py4dgeo 0.7.0__cp312-cp312-macosx_14_0_arm64.whl

py4dgeo/pbm3c2.py

@@ -0,0 +1,3870 @@
+import colorsys
+import random
+import typing
+import pprint
+import logging
+
+import numpy as np
+
+from sklearn.base import BaseEstimator, ClassifierMixin, TransformerMixin
+from sklearn.utils.validation import check_X_y, check_array, check_is_fitted
+from sklearn.utils.multiclass import unique_labels
+
+from sklearn.pipeline import Pipeline
+from sklearn.compose import make_column_selector
+
+from sklearn.ensemble import RandomForestClassifier
+from sklearn import set_config
+
+set_config(display="diagram")
+
+from abc import ABC, abstractmethod
+
+from py4dgeo import Epoch
+from py4dgeo.util import Py4DGeoError, find_file
+
+try:
+    from vedo import *
+
+    interactive_available = True
+except ImportError:
+    interactive_available = False
+
+__all__ = [
+    "Viewer",
+    "BaseTransformer",
+    "PerPointComputation",
+    "Segmentation",
+    "ExtractSegments",
+    "BuilderExtended_y",
+    "BuilderExtended_y_Visually",
+    "ClassifierWrapper",
+    "PBM3C2",
+    "build_input_scenario2_without_normals",
+    "build_input_scenario2_with_normals",
+    "PBM3C2WithSegments",
+    "set_interactive_backend",
+    "generate_random_extended_y",
+    "LLSV_PCA_COLUMNS",
+    "SEGMENTED_POINT_CLOUD_COLUMNS",
+    "SEGMENT_COLUMNS",
+    "generate_extended_y_from_prior_knowledge",
+    "generate_possible_region_pairs",
+    "DEFAULT_NO_SEGMENT",
+    "DEFAULT_STD_DEVIATION_OF_NO_CORE_POINT",
+    "add_no_corresponding_seg",
+    "config_epoch0_as_segments",
+]
+
+logger = logging.getLogger("py4dgeo")
+
+pp = pprint.PrettyPrinter(depth=4)
+
+config_epoch0_as_segments = {
+    "get_pipeline_options": True,
+    "epoch0_Transform_PerPointComputation__skip": True,
+    "epoch0_Transform_Segmentation__skip": True,
+    "epoch0_Transform_Second_Segmentation__skip": True,
+    "epoch0_Transform_ExtractSegments__skip": True,
+}
+
+
+class LLSV_PCA_COLUMNS:
+    X_COLUMN = 0
+    Y_COLUMN = 1
+    Z_COLUMN = 2
+    EPOCH_ID_COLUMN = 3
+    EIGENVALUE0_COLUMN = 4
+    EIGENVALUE1_COLUMN = 5
+    EIGENVALUE2_COLUMN = 6
+    EIGENVECTOR_0_X_COLUMN = 7
+    EIGENVECTOR_0_Y_COLUMN = 8
+    EIGENVECTOR_0_Z_COLUMN = 9
+    EIGENVECTOR_1_X_COLUMN = 10
+    EIGENVECTOR_1_Y_COLUMN = 11
+    EIGENVECTOR_1_Z_COLUMN = 12
+    EIGENVECTOR_2_X_COLUMN = 13
+    EIGENVECTOR_2_Y_COLUMN = 14
+    EIGENVECTOR_2_Z_COLUMN = 15
+    LLSV_COLUMN = 16
+    NUMBER_OF_COLUMNS = 17
+
+
+class SEGMENTED_POINT_CLOUD_COLUMNS:
+    X_COLUMN = 0
+    Y_COLUMN = 1
+    Z_COLUMN = 2
+    EPOCH_ID_COLUMN = 3
+    EIGENVALUE0_COLUMN = 4
+    EIGENVALUE1_COLUMN = 5
+    EIGENVALUE2_COLUMN = 6
+    EIGENVECTOR_0_X_COLUMN = 7
+    EIGENVECTOR_0_Y_COLUMN = 8
+    EIGENVECTOR_0_Z_COLUMN = 9
+    EIGENVECTOR_1_X_COLUMN = 10
+    EIGENVECTOR_1_Y_COLUMN = 11
+    EIGENVECTOR_1_Z_COLUMN = 12
+    EIGENVECTOR_2_X_COLUMN = 13
+    EIGENVECTOR_2_Y_COLUMN = 14
+    EIGENVECTOR_2_Z_COLUMN = 15
+    LLSV_COLUMN = 16
+    SEGMENT_ID_COLUMN = 17
+    STANDARD_DEVIATION_COLUMN = 18
+    NUMBER_OF_COLUMNS = 19
+
+
+class SEGMENT_COLUMNS:
+    X_COLUMN = 0
+    Y_COLUMN = 1
+    Z_COLUMN = 2
+    EPOCH_ID_COLUMN = 3
+    EIGENVALUE0_COLUMN = 4
+    EIGENVALUE1_COLUMN = 5
+    EIGENVALUE2_COLUMN = 6
+    EIGENVECTOR_0_X_COLUMN = 7
+    EIGENVECTOR_0_Y_COLUMN = 8
+    EIGENVECTOR_0_Z_COLUMN = 9
+    EIGENVECTOR_1_X_COLUMN = 10
+    EIGENVECTOR_1_Y_COLUMN = 11
+    EIGENVECTOR_1_Z_COLUMN = 12
+    EIGENVECTOR_2_X_COLUMN = 13
+    EIGENVECTOR_2_Y_COLUMN = 14
+    EIGENVECTOR_2_Z_COLUMN = 15
+    LLSV_COLUMN = 16
+    SEGMENT_ID_COLUMN = 17
+    STANDARD_DEVIATION_COLUMN = 18
+    NR_POINTS_PER_SEG_COLUMN = 19
+    NUMBER_OF_COLUMNS = 20
+
+
+# default value, for the points that are part of NO segment ( e.g. -1 )
+DEFAULT_NO_SEGMENT = -1
+
+# default standard deviation value for points that are not "core points"
+DEFAULT_STD_DEVIATION_OF_NO_CORE_POINT = -1
+
+
+def set_interactive_backend(backend="vtk"):
+    """Set the interactive backend for selection of correspondent segments.
+
+    All backends that can be used with the vedo library can be given here.
+    E.g. the following backends are available: vtk, ipyvtk, k3d, 2d, ipygany, panel, itk
+    """
+    if interactive_available:
+        from vedo import settings
+
+        settings.default_backend = backend
+
+
+def _extract_from_additional_dimensions(
+    epoch: Epoch,
+    column_names: typing.List[str],
+    required_number_of_columns: typing.List[int] = [],
+):
+    """
+    Build a numpy array using 'column_names' which are part of the 'additional_dimensions' field.
+    The result will maintain the same order or the columns found in 'column_names'.
+
+    :param epoch:
+        Epoch class.
+    :param column_names:
+        list[ str ]
+    :param required_number_of_columns:
+        list[ int ]
+        default [] , any number of parameter found gets accepted.
+        The number of columns required to consider the output valid.
+    :return
+        numpy array
+    """
+
+    result = np.empty(shape=(epoch.cloud.shape[0], 0), dtype=float)
+
+    for column in column_names:
+        if column in epoch.additional_dimensions.dtype.names:
+            result = np.concatenate(
+                (result, epoch.additional_dimensions[column]), axis=1
+            )
+        else:
+            logger.debug(
+                f"Column '{column}' not found during _extract_from_additional_dimensions()"
+            )
+
+    assert (
+        required_number_of_columns == []
+        or result.shape[1] in required_number_of_columns
+    ), "The number of column found is not a valid one."
+
+    return result
+
+
+def angle_difference_compute(normal1, normal2):
+    """
+
+    :param normal1:
+        unit vector
+    :param normal2:
+        unit vector
+    :return:
+        numpy array of angles in degrees.
+    """
+
+    # normal1, normal2 have to be unit vectors ( and that is the case as a result of the SVD process )
+    return np.arccos(np.clip(np.dot(normal1, normal2), -1.0, 1.0)) * 180.0 / np.pi
+
+
+def geodesic_distance(v1, v2):
+    """
+    Compute the shortest angular distance between 2 unit vectors.
+
+    :param v1:
+        unit vector
+    :param v2:
+        unit vector
+    :return:
+        numpy array of angles in degrees.
+    """
+
+    return min(
+        np.arccos(np.clip(np.dot(v1, v2), -1.0, 1.0)) * 180.0 / np.pi,
+        np.arccos(np.clip(np.dot(v1, -v2), -1.0, 1.0)) * 180.0 / np.pi,
+    )
+
+
+class Viewer:
+    def __init__(self):
+        self.sets = []
+        self.plt = Plotter(axes=3)
+
+    @staticmethod
+    def HSVToRGB(h, s, v):
+        """
+        Convert from HSV ( Hue Saturation Value ) color to RGB ( Red Blue Green )
+
+        :param h:
+            float [0, 1]
+        :param s:
+            float [0, 1]
+        :param v:
+            float [0, 1]
+        :return:
+            tuple [ float, float, float ]
+        """
+        return colorsys.hsv_to_rgb(h, s, v)
+
+    @staticmethod
+    def get_distinct_colors(n):
+        """
+        Return a python list of 'n' distinct colors.
+
+        :param n:
+            number of colors.
+        :return:
+            python list of tuple [ float, float, float ]
+        """
+
+        huePartition = 1.0 / (n + 1)
+        return [
+            Viewer.HSVToRGB(huePartition * value, 1.0, 1.0) for value in range(0, n)
+        ]
+
+    @staticmethod
+    def read_np_ndarray_from_xyz(input_file_name: str) -> np.ndarray:
+        """
+        The reconstructed np.ndarray.
+        :param input_file_name:
+            The output file name.
+        :return:
+            np.ndarray
+        """
+
+        # Resolve the given path
+        filename = find_file(input_file_name)
+
+        # Read it
+        try:
+            logger.info(f"Reading np.ndarray from file '{filename}'")
+            np_ndarray = np.genfromtxt(filename, delimiter=",")
+        except ValueError:
+            raise Py4DGeoError("Malformed file: " + str(filename))
+
+        return np_ndarray
+
+    @staticmethod
+    def segmented_point_cloud_visualizer(
+        X: np.ndarray, columns=SEGMENTED_POINT_CLOUD_COLUMNS
+    ):
+        """
+        Visualize a segmented point cloud. ( the resulting point cloud after the segmentation process )
+
+        :param X:
+            numpy array (n_points, 19) with the following column structure:
+            [
+                x, y, z ( 3 columns ),
+                EpochID ( 1 column ),
+                Eigenvalues( 3 columns ), -> that correspond to the next 3 Eigenvectors
+                Eigenvectors( 3 columns ) X 3 -> in descending order using vector norm 2,
+                Lowest local surface variation ( 1 column ),
+                Segment_ID ( 1 column ),
+                Standard deviation ( 1 column )
+            ]
+        :return:
+        """
+
+        X_Y_Z_Columns = [columns.X_COLUMN, columns.Y_COLUMN, columns.Z_COLUMN]
+
+        viewer = Viewer()
+
+        nr_segments = int(X[:, columns.SEGMENT_ID_COLUMN].max())
+        colors = Viewer.get_distinct_colors(nr_segments + 1)
+
+        for i in range(0, nr_segments + 1):
+            mask = X[:, columns.SEGMENT_ID_COLUMN] == float(i)
+            # x,y,z
+            set_cloud = X[mask, :][:, X_Y_Z_Columns]
+
+            viewer.sets = viewer.sets + [Points(set_cloud, colors[i], alpha=1, r=10)]
+
+        viewer.plt.show(viewer.sets).close()
+
+    @staticmethod
+    def segments_visualizer(X: np.ndarray, columns=SEGMENT_COLUMNS):
+        """
+        Segments visualizer.
+
+        :param X:
+            Each row is a segment, numpy array (1, 20) with the following column structure:
+                [
+                    x, y, z ( 3 columns ), -> segment, core point
+                    EpochID ( 1 column ),
+                    Eigenvalues( 3 columns ), -> that correspond to the next 3 Eigenvectors
+                    Eigenvectors( 3 columns ) X 3 -> in descending order using vector norm 2,
+                    Lowest local surface variation ( 1 column ),
+                    Segment_ID ( 1 column ),
+                    Standard deviation ( 1 column ),
+                    Number of points found in Segment_ID segment ( 1 column )
+                ]
+        :param columns:
+        """
+
+        viewer = Viewer()
+
+        nr_segments = X.shape[0]
+        colors = [(1, 0, 0), (0, 1, 0)]
+
+        viewer.plt.add_callback("KeyPress", viewer.toggle_transparency)
+
+        for i in range(0, nr_segments):
+            if X[i, columns.EPOCH_ID_COLUMN] == 0:
+                color = colors[0]
+            else:
+                color = colors[1]
+
+            ellipsoid = Ellipsoid(
+                pos=(X[i, 0], X[i, 1], X[i, 2]),
+                axis1=[
+                    X[i, columns.EIGENVECTOR_0_X_COLUMN]
+                    * X[i, columns.EIGENVALUE0_COLUMN]
+                    * 0.5,
+                    X[i, columns.EIGENVECTOR_0_Y_COLUMN]
+                    * X[i, columns.EIGENVALUE0_COLUMN]
+                    * 0.5,
+                    X[i, columns.EIGENVECTOR_0_Z_COLUMN]
+                    * X[i, columns.EIGENVALUE0_COLUMN]
+                    * 0.3,
+                ],
+                axis2=[
+                    X[i, columns.EIGENVECTOR_1_X_COLUMN]
+                    * X[i, columns.EIGENVALUE1_COLUMN]
+                    * 0.5,
+                    X[i, columns.EIGENVECTOR_1_Y_COLUMN]
+                    * X[i, columns.EIGENVALUE1_COLUMN]
+                    * 0.5,
+                    X[i, columns.EIGENVECTOR_1_Z_COLUMN]
+                    * X[i, columns.EIGENVALUE1_COLUMN]
+                    * 0.5,
+                ],
+                axis3=[
+                    X[i, columns.EIGENVECTOR_2_X_COLUMN] * 0.1,
+                    X[i, columns.EIGENVECTOR_2_Y_COLUMN] * 0.1,
+                    X[i, columns.EIGENVECTOR_2_Z_COLUMN] * 0.1,
+                ],
+                res=24,
+                c=color,
+                alpha=1,
+            )
+            # ellipsoid.caption(txt=str(i), size=(0.1, 0.05))
+            ellipsoid.id = X[i, columns.SEGMENT_ID_COLUMN]
+            ellipsoid.epoch = X[i, columns.EPOCH_ID_COLUMN]
+            ellipsoid.isOn = True
+
+            viewer.sets = viewer.sets + [ellipsoid]
+
+        viewer.plt.show(
+            viewer.sets,
+            Text2D(
+                "'z' - toggle transparency on/off "
+                "'g' - toggle on/off red ellipsoids "
+                "'d' - toggle on/off green ellipsoids",
+                pos="top-left",
+                bg="k",
+                s=0.7,
+            ),
+        ).close()
+
+    def toggle_transparency(self, evt):
+        if evt.keyPressed == "z":
+            logger.info("transparency toggle")
+            for segment in self.sets:
+                if segment.alpha() < 1.0:
+                    segment.alpha(1)
+                else:
+                    segment.alpha(0.5)
+            self.plt.render()
+
+        if evt.keyPressed == "g":
+            logger.info("toggle red")
+            for segment in self.sets:
+                if segment.epoch == 0:
+                    if segment.isOn:
+                        segment.off()
+                    else:
+                        segment.on()
+                    segment.isOn = not segment.isOn
+            self.plt.render()
+
+        if evt.keyPressed == "d":
+            logger.info("toggle green")
+            for segment in self.sets:
+                if segment.epoch == 1:
+                    if segment.isOn:
+                        segment.off()
+                    else:
+                        segment.on()
+                    segment.isOn = not segment.isOn
+            self.plt.render()
+
+
+def generate_random_extended_y(
+    X,
+    extended_y_file_name="locally_generated_extended_y.csv",
+    ratio=1 / 3,
+    low=0,
+    high=1,
+    columns=SEGMENT_COLUMNS,
+):
+    """
+        Generate a subset (1/3 from the total possible pairs) of random tuples of segments ID
+        (where each ID gets to be extracted from a different epoch) which are randomly labeled
+        between low and high)
+
+    :param X:
+        (n_segments, 20)
+        Each row contains a segment.
+    :param extended_y_file_name:
+        Name of the file where the serialized result is saved.
+    :param ratio:
+        The size of the pairs' subset size.
+    :param low:
+        Default minimum random value used as label
+    :param high:
+        Default maximum random value used as label
+    :param columns:
+        Column mapping used by each segment.
+    :return:
+        numpy (m_pairs, 3)
+            Where each row contains tuples of set0 segment id, set1 segment id, rand 0/1.
