def __init__(self, parent=None):
super().__init__(parent)
self._channels = {}
self._frameSel = multicolor.FrameSelector("")
self._registrator = multicolor.Registrator()
self.channelsChanged.connect(self._imageDataChanged)
self.registratorChanged.connect(self._imageDataChanged)
self.excitationSeqChanged.connect(self._imageDataChanged)
def __init__(self, parent=None):
super().__init__(parent)
self._smData = None
self._filterTable = pd.DataFrame(columns=["track_len", "manual"])
self._frameSel = multicolor.FrameSelector("")
self._trackLengthRange = [0, np.inf]
self._showManuallyFiltered = True
self.showManuallyFilteredChanged.connect(self._updateFiltered)
self.filterTableChanged.connect(self._updateFiltered)
def test_restore_frame_numbers(self, selector, flex_selector):
"""multicolor.FrameSelector.restore_frame_numbers"""
ar = np.arange(14)
ar = ar[ar != 7]
df = pd.DataFrame(ar[:, None], columns=["frame"])
exp = [1, 2, 3, 4, 5, 6, 8, 10, 11, 12, 13, 15, 16]
df2 = df.copy()
selector.restore_frame_numbers(df2, "da")
np.testing.assert_array_equal(df2["frame"], exp)
df3 = df.copy()
flex_selector.restore_frame_numbers(
df3, "da", n_frames=len(selector.excitation_seq))
np.testing.assert_array_equal(df3["frame"], exp)
df4 = df.copy()
with pytest.raises(ValueError):
selector.restore_frame_numbers(df4, "")
with pytest.raises(ValueError):
flex_selector.restore_frame_numbers(df4, "")
null_selector = multicolor.FrameSelector("")
df5 = df.copy()
null_selector.restore_frame_numbers(df5, "d")
pd.testing.assert_frame_equal(df5, df)
def test_eval_seq(self, selector):
"""multicolor.FrameSelector.eval_seq"""
np.testing.assert_array_equal(
selector.eval_seq(),
np.fromiter(selector.excitation_seq, "U1"))
np.testing.assert_array_equal(
multicolor.FrameSelector("a +bc * 3 + 2*de").eval_seq(),
np.fromiter("abcbcbcdede", "U1"))
np.testing.assert_array_equal(
multicolor.FrameSelector("a +bc * ? + 2*de").eval_seq(9),
np.fromiter("abcbcdede", "U1"))
with pytest.raises(ValueError):
multicolor.FrameSelector("a +bc * ? + 2*de").eval_seq(10)
np.testing.assert_array_equal(
multicolor.FrameSelector("a + ? * bc + de").eval_seq(9),
np.fromiter("abcbcbcde", "U1"))
np.testing.assert_array_equal(
multicolor.FrameSelector("a + ? * bc + de").eval_seq(-1),
np.fromiter("abcde", "U1"))
assert multicolor.FrameSelector("").eval_seq().size == 0
def test_select(self, selector, flex_selector, call_results):
"""multicolor.FrameSelector.select"""
ar = np.arange(21)
n = len(selector.excitation_seq)
for k, v in call_results.items():
r = selector.select(ar, k)
np.testing.assert_array_equal(r, v)
assert isinstance(r, np.ndarray)
fr = flex_selector.select(ar, k, n_frames=n)
np.testing.assert_array_equal(fr, v)
assert isinstance(fr, np.ndarray)
lst = list(ar)
for k, v in call_results.items():
r = selector.select(lst, k)
np.testing.assert_array_equal(r, v)
assert isinstance(r, helper.Slicerator)
fr = flex_selector.select(lst, k, n_frames=n)
np.testing.assert_array_equal(fr, v)
assert isinstance(fr, helper.Slicerator)
df = pd.DataFrame(ar[:, None], columns=["frame"])
for k, v in call_results.items():
r = selector.select(df, k)
pd.testing.assert_frame_equal(r, df.loc[v])
fr = flex_selector.select(df, k, n_frames=n)
pd.testing.assert_frame_equal(fr, df.loc[v])
# Selecting multiple frame types
np.testing.assert_equal(selector.select(ar, "da"), call_results["da"])
np.testing.assert_array_equal(selector.select(lst, "da"),
call_results["da"])
pd.testing.assert_frame_equal(selector.select(df, "da"),
df.loc[call_results["da"]])
# Empty sequence
null_selector = multicolor.FrameSelector("")
np.testing.assert_equal(null_selector.select(ar, "d"), ar)
np.testing.assert_array_equal(null_selector.select(lst, "d"), lst)
pd.testing.assert_frame_equal(null_selector.select(df, "d"), df)
