# WARNING (31th March 2023)
It seems that the various Jupyter Notebooks which use the ipympl library have a problem with the latest versions of the anaconda distribution (starting with `python 3.9`), and probably with other distribution as well.
Try the following possibilities if you have problem with the graphic and/or the interaction in the Spike Notebooks
1. the team developping jupyter is migrating the notebook to a new technology and Spike is not yet adapted to this new environment.
In the meantime, use `nbclassic` instead of `notebook` to launch the various notebooks
```
jupyter-nbclassic TheNooteBook.ipynb
```
2. The interaction is based on the optionnal `ipympl` extension, and some people have instabilities in the interaction
*upgrading ipympl to the 0.9.3 version seems to solve the difficulty:*
```
pip install ipympl==0.9.3
```
or alternatively
```
conda config --env --add channels conda-forge
conda install ipympl=0.9.3
```
Depending on your set-up (jupyter version) it might work either in `jupyter lab`, `jupyter notebook` or `jupyter nbclassic`, or even all of them.
# 1/ What is SPIKE ? #
**SPIKE** a collaborative development for a FT-spectroscopy processing library.
*This is the version 0.99.33 - Octobre 2023*
**SPIKE** allows the processing, the display and the analysis of data-sets obtained from various Fourier-Transform spectroscopies. The name stands for **S**pectrometry **P**rocessing **I**nnovative **KE**rnel.
It allows the <b>processing</b> of **1D** and **2D** FT spectroscopies, mostly **NMR** and **FTICR-MS**, but also **Orbitrap**, and other to come.
It implements all needed tools for Data analysis (Fourier Transform, Baseline correction, noise reduction, peak-picking, etc...)
To our knowledge, it is the first program freely available allowing the processing, display and analysis of 2D-FT-ICR (Fourier Transform Ion Cyclotron Resonance), as well as Orbitrap time domain data processing.
It is written in python3 currently developed in python 3.11 (python 2.7 has been tested up to version 0.99.10).
It is tested in python versions from 3.7 to 3.11.
It is mostly a library for processing, analysis and display of spectral data-sets.
The natural interface is either a python program or a `jupyter notebook` as an interactive front-end.
### SpI *(Spike Interactive)*
An additional program, called **SP**ike **I**nteractive (or **SpI** ) is also developed, it consists in a set of stand alone jupyter Notebooks which allow to use SPIKE process and analyse NMR and MS datasets without any programming knowledge.
It provides simple interactive environment which implement basic analysis can be found in the [SpI](Notebooks) directory.
A part of SpI is also contained in the [`Interactive`](spike/Interactive) directory in the source tree.
It is still in very active development, but also the basis for our research.
Many features are missing, and many other while present, are not fully fixed.
However, considering the amount of efforts already present in this code, we decided to make it available.
We believe that even in this current development stage, this program might prove useful for certain usages.
# 2/ Documentation
Basic presentation of functionalities can be found [Here](Presentation.md)
A complete documentation, with the full API, can be found [Here](http://softwares.casc4de.eu/spike/spikedoc/).
We try to keep it up to date, but it may lag a little behind the current program state.
Most of the documentation is in the code itself, available directly while programming (*try* `function_name?` *in* `jupyter notebook`).
Another source of documentation are [Notebooks](Notebooks) directory.
There are two type of Notebooks, fully developed ones, with interactive tools, which can be used as is,
and example Notebooks, meant for pedagogic purposes.
This is an ongoing effort, and always short of what we'd like to do.
### Release Notes
Can be found [Here](release_notes.md)
# 3/ How to get SPIKE ? ##
### simple installation
You might have python installed on your system, however, SPIKE relies on a whole set of scientific libraries which may dont be installed (see **Dependencies** below).
We advise to install a scientific python environment such as [Anaconda](https://www.anaconda.com/) or [Enthough](https://www.enthought.com/).
Then install SPIKE with the following command in the terminal:
pip install spike-py
This will install the latest version on your machine. *(be sure to use the pip command which came with the scientific python environment)*.
