charlesll / rampy

Python software for spectral data processing (IR, Raman, XAS...)

RamPy

=======

Rampy is a Python library that aims at helping processing spectroscopic data, such as Raman, Infrared or XAS spectra.

• Documentation: http://charlesll.github.io/rampy/html/index.html
• Examples https://github.com/charlesll/rampy/tree/master/examples
• Source code: https://github.com/charlesll/rampy/tree/master/rampy
• Contributing: https://github.com/charlesll/rampy/blob/master/CONTRIBUTING.md
• Bug reports: https://github.com/charlesll/rampy/issues
• Contact [email protected]

Rampy offers various functions to, for instance, subtract baselines, resample and smooth spectra... It aims at facilitating the use of Python in processing spectroscopic data. It integrates within a workflow that uses Numpy/Scipy/Matplotlib as well as optimisation libraries such as lmfit, emcee or PyMC3, for instance.

See the documentation for more information.

rampy's Issues

pseudovoigt() not working with arrays

While they were not originally designed to do so, it is possible to pass arrays of x and parameters to gaussian() or lorentzian().

This does not work with pseudovoigt() because of the test line 105 of functions.py

Re

Re

The log baseline needs to be checked

log version of baseline needs improvement and to be included in tests.

Add mlclassification function

As there is mlregressor and mlexplorer functions, I want to add a mlclassification function.

In particular, this could make use of 1D CNN via Keras.

Any comment/feedback/help welcome!

rubberband option in baseline not working with Python 3 kernel

There is a problem with ConvexHull line 201...

rampy.normalize error when asking "area"

y_fit = rp.normalise(y_fit,x=x_fit,method="area") yields an error:

184 if method == "area": --> 185 if x == 0: 186 raise TypeError("Input x values for area normalisation") 187 y = y/np.trapz(y,x)
I will correct this error in rampy v0.4.3, releasing it today.

ModuleNotFoundError: No module named 'rampy'

Hello, I am trying to import the rampy package but I get an error. I am launching it from Google Collaborator. It worked fine last year.

!pip install rampy
import rampy

Requirement already satisfied: rampy in /usr/local/lib/python3.10/dist-packages (0.5.1)
Requirement already satisfied: numpy>=1.12 in /usr/local/lib/python3.10/dist-packages (from rampy) (1.23.5)
Requirement already satisfied: scipy in /usr/local/lib/python3.10/dist-packages (from rampy) (1.11.4)
Requirement already satisfied: scikit-learn in /usr/local/lib/python3.10/dist-packages (from rampy) (1.2.2)
Requirement already satisfied: pandas in /usr/local/lib/python3.10/dist-packages (from rampy) (1.5.3)
Requirement already satisfied: xlrd in /usr/local/lib/python3.10/dist-packages (from rampy) (2.0.1)
Requirement already satisfied: matplotlib in /usr/local/lib/python3.10/dist-packages (from rampy) (3.7.1)
Requirement already satisfied: contourpy>=1.0.1 in /usr/local/lib/python3.10/dist-packages (from matplotlib->rampy) (1.2.0)
Requirement already satisfied: cycler>=0.10 in /usr/local/lib/python3.10/dist-packages (from matplotlib->rampy) (0.12.1)
Requirement already satisfied: fonttools>=4.22.0 in /usr/local/lib/python3.10/dist-packages (from matplotlib->rampy) (4.47.2)
Requirement already satisfied: kiwisolver>=1.0.1 in /usr/local/lib/python3.10/dist-packages (from matplotlib->rampy) (1.4.5)
Requirement already satisfied: packaging>=20.0 in /usr/local/lib/python3.10/dist-packages (from matplotlib->rampy) (23.2)
Requirement already satisfied: pillow>=6.2.0 in /usr/local/lib/python3.10/dist-packages (from matplotlib->rampy) (9.4.0)
Requirement already satisfied: pyparsing>=2.3.1 in /usr/local/lib/python3.10/dist-packages (from matplotlib->rampy) (3.1.1)
Requirement already satisfied: python-dateutil>=2.7 in /usr/local/lib/python3.10/dist-packages (from matplotlib->rampy) (2.8.2)
Requirement already satisfied: pytz>=2020.1 in /usr/local/lib/python3.10/dist-packages (from pandas->rampy) (2023.3.post1)
Requirement already satisfied: joblib>=1.1.1 in /usr/local/lib/python3.10/dist-packages (from scikit-learn->rampy) (1.3.2)
Requirement already satisfied: threadpoolctl>=2.0.0 in /usr/local/lib/python3.10/dist-packages (from scikit-learn->rampy) (3.2.0)
Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.10/dist-packages (from python-dateutil>=2.7->matplotlib->rampy) (1.16.0)

ModuleNotFoundError Traceback (most recent call last)
in <cell line: 3>()
1 get_ipython().system('pip install rampy')
2
----> 3 import rampy

ModuleNotFoundError: No module named 'rampy'

If I use:
!apt install rampy
import rampy

Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
E: Unable to locate package rampy

ModuleNotFoundError Traceback (most recent call last)
in <cell line: 3>()
1 get_ipython().system('apt install rampy')
2
----> 3 import rampy

ModuleNotFoundError: No module named 'rampy'

Does anyone know how to fix this or what is wrong?

