SIXPACK Download

Windows

Latest release v1.5.6 (Windows 10, 32 bit only!)

32 bit .exe in .zip file (Windows 10 only!)

Mac

PLEASE READ THE NOTES FOR YOUR OS CAREFULLY BEFORE CHOOSING YOUR DOWNLOAD!

MacOS has gone through several major changes over the last few years. This greatly affects the compatibility of SMAK. The best way (in general)

is to run SIXPACK via Wine (see notes below) as we are essentially retiring support for Mac DMG installations. We are working on a source code install for the future.

See below for the best ways to get SMAK on a Mac depending on you OS version.

Catalina 10.15 and later

Sorry but there is no native version of SIXPACK available for Catalina at this time. WineHQ (see below) now comes in a 64 bit version which may work with Catalina and later but this is currently untested.

Alternate solution - Crossover:

There is a paid alternative to Wine called Crossover by Codeweavers (https://www.codeweavers.com/products). The basic plan is ~$40 for an install of only the latest version of the software (no future updates included) but it has the advantage of not requiring a Windows operating system and runs "natively" within MacOS, i.e. runs the program as though it were a native Mac app even though it uses the Windows .exe install file. We have tried Crossover and it appears to work really well and Nick found it to be super fast, faster than running on Parallels and Win 10. SMAK will even appear as a regular app in Launchpad.

IMPORTANT - Only SIXPACK v1.40 currently works with Crossover. We don't know why 1.5 doesn't run after installation.

Crossover installation Instructions:

The installation for SIXPACK is a little funky as Apple have gotten tighter when trying to install apps from unidentified developers (Sam didn't want to pay the costs associated to be an official Apple app developer). So we temporarily have to tell MacOS to allow installations from "Anywhere" (this used to be an option before Catalina and we are just temporarily reinstating this option). Below are images of the Mac Security Preferences, note the different options under "Allow apps downloaded from:" in the two images.

If you try to open SMAK without doing this, you will get constantly prompted to allow every single bit of Python within the SMAK folder (~450 files), not useful and the memory is not retained so you would just have to do it all again next time you open SMAK.

Follow these steps:

Download and install Crossover (https://www.codeweavers.com/support/wiki/mac/mactutorial/install)
Before we start working with Crossover, we now have to reinstate the option to allow installations of apps from "Anywhere" within MacOS.
Open the Terminal app.
Type the following command syntax: sudo spctl --master-disable
Hit Return
Authenticate with your computer admin password (see left).
Hit Return.
Go to System Preferences and click on "Security and Privacy".
You should see the "Anywhere" option as in the image above (right)
"Anywhere" should already be selected.
If not you have to hit the padlock icon and enter your admin password.
Click the "Anywhere" option.
You may have to click an "Allow" button that might have appeared to the right of the "Anywhere" in System Preferences.
We have now allowed SMAK to open without any future security blocks from MacOS
Follow the Crossover instructions for installing an unknown application (https://www.codeweavers.com/support/wiki/mac/mactutorial/unknown_install).
- For the bottle selection, this is simply which Windows OS you choose to emulate. YOU MUST CHOOSE THE CORRECT BOTTLE FOR THE VERSION OF SIXPACK YOU DOWNLOADED. Don't just accept the version it defaults to. For SIXPACK 1.40 you are safe with the Windows 7 32-bit bottle.
- When prompted to select an executable file, select the smak.exe file within the SMAK folder you downloaded from this page.
If no application icon shortcuts are created in Crossover, you can try manually launching your Windows program using Crossover Run Command.
Double click the Run Command icon.
In the Run Command window (right) click the browse button and navigate to the smak.exe file
Click "Run" and SMAK should open
Also click "Save Command as a Launcher" and you will now get an application icon.

We will now put the default Security settings back.

In Terminal type of the following command syntax: sudo spctl --master-enable
Hit Return.
Authenticate with your computer admin password.
Hit Return.
Exit Terminal.
- In System Preferences hit the back button then go back into Security and Privacy. The “Anywhere” option should have gone away.

