Cleanup NGL Viewer class (orest-d#11)

A lot of the functionality previously contained in the Structure class
is now moved to the Viewer3d class. The main reason for this change is
that the structure class does not need to now about NGL at all.
Also the interface is much leaner and more options can be choosen by the
user afterwards if desired and don't expand the default interface.

pyproject.toml

@@ -2,7 +2,10 @@
 name = "py4vasp"
 version = "0.1.0"
 description = ""
-authors = ["Martin Schlipf <martin.schlipf@gmail.com>"]
+authors = [
+ "Martin Schlipf <martin.schlipf@gmail.com>",
+ "Orest Dubay <orest-d@users.noreply.github.com>"
+]
 
 [tool.poetry.dependencies]
 python = "^3.7"
@@ -31,7 +34,9 @@ numpy = {channel = "anaconda"}
 pandas = {channel = "anaconda"}
 cufflinks = {channel = "conda-forge", name = "cufflinks-py"}
 mdtraj = {channel = "conda-forge"}
+nglview = {channel = "conda-forge"}
 ase = {channel = "conda-forge"}
+pymatgen = {channel = "conda-forge"}
 sphinx = {channel = "anaconda"}
 
 [build-system]

src/py4vasp/data/__init__.py

@@ -22,6 +22,7 @@
 from .energy import Energy
 from .kpoints import Kpoints
 from .projectors import Projectors
+from .viewer3d import Viewer3d
 from .structure import Structure
 
 import plotly.io as pio

src/py4vasp/data/structure.py

@@ -1,56 +1,10 @@
 from py4vasp.data import _util
-from py4vasp.exceptions import RefinementException
-import functools
-import numpy as np
-
-
-class StructureViewer:
- """Collection of data and elements to be displayed in a structure viewer"""
-
- def __init__(self, structure, show_cell=True, supercell=None, show_axes=False, axes_length=3, arrows=None):
- self.structure = structure
- self.show_cell = show_cell
- self.supercell = supercell
- self.show_axes = show_axes
- self.axes_length = axes_length
- self.arrows = arrows
-
- def with_arrows(self, arrows):
- self.arrows = arrows
- return self
-
- def show(self):
- import nglview
- from nglview.shape import Shape
-
- structure = self.structure.to_pymatgen()
- if self.supercell is not None:
- structure.make_supercell(self.supercell)
-
- view = nglview.show_pymatgen(structure)
- if self.show_cell:
- view.add_representation(repr_type="unitcell")
- if self.show_axes or self.arrows is not None:
- shape = Shape(view=view)
- if self.show_axes:
- shape.add_arrow(
- [0, 0, 0], [self.axes_length, 0, 0], [1, 0, 0], 0.2)
- shape.add_arrow(
- [0, 0, 0], [0, self.axes_length, 0], [0, 1, 0], 0.2)
- shape.add_arrow(
- [0, 0, 0], [0, 0, self.axes_length], [0, 0, 1], 0.2)
- if self.arrows is not None:
- for (x, y, z), (vx, vy, vz) in zip(structure.cart_coords, self.arrows):
- shape.add_arrow(
- [x, y, z], [x+vx, y+vy, z+vz], [0.1, 0.1, 0.8], 0.2)
-
- return view
+from py4vasp.data import Viewer3d
 
 
 class Structure:
  def __init__(self, raw_structure):
  self._raw = raw_structure
- self.structure_viewer = None
 
  def read(self):
  return self.to_dict()
@@ -64,23 +18,18 @@ def to_dict(self):
 
  def __len__(self):
  return len(self._raw.cartesian_positions)
- 
+
  def to_pymatgen(self):
  import pymatgen as mg
+
  return mg.Structure(
  lattice=mg.Lattice(self._raw.cell.lattice_vectors),
  species=[specie.decode("ascii") for specie in self._raw.species],
  coords=self._raw.cartesian_positions,
- coords_are_cartesian=True
+ coords_are_cartesian=True,
  )
 
