Merge a54f2a1 into bca4aa3

sparks-baird · Jun 9, 2022 · 4339b11 · 4339b11
2 parents bca4aa3 + a54f2a1
commit 4339b11
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diff --git a/scripts/run_grayskull.py b/scripts/run_grayskull.py
@@ -94,8 +94,3 @@
 if personal_conda_channel:
     my_recipe.save(fpath2)
     copyfile("LICENSE.txt", join(dirname(fpath2), "LICENSE.txt"))
-
-# %% Code Graveyard
-# blank_id = bld.value.index("")
-# last_id = len(bld.value) - 1
-# bld.value[blank_id], bld.value[last_id] = bld.value[last_id], bld.value[blank_id]
diff --git a/src/xtal2png/core.py b/src/xtal2png/core.py
@@ -774,162 +774,3 @@ def run():
     #     python -m xtal2png.core example.cif
     #
     run()
-
-
-# %% Code Graveyard
-# @classmethod
-# def scale_array(data: np.ndarray):
-#     """Scale the 3D xtal array values as preprocessing step for PNG format.
-
-#     Parameters
-#     ----------
-#     data : np.ndarray
-#         Unscaled 3D array of crystallographic information.
-
-#     Returns
-#     -------
-#     _type_
-#         _description_
-#     """
-#     #
-
-# @classmethod
-# def unscale_array(data: np.ndarray):
-#     """Unscale the 3D xtal array values as part of conversion from PNG to Structure.
-
-#     Parameters
-#     ----------
-#     data : np.ndarray
-#         Scaled 3D array of crystallographic information.
-
-#     Returns
-#     -------
-#     _type_
-#         _description_
-#     """
-#     #
-
-# atomic_numbers = list(zip_longest(*atomic_numbers, fillvalue=0))
-
-# atom_scaler = MinMaxScaler(feature_range=atom_range)
-# frac_scaler = MinMaxScaler(feature_range=frac_range)
-# abc_scaler = MinMaxScaler(feature_range=abc_range)
-# angles_scaler = MinMaxScaler(feature_range=angles_range)
-# space_group_scaler = MinMaxScaler(feature_range=space_group_range)
-# distance_scaler = MinMaxScaler(feature_range=distance_range)
-
-# atom_scaled = atom_scaler.fit_transform(atomic_numbers)
-# frac_scaled = frac_scaler.fit_transform(frac_coords)
-# abc_scaled = abc_scaler.fit_transform(abc)
-# angles_scaled = angles_scaler.fit_transform(angles)
-# space_group_scaled = space_group_scaler.fit_transform(space_group)
-# distance_scaled = distance_scaler.fit_transform(distance_matrix)
-
-# atomic_numbers: NDArray[np.int_] = np.array([])
-# frac_coords: NDArray[np.float] = np.array([])
-# abc: NDArray[np.float] = np.array([])
-# angles: NDArray[np.float] = np.array([])
-# space_group: NDArray[np.int_] = np.array([])
-# distance_matrix: NDArray[np.float] = np.array([])
-
-# (
-#     atom_scaled,
-#     frac_scaled,
-#     abc_scaled,
-#     angles_scaled,
-#     space_group_scaled,
-#     distance_scaled,
-# )
-# id_blocks = [b * i for i, b in enumerate(id_blocks)]
-
-# def mask_png(self, keep_keys:List[str]=[ATOM_KEY]):
-#     self.data[self.id_data == self.id_mapper[ATOM_KEY]]
-
-# id_mapper = dict(
-#     atom=ATOM_ID,
-#     frac=FRAC_ID,
-#     abc=ABC_ID,
-#     angles=ANGLES_ID,
-#     volume=VOLUME_ID,
-#     space_group=SPACE_GROUP_ID,
-#     distance=DISTANCE_ID,
-# )
-
-
-# (
-#     atom_ids,
-#     frac_ids,
-#     abc_ids,
-#     angles_ids,
-#     volume_ids,
-#     space_group_ids,
-#     distance_ids,
-# )
-
-# [
-#     data[
-#         min(i[0]) : max(i[0]) + 1,
-#     ]
-#     for i in ids
-# ]
-
-# (
-#     atom_vert,
-#     frac_vert,
-#     abc_vert,
-#     angles_vert,
-#     volume_vert,
-#     space_group_vert,
-#     distance_vert,
-# )
-
-# (
-#     atom_horz,
-#     frac_horz,
-#     abc_horz,
-#     angles_horz,
-#     volume_horz,
-#     space_group_horz,
-#     distance_horz,
-# )
-
-# atom_arr = (atom_vert.swapaxes(1, 2) + atom_horz) / 2
-# frac_arr = (frac_vert.swapaxes(1, 2) + frac_horz) / 2
-# abc_arr = (abc_vert.swapaxes(1, 2) + abc_horz) / 2
-
-# ids = [np.where(id_data == id_mapper[key]) for key in keys]
-
-# orig_shape = data.shape
-# data.flatten()[np.where(id_data.flatten() == 1)[0]]
-
-# atom_scaled = np.array(atomic_numbers)
-# frac_scaled = frac_coords
-# abc_scaled = np.array(abc)
-# angles_scaled = np.array(angles)
-# volume_scaled = np.array(volume)
-# space_group_scaled = np.array(space_group)
-# distance_scaled = distance_matrix
-
-# def count_zero(X):
-#     num_zeros = np.count_nonzero(at == 0)
-#     return num_zeros
-# num_zeros = np.count_nonzero(at == 0)
-
-
-# atomic_numbers = []
-# frac_coords = []
-# abc = []
-# angles = []
-# volume = []
-# space_group = []
-# distance_matrix = []
-
-# atomic_numbers.append(at)
-# frac_coords.append(fr)
-# abc.append(abc_tmp[i])
-# angles.append(angles_tmp[i])
-# volume.append(volume_tmp[i])
-# space_group.append(space_group_tmp[i])
-# distance_matrix.append(di_cropped)
-
-# abc: List[List[float]] = []
diff --git a/tests/xtal2png_test.py b/tests/xtal2png_test.py
@@ -201,9 +201,3 @@ def test_plot_and_save():
     test_png2xtal_single()
 
 1 + 1
-
-# %% Code Graveyard
-#     xc = XtalConverter()
-#     data = xc.xtal2png(example_structures, show=True, save=True)
-#     decoded_structures = xc.png2xtal(data, save=False)
-#     return decoded_structures