If you are not comfortable with this you can also run an emulator such as Parallels (paid) or VirtualBox (free) which requires a valid Windows operating system installations. Or you can use a Windows machine.

We are working on a stable Python source distribution.

Mojave 10.14 and older via Wine (Recommended Solution)

With the advent of MacOS High Sierra and the APFS file system, SMAK/SIXPACK for Mac using the dmg will no longer function natively with MacOS. SMAK for Mac will also cease to function if you upgrade to High Sierra and will also not work if you try to do a fresh install in High Sierra. It will go through the installation process but will not open, resulting in some error message.

But all is not lost, we have a recommended solution allow you to keep using SMAK on a Mac using these OS versions!

There is free mini emulator program called WineHQ that allows Windows applications to run on a Mac (running these older OS versions) without a Windows operating system.

Running SMAK via Wine

Installation tips are below. Note that some installations may only be able to run the Windows 32 bit version of Wine.

Command line (recommended, terminal readout):

Install the latest version of Xquartz from Apple if you don’t already have it. You will already have it if you were running SMAK before on your computer but if you have a new computer and this is a new install then you may not have it: https://www.xquartz.org.
Download Wine from this link: https://wiki.winehq.org/MacOS. and install it.
Download the latest version of SMAK above by clicking the download button (yes really, the Windows version). A zip file will start to download. Macs automatically unzip the file and you should see a folder called smak-64-166 or smak-32-166.
Place the this folder in your Applications folder.
Double click on the Wine application and it will open a Terminal window with the command line "wine"
Now you have to tell Wine where the smak.exe is. Copy the appropriate line below (depending on which version of SMAK you dowloaded) into Terminal:
- cd /Applications/smak-64-166
- cd /Applications/smak-32-166
Now type "wine smak.exe"
SMAK should now open.

Traditional (no terminal readout):

Follow step 1-4 above
We recommend making an alias to the smak.exe file within the smak folder. Right click or control click the smak.exe file and select “Make Alias”.
Place that alias in the main Applications folder.
Select the alias (not double click) and hit “command I” to bring up the “Info” window for the alias. In this window select “Open with” and select “Wine Stable” from the available options.

Now whenever you double click the smak.exe alias, Wine and SMAK should open together.

Troubleshooting Wine when upgrading OS

Nick found that when he upgraded from MacOS High Sierra to Mojave, version 1.4 of SMAK and Wine worked fine. But when he tried to open version 1.5. Wine would open and then close without doing anything.

The solution involved doing a deep uninstall of Wine and reinstalling. This involves deleting a hidden file within the Mac “home” folder via Terminal.

Drag the Wine Stable app from the Applications folder to the Trash. Empty the trash.
Open Terminal
Type or copy and paste the following command lines one at a time, hitting enter after each:
- cd
- rm -rf .wine
- rm -f ~/.config/menus/applications-merged/wine*
- rm -rf ~/.local/share/applications/wine
- rm -f ~/.local/share/desktop-directories/wine*
- rm -f ~/.local/share/icons/????_*.{xpm,png}
- rm -f ~/.local/share/icons/*-x-wine-*.{xpm,png} }}}
Reinstall Wine.

For reference, these commands lines simply tell the system to delete (rm for remove) the files defined by the path that follows the rm command. These files (among millions of others for you whole computer) are hidden to the user under normal circumstances and can only be deleted via this method.

Mac DMG Installations for OSX El Capitan 10.11, Sierra 10.12

Read before installation!

The Mac dmg installs only work on systems before Sierra 10.12. Regardless we don't recommend you use these as you will only be able to use older versions of SMAK and we will not be supporting issues with those older versions (we will just recommend you run the latest version of SMAK via Wine).

If you really want to do the old dmg install, note that with El Capitan 10.11 and Sierra 10.12, Apple started using "System Integrity Protection"which would block non-Apple authorized software installs. You will NOT be able run SMAK via the regular dmg install without a few preliminary steps. You can ignore this if your system is Yosemite 10.10 or older.

1) First you can temporarily disable the SIP to perform the "tile" installation, and then enable SIP again afterwards. This link describes the process that you need to follow. There is no harm in disable SIP temporarily, just following the instructions for re-enabling it once you are done with the install.