+    """
+
+    mask_epoch0 = X[:, columns.EPOCH_ID_COLUMN] == 0
+    mask_epoch1 = X[:, columns.EPOCH_ID_COLUMN] == 1
+
+    epoch0_set = X[mask_epoch0, :]  # all
+    epoch1_set = X[mask_epoch1, :]  # all
+
+    ratio = np.clip(ratio, 0, 1)
+    nr_pairs = round(min(epoch0_set.shape[0], epoch1_set.shape[0]) * ratio)
+
+    indx0_seg_id = random.sample(range(epoch0_set.shape[0]), nr_pairs)
+    indx1_seg_id = random.sample(range(epoch1_set.shape[0]), nr_pairs)
+
+    set0_seg_id = epoch0_set[indx0_seg_id, columns.SEGMENT_ID_COLUMN]
+    set1_seg_id = epoch1_set[indx1_seg_id, columns.SEGMENT_ID_COLUMN]
+
+    rand_y = list(np.random.randint(low, high + 1, nr_pairs))
+
+    np.savetxt(
+        extended_y_file_name,
+        np.array([set0_seg_id, set1_seg_id, rand_y]).T,
+        delimiter=",",
+    )
+
+    return np.array([set0_seg_id, set1_seg_id, rand_y]).T
+
+
+def generate_possible_region_pairs(
+    segments: np.ndarray, seg_id0_seg_id1_label: np.ndarray
+):
+    """
+    :param segments:
+        numpy array of shape (n_segments, segment_size)
+    :param seg_id0_seg_id1_label:
+        extended_y, numpy array (n_pairs, 3)
+            where each row contains: (id_segment_epoch0, id_segment_epoch1, label=0/1)
+    :return:
+        numpy array of shape (m_pairs, 7) where each row contain:
+            pairs_of_points[i, :3] -> a proposed position of a segment from epoch 0
+            pairs_pf_points[i, 3:] -> a proposed position of a segment from epoch 1
+            label: 0/1
+    """
+
+    segment_pairs = seg_id0_seg_id1_label
+
+    out = np.empty(shape=(0, 7))
+    for row in range(segment_pairs.shape[0]):
+        id_epoch0 = int(segment_pairs[row, 0])
+        id_epoch1 = int(segment_pairs[row, 1])
+        label = int(segment_pairs[row, 2])
+        points = np.hstack(
+            (
+                segments[id_epoch0, 0:3] + np.random.normal(0, 1),
+                segments[id_epoch1, 3:6] + np.random.normal(0, 1),
+                label,
+            )
+        )
+        out = np.vstack((out, points))
+
+    return out
+
+
+def generate_extended_y_from_prior_knowledge(
+    segments: np.ndarray,
+    pairs_of_points: np.ndarray,
+    threshold_max_distance: float,
+    columns=SEGMENT_COLUMNS,
+) -> np.ndarray:
+    """
+    :param segments:
+        numpy array of shape (n_segments, segment_size)
+    :param pairs_of_points:
+        numpy array of shape (m_pairs, 7) where each row contain:
+            pair_of_points[i, :3] -> a proposed position of a segment from epoch 0
+            pair_pf_points[i, 3:] -> a proposed position of a segment from epoch 1
+            label: 0/1
+    :param threshold_max_distance:
+        the radios accepted threshold for possible segments
+    :param columns:
+        Column mapping used by each segment.
+    :return:
+        extended_y, numpy array (n_pairs, 3)
+            where each row contains: (id_segment_epoch0, id_segment_epoch1, label=0/1)
+    """
+
+    extended_y = np.empty(shape=(0, 3), dtype=float)
+
+    # split points(segments) between epoch0 and epoch1
+    epoch0_mask = segments[:, columns.EPOCH_ID_COLUMN] == 0
+    epoch1_mask = segments[:, columns.EPOCH_ID_COLUMN] == 1
+
+    X_Y_Z_Columns = [columns.X_COLUMN, columns.Y_COLUMN, columns.Z_COLUMN]
+
+    epoch0_set = segments[epoch0_mask][X_Y_Z_Columns]
+    epoch1_set = segments[epoch1_mask][X_Y_Z_Columns]
+
+    # generate kd-tree for each of the 2 sets
+    epoch0 = Epoch(epoch0_set.T)
+    epoch0.build_kdtree()
+    epoch1 = Epoch(epoch1_set.T)
+    epoch1.build_kdtree()
+
+    # search for the near segments and build the 'extended y'
+    for row in pairs_of_points:
+        seg_epoch0, seg_epoch1, label = np.split(ary=row, indices_or_sections=[3, 6])
+        label = label[0]
+
+        candidates_seg_epoch0 = epoch0.kdtree.radius_search(
+            seg_epoch0, threshold_max_distance
+        )
+        candidates_seg_epoch1 = epoch1.kdtree.radius_search(
+            seg_epoch1, threshold_max_distance
+        )
+
+        if len(candidates_seg_epoch0) > 0 and len(candidates_seg_epoch1) > 0:
+            indx_min_epoch0 = candidates_seg_epoch0[
+                np.linalg.norm(
+                    epoch0.cloud[candidates_seg_epoch0] - seg_epoch0
+                ).argmin()
+            ]
+            indx_min_epoch1 = candidates_seg_epoch1[
+                np.linalg.norm(
+                    epoch1.cloud[candidates_seg_epoch0] - seg_epoch1
+                ).argmin()
+            ]
+
+            extended_y = np.vstack(
+                (
+                    extended_y,
+                    # index segment epoch0 , index segment epoch1, label=0/1
+                    np.array([indx_min_epoch0, indx_min_epoch1, label]),
+                )
+            )
+
+    return extended_y
+
+
+def add_no_corresponding_seg(
+    segments: np.ndarray,
+    extended_y: np.ndarray = None,
+    threshold_max_distance: float = 3,
+    algorithm="closest",
+    extended_y_file_name: str = "extended_y.csv",
+    columns=SEGMENT_COLUMNS,
+):
+    """
+    :param segments:
+        numpy array of shape (n_segments, segment_size)
+    :param extended_y:
+        numpy array (n_pairs, 3)
+            where each row contains: (id_segment_epoch0, id_segment_epoch1, label=0/1)
+    :param threshold_max_distance:
+        the radios accepted threshold for possible segments
+    :param algorithm:
+        closest - select the closest segment, not used as the corresponding segment
+        random - select a random segment, from proximity (threshold_max_distance),
+        not used already as a corresponding segment
+    :param columns:
+        Column mapping used by each segment.
+    :param extended_y_file_name:
+        In case 'extended_y' is None, this file is used as input fallback.
+    :return:
+        extended_y, numpy array (n_pairs, 3)
+            where each row contains: (id_segment_epoch0, id_segment_epoch1, label=0/1)
+    """
+
+    assert (
+        algorithm == "closest" or algorithm == "random"
+    ), "'selection' parameter can be 'closest/random'"
+
+    if extended_y is None:
+        # Resolve the given path
+        filename = find_file(extended_y_file_name)
+        # Read it
+        try:
+            logger.info(
+                f"Reading tuples of (segment epoch0, segment epoch1, label) from file '{filename}'"
+            )
+            extended_y = np.genfromtxt(filename, delimiter=",")
+        except ValueError:
+            raise Py4DGeoError("Malformed file: " + str(filename))
+
+    # construct the corresponding pairs from the set of all pairs
+    extended_y_with_label_1 = extended_y[extended_y[:, 2] == 1]
+
+    new_extended_y = np.empty(shape=(0, 3), dtype=float)
+
+    # split points(segments) between epoch0 and epoch1
+    epoch0_mask = segments[:, columns.EPOCH_ID_COLUMN] == 0
+    epoch1_mask = segments[:, columns.EPOCH_ID_COLUMN] == 1
+
+    # compute index of each segment as part of 'segments'
+    epoch0_index = np.asarray(epoch0_mask).nonzero()[0]
+    epoch1_index = np.asarray(epoch1_mask).nonzero()[0]
+
+    X_Y_Z_Columns = [columns.X_COLUMN, columns.Y_COLUMN, columns.Z_COLUMN]
+
+    epoch0_set = segments[epoch0_mask][X_Y_Z_Columns]
+    epoch1_set = segments[epoch1_mask][X_Y_Z_Columns]
+
+    epoch0_set = epoch0_set.T
+    # generate kd-tree
+    epoch1 = Epoch(epoch1_set.T)
+    epoch1.build_kdtree()
+
+    # search for the near segments and build the 'extended y'
+    # for row in pairs_of_points:
+    for index, row in enumerate(epoch0_set):
+        index_seg_epoch0 = epoch0_index[index]
+
+        candidates_seg_epoch1 = epoch1.kdtree.radius_search(row, threshold_max_distance)
+
+        indexes_seg_epoch1 = epoch1_index[candidates_seg_epoch1]
+
+        if len(indexes_seg_epoch1) == 0:
+            continue
+
+        if algorithm == "closest":
+            index = (
+                (extended_y[:, 0] == index_seg_epoch0)
+                & (extended_y[:, 1] == indexes_seg_epoch1[0])
+                & (extended_y[:, 2] == 1)
+            )
+
+            if not index.any():
+                new_extended_y = np.vstack(
+                    (new_extended_y, (index_seg_epoch0, indexes_seg_epoch1[0], 0))
+                )
+            else:
+                if len(candidates_seg_epoch1) > 1:
+                    new_extended_y = np.vstack(
+                        (new_extended_y, (index_seg_epoch0, indexes_seg_epoch1[1], 0))
+                    )
+
+        if algorithm == "random":
+            while True:
+                rand_point = np.random.randint(low=0, high=len(indexes_seg_epoch1))
+                index = (
+                    (extended_y[:, 0] == index_seg_epoch0)
+                    & (extended_y[:, 1] == indexes_seg_epoch1[rand_point])
+                    & (extended_y[:, 2] == 1)
+                )
+
+                if not index.any():
+                    new_extended_y = np.vstack(
+                        (
+                            new_extended_y,
+                            (index_seg_epoch0, indexes_seg_epoch1[rand_point], 0),
+                        )
+                    )
+                    break
+
+    return np.vstack((extended_y, new_extended_y))
+
+
+class BaseTransformer(TransformerMixin, BaseEstimator, ABC):
+    def __init__(self, skip=False, output_file_name=None, columns=None):
+        """
+        :param skip:
+            Whether the current transform is applied or not.
+        :param output_file_name:
+            File where the result of the 'Transform()' method, a numpy array, is dumped.
+        """
+
+        self.skip = skip
+        self.output_file_name = output_file_name
+        self.columns = columns
+        super(BaseTransformer, self).__init__()
+
+    @abstractmethod
+    def _fit(self, X, y=None):
+        """
+        X : {array-like, sparse matrix}, shape (n_samples, n_features)
+            The training input samples.
+        y : None
+            There is no need of a target in a transformer, yet the pipeline API
+            requires this parameter.
+        Returns
+        -------
+        self : object
+            Returns self.
+        """
+        pass
+
+    @abstractmethod
+    def _transform(self, X):
+        """
+        X : {array-like, sparse-matrix}, shape (n_samples, n_features)
+            The input samples.
+        Returns
+        -------
+        X_transformed : array, shape (n_samples, n_features)
+        """
+        pass
+
+    def fit(self, X, y=None):
+        if self.skip:
+            return self
+
+        X = check_array(X, accept_sparse=True)
+        self.n_features_ = X.shape[1]
+
+        # Return the transformer
+        logger.info("Transformer Fit")
+
+        return self._fit(X, y)
+
+    def transform(self, X):
+        """
+        param: X
+            numpy array
+        """
+
+        if self.skip:
+            if self.output_file_name != None:
+                logger.debug(
+                    f"The output file, {self.output_file_name} "
+                    f"was set but the transformation process is skipped! (no output)"
+                )
+            return X
+
+        # Check if fit had been called
+        check_is_fitted(self, "n_features_")
+
+        # Input validation
+        X = check_array(X, accept_sparse=True)
+
+        # Check that the input is of the same shape as the one passed
+        # during fit.
+        if X.shape[1] != self.n_features_:
+            raise Py4DGeoError(
+                "Shape of input is different from what was seen in `fit`"
+            )
+
+        logger.info("Transformer Transform")
+
+        out = self._transform(X)
+
+        if self.output_file_name != None:
+            np.savetxt(self.output_file_name, out, delimiter=",")
+            logger.info(f"Saving Transform output in file: {self.output_file_name}")
+
+        return out
+
+
+class PerPointComputation(BaseTransformer):
+    def __init__(
+        self, skip=False, radius=10, output_file_name=None, columns=LLSV_PCA_COLUMNS
+    ):
+        """
+
+        :param skip:
+            Whether the current transform is applied or not.
+        :param radius:
+            The radius used to extract the neighbour points using KD-tree.
+        :param output_file_name:
+            File where the result of the 'Transform()' method, a numpy array, is dumped.
+        """
+
+        super(PerPointComputation, self).__init__(
+            skip=skip, output_file_name=output_file_name, columns=columns
+        )
+        self.radius = radius
+
+    def _llsv_and_pca(self, x, X):
+        """
+        Compute PCA (implicitly, the normal vector as well) and lowest local surface variation
+        for point "x" using the set "X" as input.
+
+        :param x:
+            a reference to a row, part of the returned structure, of the following form:
+                [
+                    x, y, z,
+                    EpochID,
+                    Eigenvalues( 3 columns ),
+                    Eigenvectors( 3 columns ) X 3 -> in descending order using vector norm 2,
+                    Lowest local surface variation ( 1 column )
+                ]
+        :param X:
+            Subset of the point cloud of numpy array (m_samples, 3), that is found around 'x'(x,y,z) inside a 'radius'.
+        :return:
+            return a populated x with
+            (Eigenvalues, Eigenvectors, Lowest local surface variation)
+        """
+
+        size = X.shape[0]
+
+        # compute mean
+        X_avg = np.mean(X, axis=0)
+        B = X - np.tile(X_avg, (size, 1))
+
+        # Find principal components (SVD)
+        U, S, VT = np.linalg.svd(B.T / np.sqrt(size), full_matrices=0)
+
+        x[-13:] = np.hstack(
+            (
+                S.reshape(1, -1),
+                U[:, 0].reshape(1, -1),
+                U[:, 1].reshape(1, -1),
+                U[:, 2].reshape(1, -1),
+                (S[-1] / np.sum(S)).reshape(1, -1),
+            )
+        )
+
+        return x
+
+    def _fit(self, X, y=None):
+        """
+
+        :param X:
+        :param y:
+        :return:
+        """
+
+        return self
+
+    def _transform(self, X):
+        """
+        Extending X matrix by adding eigenvalues, eigenvectors, and lowest local surface variation columns.
+
+        :param X:
+            A numpy array with x, y, z, EpochID columns.
+        :return:
+            numpy matrix extended containing the following columns:
+                x, y, z ( 3 columns ),
+                EpochID ( 1 column ),
+                Eigenvalues( 3 columns ),
+                Eigenvectors( 3 columns ) X 3 [ in descending normal order ],
+                Lowest local surface variation( 1 column )
+        """
+
+        X_Y_Z_Columns = [
+            self.columns.X_COLUMN,
+            self.columns.Y_COLUMN,
+            self.columns.Z_COLUMN,
+        ]
+
+        mask_epoch0 = X[:, self.columns.EPOCH_ID_COLUMN] == 0
+        mask_epoch1 = X[:, self.columns.EPOCH_ID_COLUMN] == 1
+
+        epoch0_set = X[mask_epoch0, :-1]
+        epoch1_set = X[mask_epoch1, :-1]
+
+        # currently, Epoch class doesn't accept the empty point set, as a constructor parameter.
+        _epoch = [
+            Epoch(epoch_set)
+            for epoch_set in [epoch0_set, epoch1_set]
+            if epoch_set.shape[0] > 0
+        ]
+
+        for current_epoch in _epoch:
+            current_epoch.build_kdtree()
+
+        # add extra columns
+        # Eigenvalues( 3 columns ) |
+        # Eigenvectors( 3 columns ) X 3 [ in descending normal order ] |
+        # Lowest local surface variation( 1 column )
+        # Total 13 new columns
+        new_columns = np.zeros((X.shape[0], 13))
+        X = np.hstack((X, new_columns))
+
+        # this process can be parallelized!
+        return np.apply_along_axis(
+            lambda x: self._llsv_and_pca(
+                x,
+                _epoch[int(x[self.columns.EPOCH_ID_COLUMN])].cloud[
+                    _epoch[int(x[self.columns.EPOCH_ID_COLUMN])].kdtree.radius_search(
+                        x[X_Y_Z_Columns], self.radius
+                    )
+                ],
+            ),
+            1,
+            X,
+        )
+
+
+class Segmentation(BaseTransformer):
+    def __init__(
+        self,
+        skip=False,
+        radius=2,
+        angle_diff_threshold=1,
+        distance_3D_threshold=1.5,
+        distance_orthogonal_threshold=1.5,
+        llsv_threshold=1,
+        roughness_threshold=5,
+        max_nr_points_neighborhood=100,
+        min_nr_points_per_segment=5,
+        with_previously_computed_segments=False,
+        output_file_name=None,
+        columns=SEGMENTED_POINT_CLOUD_COLUMNS,
+    ):
+        """
+
+        :param skip:
+            Whether the current transform is applied or not.
+        :param radius:
+            The radius used to extract the neighbour points using KD-tree during segmentation process.
+        :param angle_diff_threshold:
+            Angular deviation threshold for a point candidate’s local normal vector to the normal vector
+            of the initial seed point.
+        :param distance_3D_threshold:
+            Norm 2 distance threshold of the point candidate to the current set of points,
+            during the segmentation process.
+        :param distance_orthogonal_threshold:
+            Orthogonal distance threshold of the point candidate to the current plane segment
+            used during the segmentation process.
+        :param llsv_threshold:
+            The threshold on local surface variation.
+        :param roughness_threshold:
+            Threshold on local roughness.
+        :param max_nr_points_neighborhood:
+            The maximum number of points in the neighborhood of the point the candidate used
+            for checking during the segmentation process.
+        :param min_nr_points_per_segment:
+            The minimum number of points required to consider a segment as valid.
+        :param with_previously_computed_segments:
+            Used for differentiating between the first and the second segmentation.
+            ( must be refactored!!! )
+        param output_file_name:
+            File where the result of the 'Transform()' method, a numpy array, is dumped.
