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

beratools/tools/rpy_normalized_lidar_by.py

@@ -1,56 +1,56 @@
-import os
-import time
-
-from beratools.tools.common import *
-from beratools.tools.r_interface import *
-
-def normalized_lidar(callback, in_las_folder, out_folder, style, 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.
-    if style == 'tin':
-        r_normalized_lidar = robjects.globalenv['normalized_lidar_knnidw']
-    elif style == 'knnidw':
-        r_normalized_lidar = robjects.globalenv['normalized_lidar_tin']
-    else:
-        r_normalized_lidar = robjects.globalenv['normalized_lidar_kriging']
-
-    # Invoking the R function
-    r_normalized_lidar(in_las_folder, out_folder, rprocesses)
-
-
-if __name__ == '__main__':
-    start_time = time.time()
-    print('Normalize Lidar data processing\n @ {}'
-          .format(time.strftime("%a, %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()
-
-    if in_args.input["style"] in ["tin", "knnidw", "kriging"]:
-        style = in_args.input["style"]
-    else:
-        print("Warning! invalid alogrithm, default algorthim will be used.")
-        in_args.input["style"] = "tin"
-
-    in_las_folder = in_args.input["in_las_folder"]
-    out_folder = in_args.input["out_folder"]
-    check_las_files_existence(in_las_folder)
-
-    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")
-
-    normalized_lidar(print, **in_args.input, processes=int(in_args.processes), verbose=in_verbose)
-
-    print('Normalize Lidar data processing is done in {} seconds)'
-          .format(round(time.time() - start_time, 5)))
+import os
+import time
+
+from beratools.tools.common import *
+from beratools.tools.r_interface import *
+
+def normalized_lidar(callback, in_las_folder, out_folder, style, 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.
+    if style == 'tin':
+        r_normalized_lidar = robjects.globalenv['normalized_lidar_knnidw']
+    elif style == 'knnidw':
+        r_normalized_lidar = robjects.globalenv['normalized_lidar_tin']
+    else:
+        r_normalized_lidar = robjects.globalenv['normalized_lidar_kriging']
+
+    # Invoking the R function
+    r_normalized_lidar(in_las_folder, out_folder, rprocesses)
+
+
+if __name__ == '__main__':
+    start_time = time.time()
+    print('Normalize Lidar data processing\n @ {}'
+          .format(time.strftime("%a, %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()
+
+    if in_args.input["style"] in ["tin", "knnidw", "kriging"]:
+        style = in_args.input["style"]
+    else:
+        print("Warning! invalid alogrithm, default algorthim will be used.")
+        in_args.input["style"] = "tin"
+
+    in_las_folder = in_args.input["in_las_folder"]
+    out_folder = in_args.input["out_folder"]
+    check_las_files_existence(in_las_folder)
+
+    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")
+
+    normalized_lidar(print, **in_args.input, processes=int(in_args.processes), verbose=in_verbose)
+
+    print('Normalize Lidar data processing is done in {} seconds)'
+          .format(round(time.time() - start_time, 5)))

beratools/tools/rpy_percent_above_dbh.py

@@ -1,80 +1,80 @@
-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)))
+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 +1,88 @@
-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)))
+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 +1,94 @@
-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)))
+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)))