2) Download this zip file and install the folder to your "/System/Library/Tcl" directory. On some Macs the directory may also be "/Library/Tcl".

3) You may also need to install a newer Apple flavor of X11, xQuartz. This should install into your Applications-Utilities folder. Many users have reported that they need to duplicate this program to also be titled X11 (so... select "xQuartz" in a Finder window, copy/paste, rename the new file to "X11").

4) Open the dmg file and drag the application bundle to your "Applications" folder. It will not run from the .dmg file or any other location on your filesystem.

Troubleshooting DMGs

If you have found that SMAK has suddenly stopped working or fails to run after all of this... You may have upgraded your system as of late. There is a known apparent error (that manifests itself as a "gestalt" version error in the console) with upgrading the Apple OS. While it is unclear what the best way to resolve this, some Google rumors suggest reinstalling your OS. From my personal experience of updating from Mavericks to Sierra, I was able to get everything working by

Reinstalling the OS
Reinstalling the Tcl Tile package (as noted above)
Installing or reinstalling xQuartz.

Please let me know if these things work or don't work.

Currently, there is no 64-bit version for windows 10.
We recommend opening it with Windows 8 settings on your Windows 10 machine if it does not run after installation.

Screen Shot 2020-06-30 at 1.45.20 AM.png

Screen Shot 2020-06-30 at 1.44.22 AM.png

Screen Shot 2020-06-30 at 1.43.35 AM.png

Version History

4/6/20: Version 1.5.6: Minor updates. Fixed a few bugs in PCA. Added support for SOLEIL NXS data formats.

8/12/16: Version 1.40: Minor updates. Fixed a few other XDI bugs. Added a "red dot" to the active file in PCA score plots. Fixed some bugs with constant error windows popping up in various places, so it should be a lot nicer. Also made legends work again in the plots, for better or worse.

3/28/16: Version 1.30: Minor updates. Fixed bug in the XDI formats that prevented beam line data to be transferred to averagd and processed data files. Increased the ability of SSRL data formats to read up to six SCAs.

2/29/16: Version 1.20: Major release. Fixes bugs that have plagued that previous veriosm. Major bux fix that prevented Lytle only data from SSRL to be loaded. Support now added for the X-ray Data interchange format. Additioanlly, all save files will include a "standard" SIXPACK text file, as well as an XDI file. The parameters for background subtraction will be saved in the XDI metadata. Aslo updated the PCA routine so that the previous limit of the number of data files that could be analyzed at a single PCA run was increased. THe number will still depend on the range of data and the density of data points, but the limit is increased form approxiately 30 to around 100. Added support to read text files universally between Mac/Unix and Windows text formats.

7/25/14: Version 1.10: Major re-release to fix many bugs from the 1.0x verions. Fixed screen sizing, viewing and editing of raw data. Can plot/average custom columns so that you are not restricted to the default data types. Can view scatter plots of PCA scores in PCA module, including 3-D plots. Can also choose which samples to plot in PCA. There's a lot of other nasty things that were fixed, so hopfully I got them all.

7/14/12: Version 1.01: Quick bug-fixes. Plotter in the viewer does not plot too many multiples now. Least squares fitter is fixed for fitting routines. Connections to IFEFFIT libraries is fixed - caused blank sceens on startup. Fixed copy-paste of graph data from PCA module.

7/9/12: Version 1.00: Major re-release! Now with Windows specific codes removed and released in both Windows and MacOSX flavors! Graphics now rely on the matplotlib library rather than the out of support BLT graphics libraries, so navigation is new. Continued support for better handling of multiple files - can do save all for background subtraction modules. WARNING: The FEFF6L support for the Mac version is still untested and likely to be broken. I will be working on fixing this soon!

10/28/10: Version 0.68: Minor tweaks. Added a proper r-value for the linear combination fitting. In the data viewer, can now select to average data in groups. This is best used when wanting to average a ton of data files quickly (i.e. from a lot of microXANES points). Any files that have the same root (filename before the last underscore "_") in the name will be average together. This way one can load all the XANES points (including multiple scans of each point) and all the data will average in groups properly. Saves time over adding two files, averaging, clearing, loading, etc...

