Refactor spline properties to the property props

cylindra/_custom_layers.py

@@ -1,4 +1,5 @@
 from __future__ import annotations
+from contextlib import contextmanager
 
 from typing import TYPE_CHECKING, Any, NamedTuple
 import weakref
@@ -120,6 +121,8 @@ def __init__(self, data: Molecules, **kwargs):
         self._molecules = data
         self._colormap_info: ColormapInfo | None = None
         self._source_component: weakref.ReferenceType[BaseComponent] | None = None
+        self._old_name: str | None = None  # for undo/redo
+        self._undo_renaming = False
         super().__init__(data.pos, **kwargs)
         features = data.features
         if features is not None and len(features) > 0:
@@ -151,6 +154,33 @@ def features(self, features):
         Points.features.fset(self, df)
         self._molecules.features = df
 
+    @property
+    def name(self) -> str:
+        return super().name
+
+    @name.setter
+    def name(self, name: str) -> None:
+        if self.name == name:
+            return None
+        self._old_name = self.name
+        if not name:
+            name = self._basename()
+        self._name = str(name)
+        self.events.name()
+
+    @contextmanager
+    def _undo_context(self):
+        was_renaming = self._undo_renaming
+        self._undo_renaming = True
+        try:
+            yield
+        finally:
+            self._undo_renaming = was_renaming
+
+    def _rename(self, name: str):
+        with self._undo_context():
+            self.name = name
+
     @property
     def source_component(self) -> BaseComponent | None:
         """The source tomographic component object."""
@@ -171,6 +201,7 @@ def source_component(self, obj: BaseComponent | None):
 
     @property
     def source_spline(self) -> CylSpline | None:
+        """The source component but limited to splines."""
         from cylindra.components import CylSpline
 
         src = self.source_component

cylindra/components/cyl_spline.py

@@ -1,8 +1,7 @@
 from __future__ import annotations
 
-from typing import Callable, Any, TYPE_CHECKING
+from typing import Any
 import numpy as np
-from numpy.typing import ArrayLike
 import polars as pl
 
 from .spline import Spline
@@ -14,32 +13,29 @@
 from cylindra.utils import roundint
 from cylindra.components.cylindric import CylinderModel
 
-if TYPE_CHECKING:
-    Degenerative = Callable[[ArrayLike], Any]
-
 
 class CylSpline(Spline):
     """A spline object with cylindrical structure."""
 
     @property
     def radius(self) -> nm | None:
         """Average radius of the cylinder."""
-        return self.get_globalprops(H.radius, None)
+        return self.props.get_glob(H.radius, None)
 
     @radius.setter
     def radius(self, value: nm | None):
         if value is None:
             if H.radius in self.globalprops.columns:
-                self.drop_globalprops(H.radius)
+                self.props.drop_glob(H.radius)
             return None
         col = pl.Series(H.radius, [value]).cast(pl.Float32)
-        self._globalprops = self.globalprops.with_columns(col)
+        self.props.glob = self.props.glob.with_columns(col)
         return None
 
     @property
     def orientation(self) -> Ori:
         """Orientation of the spline."""
-        return Ori(str(self.get_globalprops(H.orientation, "none")))
+        return Ori(str(self.props.get_glob(H.orientation, "none")))
 
     @orientation.setter
     def orientation(self, value: Ori | str | None):
@@ -48,7 +44,7 @@ def orientation(self, value: Ori | str | None):
         else:
             value = Ori(value)
         col = pl.Series(H.orientation, [str(value)])
-        self._globalprops = self.globalprops.with_columns(col)
+        self.props.glob = self.props.glob.with_columns(col)
         return None
 
     def invert(self) -> CylSpline:
@@ -62,11 +58,9 @@ def invert(self) -> CylSpline:
         """
         # NOTE: invert() calls clip() internally.
         # We don't have to invert the orientation here.
-        return (
-            super()
-            .invert()
-            .update_localprops(self.localprops[::-1], self.localprops_window_size)
-        )
+        new = super().invert()
+        new.props.update_loc(self.props.loc[::-1], self.props.window_size)
+        return new
 
     def clip(self, start: float, stop: float) -> CylSpline:
         """
@@ -91,7 +85,7 @@ def clip(self, start: float, stop: float) -> CylSpline:
         """
         clipped = super().clip(start, stop)
 