- def plot(self, show_cell=True, supercell=None, show_axes=False, axes_length=3):
- self.structure_viewer = StructureViewer(
- self, show_cell=show_cell, supercell=supercell, show_axes=show_axes, axes_length=axes_length)
- return self.structure_viewer.show()
-
- def plot_arrows(self, arrows):
- if self.structure_viewer is None:
- self.plot()
- self.structure_viewer = self.structure_viewer.with_arrows(arrows)
- return self.structure_viewer.show()
+ def plot(self, supercell=None):
+ viewer = Viewer3d(self, supercell=supercell)
+ viewer.show_cell()
+ return viewer

src/py4vasp/data/viewer3d.py

@@ -0,0 +1,73 @@
+from typing import NamedTuple
+import nglview
+import numpy as np
+
+
+class _Arrow3d(NamedTuple):
+ tail: np.ndarray
+ tip: np.ndarray
+ color: np.ndarray
+ radius: float = 0.2
+
+
+_x_axis = _Arrow3d(tail=np.zeros(3), tip=np.array((3, 0, 0)), color=[1, 0, 0])
+_y_axis = _Arrow3d(tail=np.zeros(3), tip=np.array((0, 3, 0)), color=[0, 1, 0])
+_z_axis = _Arrow3d(tail=np.zeros(3), tip=np.array((0, 0, 3)), color=[0, 0, 1])
+
+
+class Viewer3d:
+ """Collection of data and elements to be displayed in a structure viewer"""
+
+ def __init__(self, structure, supercell=None):
+ self._structure = structure
+ self._axes = None
+ self._arrows = []
+ self.supercell = supercell
+ self._ngl = self.show()
+
+ def _ipython_display_(self):
+ self._ngl._ipython_display_()
+
+ def show_cell(self):
+ self._ngl.add_unitcell()
+
+ def hide_cell(self):
+ self._ngl.remove_unitcell()
+
+ def show_axes(self):
+ if self._axes is not None:
+ return
+ self._axes = (
+ self._make_arrow(_x_axis),
+ self._make_arrow(_y_axis),
+ self._make_arrow(_z_axis),
+ )
+
+ def hide_axes(self):
+ if self._axes is None:
+ return
+ for axis in self._axes:
+ self._ngl.remove_component(axis)
+ self._axes = None
+
+ def show_arrows_at_atoms(self, arrows, color=[0.1, 0.1, 0.8]):
+ structure = self._structure.to_pymatgen()
+ for tail, arrow in zip(structure.cart_coords, arrows):
+ tip = tail + arrow
+ arrow = _Arrow3d(tail, tip, color)
+ self._arrows.append(self._make_arrow(arrow))
+
+ def hide_arrows_at_atoms(self):
+ for arrow in self._arrows:
+ self._ngl.remove_component(arrow)
+ self._arrows = []
+
+ def _make_arrow(self, arrow):
+ return self._ngl.shape.add_arrow(*arrow)
+
+ def show(self):
+ structure = self._structure.to_pymatgen()
+ if self.supercell is not None:
+ structure.make_supercell(self.supercell)
+ view = nglview.show_pymatgen(structure)
+ return view

src/py4vasp/raw/file.py

@@ -138,9 +138,9 @@ def structure(self):
  """
  self._assert_not_closed()
  return raw.Structure(
- cell = self.cell(),
- cartesian_positions = self._h5f["results/positions/cartesian_positions"],
- species = self._h5f["results/positions/species"],
+ cell=self.cell(),
+ cartesian_positions=self._h5f["results/positions/cartesian_positions"],
+ species=self._h5f["results/positions/species"],
  )
 
  def energy(self):

src/py4vasp/raw/rawdata.py

@@ -42,13 +42,15 @@ class Cell:
  "Lattice vectors defining the unit cell."
  __eq__ = _dataclass_equal
 
+
 @dataclass
 class Structure:
  cell: Cell
  cartesian_positions: np.ndarray
  species: np.ndarray = None
  __eq__ = _dataclass_equal
 
+
 @dataclass
 class Kpoints:
  "**k** points at which wave functions are calculated."

