Warning

You are reading the documentation related to the development version. Go here if you are looking for the documentation of the stable release.

Reading datasets

In this example, we show the use of the generic read method to create dataset either from local or remote files.

First we need to import the spectrochempy API package

import spectrochempy as scp

Import dataset from local files

Read a IR data recorded in Omnic format (.spg extension). We just pass the file name as parameter.

dataset = scp.read("irdata/nh4y-activation.spg")
dataset

name	nh4y-activation
author	runner@fv-az1501-19
created	2024-04-28 03:07:18+02:00
description	Omnic title: NH4Y-activation.SPG Omnic filename: /home/runner/.spectrochempy/testdata/irdata/nh4y-activation.spg
history	2024-04-28 03:07:18+02:00> Imported from spg file /home/runner/.spectrochempy/testdata/irdata/nh4y-activation.spg. 2024-04-28 03:07:18+02:00> Sorted by date
DATA
title	absorbance
values	[[ 2.057 2.061 ... 2.013 2.012] [ 2.033 2.037 ... 1.913 1.911] ... [ 1.794 1.791 ... 1.198 1.198] [ 1.816 1.815 ... 1.24 1.238]] a.u.
shape	(y:55, x:5549)
DIMENSION `x`
size	5549
title	wavenumbers
coordinates	[ 6000 5999 ... 650.9 649.9] cm⁻¹
DIMENSION `y`
size	55
title	acquisition timestamp (GMT)
coordinates	[1.468e+09 1.468e+09 ... 1.468e+09 1.468e+09] s
labels	[[ 2016-07-06 19:03:14+00:00 2016-07-06 19:13:14+00:00 ... 2016-07-07 04:03:17+00:00 2016-07-07 04:13:17+00:00] [ vz0466.spa, Wed Jul 06 21:00:38 2016 (GMT+02:00) vz0467.spa, Wed Jul 06 21:10:38 2016 (GMT+02:00) ... vz0520.spa, Thu Jul 07 06:00:41 2016 (GMT+02:00) vz0521.spa, Thu Jul 07 06:10:41 2016 (GMT+02:00)]]

_ = dataset.plot(style="paper")

When using read, we can pass filename as a str or a Path object.

from pathlib import Path

filename = Path("irdata/nh4y-activation.spg")
dataset = scp.read(filename)

Note that is the file is not found in the current working directory, SpectroChemPy will try to find it in the datadir directory defined in preferences :

datadir = scp.preferences.datadir
datadir

PosixPath('/home/runner/.spectrochempy/testdata')

If the supplied argument is a directory, then the whole directory is read at once. By default, the different files will be merged along the first dimension (y). However, for this to work, the second dimension (x) must be compatible (same size) or else a WARNING appears. To avoid the warning and get individual spectra, you can set merge to False .

dataset_list = scp.read("irdata", merge=False)
dataset_list

[NDDataset: [float64] a.u. (shape: (y:19, x:3112)), NDDataset: [float64] a.u. (shape: (y:55, x:5549)), NDDataset: [float64] unitless (shape: (y:1, x:3736))]

to get full details on the parameters that can be used, look at the API documentation: spectrochempy.read .

Import dataset from remote files

To download and read file from remote server you can use urls.

dataset_list = scp.read("http://www.eigenvector.com/data/Corn/corn.mat")

In this case the matlab data contains 7 arrays that have been automatically transformed to NDDataset .

for nd in dataset_list:
    print(f"{nd.name} : {nd.shape}")

m5nbs : (3, 700)
mp5nbs : (4, 700)
mp6nbs : (4, 700)
propvals : (80, 4)
m5spec : (80, 700)
mp5spec : (80, 700)
mp6spec : (80, 700)

The eigenvector.com website contains the same data in a compressed (zipped) format: corn.mat_.zip . This can also be used by the read method.

dataset_list = scp.read(
    "https://eigenvector.com/wp-content/uploads/2019/06/corn.mat_.zip"
)
_ = dataset_list[-1].plot()
_ = dataset_list[-2].plot()
_ = dataset_list[-3].plot()
_ = dataset_list[-4].plot()

• 
• 
• 
• 

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

# scp.show()