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Reading Renishaw WiRE files

This example shows how to read a Renishaw WiRE files (.wdf format).

The spectral data used has been downloaded from https://github.com/alchem0x2A/py-wdf-reader (MIT License) and stored in the local directory ramandata/wire.

The examples given here is a modified version of the original examples: See https://github.com/alchem0x2A/py-wdf-reader/blob/master/examples

First we need to import the spectrochempy API package

import spectrochempy as scp

Import dataset from local files Read Raman data recorded in WiRe format (.wdf extension). We just pass the file name as parameter.

First read a single spectrum (measurement type : single)

dataset = scp.read_wire("ramandata/wire/sp.wdf")  # or read_wdf (or read)
_ = dataset.plot()

Now read a series of spectra (measurement type : series) from a Z-depth scan.

dataset = scp.read_wdf("ramandata/wire/depth.wdf")
_ = dataset.plot(method="image")

In this example, the diverging colormap is triggered because the dataset contains few, but some negative values. If the smaller lobe is at larger than diverging_margin (default 5%) of the total # range, i.e. if the following condition is satisfied:

min(|vmin|, |vmax|) / (vmax - vmin) > margin

Then a diverging colormap is used.

To avoid this behavior, you can explicitly enforce a sequential colormap, for example “viridis”:

_ = dataset.plot_image(cmap="cividis")

Alternatively, you can increase the diverging_margin that determines when the diverging colormap is applied. Then the default sequential colormap (`viridis’) will be used:

_ = dataset.plot(method="image", diverging_margin=0.1)

filter blank spectra

import numpy as np

keep_rows = np.where(dataset.data.mean(axis=1) > 0)[0]
dataset = dataset[keep_rows]
_ = dataset.plot_image()

extract a line scan data from a StreamLine HR measurement

dataset = scp.read("ramandata/wire/line.wdf")
_ = dataset.plot_image()

finally extract grid scan data from a StreamLine HR measurement

dataset = scp.read_wdf("ramandata/wire/mapping.wdf")
# plot the dataset as an image (summming all wavenumbers)
_ = dataset.sum(dim=2).plot_image(equal_aspect=True)
# plot the image taken at 1529cm-1
_ = dataset[..., 1529.0].plot_image(equal_aspect=True)

• 
• 

/home/runner/work/spectrochempy/spectrochempy/src/spectrochempy/core/readers/read_wire.py:190: UserWarning: Map area type is not specified, will assume a xy (column major) scan for the mapping data.
  warning_(

This ends the example ! The following line can be uncommented if no plot shows when running the .py script with python

# scp.show()