# -*- coding: utf-8 -*-
# ======================================================================================
# Copyright (©) 2015-2023 LCS - Laboratoire Catalyse et Spectrochimie, Caen, France.
# CeCILL-B FREE SOFTWARE LICENSE AGREEMENT
# See full LICENSE agreement in the root directory.
# ======================================================================================
"""
In this module, methods are provided to download external datasets
from public database.
"""
__all__ = ["load_iris", "download_nist_ir"]
__dataset_methods__ = __all__
from pathlib import Path
import requests
from spectrochempy.application import error_, info_
from spectrochempy.core.dataset.coord import Coord
from spectrochempy.core.dataset.nddataset import NDDataset
from spectrochempy.core.readers.read_jcamp import read_jcamp
from spectrochempy.utils.misc import is_iterable
[docs]def load_iris():
"""
Upload the classical "iris" dataset.
The "IRIS" dataset is a classical example for machine learning.
It is read from the `scikit-learn` package.
Returns
-------
dataset
The `IRIS` dataset.
See Also
--------
read : Read data from experimental data.
"""
from sklearn.datasets import load_iris as sklearn_iris
data = sklearn_iris()
coordx = Coord(
labels=["sepal_length", "sepal width", "petal_length", "petal_width"],
title="features",
)
labels = [data.target_names[i] for i in data.target]
coordy = Coord(labels=labels, title="samples")
new = NDDataset(
data.data,
coordset=[coordy, coordx],
title="size",
name="`IRIS` Dataset",
units="cm",
)
new.history = "Loaded from scikit-learn datasets"
return new
[docs]def download_nist_ir(CAS, index="all"):
"""
Upload IR spectra from NIST webbook
Parameters
----------
CAS : int or str
the CAS number, can be given as "XXXX-XX-X" (str), "XXXXXXX" (str), XXXXXXX (int)
index : str or int or tuple of ints
If set to 'all' (default, import all available spectra for the compound
corresponding to the index, or a single spectrum, or selected spectra.
Returns
-------
list of NDDataset or NDDataset
The dataset(s).
See Also
--------
read : Read data from experimental data.
"""
if isinstance(CAS, str) and "-" in CAS:
CAS = CAS.replace("-", "")
if index == "all":
# test urls and return list if any...
index = []
i = 0
while "continue":
url = (
f"https://webbook.nist.gov/cgi/cbook.cgi?JCAMP=C{CAS}&Index={i}&Type=IR"
)
try:
response = requests.get(url, timeout=10)
if b"Spectrum not found" in response.content[:30]:
break
else:
index.append(i)
i += 1
except OSError:
raise OSError("Cannot connect to the NIST server... ")
if len(index) == 0:
error_(IOError, "NIST IR: no spectrum found")
return
elif len(index) == 1:
info_("NIST IR: 1 spectrum found")
else:
info_("NISTR IR: {len(index)} spectra found")
elif isinstance(index, int):
index = [index]
elif not is_iterable(index):
raise ValueError("index must be 'all', int or iterable of int")
out = []
for i in index:
# sample adress (water, spectrum 1)
# https://webbook.nist.gov/cgi/cbook.cgi?JCAMP=C7732185&Index=1&Type=IR
url = f"https://webbook.nist.gov/cgi/cbook.cgi?JCAMP=C{CAS}&Index={i}&Type=IR"
try:
response = requests.get(url, stream=True, timeout=10)
if b"Spectrum not found" in response.content[:30]:
error_(
IOError, f"NIST IR: Spectrum {i} does not exist... please check !"
)
if i == index[-1] and out == []:
return None
else:
break
except OSError:
error_("OSError: Cannot connect... ")
return None
# Load data
txtdata = ""
for rd in response.iter_content():
txtdata += rd.decode("utf8")
with open("temp.jdx", "w") as f:
f.write(txtdata)
try:
ds = read_jcamp("temp.jdx")
# replace the default entry ":imported from jdx file":
ds.history[0] = f"Downloaded from NIST: {url}"
out.append(ds)
(Path(".") / "temp.jdx").unlink()
except Exception:
raise IOError(
"Can't read this JCAMP file: please report the issue to Spectrochempy developpers"
)
if len(out) == 1:
return out[0]
else:
return out