If you already have SPIKE installed and want to upgrade to the last version do:
pip install -U spike-py
### Installing from `github`
The`pip` instalation is always less recent than the github version, if you need the latest version, you simply instal it in the following way:
- Get the last version on `github`, using `git` (prefered)
git clone https://github.com/spike-project/spike.git
- then go to the spike directory and type the following command (new syntax due to changes in development team)
pip install -e
This method allows you to update your `Spike` distibution from `github` and always use the latest version by doing
git pull; git update
in your spike directory.
Alternatively, you can simply download the archive
wget https://github.com/spike-project/spike/archive/refs/heads/master.zip
unzip master.zip
cd spike
pip install -e
### Installing additional tools
Several additional tools may be of interest.
**a/ Interactive jupyter notebooks from SpI**
can be found in the [Notebooks](Notebooks) directory or on [github](https://github.com/spike-project/spike/tree/master/Notebooks).
You will find there fully developed interactive notebooks allowing data analysis without any knowledge in python programming, as well as examples to starting writing small pyhton programs for specific needs.
First the tool `ipympl` needs to be installed (it may not be installed along the scientific environment)
To install it, simply do (check warning above):
pip install ipympl
Then copy the related NotBooks to a directory by typing in a terminal in this directory.
python -m spike.installSpI
this will copy all the tools, you can safely remove the unneeded one, as the same command will always bring you all the notebooks.
**b/ additional plugins** are available in the [plugins/special](spike/plugins/special) directory in the source tree. [check on github](https://github.com/spike-project/spike/tree/master/spike/plugins/specials).
If you want to use them, create a directory called `Spike` in your HOME directory, and a directory called `plugins` in this one (hence `$HOME/Spike/plugins`), and put then there, they will be directly activated.
You can also develop your own plugins and put them here.
Note that some plugins or extension require additional libraries (`ipympl`, `MPI`, `bokeh`, `mayavi`, ...)
### Licenses
The Spike program is distributed under the [`CeCILL 2.1 FREE SOFTWARE LICENSE AGREEMENT`](http://www.cecill.info)
Which is the GPL license adapted to the French law.
It includes the following additional programs/algorithms:
- [urQRd](http://urqrd.igbmc.fr/) L.Chiron and M-A Delsuc (denoising of large harmonic signals) under CeCiLL licence
- [PALMA](https://github.com/delsuc/PALMA) A.Cherni and M-A.Delsuc (Processing of DOSY based on ILT) under CeCiLL licence
- [progressbar](https://github.com/niltonvolpato/python-progressbar) N.Volpato - under LGPL licence
### source and dependencies
The SPIKE source is available at https://github.com/spike-project/spike
SPIKE is written in pure Python, and relies on several external libraries:
- matplotlib
- numpy
- scipy
- tables
- pandas
It is compatible and fully tested with python 3.7 and 3.10
### developping for SPIKE
check [Here](DevelopmentGuide.md)
# 4/ Citing SPIKE
If you happen to use SPIKE successfully for your research, please cite it, and refer to this site, as well as the following possible references :
- **Main Reference**: first publication of the program itself - *rejected from Anal. Chem. with no real critics except that Reviewer 1 said "too much NMR", Reviewer 2 said "too much MS", !! so I decided to let it on ArXiV*)
1. Chiron L., Coutouly M-A., Starck J-P., Rolando C., Delsuc M-A. SPIKE a Processing Software dedicated to Fourier Spectroscopies https://arxiv.org/abs/1608.06777 (2016)
Other references are also related
- The renewal of Gifa:
2. Delsuc M-A. "Gifa V.4: A complete package for NMR data set processing" (2020) https://doi.org/10.5281/zenodo.3904595
- presentation of the automation possibilities in NMR
3. Margueritte, L., Markov, P., Chiron, L., Starck, J.-P., Vonthron Sénécheau, C., Bourjot, M., & Delsuc, M.-A. (2018). "Automatic differential analysis of NMR experiments in complex samples." Magn. Reson. Chem., 80(5), 1387. http://doi.org/10.1002/mrc.4683
- first version of the 2D FT-ICR-MS processing
4. van Agthoven, M. A., Chiron, L., Coutouly, M.-A., Delsuc, M.-A. & Rolando, C. "Two-Dimensional ECD FT-ICR"
Mass Spectrometry of Peptides and Glycopeptides." _Anal Chem_ **84**, 5589-95 (2012).
