sample concentration in RAW when the image is loaded
- Fixed a problem where ambimeter in the ATSAS 2.7.2 package could not be run
- Fixed numerous small and large visual problems with running RAW on linux with wxpython 3.0. I now believe that RAW can be considered compatible with wxpython 3.0 on all platforms, but there are still occasional sizing issues on Linux that it does not handle perfectly
- Fixed a bug where damaver and damclust would not run if the directory path contained a space
We’re releasing the latest version of RAW, 1.0.3 today. This includes several minor bug fixes. The timing of the release is done so that the version being demoed at the ACA meeting (http://www.amercrystalassn.org/2016-scientific-program#SAXS) will be identical to the latest release.
- 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 file type 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.
We’re happy to announce that we’re releasing RAW 1.0.2. This is another version focusing on small bug fixes and speed improvements, to try to increase the stability and usability of the software. As always, please report any bugs you find to us, so we can fix them!
The one major change is the inclusion of the fabIO package (https://pypi.python.org/pypi/fabio) for opening images. This has allowed us to support a number of new image types. RAW now supports images in the following formats:
- Pilatus TIff
- ADSC Quantum
- Gatan Digital Micrograph
- ESRF EDF
- Nonius KappCCD
- Fit2D spreadsheet
- General Eelctric
- Hamamatsu CCD
- ILL SANS D11
- MarCCD 165
- Numpy 2D Array
- Oxford Diffraction
- Portable aNy Map
- Rigaku SAXS format
- 16 bit TIF
- 32 bit TIF
- 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.
- Updated 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 toolbar.
- 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 lots of items.
- The file panel now automatically refreshes 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 between 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.
We’re very happy to announce that we are releasing RAW 1.0.1. This is a minor release, concentrating on bug fixes and small changes to the user interface.
There is one very exciting piece of news, which is that this release comes with a prebuilt windows installer (.msi file)! This should make it much easier for those on windows to install the program. We’re currently working on a similar thing for OS X.
We are also happy to announce that, to the best of our testing, RAW is compatible with wxpython 3.0 on OS X and Windows (Linux is still a work in progress).
- 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 intermittent 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.
Very exciting news, we’re moving the project out of beta! That doesn’t mean there aren’t still bugs, or that we’re done adding features. But it does mean that we’re happy with the current build (and that we ran out of numbers to increment in beta).
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.
All other changes:¶
- 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 integrated 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.
We are proud to announce that RAW version 1.0.0b has been released for download! This version includes a huge number of new features and bug fixes.
Our favorite new features are:
- 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.
We have also made significant improvements to speed and responsiveness:
- Sped up loading and plotting for large numbers of files on a test machine by a factor of ~30
- Sped up subtraction of large numbers of scattering profiles by a factor of ~4
- Improved responsiveness when large numbers of scattering profiles are plotted.
Also, there are new, up-to-date install guides available for Windows, Mac, and Linux. Check them out in the files tab.
Finally, we have cleaned up both the code repository and the files area.
If you have questions, or feedback, please contact us!
SEC-SAXS data processing:
Added capability to process SEC-SAXS data. This included adding a new SEC tab in the control panel, a new SEC plot, and a new SECM data class.
SEC-SAXS data is collected by continuous framing of the detector while sample is being pumped through a column. The output of that column is connected to the SAXS cell. The new RAW addition allows users to load all of the detector images collected during column elution into a new data type, the SECM. The overall frame intensity is plotted vs. frame number or time, and this should look very similar to the UV-chromatograph that an FPLC produces. The users can then select a range of frames from this curve, and send them to the main plot for processing as normal.
Additionally, the users can select a specified buffer range, and an average window size. The window is then slid across the curve, and the scattering profiles within the window are averaged. The averaged buffer is subtracted from the curves in the window, and radius of gyration, molecular weight, and I(0) are automatically calculated. These are then plotted on the same plot as the ‘SAXS chromatograph’ (intensity vs. frame #), allowing users to quickly get a feel for what is in each peak they measured.
Major code additions:
- There is now a SEC Panel, SEC Item panel, and SEC Control panel class, based on the Manipulation panel and Item Panel in RAW.py.
- There is now a new plot class in RAWPlot.py, the SECPlot, which allows for multiple axes on the same plot, and handles the various plotting options.
