GXSM / News: Recent posts

All new SPM control hardware 4 Gxsm 4 -- RedPitaya based and a 100% FPGA level core control:

https://github.com/pyzahl/Gxsm4/discussions/8

The Gxsm Team
-P

This workshop aims to bring the SPM user community together to share latest science from HR-AFM to various SPM niche sciences. We discuss capabilities for remote or autonomous control of instruments and analysis of data.

The field of “Scanning Probe Microscopy (SPM)” is continuing to grow into diverse facets of scientific data acquisition. “Home built” or specialized microscope instruments require the control of various types of (nano) positioning mechanisms in combination with line by line imaging. In this meeting we would like to showcase capabilities of existing facilities, and particularly look forward towards new demands and opportunities in the field.
We plan on engaging participants to present their particular application and problems and provide an opportunity to meet the developers of existing facilities (in particular the developers of open source GXSM project *) in a dedicated “hack-a-day” like session — having virtually hands on microscope operation demonstrations.... read more

I like to ask the Gxsm community to help, participate and present again in 2023.
We are in the early planning and workshop proposal phase and do need potential speakers!

FYI: 2023 User Meeting. This year, the User Meeting will be held from April 24 - 28, 2023, and will be virtual.

Please speak up and contact us if you are interested!

-Py

All further code base maintenance will be continued at the transferred SVN at GitHub as of 20220420.

Here:

https://github.com/pyzahl/Gxsm3

SPM user community meetup: “hands on open” source SPM software virtual “Hack a day” learning session and future outlook on artificial intelligence driven autonomous SPM

The special workshop is currently scheduled for Wednesday, May 25, 2022, from 8 a.m. to 12 p.m. EST and Thursday, May 26, 2022, from 8 a.m. to 12 p.m. EST

and will be taking place in the context of "The NSLS-II and CFN Users’ Meeting at the Brookhaven National Laboratory" and will be held from May 23 – 26, 2022 and will be completely virtual.... read more

Happy New Year Every One!

There was a big Christmas/New Year's hack happening to bring alive a all renewed cutting edge GTK4 based Gxsm4.
Under the hood this includes a whole lot of porting, cleanups and code reorganizations. Besides primitive the gtk4 porting, parts required reworking functionalities as different -- but potentially better via nicer and cleaner code! And the biggest move to a all new build system called Meson/Ninja making building and maintaining a blast.
A few new or improved GUI features. Besides a minor but refreshed look. And still a few details to be smoothed out. So be careful with production use at this time!... read more

Update on the latest high speed PAC-PLL (Red Pitaya based) Gxsm / MK3-A810 add on with digital hi speed serial link.

After a long struggle redesigning and porting to the latest Vivado 2019.2 Xilinx FPGA development platform the feat it finally done and all seam working fine now.

Under the high speed FPGA hood:

• Reorganization, rebuild/design of almost every module under the hood. Better modularity and better timing pereformance.
• New input interpolation filter
• Redesigned DC-filter
• Better pipelined PAC/LMS
• Optimized controller structures
• Totally redesigend signal combine/selection and decimation module, more flexibility, more efficient
• Cleaned up BRAM interface
• McBSP serial link functionally unchanged and working great again after temporary design/timing hickups with new development tool
• Additional new delta-frequency controller for generic use, output via McBSP link to DSP -- good for NC-AFM dF control or SQDM, etc...
  ** NEW: optimized new version of the hi-speed serial (real time) RP-PAC-PLL to DSP data interface been build in a small series and can be made available at cost. Please contact the GXSM team.... read more

Update:

today merged trunk with Gxsm-3.0-20191124-spmscancontrol-dev

going to Version Gxsm 3.52.0 Map ExplorerHD.

Key Features:

• major revised and rewritten SPM Scancontrol Plugin with minor adjustements to XSMHardware HwI Interface (ScanLineM) in the context of a new more modern idle processing scheme for improoved GUI response and in particular a actually now completely really non blocking "scan-start" vs. previously injecting gtk-idle-processing calls. That implied a major rework and introduction of a high-level scan state machine.
• The implemented non blocking "Scan-Start" now implies that all python remote calls to scan-start are also non-blocking.
• Attention: PyRemote "scan-start" is now NOT any more waiting until scan-completed and you must (and can!) check on scan progress. Note: I may add a special artificially blocking python call option for scan-start for convenience in future again. Be advised: PyRemote libraries are not yet adjusted to this behavior.
• New: A Python (GXSM side) gxsm-sok-server.py to be run within the Python console providing network based socket access to basic gxsm remote controls.
• And a standalone python (3.7) socket client "gxsm-scan-image-viewer-sok-client.py" with NetCDF image view capabilities, future AI implementaions are work in progress and under evaluation.
• And trigged by the gxsm community: A all new spm-simulator HwI PlugIn serving mainly as a hardware interface demonstration and template for new interface designs.... read more

