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Release v1.5
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smeerten committed Jun 23, 2024
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40 changes: 40 additions & 0 deletions CHANGELOG.md
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All notable changes to this project will be documented in this file.

## [1.5] - 2024-06-22
### Added
- Phasing: support for 2nd order phasing (credits: Florian Schreiner)
- Save to ascii: 2D data now is saved with the 2nd axis described in the header.
- MQMAS model fitting: foldF1 option site resonating outside current spectral window can show as folded signals.
- STMAS ratio for processing (apodization, shearing)
- Tool to scale Carrier and Reference frequencies as an alternative to scale SW in MQMAS experiments.
- Option in 'Fit all' action to copy parameters incrementally after each fit. This can speed up fit in case of smoothly
evolving dataset between each row.
- Option to shift axis when Rolling data. Correction of D1 folded site is now much easier.
### Changed
- WindowsRun.bat updated: Check for PYTHON4SSNAKE variable to find the python interpreter
- Better import of Bruker data (credits: Julien Trébosc):
+ Improved reference frequency loading.
+ Added better loading of nD and hypercomplex datasets.
- Behavior is changed for some MQMAS processing depending on spin and MQ.
Some shearing ratio and SW scaling sign may be different. Especially scaling
SW will never be done with negative anymore. Dimension D1 should be reversed instead
(or FID complex conjugated).
- Updated ReferenceManual
### Fixed
- Better text output for history of several functions (credits: Famlam)
- More error checking when inserting workspaces (credits: Famlam)
- Bruker spectral data: better use of NC and NC\_proc scaling factors (credits: Julien Trébosc)
- Bruker spectral data: fix detecting hypercomplex data
- Bruker digital filter problems for TopSpin v1.3 or earlier
- Bruker SF not properly read in 1D experiments
- Some fixes and warning suppression in Bruker parameter import
+ raw strings for re with \
+ allow non ascii char in parameter sets (utf-8 or latin-1)
- Windows build: fixed save figure output in PDF/SVG/EPS format
- Saving to Matlab: made sure naming is valid, so data can be loaded in Matlab (credits: Famlam)
- Saving to Matlab: fix for newer numpy/scipy versions
- Decreasing size of data now keeps the custom x-axis if set.
- Chemagnetics data: fixed loading function.
- Fixed some numpy code that was deprecated.
- Macro menu operations now work from fitting windows
- Pq calculation in Czjzek plot corrected.
- Hilbert transform now OK: FT-HT-iFT now result in identical FID as initial FID (was time reversed)
- fix bug #114: changing CSA definition in multi 1D fit now converts all rows to new definition

## [1.4] - 2022-09-25
### Added
2 changes: 1 addition & 1 deletion DocSrc/DeStijl.tex
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@@ -1,4 +1,4 @@
% Copyright 2016 - 2021 Bas van Meerten and Wouter Franssen
% Copyright 2016 - 2024 Bas van Meerten and Wouter Franssen
%
%This file is part of ssNake.
%
23 changes: 23 additions & 0 deletions DocSrc/ReferenceManual.bib
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@@ -128,3 +128,26 @@ @Article{Grimminck2011Easy
publisher={Elsevier}
}

@article{kumaresan1982estimating,
title={Estimating the parameters of exponentially damped sinusoids and pole-zero modeling in noise},
author={Kumaresan, Ramdas and Tufts, Donald},
journal={IEEE transactions on acoustics, speech, and signal processing},
volume={30},
number={6},
pages={833--840},
year={1982},
publisher={IEEE}
}

@article{amoureux_triple_1998,
title = {Triple, quintuple and higher order multiple quantum {MAS} {NMR} of quadrupolar nuclei.},
volume = {10},
doi = {10.1016/S0926-2040(97)00027-1},
number = {4},
journal = {Solid State Nucl. Magn. Reson.},
author = {Amoureux, J. P. and Fernandez, C.},
month = feb,
year = {1998},
pages = {211--223},
}

213 changes: 177 additions & 36 deletions DocSrc/ReferenceManual.tex

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4 changes: 2 additions & 2 deletions DocSrc/Title.tex
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@@ -1,4 +1,4 @@
% Copyright 2016 - 2021 Bas van Meerten and Wouter Franssen
% Copyright 2016 - 2024 Bas van Meerten and Wouter Franssen
%
%This file is part of ssNake.
%
@@ -27,7 +27,7 @@
\large Wouter Franssen \& Bas van Meerten

\vspace{1cm}
\large Version 1.4
\large Version 1.5
\vfill
\includegraphics[width=0.5\textwidth]{Images/logo.pdf}\

8 changes: 5 additions & 3 deletions README.md
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@@ -1,5 +1,9 @@
![Alt text](src/Icons/logo.gif?raw=true)

New repository location
=======================
From the release of version 1.5, official ssNake development will continue [here](https://gitlab.science.ru.nl/mrrc/nmrzoo/ssnake).

ssNake
======

@@ -44,7 +48,7 @@ This can be done either by modifying the PATH environment variable or by startin

On Windows systems, ssNake can be installed using the 'Windows installer' that we supply. This holds
a compiled version of both ssNake, and the relevant python libraries, and can be run without any
other requirements. For the installer, please visit our [website](https://www.ru.nl/science/solidstatenmr/software/ssnake/).
other requirements. The installer can be found on GitHub under 'Releases'.

