BERATools 0.2.0__py3-none-any.whl → 0.2.1__py3-none-any.whl

beratools/tools/line_footprint_functions.py

@@ -1,720 +1,733 @@
-# ---------------------------------------------------------------------------
-#    Copyright (C) 2021  Applied Geospatial Research Group
-#
-#    This program is free software: you can redistribute it and/or modify
-#    it under the terms of the GNU General Public License as published by
-#    the Free Software Foundation, version 3.
-#
-#    This program is distributed in the hope that it will be useful,
-#    but WITHOUT ANY WARRANTY; without even the implied warranty of
-#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-#    GNU General Public License for more details.
-#
-#    You should have received a copy of the GNU General Public License
-#    along with this program.  If not, see <https://gnu.org/licenses/gpl-3.0>.
-#
-# ---------------------------------------------------------------------------
-#
-# Refactor to use for produce dynamic footprint from dynamic canopy and cost raster with open source libraries
-# Prerequisite:  Line feature class must have the attribute Fields:"CorridorTh" "DynCanTh" "OLnFID"
-# line_footprint_function.py
-# Maverick Fong
-# Date: 2023-Dec
-# This script is part of the BERA toolset
-# Webpage: https://github.com/
-#
-# Purpose: Creates dynamic footprint polygons for each input line based on a least
-# cost corridor method and individual line thresholds.
-#
-# ---------------------------------------------------------------------------
-
-import time
-import numpy as np
-
-import rasterio
-from scipy import stats, ndimage
-from geopandas import GeoDataFrame
-from shapely import buffer
-from rasterio import features
-from xrspatial import convolution
-
-import skimage
-from skimage.morphology import *
-from skimage.graph import MCP_Flexible
-
-from beratools.core.constants import *
-from beratools.core.algo_centerline import *
-from beratools.tools.common import *
-
-
-def dyn_canopy_cost_raster(args):
-    raster_obj = args[0]
-    DynCanTh = args[1]
-    tree_radius = args[2]
-    max_line_dist = args[3]
-    canopy_avoid = args[4]
-    exponent = args[5]
-    res = args[6]
-    nodata = args[7]
-    line_df = args[8]
-    out_meta = args[9]
-    line_id = args[10]
-    Cut_Dist = args[11]
-    Side = args[12]
-    canopy_thresh_percentage = float(args[13]) / 100
-    line_buffer = args[14]
-
-    if Side == 'Left':
-        canopy_ht_threshold = line_df.CL_CutHt * canopy_thresh_percentage
-    elif Side == 'Right':
-        canopy_ht_threshold = line_df.CR_CutHt * canopy_thresh_percentage
-    elif Side == 'Center':
-        canopy_ht_threshold = DynCanTh * canopy_thresh_percentage
-    else:
-
-        canopy_ht_threshold = 0.5
-
-    canopy_ht_threshold = float(canopy_ht_threshold)
-    if canopy_ht_threshold <= 0:
-        canopy_ht_threshold = 0.5
-    tree_radius = float(tree_radius)  # get the round up integer number for tree search radius
-    max_line_dist = float(max_line_dist)
-    canopy_avoid = float(canopy_avoid)
-    cost_raster_exponent = float(exponent)
-
-    try:
-        clipped_rasterC, out_transformC = rasterio.mask.mask(raster_obj, [line_buffer], crop=True,
-                                                             filled=False)
-
-        in_chm = np.squeeze(clipped_rasterC, axis=0)
-
-        # make rasterio meta for saving raster later
-        out_meta = raster_obj.meta.copy()
-        out_meta.update({"driver": "GTiff",
-                         "height": in_chm.shape[0],
-                         "width": in_chm.shape[1],
-                         "nodata": BT_NODATA,
-                         "transform": out_transformC})
-
-        # print('Loading CHM ...')
-        (cell_x, cell_y) = res
-        band1_ndarray = in_chm
-
-        # print('Preparing Kernel window ...')
-        kernel = convolution.circle_kernel(cell_x, cell_y, tree_radius)
-
-        # Generate Canopy Raster and return the Canopy array
-        dyn_canopy_ndarray = dyn_np_cc_map(band1_ndarray, canopy_ht_threshold, nodata)
-
-        # Calculating focal statistic from canopy raster
-        cc_std, cc_mean = dyn_fs_raster_stdmean(dyn_canopy_ndarray, kernel, nodata)
-
-        # Smoothing raster
-        cc_smooth = dyn_smooth_cost(dyn_canopy_ndarray, max_line_dist, [cell_x, cell_y])
-        avoidance = max(min(float(canopy_avoid), 1), 0)
-        dyn_cost_ndarray = dyn_np_cost_raster(dyn_canopy_ndarray, cc_mean, cc_std,
-                                              cc_smooth, avoidance, cost_raster_exponent)
-        dyn_cost_ndarray[np.isnan(dyn_cost_ndarray)] = BT_NODATA_COST  # TODO was nodata, changed to BT_NODATA_COST
-        return (
-            line_df, dyn_canopy_ndarray, dyn_cost_ndarray, out_meta,
-            max_line_dist, nodata, line_id, Cut_Dist, line_buffer
-        )
-
-    except Exception as e:
-        print("Error in dyn_canopy_cost_raster: {}".format(e))
-        return None
-
-
-def split_line_fc(line):
-    return list(map(LineString, zip(line.coords[:-1], line.coords[1:])))
-
-
-def split_line_npart(line):
-    # Work out n parts for each line (divided by LP_SEGMENT_LENGTH)
-    n = int(np.ceil(line.length / LP_SEGMENT_LENGTH))
-    if n > 1:
-        # divided line into n-1 equal parts;
-        distances = np.linspace(0, line.length, n)
-        points = [line.interpolate(distance) for distance in distances]
-        line = LineString(points)
-        mline = split_line_fc(line)
-    else:
-        mline = line
-    return mline
-
-
-def split_into_segments(df):
-    odf = df
-    crs = odf.crs
-    if 'OLnSEG' not in odf.columns.array:
-        df['OLnSEG'] = np.nan
-
-    df = odf.assign(geometry=odf.apply(lambda x: split_line_fc(x.geometry), axis=1))
-    df = df.explode()
-
-    df['OLnSEG'] = df.groupby('OLnFID').cumcount()
-    gdf = GeoDataFrame(df, geometry=df.geometry, crs=crs)
-    gdf = gdf.sort_values(by=['OLnFID', 'OLnSEG'])
-    gdf = gdf.reset_index(drop=True)
-    return gdf
-
-
-def split_into_equal_nth_segments(df):
-    odf = df
-    crs = odf.crs
-    if 'OLnSEG' not in odf.columns.array:
-        df['OLnSEG'] = np.nan
-    df = odf.assign(geometry=odf.apply(lambda x: split_line_npart(x.geometry), axis=1))
-    df = df.explode(index_parts=True)
-
-    df['OLnSEG'] = df.groupby('OLnFID').cumcount()
-    gdf = GeoDataFrame(df, geometry=df.geometry, crs=crs)
-    gdf = gdf.sort_values(by=['OLnFID', 'OLnSEG'])
-    gdf = gdf.reset_index(drop=True)
-    return gdf
-
-
-def generate_line_args(line_seg, work_in_bufferL, work_in_bufferC, raster, tree_radius, max_line_dist,
-                       canopy_avoidance, exponent, work_in_bufferR, canopy_thresh_percentage):
-    line_argsL = []
-    line_argsR = []
-    line_argsC = []
-    line_id = 0
-    for record in range(0, len(work_in_bufferL)):
-        line_bufferL = work_in_bufferL.loc[record, 'geometry']
-        line_bufferC = work_in_bufferC.loc[record, 'geometry']
-        LCut = work_in_bufferL.loc[record, 'LDist_Cut']
-
-        clipped_rasterL, out_transformL = rasterio.mask.mask(raster, [line_bufferL], crop=True,
-                                                             nodata=BT_NODATA, filled=True)
-        clipped_rasterL = np.squeeze(clipped_rasterL, axis=0)
-
-        clipped_rasterC, out_transformC = rasterio.mask.mask(raster, [line_bufferC], crop=True,
-                                                             nodata=BT_NODATA, filled=True)
-
-        clipped_rasterC = np.squeeze(clipped_rasterC, axis=0)
-
-        # make rasterio meta for saving raster later
-        out_metaL = raster.meta.copy()
-        out_metaL.update({"driver": "GTiff",
-                          "height": clipped_rasterL.shape[0],
-                          "width": clipped_rasterL.shape[1],
-                          "nodata": BT_NODATA,
-                          "transform": out_transformL})
-
-        out_metaC = raster.meta.copy()
-        out_metaC.update({"driver": "GTiff",
-                          "height": clipped_rasterC.shape[0],
-                          "width": clipped_rasterC.shape[1],