A GXSM3.0 (via python remote) JSON based socket server/client is now operational and a all re-newed fully non blocking "spm-scancontrol" plugin was created -- what implied a major code over haul of the old spm-scancontrol plugin and a few adjustement on the HwI's (MK2 and MK3). Previously injecting "while (event-pending) gtk-main-loop();" calls while scanning -- however, that was not working for the python interface as the "start-scan" subroutine was never returning until scan stopped and thus the python interface was blocked until the scan completed or was stopped by the user... So I had to redesign the whole complex crap using a state machine design with frequent non blocking calls from a "g-idle()" task which have to complete quickly each time.... Just a major task but all good now and to be tested. The issue is I can not use real threads for GUI related stuff -- not thread safe.... read more

GXSM 3.51.11 "Map Explorer" is evolving in SVN and near stable at this time, but please still be advised that it's a major new version with a lot of reworks of old code been modernized, and aload of new features. MK2 users shall resist from updating from default SVN at this time, as not tested with the MK2. MK3 only tested. HOWEVER, big news for Mark2 (MK2) users a all new MK2 DSP code with a first ever RTEnginee4GXSM on Mark2 was brought to life in the past days. It brings a hug boost in performance under the hood due to levering DSP idle time in a much more extensive and multitasking manner and thus freeing up valuable real time for critical data processing! Very well functional and ready for testing: https://sourceforge.net/p/gxsm/svn/HEAD/tree/branches/Gxsm-3.0-20191105-MK2-RTE-backports-devel/... read more

V3.50.2 features now a automatic "world map" management (per scan channel) option. This is only enabled when the "RAD" function found in the SPM Scan Control Window is enabled. Not recommended for minimalistic or low memory systems as this performs full data remapping conversions at scan start for every channel and may take noticalble extra time on slow machines and in particular with large scan data sets.... read more

Now going to V3.50.1 with latest features in SVN tested OK.

New: at scan start previous image data (if overlapping in any means) is remappe/interpolated to new scan geometry and shown while been updated with new settings while scanning.
One of the key idea for this is not only to "look nice" and get a better view rigth away, but to potentially have a "position template" for molecules, etc. if preparing for rescanning partial regions using the Sub-Line-Scan (SLS) mode for selected region(s). This way a template is available right away and no need to eventually rescan at high resolution in STM mode everything -- slow for a high line count plus pointless usually in STM.... but ncAFM may reveal local details now easy to navigate to and select....... read more

Important note for production use -- please postpone any updates from SVN.

WARNING: Temporary experimental code in SVN for testing purpose.

New feature of mapping any previous scan data to new scan geometry as possible is under evaluation. Feel free to test and report any issues.

UPDATE: New code/recoded parts stabilized and tested. Still please use with extra caution.

-Py

After real work testing found to be good and even better than ever!

Merge from branches/Gxsm-3.0-MK3-rtl-devel, code name "Next Level RTEngine", V3.50.0 to trunc (main stream version) is completed.

New versatile MK3 DSP real time engine:
- allowing now for nested hardware interrupts (needed for PR high speed serial link) working now also relibale up to 12MHz serial clock with beta serial link hardware. (pending to be published)
- enhanced/optimized real time performance and capabilities due to more efficient and new rt and idle job management.
- more scan data thoughput is actually possible now than ever before!
- new rotation matrix protection mechanism, but allowing via a new GXSM method a delta step based rotation in real time and life even while scanning: convenient for aligning features, etc... (experimental so far), not available for MK2 at this time.
- new RT job management and monitoring tools:
GXSM includes a terminal based DSP process list view via Info+ mode in ProbeView module.
Python configuration tool has a App "DSP Manager" now including a sophisticated process view with job control and manipulation tools. Allowing manual tweaks... also including management of the new serial McBSP DSP-RP link.

How and what and why did this happened??

After some super productive long hacking nights it happend:
The all new RTENGINE4GXSM -- a new DSP RT scheduler -- is reality and already undergo first very positive lab tests!

Why? The need to more and particular more efficient use of DSP hard real time resources to serve short simple but high rep rate bursts of interrupt subroutine requests for high speed serial data package transmissions used for communication on a hard real time pixel rate basis, needed to finally make a digital link to the RedPitaya FPGA happen. Up 8 32bit channel can be boosed over fully bidirectional currently in a fraction of the time between "pixels". (~0.1ms) 1..5MHz McBSP serial clock -- possibly even faster pushing it. (Note: that needs a little custom interface hardware for line drivers going over CAT6 cable)... read more

Work on a final digital real time serial Link between the RedPitaya and MK3 is now completed and working.

