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

beratools/tools/Ht_metrics.py

@@ -1,116 +1,116 @@
-import os
-import time
-
-from beratools.tools.common import *
-
-
-class OperationCancelledException(Exception):
-    pass
-
-
-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
-
-
-def ht_metrics(callback, in_las_folder, cell_size, out_folder, processes, verbose):
-    r = robjects.r
-    import psutil
-    stats = psutil.virtual_memory()  # returns a named tuple
-    available = getattr(stats, 'available') / 1024000000
-    if 2 < processes <= 8:
-        if available <= 50:
-            rprocesses = 2
-        elif 50 < available <= 150:
-            rprocesses = 4
-        elif 150 < available <= 250:
-            rprocesses = 8
-    else:
-        rprocesses = 8
-
-    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_ht_metrics_function = robjects.globalenv['ht_metrics_lite']
-    # r_pd2cellsize =robjects.globalenv['pd2cellsize']
-    # Invoking the R function
-    # cell_size=r_pd2cellsize(in_las_folder)
-    r_ht_metrics_function(in_las_folder, cell_size, out_folder, rprocesses)
-
-
-if __name__ == '__main__':
-    start_time = time.time()
-    print('Height Metrics from LiDAR process.\n'
-          '@ {}'.format(time.strftime("%d %b %Y %H:%M:%S", time.localtime())))
-
-    r = robjects.r
-    utils = importr('utils')
-    base = importr('base')
-    utils.chooseCRANmirror(ind=12)  # select the 12th mirror in the list: Canada
-    print("Checking R packages ...")
-    CRANpacknames = ['lidR', 'rgrass', 'rlas', 'future',
-                     'terra']  # ,'comprehenr','na.tools','sf','sp']#,'devtools','gdal']#,'fasterRaster']
-    CRANnames_to_install = [x for x in CRANpacknames if not robjects.packages.isinstalled(x)]
-
-    if len(CRANnames_to_install) > 0:
-        utils.install_packages(StrVector(CRANnames_to_install))
-        packages_found = True
-    else:
-        packages_found = True
-
-    # if packages_found:
-    #    utils.update_packages(checkBuilt = True, ask=False)
-
-    del CRANpacknames, CRANnames_to_install
-
-    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
-    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")
-
-    ht_metrics(print, **in_args.input, processes=int(in_args.processes), verbose=in_verbose)
-
-    print('Height Metrics from LiDAR process is done in {} seconds)'
-          .format(round(time.time() - start_time, 5)))
+import os
+import time
+
+from beratools.tools.common import *
+
+
+class OperationCancelledException(Exception):
+    pass
+
+
+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
+
+
+def ht_metrics(callback, in_las_folder, cell_size, out_folder, processes, verbose):
+    r = robjects.r
+    import psutil
+    stats = psutil.virtual_memory()  # returns a named tuple
+    available = getattr(stats, 'available') / 1024000000
+    if 2 < processes <= 8:
+        if available <= 50:
+            rprocesses = 2
+        elif 50 < available <= 150:
+            rprocesses = 4
+        elif 150 < available <= 250:
+            rprocesses = 8
+    else:
+        rprocesses = 8
+
+    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_ht_metrics_function = robjects.globalenv['ht_metrics_lite']
+    # r_pd2cellsize =robjects.globalenv['pd2cellsize']
+    # Invoking the R function
+    # cell_size=r_pd2cellsize(in_las_folder)
+    r_ht_metrics_function(in_las_folder, cell_size, out_folder, rprocesses)
+
+
+if __name__ == '__main__':
+    start_time = time.time()
+    print('Height Metrics from LiDAR process.\n'
+          '@ {}'.format(time.strftime("%d %b %Y %H:%M:%S", time.localtime())))
+
+    r = robjects.r
+    utils = importr('utils')
+    base = importr('base')
+    utils.chooseCRANmirror(ind=12)  # select the 12th mirror in the list: Canada
+    print("Checking R packages ...")