-                          "nodata": BT_NODATA,
-                          "transform": out_transformC})
-
-        nodata = BT_NODATA
-        line_argsL.append([clipped_rasterL, float(work_in_bufferL.loc[record, 'DynCanTh']), float(tree_radius),
-                           float(max_line_dist), float(canopy_avoidance), float(exponent), raster.res, nodata,
-                           line_seg.iloc[[record]], out_metaL, line_id, LCut, 'Left', canopy_thresh_percentage,
-                           line_bufferC])
-
-        line_argsC.append([clipped_rasterC, float(work_in_bufferC.loc[record, 'DynCanTh']), float(tree_radius),
-                           float(max_line_dist), float(canopy_avoidance), float(exponent), raster.res, nodata,
-                           line_seg.iloc[[record]], out_metaC, line_id, 10, 'Center', canopy_thresh_percentage,
-                           line_bufferC])
-
-        line_id += 1
-
-    line_id = 0
-    for record in range(0, len(work_in_bufferR)):
-        line_bufferR = work_in_bufferR.loc[record, 'geometry']
-        RCut = work_in_bufferR.loc[record, 'RDist_Cut']
-        clipped_rasterR, out_transformR = rasterio.mask.mask(raster, [line_bufferR], crop=True,
-                                                             nodata=BT_NODATA, filled=True)
-        clipped_rasterR = np.squeeze(clipped_rasterR, axis=0)
-
-        # make rasterio meta for saving raster later
-        out_metaR = raster.meta.copy()
-        out_metaR.update({"driver": "GTiff",
-                          "height": clipped_rasterR.shape[0],
-                          "width": clipped_rasterR.shape[1],
-                          "nodata": BT_NODATA,
-                          "transform": out_transformR})
-        line_bufferC = work_in_bufferC.loc[record, 'geometry']
-        clipped_rasterC, out_transformC = rasterio.mask.mask(raster, [line_bufferC], crop=True,
-                                                             nodata=BT_NODATA, filled=True)
-
-        clipped_rasterC = np.squeeze(clipped_rasterC, axis=0)
-        out_metaC = raster.meta.copy()
-        out_metaC.update({"driver": "GTiff",
-                          "height": clipped_rasterC.shape[0],
-                          "width": clipped_rasterC.shape[1],
-                          "nodata": BT_NODATA,
-                          "transform": out_transformC})
-
-        nodata = BT_NODATA
-        # TODO deal with inherited nodata and BT_NODATA_COST
-        # TODO convert nodata to BT_NODATA_COST
-        line_argsR.append([clipped_rasterR, float(work_in_bufferR.loc[record, 'DynCanTh']), float(tree_radius),
-                           float(max_line_dist), float(canopy_avoidance), float(exponent), raster.res, nodata,
-                           line_seg.iloc[[record]], out_metaR, line_id, RCut, 'Right', canopy_thresh_percentage,
-                           line_bufferC])
-
-        print(' "PROGRESS_LABEL Preparing... {} of {}" '.format(line_id + 1 + len(work_in_bufferL),
-                                                                len(work_in_bufferL) + len(work_in_bufferR)),
-              flush=True)
-        print(
-            ' %{} '.format((line_id + 1 + len(work_in_bufferL)) / (len(work_in_bufferL) + len(work_in_bufferR)) * 100),
-            flush=True)
-
-        line_id += 1
-
-    return line_argsL, line_argsR, line_argsC
-
-#
-# def find_corridor_threshold_boundary(canopy_clip, least_cost_path, corridor_raster):
-#     threshold = -1
-#     thresholds = [-1] * 10
-#
-#     # morphological filters to get polygons from canopy raster
-#     canopy_bin = np.where(np.isclose(canopy_clip, 1.0), True, False)
-#     clean_holes = remove_small_holes(canopy_bin)
-#     clean_obj = remove_small_objects(clean_holes)
-#
-#     polys = features.shapes(skimage.img_as_ubyte(clean_obj), mask=clean_obj)
-#     polys = [shape(poly).segmentize(FP_SEGMENTIZE_LENGTH) for poly, _ in polys]
-#
-#     # perpendicular segments intersections with polygons
-#     size = corridor_raster.shape
-#     pts = []
-#     for poly in polys:
-#         pts.extend(list(poly.exterior.coords))
-#
-#     index_0 = []
-#     index_1 = []
-#     for pt in pts:
-#         if int(pt[0]) < size[1] and int(pt[1]) < size[0]:
-#             index_0.append(int(pt[0]))
-#             index_1.append(int(pt[1]))
-#
-#     try:
-#         thresholds = corridor_raster[index_1, index_0]
-#     except Exception as e:
-#         print(e)
-#
-#     # trimmed mean of values at intersections
-#     threshold = stats.trim_mean(thresholds, 0.3)
-#
-#     return threshold
-
-
-def find_corridor_threshold(raster):
-    """
-    Find the optimal corridor threshold by raster histogram
-    Parameters
-    ----------
-    raster : corridor raster
-
-    Returns
-    -------
-    corridor_threshold : float
-
-    """
-    corridor_threshold = -1.0
-    hist, bins = np.histogram(raster.flatten(), bins=100, range=(0, 100))
-    CostStd = np.nanstd(raster.flatten())
-    half_count = np.sum(hist) / 2
-    sub_count = 0
-
-    for count, bin_no in zip(hist, bins):
-        sub_count += count
-        if sub_count > half_count:
-            break
-
-        corridor_threshold = bin_no
-
-    return corridor_threshold
-
-
-def process_single_line_relative(segment):
-    in_chm = rasterio.open(segment[0])
-    #
-    segment[0] = in_chm
-    DynCanTh = segment[1]
-
-    # Segment args from mulitprocessing:
-    # [clipped_chm, float(work_in_bufferR.loc[record, 'DynCanTh']), float(tree_radius),
-    # float(max_line_dist), float(canopy_avoidance), float(exponent), raster.res, nodata,
-    # line_seg.iloc[[record]], out_meta, line_id,RCut,Side,canopy_thresh_percentage,line_buffer]
-
-    # this will change segment content, and parameters will be changed
-    segment = dyn_canopy_cost_raster(segment)
-    # Segment after Clipped Canopy and Cost Raster
-    # line_df, dyn_canopy_ndarray, dyn_cost_ndarray, out_meta, max_line_dist, nodata, line_id,Cut_Dist,line_buffer
-
-    # this function takes single line to work the line footprint
-    # (regardless it process the whole line or individual segment)
-    df = segment[0]
-    in_canopy_r = segment[1]
-    in_cost_r = segment[2]
-    out_meta = segment[3]
-
-    # in_transform = segment[3]
-    if np.isnan(in_canopy_r).all():
-        print("Canopy raster empty")
-
-    if np.isnan(in_cost_r).all():
-        print("Cost raster empty")
-
-    in_meta = segment[3]
-    exp_shk_cell = segment[4]
-    no_data = segment[5]
-    line_id = segment[6]
-    Cut_Dist = segment[7]
-    line_bufferR = segment[8]
-
-    shapefile_proj = df.crs
-    in_transform = in_meta['transform']
-
-    FID = df['OLnSEG']  # segment line feature ID
-    OID = df['OLnFID']  # original line ID for segment line
-
-    segment_list = []
-
-    feat = df.geometry.iloc[0]
-    for coord in feat.coords:
-        segment_list.append(coord)
-
-    cell_size_x = in_transform[0]
-    cell_size_y = -in_transform[4]
-
-    # Work out the corridor from both end of the centerline
-    try:
-        # TODO: further investigate and submit issue to skimage
-        # There is a severe bug in skimage find_costs
-        # when nan is present in clip_cost_r, find_costs cause access violation
-        # no message/exception will be caught
-        # change all nan to BT_NODATA_COST for workaround
-        remove_nan_from_array(in_cost_r)
-
-        # generate 1m interval points along line
-        distance_delta = 1
-        distances = np.arange(0, feat.length, distance_delta)
-        multipoint_along_line = [feat.interpolate(distance) for distance in distances]
-
-        # Rasterize points along line
-        rasterized_points_Alongln = features.rasterize(multipoint_along_line, out_shape=in_cost_r.shape,
-                                                       transform=in_transform,
-                                                       fill=0, all_touched=True, default_value=1)
-        points_Alongln = np.transpose(np.nonzero(rasterized_points_Alongln))
-
-        # Find minimum cost paths through an N-d costs array.