2/19/10: Version 0.67: Added a “cycle” fit preliminary routine in the least squares fitting. This option will do a set of LC fits for each standard that is NOT checked, and force all standards that are selected to be included in the fit. The quality of fit is reported for each fit. The thought (from Chris Kim) is that with a library of standards, the most important component can be added progressively as each cycle fit is done. Also added options to turn of the legend display in the PCA and SamView plot windows – needed for showing large numbers of graph traces.

8/28/09: Version 0.66: Missed a few numbers there in versions in the official release. Few updates: Added an r-factor for least squares fitting. It is simply the sum of the square of the residuals divided by the sum of the squares of the dataset. Updated file import formats that needed new versions. Added a “MatrixFit” least squares fitting – will calculate the least squares fit of all possible permutations of the selected component list. Returns a new window with a list of the fit permutations and their r-factor quality of fit. Added a “check all” and “check none” option in the background subtraction routine. Default in PCA is now to NOT select all the components after the calculation. SamView has option to save each file opened as an individual average file – good for large numbers of microprobe XANES data.

3/07/08: Version 0.63: Minor update to correct some errors with Tix file windows crashing the plotter.

10/29/07: Version 0.62: Minor update to correct comment format for new SSRL ASCII files.

9/08/07: Version 0.61: Minor update to correct auto-format reader for NSLS multi-element detectors. Removed links to old defunct websites on startup to shorten the delay on starting the program.

6/14/07: Version 0.60: Minor update to correct for PC based SSRL data files. Also updated the version of Tix parameters os that the screen sizes and widgets are smaller.

1/30/07: Version 0.59: Minor update to properly read most current file formats from GSE-CARS at APS.

1/24/07: Version 0.58: Added a support of the new PC based SSRL binary format. Better selection of multiple SCAs in some data formats. Indicator bar in the FEFF fitting routine to show when FEFFIT is working. Added a pulldown menu for selecting files to plot in the background subtraction routine.

5/24/06: Version 0.57: Fixed a few minor bugs in the startup sequence and fixed an error in the plotter routines which cause an error to be raised.

5/22/06: Version 0.56: Fixed a few bugs found in Linux installations from the source code. Added a few improvements to the data importer of SamView for several data formats. Added a few missing files that were vacant from the last release.

2/27/06: Version 0.55: Fixed bug from IFEFFIT upgrade and missing .dll from very latest update. Many changes since I've been so slow on updating. Highlights include… Upgraded the IFEFFIT version to 1.2.8. Added upper and lower limits on deadtime regions, fixed problems with averaging/truncating files with different lengths, added gain adjustment for averaging files under different amplifier conditions. Reads recent changes to SSRL file formats correctly. Background removal now passes all pred-edge and post-edge variables correctly to IFEFFIT. Added capability to set variables in EXAFS fitting as restraint variables (toggle switch). Command line interface to IFEFFIT added under Help menus.

8/26/04: Version 0.52: Bugfix in EXAFS fitting module regarding calculation of residuals. Also completed the save components menubar item in PCA.

8/24/04: Version 0.51: Note logo changes to splash screen and icons. Upgraded IFEFFIT version distributed with Sixpack to 1.2.6. Added the NSLS BSIF binary 1-D format for beamline X26A. SamView now supports averaging files of different lengths, with option for truncation or merging of entire data lengths. Files must still have the same initial energy spacings to work properly. Users with small screens may double click on cursor readout to raise a popup cursor position window. Background subtraction routine has mu option to shift energy positions. PCA routine now has 5 significant digits in the IND function display. EXAFS fitting routine has option to display the k-space residuals in the plot window.

3/24/04: Version 0.50: Fixed 'apply to all' bug in the auto-read of multiple fluorescence detectors in the SSRL data format readers. Added menu item to apply current selected active fluorescence channels to all data files. Added a results summary window in the background subtraction routine to permit easy copying of parameters to word prcessors for note taking.

