def test_peakat(self):
data = Orange.data.Table([[1, 2, 3, 1, 1, 1]])
i = Integrate(methods=Integrate.PeakAt, limits=[[0, 5]])(data)
self.assertEqual(i[0][0], 1)
np.testing.assert_equal(i.domain[0].compute_value.baseline(data)[1], 0)
i = Integrate(methods=Integrate.PeakAt, limits=[[1.4, None]])(data)
self.assertEqual(i[0][0], 2)
i = Integrate(methods=Integrate.PeakAt, limits=[[1.6, None]])(data)
self.assertEqual(i[0][0], 3)
def test_empty(self):
data = Orange.data.Table([[1, 2, 3, 1, 1, 1]])
i = Integrate(method=Integrate.Simple, limits=[[10, 16]])(data)
self.assertEqual(i[0][0], 0)
i = Integrate(method=Integrate.Baseline, limits=[[10, 16]])(data)
self.assertEqual(i[0][0], 0)
i = Integrate(method=Integrate.PeakMax, limits=[[10, 16]])(data)
self.assertEqual(i[0][0], np.nan)
i = Integrate(method=Integrate.PeakBaseline, limits=[[10, 16]])(data)
self.assertEqual(i[0][0], np.nan)
def test_names(self):
data = Orange.data.Table([[1, 2, 3, 1, 1, 1]])
i = Integrate(methods=[Integrate.Simple, Integrate.Baseline],
limits=[[0, 5], [0, 6]])(data)
self.assertEqual(i.domain[0].name, "0 - 5")
self.assertEqual(i.domain[1].name, "0 - 6")
i = Integrate(methods=[Integrate.Simple, Integrate.Baseline],
limits=[[0, 5], [0, 6]], names=["simple", "baseline"])(data)
self.assertEqual(i.domain[0].name, "simple")
self.assertEqual(i.domain[1].name, "baseline")
def test_empty_interval(self):
data = Orange.data.Table([[1, 2, 3, 1, 1, 1]])
i = Integrate(methods=Integrate.Simple, limits=[[10, 16]])(data)
self.assertEqual(i[0][0], 0)
i = Integrate(methods=Integrate.Baseline, limits=[[10, 16]])(data)
self.assertEqual(i[0][0], 0)
i = Integrate(methods=Integrate.PeakMax, limits=[[10, 16]])(data)
self.assertEqual(i[0][0], np.nan)
i = Integrate(methods=Integrate.PeakBaseline, limits=[[10, 16]])(data)
self.assertEqual(i[0][0], np.nan)
i = Integrate(methods=Integrate.PeakAt, limits=[[10, 16]])(data)
self.assertEqual(i[0][0], 1) # get the rightmost one
def test_peakx(self):
d1 = Orange.data.Table([[1, 2, 3, 1, 1, 1]])
d2 = Orange.data.Table([[1, 2, 3, np.nan, 1, 1]])
for data in d1, d2:
i = Integrate(methods=Integrate.PeakX, limits=[[0, 5]])(data)
self.assertEqual(i[0][0], 2)
np.testing.assert_equal(i.domain[0].compute_value.baseline(data)[1], 0)
def test_different_integrals(self):
data = Orange.data.Table([[1, 2, 3, 1, 1, 1]])
i = Integrate(methods=[Integrate.Simple, Integrate.Baseline],
limits=[[0, 5], [0, 5]])(data)
self.assertEqual(i[0][0], 8)
np.testing.assert_equal(i.domain[0].compute_value.baseline(data)[1], 0)
np.testing.assert_equal(i.domain[1].compute_value.baseline(data)[1], 1)
def test_repeated(self):
data = Orange.data.Table([[1, 2, 3, 1, 1, 1]])
i = Integrate(methods=[Integrate.Simple, Integrate.Baseline],
limits=[[0, 5], [0, 6]],
names=["int", "int"])(data)
self.assertEqual(i.domain[0].name, "int")
self.assertEqual(i.domain[1].name, "int (2)")
def test_baseline(self):
data = Orange.data.Table([[1, 2, 3, 1, 1, 1], [1, 2, 3, 1, np.nan, 1],
[1, 2, 3, 1, 1, np.nan]])
i = Integrate(methods=Integrate.Baseline, limits=[[0, 5]])(data)
self.assertEqual(i[0][0], 3)
self.assertEqual(i[1][0], 3)
self.assertEqual(i[2][0], 3)
np.testing.assert_equal(i.domain[0].compute_value.baseline(data)[1], 1)
def test_repeated(self):
data = Orange.data.Table([[1, 2, 3, 1, 1, 1]])
i = Integrate(methods=[Integrate.Simple, Integrate.Baseline],
limits=[[0, 5], [0, 6]], names=["int", "int"])(data)
self.assertEqual(i.domain[0].name, "int")
# after Orange 3.6.0 get_next_name returned different results
nn = get_next_name(["int"], "int")
self.assertEqual(i.domain[1].name, nn)
def test_metas_output(self):
data = Orange.data.Table([[1, 2, 3, 1, 1, 1]])
i = Integrate(methods=[Integrate.Simple, Integrate.Baseline],
limits=[[0, 5], [0, 6]], metas=True)(data)
metavars = [a.name for a in i.domain.metas]