-        mcp_flexible1 = MCP_Flexible(in_cost_r, sampling=(cell_size_x, cell_size_y), fully_connected=True)
-        flex_cost_alongLn, flex_back_alongLn = mcp_flexible1.find_costs(starts=points_Alongln)
-
-        # Generate corridor
-        # corridor = source_cost_acc + dest_cost_acc
-        corridor = flex_cost_alongLn  # +flex_cost_dest #cum_cost_tosource+cum_cost_todestination
-        corridor = np.ma.masked_invalid(corridor)
-
-        # Calculate minimum value of corridor raster
-        if not np.ma.min(corridor) is None:
-            corr_min = float(np.ma.min(corridor))
-        else:
-            corr_min = 0.5
-
-        # normalize corridor raster by deducting corr_min
-        corridor_norm = corridor - corr_min
-
-        # Set minimum as zero and save minimum file
-        # corridor_th_value = find_corridor_threshold(corridor_norm)
-        corridor_th_value = (Cut_Dist / cell_size_x)
-        if corridor_th_value < 0:  # if no threshold found, use default value
-            corridor_th_value = (FP_CORRIDOR_THRESHOLD / cell_size_x)
-
-        # corridor_th_value = FP_CORRIDOR_THRESHOLD
-        corridor_thresh = np.ma.where(corridor_norm >= corridor_th_value, 1.0, 0.0)
-        corridor_thresh_cl = np.ma.where(corridor_norm >= (corridor_th_value + (5 / cell_size_x)), 1.0, 0.0)
-
-        # find contiguous corridor polygon for centerline
-        corridor_poly_gpd = find_corridor_polygon(corridor_thresh_cl, in_transform, df)
-
-        # Process: Stamp CC and Max Line Width
-        # Original code here
-        # RasterClass = SetNull(IsNull(CorridorMin),((CorridorMin) + ((Canopy_Raster) >= 1)) > 0)
-        temp1 = (corridor_thresh + in_canopy_r)
-        raster_class = np.ma.where(temp1 == 0, 1, 0).data
-
-        # BERA proposed Binary morphology
-        # RasterClass_binary=np.where(RasterClass==0,False,True)
-        if exp_shk_cell > 0 and cell_size_x < 1:
-            # Process: Expand
-            # FLM original Expand equivalent
-            cell_size = int(exp_shk_cell * 2 + 1)
-
-            expanded = ndimage.grey_dilation(raster_class, size=(cell_size, cell_size))
-
-            # BERA proposed Binary morphology Expand
-            # Expanded = ndimage.binary_dilation(RasterClass_binary, iterations=exp_shk_cell,border_value=1)
-
-            # Process: Shrink
-            # FLM original Shrink equivalent
-            file_shrink = ndimage.grey_erosion(expanded, size=(cell_size, cell_size))
-
-            # BERA proposed Binary morphology Shrink
-            # fileShrink = ndimage.binary_erosion((Expanded),iterations=Exp_Shk_cell,border_value=1)
-        else:
-            print('No Expand And Shrink cell performed.')
-
-            file_shrink = raster_class
-
-        # Process: Boundary Clean
-        clean_raster = ndimage.gaussian_filter(file_shrink, sigma=0, mode='nearest')
-
-        # creat mask for non-polygon area
-        mask = np.where(clean_raster == 1, True, False)
-
-        # Process: ndarray to shapely Polygon
-        out_polygon = features.shapes(clean_raster, mask=mask, transform=in_transform)
-
-        # create a shapely multipolygon
-        multi_polygon = []
-        for poly, value in out_polygon:
-            multi_polygon.append(shape(poly))
-        poly = MultiPolygon(multi_polygon)
-
-        # create a pandas dataframe for the FP
-        out_data = pd.DataFrame({'OLnFID': OID, 'OLnSEG': FID, 'CorriThresh': corridor_th_value, 'geometry': poly})
-        out_gdata = GeoDataFrame(out_data, geometry='geometry', crs=shapefile_proj)
-
-        return out_gdata, corridor_poly_gpd
-
-    except Exception as e:
-        print('Exception: {}'.format(e))
-
-
-def multiprocessing_footprint_relative(line_args, processes):
-    try:
-        total_steps = len(line_args)
-
-        feats = []
-        # chunksize = math.ceil(total_steps / processes)
-        with Pool(processes=processes) as pool:
-            step = 0
-            # execute tasks in order, process results out of order
-            for result in pool.imap_unordered(process_single_line_relative, line_args):
-                if BT_DEBUGGING:
-                    print('Got result: {}'.format(result), flush=True)
-                feats.append(result)
-                step += 1
-                print(' "PROGRESS_LABEL Dynamic Segment Line Footprint {} of {}" '.format(step, total_steps),
-                      flush=True)
-                print(' %{} '.format(step / total_steps * 100), flush=True)
-        return feats
-    except OperationCancelledException:
-        print("Operation cancelled")
-        return None
-
-
-def main_line_footprint_relative(callback, in_line, in_chm, max_ln_width, exp_shk_cell, out_footprint, out_centerline,
-                                 tree_radius, max_line_dist, canopy_avoidance, exponent, full_step,
-                                 canopy_thresh_percentage, processes, verbose):
-    # use_corridor_th_col = True
-    line_seg = GeoDataFrame.from_file(in_line)
-
-    # If Dynamic canopy threshold column not found, create one
-    if 'DynCanTh' not in line_seg.columns.array:
-        print("Please create field {} first".format('DynCanTh'))
-        exit()
-    if not float(canopy_thresh_percentage):
-        canopy_thresh_percentage = 50
-    else:
-        canopy_thresh_percentage = float(canopy_thresh_percentage)
-
-    if float(canopy_avoidance) <= 0.0:
-        canopy_avoidance = 0.0
-    if float(exponent) <= 0.0:
-        exponent = 1.0
-    # If OLnFID column is not found, column will be created
-    if 'OLnFID' not in line_seg.columns.array:
-        print("Created {} column in input line data.".format('OLnFID'))
-        line_seg['OLnFID'] = line_seg.index
-
-    if 'OLnSEG' not in line_seg.columns.array:
-        line_seg['OLnSEG'] = 0
-
-    print('%{}'.format(10))
-
-    # check coordinate systems between line and raster features
-    with rasterio.open(in_chm) as raster:
-        line_args = []
-
-        if compare_crs(vector_crs(in_line), raster_crs(in_chm)):
-            proc_segments = False
-            if proc_segments:
-                print("Splitting lines into segments...")
-                line_seg_split = split_into_segments(line_seg)
-                print("Splitting lines into segments...Done")
-            else:
-                if full_step:
-                    print("Tool runs on input lines......")
-                    line_seg_split = line_seg
-                else:
-                    print("Tool runs on input segment lines......")
