def test_fsm_format():
filename = load_fsm_path()
R = Request(filename)
F = formats['FSM']
assert F.can_read(R)
reader = F.get_reader(R)
assert reader.get_length() == 7998
assert reader.get_meta_data()['signature'] == b'PEPE'
spec = reader.get_data()
assert spec.spectrum.shape == (7998, 1641)
assert spec.wavelength.shape == (1641, )
spec = reader.get_data(0)
assert spec.spectrum.shape == (1641, )
assert spec.wavelength.shape == (1641, )
assert spec.spectrum[0] == pytest.approx(38.656551)
def test_load_fsm_path():
path_data = load_fsm_path()
assert 'datasets/data/spectra.fsm' in path_data
"""
==============================================
Read FSM Perkin Elmer Spotlight IR binary file
==============================================
This example shows how to read FSM file and plot the results.
"""
from __future__ import print_function
import matplotlib.pyplot as plt
from specio import specread
from specio.datasets import load_fsm_path
# Find the path to the FSM toy data
fsm_filename = load_fsm_path()
print(fsm_filename)
# Read the data
spectra = specread(fsm_filename)
# Plot the first spectra
plt.plot(spectra.wavelength,
spectra.spectrum[0])
plt.show()
"""Test that all spectra files are retrieved."""
# Copyright (c) 2017
# Authors: Guillaume Lemaitre <*****@*****.**>
# License: BSD 3 clause
from os.path import join
import pytest
from specio.datasets import load_fsm_path
from specio.datasets import load_mzml_path
from specio.datasets import load_sp_path
from specio.datasets import load_spc_path
from specio.datasets import load_csv_path
@pytest.mark.parametrize("path_data,extension", [(load_fsm_path(), 'fsm'),
(load_mzml_path(), 'mzml'),
(load_sp_path(), 'sp'),
(load_spc_path(), 'spc'),
(load_csv_path(), 'csv')])
def test_load_spectra_path(path_data, extension):
assert join('datasets', 'data', 'spectra.' + extension) in path_data
if isinstance(spec.meta, tuple):
for m in spec.meta:
if filename_cmp:
assert m['filename'] == basename(filename)
else:
assert m['filename']
else:
if filename_cmp:
assert spec.meta['filename'] == basename(filename)
else:
assert spec.meta['filename']
@pytest.mark.parametrize(
"filename,filename_cmp,spectrum_shape,wavelength_shape",
[(load_fsm_path(), True, (7998, 1641), (1641,)),
(load_spc_path(), True, (1911,), (1911,)),
(load_sp_path(), True, (3301,), (3301,)),
pytest.param(load_mzml_path(), True, (282,), (282,),
marks=skip_windows_py27()),
(load_csv_path(), False, (84, 1732,), (1732,))])
def test_specread(filename, filename_cmp, spectrum_shape, wavelength_shape):
spec = specread(filename)
if isinstance(spec, Spectrum):
_check_spectra(spec, filename, filename_cmp, spectrum_shape,
wavelength_shape)
elif isinstance(spec, list):
assert all([isinstance(sp, Spectrum) for sp in spec])
sp = spec[0]
_check_spectra(sp, filename, filename_cmp, spectrum_shape,
wavelength_shape)