+        """
+
+        super(Segmentation, self).__init__(
+            skip=skip, output_file_name=output_file_name, columns=columns
+        )
+
+        self.radius = radius
+        self.angle_diff_threshold = angle_diff_threshold
+        self.distance_3D_threshold = distance_3D_threshold
+        self.distance_orthogonal_threshold = distance_orthogonal_threshold
+        self.llsv_threshold = llsv_threshold
+        self.roughness_threshold = roughness_threshold
+        self.max_nr_points_neighborhood = max_nr_points_neighborhood
+        self.min_nr_points_per_segment = min_nr_points_per_segment
+        self.with_previously_computed_segments = with_previously_computed_segments
+
+    def angle_difference_check(self, normal1, normal2):
+        """
+        Check whether the angle between 2 normalized vectors is less than
+        the used segmentation threshold "angle_diff_threshold" (in degrees)
+
+        :param normal1:
+            normalized vector
+        :param normal2:
+            normalized vector
+        :return:
+            True/False
+        """
+
+        # normal1, normal2 have to be unit vectors (and that is the case as a result of the SVD process)
+        return angle_difference_compute(normal1, normal2) <= self.angle_diff_threshold
+
+    def distance_3D_set_check(
+        self, point, segment_id, X, X_Y_Z_Columns, SEGMENT_ID_COLUMN
+    ):
+        """
+        Check whether the distance between the candidate point and all the points, currently part of the segment
+        is less than the 'distance_3D_threshold'.
+
+        :param point:
+            Numpy array (3, 1) candidate point during segmentation process.
+        :param segment_id:
+            The segment ID for which the candidate point is considered.
+        :param X:
+            numpy array (n_samples, 19)
+        :param X_Y_Z_Columns:
+            python list containing the indexes of the X,Y,Z columns.
+        :param SEGMENT_ID_COLUMN:
+            The column index used as the segment id.
+        :return:
+            True/False
+        """
+
+        point_mask = X[:, SEGMENT_ID_COLUMN] == segment_id
+
+        # can be optimized by changing the norm
+        return (
+            np.min(
+                np.linalg.norm(X[point_mask, :3] - point.reshape(1, 3), ord=2, axis=1)
+            )
+            <= self.distance_3D_threshold
+        )
+
+    def compute_distance_orthogonal(self, candidate_point, plane_point, plane_normal):
+        """
+        Compute the orthogonal distance between the candidate point and the segment represented by its plane.
+
+        :param candidate_point:
+            numpy array (3, 1) candidate point during segmentation process.
+        :param plane_point:
+            numpy array (3, 1) representing a point (most likely, a core point), part of the segment.
+        :param plane_normal:
+            numpy array (3, 1)
+        :return:
+            True/False
+        """
+
+        d = -plane_point.dot(plane_normal)
+        distance = (plane_normal.dot(candidate_point) + d) / np.linalg.norm(
+            plane_normal
+        )
+
+        return distance
+
+    def distance_orthogonal_check(self, candidate_point, plane_point, plane_normal):
+        """
+        Check whether the orthogonal distance between the candidate point and the segment represented by its plane
+        is less than the 'distance_orthogonal_threshold'.
+
+        :param candidate_point:
+            numpy array (3, 1) candidate point during segmentation process.
+        :param plane_point:
+            numpy array (3, 1) representing a point (most likely, a core point), part of the segment.
+        :param plane_normal:
+             numpy array (3, 1)
+        :return:
+            True/False
+        """
+
+        distance = self.compute_distance_orthogonal(
+            candidate_point, plane_point, plane_normal
+        )
+        return distance - self.distance_orthogonal_threshold <= 0
+
+    def lowest_local_surface_variance_check(self, llsv):
+        """
+        Check lowest local surface variance threshold.
+
+        :param llsv:
+            lowest local surface variance
+        :return:
+            True/False
+        """
+
+        return llsv <= self.llsv_threshold
+
+    def _fit(self, X, y=None):
+        """
+
+        :param X:
+        :param y:
+        :return:
+        """
+
+        return self
+        pass
+
+    def _transform(self, X):
+        """
+        It applies the segmentation process.
+
+        :param X:
+            Rows of points from Epoch0 and Epoch1
+            X = (
+                    X0, Rows of points from Epoch 0
+                    X1  Rows of points from Epoch 1     <- OPTIONAL
+                )
+            It is assumed that rows for Epoch0 and Epoch1 are not interleaved!
+
+            numpy array (n_points, 17) with the following column structure:
+            [
+                x, y, z ( 3 column ),
+                EpochID ( 1 column ),
+                Eigenvalues( 3 columns ), -> that correspond to the next 3 Eigenvectors
+                Eigenvectors( 3 columns ) X 3 -> in descending order using vector norm 2,
+                Lowest local surface variation ( 1 column )
+            ]
+        :return:
+            numpy array (n_points, 19) with the following column structure:
+            [
+                x, y, z ( 3 columns ),
+                EpochID ( 1 column ),
+                Eigenvalues( 3 columns ), -> that correspond to the next 3 Eigenvectors
+                Eigenvectors( 3 columns ) X 3 -> in descending order using vector norm 2,
+                Lowest local surface variation ( 1 column ),
+                Segment_ID ( 1 column ),
+                Standard deviation ( 1 column )
+            ]
+        """
+
+        X_Y_Z_Columns = [
+            self.columns.X_COLUMN,
+            self.columns.Y_COLUMN,
+            self.columns.Z_COLUMN,
+        ]
+
+        Normal_Columns = [
+            self.columns.EIGENVECTOR_2_X_COLUMN,
+            self.columns.EIGENVECTOR_2_Y_COLUMN,
+            self.columns.EIGENVECTOR_2_Z_COLUMN,
+        ]
+
+        # the new columns are added only if they weren't already been added previously
+        if not self.with_previously_computed_segments:
+            new_column_segment_id = np.full(
+                (X.shape[0], 1), DEFAULT_NO_SEGMENT, dtype=float
+            )
+            X = np.hstack((X, new_column_segment_id))
+
+            new_column_std_deviation = np.full(
+                (X.shape[0], 1), DEFAULT_STD_DEVIATION_OF_NO_CORE_POINT, dtype=float
+            )
+            X = np.hstack((X, new_column_std_deviation))
+
+        mask_epoch0 = X[:, self.columns.EPOCH_ID_COLUMN] == 0
+        mask_epoch1 = X[:, self.columns.EPOCH_ID_COLUMN] == 1
+
+        assert (
+            mask_epoch0.shape[0] > 0
+        ), "The input X must contain at least elements from Epoch 0, e.g. EPOCH_ID_COLUMN==0"
+
+        logger.debug(
+            f"'X' contains {np.count_nonzero(mask_epoch0)} elements from Epoch 0 "
+            f"and {np.count_nonzero(mask_epoch1)} from Epoch 1"
+        )
+
+        epoch0_set = X[mask_epoch0][:, X_Y_Z_Columns]
+        epoch1_set = X[mask_epoch1][:, X_Y_Z_Columns]
+
+        _epoch = [
+            Epoch(epoch_set)
+            for epoch_set in [epoch0_set, epoch1_set]
+            if epoch_set.shape[0] > 0
+        ]
+
+        for current_epoch in _epoch:
+            current_epoch.build_kdtree()
+
+        # sort by the "Lowest local surface variation"
+        sort_indx_epoch0 = X[mask_epoch0, self.columns.LLSV_COLUMN].argsort()
+        sort_indx_epoch1 = X[mask_epoch1, self.columns.LLSV_COLUMN].argsort()
+        sort_indx_epoch = [sort_indx_epoch0, sort_indx_epoch1]
+
+        # it is assumed that the rows for Epoch0 and rows for Epoch1 are not interleaved!
+        offset_in_X = [0, sort_indx_epoch0.shape[0]]
+
+        # initialization required between multiple Segmentations
+        seg_id = np.max(X[:, self.columns.SEGMENT_ID_COLUMN])
+
+        for epoch_id in range(len(_epoch)):
+            for indx_row in sort_indx_epoch[epoch_id] + offset_in_X[epoch_id]:
+                # no part of a segment yet
+                if X[indx_row, self.columns.SEGMENT_ID_COLUMN] < 0:
+                    seg_id += 1
+                    X[indx_row, self.columns.SEGMENT_ID_COLUMN] = seg_id
+
+                    cumulative_distance_for_std_deviation = 0
+                    nr_points_for_std_deviation = 0
+
+                    indx_kd_tree_list = _epoch[epoch_id].kdtree.radius_search(
+                        X[indx_row, X_Y_Z_Columns], self.radius
+                    )[: self.max_nr_points_neighborhood]
+                    for indx_kd_tree in indx_kd_tree_list:
+                        if (
+                            X[
+                                indx_kd_tree + offset_in_X[epoch_id],
+                                self.columns.SEGMENT_ID_COLUMN,
+                            ]
+                            < 0
+                            and self.angle_difference_check(
+                                X[indx_row, Normal_Columns],
+                                X[indx_kd_tree + offset_in_X[epoch_id], Normal_Columns],
+                            )
+                            and self.distance_3D_set_check(
+                                X[indx_kd_tree + offset_in_X[epoch_id], X_Y_Z_Columns],
+                                seg_id,
+                                X,
+                                X_Y_Z_Columns,
+                                self.columns.SEGMENT_ID_COLUMN,
+                            )
+                            and self.distance_orthogonal_check(
+                                X[indx_kd_tree + offset_in_X[epoch_id], X_Y_Z_Columns],
+                                X[indx_row, X_Y_Z_Columns],
+                                X[indx_row, Normal_Columns],
+                            )
+                            and self.lowest_local_surface_variance_check(
+                                X[
+                                    indx_kd_tree + offset_in_X[epoch_id],
+                                    self.columns.LLSV_COLUMN,
+                                ]
+                            )
+                        ):
+                            X[
+                                indx_kd_tree + offset_in_X[epoch_id],
+                                self.columns.SEGMENT_ID_COLUMN,
+                            ] = seg_id
+                            cumulative_distance_for_std_deviation += (
+                                self.compute_distance_orthogonal(
+                                    X[
+                                        indx_kd_tree + offset_in_X[epoch_id],
+                                        X_Y_Z_Columns,
+                                    ],
+                                    X[indx_row, X_Y_Z_Columns],
+                                    X[indx_row, Normal_Columns],
+                                )
+                                ** 2
+                            )
+                            nr_points_for_std_deviation += 1
+
+                    nr_points_segment = np.count_nonzero(
+                        X[:, self.columns.SEGMENT_ID_COLUMN] == seg_id
+                    )
+
+                    # not enough points or 'roughness_threshold' exceeded
+                    if (
+                        nr_points_segment < self.min_nr_points_per_segment
+                        or cumulative_distance_for_std_deviation
+                        / nr_points_for_std_deviation
+                        >= self.roughness_threshold
+                    ):
+                        mask_seg_id = X[:, self.columns.SEGMENT_ID_COLUMN] == seg_id
+                        X[mask_seg_id, self.columns.SEGMENT_ID_COLUMN] = (
+                            DEFAULT_NO_SEGMENT
+                        )
+                        # since we don't have a new segment
+                        seg_id -= 1
+                    else:
+                        X[indx_row, self.columns.STANDARD_DEVIATION_COLUMN] = (
+                            cumulative_distance_for_std_deviation
+                            / nr_points_for_std_deviation
+                        )
+        return X
+
+
+class PostPointCloudSegmentation(BaseTransformer):
+    def __init__(
+        self,
+        skip=False,
+        compute_normal=True,
+        output_file_name=None,
+        columns=SEGMENTED_POINT_CLOUD_COLUMNS,
+    ):
+        """
+        :param skip:
+            Whether the current transform is applied or not.
+        :param compute_normal:
+
+        :param output_file_name:
+            File where the result of the 'Transform()' method, a numpy array, is dumped.
+        :param columns:
+
+        """
+
+        super().__init__(skip=skip, output_file_name=output_file_name, columns=columns)
+        self.compute_normal = compute_normal
+
+    def compute_distance_orthogonal(self, candidate_point, plane_point, plane_normal):
+        """
+        Compute the orthogonal distance between the candidate point and the segment represented by its plane.
+
+        :param candidate_point:
+            numpy array (3, 1) candidate point during segmentation process.
+        :param plane_point:
+            numpy array (3, 1) representing a point (most likely, a core point), part of the segment.
+        :param plane_normal:
+            numpy array (3, 1)
+        :return:
+            True/False
+        """
+
+        d = -plane_point.dot(plane_normal.T)
+        distance = (plane_normal.dot(candidate_point) + d) / np.linalg.norm(
+            plane_normal
+        )
+
+        return distance
+
+    def pca_compute_normal_and_mean(self, X):
+        """
+            Perform PCA.
+            The order of the eigenvalues and eigenvectors is consistent.
+
+        :param X:
+            numpy array of shape (n_points, 3) with [x, y, z] columns.
+        :return:
+            a tuple of:
+                Eig. values as numpy array of shape (1, 3)
+                Eig. vector0 as numpy array of shape (1, 3)
+                Eig. vector1 as numpy array of shape (1, 3)
+                Eig. vector2 (normal vector) as numpy array of shape (1, 3)
+                Position of the normal vector as numpy array of shape (1, 3),
+                    approximated as the mean of the input points.
+        """
+
+        size = X.shape[0]
+
+        # compute mean
+        X_avg = np.mean(X, axis=0)
+        B = X - np.tile(X_avg, (size, 1))
+
+        # Find principal components (SVD)
+        U, S, VT = np.linalg.svd(B.T / np.sqrt(size), full_matrices=0)
+
+        assert S[0] != 0, "eig. value should not be 0!"
+        assert S[1] != 0, "eig. value should not be 0!"
+        assert S[2] != 0, "eig. value should not be 0!"
+
+        # Eig. values,
+        # Eig. Vector0, Eig. Vector1, Eig. Vector2( the norma vector),
+        # 'position' of the normal vector
+        return (
+            S.reshape(1, -1),
+            U[:, 0].reshape(1, -1),
+            U[:, 1].reshape(1, -1),
+            U[:, 2].reshape(1, -1),
+            X_avg.reshape(1, -1),
+        )
+
+    def _fit(self, X, y=None):
+        """
+        :param X:
+        :param y:
+        :return:
+        """
+
+        return self
+        pass
+
+    def _transform(self, X):
+        """
+
+        :param X:
+        :return:
+        """
+
+        X_Y_Z_Columns = [
+            self.columns.X_COLUMN,
+            self.columns.Y_COLUMN,
+            self.columns.Z_COLUMN,
+        ]
+
+        Eigval = [
+            self.columns.EIGENVALUE0_COLUMN,
+            self.columns.EIGENVALUE1_COLUMN,
+            self.columns.EIGENVALUE2_COLUMN,
+        ]
+
+        Eigvec0 = [
+            self.columns.EIGENVECTOR_0_X_COLUMN,
+            self.columns.EIGENVECTOR_0_Y_COLUMN,
+            self.columns.EIGENVECTOR_0_Z_COLUMN,
+        ]
+
+        Eigvec1 = [
+            self.columns.EIGENVECTOR_1_X_COLUMN,
+            self.columns.EIGENVECTOR_1_Y_COLUMN,
+            self.columns.EIGENVECTOR_1_Z_COLUMN,
+        ]
+
+        Normal_Columns = [
+            self.columns.EIGENVECTOR_2_X_COLUMN,
+            self.columns.EIGENVECTOR_2_Y_COLUMN,
+            self.columns.EIGENVECTOR_2_Z_COLUMN,
+        ]
+
+        highest_segment_id_used = int(X[:, self.columns.SEGMENT_ID_COLUMN].max())
+
+        for i in range(0, highest_segment_id_used + 1):
+            mask = X[:, self.columns.SEGMENT_ID_COLUMN] == float(i)
+            # extract all points, that are part of the same segment
+            set_cloud = X[mask, :][:, X_Y_Z_Columns]
+
+            eig_values, e0, e1, normal, position = self.pca_compute_normal_and_mean(
+                set_cloud
+            )
+
+            indexes = np.where(mask == True)[0]
+
+            # compute the closest point from the current segment to calculated "position"
+            indx_min_in_indexes = np.linalg.norm(
+                x=set_cloud - position, axis=1
+            ).argmin()
+            indx_min_in_X = indexes[indx_min_in_indexes]
+
+            X[indx_min_in_X, Eigval] = eig_values
+            X[indx_min_in_X, Eigvec0] = e0
+            X[indx_min_in_X, Eigvec1] = e1
+
+            if self.compute_normal:
+                X[indx_min_in_X, Normal_Columns] = normal
+
+            cumulative_distance_for_std_deviation = 0
+            nr_points_for_std_deviation = indexes.shape[0] - 1
+            for indx in indexes:
+                cumulative_distance_for_std_deviation += (
+                    self.compute_distance_orthogonal(
+                        X[indx, X_Y_Z_Columns],
+                        X[indx_min_in_X, X_Y_Z_Columns],
+                        normal.reshape(1, -1),
+                    )
+                    ** 2
+                )
+
+            X[indx_min_in_X, self.columns.STANDARD_DEVIATION_COLUMN] = (
+                cumulative_distance_for_std_deviation / nr_points_for_std_deviation
+            )
+
+        return X
+
+
+class ExtractSegments(BaseTransformer):
+    def __init__(self, skip=False, output_file_name=None, columns=SEGMENT_COLUMNS):
+        """
+
+        :param skip:
+            Whether the current transform is applied or not.
+        :param output_file_name:
+            File where the result of the 'Transform()' method, a numpy array, is dumped.
+        """
+
+        super(ExtractSegments, self).__init__(
+            skip=skip, output_file_name=output_file_name, columns=columns
+        )
+
+    def _fit(self, X, y=None):
+        """
+
+        :param X:
+        :param y:
+        :return:
+        """
+
+        return self
+        pass
+
+    def _transform(self, X):
+        """
+        Transform the numpy array of 'point cloud' to numpy array of 'segments' and extend the structure by adding
+        a new column containing the 'number of points found in Segment_ID'. During this process, only one point
+        that is part of a segment ( the core point ) is maintained, while all the others are discarded.