Thanks!
Laura

read_horiba function may return bad raman shifts (as string)

We need to change in the function:

lambdas=df.columns.values[2:]

to

lambdas=df.columns.values[2:].values

For now, a quick fix is to add the line

my_map.w = my_map.w.astype(float)

after generating your map object.

Bug in tlcorrection

If using normalisation="no" in tlcorrection, this yields an error as ycorr is not calculated.

Add parametric and non-parametric bootstrap functions

Like in Spectra.jl... But is it really good? Slow? May speed up thing with the use of Cython?

emcee error analysis in peak fitting example

To replace bootstrapping

Code quality needs improvement

Here is an incomplete list of the issues in the project.

1. https://github.com/charlesll/rampy/blob/master/rampy/filters.py#L94
   say 1000 times "eval is a performance and security issue, it is almost never needed, I will never use eval for anything for which there exist other means, and even if I had to use eval, I promise to be very cautionous" . There is getattr for your use case.

2. https://github.com/charlesll/rampy/blob/master/setup.py#L18
   Say 1000 times "I will be extremily careful when referencing other packages. I will always make sure that the package I reference is the one meant". There already has been malware spread by exploiting people making typos in package names.

3. https://github.com/charlesll/rampy/blob/master/rampy/filters.py#L88
   checking in an array is inefficient, you need a preconstructed frozenset

4. ./raw/ WUT? I guess this path is valid only for your computer.

5. https://github.com/charlesll/rampy/blob/master/rampy/filters.py#L173 - repeated line, should be refactored

6. https://github.com/charlesll/rampy/blob/master/rampy/__init__.pyc - pyc files must not be present in a repo. (P.S. I see that you use Windows, your user name is charles and you still use python 2.7 in 2019 even though it is completely unneeded and is being dropped)

merge with scikit-spectra

https://github.com/hugadams/scikit-spectra

but it seems to be abandoned (you may want to become a new maintainer). It may make sense to merge some pieces of your code into it and then retire rampy.

path error in rameau

path_in in rameau is an optional argument, but actually is not used in the code.

This should be corrected asap.

Rameau error when not setting p values for predictions

Lines 175 and 185, we test if p.size > 0 but if we want to use the default values, this does not work as p is an empty list.

synergies with infrared emission code?

Hello,

I see that rampy is used to process IR spectra, but I do not know the needs of the geophysicist community : I've developed a high-resolution infrared emission code for gases, called RADIS. Do you ever need to calculate such spectra?

In that case, I'm considering updating my code (https://github.com/radis/radis) to make the output compatible with the rampy analysis tools

multigaussian function is not good and needs a re-write

the multigaussian function is not functional. It needs either to be dropped, or re-written.

add ATR correction

Implementation of the ATR infrared correction for treating ATR spectra would be great!

[Suggestion] Applying the neighbour parameter to the averaging function

Description of the suggestion
In the current state, the neigh parameter in the despiking function is only used to define the numbers of points around the spikes to calculate the replacement value for the spike.

Use case/Problem
The despiking function does not work as intended on our dataset, as the spikes seem to be broader than the default window size for the smoothing function.

Suggestion
A more flexible approach would be to allow the user to specify the window size for the smoothing function.
My suggestion would be to pass the neigh parameter to the smoothing function.

I will provide a PR in a due course.

Raman maps from Renishaw spectrometer

I think it is valuable to add new functionality- possibility to read and analyse Raman maps taken from spectrometers like Renishaw or Horiba. I have already done it on Ammon1/spectroscopy repo. Part of it is reading of (quite havy Renishaw type of files) and change it to Horiba-like (much more elegant). Next step is to make possibility to analize peak params and save it as maps of params-very usefull in Raman spectroscopy in solid state physics.
My code is based on pandas and numpy. It is not very elegant because it is quite old but I may update and upgrade it.

Documentation needs updates

The documentation is sparse and needs updates...

Incorrect data path in example

The data path is incorrect in the 4th code cell of Raman_spectrum_fitting, causing import to fail.

Import line should be:

inputsp = np.genfromtxt("data/LS4.txt",skip_header=20, skip_footer=43)

rampy maps : need an area function

We need to add a function to calculate the area under the spectra given wavenumbers.

Move the metadata into setup.cfg

https://github.com/gvalkov/setuptools-py2cfg automates setup.cfg generation. Reading some metadata from files can also be configured via it. Your setup.py should look like

from setuptools import setup
setup(use_scm_version=True)