- first version of the python set-up on which the current SPIKE is loosely based
5. Tramesel, D., Catherinot, V. & Delsuc, M.-A. "Modeling of NMR processing, toward efficient unattended processing of NMR experiments. _J Magn Reson_ **188**, 56-67 (2007).
ref 1) is a general purpose reference, the other ones are more specific.
# 5/ Contents of this repository
- [`spike/`](spike) - the python code of the program itself
- [`doc/`](doc) - a directory containing various files used to generate the documentation
- [`Notebooks/`](Notebooks) - the repository of the **SpI** notebooks
- miscelaneous:
- `QC.py` `QC.txt` a small utility to check the quality of the code using pylint.
# 6/ Origin of the program
**SPIKE** is originated from the _Gifa_ program, developed by M-A Delsuc and others in `FORTRAN 77` since the late eighties, it still shares similarities, such as command names, or internal data organisation.
_Gifa_ was abandoned around 2005, but it actually experienced a revival in 2020 thanks to the " *ten years challenge* " organised by the [ReScience C Journal](https://rescience.github.io/read/). You can find an installable and runnable version here: https://github.com/delsuc/Gifa
_Gifa_ has known several mutations, and finally ended as a partial rewrite called **NPK**.
The [NPK](http://abcis.cbs.cnrs.fr/NPK/) program is based on some of the original `FORTRAN` code, wrapped in Java and Python, which allows to control all the program possibilities from the Python level.
NPK is purely a computing kernel, with no graphical possibilities, and has been used as a kernel embedded in the commercial program NMRNoteBook, commercialized by NMRTEC.
However, NPK was showing many weaknesses, mostly due to the 32bits organization, and a poor file format. So, when a strong scientific environment became available in Python, a rewrite in pure Python was undertaken. To this initial project, called NPK-V2, many new functionalities were added, and mostly the capability to work in other spectroscopies than NMR.
At some point in 2014, we chose to fork NPK-V2 to SPIKE, and made it public.
# 6/ Authors and Licence
Current Active authors for SPIKE are:
- Marc-André Delsuc `madelsuc -at- unistra.fr`
- Laura Duciel `laura.duciel -at- casc4de.eu`
Previous authors:
- Christian Rolando `christian.rolando -at- univ-lille1.fr`
- Lionel Chiron `Lionel.Chiron -at- casc4de.eu`
- Petar Markov `petar.markov -at- igbmc.fr`
- Marie-Aude Coutouly . `Marie-Aude.COUTOULY - at- datastorm.fr`
Covered code is provided under this license on an "as is" basis, without warranty of any kind, either expressed or implied, including, without limitation, warranties that the covered code is free of defects. The entire risk as to the quality and performance of the covered code is with you. Should any covered code prove defective in any respect, you (not the initial developer or any other contributor) assume the cost of any necessary servicing, repair or correction.