-        clipped._globalprops = self.globalprops.clone()
+        clipped.props.glob = self.props.glob.clone()
         if start > stop:
             clipped.orientation = Ori.invert(self.orientation)
         else:
@@ -227,7 +221,7 @@ def update_props(
         # update H.start
         if rise is not None:
             r = radius if radius is not None else self.radius
-            if r is not None and self.has_localprops([H.rise, H.spacing, H.skew]):
+            if r is not None and self.props.has_loc([H.rise, H.spacing, H.skew]):
                 _start_loc = rise_to_start(
                     rise=np.deg2rad(ldf[H.rise].to_numpy()),
                     space=ldf[H.spacing].to_numpy(),
@@ -237,7 +231,7 @@ def update_props(
                 ldf = ldf.with_columns(
                     pl.Series(_start_loc).cast(pl.Float32).alias(H.start)
                 )
-            if r is not None and self.has_globalprops([H.rise, H.spacing, H.skew]):
+            if r is not None and self.props.has_glob([H.rise, H.spacing, H.skew]):
                 _start_glob = rise_to_start(
                     rise=np.deg2rad(gdf[H.rise].to_numpy()),
                     space=gdf[H.spacing].to_numpy(),
@@ -248,8 +242,8 @@ def update_props(
                     pl.Series(_start_glob).cast(pl.Float32).alias(H.start)
                 )
 
-        self._localprops = ldf
-        self._globalprops = gdf
+        self.props.loc = ldf
+        self.props.glob = gdf
         return self
 
     def _need_rotation(self, orientation: Ori | str | None) -> bool:
@@ -274,4 +268,4 @@ def rise_to_start(rise: float, space: nm, skew: float, perimeter: nm) -> float:
 def _get_globalprops(spl: CylSpline, kwargs: dict[str, Any], name: str):
     if name in kwargs:
         return kwargs[name]
-    return spl.get_globalprops(name)
+    return spl.props.get_glob(name)

cylindra/components/cyl_tomogram.py

@@ -519,7 +519,7 @@ def refine(
             self.set_radius(i=i, binsize=binsize)
 
         _required = [H.spacing, H.skew, H.nPF]
-        if not spl.has_globalprops(_required):
+        if not spl.props.has_glob(_required):
             self.global_ft_params(i=i, binsize=binsize)
 
         spl.make_anchors(max_interval=max_interval)
@@ -529,9 +529,9 @@ def refine(
         # Calculate Fourier parameters by cylindrical transformation along spline.
         # Skew angles are divided by the angle of single protofilament and the residual
         # angles are used, considering missing wedge effect.
-        interv = spl.get_globalprops(H.spacing) * 2
-        skew = spl.get_globalprops(H.skew)
-        npf = roundint(spl.get_globalprops(H.nPF))
+        interv = spl.props.get_glob(H.spacing) * 2
+        skew = spl.props.get_glob(H.skew)
+        npf = roundint(spl.props.get_glob(H.nPF))
 
         LOGGER.info(
             f" >> Parameters: spacing = {interv/2:.2f} nm, skew = {skew:.3f} deg, PF = {npf}"
@@ -754,7 +754,7 @@ def local_radii(
             r_peak_sub = (imax_sub + 0.5) / nbin * r_max
             radii.append(r_peak_sub)
         out = pl.Series(H.radius, radii, dtype=pl.Float32)
-        spl.update_localprops([out], size)
+        spl.props.update_loc([out], size)
         return out
 
     @batch_process
@@ -814,8 +814,7 @@ def local_ft_params(
             pl.Series(H.splPos, spl.anchors, dtype=pl.Float32),
             pl.Series(H.splDist, spl.distances(), dtype=pl.Float32),
         )
-
-        spl.update_localprops(lprops, ft_size)
+        spl.props.update_loc(lprops, ft_size)
 
         return lprops
 
@@ -1017,7 +1016,7 @@ def infer_polarity(
             polar = mask_spectra(polar)
         img_flat = polar.proj("y")
 
