BERATools 0.2.3__py3-none-any.whl → 0.2.5__py3-none-any.whl

beratools/tools/rpy_percent_above_dbh.py

@@ -1,80 +0,0 @@
-import os
-import time
-
-from beratools.tools.common import *
-from beratools.tools.r_interface import *
-
-def percentage_aboveDBH(callback, in_las_folder, is_normalized, out_folder, DBH, cell_size, processes, verbose):
-    rprocesses = r_processes(processes)
-
-    # assign R script file to local variable
-    Beratools_R_script = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'Beratools_r_script.r')
-    # Defining the R script and loading the instance in Python
-    r['source'](Beratools_R_script)
-    # Loading the function defined in R script.
-    r_percentage_aboveDBH = robjects.globalenv['percentage_aboveDBH']
-    # Invoking the R function
-    r_percentage_aboveDBH(in_las_folder, is_normalized, out_folder, DBH, cell_size, rprocesses)
-
-
-if __name__ == '__main__':
-    start_time = time.time()
-    print('Finding percentage returns above DBH height process\n @ {}'
-          .format(time.strftime("%d %b %Y %H:%M:%S", time.localtime())))
-
-    packages = ['lidR', 'future', 'terra']
-    check_r_packages_installation(packages)
-
-    print("Checking input parameters ...")
-    in_args, in_verbose = check_arguments()
-    in_las_folder = in_args.input["in_las_folder"]
-
-    try:
-        DBH = float(in_args.input["DBH"])
-        if DBH < 0:
-            raise ValueError
-        else:
-            in_args.input["DBH"] = DBH
-    except ValueError:
-        print("Invalid input of DBH, default value is used")
-        in_args.input["DBH"] = 1.3
-
-    try:
-        is_normalized = bool(in_args.input["is_normalized"])
-
-    except ValueError:
-        print("Invalid input of checking normalized data box, normalize data will be carried")
-        in_args.input["is_normalized"] = False
-
-    try:
-        cell_size = float(in_args.input["cell_size"])
-        in_args.input["cell_size"] = cell_size
-    except ValueError:
-        print("Invalid input of cell size, default value is used")
-        in_args.input["cell_size"] = 5.0
-
-    out_folder = in_args.input["out_folder"]
-
-    if not os.path.exists(in_las_folder):
-        print("Error! Cannot locate Las folder, please check.")
-        exit()
-    else:
-        found = False
-        for files in os.listdir(in_las_folder):
-            if files.endswith(".las") or files.endswith(".laz"):
-                found = True
-                break
-        if not found:
-            print("Error! Cannot locate input LAS file(s), please check!")
-            exit()
-
-    if not os.path.exists(out_folder):
-        print("Warning! Cannot locate output folder, It will be created.")
-        os.makedirs(out_folder)
-
-    print("Checking input parameters ... Done")
-
-    percentage_aboveDBH(print, **in_args.input, processes=int(in_args.processes), verbose=in_verbose)
-
-    print('Finding percentage returns above DBH height process is done in {} seconds)'
-          .format(round(time.time() - start_time, 5)))

beratools/tools/rpy_points2trees.py

@@ -1,88 +0,0 @@
-import os
-import time
-
-from beratools.tools.common import *
-from beratools.tools.r_interface import *
-
-def points2trees(callback, in_las_folder, is_normalized, hmin, cell_size, do_nCHM, out_folder, processes, verbose):
-    rprocesses = r_processes(processes)
-
-    # assign R script file to local variable
-    Beratools_R_script = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'Beratools_r_script.r')
-    # Defining the R script and loading the instance in Python
-    r['source'](Beratools_R_script)
-    # Loading the function defined in R script.
-    r_points2trees = robjects.globalenv['points2trees']
-    r_pd2cellsize = robjects.globalenv['pd2cellsize']
-    # Invoking the R function
-    if do_nCHM:
-        CHMcell_size = r_pd2cellsize(in_las_folder, rprocesses)
-        print("CHM raster output cell size is: {}m".format(CHMcell_size))
-        r_points2trees(in_las_folder, is_normalized, hmin, out_folder, rprocesses, CHMcell_size, cell_size)
-    else:
-        CHMcell_size = -999
-        r_points2trees(in_las_folder, is_normalized, hmin, out_folder, rprocesses, CHMcell_size, cell_size)
-
-
-if __name__ == '__main__':
-    start_time = time.time()
-    print('Starting tree detection from LAS processing\n @ {}'
-          .format(time.strftime("%d %b %Y %H:%M:%S", time.localtime())))
-
-    packages = ['lidR', 'rgrass', 'rlas', 'future', 'terra', 'sp']
-    check_r_packages_installation(packages)
-
-    print("Checking input parameters ...")
-    in_args, in_verbose = check_arguments()
-    in_las_folder = in_args.input["in_las_folder"]
-
-    try:
-        hmin = float(in_args.input["hmin"])
-        if hmin >= 20:
-            print("Invalid input of minimum height (<=20) of a tree, maximum is used")
-            in_args.input["hmin"] = 20.0
-        else:
-            in_args.input["hmin"] = hmin
-    except ValueError:
-        print("Invalid input of minimum height (<=20) of a tree, default is used")
-        in_args.input["hmin"] = 3.0
-
-    try:
-        is_normalized = bool(in_args.input["is_normalized"])
-
-    except ValueError:
-        print("Invalid input of checking normalized data box, normalize data will be carried")
-        in_args.input["is_normalized"] = False
-
-    try:
-        cell_size = float(in_args.input["cell_size"])
-        in_args.input["cell_size"] = cell_size
-    except ValueError:
-        print("Invalid input of minimum height of a tree, default is used")
-        in_args.input["cell_size"] = 5.0
-
-    out_folder = in_args.input["out_folder"]
-
-    if not os.path.exists(in_las_folder):
-        print("Error! Cannot locate Las folder, please check.")
-        exit()
-    else:
-        found = False
-        for files in os.listdir(in_las_folder):
-            if files.endswith(".las") or files.endswith(".laz"):
-                found = True
-                break
-        if not found:
-            print("Error! Cannot locate input LAS file(s), please check!")
-            exit()
-
-    if not os.path.exists(out_folder):
-        print("Warning! Cannot locate output folder, It will be created.")
-        os.makedirs(out_folder)
-
-    print("Checking input parameters ... Done")
-
-    points2trees(print, **in_args.input, processes=int(in_args.processes), verbose=in_verbose)
-
-    print('Tree detection from Lidar data processing is done in {} seconds)'
-          .format(round(time.time() - start_time, 5)))

beratools/tools/rpy_vegcoverage.py

@@ -1,94 +0,0 @@
-import os
-import time
-
-from beratools.tools.common import *
-from beratools.tools.r_interface import *
-
-def veg_cover_percentage(callback, in_las_folder, is_normalized, out_folder, hmin, hmax, cell_size, processes, verbose):
-    rprocesses = r_processes(processes)
-
-    # assign R script file to local variable
-    Beratools_R_script = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'Beratools_r_script.r')
-    # Defining the R script and loading the instance in Python
-    r['source'](Beratools_R_script)
-    # Loading the function defined in R script.
-    r_veg_metrics = robjects.globalenv['veg_cover_percentage']
-    # Invoking the R function
-    r_veg_metrics(in_las_folder, is_normalized, out_folder, hmin, hmax, cell_size, rprocesses)
-
-
-if __name__ == '__main__':
-    start_time = time.time()
-    print('Finding Vegetation Coverage from Lidar data process\n @ {}'
-          .format(time.strftime("%d %b %Y %H:%M:%S", time.localtime())))
-
-    packages = ['lidR', 'future', 'terra']
-    check_r_packages_installation(packages)
-
-    print("Checking input parameters ...")
-    in_args, in_verbose = check_arguments()
-    in_las_folder = in_args.input["in_las_folder"]
-
-    try:
-        hmin = float(in_args.input["hmin"])
-        if hmin < 0:
-            raise ValueError
-        else:
-            in_args.input["hmin"] = hmin
-    except ValueError:
-        print("Invalid input of minimum height of a tree, default value is used")
-        in_args.input["hmin"] = 3.0
-
-    try:
-        hmax = float(in_args.input["hmax"])
-        if hmax <= hmin:
-            raise ValueError
-        else:
-            in_args.input["hmax"] = hmax
-    except ValueError:
-        print("Invalid input of maximum height of a tree, default value is used")
-        if hmin < 10:
-            in_args.input["hmax"] = 10.0
-        else:
-            in_args.input["hmin"] = 3.0
-            in_args.input["hmax"] = 10.0
-
-    try:
-        is_normalized = bool(in_args.input["is_normalized"])
-
-    except ValueError:
-        print("Invalid input of checking normalized data box, normalize data will be carried")
-        in_args.input["is_normalized"] = False
-
-    try:
-        cell_size = float(in_args.input["cell_size"])
-        in_args.input["cell_size"] = cell_size
-    except ValueError:
-        print("Invalid input of cell size, default value is used")
-        in_args.input["cell_size"] = 5.0
-
-    out_folder = in_args.input["out_folder"]
-
-    if not os.path.exists(in_las_folder):
-        print("Error! Cannot locate Las folder, please check.")
-        exit()
-    else:
-        found = False
-        for files in os.listdir(in_las_folder):
-            if files.endswith(".las") or files.endswith(".laz"):
-                found = True
-                break
-        if not found:
-            print("Error! Cannot locate input LAS file(s), please check!")
-            exit()
-
-    if not os.path.exists(out_folder):
-        print("Warning! Cannot locate output folder, It will be created.")
-        os.makedirs(out_folder)
-
-    print("Checking input parameters ... Done")
-
-    veg_cover_percentage(print, **in_args.input, processes=int(in_args.processes), verbose=in_verbose)
-
-    print('Finding Vegetation Coverage from Lidar data process is done in {} seconds)'
-          .format(round(time.time() - start_time, 5)))

beratools/tools/tiler.py

@@ -1,48 +0,0 @@
-"""
-Copyright (C) 2025 Applied Geospatial Research Group.
-
-This script is licensed under the GNU General Public License v3.0.
-See <https://gnu.org/licenses/gpl-3.0> for full license details.
-
-Author: Richard Zeng
-
-Description:
-    This script is part of the BERA Tools.
-    Webpage: https://github.com/appliedgrg/beratools
-
-    The purpose of this script is to split input vector and raster data into
-    smaller tiles based on a specified tile size and buffer distance.
-"""
-
-import time
-
-import beratools.tools.common as bt_common
-import beratools.core.algo_tiler as bt_tiler
-
-def tiler(
-    in_line,
-    in_raster,
-    out_file,
-    n_clusters,
-    processes,
-    verbose,
-    tile_buffer=50,
-    in_layer=None,
-):
-    clustering = bt_tiler.DensityBasedClustering(
-        in_line=in_line,
-        in_raster=in_raster,
-        out_file=out_file,
-        n_clusters=int(n_clusters),
-        tile_buffer=tile_buffer,
-        layer=in_layer,
-    )
-
-    clustering.run()
-
-
-if __name__ == "__main__":
-    in_args, in_verbose = bt_common.check_arguments()
-    start_time = time.time()
-    tiler(**in_args.input, processes=int(in_args.processes), verbose=in_verbose)
-    print("Elapsed time: {}".format(time.time() - start_time))

beratools/tools/zonal_threshold.py

@@ -1,144 +0,0 @@
-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-0.2.3.dist-info/METADATA

@@ -1,108 +0,0 @@
-Metadata-Version: 2.4
-Name: BERATools
-Version: 0.2.3
-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 :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Requires-Python: >=3.10
-Requires-Dist: bera-centerlines
-Requires-Dist: gdal>=3.9.2
-Requires-Dist: geopandas
-Requires-Dist: pip
-Requires-Dist: psutil
-Requires-Dist: pyogrio>=0.9.0
-Requires-Dist: pyqt5
-Requires-Dist: pyqtlet2
-Requires-Dist: pytest
-Requires-Dist: pyyaml
-Requires-Dist: rioxarray
-Requires-Dist: scikit-image>=0.24.0
-Requires-Dist: tqdm
-Requires-Dist: xarray-spatial
-Description-Content-Type: text/markdown
-
-# BERA Tools
-<div align="center">
-BERA Tools is successor of [Forest Line Mapper](https://github.com/appliedgrg/flm). It is a toolset for enhanced delineation and attribution of linear disturbances in forests.
-
-[![GitHub Workflow Status (Build)](https://img.shields.io/github/actions/workflow/status/appliedgrg/bera-tools/python-tests.yml?branch=develop&style=for-the-badge)](https://github.com/appliedgrg/bera-tools/actions/workflows/python-tests.yml)
-[![Read the Docs](https://img.shields.io/readthedocs/bera-tools?style=for-the-badge&logo=readthedocs&logoColor=white)](https://bera-tools.readthedocs.io/en/latest/)
-<br>
-[![Conda Version](https://img.shields.io/conda/v/AppliedGRG/beratools?style=for-the-badge&logo=anaconda&color=green)](https://anaconda.org/AppliedGRG/beratools)
-[![Python - Version](https://img.shields.io/badge/PYTHON-3.9+-blue?style=for-the-badge&logo=python&logoColor=white)](https://www.python.org/downloads/release/python-390/)
-<br>
-[![License: MIT](https://img.shields.io/github/license/appliedgrg/bera-tools?style=for-the-badge&color=blue)](https://github.com/appliedgrg/bera-tools/blob/main/LICENSE)
-
-</div>
-<!--![Banner](docs/files/images/BERALogo.png)-->
-
-## [Quick Start](https://beratools.readthedocs.io/en/latest/installation.html)
-
-BERA Tools is built upon open-source Python libraries. Anaconda is used to manage runtime environments.
-
-Installation Steps:
-
-- Install Miniconda. Download Miniconda from [Miniconda](https://docs.anaconda.com/miniconda/) and install on your machine.
-- Launch **Anaconda Prompt**. Run the following command to create a new environment. **BERA Tools** will be installed in the new environment at the same time. Download the file [conda_environment.yml](https://github.com/RichardQZeng/BTools/blob/main/conda_environment.yml) first.
-
-   ```bash
-   $ conda env create -f conda_environment.yml
-   ```
-
-   Wait until the installation is done.
-- Activate the **bera** environment and launch BERA Tools:
-
-  ```bash
-  $ conda activate bera
-  $ beratools
-  ```
-
-
-## User Guide
-
-Check the online [User Guide](https://beratools.readthedocs.io/en/latest/) for more information.
-
-## Technical Documentation
-
-BERA Tools provides a series of tools for forest lines processing. Please refer to the technical documentation for programming APIs and algorithms details.
-
-Check the link for more information:  [Technical Documentation](https://beratools.readthedocs.io/en/latest/)
-
-## Credits
-
-This tool is part of the [**Boreal Ecosystem Recovery and Assessment (BERA)**](http://www.beraproject.org/) Project, and is being actively developed by the [**Applied Geospatial Research Group**](https://www.appliedgrg.ca/).
-
-![Logos](docs/files/images/BERALogo.png)
-*Copyright (C) 2025  Applied Geospatial Research Group*

beratools-0.2.3.dist-info/RECORD

@@ -1,74 +0,0 @@
-beratools/__init__.py,sha256=Mdv1nAvOXx6fFOvIS_3Qob8L_hjZxvsne1JXzaSm5Ao,90
-beratools/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-beratools/core/algo_centerline.py,sha256=mIHUsda68Pya7I51ZAb_xtF-5DYW1jebzh72r9tjSas,15582
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beratools-0.2.3.dist-info/entry_points.txt

@@ -1,2 +0,0 @@
-[console_scripts]
-BERATools = beratools.gui:gui_main

beratools-0.2.3.dist-info/licenses/LICENSE

@@ -1,22 +0,0 @@
-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
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-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
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-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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-SOFTWARE.
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