+    CRANpacknames = ['lidR', 'rgrass', 'rlas', 'future',
+                     'terra']  # ,'comprehenr','na.tools','sf','sp']#,'devtools','gdal']#,'fasterRaster']
+    CRANnames_to_install = [x for x in CRANpacknames if not robjects.packages.isinstalled(x)]
+
+    if len(CRANnames_to_install) > 0:
+        utils.install_packages(StrVector(CRANnames_to_install))
+        packages_found = True
+    else:
+        packages_found = True
+
+    # if packages_found:
+    #    utils.update_packages(checkBuilt = True, ask=False)
+
+    del CRANpacknames, CRANnames_to_install
+
+    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
+    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")
+
+    ht_metrics(print, **in_args.input, processes=int(in_args.processes), verbose=in_verbose)
+
+    print('Height Metrics from LiDAR process is done in {} seconds)'
+          .format(round(time.time() - start_time, 5)))

beratools/tools/__init__.py

@@ -1,7 +1,7 @@
-# -*- coding: utf-8 -*-
-
-import os
-import sys
-sys.path.append(os.path.dirname(os.path.realpath(__file__)))
-
-name = 'tools'
+# -*- coding: utf-8 -*-
+
+# import os
+# import sys
+# sys.path.append(os.path.dirname(os.path.realpath(__file__)))
+
+name = 'tools'

beratools/tools/batch_processing.py

@@ -1,132 +1,136 @@
-import os
-import csv
-
-from PyQt5.QtWidgets import QDialog
-from beratools.gui.batch_processing_dlg import *
-from beratools.gui.bt_data import *
-
-bt = BTData()
-
-
-# TODO: Check input file existence
-def create_tool_batch_csv(project, tool_name, tasks):
-    tool_api = tool_name
-    proj_path = Path(project)
-    script_path = str(proj_path.with_name(proj_path.stem + '_' + tool_api.replace(' ', '_') + '.csv'))
-
-    param_list = bt.get_bera_tool_parameters_list(tool_name)
-
-    all_tasks = []
-    for item in tasks:
-        task = param_list
-        in_line = Path(item['in_line'])
-        in_chm = Path(item['in_chm'])
-        path_line = in_line.with_name(in_line.stem + '_output_line.shp')
-        path_footprint = in_line.with_name(in_line.stem + '_footprint.shp')
-        path_canopy = in_chm.with_name(in_chm.stem + '_canopy.tif')
-        path_cost = in_chm.with_name(in_chm.stem + '_cost.tif')
-
-        # TODO: change to tool api
-        if tool_name == 'Canopy Cost Raster':
-            task['in_chm'] = in_chm.as_posix()
-            task['out_canopy'] = path_canopy.as_posix()
-            task['out_cost'] = path_cost.as_posix()
-        elif tool_name == 'Center Line':
-            task['in_line'] = in_line.as_posix()
-            task['in_cost'] = path_cost.as_posix()
-            task['out_line'] = path_line.as_posix()
-        elif tool_name == 'Line Footprint by Static Threshold':
-            task['in_line'] = path_line.as_posix()
-            task['in_canopy'] = path_canopy.as_posix()
-            task['in_cost'] = path_cost.as_posix()
-            task['out_footprint'] = path_footprint.as_posix()
-        elif tool_name == 'Line Footprint by Dynamic Threshold':
-            task['in_line'] = path_line.as_posix()
-            task['in_chm'] = in_chm.as_posix()
-            task['out_footprint'] = in_line.with_name(in_line.stem + '_dyn_footprint.shp')
-        elif tool_name == 'Forest Line Attributes':
-            task['in_line'] = path_line.as_posix()
-            task['in_chm'] = in_chm.as_posix()
-            task['in_footprint'] = path_footprint.as_posix()
-            task['out_line'] = in_line.with_name(in_line.stem + '_line_attributes.shp').as_posix()
-        elif tool_name == 'Raster Line Attributes':
-            task['in_line'] = path_line.as_posix()
-            task['in_chm'] = in_chm.as_posix()
-            task['out_line'] = in_line.with_name(in_line.stem + '_raster_attributes.shp').as_posix()
-
-        all_tasks.append(task.copy())