Users that have installed python via the Anaconda progrom descibed above can do the following:
To install ssNake, copy the ssNake directory to your favourite location (C:\Program Files\, for example).
@@ -83,8 +87,6 @@ Contact

For question and suggestions mail to: ssnake@science.ru.nl

Or use the GitHib [discussion forum](https://github.com/smeerten/ssnake/discussions)

License
-------

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2 changes: 1 addition & 1 deletion Tutorial/src/DeStijl.tex
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@@ -1,4 +1,4 @@
% Copyright 2016 - 2021 Bas van Meerten and Wouter Franssen
% Copyright 2016 - 2024 Bas van Meerten and Wouter Franssen
%
%This file is part of ssNake.
%
4 changes: 2 additions & 2 deletions Tutorial/src/Title.tex
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@@ -1,4 +1,4 @@
% Copyright 2016 - 2021 Bas van Meerten and Wouter Franssen
% Copyright 2016 - 2024 Bas van Meerten and Wouter Franssen
%
%This file is part of ssNake.
%
@@ -27,7 +27,7 @@
\large Wouter Franssen \& Bas van Meerten

\vspace{1cm}
\large Version 1.4
\large Version 1.5
\vfill
\includegraphics[width=0.7\textwidth]{Images/logo.pdf}\

2 changes: 1 addition & 1 deletion Tutorial/src/Tutorial.tex
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@@ -1,4 +1,4 @@
% Copyright 2016 - 2021 Bas van Meerten and Wouter Franssen
% Copyright 2016 - 2024 Bas van Meerten and Wouter Franssen
%
%This file is part of ssNake.
%
2 changes: 1 addition & 1 deletion src/Czjzek.py
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@@ -1,7 +1,7 @@
#!/usr/bin/env python3
# -*- coding: utf-8 -*-

# Copyright 2016 - 2022 Bas van Meerten and Wouter Franssen
# Copyright 2016 - 2024 Bas van Meerten and Wouter Franssen

# This file is part of ssNake.
#
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125 changes: 125 additions & 0 deletions src/Icons/Sources/ScaleFreqRef.svg
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10 changes: 6 additions & 4 deletions src/WindowsBuild/ssNake.spec
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@@ -19,12 +19,14 @@ basePath = 'c:\\Users\\Emulator\\Desktop\\ssNakeBuild\\ssnake\\src\\'
# plugins --> pltforms: only need qwindows

a = Analysis([basePath + 'ssNake.py'],
pathex=['C:\\Users\\Emulator\\AppData\\Local\\Programs\\Python\\Python36\\Lib\\site-packages\\scipy\\extra-dll', 'C:\\Users\\Emulator\\Desktop'],
pathex=['C:\\Users\\Emulator\\AppData\\Local\\Programs\\Python\\Python38\\Lib\\site-packages\\scipy\\.libs','C:\\Users\\Emulator\\Desktop'],
binaries=[],
datas=[(basePath + 'IsotopeProperties', '.'),(basePath + 'licenseHtml.txt','.'),
(basePath + '\\Icons','Icons'),
(basePath + 'References.txt','.')],
hiddenimports=['spectrum','fitting', 'updateWindow','saveFigure','loadIsotopes','scipy.optimize', 'scipy._lib.messagestream'],
(basePath + 'References.txt','.'),
(basePath + 'Tooltips','.')],
hiddenimports=['spectrum','fitting', 'updateWindow','saveFigure','loadIsotopes','scipy.optimize', 'scipy._lib.messagestream',
'matplotlib.backends.backend_svg','matplotlib.backends.backend_ps','matplotlib.backends.backend_pdf'],
hookspath=[],
runtime_hooks=[],
excludes=['tkinter','PyQt5.QtWebEngineWidgets','PyQt5.QtWebEngineCore','PyQt5.QtWebEngine','PyQt5.QtDesigner',
@@ -34,7 +36,7 @@ a = Analysis([basePath + 'ssNake.py'],
'PyQt5.QtNfc','PyQt5.QtNetworkAuth','PyQt5.QtNetwork','PyQt5.QtMultimediaWidgets','PyQt5.QtMultimedia',
'PyQt5.QtLocation','PyQt5.QtHelp','PyQt5.QtDBus','PyQt5.QtBluetooth',
'PyQt4','h5py.tests','pytz',
'matplotlib.backends._tkagg','lib2to3','ssl','numba'],
'matplotlib.backends._tkagg','lib2to3','numba'],
win_no_prefer_redirects=False,
win_private_assemblies=False,
cipher=block_cipher)
34 changes: 26 additions & 8 deletions src/WindowsRun.bat
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@@ -1,17 +1,35 @@
REM Check for a user defined environnment variable (PYTHON4SSNAKE) containing the location of python interpreter.
REM Else this script will start ssNake only if pyw.exe or pythonw.exe is found in current path search.
REM Otherwise it will quit
@echo off
set mypath=%cd%
cd ..\..

IF DEFINED PYTHON4SSNAKE (
set PYTHONW=%PYTHON4SSNAKE%
goto run_ssnake
)

where /q pyw
IF ERRORLEVEL 1 (
ECHO 'pyw' is missing, try 'pythonw'
where /q pythonw
IF ERRORLEVEL 1 (
ECHO 'pythonw' also missing. Abort.
) ELSE (
start pythonw "%mypath%"\ssNake.py
)
ECHO 'pyw' not in search path, try 'pythonw'
) ELSE (
start pyw "%mypath%"\ssNake.py
SET PYTHONW=pyw
goto run_ssnake
)

where /q pythonw
IF ERRORLEVEL 1 (
ECHO 'pythonw' also not in search path.
) ELSE (
SET PYTHONW=pythonw
goto run_ssnake
)
ECHO No python interpreter found: about to leave
PAUSE
EXIT

:run_ssnake
REM Let's try running ssNake !!!!
start "ssNake" %PYTHONW% "%mypath%"\ssNake.py

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