def test_BilinearInterpolation(self):
mat = pyopenms.MatrixDouble()
mat.resize(2, 3, float())
mat.setValue(0, 0, 17)
mat.setValue(0, 1, 18.9)
mat.setValue(0, 2, 20.333)
mat.setValue(1, 0, -0.1)
mat.setValue(1, 1, -0.13)
mat.setValue(1, 2, -0.001)
bilip = pyopenms.BilinearInterpolation()
bilip.setData(mat)
bilip.setMapping_0(13.0, 230.0, 14.0, 250.0)
bilip.setMapping_1(15.0, 2100.0, 17.0, 2900.0)
bilip_2 = pyopenms.BilinearInterpolation()
bilip_2 = bilip
self.assertAlmostEqual(bilip_2.getScale_0(), 20)
self.assertAlmostEqual(bilip_2.getScale_1(), 400)
self.assertAlmostEqual(bilip_2.getOffset_0(), -30)
self.assertAlmostEqual(bilip_2.getOffset_1(), -3900)
self.assertAlmostEqual(bilip_2.getInsideReferencePoint_0(), 13)
self.assertAlmostEqual(bilip_2.getOutsideReferencePoint_0(), 230)
self.assertAlmostEqual(bilip_2.getInsideReferencePoint_1(), 15)
self.assertAlmostEqual(bilip_2.getOutsideReferencePoint_1(), 2100)
for i in range(mat.rows()):
for j in range(mat.cols()):
self.assertAlmostEqual(bilip.getData().getValue(i, j),
mat.getValue(i, j))
def test_value(self):
bilip_small = pyopenms.BilinearInterpolation()
bilip_big = pyopenms.BilinearInterpolation()
tmp_small = bilip_small.getData()
tmp_big = bilip_big.getData()
tmp_small.resize(5, 5, float())
tmp_big.resize(15, 15, float())
for i in range(5):
for j in range(5):
num = int(math.floor(random.random() * 100))
tmp_small.setValue(i, j, num)
tmp_big.setValue(i + 5, j + 5, num)
bilip_small.setData(tmp_small)
bilip_big.setData(tmp_big)
bilip_small.setMapping_0(0.0, 0.0, 5.0, 5.0)
bilip_small.setMapping_1(0.0, 0.0, 5.0, 5.0)
bilip_big.setMapping_0(5.0, 0.0, 10.0, 5.0)
bilip_big.setMapping_1(5.0, 0.0, 10.0, 5.0)
for i in range(-50, 101):
p = i / 10.0
for j in range(-50, 101):
q = j / 10.0
self.assertAlmostEqual(bilip_small.value(p, q),
bilip_big.value(p, q))
def test_addValue(self):
for i in range(-50, 101):
p = i / 10.0
for j in range(-50, 101):
q = j / 10.0
bilip_small = pyopenms.BilinearInterpolation()
tmp = bilip_small.getData()
tmp.resize(5, 5, float())
bilip_small.setData(tmp)
bilip_small.setMapping_0(0.0, 0.0, 5.0, 5.0)
bilip_small.setMapping_1(0.0, 0.0, 5.0, 5.0)
bilip_small.addValue(p, q, 100)
bilip_big = pyopenms.BilinearInterpolation()
tmp = bilip_big.getData()
tmp.resize(15, 15, float())
bilip_big.setData(tmp)
bilip_big.setMapping_0(5.0, 0.0, 10.0, 5.0)
bilip_big.setMapping_1(5.0, 0.0, 10.0, 5.0)
bilip_big.addValue(p, q, 100)
big_submatrix = pyopenms.MatrixDouble()
big_submatrix.resize(5, 5, float())
for m in range(5):
for n in range(5):
big_submatrix.setValue(m, n,
bilip_big.getData().getValue(m+5,
n+5))
for m in range(bilip_small.getData().rows()):
for n in range(bilip_small.getData().cols()):
self.assertAlmostEqual(bilip_small.getData().getValue(m, n),
big_submatrix.getValue(m, n))
def test_getData_setData(self):
bilip = pyopenms.BilinearInterpolation()
tmp = bilip.getData()
tmp.resize(2, 3, float())
tmp.setValue(1, 2, 10012)
tmp.setValue(0, 0, 10000)
tmp.setValue(1, 0, 10010)
bilip.setData(tmp)
bilip_2 = pyopenms.BilinearInterpolation(bilip)
self.assertAlmostEqual(bilip_2.getData().getValue(1, 2), 10012)
self.assertAlmostEqual(bilip_2.getData().getValue(0, 0), 10000)
self.assertAlmostEqual(bilip_2.getData().getValue(1, 0), 10010)
def test_setMapping_0(self):
bilip = pyopenms.BilinearInterpolation()
bilip.setMapping_0(1.0, 2.0, 3.0, 8.0)
self.assertAlmostEqual(bilip.getScale_0(), 3)
self.assertAlmostEqual(bilip.getOffset_0(), -1)
self.assertAlmostEqual(bilip.getScale_1(), 1)
self.assertAlmostEqual(bilip.getOffset_1(), 0)
bilip2 = pyopenms.BilinearInterpolation()
bilip2.setMapping_0(3.0, 1.0, 2.0)
self.assertAlmostEqual(bilip2.getScale_0(), 3)
self.assertAlmostEqual(bilip2.getOffset_0(), -1)
self.assertAlmostEqual(bilip2.getScale_1(), 1)
self.assertAlmostEqual(bilip2.getOffset_1(), 0)
