General: Fixed import errors

Author: Somerandomguy10111

exports.py

@@ -1,56 +0,0 @@
-@classmethod
-def make_empty(cls, is_simulated: bool = False, num_phases: int = 1) -> PowderExperiment:
-    phases = []
-    for j in range(num_phases):
-        lengths = (float('nan'), float('nan'), float('nan'))
-        angles = (float('nan'), float('nan'), float('nan'))
-        base = CrystalBasis.empty()
-
-        p = CrystalStructure(lengths=lengths, angles=angles, basis=base)
-        phases.append(p)
-
-    xray_info = XrayInfo.mk_empty()
-    return cls(phases=phases, crystallite_size=None, temp_in_celcius=None, xray_info=xray_info,
-               is_simulated=is_simulated)
-
-
-def get_list_repr(self) -> list:
-    list_repr = []
-    structure = self.phases[0]
-
-    a, b, c = structure.lengths
-    alpha, beta, gamma = structure.angles
-    lattice_params = [a, b, c, alpha, beta, gamma]
-    list_repr += lattice_params
-
-    base = structure.basis
-    padded_base = self.get_padded_base(base=base, nan_padding=base.is_empty())
-    for atomic_site in padded_base:
-        list_repr += atomic_site.as_list()
-
-    if structure.spacegroup is None:
-        spg_logits_list = [float('nan') for _ in range(NUM_SPACEGROUPS)]
-    else:
-        spg_logits_list = [1000 if j + 1 == structure.spacegroup else 0 for j in range(NUM_SPACEGROUPS)]
-    list_repr += spg_logits_list
-
-    list_repr += self.xray_info.as_list()
-    list_repr += [self.is_simulated]
-
-    return list_repr
-
-@staticmethod
-def get_padded_base(base: CrystalBasis, nan_padding : bool) -> CrystalBasis:
-    def make_padding_site():
-        if nan_padding:
-            site = AtomSite.make_placeholder()
-        else:
-            site = AtomSite.make_void()
-        return site
-
-    delta = MAX_ATOMIC_SITES - len(base)
-    if delta < 0:
-        raise ValueError(f'Base is too large! Size = {len(base)} exceeds MAX_ATOMIC_SITES = {MAX_ATOMIC_SITES}')
-
-    padded_base = base + [make_padding_site() for _ in range(delta)]
-    return padded_base

tests/t_crystal/t_basis.py

@@ -1,6 +1,6 @@
 from holytools.devtools import Unittest
 
-from xrdpattern.crystal import CrystalBasis, AtomSite, Atom, CrystalExamples
+from xrdpattern.crystal import CrystalBasis, AtomSite, CrystalExamples
 
 
 # ---------------------------------------------------------
@@ -9,8 +9,6 @@ class TestCrystalBase(Unittest):
     def test_scattering_params(self):
         mock_base = CrystalBasis([
             AtomSite(x=0.5, y=0.5, z=0.5, occupancy=1.0, species_str="Si0"),
-            AtomSite(x=0.1, y=0.1, z=0.1, occupancy=1.0, species_str=Atom.placeholder_symbol),
-            AtomSite(x=0.9, y=0.9, z=0.9, occupancy=1.0, species_str=Atom.void_symbol)
         ])
         real_base = CrystalExamples.get_base()
 

tests/t_crystal/t_calculation.py

@@ -81,8 +81,6 @@ def to_clustered_pymatgen(crystal : CrystalStructure) -> Structure:
         alpha, beta, gamma = crystal.angles
         lattice = Lattice.from_parameters(a, b, c, alpha, beta, gamma)
 
-        non_void_sites = crystal.basis.get_non_void_sites()
-
         EPSILON = 0.001
         clusters: list[list[AtomSite]] = []
 
@@ -92,7 +90,7 @@ def matching_cluster(the_site):
                     return cl
             return None
 
-        for site in non_void_sites:
+        for site in crystal.basis.atom_sites:
             match = matching_cluster(site)
             if match:
                 match.append(site)

tests/t_parsing/t_parser.py

@@ -21,8 +21,8 @@ def test_obj_ok(self):
 
     def test_metadata_ok(self):
         metadata = self.pattern.powder_experiment
-        primary_wavelength = metadata.primary_wavelength
-        secondary_wavelength = metadata.secondary_wavelength
+        primary_wavelength = metadata.xray_info.primary_wavelength
+        secondary_wavelength = metadata.xray_info.secondary_wavelength
 
         for prop in [primary_wavelength, secondary_wavelength]:
             self.assertIsNotNone(obj=prop)

xrdpattern/xrd/__init__.py

@@ -1,2 +1,3 @@
-from .experiment import XrayInfo, XrdAnode, Metadata, PowderExperiment
+from .experiment import XrayInfo, Metadata, PowderExperiment
 from .data import XrdData, LabelType
+from .xray import XrdAnode, XrayInfo

xrdpattern/xrd/data.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import json
-import math
 from dataclasses import dataclass, fields, field
 from enum import Enum
 
@@ -11,8 +10,9 @@
 
 from xrdpattern.crystal import CrystalStructure
 from xrdpattern.serialization import Serializable
-from xrdpattern.xrd.experiment import PowderExperiment
 from xrdpattern.xrd import Metadata
+from xrdpattern.xrd.experiment import PowderExperiment
+
 
 # -------------------------------------------
 
@@ -82,19 +82,21 @@ def get_name(self) -> str:
     def get_phase(self, phase_num : int) -> CrystalStructure:
         return self.powder_experiment.phases[phase_num]
 
+
     def has_label(self, label_type: LabelType) -> bool:
-        if label_type == LabelType.composition:
-            return self.primary_phase.chemical_composition is not None
-        if label_type == LabelType.lattice:
-            return
-        if label_type == LabelType.atom_coords:
-            return len(self.primary_phase.basis) > 0
-        if label_type == LabelType.spg:
-            spg_explicit = self.primary_phase.spacegroup is not None
-            spg_implicit = self.has_label(label_type=LabelType.lattice) and self.has_label(
-                label_type=LabelType.atom_coords)
-            return spg_explicit or spg_implicit
-        return False
+        raise NotImplementedError
+        # if label_type == LabelType.composition:
+        #     return self.primary_phase.chemical_composition is not None
+        # if label_type == LabelType.lattice:
+        #     return
+        # if label_type == LabelType.atom_coords:
+        #     return len(self.primary_phase.basis) > 0
+        # if label_type == LabelType.spg:
+        #     spg_explicit = self.primary_phase.spacegroup is not None
+        #     spg_implicit = self.has_label(label_type=LabelType.lattice) and self.has_label(
+        #         label_type=LabelType.atom_coords)
+        #     return spg_explicit or spg_implicit
+        # return False
 
     def is_labeled(self) -> bool:
         return any(self.has_label(label_type=lt) for lt in LabelType)