-                    line_seg_split = split_into_Equal_Nth_segments(line_seg, 250)
-
-            print('%{}'.format(20))
-
-            work_in_bufferL1 = GeoDataFrame.copy(line_seg_split)
-            work_in_bufferL2 = GeoDataFrame.copy(line_seg_split)
-            work_in_bufferR1 = GeoDataFrame.copy(line_seg_split)
-            work_in_bufferR2 = GeoDataFrame.copy(line_seg_split)
-            work_in_bufferC = GeoDataFrame.copy(line_seg_split)
-            work_in_bufferL1['geometry'] = buffer(work_in_bufferL1['geometry'], distance=float(max_ln_width) + 1,
-                                                  cap_style=3, single_sided=True)
-
-            work_in_bufferL2['geometry'] = buffer(work_in_bufferL2['geometry'], distance=-1,
-                                                  cap_style=3, single_sided=True)
-
-            work_in_bufferL = GeoDataFrame(pd.concat([work_in_bufferL1, work_in_bufferL2]))
-            work_in_bufferL = work_in_bufferL.dissolve(by=['OLnFID', 'OLnSEG'], as_index=False)
-
-            work_in_bufferR1['geometry'] = buffer(work_in_bufferR1['geometry'], distance=-float(max_ln_width) - 1,
-                                                  cap_style=3, single_sided=True)
-            work_in_bufferR2['geometry'] = buffer(work_in_bufferR2['geometry'], distance=1,
-                                                  cap_style=3, single_sided=True)
-
-            work_in_bufferR = GeoDataFrame(pd.concat([work_in_bufferR1, work_in_bufferR2]))
-            work_in_bufferR = work_in_bufferR.dissolve(by=['OLnFID', 'OLnSEG'], as_index=False)
-
-            work_in_bufferC['geometry'] = buffer(work_in_bufferC['geometry'], distance=float(max_ln_width),
-                                                 cap_style=3, single_sided=False)
-            print("Prepare arguments for Dynamic FP ...")
-            # line_argsL, line_argsR,line_argsC= generate_line_args(line_seg_split, work_in_bufferL,work_in_bufferC,
-            #                                                       raster, tree_radius, max_line_dist,
-            #                                                       canopy_avoidance, exponent, work_in_bufferR,
-            #                                                       canopy_thresh_percentage)
-
-            line_argsL, line_argsR, line_argsC = generate_line_args_DFP_NoClip(line_seg_split, work_in_bufferL,
-                                                                               work_in_bufferC, raster, in_chm,
-                                                                               tree_radius, max_line_dist,
-                                                                               canopy_avoidance, exponent,
-                                                                               work_in_bufferR,
-                                                                               canopy_thresh_percentage)
-
-        else:
-            print("Line and canopy raster spatial references are not same, please check.")
-            exit()
-        # pass center lines for footprint
-        print("Generating Dynamic footprint ...")
-
-        feat_listL = []
-        feat_listR = []
-        feat_listC = []
-        poly_listL = []
-        poly_listR = []
-        footprint_listL = []
-        footprint_listR = []
-        footprint_listC = []
-        # PARALLEL_MODE = ParallelMode.SEQUENTIAL
-        if PARALLEL_MODE == ParallelMode.MULTIPROCESSING:
-            # feat_listC = multiprocessing_footprint_relative(line_argsC, processes)
-            feat_listL = multiprocessing_footprint_relative(line_argsL, processes)
-            # feat_listL = execute_multiprocessing(process_single_line_relative,'Footprint',line_argsL, processes)
-            feat_listR = multiprocessing_footprint_relative(line_argsR, processes)
-            # feat_listR = execute_multiprocessing(process_single_line_relative, 'Footprint', line_argsR, processes)
-
-        elif PARALLEL_MODE == ParallelMode.SEQUENTIAL:
-            step = 1
-            total_steps = len(line_argsL)
-            print("There are {} result to process.".format(total_steps))
-            for row in line_argsL:
-                feat_listL.append(process_single_line_relative(row))
-                print("Footprint (left side) for line {} is done".format(step))
-                print(' "PROGRESS_LABEL Dynamic Line Footprint {} of {}" '.format(step, total_steps), flush=True)
-                print(' %{} '.format((step / total_steps) * 100))
-                step += 1
-            step = 1
-            total_steps = len(line_argsR)
-            for row in line_argsR:
-                feat_listR.append(process_single_line_relative(row))
-                print("Footprint for (right side) line {} is done".format(step))
-                print(' "PROGRESS_LABEL Dynamic Line Footprint {} of {}" '.format(step, total_steps), flush=True)
-                print(' %{} '.format((step / total_steps) * 100))
-                step += 1
-
-    print('%{}'.format(80))
-    print("Task done.")
-
-    for feat in feat_listL:
-        if feat:
-            footprint_listL.append(feat[0])
-            poly_listL.append(feat[1])
-
-    for feat in feat_listR:
-        if feat:
-            footprint_listR.append(feat[0])
-            poly_listR.append(feat[1])
-
-    print('Writing shapefile ...')
-    resultsL = GeoDataFrame(pd.concat(footprint_listL))
-    resultsL['geometry'] = resultsL['geometry'].buffer(0.005)
-    resultsR = GeoDataFrame(pd.concat(footprint_listR))
-    resultsR['geometry'] = resultsR['geometry'].buffer(0.005)
-    resultsL = resultsL.sort_values(by=['OLnFID', 'OLnSEG'])
-    resultsR = resultsR.sort_values(by=['OLnFID', 'OLnSEG'])
-    resultsL = resultsL.reset_index(drop=True)
-    resultsR = resultsR.reset_index(drop=True)
-    #
-
-    resultsAll = GeoDataFrame(pd.concat([resultsL, resultsR]))
-    dissolved_results = resultsAll.dissolve(by='OLnFID', as_index=False)
-    dissolved_results['geometry'] = dissolved_results['geometry'].buffer(-0.005)
-    print("Saving output ...")
-    dissolved_results.to_file(out_footprint)
-    print("Footprint file saved")
-
-    # dissolved polygon group by column 'OLnFID'
-    print("Generating centerlines from corridor polygons ...")
-    resultsCL = GeoDataFrame(pd.concat(poly_listL))
-    resultsCL['geometry'] = resultsCL['geometry'].buffer(0.005)
-    resultsCR = GeoDataFrame(pd.concat(poly_listR))
-    resultsCR['geometry'] = resultsCR['geometry'].buffer(0.005)
-
-    resultsCLR = GeoDataFrame(pd.concat([resultsCL, resultsCR]))
-    resultsCLR = resultsCLR.dissolve(by='OLnFID', as_index=False)
-    resultsCLR = resultsCLR.sort_values(by=['OLnFID', 'OLnSEG'])
-    resultsCLR = resultsCLR.reset_index(drop=True)
-    resultsCLR['geometry'] = resultsCLR['geometry'].buffer(-0.005)
-
-    # out_centerline=False
-    # save lines to file
-    if out_centerline:
-        poly_centerline_gpd = find_centerlines(resultsCLR, line_seg, processes)
-        poly_gpd = poly_centerline_gpd.copy()
-        centerline_gpd = poly_centerline_gpd.copy()
-
-        centerline_gpd = centerline_gpd.set_geometry('centerline')
-        centerline_gpd = centerline_gpd.drop(columns=['geometry'])
-        centerline_gpd.crs = poly_centerline_gpd.crs
-        centerline_gpd.to_file(out_centerline)
-        print("Centerline file saved")
-
-        # save polygons
-        path = Path(out_centerline)
-        path = path.with_stem(path.stem + '_poly')
-        poly_gpd = poly_gpd.drop(columns=['centerline'])
-        poly_gpd.to_file(path)
-
-    print('%{}'.format(100))
-
-
-if __name__ == '__main__':
-    start_time = time.time()
-    print('Dynamic Footprint processing started')
-    print('Current time: {}'.format(time.strftime("%d %b %Y %H:%M:%S", time.localtime())))
-
-    in_args, in_verbose = check_arguments()
-    main_line_footprint_relative(print, **in_args.input, processes=int(in_args.processes), verbose=in_verbose)
-
-    print('%{}'.format(100))
-    print('Dynamic Footprint processing finished')
-    print('Current time: {}'.format(time.strftime("%d %b %Y %H:%M:%S", time.localtime())))
-    print('Total processing time (seconds): {}'.format(round(time.time() - start_time, 3)))
+# ---------------------------------------------------------------------------
+#    Copyright (C) 2021  Applied Geospatial Research Group
+#
+#    This program is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, version 3.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with this program.  If not, see <https://gnu.org/licenses/gpl-3.0>.
+#
+# ---------------------------------------------------------------------------
+#
+# Refactor to use for produce dynamic footprint from dynamic canopy and cost raster with open source libraries
+# Prerequisite:  Line feature class must have the attribute Fields:"CorridorTh" "DynCanTh" "OLnFID"
+# line_footprint_function.py
+# Maverick Fong
+# Date: 2023-Dec
+# This script is part of the BERA toolset
+# Webpage: https://github.com/
+#
+# Purpose: Creates dynamic footprint polygons for each input line based on a least
+# cost corridor method and individual line thresholds.
+#
+# ---------------------------------------------------------------------------
+
+import time
+import numpy as np
+
+import rasterio
+from scipy import stats, ndimage
+from geopandas import GeoDataFrame
+from shapely import buffer
+from rasterio import features
+from xrspatial import convolution
+
+import skimage
+from skimage.morphology import *
+from skimage.graph import MCP_Flexible
+
+from beratools.core.constants import *
+from beratools.core.algo_centerline import *
+from beratools.tools.common import *
+from beratools.core.tool_base import *
+
+
+def dyn_canopy_cost_raster(args):
+    # raster_obj = args[0]
+    in_chm_raster=args[0]
+    DynCanTh = args[1]
+    tree_radius = args[2]
+    max_line_dist = args[3]
+    canopy_avoid = args[4]
+    exponent = args[5]
+    res = args[6]
+    nodata = args[7]
+    line_df = args[8]
+    out_meta = args[9]
+    line_id = args[10]
+    Cut_Dist = args[11]
+    Side = args[12]
+    canopy_thresh_percentage = float(args[13]) / 100
+    line_buffer = args[14]
+
+    if Side == 'Left':
+        canopy_ht_threshold = line_df.CL_CutHt * canopy_thresh_percentage
+    elif Side == 'Right':
+        canopy_ht_threshold = line_df.CR_CutHt * canopy_thresh_percentage
+    elif Side == 'Center':
+        canopy_ht_threshold = DynCanTh * canopy_thresh_percentage
+    else:
+
+        canopy_ht_threshold = 0.5
+
+    canopy_ht_threshold = float(canopy_ht_threshold)
+    if canopy_ht_threshold <= 0:
+        canopy_ht_threshold = 0.5
+    tree_radius = float(tree_radius)  # get the round up integer number for tree search radius
+    max_line_dist = float(max_line_dist)
+    canopy_avoid = float(canopy_avoid)
+    cost_raster_exponent = float(exponent)
+
+    try:
+
+        clipped_rasterC, out_meta = clip_raster(in_chm_raster, line_buffer, 0)
+
+        #clipped_rasterC, out_transformC = rasterio.mask.mask(raster_obj, [line_buffer], crop=True,
+        #                                                     filled=False)
+
+        in_chm = np.squeeze(clipped_rasterC, axis=0)
+
+        # # make rasterio meta for saving raster later
+        # out_meta = raster_obj.meta.copy()
+        # out_meta.update({"driver": "GTiff",
+        #                  "height": in_chm.shape[0],
+        #                  "width": in_chm.shape[1],
+        #                  "nodata": BT_NODATA,
+        #                  "transform": out_transformC})
+
+        # print('Loading CHM ...')
+        cell_x, cell_y = out_meta['transform'][0], -out_meta['transform'][4]
+
+        # print('Preparing Kernel window ...')
+        kernel = convolution.circle_kernel(cell_x, cell_y, tree_radius)
+
+        # Generate Canopy Raster and return the Canopy array
+        dyn_canopy_ndarray = dyn_np_cc_map(in_chm, canopy_ht_threshold, BT_NODATA)
+
+        # Calculating focal statistic from canopy raster
+        cc_std, cc_mean = dyn_fs_raster_stdmean(dyn_canopy_ndarray, kernel, BT_NODATA)
+
+        # Smoothing raster
+        cc_smooth = dyn_smooth_cost(dyn_canopy_ndarray, max_line_dist, [cell_x, cell_y])
+        avoidance = max(min(float(canopy_avoid), 1), 0)
+        cost_clip = dyn_np_cost_raster(dyn_canopy_ndarray, cc_mean, cc_std,
+                                              cc_smooth, avoidance, cost_raster_exponent)
+        negative_cost_clip = np.where(np.isnan(cost_clip), -9999, cost_clip)  # TODO was nodata, changed to BT_NODATA_COST
+        return (
+            line_df, dyn_canopy_ndarray, negative_cost_clip, out_meta,
+            max_line_dist, nodata, line_id, Cut_Dist, line_buffer
+        )
+
+    except Exception as e:
+        print("Error in createing (dynamic) cost raster @ {}: {}".format(line_id,e))
+        return None
+
+
+def split_line_fc(line):
+    return list(map(LineString, zip(line.coords[:-1], line.coords[1:])))
+
+
+def split_line_npart(line):
+    # Work out n parts for each line (divided by LP_SEGMENT_LENGTH)
+    n = int(np.ceil(line.length / LP_SEGMENT_LENGTH))
+    if n > 1:
+        # divided line into n-1 equal parts;
+        distances = np.linspace(0, line.length, n)
+        points = [line.interpolate(distance) for distance in distances]
+        line = LineString(points)
+        mline = split_line_fc(line)
+    else:
+        mline = line
+    return mline
+
+
+def split_into_segments(df):
+    odf = df
+    crs = odf.crs
+    if 'OLnSEG' not in odf.columns.array:
+        df['OLnSEG'] = np.nan
+
+    df = odf.assign(geometry=odf.apply(lambda x: split_line_fc(x.geometry), axis=1))
+    df = df.explode()
+
+    df['OLnSEG'] = df.groupby('OLnFID').cumcount()
+    gdf = GeoDataFrame(df, geometry=df.geometry, crs=crs)
+    gdf = gdf.sort_values(by=['OLnFID', 'OLnSEG'])
+    gdf = gdf.reset_index(drop=True)
+    return gdf
+
+
+def split_into_equal_nth_segments(df):
+    odf = df
+    crs = odf.crs
+    if 'OLnSEG' not in odf.columns.array:
+        df['OLnSEG'] = np.nan
+    df = odf.assign(geometry=odf.apply(lambda x: split_line_npart(x.geometry), axis=1))
+    df = df.explode(index_parts=True)
+
+    df['OLnSEG'] = df.groupby('OLnFID').cumcount()
+    gdf = GeoDataFrame(df, geometry=df.geometry, crs=crs)
+    gdf = gdf.sort_values(by=['OLnFID', 'OLnSEG'])
+    gdf = gdf.reset_index(drop=True)
+    return gdf
+
+
+def generate_line_args(line_seg, work_in_bufferL, work_in_bufferC, raster, tree_radius, max_line_dist,
+                       canopy_avoidance, exponent, work_in_bufferR, canopy_thresh_percentage):
+    line_argsL = []
+    line_argsR = []
+    line_argsC = []
+    line_id = 0
+    for record in range(0, len(work_in_bufferL)):
+        line_bufferL = work_in_bufferL.loc[record, 'geometry']
+        line_bufferC = work_in_bufferC.loc[record, 'geometry']
+        LCut = work_in_bufferL.loc[record, 'LDist_Cut']
+
+        clipped_rasterL, out_transformL = rasterio.mask.mask(raster, [line_bufferL], crop=True,
+                                                             nodata=BT_NODATA, filled=True)
+        clipped_rasterL = np.squeeze(clipped_rasterL, axis=0)
+
+        clipped_rasterC, out_transformC = rasterio.mask.mask(raster, [line_bufferC], crop=True,
+                                                             nodata=BT_NODATA, filled=True)
+
+        clipped_rasterC = np.squeeze(clipped_rasterC, axis=0)
+
+        # make rasterio meta for saving raster later
+        out_metaL = raster.meta.copy()
+        out_metaL.update({"driver": "GTiff",
+                          "height": clipped_rasterL.shape[0],
+                          "width": clipped_rasterL.shape[1],
+                          "nodata": BT_NODATA,
+                          "transform": out_transformL})
+
+        out_metaC = raster.meta.copy()
+        out_metaC.update({"driver": "GTiff",
+                          "height": clipped_rasterC.shape[0],
+                          "width": clipped_rasterC.shape[1],
+                          "nodata": BT_NODATA,
+                          "transform": out_transformC})
+
+        nodata = BT_NODATA
+        line_argsL.append([clipped_rasterL, float(work_in_bufferL.loc[record, 'DynCanTh']), float(tree_radius),
+                           float(max_line_dist), float(canopy_avoidance), float(exponent), raster.res, nodata,
+                           line_seg.iloc[[record]], out_metaL, line_id, LCut, 'Left', canopy_thresh_percentage,
+                           line_bufferC])
+
+        line_argsC.append([clipped_rasterC, float(work_in_bufferC.loc[record, 'DynCanTh']), float(tree_radius),
+                           float(max_line_dist), float(canopy_avoidance), float(exponent), raster.res, nodata,
+                           line_seg.iloc[[record]], out_metaC, line_id, 10, 'Center', canopy_thresh_percentage,
+                           line_bufferC])
+
+        line_id += 1
+
+    line_id = 0
+    for record in range(0, len(work_in_bufferR)):
+        line_bufferR = work_in_bufferR.loc[record, 'geometry']
+        RCut = work_in_bufferR.loc[record, 'RDist_Cut']
+        clipped_rasterR, out_transformR = rasterio.mask.mask(raster, [line_bufferR], crop=True,
+                                                             nodata=BT_NODATA, filled=True)
+        clipped_rasterR = np.squeeze(clipped_rasterR, axis=0)
+
+        # make rasterio meta for saving raster later
+        out_metaR = raster.meta.copy()
+        out_metaR.update({"driver": "GTiff",
+                          "height": clipped_rasterR.shape[0],
+                          "width": clipped_rasterR.shape[1],
+                          "nodata": BT_NODATA,
+                          "transform": out_transformR})
+        line_bufferC = work_in_bufferC.loc[record, 'geometry']
+        clipped_rasterC, out_transformC = rasterio.mask.mask(raster, [line_bufferC], crop=True,
+                                                             nodata=BT_NODATA, filled=True)
+
+        clipped_rasterC = np.squeeze(clipped_rasterC, axis=0)
+        out_metaC = raster.meta.copy()
+        out_metaC.update({"driver": "GTiff",
+                          "height": clipped_rasterC.shape[0],
+                          "width": clipped_rasterC.shape[1],
+                          "nodata": BT_NODATA,
+                          "transform": out_transformC})
+
+        nodata = BT_NODATA
+        # TODO deal with inherited nodata and BT_NODATA_COST
+        # TODO convert nodata to BT_NODATA_COST
+        line_argsR.append([clipped_rasterR, float(work_in_bufferR.loc[record, 'DynCanTh']), float(tree_radius),
+                           float(max_line_dist), float(canopy_avoidance), float(exponent), raster.res, nodata,
+                           line_seg.iloc[[record]], out_metaR, line_id, RCut, 'Right', canopy_thresh_percentage,
+                           line_bufferC])
+
+        print(' "PROGRESS_LABEL Preparing... {} of {}" '.format(line_id + 1 + len(work_in_bufferL),
+                                                                len(work_in_bufferL) + len(work_in_bufferR)),
+              flush=True)
+        print(
+            ' %{} '.format((line_id + 1 + len(work_in_bufferL)) / (len(work_in_bufferL) + len(work_in_bufferR)) * 100),
+            flush=True)
+
+        line_id += 1
+
+    return line_argsL, line_argsR, line_argsC
+
+#
+# def find_corridor_threshold_boundary(canopy_clip, least_cost_path, corridor_raster):
+#     threshold = -1
+#     thresholds = [-1] * 10
+#
+#     # morphological filters to get polygons from canopy raster
+#     canopy_bin = np.where(np.isclose(canopy_clip, 1.0), True, False)
+#     clean_holes = remove_small_holes(canopy_bin)
+#     clean_obj = remove_small_objects(clean_holes)
+#
+#     polys = features.shapes(skimage.img_as_ubyte(clean_obj), mask=clean_obj)
+#     polys = [shape(poly).segmentize(FP_SEGMENTIZE_LENGTH) for poly, _ in polys]
+#
+#     # perpendicular segments intersections with polygons
+#     size = corridor_raster.shape
+#     pts = []
+#     for poly in polys:
+#         pts.extend(list(poly.exterior.coords))
+#
+#     index_0 = []
+#     index_1 = []
+#     for pt in pts:
+#         if int(pt[0]) < size[1] and int(pt[1]) < size[0]:
+#             index_0.append(int(pt[0]))
+#             index_1.append(int(pt[1]))
+#
+#     try:
+#         thresholds = corridor_raster[index_1, index_0]
+#     except Exception as e:
+#         print(e)
+#
+#     # trimmed mean of values at intersections
+#     threshold = stats.trim_mean(thresholds, 0.3)
+#
+#     return threshold
+
+
+def find_corridor_threshold(raster):
+    """
+    Find the optimal corridor threshold by raster histogram
+    Parameters
+    ----------
+    raster : corridor raster
+
+    Returns
+    -------
+    corridor_threshold : float
+
+    """
+    corridor_threshold = -1.0
+    hist, bins = np.histogram(raster.flatten(), bins=100, range=(0, 100))
+    CostStd = np.nanstd(raster.flatten())
+    half_count = np.sum(hist) / 2
+    sub_count = 0
+
+    for count, bin_no in zip(hist, bins):
+        sub_count += count
+        if sub_count > half_count:
+            break
+
+        corridor_threshold = bin_no
+
+    return corridor_threshold
+
+
+def process_single_line_relative(segment):
+    # in_chm = rasterio.open(segment[0])
+
+    # segment[0] = in_chm
+    #DynCanTh = segment[1]
+
+    # Segment args from mulitprocessing:
+    # [clipped_chm, float(work_in_bufferR.loc[record, 'DynCanTh']), float(tree_radius),
+    # float(max_line_dist), float(canopy_avoidance), float(exponent), raster.res, nodata,
+    # line_seg.iloc[[record]], out_meta, line_id,RCut,Side,canopy_thresh_percentage,line_buffer]
+
+    # this will change segment content, and parameters will be changed
+    segment = dyn_canopy_cost_raster(segment)
+    if segment is None:
+        return None
+    # Segement after Clipped Canopy and Cost Raster
+    # line_df, dyn_canopy_ndarray, negative_cost_clip, out_meta, max_line_dist, nodata, line_id,Cut_Dist,line_buffer
+
+    # this function takes single line to work the line footprint
+    # (regardless it process the whole line or individual segment)
+    df = segment[0]
+    in_canopy_r = segment[1]
+    in_cost_r = segment[2]
+    out_meta = segment[3]
+
+    # in_transform = segment[3]
+    if np.isnan(in_canopy_r).all():
+        print("Canopy raster empty")
+
+    if np.isnan(in_cost_r).all():
+        print("Cost raster empty")
+
+    in_meta = segment[3]
+    exp_shk_cell = segment[4]
+    no_data = segment[5]
+    line_id = segment[6]
+    Cut_Dist = segment[7]
+    line_bufferR = segment[8]
+
+    shapefile_proj = df.crs
+    in_transform = in_meta['transform']
+
+    FID = df['OLnSEG']  # segment line feature ID
+    OID = df['OLnFID']  # original line ID for segment line
+
+    segment_list = []
+
+    feat = df.geometry.iloc[0]
+    for coord in feat.coords:
+        segment_list.append(coord)
+
+    cell_size_x = in_transform[0]
+    cell_size_y = -in_transform[4]
+
+    # Work out the corridor from both end of the centerline
+    try:
+        # TODO: further investigate and submit issue to skimage
+        # There is a severe bug in skimage find_costs
+        # when nan is present in clip_cost_r, find_costs cause access violation
+        # no message/exception will be caught
+        # change all nan to BT_NODATA_COST for workaround
+        if len(in_cost_r.shape) > 2:
+            in_cost_r = np.squeeze(in_cost_r, axis=0)
+        remove_nan_from_array(in_cost_r)
+        in_cost_r[in_cost_r==no_data]=np.inf
+
+        # generate 1m interval points along line
+        distance_delta = 1
+        distances = np.arange(0, feat.length, distance_delta)
+        multipoint_along_line = [feat.interpolate(distance) for distance in distances]
+        multipoint_along_line.append(Point(segment_list[-1]))
+        # Rasterize points along line
+        rasterized_points_Alongln = features.rasterize(multipoint_along_line, out_shape=in_cost_r.shape,
+                                                       transform=in_transform,
+                                                       fill=0, all_touched=True, default_value=1)
+        points_Alongln = np.transpose(np.nonzero(rasterized_points_Alongln))
+
+        # Find minimum cost paths through an N-d costs array.
+        mcp_flexible1 = MCP_Flexible(in_cost_r, sampling=(cell_size_x, cell_size_y), fully_connected=True)
+        flex_cost_alongLn, flex_back_alongLn = mcp_flexible1.find_costs(starts=points_Alongln)
+
+        # Generate corridor
+        # corridor = source_cost_acc + dest_cost_acc
+        corridor = flex_cost_alongLn  # +flex_cost_dest #cum_cost_tosource+cum_cost_todestination
+        corridor = np.ma.masked_invalid(corridor)
+
+
+        # Calculate minimum value of corridor raster
+        if not np.ma.min(corridor) is None:
+            corr_min = float(np.ma.min(corridor))
+        else:
+            corr_min = 0.5
+
+        # normalize corridor raster by deducting corr_min
+        corridor_norm = corridor - corr_min
+
+        # Set minimum as zero and save minimum file
+        # corridor_th_value = find_corridor_threshold(corridor_norm)
+        corridor_th_value = (Cut_Dist / cell_size_x)
+        if corridor_th_value < 0:  # if no threshold found, use default value
+            corridor_th_value = (FP_CORRIDOR_THRESHOLD / cell_size_x)
+
+        # corridor_th_value = FP_CORRIDOR_THRESHOLD
+        corridor_thresh = np.ma.where(corridor_norm >= corridor_th_value, 1.0, 0.0)
+        corridor_thresh_cl = np.ma.where(corridor_norm >= (corridor_th_value + (5 / cell_size_x)), 1.0, 0.0)
+
+        # find contiguous corridor polygon for centerline
+        corridor_poly_gpd = find_corridor_polygon(corridor_thresh_cl, in_transform, df)
+
+        # Process: Stamp CC and Max Line Width
+        # Original code here
+        # RasterClass = SetNull(IsNull(CorridorMin),((CorridorMin) + ((Canopy_Raster) >= 1)) > 0)
+        temp1 = (corridor_thresh + in_canopy_r)
+        raster_class = np.ma.where(temp1 == 0, 1, 0).data
+
+        # BERA proposed Binary morphology
+        # RasterClass_binary=np.where(RasterClass==0,False,True)
+        if exp_shk_cell > 0 and cell_size_x < 1:
+            # Process: Expand
+            # FLM original Expand equivalent
+            cell_size = int(exp_shk_cell * 2 + 1)
+
+            expanded = ndimage.grey_dilation(raster_class, size=(cell_size, cell_size))
+
+            # BERA proposed Binary morphology Expand
+            # Expanded = ndimage.binary_dilation(RasterClass_binary, iterations=exp_shk_cell,border_value=1)
+
+            # Process: Shrink
+            # FLM original Shrink equivalent
+            file_shrink = ndimage.grey_erosion(expanded, size=(cell_size, cell_size))
+
+            # BERA proposed Binary morphology Shrink
+            # fileShrink = ndimage.binary_erosion((Expanded),iterations=Exp_Shk_cell,border_value=1)
+        else:
+            print('No Expand And Shrink cell performed.')
+
+            file_shrink = raster_class
+
+        # Process: Boundary Clean
+        clean_raster = ndimage.gaussian_filter(file_shrink, sigma=0, mode='nearest')
+
+        # creat mask for non-polygon area
+        mask = np.where(clean_raster == 1, True, False)
+        if clean_raster.dtype == np.int64:
+            clean_raster = clean_raster.astype(np.int32)
+
+        # Process: ndarray to shapely Polygon
+        out_polygon = features.shapes(clean_raster, mask=mask, transform=in_transform)
+
+        # create a shapely multipolygon
+        multi_polygon = []
+        for poly, value in out_polygon:
+            multi_polygon.append(shape(poly))
+        poly = MultiPolygon(multi_polygon)
+
+        # create a pandas dataframe for the FP
+        out_data = pd.DataFrame({'OLnFID': OID, 'OLnSEG': FID, 'CorriThresh': corridor_th_value, 'geometry': poly})
+        out_gdata = GeoDataFrame(out_data, geometry='geometry', crs=shapefile_proj)
+
+        return out_gdata, corridor_poly_gpd
+
+    except Exception as e:
+        print('Exception: {}'.format(e))
+
+
+def multiprocessing_footprint_relative(line_args, processes):
+    try:
+        total_steps = len(line_args)
+
+        feats = []
+        # chunksize = math.ceil(total_steps / processes)
+        with Pool(processes=processes) as pool:
+            step = 0
+            # execute tasks in order, process results out of order
+            for result in pool.imap_unordered(process_single_line_relative, line_args):
+                if BT_DEBUGGING:
+                    print('Got result: {}'.format(result), flush=True)
+                if result != None:
+                    feats.append(result)
+                step += 1
+                print(' "PROGRESS_LABEL Dynamic Segment Line Footprint {} of {}" '.format(step, total_steps),
+                      flush=True)
+                print(' %{} '.format(step / total_steps * 100), flush=True)
+        return feats
+    except OperationCancelledException:
+        print("Operation cancelled")
+        return None
+
+
+def main_line_footprint_relative(callback, in_line, in_chm, max_ln_width, exp_shk_cell, out_footprint, out_centerline,
+                                 tree_radius, max_line_dist, canopy_avoidance, exponent, full_step,
+                                 canopy_thresh_percentage, processes, verbose):
+    # use_corridor_th_col = True
+    line_seg = GeoDataFrame.from_file(in_line)
+
+    # If Dynamic canopy threshold column not found, create one
+    if 'DynCanTh' not in line_seg.columns.array:
+        print("Please create field {} first".format('DynCanTh'))
+        exit()
+    if not float(canopy_thresh_percentage):
+        canopy_thresh_percentage = 50
+    else:
+        canopy_thresh_percentage = float(canopy_thresh_percentage)
+
+    if float(canopy_avoidance) <= 0.0:
+        canopy_avoidance = 0.0
+    if float(exponent) <= 0.0:
+        exponent = 1.0
+    # If OLnFID column is not found, column will be created
+    if 'OLnFID' not in line_seg.columns.array:
+        print("Created {} column in input line data.".format('OLnFID'))
+        line_seg['OLnFID'] = line_seg.index
+
+    if 'OLnSEG' not in line_seg.columns.array:
+        line_seg['OLnSEG'] = 0
+
+    print('%{}'.format(10))
+
+    # check coordinate systems between line and raster features
+    with rasterio.open(in_chm) as raster:
+        line_args = []
+
+        if compare_crs(vector_crs(in_line), raster_crs(in_chm)):
+            proc_segments = False
+            if proc_segments:
+                print("Splitting lines into segments...")
+                line_seg_split = split_into_segments(line_seg)
+                print("Splitting lines into segments...Done")
+            else:
+                if full_step:
+                    print("Tool runs on input lines......")
+                    line_seg_split = line_seg
+                else:
+                    print("Tool runs on input segment lines......")
