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

beratools/tools/lapis_all.py

@@ -1,103 +0,0 @@
-
-from random import random
-import time
-from multiprocessing.pool import Pool
-from numpy import mean
-from beratools.tools.common import *
-import json
-
-
-class OperationCancelledException(Exception):
-    pass
-
-
-def lapis_all(args, callback=print, processes=None, verbose=None):
-    lapis_path = '../third_party/Lapis_0_8/Lapis.exe'
-    lapis_path = Path(__file__).parent.joinpath(lapis_path).resolve()
-    ini_file = Path(__file__).parents[2].joinpath(r'.\.data\lapis.ini').resolve().as_posix()
-
-    arg_parsed = json.loads(args)
-    in_dtm = arg_parsed['in_dtm']
-    in_las = arg_parsed['in_las']
-    out_dir = arg_parsed['out_dir']
-
-    f = open(ini_file, 'w')
-    f.write('#Data options\n')
-    f.write('dem=' + in_dtm + '\n')
-    f.write('dem-units = unspecified' + '\n')
-    f.write('dem-algo = raster' + '\n')
-    f.write('las=' + in_las + '\n')
-    f.write('las-units=unspecified' + '\n')
-    f.write('output=' + out_dir + '\n')
-
-    f.write('\n # Computer-specific options\n')
-    f.write('thread=50' + '\n')
-    f.write('bench=' + '\n')
-
-    f.write('\n # Processing options\n')
-    f.write('xres=0.15' + '\n')
-    f.write('yres=0.15' + '\n')
-    f.write('xorigin=0' + '\n')
-    f.write('yorigin=0' + '\n')
-    f.write('csm-cellsize=0.15' + '\n')
-    f.write('footprint=0.1' + '\n')
-    f.write('smooth=1' + '\n')
-    f.write('minht=-8' + '\n')
-    f.write('maxht=100' + '\n')
-    f.write('class=~7, 9, 18' + '\n')
-    f.write('max-scan-angle=32' + '\n')
-    f.write('user-units=meters' + '\n')
-    f.write('canopy=3' + '\n')
-    f.write('strata=0.5, 1, 2, 4, 8, 16, 32, 48, 64,' + '\n')
-    f.write('min-tao-dist=1' + '\n')
-    f.write('id-algo=highpoint' + '\n')
-    f.write('seg-algo=watershed' + '\n')
-    f.write('topo-scale=500, 1000, 2000,' + '\n')
-    f.write('fine-int=' + '\n')
-
-    args = lapis_path.as_posix() + ' --ini-file' + ' ' + ini_file
-
-    callback('Lapis parameters returned.')
-    return args
-
-
-# task executed in a worker process
-def worker(task_data):
-    # report a message
-    value = mean(task_data)
-    print(f'Task {len(task_data)} with {value} executed', flush=True)
-
-    # block for a moment
-    time.sleep(value * 10)
-
-    # return the generated value
-    return value
-
-
-# protect the entry point
-def execute_multiprocessing():
-    # create and configure the process pool
-    data = [[random() for n in range(100)] for i in range(300)]
-    try:
-        total_steps = 300
-        with Pool() as pool:
-            step = 0
-            # execute tasks in order, process results out of order
-            for result in pool.imap_unordered(worker, data):
-                print(f'Got result: {result}', flush=True)
-                step += 1
-                print(step)
-                print('%{}'.format(step/total_steps*100))
-
-    except OperationCancelledException:
-        print("Operation cancelled")
-
-
-if __name__ == '__main__':
-    # in_args, in_verbose = check_arguments()
-    # start_time = time.time()
-    # lapis_all(print, **in_args.input, processes=int(in_args.processes), verbose=in_verbose)
-    #
-    # print('Elapsed time: {}'.format(time.time() - start_time))
-
-    pass

