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'''
Runs unit tests of functions associated with spectral databases.
To run the unit tests, type the following from the system command line:
# python -m spectral.tests.database
Note that the ECOSTRESS database must be requested so if the data files are
not located on the local file system, these tests will be skipped.
'''
from __future__ import absolute_import, division, print_function, unicode_literals
import numpy as np
import os
from numpy.testing import assert_almost_equal
import spectral as spy
from spectral.io.aviris import read_aviris_bands
from spectral.tests import testdir
from spectral.tests.spytest import SpyTest
ECOSTRESS_DATA_DIR = os.path.join(os.path.split(__file__)[0],
'data/ecostress')
ECOSTRESS_DB = os.path.join(testdir, 'ecostress.db')
USGS_DATA_DIR = os.path.join(os.path.split(__file__)[0],
'data/usgs/ASCIIdata')
USGS_DB = os.path.join(testdir, 'usgs.db')
AVIRIS_BAND_FILE = os.path.join(os.path.split(__file__)[0], 'data/92AV3C.spc')
class ECOSTRESSDatabaseCreationTest(SpyTest):
'''Tests ECOSTRESS database creation from text files.'''
def __init__(self):
pass
def setup(self):
if not os.path.isdir(testdir):
os.makedirs(testdir)
if os.path.exists(ECOSTRESS_DB):
os.remove(ECOSTRESS_DB)
def test_create_database(self):
'''Test creating new database from ECOSTRESS data files.'''
db = spy.EcostressDatabase.create(ECOSTRESS_DB,
ECOSTRESS_DATA_DIR)
assert(list(db.query('SELECT COUNT() FROM Spectra'))[0][0] == 3)
class ECOSTRESSDatabaseTest(SpyTest):
'''Tests that ECOSTRESS database works properly'''
def __init__(self):
pass
def setup(self):
self.db = spy.EcostressDatabase(ECOSTRESS_DB)
def test_read_signatures(self):
'''Can get spectra from the opened database.'''
assert(list(self.db.query('SELECT COUNT() FROM Spectra'))[0][0] == 3)
def test_create_envi_lib(self):
'''Can resample spectra and create an ENVI spectral library.'''
bands = read_aviris_bands(AVIRIS_BAND_FILE)
cursor = self.db.query('SELECT SpectrumID FROM Spectra')
ids = [r[0] for r in cursor]
bands.centers = [x / 1000. for x in bands.centers]
bands.bandwidths = [x / 1000. for x in bands.bandwidths]
slib = self.db.create_envi_spectral_library(ids, bands)
assert(slib.spectra.shape == (3, 220))
class USGSDatabaseCreationTest(SpyTest):
'''Tests USGS database creation from text files.'''
def __init__(self):
pass
def setup(self):
if not os.path.isdir(testdir):
os.makedirs(testdir)
if os.path.exists(USGS_DB):
os.remove(USGS_DB)
def test_create_database(self):
'''Test creating new database from USGS data files.'''
db = spy.USGSDatabase.create(USGS_DB, USGS_DATA_DIR)
assert(list(db.query('SELECT COUNT() FROM Samples'))[0][0] == 8)
assert(list(db.query('SELECT COUNT() FROM SpectrometerData'))
[0][0] == 13)
class USGSDatabaseTest(SpyTest):
'''Tests that USGS database works properly'''
def __init__(self):
pass
def setup(self):
self.db = spy.USGSDatabase(USGS_DB)
def test_read_signatures(self):
'''Can get spectra from the opened database.'''
assert(list(self.db.query('SELECT COUNT() FROM Samples'))[0][0] == 8)
assert(list(self.db.query('SELECT COUNT() FROM SpectrometerData'))
[0][0] == 13)
some_sample = list(self.db.query('''SELECT Chapter, FileName,
AssumedWLSpmeterDataID,
NumValues, MinValue, MaxValue
FROM Samples
WHERE LibName='liba' AND Record=1 AND
Description='Material a b0 0 ASDFRa AREF' AND
Spectrometer='ASDFR' AND Purity='a' AND MeasurementType='AREF'
'''))[0]
assert(some_sample[0] == 'ChapterB_b0')
assert(some_sample[1] == 'liba_Material_a_b0_0_ASDFRa_AREF.txt')
assert(some_sample[3] == 24)
assert_almost_equal(some_sample[4], 0.33387077)
assert_almost_equal(some_sample[5], 0.51682192)
some_spectrometer_data = list(self.db.query('''SELECT LibName, Record, MeasurementType, Unit,
Name, Description, FileName, NumValues, MinValue, MaxValue
FROM SpectrometerData
WHERE SpectrometerDataID=?
''', (some_sample[2],)))[0]
assert(some_spectrometer_data[0] == 'liba')
assert(some_spectrometer_data[1] == 13)
assert(some_spectrometer_data[2] == 'Wavelengths')
assert(some_spectrometer_data[3] == 'micrometer')
assert(some_spectrometer_data[4] == 'ASD')
assert(some_spectrometer_data[5] == 'Wavelengths ASD 0.35-2.5 um')
assert(some_spectrometer_data[6] ==
'liba_Wavelengths_ASD_0.35-2.5_um.txt')
assert(some_spectrometer_data[7] == 24)
assert_almost_equal(some_spectrometer_data[8], 0.35)
assert_almost_equal(some_spectrometer_data[9], 2.5)
def test_get_spectrum(self):
some_sample_id = list(self.db.query('''SELECT SampleID
FROM Samples
WHERE LibName='libc' AND Description='Material D 2 AVIRISb RTGC'
'''))[0][0]
(x, y) = self.db.get_spectrum(some_sample_id)
assert(len(x) == len(y))
assert(len(y) == 7)
assert_almost_equal(y[0], 0.010381651)
assert_almost_equal(x[-1], 2.2020326)
def test_create_envi_lib(self):
'''Can resample spectra and create an ENVI spectral library.'''
bands = read_aviris_bands(AVIRIS_BAND_FILE)
cursor = self.db.query('SELECT SampleID FROM Samples')
ids = [r[0] for r in cursor]
bands.centers = [x / 1000. for x in bands.centers]
bands.bandwidths = [x / 1000. for x in bands.bandwidths]
slib = self.db.create_envi_spectral_library(ids, bands)
assert(slib.spectra.shape == (8, 220))
def run():
print('\n' + '-' * 72)
print('Running database tests.')
print('-' * 72)
for T in [ECOSTRESSDatabaseCreationTest, ECOSTRESSDatabaseTest, USGSDatabaseCreationTest, USGSDatabaseTest]:
T().run()
if __name__ == '__main__':
from spectral.tests.run import parse_args, reset_stats, print_summary
import logging
logging.getLogger('spectral').setLevel(logging.ERROR)
parse_args()
reset_stats()
run()
print_summary()
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