BERATools 0.2.0__tar.gz

beratools-0.2.0/.gitignore

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+/.idea
+/.vscode
+/.spyproject
+/data
+.data
+/beratools/gui/icons/grass
+/beratools/__pycache__
+/beratools/tools/__pycache__
+/beratools/gui/__pycache__
+*.pyc
+*.whl
+0.5.1
+/dist
+.project
+.pydevproject
+BERATools.bat

beratools-0.2.0/LICENSE

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+MIT License
+
+Copyright (c) 2023, AppliedGRG
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+

beratools-0.2.0/PKG-INFO

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+Metadata-Version: 2.3
+Name: BERATools
+Version: 0.2.0
+Summary: An advanced forest line feature analysis platform
+Project-URL: Homepage, https://github.com/RichardQZeng/BTools
+Author-email: AppliedGRG <appliedgrg@gmail.com>, Richard Zeng <richardqzeng@gmail.com>
+License: MIT License
+        
+        Copyright (c) 2023, AppliedGRG
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+License-File: LICENSE
+Keywords: BERA,Line
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.9
+Requires-Dist: dask
+Requires-Dist: distributed
+Requires-Dist: geopandas
+Requires-Dist: label-centerlines
+Requires-Dist: pip
+Requires-Dist: psutil
+Requires-Dist: pyogrio>=0.9.0
+Requires-Dist: pyqt5
+Requires-Dist: rioxarray
+Requires-Dist: rpy2
+Requires-Dist: scikit-image>=0.24.0
+Requires-Dist: xarray-spatial
+Description-Content-Type: text/markdown
+
+- HTML documentation is generated from .rst files with Sphinx
+
+$ sphinx-build -b html ./sphinx/rst OutDir/sphinx/html
+Or use the target doc in the cmake build system
+$ make doc
+
+Sphinx setup:
+Please follow the http://sphinx-doc.org/latest/install.html guide.
+

beratools-0.2.0/README.md

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+- HTML documentation is generated from .rst files with Sphinx
+
+$ sphinx-build -b html ./sphinx/rst OutDir/sphinx/html
+Or use the target doc in the cmake build system
+$ make doc
+
+Sphinx setup:
+Please follow the http://sphinx-doc.org/latest/install.html guide.
+

beratools-0.2.0/beratools/__init__.py

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+from beratools.core import *
+from beratools.tools import *
+from beratools.gui import *
+from beratools.third_party import *
+from beratools.core import logger
+
+__author__ = """AppliedGRG"""
+__email__ = 'appliedgrg@gmail.com'
+__version__ = '0.2.0'

