NDDataset creation and plotting example

In this example, we create a 3D NDDataset from scratch, and then we plot one section (a 2D plane)

Creation

Now we will create a 3D NDDataset from scratch

Data

here we make use of numpy array functions to create the data for coordinates axis and the array of data

import numpy as np

As usual, we start by loading the spectrochempy library

import spectrochempy as scp

c0 = np.linspace(200.0, 300.0, 3)
c1 = np.linspace(0.0, 60.0, 100)
c2 = np.linspace(4000.0, 1000.0, 100)
nd_data = np.array(
    [
        np.array([np.sin(2.0 * np.pi * c2 / 4000.0) * np.exp(-y / 60) for y in c1]) * t
        for t in c0
    ]
)

Coordinates

The Coord object allow making an array of coordinates with additional metadata such as units, labels, title, etc

coord0 = scp.Coord(
    data=c0, labels=["cold", "normal", "hot"], units="K", title="temperature"
)
coord1 = scp.Coord(data=c1, labels=None, units="minutes", title="time-on-stream")
coord2 = scp.Coord(data=c2, labels=None, units="cm^-1", title="wavenumber")

Labels can be useful for instance for indexing

a = coord0["normal"]
print(a)

Coord: [float64] K (size: 1)

nd-Dataset

The NDDataset object allow making the array of data with units, etc…

mydataset = scp.NDDataset(
    nd_data, coordset=[coord0, coord1, coord2], title="Absorbance", units="absorbance"
)
mydataset.description = """Dataset example created for this tutorial.
It's a 3-D dataset (with dimensionless intensity: absorbance )"""
mydataset.name = "An example from scratch"
mydataset.author = "Blake and Mortimer"
print(mydataset)

NDDataset: [float64] a.u. (shape: (z:3, y:100, x:100))

We want to plot a section of this 3D NDDataset:

NDDataset can be sliced like conventional numpy-array…

new = mydataset[..., 0]

or maybe more conveniently in this case, using an axis labels:

new = mydataset["hot"]

To plot a dataset, use the plot command (generic plot). As the section NDDataset is 2D, a contour plot is displayed by default.

new.plot()

<_Axes: xlabel='wavenumber $\\mathrm{/\\ \\mathrm{cm}^{-1}}$', ylabel='Absorbance $\\mathrm{/\\ \\mathrm{a.u.}}$'>

But it is possible to display image

sphinx_gallery_thumbnail_number = 2

new.plot(method="image")

<_Axes: xlabel='wavenumber $\\mathrm{/\\ \\mathrm{cm}^{-1}}$', ylabel='time-on-stream $\\mathrm{/\\ \\mathrm{min}}$'>

or stacked plot

new.plot(method="stack")

<_Axes: xlabel='wavenumber $\\mathrm{/\\ \\mathrm{cm}^{-1}}$', ylabel='Absorbance $\\mathrm{/\\ \\mathrm{a.u.}}$'>

Note that the scp allows one to use this syntax too:

scp.plot_stack(new)

<_Axes: xlabel='wavenumber $\\mathrm{/\\ \\mathrm{cm}^{-1}}$', ylabel='Absorbance $\\mathrm{/\\ \\mathrm{a.u.}}$'>

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

scp.show()