Peak finder

You can use this notebook to find peaks in your data.

Getting everything set up

uv

If you downloaded or cloned this repository, simply run:

uv sync

To set up your virtual environment. You can also add the dependencies listed in pyproject.toml to an existing project's environment.

Run the notebook from Visual Studio Code by selecting the peak-finder .venv as the environment for the kernel or run Jupyter Lab with

uv run jupyter-lab peak-finder.ipynb

uvx

If you just have a copy of the notebook and want to run Jupyter Lab with the required dependencies but without installing anything run

uvx --from jupyterlab --with ipympl,matplotlib,numpy,pandas,scipy jupyter-lab peak-finder.ipynb

Conda (Anaconda or Miniconda)

To create a conda environment with Jupyter Lab and all dependencies, run:

$ conda env create -f environment.yml

Run Jupyter Lab with

$ conda activate peak-finder
$ jupyter lab peak-finder.ipynb

and load the notebook, or run the notebook from e.g. Visual Studio Code while selecting the peak-finder conda environment.

Running the notebook

At the bottom of the notebook you will find this line:

find_peaks("example-datafile.csv")

Change example-datafile.csv to point at your data file or just run the notebook with the example data. You should see something like this:

You can zoom into parts of your dataset and tweak the settings until you're satisfied with the detected peaks.