Downloading code and datasets from this page signifies acceptance of the hereunder License Agreement. The code distributed here is covered under the CeCILL license : http://www.cecill.info/index.en.html
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"description": "\n\n# WARNING (31th March 2023)\nIt seems that the various Jupyter Notebooks which use the ipympl library have a problem with the latest versions of the anaconda distribution (starting with `python 3.9`), and probably with other distribution as well.\n\nTry the following possibilities if you have problem with the graphic and/or the interaction in the Spike Notebooks\n\n1. the team developping jupyter is migrating the notebook to a new technology and Spike is not yet adapted to this new environment.\n In the meantime, use `nbclassic` instead of `notebook` to launch the various notebooks\n ```\n jupyter-nbclassic TheNooteBook.ipynb\n ```\n2. The interaction is based on the optionnal `ipympl` extension, and some people have instabilities in the interaction\n*upgrading ipympl to the 0.9.3 version seems to solve the difficulty:*\n ```\n pip install ipympl==0.9.3\n ```\nor alternatively\n ```\n conda config --env --add channels conda-forge\n conda install ipympl=0.9.3\n ```\nDepending on your set-up (jupyter version) it might work either in `jupyter lab`, `jupyter notebook` or `jupyter nbclassic`, or even all of them.\n\n# 1/ What is SPIKE ? #\n\n**SPIKE** a collaborative development for a FT-spectroscopy processing library.\n\n*This is the version 0.99.33 - Octobre 2023*\n\n**SPIKE** allows the processing, the display and the analysis of data-sets obtained from various Fourier-Transform spectroscopies. The name stands for **S**pectrometry **P**rocessing **I**nnovative **KE**rnel.\n\nIt allows the <b>processing</b> of **1D** and **2D** FT spectroscopies, mostly **NMR** and **FTICR-MS**, but also **Orbitrap**, and other to come.\n\nIt implements all needed tools for Data analysis (Fourier Transform, Baseline correction, noise reduction, peak-picking, etc...)\n\nTo our knowledge, it is the first program freely available allowing the processing, display and analysis of 2D-FT-ICR (Fourier Transform Ion Cyclotron Resonance), as well as Orbitrap time domain data processing.\n\nIt is written in python3 currently developed in python 3.11 (python 2.7 has been tested up to version 0.99.10).\nIt is tested in python versions from 3.7 to 3.11.\n\nIt is mostly a library for processing, analysis and display of spectral data-sets.\nThe natural interface is either a python program or a `jupyter notebook` as an interactive front-end.\n\n\n### SpI *(Spike Interactive)*\nAn additional program, called **SP**ike **I**nteractive (or **SpI** ) is also developed, it consists in a set of stand alone jupyter Notebooks which allow to use SPIKE process and analyse NMR and MS datasets without any programming knowledge.\n\nIt provides simple interactive environment which implement basic analysis can be found in the [SpI](Notebooks) directory.\nA part of SpI is also contained in the [`Interactive`](spike/Interactive) directory in the source tree.\n\nIt is still in very active development, but also the basis for our research.\n\nMany features are missing, and many other while present, are not fully fixed.\nHowever, considering the amount of efforts already present in this code, we decided to make it available.\nWe believe that even in this current development stage, this program might prove useful for certain usages.\n\n# 2/ Documentation\nBasic presentation of functionalities can be found [Here](Presentation.md)\n\nA complete documentation, with the full API, can be found [Here](http://softwares.casc4de.eu/spike/spikedoc/).\nWe try to keep it up to date, but it may lag a little behind the current program state.\n\nMost of the documentation is in the code itself, available directly while programming (*try* `function_name?` *in* `jupyter notebook`).\n\nAnother source of documentation are [Notebooks](Notebooks) directory.\nThere are two type of Notebooks, fully developed ones, with interactive tools, which can be used as is,\nand example Notebooks, meant for pedagogic purposes.\nThis is an ongoing effort, and always short of what we'd like to do.