self.assertTrue("0 - 5" in metavars and "0 - 6" in metavars)
self.assertEqual(i[0]["0 - 5"], 8)
self.assertEqual(i[0]["0 - 6"], 3)
def test_area_norm(self):
data = Orange.data.Table([[2, 1, 2, 2, 3]])
p = Normalize(method=Normalize.Area, int_method=Integrate.PeakMax, lower=0, upper=4)(data)
np.testing.assert_equal(p.X, data.X / 3)
p = Normalize(method=Normalize.Area, int_method=Integrate.Simple, lower=0, upper=4)(data)
np.testing.assert_equal(p.X, data.X / 7.5)
p = Normalize(method=Normalize.Area, int_method=Integrate.Simple, lower=0, upper=2)(data)
q = Integrate(methods=Integrate.Simple, limits=[[0, 2]])(p)
np.testing.assert_equal(q.X, np.ones_like(q.X))
def show_data(self):
self.img.clear()
if self.data:
xat = self.data.domain[self.attr_x]
yat = self.data.domain[self.attr_y]
ndom = Orange.data.Domain([xat, yat])
datam = Orange.data.Table(ndom, self.data)
coorx = datam.X[:, 0]
coory = datam.X[:, 1]
lsx = values_to_linspace(coorx)
lsy = values_to_linspace(coory)
l1, l2 = self.parent.lowlim, self.parent.highlim
gx = getx(self.data)
if l1 is None:
l1 = min(gx) - 1
if l2 is None:
l2 = max(gx) + 1
l1, l2 = min(l1, l2), max(l1, l2)
imethod = self.parent.integration_methods[
self.parent.integration_method]
datai = Integrate(method=imethod, limits=[[l1, l2]])(self.data)
di = {}
if self.parent.curveplot.selected_indices:
ind = list(self.parent.curveplot.selected_indices)[0]
di = datai.domain.attributes[0].compute_value.draw_info(
self.data[ind:ind + 1])
self.refresh_markings(di)
d = datai.X[:, 0]
# set data
imdata = np.ones((lsy[2], lsx[2])) * float("nan")
xindex = index_values(coorx, lsx)
yindex = index_values(coory, lsy)
imdata[yindex, xindex] = d
levels = get_levels(imdata)
self.update_color_schema()
self.img.setImage(imdata, levels=levels)
# shift centres of the pixels so that the axes are useful
shiftx = (lsx[1] - lsx[0]) / (2 * (lsx[2] - 1))
shifty = (lsy[1] - lsy[0]) / (2 * (lsy[2] - 1))
left = lsx[0] - shiftx
bottom = lsy[0] - shifty
width = (lsx[1] - lsx[0]) + 2 * shiftx
height = (lsy[1] - lsy[0]) + 2 * shifty
self.img.setRect(QRectF(left, bottom, width, height))
import Orange
from orangecontrib.infrared.preprocess import Absorbance, Transmittance, \
Integrate, Interpolate, Cut, SavitzkyGolayFiltering, \
GaussianSmoothing, PCADenoising, RubberbandBaseline, \
Normalize
# Preprocessors that work per sample and should return the same
# result for a sample independent of the other samples
PREPROCESSORS_INDEPENDENT_SAMPLES = [
Interpolate(np.linspace(1000, 1800, 100)),
SavitzkyGolayFiltering(window=9, polyorder=2, deriv=2),
Cut(lowlim=1000, highlim=1800),
GaussianSmoothing(sd=3.),
Absorbance(),
Transmittance(),
Integrate(limits=[[900, 100], [1100, 1200], [1200, 1300]]),
RubberbandBaseline(),
Normalize(method=Normalize.Vector),
]
# Preprocessors that use groups of input samples to infer
# internal parameters.
PREPROCESSORS_GROUPS_OF_SAMPLES = [
PCADenoising(components=2),
]
PREPROCESSORS = PREPROCESSORS_INDEPENDENT_SAMPLES + PREPROCESSORS_GROUPS_OF_SAMPLES
class TestTransmittance(unittest.TestCase):
def test_domain_conversion(self):
def test_simple(self):
data = Orange.data.Table([[1, 2, 3, 1, 1, 1]])
i = Integrate(method=Integrate.Simple, limits=[[0, 5]])(data)
self.assertEqual(i[0][0], 8)
np.testing.assert_equal(i.domain[0].compute_value.baseline(data)[1],
[[0, 0, 0, 0, 0, 0]])
def test_peakxbaseline(self):
data = Orange.data.Table([[1, 2, 3, 1, 1, 1]])
i = Integrate(methods=Integrate.PeakXBaseline, limits=[[0, 5]])(data)
self.assertEqual(i[0][0], 2)
np.testing.assert_equal(i.domain[0].compute_value.baseline(data)[1],
[[1, 1, 1, 1, 1, 1]])
def createinstance(cls, params):
params = dict(params)
values = []
for ind, (name, _) in enumerate(cls.integrator.parameters()):
values.append(params.get(name, 0.))