beratools-0.2.0/beratools/core/algo_centerline.py

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+import numpy as np
+from rasterio import features
+import shapely
+from shapely.geometry import shape
+from shapely.ops import unary_union, substring, linemerge, nearest_points, split
+from shapely.geometry import Point, MultiPoint, Polygon, MultiPolygon, LineString, MultiLineString
+# from beratools.third_party.label_centerlines import get_centerline
+from label_centerlines import get_centerline
+
+from beratools.core.tool_base import *
+from beratools.core.constants import *
+from beratools.tools.common import generate_perpendicular_line_precise
+
+
+def centerline_is_valid(centerline, input_line):
+    """
+    Check if centerline is valid
+    Parameters
+    ----------
+    centerline :
+    input_line : shapely LineString
+        This can be input seed line or least cost path. Only two end points are used.
+
+    Returns
+    -------
+
+    """
+    if not centerline:
+        return False
+
+    # centerline length less the half of least cost path
+    if (centerline.length < input_line.length / 2 or
+            centerline.distance(Point(input_line.coords[0])) > BT_EPSILON or
+            centerline.distance(Point(input_line.coords[-1])) > BT_EPSILON):
+        return False
+
+    return True
+
+
+def snap_end_to_end(in_line, line_reference):
+    if type(in_line) is MultiLineString:
+        in_line = linemerge(in_line)
+        if type(in_line) is MultiLineString:
+            print(f'algo_centerline: MultiLineString found {in_line.centroid}, pass.')
+            return None
+
+    pts = list(in_line.coords)
+    if len(pts) < 2:
+        print('snap_end_to_end: input line invalid.')
+        return in_line
+
+    line_start = Point(pts[0])
+    line_end = Point(pts[-1])
+    ref_ends = MultiPoint([line_reference.coords[0], line_reference.coords[-1]])
+
+    _, snap_start = nearest_points(line_start, ref_ends)
+    _, snap_end = nearest_points(line_end, ref_ends)
+
+    if in_line.has_z:
+        snap_start = shapely.force_3d(snap_start)
+        snap_end = shapely.force_3d(snap_end)
+    else:
+        snap_start = shapely.force_2d(snap_start)
+        snap_end = shapely.force_2d(snap_end)
+
+    pts[0] = snap_start.coords[0]
+    pts[-1] = snap_end.coords[0]
+
+    return LineString(pts)
+
+
+def find_centerline(poly, input_line):
+    """
+    Parameters
+    ----------
+    poly : Polygon
+    input_line : LineString
+        Least cost path or seed line
+
+    Returns
+    -------
+
+    """
+    default_return = input_line, CenterlineStatus.FAILED
+    if not poly:
+        print('find_centerline: No polygon found')
+        return default_return
+
+    poly = shapely.segmentize(poly, max_segment_length=CL_SEGMENTIZE_LENGTH)
+
+    poly = poly.buffer(CL_POLYGON_BUFFER)  # buffer polygon to reduce MultiPolygons
+    if type(poly) is MultiPolygon:
+        print('MultiPolygon encountered, skip.')
+        return default_return
+
+    exterior_pts = list(poly.exterior.coords)
+
+    if CL_DELETE_HOLES:
+        poly = Polygon(exterior_pts)
+    if CL_SIMPLIFY_POLYGON:
+        poly = poly.simplify(CL_SIMPLIFY_LENGTH)
+
+    line_coords = list(input_line.coords)
+
+    # TODO add more code to filter voronoi vertices
+    src_geom = Point(line_coords[0]).buffer(CL_BUFFER_CLIP*3).intersection(poly)
+    dst_geom = Point(line_coords[-1]).buffer(CL_BUFFER_CLIP*3).intersection(poly)
+    src_geom = None
+    dst_geom = None
+
+    try:
+        centerline = get_centerline(poly, segmentize_maxlen=1, max_points=3000,
+                                    simplification=0.05, smooth_sigma=CL_SMOOTH_SIGMA, max_paths=1,
+                                    src_geom=src_geom, dst_geom=dst_geom)
+    except Exception as e:
+        print(e)
+        return default_return
+
+    if not centerline:
+        return default_return
+
+    if type(centerline) is MultiLineString:
+        if len(centerline.geoms) > 1:
+            print(" Multiple centerline segments detected, no further processing.")
+            return centerline, CenterlineStatus.SUCCESS  # TODO: inspect
+        elif len(centerline.geoms) == 1:
+            centerline = centerline.geoms[0]
+        else:
+            return default_return
+
+    cl_coords = list(centerline.coords)
+
+    # trim centerline at two ends
+    head_buffer = Point(cl_coords[0]).buffer(CL_BUFFER_CLIP)
+    centerline = centerline.difference(head_buffer)
+
+    end_buffer = Point(cl_coords[-1]).buffer(CL_BUFFER_CLIP)
+    centerline = centerline.difference(end_buffer)
+
+    if not centerline:
+        print('No centerline detected, use input line instead.')
+        return default_return
+    try:
+        if centerline.is_empty:
+            print('Empty centerline detected, use input line instead.')
+            return default_return
+    except Exception as e:
+        print(e)
+
+    centerline = snap_end_to_end(centerline, input_line)
+
+    # Check if centerline is valid. If not, regenerate by splitting polygon into two halves.
+    if not centerline_is_valid(centerline, input_line):
+        try:
+            print(f'Regenerating line ...')
+            centerline = regenerate_centerline(poly, input_line)
+            return centerline, CenterlineStatus.REGENERATE_SUCCESS
+        except Exception as e:
+            print('find_centerline:  Exception occurred. \n {}'.format(e))
+            return input_line, CenterlineStatus.REGENERATE_FAILED
+
+    return centerline, CenterlineStatus.SUCCESS
+
+
+# def find_route(array, start, end, fully_connected, geometric):
+#     route_list, cost_list = route_through_array(array, start, end, fully_connected, geometric)
+#     return route_list, cost_list
+
+
+def find_corridor_polygon(corridor_thresh, in_transform, line_gpd):
+    # Threshold corridor raster used for generating centerline
+    corridor_thresh_cl = np.ma.where(corridor_thresh == 0.0, 1, 0).data
+    corridor_mask = np.where(1 == corridor_thresh_cl, True, False)
+    poly_generator = features.shapes(corridor_thresh_cl, mask=corridor_mask, transform=in_transform)
+    corridor_polygon = []
+
+    try:
+        for poly, value in poly_generator:
+            if shape(poly).area > 1:
+                corridor_polygon.append(shape(poly))
+    except Exception as e:
+        print(e)
+
+    if corridor_polygon:
+        corridor_polygon = (unary_union(corridor_polygon))
+        if type(corridor_polygon) is MultiPolygon:
+            poly_list = shapely.get_parts(corridor_polygon)
+            merge_poly = poly_list[0]
+            for i in range(1, len(poly_list)):
+                if shapely.intersects(merge_poly, poly_list[i]):
+                    merge_poly = shapely.union(merge_poly, poly_list[i])
+                else:
+                    buffer_dist = poly_list[i].distance(merge_poly) + 0.1
+                    buffer_poly = poly_list[i].buffer(buffer_dist)
+                    merge_poly = shapely.union(merge_poly, buffer_poly)
+            corridor_polygon = merge_poly
+    else:
+        corridor_polygon = None
+
+    # create GeoDataFrame for centerline
+    corridor_poly_gpd = gpd.GeoDataFrame.copy(line_gpd)
+    corridor_poly_gpd.geometry = [corridor_polygon]
+
+    return corridor_poly_gpd
+
+
+def process_single_centerline(row_and_path):
+    """
+
+    Parameters
+    ----------
+    row_and_path:
+        list of row (polygon and props) and least cost path
+        first is geopandas row, second is input line, (least cost path)
+
+    Returns
+    -------
+
+    """
+    row = row_and_path[0]
+    lc_path = row_and_path[1]
+
+    poly = row.geometry.iloc[0]
+    centerline, status = find_centerline(poly, lc_path)
+    row['centerline'] = centerline
+
+    return row
+
+
+def find_centerlines(poly_gpd, line_seg, processes):
+    centerline = None
+    centerline_gpd = []
+    rows_and_paths = []
+
+    try:
+        for i in poly_gpd.index:
+            row = poly_gpd.loc[[i]]
+            poly = row.geometry.iloc[0]
+            if 'OLnSEG' in line_seg.columns:
+                line_id, Seg_id = row['OLnFID'].iloc[0], row['OLnSEG'].iloc[0]
+                lc_path = line_seg.loc[(line_seg.OLnFID == line_id) & (line_seg.OLnSEG == Seg_id)]['geometry'].iloc[0]
+            else:
+                line_id = row['OLnFID'].iloc[0]
+                lc_path = line_seg.loc[(line_seg.OLnFID == line_id)]['geometry'].iloc[0]
+
+            rows_and_paths.append((row, lc_path))
+    except Exception as e:
+        print(e)
+
+    total_steps = len(rows_and_paths)
+    step = 0
+
+    # if PARALLEL_MODE == ParallelMode.MULTIPROCESSING:
+    #     with Pool(processes=processes) as pool:
+    #         # execute tasks in order, process results out of order
+    #         for result in pool.imap_unordered(process_single_centerline, rows_and_paths):
+    #             centerline_gpd.append(result)
+    #             step += 1
+    #             print(' "PROGRESS_LABEL Centerline {} of {}" '.format(step, total_steps), flush=True)
+    #             print(' %{} '.format(step / total_steps * 100))
+    #             print('Centerline No. {} done'.format(step))
+    # elif PARALLEL_MODE == ParallelMode.SEQUENTIAL:
+    #     for item in rows_and_paths:
+    #         row_with_centerline = process_single_centerline(item)
+    #         centerline_gpd.append(row_with_centerline)
+    #         step += 1
+    #         print(' "PROGRESS_LABEL Centerline {} of {}" '.format(step, total_steps), flush=True)
+    #         print(' %{} '.format(step / total_steps * 100))
+    #         print('Centerline No. {} done'.format(step))
+    centerline_gpd = execute_multiprocessing(process_single_centerline, rows_and_paths,
+                                             'find_centerlines', processes, 1)
+    return pd.concat(centerline_gpd)
+
+
+def regenerate_centerline(poly, input_line):
+    """
+    Regenerates centerline when initial
+    ----------
+    poly : line is not valid
+    Parameters
+    input_line : shapely LineString
+        This can be input seed line or least cost path. Only two end points will be used
+
+    Returns
+    -------
+
+    """
+    line_1 = substring(input_line, start_dist=0.0, end_dist=input_line.length / 2)
+    line_2 = substring(input_line, start_dist=input_line.length / 2, end_dist=input_line.length)
+
+    pts = shapely.force_2d([Point(list(input_line.coords)[0]),
+                            Point(list(line_1.coords)[-1]),
+                            Point(list(input_line.coords)[-1])])
+    perp = generate_perpendicular_line_precise(pts)
+
+    # MultiPolygon is rare, but need to be dealt with
+    # remove polygon of area less than CL_CLEANUP_POLYGON_BY_AREA
+    poly = poly.buffer(CL_POLYGON_BUFFER)
+    if type(poly) is MultiPolygon:
+        poly_geoms = list(poly.geoms)
+        poly_valid = [True] * len(poly_geoms)
+        for i, item in enumerate(poly_geoms):
+            if item.area < CL_CLEANUP_POLYGON_BY_AREA:
+                poly_valid[i] = False
+
+        poly_geoms = list(compress(poly_geoms, poly_valid))
+        if len(poly_geoms) != 1:  # still multi polygon
+            print('regenerate_centerline: Multi or none polygon found, pass.')
+
+        poly = Polygon(poly_geoms[0])
+
+    poly_exterior = Polygon(poly.buffer(CL_POLYGON_BUFFER).exterior)
+    poly_split = split(poly_exterior, perp)
+
+    if len(poly_split.geoms) < 2:
+        print('regenerate_centerline: polygon split failed, pass.')
+        return None
+
+    poly_1 = poly_split.geoms[0]
+    poly_2 = poly_split.geoms[1]
+
+    # find polygon and line pairs
+    pair_line_1 = line_1
+    pair_line_2 = line_2
+    if not poly_1.intersects(line_1):
+        pair_line_1 = line_2
+        pair_line_2 = line_1
+    elif poly_1.intersection(line_1).length < line_1.length / 3:
+        pair_line_1 = line_2
+        pair_line_2 = line_1
+
+    center_line_1 = find_centerline(poly_1, pair_line_1)
+    center_line_2 = find_centerline(poly_2, pair_line_2)
+
+    center_line_1 = center_line_1[0]
+    center_line_2 = center_line_2[0]
+
+    if not center_line_1 or not center_line_2:
+        print('Regenerate line: centerline is None')
+        return None
+
+    try:
+        if center_line_1.is_empty or center_line_2.is_empty:
+            print('Regenerate line: centerline is empty')
+            return None
+    except Exception as e:
+        print(e)
+
+    print(f'Centerline is regenerated.')
+    return linemerge(MultiLineString([center_line_1, center_line_2]))
+

