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

beratools/tools/r_generate_pd_focalraster.r

@@ -1,101 +0,0 @@
-#create a 'generate_pd' function
-generate_pd <- function(ctg, radius_fr_CHM, focal_radius, cell_size, cache_folder,
-                        cut_ht, PD_Ground_folder, PD_Total_folder, rprocesses) {
-    library(terra)
-    library(lidR)
-
-    plan(multisession, workers = rprocesses)
-    set_lidr_threads(rprocesses)
-
-    opts <- paste0("-drop_class 7")
-
-    print("Processing using R packages.")
-
-    folder <- paste0(cache_folder, "/nlidar/n_{*}")
-    opt_output_files(ctg) <- opt_output_files(ctg) <- folder
-    opt_laz_compression(ctg) <- FALSE
-    opt_filter(ctg) <- "-drop_class 7"
-    opt_chunk_alignment(ctg) <- c(0, 0)
-
-
-    #normalized LAS with pulse info
-    print("Indexing LAS Tiles ...")
-    lidR:::catalog_laxindex(ctg)
-    print("Normalize point cloud using K-nearest neighbour IDW ...")
-    normalize_height(ctg, algorithm = knnidw())
-
-    print("Generating point density (total focal sum) raster ...")
-
-    pd_total <- function(chunk, radius, cell_size)
-    {
-        las <- readLAS(chunk)
-        if (is.empty(las)) return(NULL)
-
-        las_1 <- filter_poi(readLAS(chunk), buffer == 0)
-        hull <- st_convex_hull(las_1)
-        # bbox <- ext(las_1)
-
-        # convert to SpatialPolygons
-        bbox <- vect(hull)
-
-        las <- filter_poi(las, Classification != 7L)
-        #las <- retrieve_pulses(las)
-        density_raster_total <- rasterize_density(las, res = cell_size, pkg = "terra")[[1]]
-
-        tfw <- focalMat(density_raster_total, radius, "circle")
-
-        tfw[tfw > 0] = 1
-        tfw[tfw == 0] = NA
-
-        Total_focal <- focal(density_raster_total, w = tfw, fun = "sum", na.rm = TRUE, na.policy = "omit", fillvalue = NA, expand = FALSE)
-        Total_focal <- crop(Total_focal, bbox)
-    }
-
-    opt <- list(need_output_file =TRUE, autocrop = TRUE)
-    opt_chunk_alignment(ctg) <- c(0,0)
-    ctg@output_options$drivers$SpatRaster$param$overwrite <- TRUE
-    opt_output_files(ctg) <- paste0(PD_Total_folder,"/{*}_PD_Tfocalsum")
-    opt_stop_early(ctg) <- FALSE
-    catalog_apply(ctg, pd_total, radius = focal_radius, cell_size = cell_size, .options = opt)
-
-    #load normalized LAS for ground point density
-    ht <- paste0("-drop_class 7 -drop_z_above ", cut_ht)
-    ctg2 <- readLAScatalog(paste0(cache_folder, "/nlidar"), filter = ht)
-    lidR:::catalog_laxindex(ctg2)
-
-
-    print("Generating point density (ground focal sum) raster ...")
-
-    pd_ground <- function(chunk, radius, cell_size, cut_ht)
-    {
-        las <- readLAS(chunk)
-        if (is.empty(las)) return(NULL)
-
-        las_1 <- filter_poi(readLAS(chunk), buffer == 0)
-        hull <- st_convex_hull(las_1)
-
-        # convert to SpatialPolygons
-        bbox <- vect(hull)
-        # bbox <- ext(las_1)
-
-        #las <- retrieve_pulses(las)
-        density_raster_ground <- rasterize_density(las, res = cell_size, pkg = "terra")[[1]]
-
-
-        gfw <- focalMat(density_raster_ground, radius, "circle")
-        gfw[gfw > 0] = 1
-        gfw[gfw == 0] = NA
-
-        Ground_focal <- focal(density_raster_ground, w = gfw, fun = "sum", na.policy = "omit", na.rm = TRUE, fillvalue = NA, expand = FALSE)
-        ground_focal <- crop(Ground_focal, bbox)
-
-    }
-    opt <- list(need_output_file =TRUE, autocrop = TRUE)
-    opt_chunk_alignment(ctg2) <- c(0,0)
-    ctg2@output_options$drivers$SpatRaster$param$overwrite <- TRUE
-    opt_output_files(ctg2) <- paste0(PD_Ground_folder,"/{*}_PD_Gfocalsum")
-    opt_stop_early(ctg2) <- FALSE
-    catalog_apply(ctg2, pd_ground,radius=focal_radius,cell_size=cell_size,cut_ht=cut_ht,.options=opt)
-    # reset R mutilsession back to default
-    plan("default")
-}