def test_getInsideReferencePoint_0(self):
bilip = pyopenms.BilinearInterpolation()
bilip.setMapping_0(1.0, 4.0, 3.0, 8.0)
self.assertAlmostEqual(bilip.getInsideReferencePoint_0(), 1)
self.assertAlmostEqual(bilip.getOutsideReferencePoint_0(), 4)
self.assertAlmostEqual(bilip.getInsideReferencePoint_1(), 0)
self.assertAlmostEqual(bilip.getOutsideReferencePoint_1(), 0)
def setSpectra(self, msexperiment):
msexperiment.updateRanges()
# resolution: mz_res Da in m/z, rt_res seconds in RT dimension
mz_res = 1.0
rt_res = 1.0
# size of image
cols = 1.0 / mz_res * msexperiment.getMaxMZ()
rows = 1.0 / rt_res * msexperiment.getMaxRT()
# create regular spaced data to turn spectra into an image
"""se_comment: max_intensity was never used"""
"""max_intensity = msexperiment.getMaxInt()"""
bilip = pyopenms.BilinearInterpolation()
tmp = bilip.getData()
tmp.resize(int(rows), int(cols), float())
bilip.setData(tmp)
bilip.setMapping_0(0.0, 0.0, rows - 1, msexperiment.getMaxRT())
bilip.setMapping_1(0.0, 0.0, cols - 1, msexperiment.getMaxMZ())
img = pg.ImageItem(autoDownsample=True)
self.addItem(img)
for spec in msexperiment:
if spec.getMSLevel() == 1:
mzs, ints = spec.get_peaks()
rt = spec.getRT()
for i in range(0, len(mzs)):
bilip.addValue(rt, mzs[i], ints[i]) # slow
data = np.ndarray(shape=(int(cols), int(rows)), dtype=np.float64)
grid_data = bilip.getData()
for i in range(int(rows)):
for j in range(int(cols)):
data[j][i] = grid_data.getValue(i, j) # slow
# Set a custom color map
pos = np.array([0.0, 0.01, 0.05, 0.1, 1.0])
color = np.array(
[
(255, 255, 255, 0),
(255, 255, 0, 255),
(255, 0, 0, 255),
(0, 0, 255, 255),
(0, 0, 0, 255),
],
dtype=np.ubyte,
)
cmap = pg.ColorMap(pos, color)
img.setLookupTable(cmap.getLookupTable(0.0, 1.0, 256))
img.setImage(data)
def test_supportMax_1(self):
bilip = pyopenms.BilinearInterpolation()
bilip.setMapping_1(3.0, 1.0, 2.0)
bilip.setMapping_0(5.0, 3.0, 4.0)
tmp = bilip.getData()
tmp.resize(3, 2, float())
bilip.setData(tmp)
self.assertAlmostEqual(bilip.index2key_1(0), -1)
self.assertAlmostEqual(bilip.index2key_1(1), 2)
self.assertAlmostEqual(bilip.supportMin_1(), -4)
self.assertAlmostEqual(bilip.supportMax_1(), 5)
self.assertAlmostEqual(bilip.index2key_0(0), -11)
self.assertAlmostEqual(bilip.index2key_0(2), -1)
self.assertAlmostEqual(bilip.supportMin_0(), -16)
self.assertAlmostEqual(bilip.supportMax_0(), 4)
def test_empty(self):
bilip = pyopenms.BilinearInterpolation()
self.assertTrue(bilip.empty())
tmp = bilip.getData()
tmp.resize(1, 2, float())
bilip.setData(tmp)
self.assertFalse(bilip.empty())
tmp = bilip.getData()
tmp.resize(0, 0, float())
bilip.setData(tmp)
self.assertTrue(bilip.empty())
tmp = bilip.getData()
tmp.resize(1, 2, float())
bilip.setData(tmp)
self.assertFalse(bilip.empty())
tmp = bilip.getData()
tmp.resize(1, 0, float())
bilip.setData(tmp)
self.assertTrue(bilip.empty())
tmp = bilip.getData()
tmp.resize(1, 2, float())
bilip.setData(tmp)
self.assertFalse(bilip.empty())
tmp = bilip.getData()
tmp.resize(0, 0, float())
bilip.setData(tmp)
self.assertTrue(bilip.empty())
tmp = bilip.getData()
tmp.resize(2, 2, float())
bilip.setData(tmp)
self.assertFalse(bilip.empty())
tmp = bilip.getData()
tmp.clear()
bilip.setData(tmp)
self.assertTrue(bilip.empty())
def test_key2index_0(self):
bilip = pyopenms.BilinearInterpolation()
bilip.setMapping_0(3.0, 1.0, 2.0)
self.assertAlmostEqual(bilip.key2index_0(-1), 0)
self.assertAlmostEqual(bilip.key2index_1(0), 0)
def test_setScale_0(self):
bilip = pyopenms.BilinearInterpolation()
bilip.setScale_0(987)
self.assertAlmostEqual(bilip.getScale_0(), 987)
def test_index2key_1(self):
bilip = pyopenms.BilinearInterpolation()
bilip.setMapping_1(3.0, 1.0, 2.0)
self.assertAlmostEqual(bilip.index2key_1(0), -1)
self.assertAlmostEqual(bilip.index2key_0(0), 0)