# Empty `which`
np.testing.assert_array_equal(selector.select(ar, ""), [])
np.testing.assert_array_equal(selector.select(lst, ""), [])
pd.testing.assert_frame_equal(selector.select(df, ""), df.iloc[:0])
np.testing.assert_array_equal(flex_selector.select(ar, ""), [])
np.testing.assert_array_equal(flex_selector.select(lst, ""), [])
pd.testing.assert_frame_equal(flex_selector.select(df, "", n_frames=n),
df.iloc[:0])
# For non-DataFrames, n_frames is deduced from length
ar2 = np.arange(10)
np.testing.assert_equal(flex_selector.select(ar2, "c"), [0])
np.testing.assert_equal(flex_selector.select(ar2, "d"),
[1, 2, 3, 4, 5, 6, 7])
np.testing.assert_equal(flex_selector.select(ar2, "a"), [8, 9])
# For DataFrames, there should be an error
with pytest.raises(ValueError):
flex_selector.select(df, "d")
# drop a frame which should leave a gap when renumbering
drop_frame = 3
df2 = df.drop(drop_frame)
for k, v in call_results.items():
data = np.arange(len(v))[:, None]
# deal with dropped frame
v = np.array(v)
mask = v != drop_frame
v = v[mask]
data = data[mask]
r = selector.select(df2, k, renumber=True)
np.testing.assert_equal(r.index, v)
np.testing.assert_equal(r.to_numpy(), data)
fr = flex_selector.select(df2, k, renumber=True, n_frames=n)
np.testing.assert_equal(fr.index, v)
np.testing.assert_equal(fr.to_numpy(), data)
def test_renumber(self, selector, call_results):
"""multicolor.FrameSelector._renumber, renumber_frames"""
drop_frame = 3
seq = np.fromiter(selector.excitation_seq, "U1")
for k, v in call_results.items():
v = np.array(v)
mask = v != drop_frame
v = v[mask]
v2 = np.arange(len(mask))[mask]
r = multicolor.FrameSelector._renumber(seq, v, k, restore=False)
rr = selector.renumber_frames(v, k, restore=False)
for cr in r, rr:
np.testing.assert_equal(cr, v2)
r2 = multicolor.FrameSelector._renumber(seq, v2, k, restore=True)
rr2 = selector.renumber_frames(v2, k, restore=True)
for cr in r2, rr2:
np.testing.assert_equal(cr, v)
# Check behavior in case a frame number not belonging to excitation
# type given by `which` parameter is in the list
bad = np.array([0, 2, 3, 4])
r = multicolor.FrameSelector._renumber(
np.array(["d", "a"]), bad, "d", restore=False)
r2 = multicolor.FrameSelector("da").renumber_frames(
bad, "d", restore=False)
for cr in r, r2:
np.testing.assert_array_equal(cr, [0, 1, -1, 2])
# There was a bug when the max frame number was divisible by the
# length of the excitation sequence, resulting in f_map_inv being too
# short. Ensure that this is fixed by using an array with max == 10
# and the sequence "da".
ar = np.arange(0, 11, 2)
r = multicolor.FrameSelector._renumber(
np.array(["d", "a"]), ar, "d", restore=False)
r2 = multicolor.FrameSelector("da").renumber_frames(
ar, "d", restore=False)
for cr in r, r2:
np.testing.assert_equal(cr, np.arange(len(ar)))
# Test empty sequence and empty `which`
ar2 = np.arange(21)
r = multicolor.FrameSelector._renumber(
np.array([], dtype="U1"), ar2, "d", restore=False)
r2 = multicolor.FrameSelector("").renumber_frames(
ar2, "d", restore=False)
for cr in r, r2:
np.testing.assert_array_equal(cr, ar2)
r = multicolor.FrameSelector._renumber(
np.array(["d", "a"], dtype="U1"), ar2, "", restore=False)
r2 = multicolor.FrameSelector("da").renumber_frames(
ar2, "", restore=False)
for cr in r, r2:
np.testing.assert_array_equal(cr, np.full(ar2.size, -1, dtype=int))
with pytest.raises(ValueError):
multicolor.FrameSelector._renumber(
np.array(["d", "a"], dtype="U1"), ar2, "", restore=True)
with pytest.raises(ValueError):
multicolor.FrameSelector("da").renumber_frames(
ar2, "", restore=True)
def flex_selector(self):
return multicolor.FrameSelector("c + d*? + a*2")
def selector(self):
return multicolor.FrameSelector("cddddaa")