-
-    header = list(task.keys())
-
-    with open(script_path, 'w', newline='') as csv_file:
-        writer = csv.DictWriter(csv_file, fieldnames=header)
-        writer.writeheader()
-        writer.writerows(all_tasks)
-
-    return script_path
-
-
-def batch_processing(callback, batch_tool_name, in_project, processes, verbose):
-    proj_data = None
-    proj_tool_name = None
-    proj_tasks = None
-    if in_project and os.path.exists(in_project):
-        with open(in_project, 'r') as project_file:
-            proj_data = json.load(project_file)
-
-    csv_file = create_tool_batch_csv(in_project, batch_tool_name, proj_data['tasks'])
-    dialog = BPDialog(batch_tool_name)
-    dialog.open_csv(csv_file)
-
-    flag = dialog.exec()
-
-    # import tasks data
-    data = pd.read_csv(csv_file)
-    task_data = data.to_dict(orient='records')
-
-    if flag == QDialog.Accepted and task_data:
-        steps = len(task_data)
-        step = 0
-
-        print('{} tasks are prepared'.format(steps))
-        print('-----------------------------------')
-
-        step = 0
-        total_steps = len(task_data)
-        for task in task_data:
-            print('Starting task #{} ...'.format(step))
-            print(' "PROGRESS_LABEL {} task {} of {}" '.format(batch_tool_name, step, total_steps), flush=True)
-            print(' %{} '.format(step / steps * 100), flush=True)
-            task = generate_task_params(task)
-            code = execute_task(bt.get_bera_tool_api(batch_tool_name), task)
-            step += 1
-            # task is cancelled
-            if code == 2:
-                break
-
-        print(' "PROGRESS_LABEL {} {} tasks finished" '.format(batch_tool_name, total_steps), flush=True)
-        print(' %{} '.format(0), flush=True)
-
-    print('Tasks finished.', flush=True)
-
-
-def execute_task(tool_api, task):
-    # return 2 if task is cancelled
-    return bt.run_tool(tool_api, task, None, False)
-
-
-def generate_task_params(task):
-    """
-    When project tool_api is tiler, tool parameters are missing.
-    This function will retrieve default arguments
-    and generate new file names such as cost/canopy/centerline file names
-    """
-    updated_task = task
-    return updated_task
-
-
-if __name__ == '__main__':
-    in_args, in_verbose = check_arguments()
-    app = QApplication(sys.argv)
-    batch_processing(print, **in_args.input, processes=int(in_args.processes), verbose=in_verbose)
-    sys.exit(app.exec_())
+import csv
+import json
+import os
+import sys
+from pathlib import Path
+
+import pandas as pd
+from PyQt5 import QtWidgets
+
+import beratools.tools.common as bt_common
+from beratools.gui.batch_processing_dlg import BPDialog
+from beratools.gui.bt_data import BTData
+
+bt = BTData()
+
+
+# TODO: Check input file existence
+def create_tool_batch_csv(project, tool_name, tasks):
+    tool_api = tool_name
+    proj_path = Path(project)
+    script_path = str(proj_path.with_name(proj_path.stem + '_' + tool_api.replace(' ', '_') + '.csv'))
+
+    param_list = bt.get_bera_tool_parameters_list(tool_name)
+
+    all_tasks = []
+    for item in tasks:
+        task = param_list
+        in_line = Path(item['in_line'])
+        in_chm = Path(item['in_chm'])
+        path_line = in_line.with_name(in_line.stem + '_output_line.shp')
+        path_footprint = in_line.with_name(in_line.stem + '_footprint.shp')
+        path_canopy = in_chm.with_name(in_chm.stem + '_canopy.tif')
+        path_cost = in_chm.with_name(in_chm.stem + '_cost.tif')
+
+        # TODO: change to tool api
+        if tool_name == 'Canopy Cost Raster':
+            task['in_chm'] = in_chm.as_posix()
+            task['out_canopy'] = path_canopy.as_posix()
+            task['out_cost'] = path_cost.as_posix()