- There is a SECM class in SASM.py, which is the data structure for this new thing.
- There is a new SASCalc.py file, which contains the autorg and automw functions. The autorg is pure python, based on the ATSAS package autorg function. It could probably use some tuning of the various parameters. The automw is also purely python, and based on the Rambo & Tainer correlation volume method for determining molecular weight.
- There is a new save/load format, extension .sec, for saving SEC objects.
- The SEC data is saved when the workspace is saved.
- Various bits and pieces everywhere have been adjusted to accommodate these new panels.
Online mode filtering:
- Added an online mode section in the advanced option panel. This allows you to turn on online filtering, and give a set of strings that allow you to ignore certain files when they enter the watched folder. You can either set a list of strings in the file name to ignore, or a list of strings that must be in the file name, or some combination. You can also set the location where these strings must occur: at the start, end, or anywhere.
- Added a new analysis panel for finding MW. It has methods for MW by I(0) ratio (also in Guinier plot), MW by the Rambo & Tainer method of the volume of correlation, MW by the Porod volume (corrected by the method of Fisher), and MW by absolute intensity.
- Users can modify default calculation values for the MW in the advanced options MW panel.
- Changed the loadAndPlot function so that it only updates the curves on the plot every 20 curves loaded (and at the end), and only updates the legend after all the curves are loaded. On my machine, for ~400 data files (pilatus 100K tiffs) this sped up loading and plotting by ~30x (~40 s vs. 20 minutes & 15 s).
- Changed the subtractItems function so that it only updates the curves on the plot every 20 curves loaded (and at the end), and only updates the legend after all the curves are loaded, as with the _loadAndPlot function. On my machine, this sped up subtraction by ~4x (1 min 7 s vs. 4 min 5 s for ~400 manipulation items).
- Updated online mode to take advantage of the faster plotting, by passing all of the files to be plotted to ‘loadAndPlot’ at once, rather than one at a time (will only matter if files are coming in faster than the online mode update timer)
- Changed the legend to be off by default (since it significantly hinders performance). Changed the update legend and the legend plot options dialog functions so that this all still works. This seemed to improve load in performance for ~400 data files by ~15% (35 s compared to 40 s).
- Removed all attempts to compile unused extensions.
- Added in try/except cycles for importing and compiling compiled extensions.
- Rewrote compiled extensions scipy.weave code (essentially c code) as pure python.
- Set it so that if RAW is unable to compile extensions, it displays a warning message to users on startup, and then runs with the pure python versions.
- Compilation is particularly an issue on windows, so hopefully this will make deploying to windows much easier (even though the program will run slower). Particularly for versions where a windows installer is not available.
- This required the inclusion of a RAWGlobals file, which contains a variable that notes whether or not the compiled extensions were successfully imported.
- Switched from PIL to pillow. PIL is not longer under active development, pillow is a fork of PIL that is still supported. Also, pillow is included in the default enthought python installation, while PIL no longer is.
- Fixed an issue where integrated scattering profiles could end up with different numbers of points. This was simply disabling the zero trim command in the integration routine.
- Added in an option to skip points at the end of a scattering profile (identical to the skip at the beginning). This was needed after the removal of the zero trim command when you have entire range of high q masked out (such as to eliminate shadowing from the beam pipe). This setting is accessible in the advanced options calibration dialog.
- Added in a parse function and header profile for log files from the BioCAT beamline.
- Removed the requirement that the beam position be an integer.
- Added in the ability to add a ‘zero line’ to the main plots (a horizontal line at y=0), in the plot options dialog.
- Fixed the plot options dialog so that it can be opened when no items are loaded in the plot.
- Fixed how the plot options dialog handles legend settings, so it doesn’t break if there are no curves already plotted.
- Fixed plot options so that setting x limits and y limits when auto limits is not checked actually affects the graph. Also fixed the limits so that they properly acquire the current axis limits when plot options is opened.
- Made it so that turning auto fitting axes back on forces the plot to autofit the axes when the plot option dialog is closed with the okay button.
- Fixed a bug where the legend would turn on when an item was hid/shown in the manipulation panel, even if the legend was previously turned off.
- Fixed a bug where error bars didn’t turn off when an item was hidden in the manipulation panel with error bars turned on.
- Made it so that the borders check boxes in the plot options window actually cause the borders (and tick marks) to turn on and off in the plot.