+
+        :param X:
+            numpy array (n_points, 19) with the following column structure:
+            [
+                x, y, z ( 3 columns ), -> point from cloud
+                EpochID ( 1 column ),
+                Eigenvalues( 3 columns ), -> that correspond to the next 3 Eigenvectors
+                Eigenvectors( 3 columns ) X 3 -> in descending order using vector norm 2,
+                Lowest local surface variation ( 1 column ),
+                Segment_ID ( 1 column ),
+                Standard deviation ( 1 column )
+            ]
+        :return:
+            numpy array (n_segments, 20) with the following column structure:
+            [
+                x, y, z ( 3 columns ), -> segment, core point
+                EpochID ( 1 column ),
+                Eigenvalues( 3 columns ), -> that correspond to the next 3 Eigenvectors
+                Eigenvectors( 3 columns ) X 3 -> in descending order using vector norm 2,
+                Lowest local surface variation ( 1 column ),
+                Segment_ID ( 1 column ),
+                Standard deviation ( 1 column ),
+                Number of points found in Segment_ID segment ( 1 column )
+            ]
+        """
+
+        max_segment_id = int(X[:, self.columns.SEGMENT_ID_COLUMN].max())
+        X_Segments = np.empty(
+            (int(max_segment_id) + 1, self.columns.NUMBER_OF_COLUMNS), dtype=float
+        )
+
+        for i in range(0, max_segment_id + 1):
+            mask = X[:, self.columns.SEGMENT_ID_COLUMN] == float(i)
+            set_cloud = X[mask, :]  # all
+            nr_points = set_cloud.shape[0]
+
+            # arg_min = set_cloud[:, LLSV_COLUMN].argmin()
+            # X_Segments[i, :-1] = set_cloud[arg_min, :]
+
+            # find the CoM point, e.g. the point which has STD != DEFAULT_STD_DEVIATION_OF_NO_CORE_POINT
+            mask_std = (
+                set_cloud[:, self.columns.STANDARD_DEVIATION_COLUMN]
+                != DEFAULT_STD_DEVIATION_OF_NO_CORE_POINT
+            )
+            set_cloud_std = set_cloud[mask_std, :]
+            assert (
+                set_cloud_std.shape[0] == 1
+            ), "Only one element within a segment should have the standard deviation computed!"
+            X_Segments[i, :-1] = set_cloud_std[0, :]
+
+            X_Segments[i, self.columns.NR_POINTS_PER_SEG_COLUMN] = nr_points
+
+        return X_Segments
+
+
+class BuilderExtended_y(ABC):
+    def __init__(self, columns):
+        super().__init__()
+        self.columns = columns
+
+    @abstractmethod
+    def generate_extended_y(self, X):
+        """
+        Generates tuples of ( segment index epoch 0, segment index epoch 1, 0/1 label )
+
+        :param X:
+            numpy array of shape (n_segments, segment_features_size) containing all the segments for both,
+            epoch 0 and epoch 1. Each row is a segment.
+        :return:
+            numpy array with shape (n_segments, 3)
+        """
+        pass
+
+
+class BuilderExtended_y_Visually(BuilderExtended_y):
+    def __init__(self, columns=SEGMENT_COLUMNS):
+        super(BuilderExtended_y_Visually, self).__init__(columns=columns)
+
+        self.current_pair = [None] * 2
+        self.constructed_extended_y = np.empty(shape=(0, 3))
+
+    def toggle_transparenct(self, evt):
+        if evt.keyPressed == "z":
+            # transparency toggle
+            for segment in self.sets:
+                if segment.alpha() < 1.0:
+                    segment.alpha(1)
+                else:
+                    segment.alpha(0.5)
+            self.plt.render()
+
+        if evt.keyPressed == "g":
+            # toggle red
+            for segment in self.sets:
+                if segment.epoch == 0:
+                    if segment.isOn == True:
+                        segment.off()
+                    else:
+                        segment.on()
+                    segment.isOn = not segment.isOn
+            self.plt.render()
+
+        if evt.keyPressed == "d":
+            # toggle green
+            for segment in self.sets:
+                if segment.epoch == 1:
+                    if segment.isOn == True:
+                        segment.off()
+                    else:
+                        segment.on()
+                    segment.isOn = not segment.isOn
+            self.plt.render()
+
+    def controller(self, evt):
+        """
+
+        :param evt:
+        :return:
+        """
+        if not evt.actor:
+            # no hit, return
+            return
+        logger.debug("point coords =%s", str(evt.picked3d), exc_info=1)
+        if evt.isPoints:
+            logger.debug("evt.actor = s", str(evt.actor))
+            self.current_pair[int(evt.actor.epoch)] = evt.actor.id
+
+        if self.current_pair[0] != None and self.current_pair[1] != None:
+            # we have a pair
+            self.add_pair_button.status(self.add_pair_button.states[1])
+        else:
+            # we don't
+            self.add_pair_button.status(self.add_pair_button.states[0])
+
+    def event_add_pair_button(self):
+        """
+
+        :return:
+        """
+
+        if self.current_pair[0] != None and self.current_pair[1] != None:
+            try:
+                self.constructed_extended_y = np.vstack(
+                    (
+                        self.constructed_extended_y,
+                        np.array(
+                            [
+                                self.current_pair[0],
+                                self.current_pair[1],
+                                int(self.label.status()),
+                            ]
+                        ),
+                    )
+                )
+
+                self.current_pair[0] = None
+                self.current_pair[1] = None
+                self.label.status(self.label.states[0])  # firs state "None"
+
+                self.add_pair_button.switch()
+            except:
+                logger.error("You must select 0 or 1 as label")
+
+    def segments_visualizer(self, X):
+        """
+
+        :param X:
+        :return:
+        """
+
+        self.sets = []
+
+        nr_segments = X.shape[0]
+        colors = [(1, 0, 0), (0, 1, 0)]
+        self.plt = Plotter(axes=3)
+
+        self.plt.add_callback("EndInteraction", self.controller)
+        self.plt.add_callback("KeyPress", self.toggle_transparenct)
+
+        for i in range(0, nr_segments):
+            # mask = X[:, 17] == float(i)
+            # set_cloud = X[mask, :3]  # x,y,z
+
+            if X[i, self.columns.EPOCH_ID_COLUMN] == 0:
+                color = colors[0]
+            else:
+                color = colors[1]
+
+            # self.sets = self.sets + [Points(set_cloud, colors[i], alpha=1, r=10)]
+
+            # self.sets = self.sets + [ Point( pos=(X[i, 0],X[i, 1],X[i, 2]), r=15, c=colors[i], alpha=1 ) ]
+            ellipsoid = Ellipsoid(
+                pos=(X[i, 0], X[i, 1], X[i, 2]),
+                axis1=[
+                    X[i, self.columns.EIGENVECTOR_0_X_COLUMN]
+                    * X[i, self.columns.EIGENVALUE0_COLUMN]
+                    * 0.5,
+                    X[i, self.columns.EIGENVECTOR_0_Y_COLUMN]
+                    * X[i, self.columns.EIGENVALUE0_COLUMN]
+                    * 0.5,
+                    X[i, self.columns.EIGENVECTOR_0_Z_COLUMN]
+                    * X[i, self.columns.EIGENVALUE0_COLUMN]
+                    * 0.3,
+                ],
+                axis2=[
+                    X[i, self.columns.EIGENVECTOR_1_X_COLUMN]
+                    * X[i, self.columns.EIGENVALUE1_COLUMN]
+                    * 0.5,
+                    X[i, self.columns.EIGENVECTOR_1_Y_COLUMN]
+                    * X[i, self.columns.EIGENVALUE1_COLUMN]
+                    * 0.5,
+                    X[i, self.columns.EIGENVECTOR_1_Z_COLUMN]
+                    * X[i, self.columns.EIGENVALUE1_COLUMN]
+                    * 0.5,
+                ],
+                axis3=[
+                    X[i, self.columns.EIGENVECTOR_2_X_COLUMN] * 0.1,
+                    X[i, self.columns.EIGENVECTOR_2_Y_COLUMN] * 0.1,
+                    X[i, self.columns.EIGENVECTOR_2_Z_COLUMN] * 0.1,
+                ],
+                res=24,
+                c=color,
+                alpha=1,
+            )
+
+            ellipsoid.id = X[i, self.columns.SEGMENT_ID_COLUMN]
+            ellipsoid.epoch = X[i, self.columns.EPOCH_ID_COLUMN]
+            ellipsoid.isOn = True
+            self.sets = self.sets + [ellipsoid]
+
+        self.label = self.plt.add_button(
+            lambda: self.label.switch(),
+            states=["Label (0/1)", "0", "1"],  # None
+            c=["w", "w", "w"],
+            bc=["bb", "lr", "lg"],
+            pos=(0.90, 0.25),
+            size=24,
+        )
+
+        self.add_pair_button = self.plt.add_button(
+            self.event_add_pair_button,
+            states=["Select pair", "Add pair"],
+            c=["w", "w"],
+            bc=["lg", "lr"],
+            pos=(0.90, 0.15),
+            size=24,
+        )
+
+        self.plt.show(
+            self.sets,
+            Text2D(
+                "Select multiple pairs of red-green Ellipsoids with their corresponding labels (0/1) "
+                "and then press 'Select pair'\n"
+                "'z' - toggle transparency on/off 'g' - toggle on/off red ellipsoids 'd' toggle on/off red ellipsoids",
+                pos="top-left",
+                bg="k",
+                s=0.7,
+            ),
+        ).close()
+        return self.constructed_extended_y
+
+    def generate_extended_y(self, X):
+        """
+        :param X:
+        :return:
+        """
+
+        return self.segments_visualizer(X)
+
+
+class ClassifierWrapper(ClassifierMixin, BaseEstimator):
+    def __init__(
+        self,
+        neighborhood_search_radius=3,
+        threshold_probability_most_similar=0.8,
+        diff_between_most_similar_2=0.1,
+        classifier=RandomForestClassifier(),
+        columns=SEGMENT_COLUMNS,
+    ):
+        """
+        :param neighborhood_search_radius:
+            Maximum accepted Euclidean distance for any candidate segments.
+        :param threshold_probability_most_similar:
+            Lower bound probability threshold for the most similar ( candidate ) plane.
+        :param diff_between_most_similar_2:
+            Lower bound threshold of difference between first 2, most similar planes.
+        :param classifier:
+            The classifier used, default is RandomForestClassifier. ( sk-learn )
+        :param columns:
+            Column mapping used by seg_epoch0 and seg_epoch0
+        """
+
+        super().__init__()
+
+        self.neighborhood_search_radius = neighborhood_search_radius
+        self.threshold_probability_most_similar = threshold_probability_most_similar
+        self.diff_between_most_similar_2 = diff_between_most_similar_2
+        self.classifier = classifier
+        self.columns = columns
+
+    def compute_similarity_between(
+        self, seg_epoch0: np.ndarray, seg_epoch1: np.ndarray
+    ) -> np.ndarray:
+        """
+        Similarity function between 2 segments.
+
+        :param seg_epoch0:
+            segment from epoch0, numpy array (1, 20) with the following column structure:
+                [
+                    x, y, z ( 3 columns ), -> segment, core point
+                    EpochID ( 1 column ),
+                    Eigenvalues( 3 columns ), -> that correspond to the next 3 Eigenvectors
+                    Eigenvectors( 3 columns ) X 3 -> in descending order using vector norm 2,
+                    Lowest local surface variation ( 1 column ),
+                    Segment_ID ( 1 column ),
+                    Standard deviation ( 1 column ),
+                    Number of points found in Segment_ID segment ( 1 column )
+                ]
+        :param seg_epoch1:
+            segment from epoch1, same structure as 'seg_epoch0'
+        :return:
+            numpy array of shape (6,) containing:
+                angle, -> angle between plane normal vectors
+                points_density_diff, -> difference between points density between pairs of segments
+                eigen_value_smallest_diff, -> difference in the quality of plane fit (smallest eigenvalue)
+                eigen_value_largest_diff, -> difference in plane extension (largest eigenvalue)
+                eigen_value_middle_diff, -> difference in orthogonal plane extension (middle eigenvalue)
+                nr_points_diff, -> difference in number of points per plane
+        """
+
+        Normal_Columns = [
+            self.columns.EIGENVECTOR_2_X_COLUMN,
+            self.columns.EIGENVECTOR_2_Y_COLUMN,
+            self.columns.EIGENVECTOR_2_Z_COLUMN,
+        ]
+
+        angle = angle_difference_compute(
+            seg_epoch0[Normal_Columns], seg_epoch1[Normal_Columns]
+        )
+
+        points_density_seg_epoch0 = seg_epoch0[
+            self.columns.NR_POINTS_PER_SEG_COLUMN
+        ] / (
+            seg_epoch0[self.columns.EIGENVALUE0_COLUMN]
+            * seg_epoch0[self.columns.EIGENVALUE1_COLUMN]
+        )
+
+        points_density_seg_epoch1 = seg_epoch1[
+            self.columns.NR_POINTS_PER_SEG_COLUMN
+        ] / (
+            seg_epoch1[self.columns.EIGENVALUE0_COLUMN]
+            * seg_epoch1[self.columns.EIGENVALUE1_COLUMN]
+        )
+
+        points_density_diff = abs(points_density_seg_epoch0 - points_density_seg_epoch1)
+
+        eigen_value_smallest_diff = abs(
+            seg_epoch0[self.columns.EIGENVALUE2_COLUMN]
+            - seg_epoch1[self.columns.EIGENVALUE2_COLUMN]
+        )
+        eigen_value_largest_diff = abs(
+            seg_epoch0[self.columns.EIGENVALUE0_COLUMN]
+            - seg_epoch1[self.columns.EIGENVALUE0_COLUMN]
+        )
+        eigen_value_middle_diff = abs(
+            seg_epoch0[self.columns.EIGENVALUE1_COLUMN]
+            - seg_epoch1[self.columns.EIGENVALUE1_COLUMN]
+        )
+
+        nr_points_diff = abs(
+            seg_epoch0[self.columns.NR_POINTS_PER_SEG_COLUMN]
+            - seg_epoch1[self.columns.NR_POINTS_PER_SEG_COLUMN]
+        )
+
+        return np.array(
+            [
+                angle,
+                points_density_diff,
+                eigen_value_smallest_diff,
+                eigen_value_largest_diff,
+                eigen_value_middle_diff,
+                nr_points_diff,
+            ]
+        )
+
+    def _build_X_similarity(self, y_row, X):
+        """
+
+        :param y_row:
+            numpy array of ( segment epoch0 id, segment epoch1 id, label(0/1) )
+        :param X:
+            numpy array of shape (n_segments, segment_features_size) containing all the segments for both,
+            epoch 0 and epoch 1. Each row is a segment.
+        :return:
+            numpy array containing the similarity value between 2 segments.
+        """
+
+        seg_epoch0 = X[int(y_row[0]), :]
+        seg_epoch1 = X[int(y_row[1]), :]
+
+        return self.compute_similarity_between(seg_epoch0, seg_epoch1)
+
+    def fit(self, X, y):
+        """
+        This method takes care of the learning process by training the chosen 'classifier', using labeled data.
+
+        :param X:
+            numpy array (n_segments, segment_size)
+        :param y:
+            numpy array of shape (m_extended_y, 3) where 'extended y' has the following structure:
+        ( tuples of index segment from epoch0, index segment from epoch1, label(0/1) )
+        """
+
+        X_similarity = np.apply_along_axis(
+            lambda y_row: self._build_X_similarity(y_row, X), 1, y
+        )
+
+        # Check that X and y have correct shape
+        # X_similarity, y = check_X_y(X_similarity, y, multi_output=True)
+
+        # Store the classes seen during fit
+        # self.classes_ = unique_labels(y[:, 2])
+
+        # self.X_ = X_similarity
+        # self.y_ = y[:, 2]
+
+        logger.info(f"Fit ClassifierWrapper")
+
+        # Return the classifier
+        return self.classifier.fit(X_similarity, y[:, 2])
+
+    def predict(self, X):
+        """
+        For a set of segments from epoch 0 and epoch 1 it computes which one corresponds.
+
+        :param X:
+            numpy array (n_segments, 20) with the following column structure:
+            [
+                x, y, z ( 3 columns ), -> segment, core point
+                EpochID ( 1 column ),
+                Eigenvalues( 3 columns ), -> that correspond to the next 3 Eigenvectors
+                Eigenvectors( 3 columns ) X 3 -> in descending order using vector norm 2,
+                Lowest local surface variation ( 1 column ),
+                Segment_ID ( 1 column ),
+                Standard deviation ( 1 column ),
+                Number of points found in Segment_ID segment ( 1 column )
+            ]
+
+        :return:
+            numpy array where each row contains a pair of segments:
+                [segment epoch 0, segment epoch 1]
+        """
+
+        # Check if fit had been called
+        # check_is_fitted(self, ["X_", "y_"])
+
+        # Input validation
+        # X = check_array(X)
+
+        mask_epoch0 = X[:, self.columns.EPOCH_ID_COLUMN] == 0
+        mask_epoch1 = X[:, self.columns.EPOCH_ID_COLUMN] == 1
+
+        epoch0_set = X[mask_epoch0, :]  # all
+        epoch1_set = X[mask_epoch1, :]  # all
+
+        self.epoch1_segments = Epoch(
+            epoch1_set[
+                :, [self.columns.X_COLUMN, self.columns.Y_COLUMN, self.columns.Z_COLUMN]
+            ]
+        )
+        self.epoch1_segments.build_kdtree()
+
+        list_segments_pair = np.empty((0, epoch0_set.shape[1] + epoch1_set.shape[1]))
+
+        # this operation can be parallelized
+        for epoch0_set_row in epoch0_set:
+            list_candidates = self.epoch1_segments.kdtree.radius_search(
+                epoch0_set_row, self.neighborhood_search_radius
+            )
+
+            list_classified = np.array(
+                [
+                    self.classifier.predict_proba(
+                        self.compute_similarity_between(
+                            epoch0_set_row, epoch1_set[candidate, :]
+                        ).reshape(1, -1)
+                    )[0][1]
+                    for candidate in list_candidates
+                ]
+            )
+
+            if len(list_classified) < 2:
+                continue
+
+            most_similar = list_classified.argsort()[-2:]
+
+            if (
+                most_similar[1] >= self.threshold_probability_most_similar
+                and abs(most_similar[1] - most_similar[0])
+                >= self.diff_between_most_similar_2
+            ):
+                list_segments_pair = np.vstack(
+                    (
+                        list_segments_pair,
+                        np.hstack(
+                            (epoch0_set_row, epoch1_set[most_similar[-1], :])
+                        ).reshape(1, -1),
+                    )
+                )
+
+        return list_segments_pair
+
+
+class PBM3C2:
+    def __init__(
+        self,
+        per_point_computation=PerPointComputation(),
+        segmentation=Segmentation(),
+        second_segmentation=Segmentation(),
+        extract_segments=ExtractSegments(),
+        classifier=ClassifierWrapper(),
+    ):
+
+        logger.warning(
+            f"This method is in experimental stage and undergoing active development."
