BERATools 0.2.0__py3-none-any.whl → 0.2.2__py3-none-any.whl

beratools/tools/r_cal_lpi_elai.r

@@ -1,25 +1,25 @@
-#create a 'rlpi_elai' function
-library(terra)
-
-rlpi_elai <- function(pdTotal, pdGround, radius, scan_angle, out_lpi, out_elai) {
-
-    total_focal <- rast(pdTotal)
-    ground_focal <- rast(pdGround)
-
-    # pdTotal_SpatRaster <- rast(pdTotal)Aug 24
-    # pdGround_SpatRaster <- rast(pdGround)
-    ground_focal <- extend(ground_focal, ext(total_focal))
-
-    # lpi
-    lpi = ground_focal / total_focal
-    #lpi
-    lpi[is.infinite(lpi)] = NA
-
-    elai = -cos(((scan_angle / 2.0) / 180) * pi) / 0.5 * log(lpi)
-    elai[is.infinite(elai)] = NA
-    elai[elai == 0 | elai == -0] = 0
-
-    writeRaster(lpi, out_lpi, overwrite = TRUE)
-    writeRaster(elai, out_elai, overwrite = TRUE)
-
+#create a 'rlpi_elai' function
+library(terra)
+
+rlpi_elai <- function(pdTotal, pdGround, radius, scan_angle, out_lpi, out_elai) {
+
+    total_focal <- rast(pdTotal)
+    ground_focal <- rast(pdGround)
+
+    # pdTotal_SpatRaster <- rast(pdTotal)Aug 24
+    # pdGround_SpatRaster <- rast(pdGround)
+    ground_focal <- extend(ground_focal, ext(total_focal))
+
+    # lpi
+    lpi = ground_focal / total_focal
+    #lpi
+    lpi[is.infinite(lpi)] = NA
+
+    elai = -cos(((scan_angle / 2.0) / 180) * pi) / 0.5 * log(lpi)
+    elai[is.infinite(elai)] = NA
+    elai[elai == 0 | elai == -0] = 0
+
+    writeRaster(lpi, out_lpi, overwrite = TRUE)
+    writeRaster(elai, out_elai, overwrite = TRUE)
+
 }

beratools/tools/r_generate_pd_focalraster.r

@@ -1,101 +1,101 @@
-#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")
+#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 +1,80 @@
-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)
-
+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 +1,9 @@
-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))
+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 +1,86 @@
-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)))
+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)))