- Changed the Guinier plot panel so that it automatically updates the MW when the concentration is entered (instead of needing one of the up/down arrows to be hit in the spin control)
- Fixed a bug where the MW of a SASM object wasn’t updated when the SASM object was set as a MW standard.
- Fixed a bug in the menu creation of the file browser pane where the right click menu wouldn’t open on a mac (wxpython >=188.8.131.52)
- Fixed a bug where the concentration of a sasm object was getting improperly set when the clearinfo function in the information panel was called.
- Made the info panel Rg, MW, and I(0) boxes read only, since user modified values in those boxes aren’t saved
- Made the info panel conc box update whenever it gets text, so that if you update the concentration and click on another sasm it still saves the concentration.
- Fixed the options window not opening at the right size.
- Switched to using json to save/load sasm parameter dictionary contents in .dat files. This allows easy saving and loading of dictionaries in human readable format. So now all parameters (header, counters, analysis, etc) are loaded. NOTE: THIS IS NOT STRICTLY BACKWARD COMPATIBLE. RAW can still load old .dat files (and primus .dat files), but it cannot load analysis information out of the old files. This doesn’t really affect anything, as for the old files the analysis information didn’t load anyways.
- Modified how saving of averaged files history is done. Added in saving of subtracted files history. Now all of the averaging and subtracting manipulation history of a file is saved in the history entry of the parameters dictionary. This works even when you average or subtract files that are already averaged or subtracted. It is mostly human readable in the saved .dat file (though as you get more layers deep in averaging or subtracting it gets hard to tell what is what).
- Fixed a bug where the correct qmin and qmax weren’t loading in the Guinier window when a previous Guinier analysis had been done.
- Changed it so that when guinier or mol. weight analysis is done, if the results are different from previous analysis, the scattering profile is marked as modified to denote that the results are not saved.
- Fixed a bug where plot axes didn’t auto resize when curves were moved from the top main plot to the bottom main plot and vice versa.
- Fixed a bug where selecting ‘Help!’ in the help menu crashed RAW. No in-program help is yet available, but a message dialog now tells the user to look for help on the raw project homepage.
- Set ‘okay’ button to be selected by default in the welcome window.
- Fixed a bug where on mac, last saved settings wouldn’t load from the dialog on startup (this may have also been affecting other OSes).
- Enabled normalization by ROI counter using an ‘ROI counter mask’ (formerly called a transparent beamstop mask).
- Fixed a bug where minor tick marks weren’t turning off for log axes that weren’t shown (such as top and right) (I believe this was introduced by an updated version of matplotlib, I don’t remember seeing it before).
- Fixed the logarithmic image scale display in the image panel. It works now, and is enabled.
- Disabled nexus support to remove error on starting raw (can be easily re-enabled, it is simply commented out in a couple places in SASFileIO).
- Updated the manipulation and IFT item saves so that it offers the choice to rename the file when saving a single file, and so that there are more explicit instructions when saving multiple files.
- Fixed a bug in the rebin function, where it wasn’t setting the qrange according to the original sasm.
- Fixed a bug where comparison of q vectors to test for subtraction was done by length rather than elementwise by q.
- When scattering profiles with different q vectors are subtracted, choosing to force the subtraction now actually carries out the subtraction (with appropriate matching/rebinning of the q vectors).
- Fixed a bug so that the average function now tests the q vectors point wise, rather than by length, to make sure they actually match.
- Added a feature to export all analysis information from sasm objects as an alternative to selecting which analysis features you want to save.
- Update the old save analysis feature to be called ‘save item info’ in the menu, since it can save things that aren’t analysis. Updated the layout of that window a little bit, and added ability to save the new MW analysis info into the item.
- Added scattering profile manipulation into the tools menu: average, subtract, merge, rebin, interpolate, normalize by concentration, change q scale, set as MW standard.
- Upon quitting, RAW now checks whether there are unsaved changes to manipulation or SEC items, and asks for confirmation of quitting if there are.
- Added show image, show data, show header options to the view menu.
- File list maintains sort order upon refresh.
- Doing a Guinier fit on a scattering profile that is all zeros no long crashes RAW.
- Subtraction can handle mismatched q vectors.
- Autosave for averaged and subtracted files now available.
- Features supporting SAXSLab300 image format now available.