Remove obsolete functions

Author: tcompa

fractal_tasks_core/roi/_overlaps_common.py

@@ -62,35 +62,6 @@ def is_overlapping_2D(
     return overlap_x and overlap_y
 
 
-def is_overlapping_3D(
-    box1: Sequence[float], box2: Sequence[float], tol: float = 1e-10
-) -> bool:
-    """
-    Given two three-dimensional boxes, finds whether they overlap.
-
-    This is based on https://stackoverflow.com/a/70023212/19085332, and we
-    additionally use a finite tolerance for floating-point comparisons.
-
-    Args:
-        box1: The boundaries of the first box, written as
-            `[x_min, y_min, z_min, x_max, y_max, z_max]`.
-        box2: The boundaries of the second box, written as
-            `[x_min, y_min, z_min, x_max, y_max, z_max]`.
-        tol: Finite tolerance for floating-point comparisons.
-    """
-
-    overlap_x = is_overlapping_1D(
-        [box1[0], box1[3]], [box2[0], box2[3]], tol=tol
-    )
-    overlap_y = is_overlapping_1D(
-        [box1[1], box1[4]], [box2[1], box2[4]], tol=tol
-    )
-    overlap_z = is_overlapping_1D(
-        [box1[2], box1[5]], [box2[2], box2[5]], tol=tol
-    )
-    return overlap_x and overlap_y and overlap_z
-
-
 def _is_overlapping_1D_int(
     line1: Sequence[int],
     line2: Sequence[int],

fractal_tasks_core/roi/v1_overlaps.py

@@ -23,7 +23,6 @@
 from fractal_tasks_core.roi._overlaps_common import _is_overlapping_3D_int
 from fractal_tasks_core.roi._overlaps_common import is_overlapping_1D
 from fractal_tasks_core.roi._overlaps_common import is_overlapping_2D
-from fractal_tasks_core.roi._overlaps_common import is_overlapping_3D
 
 
 logger = logging.getLogger(__name__)
@@ -52,58 +51,6 @@ def get_overlapping_pair(
     return False
 
 
-def get_overlapping_pairs_3D(
-    tmp_df: pd.DataFrame,
-    full_res_pxl_sizes_zyx: Sequence[float],
-):
-    """
-    Finds the indices for the all overlapping FOVs pair, in three dimensions.
-
-    Note: the returned indices are positional indices, starting from 0.
-
-    Args:
-        tmp_df: Dataframe with columns `{x,y,z}_micrometer` and
-            `len_{x,y,z}_micrometer`.
-        full_res_pxl_sizes_zyx: TBD
-    """
-
-    tol = 1e-10
-    if tol > min(full_res_pxl_sizes_zyx) / 1e3:
-        raise ValueError(f"{tol=} but {full_res_pxl_sizes_zyx=}")
-
-    new_tmp_df = tmp_df.copy()
-
-    new_tmp_df["x_micrometer_max"] = (
-        new_tmp_df["x_micrometer"] + new_tmp_df["len_x_micrometer"]
-    )
-    new_tmp_df["y_micrometer_max"] = (
-        new_tmp_df["y_micrometer"] + new_tmp_df["len_y_micrometer"]
-    )
-    new_tmp_df["z_micrometer_max"] = (
-        new_tmp_df["z_micrometer"] + new_tmp_df["len_z_micrometer"]
-    )
-    # Remove columns which are not necessary for overlap checks
-    list_columns = [
-        "len_x_micrometer",
-        "len_y_micrometer",
-        "len_z_micrometer",
-        "label",
-    ]
-    new_tmp_df.drop(labels=list_columns, axis=1, inplace=True)
-
-    # Loop over all pairs, and construct list of overlapping ones
-    num_lines = len(new_tmp_df.index)
-    overlapping_list = []
-    for pos_ind_1 in range(num_lines):
-        for pos_ind_2 in range(pos_ind_1):
-            bbox_1 = new_tmp_df.iloc[pos_ind_1].to_numpy()
-            bbox_2 = new_tmp_df.iloc[pos_ind_2].to_numpy()
-            overlap = is_overlapping_3D(bbox_1, bbox_2, tol=tol)
-            if overlap:
-                overlapping_list.append((pos_ind_1, pos_ind_2))
-    return overlapping_list
-
-
 def apply_shift_in_one_direction(
     tmp_df_well: pd.DataFrame,
     line_1: Sequence[float],