beratools-0.2.0/beratools/core/constants.py

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+import numpy as np
+from enum import Flag, Enum, IntEnum, unique
+
+
+NADDatum = ['NAD83 Canadian Spatial Reference System', 'North American Datum 1983']
+
+BT_DEBUGGING = False
+BT_SHOW_ADVANCED_OPTIONS = False
+HAS_COST_RASTER = False
+
+BT_UID = 'BT_UID'
+
+BT_EPSILON = np.finfo(float).eps
+BT_NODATA_COST = np.inf
+BT_NODATA = -9999
+BT_MAXIMUM_CPU_CORES = 60  # multiprocessing has limit of 64, consider pathos
+BT_BUFFER_RATIO = 0.0  # overlapping ratio of raster when clipping lines
+BT_LABEL_MIN_WIDTH = 130
+
+GROUPING_SEGMENT = True
+LP_SEGMENT_LENGTH = 500
+
+FP_CORRIDOR_THRESHOLD = 2.5
+FP_SEGMENTIZE_LENGTH = 2.0
+FP_FIXED_WIDTH_DEFAULT = 5.0
+FP_PERP_LINE_OFFSET = 30.0
+
+# centerline
+CL_USE_SKIMAGE_GRAPH = False
+CL_DELETE_HOLES = True
+CL_SIMPLIFY_POLYGON = True
+
+CL_BUFFER_CLIP = 10.0
+CL_BUFFER_CENTROID = 3.0
+CL_SNAP_TOLERANCE = 15.0
+CL_SEGMENTIZE_LENGTH = 1.0
+CL_SIMPLIFY_LENGTH = 0.5
+CL_SMOOTH_SIGMA = 0.8
+CL_CLEANUP_POLYGON_BY_AREA = 1.0
+CL_POLYGON_BUFFER = 1e-6
+
+
+class FootprintParams(float, Enum):
+    FP_CORRIDOR_THRESHOLD = 2.5
+    FP_SEGMENTIZE_LENGTH = 2.0
+    FP_FIXED_WIDTH_DEFAULT = 5.0
+    FP_PERP_LINE_OFFSET = 30.0
+
+
+class CenterlineParams(float, Enum):
+    BUFFER_CLIP = 5.0
+    BUFFER_CENTROID = 3.0
+    SNAP_TOLERANCE = 15.0
+    SEGMENTIZE_LENGTH = 1.0
+    SIMPLIFY_LENGTH = 0.5
+    SMOOTH_SIGMA = 0.8
+    CLEANUP_POLYGON_BY_AREA = 1.0
+    POLYGON_BUFFER = 1e-6
+
+
+class CenterlineFlags(Flag):
+    USE_SKIMAGE_GRAPH = False
+    DELETE_HOLES = True
+    SIMPLIFY_POLYGON = True
+
+
+@unique
+class CenterlineStatus(IntEnum):
+    SUCCESS = 1
+    FAILED = 2
+    REGENERATE_SUCCESS = 3
+    REGENERATE_FAILED = 4
+
+
+@unique
+class ParallelMode(IntEnum):
+    SEQUENTIAL = 1
+    MULTIPROCESSING = 2
+    CONCURRENT = 3
+    DASK = 4
+    # RAY = 5
+
+
+PARALLEL_MODE = ParallelMode.MULTIPROCESSING
+
+