3/7/04: Version 0.49: Added auto-read formats for PNC-CAT and SRC beamlines. Upgraded IFEFFIT version distributed with Sixpack to 1.2.5.

12/16/03: Version 0.48: Added capability to perform self-absorption corrections to EXAFS data, given a known sample composition. This functionality was based from the code of Corwin Booth. Also included in the source code distribution is a Python native version of mucal. Additional changes made to the quick-XAS loading format from DND-CAT to more easily support variable data formats.

8/20/03: Version 0.47: Upgraded the SixPACK distribution to version 1.2.1 of IFEFFIT. NEW: Added ability to cut data from any graph in SixPACK and paste it as tab delimited text onto the clipboard. This text can then be pasted into any spreadsheet or graphing utility. Greatly enhances data transfer out of SixPACK. Added "Plot Paths" in the EXAFS fitting module which allows the user to plot the contributions from all of the FEFF paths in the fit. Added sort capability to enable reorder of the fit variables. Also fixed a few aesthetic issues.

7/27/03: Version 0.46: Fixed a few errors and added features. Fixed the stack problem with the remove variable button and fixed errors in the e0 finder. Added an error checker in the SSRL format to trap from binary files that have been corrupted by ASCII transfers. Added a computation for step height in the background subtraction routine. Updated the least-squares report page to contain all pertinent values. Added a default text in the "label" category in EXAFS fitting to prevent IFEFFIT hangups.

7/20/03: Version 0.452: Small change to add compatibility for changes in GSE-CARS format

7/14/03: Version 0.451: Small change to fix a text error in the varimax routine.

7/12/03: Version 0.45: MANY new changes. Thanks to all of those who have added valuable input!

Fitting reports both chi-square and reduced chi-square
Added "remove variable" option in EXAFS fitter
Fixed error in log function in least squares fitting routine
Added a global search and replace for FEFF paths to facilitate modifying path definitions. Useful when transftering workspaces between computers
Fixed broken library in PCA routine
Added varimax rotation to PCA routine
Report after performing target transforms on library in PCA is properly formatted
Default directories can be chosen in 'File' menus
Background subtraction routine has a linear post edge fitting option for L-edge spectroscopy
Added functionality to plot FT window parameters in k-space with data
Added ability to control number of spline knots in background subtraction
Fixed improper file name convention warnings
Added ability to apply ROI/detector choices to all files loaded in a series
Adjusted GSECARS auto-format to recognize non-adjacent ROIs. Also fixed error that occured with slight alterations in the file format

3/21/03: Version 0.43: Added arctan function to the least squares fitting module. Background subtraction routine now allows saving a first derivative of the normalized mu. Added warnings for characters in filenames that may be incompatible with IFEFFIT. Also fixed the GSE-CARS format to allow more general input with multiple ROIs.

2/13/03: Version 0.42: Fixed a few bugs in the FEFF fitting routines to allow path degeneracies to be handled better.

2/08/03: Version 0.41: Made a permanent fix for the input problems for recent files at SSRL BL 11-2. Fixed the occansional occurrence of the chi plots not plotting. Made a hack fix for some of the data scrambling that occurred when changing spline ranges in the background subtraction routine. Be sure to update Sixpack with _socket.pyd file and ensure that test.inp is in the same directory as the executable.

2/05/03: Version 0.40: Fixed a file input problem with recent files collected at SSRL BL 11-2. Also fixed a small plotting error.

2/04/03: Version 0.39: Added a version checker to the program. A status bar at the bottom of the main screen lets the user know if they have the most recent version of Sixpack or if they need to update. Also fixed some file storage errors in the least squares fitting routines. Added a library function to PCA. Users can define libraries of standard compounds. After PCA is performed, all of the files in the library will be "target transformed" to see if they fit in the vector space defined by the samples.

2/02/03: Version 0.38: Fixed minor error in fitting routine which would not plot all components of a fit in the waterfall plotting function. Also added a "self-absorption" cycle which will run the routines 10 times so you don't get excessively tired clicking the fit buttons.