+        )
+
+        """
+        :param per_point_computation:
+            lowest local surface variation and PCA computation. (computes the normal vector as well)
+        :param segmentation:
+            The object used for the first segmentation.
+        :param second_segmentation:
+            The object used for the second segmentation.
+        :param extract_segments:
+            The object used for building the segments.
+        :param classifier:
+            An instance of ClassifierWrapper class. The default wrapped classifier used is sk-learn RandomForest.
+        """
+
+        self._per_point_computation = per_point_computation
+        self._segmentation = segmentation
+        self._second_segmentation = second_segmentation
+        self._extract_segments = extract_segments
+        self._classifier = classifier
+
+        self._second_segmentation.set_params(with_previously_computed_segments=True)
+
+    def _reconstruct_input_with_normals(self, epoch, epoch_id, columns):
+        """
+        It is an adapter from [x, y, z, N_x, N_y, N_z, Segment_ID] column structure of input 'epoch'
+        to an output equivalent with the following pipeline computation:
+                ("Transform LLSV_and_PCA"), ("Transform Segmentation"), ("Transform Second Segmentation")
+
+        Note: When comparing distance results between this notebook and the base algorithm notebook, you might notice,
+        that results do not necessarily agree even if the given segmentation information is exactly
+        the same as the one computed in the base algorithm.
+        This is due to the reconstruction process in this algorithm being forced to select the segment position
+        (exported as the core point) from the segment points instead of reconstructing the correct position
+        from the base algorithm.
+
+        :param epoch:
+            Epoch object where each row has the following format: [x, y, z, N_x, N_y, N_z, Segment_ID]
+        :param epoch_id:
+            is 0 or 1 and represents one of the epochs used as part of distance computation.
+        :param columns:
+
+        :return:
+            numpy array of shape (n_points, 19) with the following column structure:
+                [
+                    x,y,z, -> Center of the Mass
+                    EPOCH_ID_COLUMN, ->0/1
+                    Eigenvalue 1, Eigenvalue 2, Eigenvalue 3,
+                    Eigenvector0 (x,y,z),
+                    Eigenvector1 (x,y,z),
+                    Eigenvector2 (x,y,z), -> Normal vector
+                    LLSV_COLUMN, -> lowest local surface variation
+                    SEGMENT_ID_COLUMN,
+                    STANDARD_DEVIATION_COLUMN
+                ]
+        """
+
+        # x, y, z, N_x, N_y, N_z, Segment_ID
+        assert epoch.shape[1] == 3 + 3 + 1, "epoch size mismatch!"
+
+        return np.hstack(
+            (
+                epoch[:, :3],  # x,y,z      X 3
+                np.full(
+                    (epoch.shape[0], 1), epoch_id, dtype=float
+                ),  # EPOCH_ID_COLUMN    X 1
+                np.full((epoch.shape[0], 3), 0, dtype=float),  # Eigenvalue X 3
+                np.full(
+                    (epoch.shape[0], 6), 0, dtype=float
+                ),  # Eigenvector0, Eigenvector1        X 6
+                epoch[:, 3:6],  # Eigenvector2      X 3
+                np.full((epoch.shape[0], 1), 0, dtype=float).reshape(
+                    -1, 1
+                ),  # LLSV_COLUMN
+                epoch[:, -1].reshape(-1, 1),  # SEGMENT_ID_COLUMN
+                np.full(
+                    (epoch.shape[0], 1),
+                    DEFAULT_STD_DEVIATION_OF_NO_CORE_POINT,
+                    dtype=float,
+                ).reshape(
+                    -1, 1
+                ),  # STANDARD_DEVIATION_COLUMN
+            )
+        )
+
+    def _reconstruct_input_without_normals(self, epoch, epoch_id, columns):
+        """
+        It is an adapter from [x, y, z, Segment_ID] column structure of input 'epoch'
+        to an output equivalent with the following pipeline computation:
+            ("Transform LLSV_and_PCA"), ("Transform Segmentation"), ("Transform Second Segmentation")
+
+        Note: When comparing distance results between this notebook and the base algorithm notebook, you might notice,
+        that results do not necessarily agree even if the given segmentation information is exactly
+        the same as the one computed in the base algorithm.
+        This is due to the reconstruction process in this algorithm being forced to select the segment position
+        (exported as the core point) from the segment points instead of reconstructing the correct position
+        from the base algorithm.
+
+        :param epoch:
+            Epoch object where each row contains by: [x, y, z, Segment_ID]
+        :param epoch_id:
+            is 0 or 1 and represents one of the epochs used as part of distance computation.
+        :param columns
+
+        :return:
+            numpy array of shape (n_points, 19) with the following column structure:
+                [
+                    x,y,z, -> Center of the Mass
+                    Epoch_ID, ->0/1
+                    Eigenvalue 1, Eigenvalue 2, Eigenvalue 3,
+                    Eigenvector0 (x,y,z),
+                    Eigenvector1 (x,y,z),
+                    Eigenvector2 (x,y,z), -> Normal vector
+                    LLSV, -> lowest local surface variation
+                    Segment_ID,
+                    Standard deviation
+                ]
+        """
+
+        # [x, y, z, Segment_ID] or [x, y, z, N_x, N_y, N_z, Segment_ID]
+        assert (
+            epoch.shape[1] == 3 + 1 or epoch.shape[1] == 3 + 3 + 1
+        ), "epoch size mismatch!"
+
+        return np.hstack(
+            (
+                epoch[:, :3],  # x,y,z     X 3
+                np.full(
+                    (epoch.shape[0], 1), epoch_id, dtype=float
+                ),  # EPOCH_ID_COLUMN X 1
+                np.full((epoch.shape[0], 3), 0, dtype=float),  # Eigenvalue X 3
+                np.full(
+                    (epoch.shape[0], 6), 0, dtype=float
+                ),  # Eigenvector0, Eigenvector1 X 6
+                np.full((epoch.shape[0], 3), 0, dtype=float),  # Eigenvector2 X 3
+                np.full((epoch.shape[0], 1), 0, dtype=float).reshape(
+                    -1, 1
+                ),  # LLSV_COLUMN
+                epoch[:, -1].reshape(-1, 1),  # SEGMENT_ID_COLUMN
+                np.full(
+                    (epoch.shape[0], 1),
+                    DEFAULT_STD_DEVIATION_OF_NO_CORE_POINT,
+                    dtype=float,
+                ).reshape(
+                    -1, 1
+                ),  # STANDARD_DEVIATION_COLUMN
+            )
+        )
+
+    @staticmethod
+    def _print_default_parameters(kwargs, pipeline_param_dict):
+        """
+        :param kwargs:
+        :param pipeline_param_dict
+        """
+
+        # print the default parameters
+        if ("get_pipeline_options", True) in kwargs.items():
+            logger.info(
+                f"----\n "
+                f"The default parameters are:\n "
+                f"{pp.pformat(pipeline_param_dict)} \n"
+                f"----\n"
+            )
+            del kwargs["get_pipeline_options"]
+
+    @staticmethod
+    def _overwrite_pipeline_parameters(
+        kwargs, pipeline, message="The pipeline parameters after overwriting are:"
+    ):
+        """
+        :param kwargs:
+        :param pipeline:
+
+        :return: unused_kwargs
+            The unused parameters / not found as part of 'pipeline'
+        """
+
+        unused_kwargs = {}
+
+        # if we have parameters
+        if len(kwargs.items()) > 0:
+            pipeline_params = pipeline.get_params()
+            # overwrite the default parameters
+            for key, value in kwargs.items():
+                if key in pipeline_params.keys():
+                    pipeline.set_params(**{key: value})
+                    logger.debug(f"The pipeline parameter '{key}' is now '{value}'")
+                else:
+                    unused_kwargs[key] = value
+            logger.info(
+                f"----\n "
+                f"{message} \n"
+                f"{pp.pformat(pipeline.get_params())} \n"
+                f"----\n"
+            )
+        else:
+            logger.info("No pipeline parameter is overwritten")
+
+        return unused_kwargs
+
+    def generate_extended_labels_interactively(
+        self,
+        epoch0: typing.Union[Epoch, None] = None,
+        epoch1: typing.Union[Epoch, None] = None,
+        builder_extended_y: BuilderExtended_y_Visually = BuilderExtended_y_Visually(),
+        **kwargs,
+    ) -> typing.Union[typing.Tuple[np.ndarray, np.ndarray], None]:
+        """
+        Given 2 Epochs, it builds a pair of (segments and 'extended y').
+
+        :param epoch0:
+            Epoch object.
+        :param epoch1:
+            Epoch object.
+        :param builder_extended_y:
+            The object is used for generating 'extended y', visually.
+        :param kwargs:
+
+            Used for customize the default pipeline parameters.
+
+            Getting the default parameters:
+            e.g. "get_pipeline_options"
+                In case this parameter is True, the method will print the pipeline options as kwargs.
+
+            e.g. "output_file_name" (of a specific step in the pipeline) default value is "None".
+                In case of setting it, the result of computation at that step is dump as xyz file.
+            e.g. "distance_3D_threshold" (part of Segmentation Transform)
+
+            this process is stateless
+
+        :return:
+            tuple [Segments, 'extended y'] | None
+
+            where:
+
+            'Segments' has the following column structure:
+                    X_COLUMN, Y_COLUMN, Z_COLUMN, -> Center of Gravity
+                    EPOCH_ID_COLUMN, -> 0/1
+                    EIGENVALUE0_COLUMN, EIGENVALUE1_COLUMN, EIGENVALUE2_COLUMN,
+                    EIGENVECTOR_0_X_COLUMN, EIGENVECTOR_0_Y_COLUMN, EIGENVECTOR_0_Z_COLUMN,
+                    EIGENVECTOR_1_X_COLUMN, EIGENVECTOR_1_Y_COLUMN, EIGENVECTOR_1_Z_COLUMN,
+                    EIGENVECTOR_2_X_COLUMN, EIGENVECTOR_2_Y_COLUMN, EIGENVECTOR_2_Z_COLUMN, -> Normal vector
+                    LLSV_COLUMN, -> lowest local surface variation
+                    SEGMENT_ID_COLUMN,
+                    STANDARD_DEVIATION_COLUMN,
+                    NR_POINTS_PER_SEG_COLUMN,
+
+            'extended y' has the following structure: (tuples of index segment from epoch0, index segment from epoch1,
+            label(0/1)) used for learning.
+        """
+
+        if not interactive_available:
+            logger.error("Interactive session not available in this environment.")
+            return
+
+        labeling_pipeline = Pipeline(
+            [
+                ("Transform_PerPointComputation", self._per_point_computation),
+                ("Transform_Segmentation", self._segmentation),
+                ("Transform_Second_Segmentation", self._second_segmentation),
+                ("Transform_ExtractSegments", self._extract_segments),
+            ]
+        )
+
+        # print the default parameters
+        PBM3C2._print_default_parameters(
+            kwargs=kwargs, pipeline_param_dict=labeling_pipeline.get_params()
+        )
+
+        # no computation
+        if epoch0 is None or epoch1 is None:
+            # logger.info("epoch0 and epoch1 are required, no parameter changes applied")
+            return
+
+        # save the default pipeline options
+        default_options = labeling_pipeline.get_params()
+
+        # overwrite the default parameters
+        unused_kwargs = PBM3C2._overwrite_pipeline_parameters(
+            kwargs=kwargs, pipeline=labeling_pipeline
+        )
+        if len(unused_kwargs) > 0:
+            logger.warning(
+                f"The parameters '{unused_kwargs.keys()}' are not part of the pipeline parameters: \n "
+                f"{pp.pformat(labeling_pipeline.get_params())}"
+            )
+
+        # apply the pipeline
+        X0 = np.hstack((epoch0.cloud[:, :], np.zeros((epoch0.cloud.shape[0], 1))))
+        X1 = np.hstack((epoch1.cloud[:, :], np.ones((epoch1.cloud.shape[0], 1))))
+        X = np.vstack((X0, X1))
+        labeling_pipeline.fit(X)
+        segments = labeling_pipeline.transform(X)
+
+        # restore the default pipeline options
+        unused_kwargs = PBM3C2._overwrite_pipeline_parameters(
+            kwargs=default_options,
+            pipeline=labeling_pipeline,
+            message="The pipeline parameters after restoration are: ",
+        )
+        assert (
+            len(unused_kwargs) == 0
+        ), "All default options should be found when default parameter restoration is done"
+
+        return segments, builder_extended_y.generate_extended_y(segments)
+
+    def export_segmented_point_cloud_and_segments(
+        self,
+        epoch0: Epoch = None,
+        epoch1: Epoch = None,
+        x_y_z_id_epoch0_file_name: typing.Union[str, None] = "x_y_z_id_epoch0.xyz",
+        x_y_z_id_epoch1_file_name: typing.Union[str, None] = "x_y_z_id_epoch1.xyz",
+        extracted_segments_file_name: typing.Union[
+            str, None
+        ] = "extracted_segments.seg",
+        concatenate_name="",
+        **kwargs,
+    ) -> typing.Union[
+        typing.Tuple[np.ndarray, typing.Union[np.ndarray, None], np.ndarray], None
+    ]:
+        """
+        For each epoch, it returns the segmentation of the point cloud as a numpy array (n_points, 4)
+        and it also serializes them using the provided file names.
+        where each row has the following structure: x, y, z, segment_id
+
+        It also generates a numpy array of segments of the form:
+                    X_COLUMN, Y_COLUMN, Z_COLUMN, -> Center of Gravity
+                    EPOCH_ID_COLUMN, -> 0/1
+                    EIGENVALUE0_COLUMN, EIGENVALUE1_COLUMN, EIGENVALUE2_COLUMN,
+                    EIGENVECTOR_0_X_COLUMN, EIGENVECTOR_0_Y_COLUMN, EIGENVECTOR_0_Z_COLUMN,
+                    EIGENVECTOR_1_X_COLUMN, EIGENVECTOR_1_Y_COLUMN, EIGENVECTOR_1_Z_COLUMN,
+                    EIGENVECTOR_2_X_COLUMN, EIGENVECTOR_2_Y_COLUMN, EIGENVECTOR_2_Z_COLUMN, -> Normal vector
+                    LLSV_COLUMN, -> lowest local surface variation
+                    SEGMENT_ID_COLUMN,
+                    STANDARD_DEVIATION_COLUMN,
+                    NR_POINTS_PER_SEG_COLUMN,
+
+        :param epoch0:
+            Epoch object | None
+        :param epoch1:
+            Epoch object | None
+        :param x_y_z_id_epoch0_file_name:
+            The output file name for epoch0, point cloud segmentation, saved as a numpy array (n_points, 4)
+            (x,y,z, segment_id)
+            | None
+        :param x_y_z_id_epoch1_file_name:
+            The output file name for epoch1, point cloud segmentation, saved as a numpy array (n_points, 4)
+            (x,y,z, segment_id)
+            | None
+        :param extracted_segments_file_name:
+            The output file name for the file containing the segments, saved as a numpy array containing
+            the column structure introduced above.
+            | None
+        :param concatenate_name:
+            String that is utilized to uniquely identify the same transformer between multiple pipelines.
+        :param kwargs:
+
+            Used for customize the default pipeline parameters.
+
+            Getting the default parameters:
+            e.g. "get_pipeline_options"
+                In case this parameter is True, the method will print the pipeline options as kwargs.
+
+            e.g. "output_file_name" (of a specific step in the pipeline) default value is "None".
+                In case of setting it, the result of computation at that step is dump as xyz file.
+            e.g. "distance_3D_threshold" (part of Segmentation Transform)
+
+            this process is stateless
+
+        :return:
+            tuple [ x_y_z_id_epoch0, x_y_z_id_epoch1 | None, extracted_segments ] | None
+        """
+
+        pipe_segmentation = Pipeline(
+            [
+                (
+                    concatenate_name + "_Transform_PerPointComputation",
+                    self._per_point_computation,
+                ),
+                (concatenate_name + "_Transform_Segmentation", self._segmentation),
+                (
+                    concatenate_name + "_Transform_Second_Segmentation",
+                    self._second_segmentation,
+                ),
+            ]
+        )
+
+        pipe_extract_segments = Pipeline(
+            [
+                (
+                    concatenate_name + "_Transform_ExtractSegments",
+                    self._extract_segments,
+                ),
+            ]
+        )
+
+        # print the default parameters
+        PBM3C2._print_default_parameters(
+            kwargs=kwargs,
+            pipeline_param_dict={
+                **pipe_segmentation.get_params(),
+                **pipe_extract_segments.get_params(),
+            },
+        )
+
+        # no computation
+        if epoch0 is None:  # or epoch1 is None:
+            # logger.info("epoch0 is required, no parameter changes applied")
+            return
+
+        # save the default pipeline options
+        default_options = {
+            **pipe_segmentation.get_params(),
+            **pipe_extract_segments.get_params(),
+        }
+        del default_options["memory"]
+        del default_options["steps"]
+        del default_options["verbose"]
+
+        # overwrite the default parameters
+        unused_kwargs = PBM3C2._overwrite_pipeline_parameters(
+            kwargs=kwargs, pipeline=pipe_segmentation
+        )
+        unused_kwargs = PBM3C2._overwrite_pipeline_parameters(
+            kwargs=unused_kwargs, pipeline=pipe_extract_segments
+        )
+        if len(unused_kwargs) > 0:
+            logger.warning(
+                f"The parameters '{unused_kwargs.keys()}' are not part of the pipeline parameters: \n "
+                f"{pp.pformat({**pipe_segmentation.get_params(), **pipe_extract_segments.get_params()})}"
+            )
+
+        # apply the pipeline
+
+        if isinstance(epoch0, Epoch):
+            X0 = np.hstack((epoch0.cloud[:, :], np.zeros((epoch0.cloud.shape[0], 1))))
+        else:
+            X0 = epoch0
+
+        if isinstance(epoch1, Epoch):
+            X1 = np.hstack((epoch1.cloud[:, :], np.ones((epoch1.cloud.shape[0], 1))))
+            X = np.vstack((X0, X1))
+        else:
+            X = X0
+
+        pipe_segmentation.fit(X)
+        # 'out' contains the segmentation of the point cloud.