return Integrate(methods=cls.integrator, limits=[values], metas=True)
def update_view(self):
self.img.clear()
self.img.setSelection(None)
self.lsx = None
self.lsy = None
self.data_points = None
self.data_values = None
self.data_imagepixels = None
if self.data and self.attr_x and self.attr_y:
xat = self.data.domain[self.attr_x]
yat = self.data.domain[self.attr_y]
ndom = Orange.data.Domain([xat, yat])
datam = Orange.data.Table(ndom, self.data)
coorx = datam.X[:, 0]
coory = datam.X[:, 1]
self.data_points = datam.X
self.lsx = lsx = values_to_linspace(coorx)
self.lsy = lsy = values_to_linspace(coory)
if lsx[-1] * lsy[-1] > IMAGE_TOO_BIG:
self.parent.Error.image_too_big(lsx[-1], lsy[-1])
return
else:
self.parent.Error.image_too_big.clear()
di = {}
if self.parent.value_type == 0: # integrals
imethod = self.parent.integration_methods[self.parent.integration_method]
l1, l2, l3 = self.parent.lowlim, self.parent.highlim, self.parent.choose
gx = getx(self.data)
if l1 is None:
l1 = min(gx) - 1
if l2 is None:
l2 = max(gx) + 1
l1, l2 = min(l1, l2), max(l1, l2)
if l3 is None:
l3 = (l1 + l2)/2
if imethod != Integrate.PeakAt:
datai = Integrate(methods=imethod, limits=[[l1, l2]])(self.data)
else:
datai = Integrate(methods=imethod, limits=[[l3, l3]])(self.data)
if self.parent.curveplot.selected_indices:
# curveplot can have a subset of curves on the input> match IDs
ind = list(self.parent.curveplot.selected_indices)[0]
dind = self.data_ids[self.parent.curveplot.data[ind].id]
di = datai.domain.attributes[0].compute_value.draw_info(self.data[dind:dind+1])
d = datai.X[:, 0]
else:
dat = self.data.domain[self.parent.attr_value]
ndom = Orange.data.Domain([dat])
d = Orange.data.Table(ndom, self.data).X[:, 0]
self.refresh_markings(di)
# set data
imdata = np.ones((lsy[2], lsx[2])) * float("nan")
# if previous or saved selection is valid for this data set keep it
if self.selection is None or len(self.selection) != len(self.data):
self.selection = np.zeros(len(self.data), dtype="bool")
xindex = index_values(coorx, lsx)
yindex = index_values(coory, lsy)
imdata[yindex, xindex] = d
self.data_values = d
self.data_imagepixels = np.vstack((yindex, xindex)).T
levels = get_levels(imdata)
self.update_color_schema()
self.img.setImage(imdata, levels=levels)
# shift centres of the pixels so that the axes are useful
shiftx = _shift(lsx)
shifty = _shift(lsy)
left = lsx[0] - shiftx
bottom = lsy[0] - shifty
width = (lsx[1]-lsx[0]) + 2*shiftx
height = (lsy[1]-lsy[0]) + 2*shifty
self.img.setRect(QRectF(left, bottom, width, height))
self.send_selection()
self.refresh_img_selection()
from orangecontrib.infrared.preprocess import Absorbance, Transmittance, \
Integrate, Interpolate, Cut, SavitzkyGolayFiltering, \
GaussianSmoothing, PCADenoising, RubberbandBaseline, \
Normalize
# Preprocessors that work per sample and should return the same
# result for a sample independent of the other samples
PREPROCESSORS_INDEPENDENT_SAMPLES = [
Interpolate(np.linspace(1000, 1700, 100)),
SavitzkyGolayFiltering(window=9, polyorder=2, deriv=2),
Cut(lowlim=1000, highlim=1800),
GaussianSmoothing(sd=3.),
Absorbance(),
Transmittance(),
Integrate(limits=[[900, 100], [1100, 1200], [1200, 1300]]),
Integrate(methods=Integrate.Simple, limits=[[1100, 1200]]),
Integrate(methods=Integrate.Baseline, limits=[[1100, 1200]]),
Integrate(methods=Integrate.PeakMax, limits=[[1100, 1200]]),
Integrate(methods=Integrate.PeakBaseline, limits=[[1100, 1200]]),
Integrate(methods=Integrate.PeakAt, limits=[[1100]]),
Integrate(methods=Integrate.PeakX, limits=[[1100, 1200]]),
Integrate(methods=Integrate.PeakXBaseline, limits=[[1100, 1200]]),
RubberbandBaseline(),
Normalize(method=Normalize.Vector),
Normalize(method=Normalize.Area, int_method=Integrate.PeakMax, lower=0, upper=10000),
]
# Preprocessors that use groups of input samples to infer
# internal parameters.
PREPROCESSORS_GROUPS_OF_SAMPLES = [