beratools/tools/least_cost_path_from_chm.py

@@ -1,152 +0,0 @@
-import time
-from xrspatial import convolution
-
-from beratools.tools.common import *
-from beratools.core.algo_centerline import *
-
-
-def LCP_centerline(callback, in_line, in_chm, line_radius,
-                   proc_segments, out_line, processes, verbose):
-    if not compare_crs(vector_crs(in_line), raster_crs(in_chm)):
-        print("Line and CHM have different spatial references, please check.")
-        return
-
-    # Read input line features
-    layer_crs = None
-    schema = None
-    input_lines = []
-
-    df, found = chk_df_multipart(gpd.GeoDataFrame.from_file(in_line), 'MultiLineString')
-    if found:
-        df.to_file(in_line)
-    else:
-        del df, found
-
-    with fiona.open(in_line) as open_line_file:
-        layer_crs = open_line_file.crs
-        schema = open_line_file.meta['schema']
-        for line in open_line_file:
-            if line.geometry:
-                if line.geometry['type'] != 'MultiLineString':
-                    input_lines.append([line.geometry, line.properties])
-                else:
-                    print('MultiLineString found.')
-                    geoms = shape(line['geometry']).geoms
-                    for item in geoms:
-                        line_part = fiona.Geometry.from_dict(item)
-                        if line_part:
-                            input_lines.append([line_part, line.properties])
-            else:
-                print(f'Line {line.id} has empty geometry.')
-
-    if proc_segments:
-        # split line segments at vertices
-        input_lines_temp = []
-        for line in input_lines:
-            line_seg = line[0]
-            line_prop = line[1]
-            line_segs = segments(line_seg.coordinates)
-            line_feats = [(line, line_prop) for line in line_segs]
-            if line_segs:
-                input_lines_temp.extend(line_feats)
-
-        input_lines = input_lines_temp
-
-    # Process lines
-    all_lines = []
-    i = 0
-    for line in input_lines:
-        all_lines.append((line, line_radius, in_chm, i))
-        i += 1
-
-    print('{} lines to be processed.'.format(len(all_lines)))
-
-    feat_geoms = []
-    feat_props = []
-    center_line_geoms = []
-    corridor_poly_list = []
-    result = execute_multiprocessing(process_single_line, all_lines, 'Centerline',
-                                     processes, 1, verbose=verbose)
-
-    for item in result:
-        geom = item[0]
-        prop = item[1]
-        center_line = item[2]
-        corridor_poly = item[3]
-
-        if geom and prop:
-            feat_geoms.append(geom)
-            feat_props.append(prop)
-            center_line_geoms.append(center_line)
-            corridor_poly_list.append(corridor_poly)
-
-    out_least_cost_path = Path(out_line)
-    out_least_cost_path = out_least_cost_path.with_stem(out_least_cost_path.stem + '_least_cost_path')
-    schema['properties']['status'] = 'int'
-
-    save_features_to_shapefile(out_least_cost_path.as_posix(), layer_crs, feat_geoms, feat_props, schema)
-
-
-def process_single_line(line_args):
-    line = line_args[0][0]
-    prop = line_args[0][1]
-    line_radius = line_args[1]
-    in_chm_raster = line_args[2]
-    line_id = line_args[3]
-    seed_line = shape(line)  # LineString
-    line_radius = float(line_radius)
-
-    chm_clip, out_meta = clip_raster(in_chm_raster, seed_line, line_radius)
-    in_chm = np.squeeze(chm_clip, axis=0)
-    cell_x, cell_y = out_meta['transform'][0], -out_meta['transform'][4]
-    kernel = convolution.circle_kernel(cell_x, cell_y, 2.5)
-    dyn_canopy_ndarray = dyn_np_cc_map(in_chm, FP_CORRIDOR_THRESHOLD, BT_NODATA)
-    cc_std, cc_mean = dyn_fs_raster_stdmean(dyn_canopy_ndarray, kernel, BT_NODATA)
-    cc_smooth = dyn_smooth_cost(dyn_canopy_ndarray, 2.5, [cell_x, cell_y])
-    avoidance = max(min(float(0.4), 1), 0)
-    cost_clip = dyn_np_cost_raster(dyn_canopy_ndarray, cc_mean, cc_std,
-                                   cc_smooth, 0.4, 1.5)
-
-    # if CL_USE_SKIMAGE_GRAPH:
-    # skimage shortest path (Cost Array elements with infinite or negative costs will simply be ignored.)
-    negative_cost_clip = np.where(np.isnan(cost_clip), -9999, cost_clip)
-    lc_path = LCP_skimage_mcp_connect(negative_cost_clip, out_meta, seed_line)
-
-    if lc_path:
-        lc_path_coords = lc_path.coords
-    else:
-        lc_path_coords = []
-
-    # search for centerline
-    if len(lc_path_coords) < 2:
-        print('No least cost path detected, use input line.')
-        prop['status'] = CenterlineStatus.FAILED.value
-        return seed_line, prop, seed_line, None
-
-    # get corridor raster
-    out_transform = out_meta['transform']
-    transformer = rasterio.transform.AffineTransformer(out_transform)
-    cell_size = (out_transform[0], -out_transform[4])
-
-    x1, y1 = lc_path_coords[0]
-    x2, y2 = lc_path_coords[-1]
-    source = [transformer.rowcol(x1, y1)]
-    destination = [transformer.rowcol(x2, y2)]
-    corridor_thresh_cl = corridor_raster(negative_cost_clip, out_meta, source, destination,
-                                         cell_size, FP_CORRIDOR_THRESHOLD)
-
-    # find contiguous corridor polygon and extract centerline
-    df = gpd.GeoDataFrame(geometry=[seed_line], crs=out_meta['crs'])
-    corridor_poly_gpd = find_corridor_polygon(corridor_thresh_cl, out_transform, df)
-    center_line, status = find_centerline(corridor_poly_gpd.geometry.iloc[0], lc_path)
-    prop['status'] = status.value
-
-    print(" Searching centerline: line {} ".format(line_id), flush=True)
-    return lc_path, prop, center_line, corridor_poly_gpd
-
-
-if __name__ == '__main__':
-    in_args, in_verbose = check_arguments()
-    start_time = time.time()
-    LCP_centerline(print, **in_args.input, processes=int(in_args.processes), verbose=in_verbose)
-    print('Elapsed time: {}'.format(time.time() - start_time))

beratools-0.2.0.dist-info/METADATA

@@ -1,63 +0,0 @@
-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.dist-info/RECORD

@@ -1,142 +0,0 @@
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