def test_locate_sample_datasets(self):
with self.assertRaises(OSError):
FileFormat.locate("iris.tab", search_dirs=[os.path.dirname(__file__)])
iris = FileFormat.locate("iris.tab", search_dirs=[get_sample_datasets_dir()])
self.assertEqual(os.path.basename(iris), "iris.tab")
# test extension adding
iris = FileFormat.locate("iris", search_dirs=[get_sample_datasets_dir()])
self.assertEqual(os.path.basename(iris), "iris.tab")
def test_locate_sample_datasets(self):
with self.assertRaises(OSError):
FileFormat.locate("iris.tab",
search_dirs=[os.path.dirname(__file__)])
iris = FileFormat.locate("iris.tab",
search_dirs=[get_sample_datasets_dir()])
self.assertEqual(os.path.basename(iris), "iris.tab")
# test extension adding
iris = FileFormat.locate("iris",
search_dirs=[get_sample_datasets_dir()])
self.assertEqual(os.path.basename(iris), "iris.tab")
def test_locate_wildcard_extension(self):
tempdir = tempfile.mkdtemp()
with self.assertRaises(OSError):
FileFormat.locate("t.wild9", search_dirs=[tempdir])
fn = os.path.join(tempdir, "t.wild8")
with open(fn, "wt") as f:
f.write("\n")
l = FileFormat.locate("t.wild8", search_dirs=[tempdir])
self.assertEqual(l, fn)
# test extension adding
l = FileFormat.locate("t", search_dirs=[tempdir])
self.assertEqual(l, fn)
shutil.rmtree(tempdir)
def test_locate_wildcard_extension(self):
tempdir = tempfile.mkdtemp()
with self.assertRaises(OSError):
FileFormat.locate("t.wild9", search_dirs=[tempdir])
fn = os.path.join(tempdir, "t.wild8")
with open(fn, "wt") as f:
f.write("\n")
l = FileFormat.locate("t.wild8", search_dirs=[tempdir])
self.assertEqual(l, fn)
# test extension adding
l = FileFormat.locate("t", search_dirs=[tempdir])
self.assertEqual(l, fn)
shutil.rmtree(tempdir)
def initialize_reader(reader, fn):
"""
Returns an initialized reader with the file that can be relative
to Orange's default data set directories.
"""
absolute_filename = FileFormat.locate(fn, Orange.data.table.dataset_dirs)
return reader(absolute_filename)
def setUp(self):
self.widget = self.create_widget(OWFFT)
self.ifg_single = Orange.data.Table("IFG_single.dpt")
self.ifg_seq = Orange.data.Table("agilent/4_noimage_agg256.seq")
fn = 'NeaReaderGSF_test/NeaReaderGSF_test O2A raw.gsf'
absolute_filename = FileFormat.locate(fn, dataset_dirs)
self.ifg_gsf = NeaReaderGSF(absolute_filename).read()
def main(argv=sys.argv):
from orangecontrib.spectroscopy.io.neaspec import NeaReaderGSF
from Orange.data.io import FileFormat
from Orange.data import dataset_dirs
fn = 'NeaReaderGSF_test/NeaReaderGSF_test O2A raw.gsf'
absolute_filename = FileFormat.locate(fn, dataset_dirs)
data = NeaReaderGSF(absolute_filename).read()
app = QApplication(list(argv))
filename = "IFG_single.dpt"
ow = OWFFT()
ow.show()
ow.raise_()
dataset = Orange.data.Table(filename)
dataset = data #ComplexFFT, this line can be commented
ow.set_data(dataset)
ow.handleNewSignals()
app.exec_()
ow.set_data(None)
ow.handleNewSignals()
return 0
def test_read(self):
fn = 'NeaReaderGSF_test/NeaReaderGSF_test O2P raw.gsf'
absolute_filename = FileFormat.locate(fn, dataset_dirs)
data = NeaReaderGSF(absolute_filename).read()
self.assertEqual(len(data), 2)
self.assertEqual("run", data.domain.metas[2].name)
self.assertEqual("O2A", data.metas[0][3])
np.testing.assert_almost_equal(data.X[0, 0], 0.734363853931427)
self.assertEqual("O2P", data.metas[1][3])
np.testing.assert_almost_equal(data.X[1, 43], 0.17290098965168)
def test_open_v2(self):
fn = "nea_test_v2.txt"
absolute_filename = FileFormat.locate(fn, dataset_dirs)
data = NeaReader(absolute_filename).read()
self.assertEqual(len(data), 12)
self.assertEqual("channel", data.domain.metas[2].name)
np.testing.assert_almost_equal(getx(data), [15., 89.])
