Merge branch '10-selection-refactoring' into 'master'

Resolve "Selection refactoring"

Closes orest-d#10

See merge request schlipf/py4vasp!10

src/py4vasp/data/__init__.py

@@ -1,5 +1,6 @@
 from .band import Band
 from .dos import Dos
+from .projectors import Projectors
 
 import plotly.io as pio
 import cufflinks as cf

src/py4vasp/data/band.py

@@ -1,17 +1,11 @@
-import re
 import functools
 import itertools
 import numpy as np
 import plotly.graph_objects as go
-from collections import namedtuple
+from .projectors import Projectors
 
 
 class Band:
- _Index = namedtuple("_Index", "spin, atom, orbital")
- _Atom = namedtuple("_Atom", "indices, label")
- _Orbital = namedtuple("_Orbital", "indices, label")
- _Spin = namedtuple("_Spin", "indices, label")
-
  def __init__(self, raw_band):
  self._raw = raw_band
  self._fermi_energy = raw_band.fermi_energy
@@ -25,58 +19,14 @@ def __init__(self, raw_band):
  self._num_lines = len(self._kpoints) // self._line_length
  self._indices = raw_band.label_indices
  self._labels = raw_band.labels
- self._has_projectors = raw_band.projectors is not None
- if self._has_projectors:
-  self._init_projectors(raw_band.projectors)
+ if raw_band.projectors is not None:
+  self._projectors = Projectors(raw_band.projectors)
+ self._projections = raw_band.projections
 
  @classmethod
  def from_file(cls, file):
  return cls(file.band())
 
- def _init_projectors(self, raw_proj):
- self._projections = raw_proj.bands
- ion_types = raw_proj.ion_types
- ion_types = [type.decode().strip() for type in ion_types]
- self._init_atom_dict(ion_types, raw_proj.number_ion_types)
- orbitals = raw_proj.orbital_types
- orbitals = [orb.decode().strip() for orb in orbitals]
- self._init_orbital_dict(orbitals)
- self._init_spin_dict()
-
- def _init_atom_dict(self, ion_types, number_ion_types):
- num_atoms = self._projections.shape[1]
- all_atoms = self._Atom(indices=range(num_atoms), label=None)
- self._atom_dict = {"*": all_atoms}
- start = 0
- for type, number in zip(ion_types, number_ion_types):
- _range = range(start, start + number)
- self._atom_dict[type] = self._Atom(indices=_range, label=type)
- for i in _range:
- # create labels like Si_1, Si_2, Si_3 (starting at 1)
- label = type + "_" + str(_range.index(i) + 1)
- self._atom_dict[str(i + 1)] = self._Atom(indices=[i], label=label)
- start += number
- # atoms may be preceeded by :
- for key in self._atom_dict.copy():
- self._atom_dict[key + ":"] = self._atom_dict[key]
-
- def _init_orbital_dict(self, orbitals):
- num_orbitals = self._projections.shape[2]
- all_orbitals = self._Orbital(indices=range(num_orbitals), label=None)
- self._orbital_dict = {"*": all_orbitals}
- for i, orbital in enumerate(orbitals):
- self._orbital_dict[orbital] = self._Orbital(indices=[i], label=orbital)
- if "px" in self._orbital_dict:
- self._orbital_dict["p"] = self._Orbital(indices=range(1, 4), label="p")
- self._orbital_dict["d"] = self._Orbital(indices=range(4, 9), label="d")
- self._orbital_dict["f"] = self._Orbital(indices=range(9, 16), label="f")
-
- def _init_spin_dict(self):
- labels = ["up", "down"] if self._spin_polarized else [None]
- self._spin_dict = {
- key: self._Spin(indices=[i], label=key) for i, key in enumerate(labels)
- }
-
  def read(self, selection=None):
  kpoints = self._kpoints[:]
  return {
@@ -124,12 +74,6 @@ def _shift_bands_by_fermi_energy(self):
  else:
  return {"bands": self._bands[0] - self._fermi_energy}
 
- def _read_projections(self, selection):
- if selection is None:
- return {}
- parts = self._parse_selection(selection)
- return self._read_elements(parts)
-
  def _scatter(self, name, kdists, lines):
  # insert NaN to split separate lines
  num_bands = lines.shape[-1]
@@ -146,24 +90,17 @@ def _kpoint_distances(self, kpoints):
  )
  return functools.reduce(concatenate_distances, kpoint_norms)
 
- def _parse_selection(self, selection):
- atom = self._atom_dict["*"]
- selection = re.sub("\s*:\s*", ": ", selection)
- for part in re.split("[ ,]+", selection):
- if part in self._orbital_dict:
- orbital = self._orbital_dict[part]
- else:
- atom = self._atom_dict[part]
- orbital = self._orbital_dict["*"]
- if ":" not in part: # exclude ":" because it starts a new atom
- for spin in self._spin_dict.values():
- yield atom, orbital, spin
+ def _read_projections(self, selection):
+ if selection is None:
+ return {}
+ return self._read_elements(selection)
 