\n\n### Release Notes\nCan be found [Here](release_notes.md)\n\n\n# 3/ How to get SPIKE ? ##\n\n### simple installation\nYou might have python installed on your system, however, SPIKE relies on a whole set of scientific libraries which may dont be installed (see **Dependencies** below).\nWe advise to install a scientific python environment such as [Anaconda](https://www.anaconda.com/) or [Enthough](https://www.enthought.com/).\nThen install SPIKE with the following command in the terminal:\n\n pip install spike-py\n\nThis will install the latest version on your machine. *(be sure to use the pip command which came with the scientific python environment)*.\n\nIf you already have SPIKE installed and want to upgrade to the last version do:\n\n pip install -U spike-py\n\n### Installing from `github`\nThe`pip` instalation is always less recent than the github version, if you need the latest version, you simply instal it in the following way:\n\n- Get the last version on `github`, using `git` (prefered)\n\n git clone https://github.com/spike-project/spike.git\n\n- then go to the spike directory and type the following command (new syntax due to changes in development team)\n\n pip install -e\n\nThis method allows you to update your `Spike` distibution from `github` and always use the latest version by doing\n\n git pull; git update\n\nin your spike directory.\n\nAlternatively, you can simply download the archive\n\n wget https://github.com/spike-project/spike/archive/refs/heads/master.zip\n unzip master.zip\n\tcd spike\n pip install -e\n \n### Installing additional tools\nSeveral additional tools may be of interest.\n\n**a/ Interactive jupyter notebooks from SpI**\ncan be found in the [Notebooks](Notebooks) directory or on [github](https://github.com/spike-project/spike/tree/master/Notebooks). \nYou will find there fully developed interactive notebooks allowing data analysis without any knowledge in python programming, as well as examples to starting writing small pyhton programs for specific needs.\n\nFirst the tool `ipympl` needs to be installed (it may not be installed along the scientific environment)\nTo install it, simply do (check warning above):\n\n pip install ipympl\n\nThen copy the related NotBooks to a directory by typing in a terminal in this directory.\n\n python -m spike.installSpI\n\nthis will copy all the tools, you can safely remove the unneeded one, as the same command will always bring you all the notebooks.\n\n\n**b/ additional plugins** are available in the [plugins/special](spike/plugins/special) directory in the source tree. [check on github](https://github.com/spike-project/spike/tree/master/spike/plugins/specials).\n\nIf you want to use them, create a directory called `Spike` in your HOME directory, and a directory called `plugins` in this one (hence `$HOME/Spike/plugins`), and put then there, they will be directly activated. \nYou can also develop your own plugins and put them here.\n\nNote that some plugins or extension require additional libraries (`ipympl`, `MPI`, `bokeh`, `mayavi`, ...)\n\n### Licenses\nThe Spike program is distributed under the [`CeCILL 2.1 FREE SOFTWARE LICENSE AGREEMENT`](http://www.cecill.info)\nWhich is the GPL license adapted to the French law.\n\nIt includes the following additional programs/algorithms:\n\n- [urQRd](http://urqrd.igbmc.fr/) L.Chiron and M-A Delsuc (denoising of large harmonic signals) under CeCiLL licence\n- [PALMA](https://github.com/delsuc/PALMA) A.Cherni and M-A.Delsuc (Processing of DOSY based on ILT) under CeCiLL licence\n- [progressbar](https://github.com/niltonvolpato/python-progressbar) N.Volpato - under LGPL licence\n\n### source and dependencies\nThe SPIKE source is available at https://github.com/spike-project/spike\n\nSPIKE is written in pure Python, and relies on several external libraries:\n\n- matplotlib\n- numpy\n- scipy\n- tables\n- pandas\n\nIt is compatible and fully tested with python 3.7 and 3.10\n\n### developping for SPIKE\ncheck [Here](DevelopmentGuide.md)\n\n\n\n# 4/ Citing SPIKE\nIf you happen to use SPIKE successfully for your research, please cite it, and refer to this site, as well as the following possible references :\n- **Main Reference**: first publication of the program itself - *rejected from Anal. Chem. with no real critics except that Reviewer 1 said \"too much NMR\", Reviewer 2 said \"too much MS\", !! so I decided to let it on ArXiV*)\n 1. Chiron L., Coutouly M-A., Starck J-P., Rolando C., Delsuc M-A. SPIKE a Processing Software dedicated to Fourier Spectroscopies https://arxiv.org/abs/1608.06777 (2016)\n\nOther references are also related\n- The renewal of Gifa:\n 2. Delsuc M-A. \"Gifa V.4: A complete package for NMR data set processing\" (2020) https://doi.org/10.5281/zenodo.3904595\n- presentation of the automation possibilities in NMR\n 3. Margueritte, L., Markov, P., Chiron, L., Starck, J.