self.assertEqual("O0A", data.metas[0][2])
np.testing.assert_almost_equal(data.X[0, 0], 92.0)
self.assertEqual("O0A", data.metas[6][2])
np.testing.assert_almost_equal(data.X[6, 0], 38.0)
def test_read(self):
fn = 'NeaReaderGSF_test/NeaReaderGSF_test O2P raw.gsf'
absolute_filename = FileFormat.locate(fn, dataset_dirs)
data = NeaReaderGSF(absolute_filename).read()
self.assertEqual(len(data), 2)
self.assertEqual("run", data.domain.metas[2].name)
self.assertEqual("O2A", data.metas[0][3])
np.testing.assert_almost_equal(data.X[0, 0], 0.734363853931427)
self.assertEqual("O2P", data.metas[1][3])
np.testing.assert_almost_equal(data.X[1, 43], 0.17290098965168)
n_ifg = int(data.attributes['Pixel Area (X, Y, Z)'][3])
self.assertEqual(n_ifg, 1024)
self.assertEqual(n_ifg, len(data.domain.attributes))
check_attributes(data)
def load_from_file():
filename = self.last_path()
if not filename:
return None, ""
if not os.path.exists(filename):
filename = os.path.basename(filename)
filename = FileFormat.locate(filename, "")
self.information("Loading '{}' from the current directory."
.format(filename))
reader = FileFormat.get_reader(filename)
if isinstance(reader, ExcelReader):
reader.select_sheet(self.xls_sheet)
try:
return load(lambda x: reader.read(), filename)
except Exception as exc:
self.warnings.setText(str(exc))
# Let us not remove from recent files: user may fix them
raise
def load_from_file():
filename = self.last_path()
if not filename:
return None, ""
if not os.path.exists(filename):
filename = os.path.basename(filename)
filename = FileFormat.locate(filename, "")
self.information(
"Loading '{}' from the current directory.".format(
filename))
reader = FileFormat.get_reader(filename)
if isinstance(reader, ExcelReader):
reader.select_sheet(self.xls_sheet)
try:
return load(lambda x: reader.read(), filename)
except Exception as exc:
self.warnings.setText(str(exc))
# Let us not remove from recent files: user may fix them
raise
def test_mosaic_ifg_read(self):
# This reader will only be selected manually due to shared .dmt extension
absolute_filename = FileFormat.locate("agilent/5_mosaic_agg1024.dmt",
Orange.data.table.dataset_dirs)
d = agilentMosaicIFGReader(absolute_filename).read()
self.assertEqual(len(d), 32)
self.assertEqual(len(d.domain.attributes), 311)
# Pixel sizes are 5.5 * 32 = 176.0 (binning to reduce test data)
self.assertAlmostEqual(
d[1]["map_x"] - d[0]["map_x"], 176.0)
self.assertAlmostEqual(
d[4]["map_y"] - d[3]["map_y"], 176.0)
# Last pixel should start at (4 - 1) * 176.0 = 528.0
self.assertAlmostEqual(d[-1]["map_x"], 528.0)
# 1 x 2 mosiac, (8 - 1) * 176.0 = 1232.0
self.assertAlmostEqual(d[-1]["map_y"], 1232.0)
self.assertAlmostEqual(d[21][0], 0.7116039)
self.assertAlmostEqual(d[26][0], 0.48532167)
# Metadata
self.assertEqual(d.metas[0, 2], 1.57980039e+04)
self.assertEqual(d.metas[0, 3], 4)
# multiple spectra
d1 = Orange.data.Table("collagen.csv")
d1.save(fn)
d2 = Orange.data.Table(fn)
np.testing.assert_equal(d1.X, d2.X)
def test_comma_delim(self):
with named_file("15,500\n30,650\n", suffix=".dpt") as fn:
d = Orange.data.Table(fn)
np.testing.assert_equal(d.X, [[500., 650.]])
try:
no_visible_image = FileFormat.locate("opus/no_visible_images.0",
Orange.data.table.dataset_dirs)
except OSError:
no_visible_image = False
try:
one_visible_image = FileFormat.locate("opus/one_visible_image.0",
Orange.data.table.dataset_dirs)
except OSError:
one_visible_image = False
@unittest.skipIf(opusFC is None, "opusFC module not installed")
class TestOpusReader(unittest.TestCase):
@unittest.skipIf(no_visible_image is False, "Missing opus/no_visible_images.0")
def test_no_visible_image_read(self):
