|v14.05||15th April 2014|
|v14.02||15th March 2014|
|v13.12||11th December 2013||NEW: PulseGen|
|v13.10||24th October 2013||1200 downloads|
|v13.07||7th July 2013|
|v13.05||4th May 2013||150000+ lines of code|
|v13.04||5th April 2013||800 downloads|
|v13.03||10th March 2013|
|v13.02||6th February 2013|
|v13.01||14th January 2013||600 downloads|
|v12.12||7th December 2012|
|v12.10||25th October 2012|
|v12.9||N/A||Youtube demo videos|
|v12.8||15th August 2012||500 downloads|
|v12.7||9th July 2012|
|v12.6||30th May 2012|
|v12.5||10th May 2012||400 downloads – NEW: cwViewer|
|v12.2||2nd March 2012||350 downloads|
|v12.1||25th January 2012|
|v11.11||19th October 2011||NEW: PowerSat GUI|
|v11.8||22nd July 2011||NEW: cwPlotter|
|v11.6||27th May 2011||NEW: PowerSat CLI|
|v11.5||19th May 2011|
|v11.4||15th April 2011|
|v11.3||18th March 2011||First public release|
NEW FEATURE: reportbuilder
reportbuilder aims to take all of the hassle out of plotting data in a repetitive manner. A graphical user interface guides file selection of the raw data files. The data is then imported, plotted with a table of the key parameters from the experiment.
Images are presented by default in vector format. Then a LaTeX (.tex) file is generated. On a Linux system the .tex file is automatically compiled to generate a formal report (PDF) on A4 paper for easy printing.
NEW FEATURE: Lcurving
Takes a DeerAnalysis L-curve result file and generates a PDF figure report
Complete rewrite of how experimental data is processed now we scan through the parameters section, find the variable that changes, then look for that variable and see how it increases. Based on whether it is a “x to y”, “x step y” or “x, y, z …” experiment the axis is then generated.
As this is terribly complicated there is a lot of commenting for this section. It should now work for almost all experiment types. But testing is the only way to tell for sure.
- CPMG support
- Error handling in figure plotting
- Better error reporting for when a file cannot be opened -
by file permission or missing file
- YUNI (y axis units) now uses a try statement – old Xepr versions will not
automatically add it to the .dsc file
- Increased robustness in file names
- PeldorPlotter2, features the same simply without the raw data
- Improved toolbar
- Additional robustness
- Better error handling and reporting
- Added “Export to Origin” options
NEW FEATURE: PulseGen
Dr. F. Mentink of the Weizmann Institute of Science, donated code for the drawing of pulse sequences easily in MatLab. This code has been implemented as a graphical user interface and allows users to draw complex pulse sequences quickly and easily. The pulse sequence can then be exported in a number of image types.
NEW FEATURE: SpecManRead
Read SpecMan *.dat/*.exp/*.d01 files into MatLab.
So far tested with the following experiments:
- Transient datasets
NEW FEATURE: VarianRead
Read Varian *.dat files into MatLab.
General update / bug fix
- Added header to output file
- Optional ‘noheader’ call
- Input arguments tidied up
- Removed extremely complex output argument and replaced with smarter use of output arguments
With PhD thesis completion, submission and defence a huge number of small changes have been implemented making for better efficiency or error handling.
All files have been updated with new/improved help sections.
New website design for clarity in coding.
Numerous minor bug fixes and improvements.
A complete setup of a PELDOR experiment includes a T1, T2 and field swept echo before the PELDOR trace. By pointing T1T2Plotter at one of these files in a folder it will automatically plot all 4 experiments as a single figure of subplots. The figure is then automatically saved to the same location as a PDF for quick printing.
Files must be saved with the file format:
For example the folder might look like:
1307-X-4PEL-050-MTSL.DTA 1307-X-FSE-050-MTSL.DTA 1307-X-T1-050-MTSL.DTA 1307-X-T2-050-MTSL.DTA
DAPlotter – DeerAnalysis Plotter
Takes the saved files from a DeerAnalysis analysis and plots the raw data, background subtracted PELDOR trace with fit and the distance distribution as a single figure of subplots. The figure is then automatically saved to the same location as a PDF for quick printing.
The Bruker EPR (folder of) data to ASCII tools now supports pulsed experiments. Data is outputted with 3 columns for x, y (real) and y (imaginary).
Numerous minor bug fixes and improvements.
- Technical documentation of all scripts link added to help menu
MISHAP – ALPHA
MISHAP has been in constant development and is near release
- When loading a file, check added to see if file has already been loaded. If so, erases previous file, preventing errors and allows for better file comparison.
- “File” > “Reset all” now clears the old data files and axes instead of opening a new instance of PowerSat and closing the old one
- Changed PS_Pi so that Pi is calculated faster and calculated automatically if nitrogen and DPPH have been loaded, allowing for single oxygen or NiEDDA experiments to be analysed and not requiring all 4 datasets to be loaded.
- Minor bug fixes, better graphic presentation.
- More error reporting added – if power saturation fails or Pi is not able to be calculated then the user is messaged.
- Added interpolation variable so that the created files can have data points at a given interval eg. 0.2 gives a data point every 0.2 G
- Changed input address – removes conflict with address command
- Added switch for output to the same folder – so that if the folder is the current folder it still works
Added interpolation variable so that the created files can have data points at a given interval eg. 0.2 gives a data point every 0.2 G
Added ‘noheader’ option for use with programs that do not like headers
Compatible with pyDipfit:
e2af(‘/folder/of/files’,'\t’, ‘.dat’, ‘noheader’, 0.2)
NEW FEATURE: eprViewer – BETA
This feature will eventually take over from cwViewer as the main viewer interface with more features and significantly better handling of pulsed experiments.
