From a02369746c5fbefef0640aff7a0a6aa349aaae2d Mon Sep 17 00:00:00 2001
From: lanery <ryanilane@gmail.com>
Date: Mon, 24 Feb 2025 14:43:21 -0800
Subject: [PATCH 1/2] Update spectra.py

- add a class method for a "generic" reader that assumes the convention that many vendors abide by in which the first column of a csv file is the wavenumber data and the second column is the intensity data
---
 ramanalysis/spectra.py | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/ramanalysis/spectra.py b/ramanalysis/spectra.py
index eb0ecdb..2bbd007 100644
--- a/ramanalysis/spectra.py
+++ b/ramanalysis/spectra.py
@@ -5,6 +5,7 @@
 from typing import cast
 
 import numpy as np
+import pandas as pd
 from scipy.signal import find_peaks, medfilt
 
 from .calibrate import (
@@ -138,6 +139,18 @@ def from_wasatch_csvfile(cls, csv_filepath: Path | str) -> RamanSpectrum:
         wavenumbers_cm1, intensities, _metadata = read_wasatch_csv(csv_filepath)
         return RamanSpectrum(wavenumbers_cm1, intensities)
 
+    @classmethod
+    def from_generic_csvfile(
+        cls,
+        csv_filepath: Path | str,
+        wavenumber_cm1_index: int = 0,
+        intensity_index: int = 1,
+        **kwargs,
+    ) -> RamanSpectrum:
+        """"""
+        data = pd.read_csv(csv_filepath, **kwargs).values  # type: ignore
+        return RamanSpectrum(wavenumbers_cm1=data[:, 0], intensities=data[:, 1])
+
     @property
     def snr(self) -> float:
         raise NotImplementedError("TODO: SNR calculation hasn't been implemented.")

From fbd3b7f4e47487ba9a9622968cf99750978c1bf9 Mon Sep 17 00:00:00 2001
From: lanery <ryanilane@gmail.com>
Date: Mon, 24 Feb 2025 16:35:28 -0800
Subject: [PATCH 2/2] Update spectra.py

- add docstring
- actually use the wavenumber and intensity index arguments to choose the appropriate columns
---
 ramanalysis/spectra.py | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/ramanalysis/spectra.py b/ramanalysis/spectra.py
index 2bbd007..ee85ff4 100644
--- a/ramanalysis/spectra.py
+++ b/ramanalysis/spectra.py
@@ -147,9 +147,21 @@ def from_generic_csvfile(
         intensity_index: int = 1,
         **kwargs,
     ) -> RamanSpectrum:
-        """"""
+        """Load a Raman spectrum from a CSV file for which there is no pre-defined reader.
+
+        Most data files from Raman spectrometer manufacturers follow a convention where the first
+        column contains the wavenumbers and the second column contains the intensities. Where
+        they vary is in e.g. the delimiter character, the number of rows of metadata, etc. This
+        function assumes this generic format and creates a spectrum object from the data by passing
+        keyword arguments to :func:`pd.read_csv` to support a range of possible formats.
+
+        See also:
+            - https://pandas.pydata.org/docs/reference/api/pandas.read_csv.html
+        """
         data = pd.read_csv(csv_filepath, **kwargs).values  # type: ignore
-        return RamanSpectrum(wavenumbers_cm1=data[:, 0], intensities=data[:, 1])
+        wavenumbers_cm1 = data[:, wavenumber_cm1_index]
+        intensities = data[:, intensity_index]
+        return RamanSpectrum(wavenumbers_cm1, intensities)
 
     @property
     def snr(self) -> float: