BERATools 0.2.0__py3-none-any.whl

beratools/tools/zonal_threshold.py

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+from multiprocessing.pool import Pool
+import geopandas
+import json
+import argparse
+import time
+import pandas
+import numpy
+import shapely
+
+from beratools.tools.common import *
+
+corridor_th_field = 'CorridorTh'
+
+
+class OperationCancelledException(Exception):
+    pass
+
+
+def zonal_threshold(callback, in_line, in_canopy_raster, canopy_search_r, min_canopy_th, max_canopy_th,
+                    out_line, processes, verbose):
+    line_seg = geopandas.GeoDataFrame.from_file(in_line)
+    # check coordinate systems between line and raster features
+    with rasterio.open(in_canopy_raster) as in_canopy:
+        if line_seg.crs.to_epsg() != in_canopy.crs.to_epsg():
+            print("Line and raster spatial references are not same, please check.")
+            exit()
+
+    del in_canopy
+
+    if not corridor_th_field in line_seg.columns.array:
+        print("Cannot find {} column in input data.\n '{}' column will be create".format(corridor_th_field,
+                                                                                         corridor_th_field))
+        line_seg[corridor_th_field] = numpy.nan
+
+    # copy original line input to another Geodataframe
+    line_buffer = geopandas.GeoDataFrame.copy((line_seg))
+    # buffer the input lines
+    buffer = shapely.buffer(line_buffer['geometry'], float(canopy_search_r), cap_style=1, quad_segs=16)
+    # replace line geometry by polygon geometry
+    line_buffer['geometry'] = buffer
+    # create a New column for Zonal Mean
+    line_buffer['ZonMean'] = numpy.nan
+    print('%{}'.format(10))
+    print("Line preparing... ")
+    #
+    line_arg = []
+
+    for row in line_buffer.index:
+        list_items = [row]  # 0
+        list_items.append(line_buffer.iloc[[row]])  # 1
+        # list_items.append(line_buffer) #1
+        list_items.append(in_canopy_raster)  # 2
+        list_items.append(canopy_search_r)  # 3
+        list_items.append(min_canopy_th)  # 4
+        list_items.append(max_canopy_th)  # 5
+        list_items.append(corridor_th_field)  # 6
+
+        line_arg.append(list_items)
+    print('%{}'.format(60))
+    print("Calculating zonal statistic ...")
+    features = []
+    # for row in range(0,len(line_arg)):
+    #     features.append(zonal_prepare(line_arg[row]))
+    features = execute_multiprocessing(line_arg)
+    print("Merging results ...")
+    results = geopandas.GeoDataFrame(pandas.concat(features))
+    results['geometry'] = line_seg['geometry']
+
+    print("Saving output ...")
+    print('%{}'.format(100))
+    # Debug save
+    geopandas.GeoDataFrame.to_file(results, out_line)
+    callback('Zonal Threshold tool done.')
+
+
+# task executed in a worker process
+def zonal_prepare(task_data):
+    # report a message
+    row_index = task_data[0]
+    df = task_data[1]
+    in_canopy_raster = task_data[2]
+    corridor_th_field = task_data[6]
+    MinValue = float(task_data[4])
+    MaxValue = float(task_data[5])
+
+    line_buffer = df['geometry']
+
+    with rasterio.open(in_canopy_raster) as in_canopy:
+        # clipped the chm base on polygon of line buffer or footprint
+        clipped_canopy, out_transform = rasterio.mask.mask(in_canopy, line_buffer, crop=True,
+                                                           nodata=BT_NODATA, filled=True)
+        clipped_canopy = numpy.squeeze(clipped_canopy, axis=0)
+
+        # mask out all -9999 value cells
+        zonal_canopy = numpy.ma.masked_where(clipped_canopy == BT_NODATA, clipped_canopy)
+
+        # Calculate the zonal mean and threshold
+        zonal_mean = numpy.ma.mean(zonal_canopy)
+        threshold = MinValue + (zonal_mean * zonal_mean) * (MaxValue - MinValue)
+        # return the generated value
+        df.loc[df.index == row_index, 'ZonMean'] = zonal_mean
+        df.loc[df.index == row_index, corridor_th_field] = threshold
+
+    return df
+
+
+# protect the entry point
+def execute_multiprocessing(line_args):
+    # create and configure the process pool
+    # data = [[random() for n in range(100)] for i in range(300)]
+    try:
+        total_steps = len(line_args)
+        features = []
+        with Pool(processes=int(args.processes)) as pool:
+            step = 0
+            # execute tasks in order, process results out of order
+            for result in pool.imap_unordered(zonal_prepare, line_args):
+                if BT_DEBUGGING:
+                    print('Got result: {}'.format(result), flush=True)
+                features.append(result)
+                step += 1
+                print('%{}'.format(step / total_steps * 100))
+        return features
+    except OperationCancelledException:
+        print("Operation cancelled")
+
+
+if __name__ == '__main__':
+    start_time = time.time()
+    print('Starting zonal threshold calculation processing @ {}'.format(
+        time.strftime("%d %b %Y %H:%M:%S", time.localtime())))
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-i', '--input', type=json.loads)
+    parser.add_argument('-p', '--processes')
+    parser.add_argument('-v', '--verbose')
+    args = parser.parse_args()
+
+    verbose = True if args.verbose == 'True' else False
+    zonal_threshold(print, **args.input, processes=int(args.processes), verbose=verbose)
+
+    print('%{}'.format(100))
+    print('Finishing zonal threshold calculation processing @ {} (or in {} second)'.format(
+        time.strftime("%d %b %Y %H:%M:%S", time.localtime()), round(time.time() - start_time, 5)))

beratools-0.2.0.dist-info/METADATA

@@ -0,0 +1,63 @@
+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.
+

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beratools-0.2.0.dist-info/WHEEL

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+Tag: py3-none-any

beratools-0.2.0.dist-info/entry_points.txt

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beratools-0.2.0.dist-info/licenses/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.
+