beratools/tools/r_interface.py

@@ -1,80 +0,0 @@
-import os
-import psutil
-
-
-# def check_r_env():
-try:  # integrated R env
-    # check R language within env
-    current_env_path = os.environ['CONDA_PREFIX']
-    # if os.path.isdir(current_env_path):
-    os.environ['R_HOME'] = os.path.join(current_env_path, r"Lib\R")
-    os.environ['R_USER'] = os.path.expanduser('~')
-    os.environ['R_LIBS_USER'] = os.path.join(current_env_path, r"Lib\R\library")
-
-except FileNotFoundError:
-    print("Warning: Please install R for this process!!")
-    exit()
-
-import rpy2.robjects as robjects
-from rpy2.robjects.packages import importr, data
-from rpy2.robjects.vectors import StrVector
-
-r = robjects.r
-
-def r_processes(processes):
-    stats = psutil.virtual_memory()  # returns a named tuple
-    available = getattr(stats, 'available') / 1024000000
-    rprocesses = processes
-
-    if 2 < processes <= 8:
-        if available <= 50:
-            rprocesses = 2
-        elif 50 < available <= 150:
-            rprocesses = 4
-        elif 150 < available <= 250:
-            rprocesses = 8
-    else:
-        rprocesses = 8
-
-    return rprocesses
-
-
-def check_las_files_existence(folder):
-    if not os.path.exists(folder):
-        print("Error! Cannot locate Las folder, please check.")
-        exit()
-    else:
-        found = False
-        for files in os.listdir(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()
-
-
-def check_r_packages_installation(packages):
-    utils = importr('utils')
-    base = importr('base')
-    utils.chooseCRANmirror(ind=12)  # select the 12th mirror in the list: Canada
-    print("Checking R packages....")
-
-    cran_names_to_install = [x for x in packages if not robjects.packages.isinstalled(x)]
-    need_fasterRaster = False
-    if len(cran_names_to_install) > 0:
-        if not 'fasterRaster' in cran_names_to_install:
-            utils.install_packages(StrVector(cran_names_to_install))
-        else:
-            cran_names_to_install.remove('fasterRaster')
-            need_fasterRaster = True
-            utils.install_packages(StrVector(cran_names_to_install))
-        packages_found = True
-    else:
-        packages_found = True
-
-    if need_fasterRaster:
-        devtools=importr('devtools')
-        devtools.install_github("adamlilith/fasterRaster", dependencies=True)
-
-    print("Checking R packages....Done")

beratools/tools/r_point_density.r

@@ -1,9 +0,0 @@
-pd_routine <- function(chunk) {
-    las <- readLAS(chunk)
-
-    if (is.empty(las)) return(NULL)
-    las <- retrieve_pulses(las)
-    output <- density(las)[1]
-    # output is a list
-    return(list(output))
-}

beratools/tools/rpy_chm2trees.py

@@ -1,86 +0,0 @@
-import os
-import time
-from multiprocessing.pool import Pool
-
-from beratools.tools.common import *
-from beratools.tools.r_interface import *
-
-
-def chm2trees(callback, in_chm_folder, Min_ws, hmin, 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_chm2trees = robjects.globalenv['chm2trees']
-
-    args_list = []
-    for root, dirs, files in sorted(os.walk(in_chm_folder)):
-        for file in files:
-            if file.endswith(".tif"):
-                result = []
-                chm_file = os.path.join(root, file)
-                chm_file = chm_file.replace("\\", "/")
-                result.append(chm_file)
-                result.append(Min_ws)
-                result.append(hmin)
-                result.append(out_folder)
-                result.append(rprocesses)
-                args_list.append(result)
-                # Invoking the R function
-                r_chm2trees(chm_file, Min_ws, hmin, out_folder, rprocesses)
-
-    del root, dirs, files
-
-
-if __name__ == '__main__':
-    start_time = time.time()
-    print('Starting tree detection from CHM processing\n @ {}'
-          .format(time.strftime("%a, %d %b %Y %H:%M:%S", time.localtime())))
-
-    packages = ['lidR', 'rgrass', 'rlas', 'future', 'terra']
-    check_r_packages_installation(packages)
-
-    print("Checking input parameters....")
-    in_args, in_verbose = check_arguments()
-    in_chm_folder = in_args.input["in_chm_folder"]
-    try:
-        ws = float(in_args.input["Min_ws"])
-        in_args.input["Min_ws"] = ws
-    except ValueError:
-        print("Invalid input of circular diameter, default is used")
-        in_args.input["Min_ws"] = 2.5
-    try:
-        hmin = float(in_args.input["hmin"])
-        in_args.input["hmin"] = hmin
-    except ValueError:
-        print("Invalid input of minimum height of a tree, default is used")
-        in_args.input["hmin"] = 3.0
-
-    out_folder = in_args.input["out_folder"]
-
-    if not os.path.exists(in_chm_folder):
-        print("Error! Cannot locate CHM raster folder, please check.")
-        exit()
-    else:
-        found = False
-        for files in os.listdir(in_chm_folder):
-            if files.endswith(".tif"):
-                found = True
-                break
-        if not found:
-            print("Error! Cannot locate input CHM raster 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")
-
-    chm2trees(print, **in_args.input, processes=int(in_args.processes), verbose=in_verbose)
-
-    print('Tree detection from CHM raster data processing is done in {} seconds)'
-          .format(round(time.time() - start_time, 5)))