1/24/03: Version 0.37: Incorporated the new IFEFFIT 1.0076. Added higher compatibility with GSE-CARS formats. Allowed user selection of Lytle vs. Ge detectors in SSRL data files that contain both sets of data. Also added a "history" function to the generic file loader so the options and column assignments are remembered between file inputs.

1/23/03: Version 0.36: Added additional auto-read formats for ALS and NSLS for single fluorescence detectors. Made the SSRL auto format more general to support varied detector formats. Abandoned use of PGPLOT to plot graphics and results. New plotter interface native with Tkinter to provide more effective cursor readouts and zoom functions. Also allows the plot window to be closed and further graphs to be created without crashing main program. Users can no longer cut and paste graphs from clipboard. However, graphs can be dumped to a gif file and imported into the document of choice. All plot interfaces in modules have a zoom history. Left click to drag new zoom view and right click to previous view. Documentation is now severely outdated!

1/21/03: Version 0.35: Many changes. Added a deglitching panel to the background subtraction panel due to popular demand. This allows basic editing of glitches. Fixed problems with changes in plot parameters not taking effect in this module as well. Added a GSE-CARS auto-read format for SamView (still preliminary). Added a zoom history to the SamView and PCA modules. Left click controls zooming in, and a right click goes back to the last zoom. Also changed least-squares fitting routine to auto-fill the x-limits if none are provided. Fixed a small error in the self-absorption correction routine that didn't work in the upgrade of the module in version 0.33. Cleaned up some of the source code as well. A new zip for the source is now present.

1/16/03: Version 0.34: Fixed memory leakage bug when calculating mu in the background subtraction routine. Also added an option to turn off grid interpolation in the least squares fitting routine. A necessary option when attempting to fit non-XAS data.

1/02/03: Version 0.33: About screen now shows proper version! Added dialog to show comments from SSRL files. Also changed the look and feel of the least-squares fitting routine. Can now use an unlimited number of component and function files. Added many functions other a simple linear function. Can allow variables in the functional expressions to be guessed or fixed. The GUI now matches the look and feel of the other modules. Fixed the install problems when used with the IFEFFIT installer. Documentation and screenshots to be updated soon!

12/15/02: Version 0.32: Fixed some minor bugs. Changed the weighting distribution on the PCA routine and added evaluation functions from Malinkowski's papers. Added a few SSRL detector specific corrections.

10/23/02: Version 0.31: Fixed minor bug to display fitting correlations in EXAFS fitting module. Documentation and screenshots are now available!

10/16/02: Version 0.30: Changes in this list now in reverse chronological order. Another major update! Main feature is addition of PCA routine. It's pretty handy. Also added scrollable windows for the SamView and PCA module for those who have smaller screens. Thanks to Francois Farges for pointing this out a while ago - I finally got to fixing it. Added a row of null radiobuttons in the generic loader so you don't need to start over if you make a mistake. Sources also updated.

10/10/02: Version 0.25: Its been too long before updating... Many additions! Thanks to many people for added feedback. Added support to rebin CS-XAS data in SamView module. Added generic file reader with scrolling windows. Small improvements on some of the interface controls, including some hiding of unnecessary windows building up. Also added window to display fit correlations in advanced fitting. Added extra file support for DND-CAT data files, including compatibility with ID line EXAFS and multi-element detectors. The file extensions of these data types are also also recognized: *.dnd = ascii and CS-XAS, *.dme = multi-element. Source codes also appropriately updated.

8/11/02: Version 0.22: Added dialog window to present fit variable correlations.

8/02/02: Version 0.21: Added support to read in generic ASCII files as raw data with assignment of data columns. Also made e0 calibration in SamView module more robust and easier to choose calibration point. Improved performance of background subtraction routine to reduce unnecessary calculations. Included support for writing FEFF input files compatible with older versions of FEFF.

7/16/02: Fixed errors in single file read in background subtraction function. Also fixed bug that showed up when performing deadtime fits on Ge detectors which have bad channels. Errors in fitting now cause a default value to created. Added these changes to the source code as well

7/9/02: First release version of SixPACK (v0.2) incorporating the 0.11 version of SamView and 2.3.1 version of SamXAS.