NEW FEATURE: MMM_figureshaper
Take DEER window distance distribution saved figures and plot them nicely, saving them automatically as an image file whilst simultaniously generating a .CSV file of the x and y axis.
FEATURE REMOVAL: MMM_rotamers (directory/_install.m/_uninstall.m)
Feature not required with new MMM release.
Various bug fixes to many scripts
Work here has been published in the new version of MMM in that the PDB read and write functions have been revamped to conform better with the PDB standard and ensure better functionality with other programs. Namely enforcing 80 character lines.
- Added a “Run later” button, so that the start of a fitting run can be defined as an exact date and time in the future.
- Better error handling
- Supports long file names
- Closing waitbar cancels queue at end of current fit
- Seperation of EasySpin stats in command window using file name
- Add fit results to the output
- Handling of non-valid file name characters in file title
Constant development has been moved to github: github.com/morganbye/EPRtoolbox This allows users to pull updates as soon as they are coded. Releases will
still be made to sourceforge as appropiate, but the toolbox_working_directory on sourceforge will be only contain unzipped versions of the last release.
Big update to BrukerRead so that it now reliably can open and plot almost all common pulsed EPR experiments including FID, FSE, PELDOR, ESEEM, HYSCORE, ENDOR, DONUT.
Many improvements for Windows users, Windows despite what the Mathworks documentation says, uses a different addressing system for positioning windows/figures. Switches have been introduced such that windows always appear on-screen and not just above it as was reported by some users.
NEW FEATURE: e2af
By request from the guys at NREL, e2a has been expanded to convert an
entire folder of Bruker files to ASCII files in one easy script.
Integration between the EPR toolbox and tools provided by ETH Zurich
(namely MMM and DeerAnalysis) has begun. This is part of a longer term
project. This work is not yet published, but can start to be seen in
changes to pdbimport/pdbexport.
Update reflecting changes in BrukerRead
A short acknowledgements section has been added to README.txt
PowerSat and cwViewer now have demonstration videos available on YouTube,
see each programs help section for links, or their webpage to view.
Another big update for PowerSat. Raw data can now be fitted using 5 different methods
- Manually defined single points
- Splitting the peak into a positive and negative peak and then fitting each with a Gaussian distribution
- Same as 2 but with a Lorentzian distribution
- Fitting the signal with a 1st derivative Gaussian distribution, the 2nd derivative is then calculated, and where the 2nd derivative = 0 then that is the turning point (peak or trough) of the 1st derivative
- Same as 4 but with a Lorentzian distribution
addnoise – renamed to avoid conflict with addnoise from EasySpin, as most users will have both installed. Minor update to help and argument inputs
Several functions have had minor tidy ups and optimisations
Massive rebuild of PowerSat, spectra can now be fitted with Gaussian peaks before the peak-to-peak height is taken. Accessibility calculations, have been improved and additional functionality for folder loading as well as full compatibility with Bruker .spc/.par files from EMX machines.
New function/window that allows you to send the currently viewable screen to EasySpin. Suitable for quick or frequently repeated EasySpin functions. The window comes complete preloaded for nitroxide spin labels
Big reworking so that it now works with .spc/.par files from Bruker EMX spectrometers, having received some files to play with
Function has been reworked so that it finds an open DeerAnalysis window by searching all MATLAB figure windows and then gets the figures. This means that it automatically obtains data arrays with no export needed.
Error handling added so that no error is presented if a user cancels the selection of a file
NEW FEATURE: sgol
Crude implementation of the Savitzky-Golay smoothing function. This allows for data to be smoothed without such pronounced problems of line/peak broadening and intensity lose found with a moving point average.
NEW FEATURE: Documentation
The toolbox now comes with a folder “doc” inside of which is index.html which gives support to all EPR Toolbox files in web page format.
- Savitzky-Golay smoothing function added to Viewing Options
- Add noise function added to Viewing Options
- x-axis can now be switched between Magnetic Field and g-value
- Export of CSV data includes g-values
NEW FEATURE: cwViewer
Massive revamp of cwPlotter into a new feature.
- Ability to load a single cw file, folder of cw files or cw file with a third dimension (such as power)
- Will handle FSEs and FIDs
- Ability to manipulate spectra in real time
- Auto-zero, normalize and smoothing functions
- Ability to stagger plots
- Export and save functions as pictures, Bruker files or CSVs
- Save/Load a workspace to continue working on files at a later date
- Better handling of pulse experiments
- Inputs changed so that ‘plot’ can be used by itself
- Figure plotting reconfigured and improved
- imaginary channel for pulse experiments
- legend is displayed for real/imaginary channels
- x-axis corrected for time or mag field depending on FSE or FID experiment with correct units/label
Changed 3rd input argument so that if a file path is specified then the script writes out to that address. Only useful really for when this script is called from other scripts; ie. in a for loop for writing many files
NEW FEATURE: DEERextract
> Extract the raw data behind plots in ETH Zurich’s DeerAnalysis
NEW FEATURE: pdbexport
> Partner script to pdbimport
NEW FEATURE: pdbimport
> Complete reworking of function
- URL read added
- direct download from pdb.org added
- complete reworking of atom and sequence handling
- better progress bar functionality
NEW FEATURE: Fsc2Read
NEW FEATURE: JeolRead < BETA release >
NEW FEATURE: BrukerWrite
NEW FEATURE: addnoise
KEY FEATURE: EPRtoolbox
NEW FEATURE: cwPlotter
> Minor bug fixes