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fix rise angle null values of calculate_lattice_structure #117

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merged 1 commit into from
Sep 5, 2024
Merged

fix rise angle null values of calculate_lattice_structure #117

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14 changes: 4 additions & 10 deletions cylindra/cylmeasure.py
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Original file line number Diff line number Diff line change
Expand Up @@ -95,15 +95,10 @@ def calc_rise(mole: Molecules, spl: CylSpline) -> pl.Series:
sign = spl.config.rise_sign
return (
calc_localvec_lat(mole, spl, fill=np.nan)
.select(
pl.arctan2("vecy", "veca")
.degrees()
.fill_nan(-float("inf"))
.alias(Mole.rise)
)
.select(pl.arctan2("vecy", "veca").degrees().alias(Mole.rise))
.to_series()
* sign
)
).fill_nan(-float("inf"))


def calc_lateral_interval(mole: Molecules, spl: CylSpline) -> pl.Series:
Expand All @@ -113,11 +108,10 @@ def calc_lateral_interval(mole: Molecules, spl: CylSpline) -> pl.Series:
.select(
(pl.col("vecy") ** 2 + pl.col("veca") ** 2)
.sqrt()
.fill_nan(-float("inf"))
.alias(Mole.lateral_interval)
)
.to_series()
)
).fill_nan(-float("inf"))


def _pad_molecules_at_seam(mole: Molecules, spl: CylSpline) -> tuple[Molecules, int]:
Expand Down Expand Up @@ -195,7 +189,7 @@ def calc_localvec_lat(
_vec_tr = _vec_tr[:-1, :]
sub0 = sub0.subset(slice(None, -1))
else:
_vec_tr[:-1, :] = fill
_vec_tr[-1, :] = fill
subsets.append(
sub0.with_features(
pl.Series("vecr", _vec_tr[:, 0], dtype=pl.Float32),
Expand Down
6 changes: 6 additions & 0 deletions tests/test_gui_0.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1189,6 +1189,12 @@ def test_calc_misc(ui: CylindraMainWidget):
all_props = cylmeasure.LatticeParameters.choices()
ui.calculate_lattice_structure(layer=layer, props=all_props)
assert layer.features[Mole.radius].std() < 0.1
# check null values
assert layer.molecules.features[Mole.spacing].is_finite().not_().sum() == 13
assert layer.molecules.features[Mole.twist].is_finite().not_().sum() == 13
assert layer.molecules.features[Mole.rise].is_finite().not_().sum() == 3
assert layer.molecules.features[Mole.lateral_interval].is_finite().not_().sum() == 3

ui.paint_molecules(layer, color_by=Mole.nth, limits=(0, 10))
colors = ui.mole_layers.last().face_color
ui.MoleculesMenu.View.plot_molecule_feature(layer, backend="qt")
Expand Down
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