+        out = pipe_segmentation.transform(X)
+
+        pipe_extract_segments.fit(out)
+        # 'extracted_segments' contains the new set of segments
+        extracted_segments = pipe_extract_segments.transform(out)
+
+        # restore the default pipeline options
+        unused_default_options = PBM3C2._overwrite_pipeline_parameters(
+            kwargs=default_options,
+            pipeline=pipe_segmentation,
+            message="The pipeline parameters after restoration are: ",
+        )
+        unused_default_options = PBM3C2._overwrite_pipeline_parameters(
+            kwargs=unused_default_options,
+            pipeline=pipe_extract_segments,
+            message="The pipeline parameters after restoration are: ",
+        )
+        assert (
+            len(unused_default_options) == 0
+        ), "All default options should be found when default parameter restoration is done"
+
+        columns = self._second_segmentation.columns
+
+        Extract_Columns = [
+            columns.X_COLUMN,
+            columns.Y_COLUMN,
+            columns.Z_COLUMN,
+            columns.SEGMENT_ID_COLUMN,
+        ]
+
+        mask_epoch0 = out[:, columns.EPOCH_ID_COLUMN] == 0
+        mask_epoch1 = out[:, columns.EPOCH_ID_COLUMN] == 1
+
+        out_epoch0 = out[mask_epoch0, :]
+        out_epoch1 = out[mask_epoch1, :]
+
+        x_y_z_id_epoch0 = out_epoch0[:, Extract_Columns]  # x,y,z, Seg_ID
+        x_y_z_id_epoch1 = out_epoch1[:, Extract_Columns]  # x,y,z, Seg_ID
+
+        if x_y_z_id_epoch0_file_name != None:
+            logger.debug(f"Save 'x_y_z_id_epoch0' in file: {x_y_z_id_epoch0_file_name}")
+            np.savetxt(x_y_z_id_epoch0_file_name, x_y_z_id_epoch0, delimiter=",")
+        else:
+            logger.debug(f"'x_y_z_id_epoch0' is not saved")
+
+        if x_y_z_id_epoch1_file_name != None:
+            logger.debug(f"Save 'x_y_z_id_epoch1' in file: {x_y_z_id_epoch1_file_name}")
+            np.savetxt(x_y_z_id_epoch1_file_name, x_y_z_id_epoch1, delimiter=",")
+        else:
+            logger.debug(f"'x_y_z_id_epoch1' is not saved")
+
+        if extracted_segments_file_name != None:
+            logger.debug(
+                f"Save 'extracted_segments' in file: {extracted_segments_file_name}"
+            )
+            np.savetxt(extracted_segments_file_name, extracted_segments, delimiter=",")
+        else:
+            logger.debug(f"'extracted_segments' is not saved")
+
+        return x_y_z_id_epoch0, x_y_z_id_epoch1, extracted_segments
+
+    def training(
+        self,
+        segments: np.ndarray = None,
+        extended_y: np.ndarray = None,
+        extracted_segments_file_name: str = "extracted_segments.seg",
+        extended_y_file_name: str = "extended_y.csv",
+    ) -> None:
+        """
+        It applies the training algorithm for the input pairs of Segments 'segments'
+        and extended labels 'extended_y'.
+
+        :param segments:
+            'Segments' numpy array of shape (n_segments, segment_size)
+
+            It has the following column structure:
+                    X_COLUMN, Y_COLUMN, Z_COLUMN, -> Center of Gravity
+                    EPOCH_ID_COLUMN, -> 0/1
+                    EIGENVALUE0_COLUMN, EIGENVALUE1_COLUMN, EIGENVALUE2_COLUMN,
+                    EIGENVECTOR_0_X_COLUMN, EIGENVECTOR_0_Y_COLUMN, EIGENVECTOR_0_Z_COLUMN,
+                    EIGENVECTOR_1_X_COLUMN, EIGENVECTOR_1_Y_COLUMN, EIGENVECTOR_1_Z_COLUMN,
+                    EIGENVECTOR_2_X_COLUMN, EIGENVECTOR_2_Y_COLUMN, EIGENVECTOR_2_Z_COLUMN, -> Normal vector
+                    LLSV_COLUMN, -> lowest local surface variation
+                    SEGMENT_ID_COLUMN,
+                    STANDARD_DEVIATION_COLUMN,
+                    NR_POINTS_PER_SEG_COLUMN,
+
+        :param extended_y:
+            numpy array of shape (m_labels, 3)
+            has the following structure: (tuples of index segment from epoch0, index segment from epoch1,
+            label(0/1))
+        :param extracted_segments_file_name:
+            In case 'X' is None segments are loaded using 'extracted_segments_file_name'.
+        :param extended_y_file_name:
+            In case 'extended_y' is None, this file is used as input fallback.
+        """
+
+        if segments is None:
+            # Resolve the given path
+            filename = find_file(extracted_segments_file_name)
+            # Read it
+            try:
+                logger.info(f"Reading segments from file '{filename}'")
+                segments = np.genfromtxt(filename, delimiter=",")
+            except ValueError:
+                raise Py4DGeoError("Malformed file: " + str(filename))
+
+        if extended_y is None:
+            # Resolve the given path
+            filename = find_file(extended_y_file_name)
+            # Read it
+            try:
+                logger.info(
+                    f"Reading tuples of (segment epoch0, segment epoch1, label) from file '{filename}'"
+                )
+                extended_y = np.genfromtxt(filename, delimiter=",")
+            except ValueError:
+                raise Py4DGeoError("Malformed file: " + str(filename))
+
+        training_pipeline = Pipeline(
+            [
+                ("Classifier", self._classifier),
+            ]
+        )
+
+        # apply the pipeline
+        training_pipeline.fit(segments, extended_y)
+
+    def predict(
+        self,
+        epoch0: Epoch = None,
+        epoch1: Epoch = None,
+        epoch_additional_dimensions_lookup: typing.Dict[str, str] = None,
+        **kwargs,
+    ) -> typing.Union[np.ndarray, None]:
+        """
+        After extracting the segments from epoch0 and epoch1, it returns a numpy array of corresponding
+        pairs of segments between epoch 0 and epoch 1.
+
+        :param epoch0:
+            Epoch object.
+        :param epoch1:
+            Epoch object.
+        :param epoch_additional_dimensions_lookup:
+            A dictionary that maps between the names of the columns used internally
+            and the names of the columns used by both epoch0 and epoch1.
+
+            No additional column is used.
+        :param kwargs:
+
+            Used for customize the default pipeline parameters.
+
+            Getting the default parameters:
+            e.g. "get_pipeline_options"
+                In case this parameter is True, the method will print the pipeline options as kwargs.
+
+            e.g. "output_file_name" (of a specific step in the pipeline) default value is "None".
+                In case of setting it, the result of computation at that step is dump as xyz file.
+            e.g. "distance_3D_threshold" (part of Segmentation Transform)
+
+            this process is stateless
+
+        :return:
+            A numpy array ( n_pairs, segment_features_size*2 ) where each row contains a pair of segments.
+            | None
+        """
+
+        pipe_classifier = Pipeline(
+            [
+                ("Classifier", self._classifier),
+            ]
+        )
+
+        # arguments used, as part of the epoch0's pipeline.
+        kwargs_epoch0 = {
+            key: val
+            for key, val in kwargs.items()
+            if key.startswith("epoch0") or key == "get_pipeline_options"
+        }
+
+        # epoch0, segments computation
+        out_for_epoch0 = self.export_segmented_point_cloud_and_segments(
+            epoch0=epoch0,
+            epoch1=None,
+            x_y_z_id_epoch0_file_name=None,
+            x_y_z_id_epoch1_file_name=None,
+            extracted_segments_file_name=None,
+            concatenate_name="epoch0",
+            **kwargs_epoch0,
+        )
+
+        # arguments used, as part of the epoch1's pipeline.
+        kwargs_epoch1 = {
+            key: val
+            for key, val in kwargs.items()
+            if key.startswith("epoch1") or key == "get_pipeline_options"
+        }
+
+        # epoch1, segments computation
+        out_for_epoch1 = self.export_segmented_point_cloud_and_segments(
+            epoch0=epoch1,
+            epoch1=None,
+            x_y_z_id_epoch0_file_name=None,
+            x_y_z_id_epoch1_file_name=None,
+            extracted_segments_file_name=None,
+            concatenate_name="epoch1",
+            **kwargs_epoch1,
+        )
+
+        # arguments used, as part of the classifier 'pipeline'
+        kwargs_classifier = {
+            key: val
+            for key, val in kwargs.items()
+            if not key.startswith("epoch0") and not key.startswith("epoch1")
+        }
+
+        # print the default parameters for 'pipe_classifier'
+        PBM3C2._print_default_parameters(
+            kwargs=kwargs_classifier, pipeline_param_dict=pipe_classifier.get_params()
+        )
+
+        # no computation
+        if epoch0 is None or epoch1 is None:
+            # logger.info("epoch0 and epoch1 are required, no parameter changes applied")
+            return
+
+        # save the default pipe_classifier options
+        default_options = pipe_classifier.get_params()
+
+        # overwrite the default parameters
+        unused_kwargs = PBM3C2._overwrite_pipeline_parameters(
+            kwargs=kwargs_classifier, pipeline=pipe_classifier
+        )
+        if len(unused_kwargs) > 0:
+            logger.error(
+                f"The parameters: '{unused_kwargs.keys()}' are not part of the pipeline parameters: \n "
+                f"{pp.pformat(pipe_classifier.get_params())}"
+            )
+
+        _0, _1, epoch0_segments = out_for_epoch0
+        _0, _1, epoch1_segments = out_for_epoch1
+
+        columns = self._extract_segments.columns
+
+        # compute segment id offset
+        max_seg_id_epoch0 = np.max(epoch0_segments[:, columns.SEGMENT_ID_COLUMN])
+        # apply offset to segment from epoch1
+        epoch1_segments[:, columns.SEGMENT_ID_COLUMN] += max_seg_id_epoch0 + 1
+
+        # enforce epoch ID as '0' for 'epoch0_segments'
+        epoch0_segments[:, columns.EPOCH_ID_COLUMN] = 0
+
+        # change the epoch ID from 0 (the default one used during the previous computation for both epochs)
+        # to 1 for 'epoch1_segments'
+        epoch1_segments[:, columns.EPOCH_ID_COLUMN] = 1
+
+        extracted_segments = np.vstack((epoch0_segments, epoch1_segments))
+
+        out = pipe_classifier.predict(extracted_segments)
+
+        # restore the default pipeline options
+        unused_default_options = PBM3C2._overwrite_pipeline_parameters(
+            kwargs=default_options,
+            pipeline=pipe_classifier,
+            message="The pipeline parameters after restoration are: ",
+        )
+        assert (
+            len(unused_default_options) == 0
+        ), "All default options should be found when default parameter restoration is done"
+
+        return out
+
+    def _compute_distances(
+        self,
+        epoch0_info: typing.Union[Epoch, np.ndarray] = None,
+        epoch1: Epoch = None,
+        alignment_error: float = 1.1,
+        epoch_additional_dimensions_lookup: typing.Dict[str, str] = None,
+        **kwargs,
+    ) -> typing.Union[typing.Tuple[np.ndarray, np.ndarray], None]:
+        """
+        Compute the distance between 2 epochs. It also adds the following properties at the end of the computation:
+            distances, corepoints (corepoints of epoch0), epochs (epoch0, epoch1), uncertainties
+
+        :param epoch0_info:
+            Epoch object.
+            | np.ndarray
+        :param epoch1:
+            Epoch object.
+        :param alignment_error:
+            alignment error reg between point clouds.
+        :param epoch_additional_dimensions_lookup:
+            A dictionary that maps between the names of the columns used internally
+            and the names of the columns used by both epoch0 and epoch1.
+        :param kwargs:
+            Used for customize the default pipeline parameters.
+
+            Getting the default parameters:
+            e.g. "get_pipeline_options"
+                In case this parameter is True, the method will print the pipeline options as kwargs.
+
+            e.g. "output_file_name" (of a specific step in the pipeline) default value is "None".
+                In case of setting it, the result of computation at that step is dump as xyz file.
+            e.g. "distance_3D_threshold" (part of Segmentation Transform)
+
+            this process is stateless
+
+        :return:
+            tuple [distances, uncertainties]
+                'distances' is np.array (nr_similar_pairs, 1)
+                'uncertainties' is np.array (nr_similar_pairs,1) and it has the following structure:
+                    dtype=np.dtype(
+                        [
+                            ("lodetection", "<f8"),
+                            ("spread1", "<f8"),
+                            ("num_samples1", "<i8"),
+                            ("spread2", "<f8"),
+                            ("num_samples2", "<i8"),
+                        ]
+                    )
+            | None
+        """
+
+        logger.info(f"PBM3C2._compute_distances(...)")
+
+        # A numpy array where each row contains a pair of segments.
+        segments_pair = self.predict(
+            epoch0_info,
+            epoch1,
+            epoch_additional_dimensions_lookup=epoch_additional_dimensions_lookup,
+            **kwargs,
+        )
+
+        columns = self._extract_segments.columns
+
+        # no computation
+        if epoch0_info is None or epoch1 is None:
+            # logger.info("epoch0 and epoch1 are required, no parameter changes applied")
+            return
+
+        size_segment = int(segments_pair.shape[1] / 2)
+        nr_pairs = segments_pair.shape[0]
+
+        epoch0_segments = segments_pair[:, :size_segment]
+        epoch1_segments = segments_pair[:, size_segment:]
+
+        # seg_id_epoch0, X_Column0, Y_Column0, Z_Column0, seg_id_epoch1, X_Column1, Y_Column1, Z_Column1, distance, uncertaintie
+        output = np.empty((0, 10), dtype=float)
+
+        for indx in range(nr_pairs):
+            segment_epoch0 = epoch0_segments[indx]
+            segment_epoch1 = epoch1_segments[indx]
+
+            t0_CoG = segment_epoch0[
+                [columns.X_COLUMN, columns.Y_COLUMN, columns.Z_COLUMN]
+            ]
+            t1_CoG = segment_epoch1[
+                [columns.X_COLUMN, columns.Y_COLUMN, columns.Z_COLUMN]
+            ]
+
+            Normal_Columns = [
+                columns.EIGENVECTOR_2_X_COLUMN,
+                columns.EIGENVECTOR_2_Y_COLUMN,
+                columns.EIGENVECTOR_2_Z_COLUMN,
+            ]
+            normal_vector_t0 = segment_epoch0[Normal_Columns]
+
+            M3C2_dist = normal_vector_t0.dot(t0_CoG - t1_CoG)
+
+            std_dev_normalized_squared_t0 = segment_epoch0[
+                columns.STANDARD_DEVIATION_COLUMN
+            ]
+            std_dev_normalized_squared_t1 = segment_epoch1[
+                columns.STANDARD_DEVIATION_COLUMN
+            ]
+
+            LoDetection = 1.96 * (
+                np.sqrt(std_dev_normalized_squared_t0 + std_dev_normalized_squared_t1)
+                + alignment_error
+            )
+
+            # seg_id_epoch0, X_Column0, Y_Column0, Z_Column0, seg_id_epoch1, X_Column1, Y_Column1, Z_Column1, distance, uncertaintie
+            args = (
+                np.array([segment_epoch0[columns.SEGMENT_ID_COLUMN]]),
+                t0_CoG,
+                np.array([segment_epoch1[columns.SEGMENT_ID_COLUMN]]),
+                t1_CoG,
+                np.array([M3C2_dist]),
+                np.array([LoDetection]),
+            )
+            row = np.concatenate(args)
+            output = np.vstack((output, row))
+
+        # We don't return this anymore. It corresponds to the output structure of the original implementation.
+        # return output
+
+        # distance vector
+        self.distances = output[:, -2]
+
+        # corepoints to epoch0 ('initial' one)
+        self.corepoints = Epoch(output[:, [1, 2, 3]])
+
+        # epochs
+        self.epochs = (epoch0_info, epoch1)
+
+        self.uncertainties = np.empty(
+            (output.shape[0], 1),
+            dtype=np.dtype(
+                [
+                    ("lodetection", "<f8"),
+                    ("spread1", "<f8"),
+                    ("num_samples1", "<i8"),
+                    ("spread2", "<f8"),
+                    ("num_samples2", "<i8"),
+                ]
+            ),
+        )
+
+        self.uncertainties["lodetection"] = output[:, -1].reshape(-1, 1)
+
+        self.uncertainties["spread1"] = np.sqrt(
+            np.multiply(
+                epoch0_segments[:, columns.STANDARD_DEVIATION_COLUMN],
+                epoch0_segments[:, columns.NR_POINTS_PER_SEG_COLUMN],
+            )
+        ).reshape(-1, 1)
+        self.uncertainties["spread2"] = np.sqrt(
+            np.multiply(
+                epoch1_segments[:, columns.STANDARD_DEVIATION_COLUMN],
+                epoch1_segments[:, columns.NR_POINTS_PER_SEG_COLUMN],
+            )
+        ).reshape(-1, 1)
+
+        self.uncertainties["num_samples1"] = (
+            epoch0_segments[:, columns.NR_POINTS_PER_SEG_COLUMN]
+            .astype(int)
+            .reshape(-1, 1)
+        )
+        self.uncertainties["num_samples2"] = (
+            epoch1_segments[:, columns.NR_POINTS_PER_SEG_COLUMN]
+            .astype(int)
+            .reshape(-1, 1)
+        )
+
+        return (self.distances, self.uncertainties)
+
+    def compute_distances(
+        self,
+        epoch0: typing.Union[Epoch, np.ndarray] = None,
+        epoch1: Epoch = None,
+        alignment_error: float = 1.1,
+        **kwargs,
+    ) -> typing.Union[typing.Tuple[np.ndarray, np.ndarray], None]:
+        """
+        Compute the distance between 2 epochs. It also adds the following properties at the end of the computation:
+            distances, corepoints (corepoints of epoch0), epochs (epoch0, epoch1), uncertainties
+
+        :param epoch0:
+            Epoch object.