beratools/tools/rpy_dsm_chm_by.py

@@ -1,81 +0,0 @@
-import os
-import time
-
-from beratools.tools.common import *
-from beratools.tools.r_interface import *
-
-def chm_by(callback, in_las_folder, is_normalized, out_folder, cell_size, 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_chm_by_algorithm = robjects.globalenv['chm_by_dsmtin']
-    else:
-        r_chm_by_algorithm = robjects.globalenv['chm_by_pitfree']
-
-    # Invoking the R function
-    r_chm_by_algorithm(in_las_folder, out_folder, cell_size, is_normalized, 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', 'future', 'terra']
-    check_r_packages_installation(packages)
-
-    print("Checking input parameters....")
-    in_args, in_verbose = check_arguments()
-    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["DSMcell_size"] = 1.0
-
-    try:
-        is_normalized = bool(in_args.input["is_normalized"])
-
-    except ValueError:
-        print("Invalid input of checking normalized data box, DSM will be created")
-        in_args.input["is_normalized"] = False
-
-    in_las_folder = in_args.input["in_las_folder"]
-
-    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 in_args.input["style"] in ["tin", "pitfree"]:
-        style = in_args.input["style"]
-    else:
-        print("Warning! invalid alogrithm, default algorthim will be used.")
-        in_args.input["style"] = "tin"
-
-    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")
-
-    chm_by(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_dtm_by.py

@@ -1,63 +0,0 @@
-import os
-import time
-
-from beratools.tools.common import *
-from beratools.tools.r_interface import *
-
-def dtm_by(callback, in_las_folder, out_folder, cell_size, 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_chm_by_algorithm = robjects.globalenv['dtm_by_tin']
-    elif style == "idw":
-        r_chm_by_algorithm = robjects.globalenv['dtm_by_knnidw ']
-    else:
-        r_chm_by_algorithm = robjects.globalenv['dtm_by_kriging']
-    # Invoking the R function
-    r_chm_by_algorithm(in_las_folder, out_folder, cell_size, 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()
-
-    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["DSMcell_size"] = 1.0
-
-    in_las_folder = in_args.input["in_las_folder"]
-    out_folder = in_args.input["out_folder"]
-    check_las_files_existence(in_las_folder)
-
-    if in_args.input["style"] in ["tin", "idw", "kriging"]:
-        style = in_args.input["style"]
-    else:
-        print("Warning! invalid alogrithm, default algorthim will be used.")
-        in_args.input["style"] = "tin"
-
-    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")
-
-    dtm_by(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_find_cellsize.py

@@ -1,43 +0,0 @@
-import os
-import sys
-import time
-
-from beratools.tools.common import *
-from beratools.tools.r_interface import *
-
-
-def find_cell_size(callback, in_las_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_pd2cellsize = robjects.globalenv['pd2cellsize']
-
-    # Invoking the R function
-    cell_size = r_pd2cellsize(in_las_folder, rprocesses)
-    print("The recommended cell size for the input liDAR data(set) is {}.".format(cell_size))
-
-
-if __name__ == '__main__':
-    start_time = time.time()
-    print('Calculate cell size from liDAR data point density processing..\n @ {}'
-          .format(time.strftime("%a, %d %b %Y %H:%M:%S", time.localtime())))
-
-    packages = ['lidR', 'future']
-    check_r_packages_installation(packages)
-
-    print("Checking input parameters....")
-    in_args, in_verbose = check_arguments()
-
-    in_las_folder = in_args.input["in_las_folder"]
-    check_las_files_existence(in_las_folder)
-
-    print("Checking input parameters....Done")
-
-    find_cell_size(print, **in_args.input, processes=int(in_args.processes), verbose=in_verbose)
-
-    print('Calculate cell size from liDAR data point density processing is done in {} seconds)'
-          .format(round(time.time() - start_time, 5)))