+        elif tool_name == 'Center Line':
+            task['in_line'] = in_line.as_posix()
+            task['in_cost'] = path_cost.as_posix()
+            task['out_line'] = path_line.as_posix()
+        elif tool_name == 'Line Footprint by Static Threshold':
+            task['in_line'] = path_line.as_posix()
+            task['in_canopy'] = path_canopy.as_posix()
+            task['in_cost'] = path_cost.as_posix()
+            task['out_footprint'] = path_footprint.as_posix()
+        elif tool_name == 'Line Footprint by Dynamic Threshold':
+            task['in_line'] = path_line.as_posix()
+            task['in_chm'] = in_chm.as_posix()
+            task['out_footprint'] = in_line.with_name(in_line.stem + '_dyn_footprint.shp')
+        elif tool_name == 'Forest Line Attributes':
+            task['in_line'] = path_line.as_posix()
+            task['in_chm'] = in_chm.as_posix()
+            task['in_footprint'] = path_footprint.as_posix()
+            task['out_line'] = in_line.with_name(in_line.stem + '_line_attributes.shp').as_posix()
+        elif tool_name == 'Raster Line Attributes':
+            task['in_line'] = path_line.as_posix()
+            task['in_chm'] = in_chm.as_posix()
+            task['out_line'] = in_line.with_name(in_line.stem + '_raster_attributes.shp').as_posix()
+
+        all_tasks.append(task.copy())
+
+    header = list(task.keys())
+
+    with open(script_path, 'w', newline='') as csv_file:
+        writer = csv.DictWriter(csv_file, fieldnames=header)
+        writer.writeheader()
+        writer.writerows(all_tasks)
+
+    return script_path
+
+
+def batch_processing(callback, batch_tool_name, in_project, processes, verbose):
+    proj_data = None
+    if in_project and os.path.exists(in_project):
+        with open(in_project, 'r') as project_file:
+            proj_data = json.load(project_file)
+
+    csv_file = create_tool_batch_csv(in_project, batch_tool_name, proj_data['tasks'])
+    dialog = BPDialog(batch_tool_name)
+    dialog.open_csv(csv_file)
+
+    flag = dialog.exec()
+
+    # import tasks data
+    data = pd.read_csv(csv_file)
+    task_data = data.to_dict(orient='records')
+
+    if flag == QtWidgets.QDialog.Accepted and task_data:
+        steps = len(task_data)
+        step = 0
+
+        print('{} tasks are prepared'.format(steps))
+        print('-----------------------------------')
+
+        step = 0
+        total_steps = len(task_data)
+        for task in task_data:
+            print('Starting task #{} ...'.format(step))
+            print(' "PROGRESS_LABEL {} task {} of {}" '.format(batch_tool_name, step, total_steps), flush=True)
+            print(' %{} '.format(step / steps * 100), flush=True)
+            task = generate_task_params(task)
+            code = execute_task(bt.get_bera_tool_api(batch_tool_name), task)
+            step += 1
+            # task is cancelled
+            if code == 2:
+                break
+
+        print(' "PROGRESS_LABEL {} {} tasks finished" '.format(batch_tool_name, total_steps), flush=True)
+        print(' %{} '.format(0), flush=True)
+
+    print('Tasks finished.', flush=True)
+
+
+def execute_task(tool_api, task):
+    # return 2 if task is cancelled
+    return bt.run_tool(tool_api, task, None, False)
+
+
+def generate_task_params(task):
+    """
+    When project tool_api is tiler, tool parameters are missing.
+    This function will retrieve default arguments
+    and generate new file names such as cost/canopy/centerline file names
+    """
+    updated_task = task
+    return updated_task
+
+
+if __name__ == '__main__':
+    in_args, in_verbose = bt_common.check_arguments()
+    app = QtWidgets.QApplication(sys.argv)
+    batch_processing(print, **in_args.input, processes=int(in_args.processes), verbose=in_verbose)
+    sys.exit(app.exec_())