+            | np.ndarray
+        :param epoch1:
+            Epoch object.
+        :param alignment_error:
+            alignment error reg between point clouds.
+        :param kwargs:
+            Used for customize the default pipeline parameters.
+
+            Getting the default parameters:
+            e.g. "get_pipeline_options"
+                In case this parameter is True, the method will print the pipeline options as kwargs.
+
+            e.g. "output_file_name" (of a specific step in the pipeline) default value is "None".
+                In case of setting it, the result of computation at that step is dump as xyz file.
+            e.g. "distance_3D_threshold" (part of Segmentation Transform)
+
+            this process is stateless
+
+        :return:
+            tuple [distances, uncertainties]
+                'distances' is np.array (nr_similar_pairs, 1)
+                'uncertainties' is np.array (nr_similar_pairs,1) and it has the following structure:
+                    dtype=np.dtype(
+                        [
+                            ("lodetection", "<f8"),
+                            ("spread1", "<f8"),
+                            ("num_samples1", "<i8"),
+                            ("spread2", "<f8"),
+                            ("num_samples2", "<i8"),
+                        ]
+                    )
+            | None
+        """
+
+        logger.info(f"PBM3C2.compute_distances(...)")
+
+        return self._compute_distances(
+            epoch0_info=epoch0,
+            epoch1=epoch1,
+            alignment_error=alignment_error,
+            epoch_additional_dimensions_lookup=None,
+            **kwargs,
+        )
+
+
+def build_input_scenario2_with_normals(
+    epoch0, epoch1, columns=SEGMENTED_POINT_CLOUD_COLUMNS
+):
+    """
+    Build a segmented point cloud with computed normals for each point.
+
+    :param epoch0:
+        x,y,z point cloud
+    :param epoch1:
+        x,y,z point cloud
+    :param columns:
+
+    :return:
+        tuple [
+                numpy array (n_point_samples, 7) new_epoch0
+                numpy array (m_point_samples, 7) new_epoch1
+        ]
+        both containing: x,y,z, N_x,N_y,N_z, Segment_ID as columns.
+    """
+
+    Normal_Columns = [
+        columns.EIGENVECTOR_2_X_COLUMN,
+        columns.EIGENVECTOR_2_Y_COLUMN,
+        columns.EIGENVECTOR_2_Z_COLUMN,
+    ]
+
+    x_y_z_Columns = [columns.X_COLUMN, columns.Y_COLUMN, columns.Z_COLUMN]
+
+    X0 = np.hstack((epoch0.cloud[:, :], np.zeros((epoch0.cloud.shape[0], 1))))
+    X1 = np.hstack((epoch1.cloud[:, :], np.ones((epoch1.cloud.shape[0], 1))))
+
+    X = np.vstack((X0, X1))
+
+    transform_pipeline = Pipeline(
+        [
+            ("Transform_PerPointComputation", PerPointComputation()),
+            ("Transform_Segmentation", Segmentation()),
+        ]
+    )
+
+    transform_pipeline.fit(X)
+    out = transform_pipeline.transform(X)
+
+    mask_epoch0 = out[:, columns.EPOCH_ID_COLUMN] == 0  # epoch0
+    mask_epoch1 = out[:, columns.EPOCH_ID_COLUMN] == 1  # epoch1
+
+    new_epoch0 = out[mask_epoch0, :]  # extract epoch0
+    new_epoch1 = out[mask_epoch1, :]  # extract epoch1
+
+    new_epoch0 = new_epoch0[
+        :, x_y_z_Columns + Normal_Columns + [columns.SEGMENT_ID_COLUMN]
+    ]
+    new_epoch1 = new_epoch1[
+        :, x_y_z_Columns + Normal_Columns + [columns.SEGMENT_ID_COLUMN]
+    ]
+
+    # x,y,z, N_x,N_y,N_z, Segment_ID
+    return new_epoch0, new_epoch1
+    pass
+
+
+def build_input_scenario2_without_normals(
+    epoch0, epoch1, columns=SEGMENTED_POINT_CLOUD_COLUMNS
+):
+    """
+        Build a segmented point cloud.
+
+    :param epoch0:
+        x,y,z point cloud
+    :param epoch1:
+        x,y,z point cloud
+    :param columns:
+
+    :return:
+        tuple [
+            numpy array (n_point_samples, 4) new_epoch0
+            numpy array (m_point_samples, 4) new_epoch1
+        ]
+        both containing: x,y,z,Segment_ID as columns.
+    """
+
+    x_y_z_Columns = [columns.X_COLUMN, columns.Y_COLUMN, columns.Z_COLUMN]
+
+    Normal_Columns = [
+        columns.EIGENVECTOR_2_X_COLUMN,
+        columns.EIGENVECTOR_2_Y_COLUMN,
+        columns.EIGENVECTOR_2_Z_COLUMN,
+    ]
+
+    X0 = np.hstack((epoch0.cloud[:, :], np.zeros((epoch0.cloud.shape[0], 1))))
+    X1 = np.hstack((epoch1.cloud[:, :], np.ones((epoch1.cloud.shape[0], 1))))
+
+    X = np.vstack((X0, X1))
+
+    transform_pipeline = Pipeline(
+        [
+            ("Transform_PerPointComputation", PerPointComputation()),
+            ("Transform_Segmentation", Segmentation()),
+        ]
+    )
+
+    transform_pipeline.fit(X)
+    out = transform_pipeline.transform(X)
+
+    mask_epoch0 = out[:, columns.EPOCH_ID_COLUMN] == 0  # epoch0
+    mask_epoch1 = out[:, columns.EPOCH_ID_COLUMN] == 1  # epoch1
+
+    new_epoch0 = out[mask_epoch0, :]  # extract epoch0
+    new_epoch1 = out[mask_epoch1, :]  # extract epoch1
+
+    new_epoch0 = new_epoch0[:, x_y_z_Columns + [columns.SEGMENT_ID_COLUMN]]
+    new_epoch1 = new_epoch1[:, x_y_z_Columns + [columns.SEGMENT_ID_COLUMN]]
+
+    # x,y,z, Segment_ID
+    return new_epoch0, new_epoch1
+    pass
+
+
+class PBM3C2WithSegments(PBM3C2):
+    def __init__(
+        self,
+        per_point_computation=PerPointComputation(),
+        segmentation=Segmentation(),
+        second_segmentation=Segmentation(),
+        extract_segments=ExtractSegments(),
+        post_segmentation=PostPointCloudSegmentation(compute_normal=True),
+        classifier=ClassifierWrapper(),
+    ):
+        """
+        :param per_point_computation:
+            lowest local surface variation and PCA computation. (computes the normal vector as well)
+        :param segmentation:
+            The object used for the first segmentation.
+        :param second_segmentation:
+            The object used for the second segmentation.
+        :param extract_segments:
+            The object used for building the segments.
+        :param post_segmentation:
+            A transform object used to 'reconstruct' the result that is achieved using the "PB_P3C2 class"
+            pipeline at the end of the point cloud segmentation.
+
+            The 'input' of this adaptor is formed by 2 epochs that contain as 'additional_dimensions'
+            a segment_id column and optionally, precomputed normals as another 3 columns.
+
+            The 'output' of this adaptor is:
+            numpy array (n_point_samples, 19) with the following column structure:
+            [
+                x, y, z ( 3 columns ),
+                EpochID ( 1 column ),
+                Eigenvalues( 3 columns ), -> that correspond to the next 3 Eigenvectors
+                Eigenvectors( 3 columns ) X 3 -> in descending order using vector norm 2,
+                Lowest local surface variation ( 1 column ),
+                Segment_ID ( 1 column ),
+                Standard deviation ( 1 column )
+            ]
+        :param classifier:
+            An instance of ClassifierWrapper class. The default wrapped classifier used is sk-learn RandomForest.
+        """
+
+        super().__init__(
+            per_point_computation=per_point_computation,
+            segmentation=segmentation,
+            second_segmentation=second_segmentation,
+            extract_segments=extract_segments,
+            classifier=classifier,
+        )
+
+        self._post_segmentation = post_segmentation
+
+    def generate_extended_labels_interactively(
+        self,
+        epoch0: Epoch = None,
+        epoch1: Epoch = None,
+        builder_extended_y: BuilderExtended_y_Visually = BuilderExtended_y_Visually(),
+        epoch_additional_dimensions_lookup: typing.Dict[str, str] = dict(
+            segment_id="segment_id", N_x="N_x", N_y="N_y", N_z="N_z"
+        ),
+        **kwargs,
+    ) -> typing.Union[typing.Tuple[np.ndarray, np.ndarray], None]:
+        """
+        Given 2 Epochs, it builds a pair of (segments and 'extended y').
+
+        :param epoch0:
+            Epoch object,
+            contains as 'additional_dimensions' a segment_id column (mandatory)
+            and optionally, precomputed normals as another 3 columns.
+        :param epoch1:
+            Epoch object,
+            contains as 'additional_dimensions' a segment_id column (mandatory)
+            and optionally, precomputed normals as another 3 columns.
+        :param builder_extended_y:
+            The object is used for generating 'extended y', visually.
+        :param epoch_additional_dimensions_lookup:
+            A dictionary that maps between the names of the columns used internally to identify:
+                segment id of the points: "segment_id"  -> Mandatory part of the epochs
+                Normal x-axes vector: "N_x"             -> Optionally part of the epochs
+                Normal y-axes vector: "N_y"             -> Optionally part of the epochs
+                Normal z-axes vector: "N_z"             -> Optionally part of the epochs
+            and the names of the columns used by both epoch0 and epoch1.
+        :param kwargs:
+
+            Used for customize the default pipeline parameters.
+
+            Getting the default parameters:
+            e.g. "get_pipeline_options"
+                In case this parameter is True, the method will print the pipeline options as kwargs.
+
+            e.g. "output_file_name" (of a specific step in the pipeline) default value is "None".
+                In case of setting it, the result of computation at that step is dump as xyz file.
+            e.g. "distance_3D_threshold" (part of Segmentation Transform)
+
+            this process is stateless
+
+        :return:
+            tuple [Segments, 'extended y'] | None
+
+            where:
+
+            'Segments' has the following column structure:
+                    X_COLUMN, Y_COLUMN, Z_COLUMN, -> Center of Gravity
+                    EPOCH_ID_COLUMN, -> 0/1
+                    EIGENVALUE0_COLUMN, EIGENVALUE1_COLUMN, EIGENVALUE2_COLUMN,
+                    EIGENVECTOR_0_X_COLUMN, EIGENVECTOR_0_Y_COLUMN, EIGENVECTOR_0_Z_COLUMN,
+                    EIGENVECTOR_1_X_COLUMN, EIGENVECTOR_1_Y_COLUMN, EIGENVECTOR_1_Z_COLUMN,
+                    EIGENVECTOR_2_X_COLUMN, EIGENVECTOR_2_Y_COLUMN, EIGENVECTOR_2_Z_COLUMN, -> Normal vector
+                    LLSV_COLUMN, -> lowest local surface variation
+                    SEGMENT_ID_COLUMN,
+                    STANDARD_DEVIATION_COLUMN,
+                    NR_POINTS_PER_SEG_COLUMN,
+
+            'extended y' has the following structure: (tuples of index segment from epoch0, index segment from epoch1,
+            label(0/1)) used for learning.
+        """
+
+        if not interactive_available:
+            logger.error("Interactive session not available in this environment.")
+            return
+
+        transform_pipeline = Pipeline(
+            [
+                ("Transform_Post_Segmentation", self._post_segmentation),
+                ("Transform_ExtractSegments", self._extract_segments),
+            ]
+        )
+
+        # print the default parameters
+        PBM3C2._print_default_parameters(
+            kwargs=kwargs, pipeline_param_dict=transform_pipeline.get_params()
+        )
+
+        # no computation
+        if epoch0 is None or epoch1 is None:
+            # logger.info("epoch0 and epoch1 are required, no parameter changes applied")
+            return
+
+        # save the default pipeline options
+        default_options = transform_pipeline.get_params()
+
+        # overwrite the default parameters
+        PBM3C2._overwrite_pipeline_parameters(
+            kwargs=kwargs, pipeline=transform_pipeline
+        )
+
+        # extract columns
+
+        epoch0_normals = _extract_from_additional_dimensions(
+            epoch=epoch0,
+            column_names=[
+                epoch_additional_dimensions_lookup["N_x"],
+                epoch_additional_dimensions_lookup["N_y"],
+                epoch_additional_dimensions_lookup["N_z"],
+            ],
+            required_number_of_columns=[0, 3],
+        )
+
+        epoch0_segment_id = _extract_from_additional_dimensions(
+            epoch=epoch0,
+            column_names=[
+                epoch_additional_dimensions_lookup["segment_id"],
+            ],
+            required_number_of_columns=[1],
+        )
+
+        epoch0 = np.concatenate(
+            (epoch0.cloud, epoch0_normals, epoch0_segment_id),
+            axis=1,
+        )
+
+        epoch1_normals = _extract_from_additional_dimensions(
+            epoch=epoch1,
+            column_names=[
+                epoch_additional_dimensions_lookup["N_x"],
+                epoch_additional_dimensions_lookup["N_y"],
+                epoch_additional_dimensions_lookup["N_z"],
+            ],
+            required_number_of_columns=[0, 3],
+        )
+
+        epoch1_segment_id = _extract_from_additional_dimensions(
+            epoch=epoch1,
+            column_names=[
+                epoch_additional_dimensions_lookup["segment_id"],
+            ],
+            required_number_of_columns=[1],
+        )
+
+        epoch1 = np.concatenate(
+            (epoch1.cloud, epoch1_normals, epoch1_segment_id),
+            axis=1,
+        )
+
+        X = None
+        for epoch_id, current_epoch in enumerate([epoch0, epoch1]):
+            if current_epoch.shape[1] == 4:
+                # [x, y, z, segment_id] columns
+                assert self._post_segmentation.compute_normal, (
+                    "The reconstruction process doesn't have, as input, the Normal vector columns, hence, "
+                    "the normal vector computation is mandatory."
+                )
+
+                logger.info(
+                    f"Reconstruct post segmentation output using [x, y, z, segment_id] "
+                    f"columns from epoch{epoch_id} "
+                )
+
+                if X is not None:
+                    X = np.vstack(
+                        (
+                            X,
+                            self._reconstruct_input_without_normals(
+                                epoch=current_epoch,
+                                epoch_id=epoch_id,
+                                columns=self._post_segmentation.columns,
+                            ),
+                        )
+                    )
+                else:
+                    X = self._reconstruct_input_without_normals(
+                        epoch=current_epoch,
+                        epoch_id=epoch_id,
+                        columns=self._post_segmentation.columns,
+                    )
+            else:
+                # [x, y, z, N_x, N_y, N_z, segment_id] columns
+                logger.info(
+                    f"Reconstruct post segmentation output using [x, y, z, N_x, N_y, N_z, segment_id] "
+                    f"columns from epoch{epoch_id}"
+                )
+
+                if X is not None:
+                    X = np.vstack(
+                        (
+                            X,
+                            self._reconstruct_input_with_normals(
+                                epoch=current_epoch,
+                                epoch_id=epoch_id,
+                                columns=self._post_segmentation.columns,
+                            ),
+                        )
+                    )
+                else:
+                    X = self._reconstruct_input_with_normals(
+                        epoch=current_epoch,
+                        epoch_id=epoch_id,
+                        columns=self._post_segmentation.columns,
+                    )
+
+        # apply the pipeline
+
+        transform_pipeline.fit(X)
+        segments = transform_pipeline.transform(X)
+
+        # restore the default pipeline options
+        unused_kwargs = PBM3C2._overwrite_pipeline_parameters(
+            kwargs=default_options,
+            pipeline=transform_pipeline,
+            message="The pipeline parameters after restoration are: ",
+        )
+        assert (
+            len(unused_kwargs) == 0
+        ), "All default options should be found when default parameter restoration is done"
+
+        return segments, builder_extended_y.generate_extended_y(segments)
+
+    def reconstruct_post_segmentation_output(
+        self,
+        epoch0: Epoch = None,
+        epoch1: Epoch = None,
+        extracted_segments_file_name: typing.Union[
+            str, None
+        ] = "extracted_segments.seg",
+        epoch_additional_dimensions_lookup: typing.Dict[str, str] = dict(
+            segment_id="segment_id", N_x="N_x", N_y="N_y", N_z="N_z"
+        ),
+        concatenate_name: str = "",
+        **kwargs,
+    ) -> typing.Union[
+        typing.Tuple[np.ndarray, typing.Union[np.ndarray, None], np.ndarray], None
+    ]:
+        """
+        'reconstruct' the result that is achieved using the "PB_P3C2 class" pipeline, by applying
+            ("Transform LLSV_and_PCA"), ("Transform Segmentation"),
+            ("Transform Second Segmentation") ("Transform ExtractSegments")
+        using, as input, segmented point clouds.