tests/data/test_structure.py

@@ -1,5 +1,6 @@
+from unittest.mock import patch
 from py4vasp.data import Structure
-from py4vasp.exceptions import RefinementException
+import py4vasp.data as data
 import py4vasp.raw as raw
 import pytest
 import numpy as np
@@ -12,19 +13,24 @@ def raw_structure():
  return raw.Structure(
  cell=raw.Cell(scale=1.0, lattice_vectors=np.eye(3)),
  cartesian_positions=np.arange(np.prod(shape)).reshape(shape),
- species=np.array(["C"]*number_atoms, dtype="S2"),
+ species=np.array(["C"] * number_atoms, dtype="S2"),
  )
 
 
+def get_messages_after_structure_information(view):
+ message_archive = view.get_state()["_ngl_msg_archive"]
+ all_messages = [(msg["methodName"], msg["args"]) for msg in message_archive]
+ return all_messages[1:] # first message is structure data
+
+
 def test_read(raw_structure, Assert):
  actual = Structure(raw_structure).read()
  assert (actual["cell"] == raw_structure.cell.lattice_vectors).all()
- Assert.allclose(actual["cartesian_positions"],
- raw_structure.cartesian_positions)
+ Assert.allclose(actual["cartesian_positions"], raw_structure.cartesian_positions)
  assert (actual["species"] == raw_structure.species).all()
 
 
-def test_to_pymatgen(raw_structure, Assert):
+def test_to_pymatgen(raw_structure):
  structure = Structure(raw_structure)
  mg_structure = structure.to_pymatgen()
  a, b, c = mg_structure.lattice.as_dict()["matrix"]
@@ -33,43 +39,11 @@ def test_to_pymatgen(raw_structure, Assert):
  assert c == [0, 0, 1]
 
 
-def test_plot(raw_structure, Assert):
- structure = Structure(raw_structure)
- assert structure.structure_viewer is None
- view = structure.plot()
- assert structure.structure_viewer is not None
-
- view = structure.plot(show_cell=False)
- assert [(msg["methodName"], msg["args"])
- for msg in view.get_state()["_ngl_msg_archive"]][1:] == []
-
- view = structure.plot(show_cell=True)
- assert [(msg["methodName"], msg["args"]) for msg in view.get_state()[
- "_ngl_msg_archive"]][1:] == [('addRepresentation', ['unitcell'])]
-
- view = structure.plot(show_cell=False, show_axes=False)
- assert [(msg["methodName"], msg["args"])
- for msg in view.get_state()["_ngl_msg_archive"]][1:] == []
-
- view = structure.plot(show_cell=False, show_axes=True, axes_length=5)
- assert [(msg["methodName"], msg["args"]) for msg in view.get_state()["_ngl_msg_archive"]][1:] == [
- ('addShape', [
- 'shape', [('arrow', [0, 0, 0], [5, 0, 0], [1, 0, 0], 0.2)]]),
- ('addShape', [
- 'shape', [('arrow', [0, 0, 0], [0, 5, 0], [0, 1, 0], 0.2)]]),
- ('addShape', [
- 'shape', [('arrow', [0, 0, 0], [0, 0, 5], [0, 0, 1], 0.2)]]),
- ]
-
-
-def test_plot_arrows(raw_structure, Assert):
- structure = Structure(raw_structure)
- assert structure.structure_viewer is None
- view = structure.plot_arrows([(0, 0, 1) for i in range(len(structure))])
- assert structure.structure_viewer is not None
- assert [(msg["methodName"], msg["args"]) for msg in view.get_state()[
- "_ngl_msg_archive"]][1] == ('addRepresentation', ['unitcell'])
- assert [(msg["methodName"], msg["args"]) for msg in view.get_state()[
- "_ngl_msg_archive"]][2] == ('addShape', ['shape', [('arrow', [0.0, 1.0, 2.0], [0.0, 1.0, 3.0], [0.1, 0.1, 0.8], 0.2)]])
- assert sum(msg["methodName"] == 'addShape' for msg in view.get_state()[
- "_ngl_msg_archive"]) == len(structure)
+def test_plot(raw_structure):
+ cm_init = patch.object(data.Viewer3d, "__init__", autospec=True, return_value=None)
+ cm_cell = patch.object(data.Viewer3d, "show_cell")
+ with cm_init as init, cm_cell as cell:
+ structure = Structure(raw_structure)
+ structure.plot()
+ init.assert_called_once()
+ cell.assert_called_once()