beratools/tools/rpy_gnd_csf.py

@@ -1,74 +0,0 @@
-import os
-import time
-
-from beratools.tools.common import *
-from beratools.tools.r_interface import *
-
-def gnd_csf(callback, in_las_folder, out_folder, slope, class_threshold, cloth_resolution, rigidness, processes,
-            verbose):
-    # 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_classify_gnd = robjects.globalenv['classify_gnd']
-    # Invoking the R function
-    r_classify_gnd(in_las_folder, out_folder, slope, class_threshold, cloth_resolution, rigidness)
-
-
-if __name__ == '__main__':
-    start_time = time.time()
-    print('Ground Classification (Cloth Simulation Filter) processing\n @ {}'
-          .format(time.strftime("%a, %d %b %Y %H:%M:%S", time.localtime())))
-
-    packages = ['lidR', 'RCSF']
-    check_r_packages_installation(packages)
-
-    print("Checking input parameters....")
-    in_args, in_verbose = check_arguments()
-    try:
-        slope = bool(in_args.input["slope"])
-        in_args.input["slope"] = slope
-    except ValueError:
-        print("Invalid input of indicate slope exists, default value is used")
-        in_args.input["slope"] = False
-
-    try:
-        class_threshold = float(in_args.input["class_threshold"])
-        in_args.input["class_threshold"] = class_threshold
-    except ValueError:
-        print("Invalid input of ground threshold, default value is used")
-        in_args.input["class_threshold"] = 0.5
-
-    try:
-        cloth_resolution = float(in_args.input["cloth_resolution"])
-        in_args.input["cloth_resolution"] = cloth_resolution
-    except ValueError:
-        print("Invalid input of distance between particles in the cloth, default value is used")
-        in_args.input["cloth_resolution"] = 0.5
-
-    try:
-        rigidness = int(in_args.input["rigidness"])
-        if rigidness in [1, 2, 3]:
-            in_args.input["rigidness"] = rigidness
-        else:
-            raise ValueError
-    except ValueError:
-        print("Invalid input of rigidness of the cloth, default value is used")
-        in_args.input["rigidness"] = 1
-
-    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")
-
-    gnd_csf(print, **in_args.input, processes=int(in_args.processes), verbose=in_verbose)
-
-    print('Ground Classification (Cloth Simulation Filter) processing is done in {} seconds)'
-          .format(round(time.time() - start_time, 5)))

beratools/tools/rpy_hummock_hollow.py

@@ -1,85 +0,0 @@
-import math
-import os
-import time
-
-
-from beratools.tools.common import *
-from beratools.tools.r_interface import *
-
-
-def hh_raster(callback, in_las_folder, Min_ws, lawn_range, cell_size, out_folder, processes, verbose):
-    rprocesses = r_processes(processes)
-
-    in_las_folder = in_las_folder.replace("\\", "/")
-    out_folder = out_folder.replace("\\", "/")
-
-    # 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_hh_function = robjects.globalenv['hh_function']
-
-    # Invoking the R function
-    r_hh_function(in_las_folder, cell_size, Min_ws, lawn_range, out_folder, rprocesses)
-
-
-if __name__ == '__main__':
-    start_time = time.time()
-    print('Hummock and Hollow detection from LiDAR process.\n'
-          '@ {}'.format(time.strftime("%d %b %Y %H:%M:%S", time.localtime())))
-
-
-    packages = ['lidR', 'rgrass', 'rlas', 'future',
-                     'terra']  # ,'comprehenr','na.tools','sf','sp']#,'devtools','gdal']#,'fasterRaster']
-    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:
-        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 will be used")
-        in_args.input["cell_size"] = 1.0
-
-    try:
-        ws = float(in_args.input["Min_ws"])
-        in_args.input["Min_ws"] = ws
-    except ValueError:
-        print("Invalid input of circular diameter, default value will be used")
-        in_args.input["Min_ws"] = 3.0
-    try:
-        lawn_range = float(in_args.input["lawn_range"])
-        in_args.input["lawn_range"] = lawn_range
-    except ValueError:
-        print("Invalid input of range height of lawns, default value will be used")
-        in_args.input["lawn_range"] = 0.1
-
-    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")
-
-    hh_raster(print, **in_args.input, processes=int(in_args.processes), verbose=in_verbose)
-
-    print('Hummock and Hollow detection from LiDAR process is done in {} seconds)'
-          .format(round(time.time() - start_time, 5)))