+
+        :param epoch0:
+            Epoch object,
+            contains as 'additional_dimensions' a segment_id column (mandatory)
+            and optionally, precomputed normals as another 3 columns.
+        :param epoch1:
+            Epoch object,
+            contains as 'additional_dimensions' a segment_id column (mandatory)
+            and optionally, precomputed normals as another 3 columns.
+        :param extracted_segments_file_name:
+            out file
+            The file has the following structure:
+            numpy array with shape (n_segments_samples, 20) where the column structure is as following:
+                [
+                    X_COLUMN, Y_COLUMN, Z_COLUMN, -> Center of Gravity
+                    EPOCH_ID_COLUMN, -> 0/1
+                    EIGENVALUE0_COLUMN, EIGENVALUE1_COLUMN, EIGENVALUE2_COLUMN,
+                    EIGENVECTOR_0_X_COLUMN, EIGENVECTOR_0_Y_COLUMN, EIGENVECTOR_0_Z_COLUMN,
+                    EIGENVECTOR_1_X_COLUMN, EIGENVECTOR_1_Y_COLUMN, EIGENVECTOR_1_Z_COLUMN,
+                    EIGENVECTOR_2_X_COLUMN, EIGENVECTOR_2_Y_COLUMN, EIGENVECTOR_2_Z_COLUMN, -> Normal vector
+                    LLSV_COLUMN, -> lowest local surface variation
+                    SEGMENT_ID_COLUMN,
+                    STANDARD_DEVIATION_COLUMN,
+                    NR_POINTS_PER_SEG_COLUMN,
+                ]
+        :param epoch_additional_dimensions_lookup:
+            A dictionary that maps between the names of the columns used internally to identify:
+                segment id of the points: "segment_id"  -> Mandatory part of the epochs
+                Normal x-axes vector: "N_x"             -> Optionally part of the epochs
+                Normal y-axes vector: "N_y"             -> Optionally part of the epochs
+                Normal z-axes vector: "N_z"             -> Optionally part of the epochs
+            and the names of the columns used by both epoch0 and epoch1.
+        :param concatenate_name:
+            String that is utilized to uniquely identify the same transformer between multiple pipelines.
+        :param kwargs:
+            Used for customize the default pipeline parameters.
+            Getting the default parameters:
+            e.g. "get_pipeline_options"
+                In case this parameter is True, the method will print the pipeline options as kwargs.
+            e.g. "output_file_name" (of a specific step in the pipeline) default value is "None".
+                In case of setting it, the result of computation at that step is dump as xyz file.
+            e.g. "distance_3D_threshold" (part of Segmentation Transform)
+
+            this process is stateless
+        :return:
+            tuple
+            [
+                numpy array with shape (n, 4|7) corresponding to epoch0 and
+                    containing [x,y,z,segment_id] | [x,y,z,N_x,N_y,N_z,segment_id],
+                numpy array with shape (m, 4|7) corresponding to epoch1 and
+                    containing [x,y,z,segment_id] | [x,y,z,N_x,N_y,N_z,segment_id] | None,
+                numpy array with shape (p, 20) corresponding to extracted_segments
+            ]
+            | None
+        """
+
+        transform_pipeline = Pipeline(
+            [
+                (
+                    concatenate_name + "_Transform_Post Segmentation",
+                    self._post_segmentation,
+                ),
+                (
+                    concatenate_name + "_Transform_ExtractSegments",
+                    self._extract_segments,
+                ),
+            ]
+        )
+
+        # print the default parameters
+        PBM3C2._print_default_parameters(
+            kwargs=kwargs, pipeline_param_dict=transform_pipeline.get_params()
+        )
+
+        # no computation
+        if epoch0 is None:  # or epoch1 is None:
+            # logger.info("epoch0 is required, no parameter changes applied")
+            return
+
+        # save the default pipeline options
+        default_options = transform_pipeline.get_params()
+
+        # overwrite the default parameters
+        PBM3C2._overwrite_pipeline_parameters(
+            kwargs=kwargs, pipeline=transform_pipeline
+        )
+
+        # extract columns
+
+        epoch0_normals = _extract_from_additional_dimensions(
+            epoch=epoch0,
+            column_names=[
+                epoch_additional_dimensions_lookup["N_x"],
+                epoch_additional_dimensions_lookup["N_y"],
+                epoch_additional_dimensions_lookup["N_z"],
+            ],
+            required_number_of_columns=[0, 3],
+        )
+
+        epoch0_segment_id = _extract_from_additional_dimensions(
+            epoch=epoch0,
+            column_names=[
+                epoch_additional_dimensions_lookup["segment_id"],
+            ],
+            required_number_of_columns=[1],
+        )
+
+        epoch0 = np.concatenate(
+            (epoch0.cloud, epoch0_normals, epoch0_segment_id),
+            axis=1,
+        )
+
+        if epoch1 != None:
+            epoch1_normals = _extract_from_additional_dimensions(
+                epoch=epoch1,
+                column_names=[
+                    epoch_additional_dimensions_lookup["N_x"],
+                    epoch_additional_dimensions_lookup["N_y"],
+                    epoch_additional_dimensions_lookup["N_z"],
+                ],
+                required_number_of_columns=[0, 3],
+            )
+
+            epoch1_segment_id = _extract_from_additional_dimensions(
+                epoch=epoch1,
+                column_names=[
+                    epoch_additional_dimensions_lookup["segment_id"],
+                ],
+                required_number_of_columns=[1],
+            )
+
+            epoch1 = np.concatenate(
+                (epoch1.cloud, epoch1_normals, epoch1_segment_id),
+                axis=1,
+            )
+
+        epochs_list = [epoch0]
+        if isinstance(epoch1, np.ndarray):
+            epochs_list.append(epoch1)
+
+        X = None
+        for epoch_id, current_epoch in enumerate(epochs_list):
+            if current_epoch.shape[1] == 4:
+                # [x, y, z, segment_id] columns
+                assert self._post_segmentation.compute_normal, (
+                    "The reconstruction process doesn't have, as input, the Normal vector columns, hence, "
+                    "the normal vector computation is mandatory."
+                )
+
+                logger.info(
+                    f"Reconstruct post segmentation output using [x, y, z, segment_id] "
+                    f"columns from epoch{epoch_id} "
+                )
+
+                if X is not None:
+                    X = np.vstack(
+                        (
+                            X,
+                            self._reconstruct_input_without_normals(
+                                epoch=current_epoch,
+                                epoch_id=epoch_id,
+                                columns=self._post_segmentation.columns,
+                            ),
+                        )
+                    )
+                else:
+                    X = self._reconstruct_input_without_normals(
+                        epoch=current_epoch,
+                        epoch_id=epoch_id,
+                        columns=self._post_segmentation.columns,
+                    )
+            else:
+                # [x, y, z, N_x, N_y, N_z, segment_id] columns
+                logger.info(
+                    f"Reconstruct post segmentation output using [x, y, z, N_x, N_y, N_z, segment_id] "
+                    f"columns from epoch{epoch_id}"
+                )
+
+                if X is not None:
+                    X = np.vstack(
+                        (
+                            X,
+                            self._reconstruct_input_with_normals(
+                                epoch=current_epoch,
+                                epoch_id=epoch_id,
+                                columns=self._post_segmentation.columns,
+                            ),
+                        )
+                    )
+                else:
+                    X = self._reconstruct_input_with_normals(
+                        epoch=current_epoch,
+                        epoch_id=epoch_id,
+                        columns=self._post_segmentation.columns,
+                    )
+
+        # apply the pipeline
+
+        transform_pipeline.fit(X)
+        extracted_segments = transform_pipeline.transform(X)
+
+        if extracted_segments_file_name is not None:
+            logger.info(f"'Segments' saved in file: {extracted_segments_file_name}")
+            np.savetxt(extracted_segments_file_name, extracted_segments, delimiter=",")
+        else:
+            logger.debug(f"No file name set as output for 'segments'")
+
+        # restore the default pipeline options
+        unused_kwargs = PBM3C2._overwrite_pipeline_parameters(
+            kwargs=default_options,
+            pipeline=transform_pipeline,
+            message="The pipeline parameters after restoration are: ",
+        )
+        assert (
+            len(unused_kwargs) == 0
+        ), "All default options should be found when default parameter restoration is done"
+
+        return epoch0, epoch1, extracted_segments
+
+    def predict(
+        self,
+        epoch0: Epoch = None,
+        epoch1: Epoch = None,
+        epoch_additional_dimensions_lookup: typing.Dict[str, str] = dict(
+            segment_id="segment_id", N_x="N_x", N_y="N_y", N_z="N_z"
+        ),
+        **kwargs,
+    ) -> typing.Union[np.ndarray, None]:
+        """
+        After the reconstruction of the result that is achieved using the "PB_P3C2 class" pipeline, by applying
+        ("Transform LLSV_and_PCA"), ("Transform Segmentation"), ("Transform Second Segmentation"), ("Transform ExtractSegments")
+        applied to the segmented point cloud of epoch0 and epoch1, it returns a numpy array of corresponding
+        pairs of segments between epoch 0 and epoch 1.
+
+        :param epoch0:
+            Epoch object,
+            contains as 'additional_dimensions' a segment_id column ( mandatory )
+            and optionally, precomputed normals as another 3 columns.
+            ( the structure must be consistent with the structure of epoch1 parameter )
+        :param epoch1:
+            Epoch object.
+            contains as 'additional_dimensions' a segment_id column ( mandatory )
+            and optionally, precomputed normals as another 3 columns.
+            ( the structure must be consistent with the structure of epoch0 parameter )
+        :param epoch_additional_dimensions_lookup:
+            A dictionary that maps between the names of the columns used internally to identify:
+                segment id of the points: "segment_id"  -> Mandatory part of the epochs
+                Normal x-axes vector: "N_x"             -> Optionally part of the epochs
+                Normal y-axes vector: "N_y"             -> Optionally part of the epochs
+                Normal z-axes vector: "N_z"             -> Optionally part of the epochs
+            and the names of the columns used by both epoch0 and epoch1.
+        :param kwargs:
+            Used for customize the default pipeline parameters.
+
+            Getting the default parameters:
+            e.g. "get_pipeline_options"
+                In case this parameter is True, the method will print the pipeline options as kwargs.
+
+            e.g. "output_file_name" (of a specific step in the pipeline) default value is "None".
+                In case of setting it, the result of computation at that step is dump as xyz file.
+            e.g. "distance_3D_threshold" (part of Segmentation Transform)
+
+            this process is stateless
+        :return:
+            A numpy array of shape ( n_pairs, segment_size*2 ) where each row contains a pair of segments.
+        """
+
+        predicting_pipeline = Pipeline(
+            [
+                ("Transform_Post_Segmentation", self._post_segmentation),
+                ("Transform_ExtractSegments", self._extract_segments),
+                ("Classifier", self._classifier),
+            ]
+        )
+
+        # print the default parameters
+        PBM3C2._print_default_parameters(
+            kwargs=kwargs, pipeline_param_dict=predicting_pipeline.get_params()
+        )
+
+        # no computation
+        if epoch0 is None or epoch1 is None:
+            # logger.info("epoch0 and epoch1 are required, no parameter changes applied")
+            return
+
+        # save the default pipeline options
+        default_options = predicting_pipeline.get_params()
+
+        # overwrite the default parameters
+        PBM3C2._overwrite_pipeline_parameters(
+            kwargs=kwargs, pipeline=predicting_pipeline
+        )
+
+        # extract columns
+
+        epoch0_normals = _extract_from_additional_dimensions(
+            epoch=epoch0,
+            column_names=[
+                epoch_additional_dimensions_lookup["N_x"],
+                epoch_additional_dimensions_lookup["N_y"],
+                epoch_additional_dimensions_lookup["N_z"],
+            ],
+            required_number_of_columns=[0, 3],
+        )
+
+        epoch0_segment_id = _extract_from_additional_dimensions(
+            epoch=epoch0,
+            column_names=[
+                epoch_additional_dimensions_lookup["segment_id"],
+            ],
+            required_number_of_columns=[1],
+        )
+
+        epoch0 = np.concatenate(
+            (epoch0.cloud, epoch0_normals, epoch0_segment_id),
+            axis=1,
+        )
+
+        epoch1_normals = _extract_from_additional_dimensions(
+            epoch=epoch1,
+            column_names=[
+                epoch_additional_dimensions_lookup["N_x"],
+                epoch_additional_dimensions_lookup["N_y"],
+                epoch_additional_dimensions_lookup["N_z"],
+            ],
+            required_number_of_columns=[0, 3],
+        )
+
+        epoch1_segment_id = _extract_from_additional_dimensions(
+            epoch=epoch1,
+            column_names=[
+                epoch_additional_dimensions_lookup["segment_id"],
+            ],
+            required_number_of_columns=[1],
+        )
+
+        epoch1 = np.concatenate(
+            (epoch1.cloud, epoch1_normals, epoch1_segment_id),
+            axis=1,
+        )
+
+        X = None
+        for epoch_id, current_epoch in enumerate([epoch0, epoch1]):
+            if current_epoch.shape[1] == 4:
+                # [x, y, z, segment_id] columns
+                assert self._post_segmentation.compute_normal, (
+                    "The reconstruction process doesn't have, as input, the Normal vector columns, hence, "
+                    "the normal vector computation is mandatory."
+                )
+
+                logger.info(
+                    f"Reconstruct post segmentation output using [x, y, z, segment_id] "
+                    f"columns from epoch{epoch_id} "
+                )
+
+                if X is not None:
+                    X = np.vstack(
+                        (
+                            X,
+                            self._reconstruct_input_without_normals(
+                                epoch=current_epoch,
+                                epoch_id=epoch_id,
+                                columns=self._post_segmentation.columns,
+                            ),
+                        )
+                    )
+                else:
+                    X = self._reconstruct_input_without_normals(
+                        epoch=current_epoch,
+                        epoch_id=epoch_id,
+                        columns=self._post_segmentation.columns,
+                    )
+            else:
+                # [x, y, z, N_x, N_y, N_z, segment_id] columns
+                logger.info(
+                    f"Reconstruct post segmentation output using [x, y, z, N_x, N_y, N_z, segment_id] "
+                    f"columns from epoch{epoch_id}"
+                )
+
+                if X is not None:
+                    X = np.vstack(
+                        (
+                            X,
+                            self._reconstruct_input_with_normals(
+                                epoch=current_epoch,
+                                epoch_id=epoch_id,
+                                columns=self._post_segmentation.columns,
+                            ),
+                        )
+                    )
+                else:
+                    X = self._reconstruct_input_with_normals(
+                        epoch=current_epoch,
+                        epoch_id=epoch_id,
+                        columns=self._post_segmentation.columns,
+                    )
+
+        # apply the pipeline
+
+        out = predicting_pipeline.predict(X)
+
+        # restore the default pipeline options
+        unused_kwargs = PBM3C2._overwrite_pipeline_parameters(
+            kwargs=default_options,
+            pipeline=predicting_pipeline,
+            message="The pipeline parameters after restoration are: ",
+        )
+        assert (
+            len(unused_kwargs) == 0
+        ), "All default options should be found when default parameter restoration is done"
+
+        return out
+
+    def compute_distances(
+        self,
+        epoch0: Epoch = None,
+        epoch1: Epoch = None,
+        alignment_error: float = 1.1,
+        epoch_additional_dimensions_lookup: typing.Dict[str, str] = dict(
+            segment_id="segment_id", N_x="N_x", N_y="N_y", N_z="N_z"
+        ),
+        **kwargs,
+    ) -> typing.Union[typing.Tuple[np.ndarray, np.ndarray], None]:
+        """
+        Compute the distance between 2 epochs. It also adds the following properties at the end of the computation:
+            distances, corepoints (corepoints of epoch0), epochs (epoch0, epoch1), uncertainties
+
+        :param epoch0:
+            Epoch object,
+            contains as 'additional_dimensions' a segment_id column (mandatory)
+            and optionally, precomputed normals as another 3 columns.
+        :param epoch1:
+            Epoch object,
+            contains as 'additional_dimensions' a segment_id column (mandatory)
+            and optionally, precomputed normals as another 3 columns.
+        :param alignment_error:
+            alignment error reg between point clouds.
+        :param epoch_additional_dimensions_lookup:
+            A dictionary that maps between the names of the columns used internally to identify:
+                segment id of the points: "segment_id"  -> Mandatory part of the epochs
+                Normal x-axes vector: "N_x"             -> Optionally part of the epochs
+                Normal y-axes vector: "N_y"             -> Optionally part of the epochs
+                Normal z-axes vector: "N_z"             -> Optionally part of the epochs
+            and the names of the columns used by both epoch0 and epoch1.
+        :param kwargs:
+            Used for customize the default pipeline parameters.
+
+            Getting the default parameters:
+            e.g. "get_pipeline_options"
+                In case this parameter is True, the method will print the pipeline options as kwargs.
+
+            e.g. "output_file_name" (of a specific step in the pipeline) default value is "None".
+                In case of setting it, the result of computation at that step is dump as xyz file.
+            e.g. "distance_3D_threshold" (part of Segmentation Transform)
+
+            this process is stateless
+
+        :return:
+            tuple [distances, uncertainties]
+                'distances' is np.array (nr_similar_pairs, 1)
+                'uncertainties' is np array (nr_similar_pairs, 1) and it has the following structure:
+                    dtype=np.dtype(
+                        [
+                            ("lodetection", "<f8"),
+                            ("spread1", "<f8"),
+                            ("num_samples1", "<i8"),
+                            ("spread2", "<f8"),
+                            ("num_samples2", "<i8"),
+                        ]
+                    )
+            | None
+        """
+
+        logger.info(f"PBM3C2WithSegments.compute_distances(...)")
+
+        return super()._compute_distances(
+            epoch0_info=epoch0,
+            epoch1=epoch1,
+            alignment_error=alignment_error,
+            epoch_additional_dimensions_lookup=epoch_additional_dimensions_lookup,
+            **kwargs,
+        )