- def _read_elements(self, parts):
+ def _read_elements(self, selection):
  res = {}
- for atom, orbital, spin in parts:
+ for select in self._projectors.parse_selection(selection):
+ atom, orbital, spin = self._projectors.select(*select)
  label = self._merge_labels([atom.label, orbital.label, spin.label])
- index = self._Index(spin.indices, atom.indices, orbital.indices)
+ index = (spin.indices, atom.indices, orbital.indices)
  res[label] = self._read_element(index)
  return res
 

src/py4vasp/data/dos.py

@@ -1,17 +1,11 @@
-import re
 import functools
 import itertools
 import numpy as np
 import pandas as pd
-from collections import namedtuple
+from .projectors import Projectors
 
 
 class Dos:
- _Index = namedtuple("_Index", "spin, atom, orbital")
- _Atom = namedtuple("_Atom", "indices, label")
- _Orbital = namedtuple("_Orbital", "indices, label")
- _Spin = namedtuple("_Spin", "indices, label")
-
  def __init__(self, raw_dos):
  self._raw = raw_dos
  self._fermi_energy = raw_dos.fermi_energy
@@ -20,56 +14,13 @@ def __init__(self, raw_dos):
  self._spin_polarized = self._dos.shape[0] == 2
  self._has_partial_dos = raw_dos.projectors is not None
  if self._has_partial_dos:
- self._init_partial_dos(raw_dos.projectors)
+ self._projectors = Projectors(raw_dos.projectors)
+ self._projections = raw_dos.projections
 
  @classmethod
  def from_file(cls, file):
  return cls(file.dos())
 
- def _init_partial_dos(self, raw_proj):
- self._partial_dos = raw_proj.dos
- ion_types = raw_proj.ion_types
- ion_types = [type.decode().strip() for type in ion_types]
- self._init_atom_dict(ion_types, raw_proj.number_ion_types)
- orbitals = raw_proj.orbital_types
- orbitals = [orb.decode().strip() for orb in orbitals]
- self._init_orbital_dict(orbitals)
- self._init_spin_dict()
-
- def _init_atom_dict(self, ion_types, number_ion_types):
- num_atoms = self._partial_dos.shape[1]
- all_atoms = self._Atom(indices=range(num_atoms), label=None)
- self._atom_dict = {"*": all_atoms}
- start = 0
- for type, number in zip(ion_types, number_ion_types):
- _range = range(start, start + number)
- self._atom_dict[type] = self._Atom(indices=_range, label=type)
- for i in _range:
- # create labels like Si_1, Si_2, Si_3 (starting at 1)
- label = type + "_" + str(_range.index(i) + 1)
- self._atom_dict[str(i + 1)] = self._Atom(indices=[i], label=label)
- start += number
- # atoms may be preceeded by :
- for key in self._atom_dict.copy():
- self._atom_dict[key + ":"] = self._atom_dict[key]
-
- def _init_orbital_dict(self, orbitals):
- num_orbitals = self._partial_dos.shape[2]
- all_orbitals = self._Orbital(indices=range(num_orbitals), label=None)
- self._orbital_dict = {"*": all_orbitals}
- for i, orbital in enumerate(orbitals):
- self._orbital_dict[orbital] = self._Orbital(indices=[i], label=orbital)
- if "px" in self._orbital_dict:
- self._orbital_dict["p"] = self._Orbital(indices=range(1, 4), label="p")
- self._orbital_dict["d"] = self._Orbital(indices=range(4, 9), label="d")
- self._orbital_dict["f"] = self._Orbital(indices=range(9, 16), label="f")
-
- def _init_spin_dict(self):
- labels = ["up", "down"] if self._spin_polarized else [None]
- self._spin_dict = {
- key: self._Spin(indices=[i], label=key) for i, key in enumerate(labels)
- }
-
  def plot(self, selection=None):
  df = self.to_frame(selection)
  if self._spin_polarized:
@@ -114,40 +65,27 @@ def _read_partial_dos(self, selection):
  if selection is None:
  return {}
  self._raise_error_if_partial_Dos_not_available()
- parts = self._parse_filter(selection)
- return self._read_elements(parts)
+ return self._read_elements(selection)
 
  def _raise_error_if_partial_Dos_not_available(self):
  if not self._has_partial_dos:
  raise ValueError(
  "Filtering requires partial DOS which was not found in HDF5 file."
  )
 
- def _parse_filter(self, selection):
- atom = self._atom_dict["*"]
- selection = re.sub("\s*:\s*", ": ", selection)
- for part in re.split("[ ,]+", selection):
- if part in self._orbital_dict:
- orbital = self._orbital_dict[part]
- else:
- atom = self._atom_dict[part]
- orbital = self._orbital_dict["*"]
- if ":" not in part: # exclude ":" because it starts a new atom
- for spin in self._spin_dict.values():
- yield atom, orbital, spin
-
- def _read_elements(self, parts):
+ def _read_elements(self, selection):
  res = {}
- for atom, orbital, spin in parts:
+ for select in self._projectors.parse_selection(selection):
+ atom, orbital, spin = self._projectors.select(*select)
  label = self._merge_labels([atom.label, orbital.label, spin.label])
- index = self._Index(spin.indices, atom.indices, orbital.indices)
+ index = (spin.indices, atom.indices, orbital.indices)
  res[label] = self._read_element(index)
  return res
 
  def _merge_labels(self, labels):
  return "_".join(filter(None, labels))
 
  def _read_element(self, index):
- sum_dos = lambda dos, i: dos + self._partial_dos[i]
+ sum_dos = lambda dos, i: dos + self._projections[i]
  zero_dos = np.zeros(len(self._energies))
  return functools.reduce(sum_dos, itertools.product(*index), zero_dos)