-- WARNING -- : EXPERIMENTAL DSP CODE : but assumed to be stable if the new feature is not enabled.

Prooven reliable up to 6.25 MHz serial clock using a 4ft CAT6 cable. Default is set to 1MHz, plenty for even regular and fast STM scan speeds no hassle:

Currently transferring 8 32bit channels, while at this time only 4 are used for FPGA Phase/Freq/Ampl/Exec in BRAM Loop Transfer Mode. Selec: [Phase,Freq].
Use 10/16.8ms setting.... read more

Just completed adding a realtime resonance/tune curve fitting to the Inet Json RedPitaya Plugin scope in tune mode. Display after 15 first samples first fit data.

This new feature needs libgsl-dev package as using Lib GSL for Levenberg-Marquardt fitting method with geodesic acceleration.

With the introduction of new real time monitoring feature in Version 3.49.1 "Defender of the Electron" -- trying to do better! More visual realtime feedback on probe status and signal conditions... It's just a beginning of some ideas and still experimental but tested OK.

Besides several minor addition and tweaks a new plugin so far name Probe-HUD -- still having it's own decoration less window (move via Window-Key + LMB) -- desigend eventually to be used dynamically as temporary scan overlay, etc...... read more

Just a hint from the developer:

Recommending to use a lighter theme for the Gnome/Gtk3 desktop.
For a more efficient/responsive and faster less animated theme, try for example "Xfce Evolution" variant "Crux".

This on has no "animations" for activting a dialog and repainting all the elements in a different shade plus the layout is more compact and saves desktop space as well.

See here:
https://www.gnome-look.org/p/1191436/
or
http://www.itgroup.ro/WSX/browser.htm?.landingpage=wsx_content/en/linux/xfce-evolution.html#wsx-backclear... read more

A Gxsm-3.0 stable release tag copy was created for

Gxsm3 Version 3.48.0 Code Name "Proton Sword"

in SVN under tags/Gxsm-3.0-20180515-stable

This version includes several details eveloved over the past 8 month. And recent GUI addition related to a finer "Autosafe" channel level selection controls. Several math/plugins were optimized, evolving NC-AFM simulation plugin, advanved addition and featured for image export including legend details/options and much more.... read more

Hang in tight:

Gxsm-3.0+MK3-A810 will soon get a explorative new high-speed AD/DA+fast processing addition, completely independent but synchronized to the MK3. Looking far into the MHz regime... Guess what -- explanding the frequency detection range for NC-AFM (but not only) -- fully scalable for using an array of those new modules.

-Py

Created copy/tag: svn/tags/Gxsm-3.0-20171027-stable

For Gxsmm-3.0 V3.47.0 Action Eclipse -- minor tweaks, import plugin addition, python template script additions, optimized stich open mode.

Be advised: current trunk SVN will be more experimental for the coming weeks and will require more frequent DSP code updates to stay in sync. Also new direct DSP based digital IO is explored with intend of pixel based external data synchornization options. Alongside with new developments for using multiple (digital) external data/signal sources along with the MK3 as scan master.... read more

With 3.47.0 "Action Eclipse" not much changed visually. Added default action/control python script templates -- more to come. And much more planned on the python level part automated instrument control side.

However, a key addition/new control level on kernel module basis was implemented. Effecting only specific interaction with the MK3 signal control/management topology. So far signal control/management had to be restricted to exactly one task -- and was/could not be enforced. Else missleading signal read back could be the result.
Most users won't care as normal operation is not effected.... read more

... better and more complete than ever now. We were supporting via embedded Python Gxsm settings and scan control since ever, but now it getting better and more involved than ever -- plus the ease of use and management of a (growing) set of default actions and tools fully customizable.

The latest addition includes a more complete set of data access commands for read/write of pixel data and new scan creation from python numpy array data. So guess what -- you can now seamlessly play with some python math directly acessing scan data and send it right back to a scan to visualize via gxsm or even do some actions depending on it...... read more

The GXSM3 build in Python command set was enhanced including some minor comand name adjustments.

Please refer to the build in gxsm.help () function for a most up-to-date information and comand list, simply use the "Help" Menuitem in the Pyton Console and execute the provide help script -- then see the consol output!

Most importantly: gnuim/export is now simply "gxsm.import () and .export ()".

New: Live scan data access function to get andput pixel values in 4D (well, so far 3D, time not yet supported, soon, stay tunded.) And a scan write function to dump am python array into a scan, int or float type versions are available.... read more