+                    line_seg_split = split_into_Equal_Nth_segments(line_seg, 250)
+
+            print('%{}'.format(20))
+
+            work_in_bufferL1 = GeoDataFrame.copy(line_seg_split)
+            work_in_bufferL2 = GeoDataFrame.copy(line_seg_split)
+            work_in_bufferR1 = GeoDataFrame.copy(line_seg_split)
+            work_in_bufferR2 = GeoDataFrame.copy(line_seg_split)
+            work_in_bufferC = GeoDataFrame.copy(line_seg_split)
+            work_in_bufferL1['geometry'] = buffer(work_in_bufferL1['geometry'], distance=float(max_ln_width) + 1,
+                                                  cap_style=3, single_sided=True)
+
+            work_in_bufferL2['geometry'] = buffer(work_in_bufferL2['geometry'], distance=-1,
+                                                  cap_style=3, single_sided=True)
+
+            work_in_bufferL = GeoDataFrame(pd.concat([work_in_bufferL1, work_in_bufferL2]))
+            work_in_bufferL = work_in_bufferL.dissolve(by=['OLnFID', 'OLnSEG'], as_index=False)
+
+            work_in_bufferR1['geometry'] = buffer(work_in_bufferR1['geometry'], distance=-float(max_ln_width) - 1,
+                                                  cap_style=3, single_sided=True)
+            work_in_bufferR2['geometry'] = buffer(work_in_bufferR2['geometry'], distance=1,
+                                                  cap_style=3, single_sided=True)
+
+            work_in_bufferR = GeoDataFrame(pd.concat([work_in_bufferR1, work_in_bufferR2]))
+            work_in_bufferR = work_in_bufferR.dissolve(by=['OLnFID', 'OLnSEG'], as_index=False)
+
+            work_in_bufferC['geometry'] = buffer(work_in_bufferC['geometry'], distance=float(max_ln_width),
+                                                 cap_style=3, single_sided=False)
+            print("Prepare arguments for Dynamic FP ...")
+            # line_argsL, line_argsR,line_argsC= generate_line_args(line_seg_split, work_in_bufferL,work_in_bufferC,
+            #                                                       raster, tree_radius, max_line_dist,
+            #                                                       canopy_avoidance, exponent, work_in_bufferR,
+            #                                                       canopy_thresh_percentage)
+
+            line_argsL, line_argsR, line_argsC = generate_line_args_DFP_NoClip(line_seg_split, work_in_bufferL,
+                                                                               work_in_bufferC, raster, in_chm,
+                                                                               tree_radius, max_line_dist,
+                                                                               canopy_avoidance, exponent,
+                                                                               work_in_bufferR,
+                                                                               canopy_thresh_percentage)
+
+        else:
+            print("Line and canopy raster spatial references are not same, please check.")
+            exit()
+        # pass center lines for footprint
+        print("Generating Dynamic footprint ...")
+
+        feat_listL = []
+        feat_listR = []
+        feat_listC = []
+        poly_listL = []
+        poly_listR = []
+        footprint_listL = []
+        footprint_listR = []
+        footprint_listC = []
+        # PARALLEL_MODE = ParallelMode.SEQUENTIAL
+        if PARALLEL_MODE == ParallelMode.MULTIPROCESSING:
+            # feat_listC = multiprocessing_footprint_relative(line_argsC, processes)
+            feat_listL = multiprocessing_footprint_relative(line_argsL, processes)
+            # feat_listL = execute_multiprocessing(process_single_line_relative,'Footprint',line_argsL, processes)
+            feat_listR = multiprocessing_footprint_relative(line_argsR, processes)
+            # feat_listR = execute_multiprocessing(process_single_line_relative, 'Footprint', line_argsR, processes)
+
+        elif PARALLEL_MODE == ParallelMode.SEQUENTIAL:
+            step = 1
+            total_steps = len(line_argsL)
+            print("There are {} result to process.".format(total_steps))
+            for row in line_argsL:
+                feat_listL.append(process_single_line_relative(row))
+                print("Footprint (left side) for line {} is done".format(step))
+                print(' "PROGRESS_LABEL Dynamic Line Footprint {} of {}" '.format(step, total_steps), flush=True)
+                print(' %{} '.format((step / total_steps) * 100))
+                step += 1
+            step = 1
+            total_steps = len(line_argsR)
+            for row in line_argsR:
+                feat_listR.append(process_single_line_relative(row))
+                print("Footprint for (right side) line {} is done".format(step))
+                print(' "PROGRESS_LABEL Dynamic Line Footprint {} of {}" '.format(step, total_steps), flush=True)
+                print(' %{} '.format((step / total_steps) * 100))
+                step += 1
+
+    print('%{}'.format(80))
+    print("Task done.")
+
+    for feat in feat_listL:
+        if feat:
+            footprint_listL.append(feat[0])
+            poly_listL.append(feat[1])
+
+    for feat in feat_listR:
+        if feat:
+            footprint_listR.append(feat[0])
+            poly_listR.append(feat[1])
+
+    print('Writing shapefile ...')
+    resultsL = GeoDataFrame(pd.concat(footprint_listL))
+    resultsL['geometry'] = resultsL['geometry'].buffer(0.005)
+    resultsR = GeoDataFrame(pd.concat(footprint_listR))
+    resultsR['geometry'] = resultsR['geometry'].buffer(0.005)
+    resultsL = resultsL.sort_values(by=['OLnFID', 'OLnSEG'])
+    resultsR = resultsR.sort_values(by=['OLnFID', 'OLnSEG'])
+    resultsL = resultsL.reset_index(drop=True)
+    resultsR = resultsR.reset_index(drop=True)
+    #
+
+    resultsAll = GeoDataFrame(pd.concat([resultsL, resultsR]))
+    dissolved_results = resultsAll.dissolve(by='OLnFID', as_index=False)
+    dissolved_results['geometry'] = dissolved_results['geometry'].buffer(-0.005)
+    print("Saving output ...")
+    dissolved_results.to_file(out_footprint)
+    print("Footprint file saved")
+
+    # dissolved polygon group by column 'OLnFID'
+    print("Generating centerlines from corridor polygons ...")
+    resultsCL = GeoDataFrame(pd.concat(poly_listL))
+    resultsCL['geometry'] = resultsCL['geometry'].buffer(0.005)
+    resultsCR = GeoDataFrame(pd.concat(poly_listR))
+    resultsCR['geometry'] = resultsCR['geometry'].buffer(0.005)
+
+    resultsCLR = GeoDataFrame(pd.concat([resultsCL, resultsCR]))
+    resultsCLR = resultsCLR.dissolve(by='OLnFID', as_index=False)
+    resultsCLR = resultsCLR.sort_values(by=['OLnFID', 'OLnSEG'])
+    resultsCLR = resultsCLR.reset_index(drop=True)
+    resultsCLR['geometry'] = resultsCLR['geometry'].buffer(-0.005)
+
+    # out_centerline=False
+    # save lines to file
+    if out_centerline:
+        poly_centerline_gpd = find_centerlines(resultsCLR, line_seg, processes)
+        poly_gpd = poly_centerline_gpd.copy()
+        centerline_gpd = poly_centerline_gpd.copy()
+
+        centerline_gpd = centerline_gpd.set_geometry('centerline')
+        centerline_gpd = centerline_gpd.drop(columns=['geometry'])
+        centerline_gpd.crs = poly_centerline_gpd.crs
+        centerline_gpd.to_file(out_centerline)
+        print("Centerline file saved")
+
+        # save polygons
+        path = Path(out_centerline)
+        path = path.with_stem(path.stem + '_poly')
+        poly_gpd = poly_gpd.drop(columns=['centerline'])
+        poly_gpd.to_file(path)
+
+    print('%{}'.format(100))
+
+
+if __name__ == '__main__':
+    start_time = time.time()
+    print('Dynamic Footprint processing started')
+    print('Current time: {}'.format(time.strftime("%d %b %Y %H:%M:%S", time.localtime())))
+
+    in_args, in_verbose = check_arguments()
+    main_line_footprint_relative(print, **in_args.input, processes=int(in_args.processes), verbose=in_verbose)
+
+    print('%{}'.format(100))
+    print('Dynamic Footprint processing finished')
+    print('Current time: {}'.format(time.strftime("%d %b %Y %H:%M:%S", time.localtime())))
+    print('Total processing time (seconds): {}'.format(round(time.time() - start_time, 3)))