-P., Vonthron Sénécheau, C., Bourjot, M., & Delsuc, M.-A. (2018). \"Automatic differential analysis of NMR experiments in complex samples.\" Magn. Reson. Chem., 80(5), 1387. http://doi.org/10.1002/mrc.4683\n- first version of the 2D FT-ICR-MS processing\n 4. van Agthoven, M. A., Chiron, L., Coutouly, M.-A., Delsuc, M.-A. & Rolando, C. \"Two-Dimensional ECD FT-ICR\" \nMass Spectrometry of Peptides and Glycopeptides.\" _Anal Chem_ **84**, 5589-95 (2012).\n- first version of the python set-up on which the current SPIKE is loosely based\n 5. Tramesel, D., Catherinot, V. & Delsuc, M.-A. \"Modeling of NMR processing, toward efficient unattended processing of NMR experiments. _J Magn Reson_ **188**, 56-67 (2007).\n\nref 1) is a general purpose reference, the other ones are more specific.\n\n\n# 5/ Contents of this repository\n\n- [`spike/`](spike) - the python code of the program itself\n- [`doc/`](doc) - a directory containing various files used to generate the documentation\n- [`Notebooks/`](Notebooks) - the repository of the **SpI** notebooks\n- miscelaneous:\n - `QC.py` `QC.txt` a small utility to check the quality of the code using pylint. \n\n\n\n# 6/ Origin of the program\n\n**SPIKE** is originated from the _Gifa_ program, developed by M-A Delsuc and others in `FORTRAN 77` since the late eighties, it still shares similarities, such as command names, or internal data organisation.\n\n_Gifa_ was abandoned around 2005, but it actually experienced a revival in 2020 thanks to the \" *ten years challenge* \" organised by the [ReScience C Journal](https://rescience.github.io/read/). You can find an installable and runnable version here: https://github.com/delsuc/Gifa\n\n_Gifa_ has known several mutations, and finally ended as a partial rewrite called **NPK**.\nThe [NPK](http://abcis.cbs.cnrs.fr/NPK/) program is based on some of the original `FORTRAN` code, wrapped in Java and Python, which allows to control all the program possibilities from the Python level.\nNPK is purely a computing kernel, with no graphical possibilities, and has been used as a kernel embedded in the commercial program NMRNoteBook, commercialized by NMRTEC.\n\nHowever, NPK was showing many weaknesses, mostly due to the 32bits organization, and a poor file format. So, when a strong scientific environment became available in Python, a rewrite in pure Python was undertaken. To this initial project, called NPK-V2, many new functionalities were added, and mostly the capability to work in other spectroscopies than NMR.\n\nAt some point in 2014, we chose to fork NPK-V2 to SPIKE, and made it public.\n\n\n# 6/ Authors and Licence\nCurrent Active authors for SPIKE are:\n\n- Marc-André Delsuc `madelsuc -at- unistra.fr`\n- Laura Duciel `laura.duciel -at- casc4de.eu`\n\nPrevious authors:\n\n- Christian Rolando `christian.rolando -at- univ-lille1.fr`\n- Lionel Chiron `Lionel.Chiron -at- casc4de.eu`\n- Petar Markov `petar.markov -at- igbmc.fr`\n- Marie-Aude Coutouly . `Marie-Aude.COUTOULY - at- datastorm.fr`\n\nCovered code is provided under this license on an \"as is\" basis, without warranty of any kind, either expressed or implied, including, without limitation, warranties that the covered code is free of defects. The entire risk as to the quality and performance of the covered code is with you. Should any covered code prove defective in any respect, you (not the initial developer or any other contributor) assume the cost of any necessary servicing, repair or correction.\n\nDownloading code and datasets from this page signifies acceptance of the hereunder License Agreement. The code distributed here is covered under the CeCILL license : http://www.cecill.info/index.en.html",
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