-        if (npf := spl.get_globalprops(H.nPF, None)) is None:
+        if (npf := spl.props.get_glob(H.nPF, None)) is None:
             # if the global properties are already calculated, use it
             # otherwise, calculate the number of PFs from the power spectrum
             ft = img_flat.fft(shift=False, dims="ra")
@@ -1245,11 +1244,11 @@ def map_centers(
             Molecules object with mapped coordinates and angles.
         """
         spl = self.splines[i]
-        if spl.has_globalprops([H.spacing, H.skew]):
+        if spl.props.has_glob([H.spacing, H.skew]):
             self.global_ft_params(i=i)
 
-        interv = spl.get_globalprops(H.spacing) * 2
-        skew = spl.get_globalprops(H.skew)
+        interv = spl.props.get_glob(H.spacing) * 2
+        skew = spl.props.get_glob(H.skew)
 
         # Set interval to the dimer length by default.
         if interval is None:
@@ -1291,7 +1290,7 @@ def get_cylinder_model(
         spl = self.splines[i]
         _required = [H.spacing, H.skew, H.rise, H.nPF]
         _missing = [k for k in _required if k not in kwargs]
-        if not spl.has_globalprops(_missing):
+        if not spl.props.has_glob(_missing):
             self.global_ft_params(i=i)
         return spl.cylinder_model(offsets=offsets, **kwargs)
 
@@ -1302,6 +1301,7 @@ def map_monomers(
         *,
         offsets: tuple[nm, float] | None = None,
         orientation: Ori | str | None = None,
+        **kwargs,
     ) -> Molecules:
         """
         Map monomers in a regular cylinder shape.
@@ -1320,7 +1320,7 @@ def map_monomers(
         Molecules
             Object that represents monomer positions and angles.
         """
-        model = self.get_cylinder_model(i, offsets=offsets)
+        model = self.get_cylinder_model(i, offsets=offsets, **kwargs)
         yy, aa = np.indices(model.shape, dtype=np.int32)
         coords = np.stack([yy.ravel(), aa.ravel()], axis=1)
         spl = self.splines[i]
@@ -1337,6 +1337,7 @@ def map_on_grid(
         *,
         offsets: tuple[nm, float] | None = None,
         orientation: Ori | str | None = None,
+        **kwargs,
     ) -> Molecules:
         """
         Map monomers in a regular cylinder shape.
@@ -1357,7 +1358,7 @@ def map_on_grid(
         Molecules
             Object that represents monomer positions and angles.
         """
-        model = self.get_cylinder_model(i, offsets=offsets)
+        model = self.get_cylinder_model(i, offsets=offsets, **kwargs)
         coords = np.asarray(coords, dtype=np.int32)
         spl = self.splines[i]
         mole = model.locate_molecules(spl, coords)
@@ -1394,10 +1395,10 @@ def map_pf_line(
             Object that represents protofilament positions and angles.
         """
         spl = self.splines[i]
-        if not spl.has_globalprops([H.spacing, H.skew]):
+        if not spl.props.has_glob([H.spacing, H.skew]):
             self.global_ft_params(i=i)
-        interv = spl.get_globalprops(H.spacing) * 2
-        skew = spl.get_globalprops(H.skew)
+        interv = spl.props.get_glob(H.spacing) * 2
+        skew = spl.props.get_glob(H.skew)
 
         if interval is None:
             interval = interv
@@ -1555,7 +1556,7 @@ def _prepare_radii(
                 raise ValueError("Global radius is not measured yet.")
             radii = np.full(spl.anchors.size, spl.radius, dtype=np.float32)
         elif radius == "local":
-            if not spl.has_localprops(H.radius):
+            if not spl.props.has_loc(H.radius):
                 raise ValueError("Local radii is not measured yet.")
             radii = spl.localprops[H.radius].to_numpy()
         else: