Add 'extract_points()' and 'update_survey_output()'
parent
ae2fa58588
commit
cf386fa875
@ -1,78 +0,0 @@
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import os
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import subprocess
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def call_lastools(tool_name, input, output=None, args=None, verbose=True):
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"""Send commands to the lastools library.
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Requires lastools in system path.
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Args:
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tool_name: name of lastools binary
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input: bytes from stdout, or path to main input data
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output: '-stdout' to pipe output, or path to main output data
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args: list of additional arguments, formatted for lastools
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verbose: show all warnings and messages from lastools (boolean)
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Returns:
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bytes of output las, if output='-stdout'
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None, if output='path/to/las/file'
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Examples:
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# Convert xyz file to las and pipe stdout to a python bytes object
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las_data = call_lastools('txt2las', input='points.xyz', output='-stdout',
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args=['-parse', 'sxyz'])
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# Clip las_data with a shapefile, and save to a new las file
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call_lastools('lasclip', input=las_data, output='points.las',
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args=['-poly', 'boundary.shp'])
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"""
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# Start building command string
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cmd = [tool_name]
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# Parse input
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if type(input) == bytes:
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# Pipe input las bytes to stdin
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cmd += ['-stdin']
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stdin = input
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else:
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# Load las from file path
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cmd += ['-i', input]
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stdin = None
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# Parse output
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if output == '-stdout':
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# Pipe output las to stdout
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cmd += ['-stdout']
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elif output:
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# Save output las to file
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cmd += ['-o', output]
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# Append additional lastools arguments, if provided
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if args:
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cmd += args
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process = subprocess.Popen(
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cmd,
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stdout=subprocess.PIPE,
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stderr=subprocess.PIPE,
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stdin=subprocess.PIPE)
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stdout, stderr = process.communicate(input=stdin)
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# Handle errors, if detected
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if process.returncode != 0:
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print("Error: {} failed on {}".format(tool_name,
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os.path.basename(input)))
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print(stderr.decode())
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elif verbose:
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# Print addional messages if verbose mode is being used
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print(stderr.decode())
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# Output piped stdout if required
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if output == '-stdout':
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return stdout
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else:
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return None
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@ -0,0 +1,166 @@
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import io
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import os
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import subprocess
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import pandas as pd
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def call_lastools(tool_name, input, output=None, args=None, verbose=True):
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"""Send commands to the lastools library.
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Requires lastools in system path.
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Args:
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tool_name: name of lastools binary
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input: bytes from stdout, or path to main input data
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output: '-stdout' to pipe output, or path to main output data
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args: list of additional arguments, formatted for lastools
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verbose: show all warnings and messages from lastools (boolean)
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Returns:
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bytes of output las, if output='-stdout'
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None, if output='path/to/las/file'
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Examples:
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# Convert xyz file to las and pipe stdout to a python bytes object
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las_data = call_lastools('txt2las', input='points.xyz', output='-stdout',
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args=['-parse', 'sxyz'])
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# Clip las_data with a shapefile, and save to a new las file
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call_lastools('lasclip', input=las_data, output='points.las',
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args=['-poly', 'boundary.shp'])
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"""
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# Start building command string
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cmd = [tool_name]
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# Parse input
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if type(input) == bytes:
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# Pipe input las bytes to stdin
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cmd += ['-stdin']
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stdin = input
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else:
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# Load las from file path
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cmd += ['-i', input]
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stdin = None
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# Parse output
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if output == '-stdout':
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# Pipe output las to stdout
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cmd += ['-stdout']
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elif output:
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# Save output las to file
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cmd += ['-o', output]
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# Append additional lastools arguments, if provided
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if args:
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cmd += args
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process = subprocess.Popen(
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cmd,
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stdout=subprocess.PIPE,
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stderr=subprocess.PIPE,
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stdin=subprocess.PIPE)
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stdout, stderr = process.communicate(input=stdin)
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# Handle errors, if detected
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if process.returncode != 0:
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print("Error: {} failed on {}".format(tool_name,
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os.path.basename(input)))
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print(stderr.decode())
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elif verbose:
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# Print addional messages if verbose mode is being used
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print(stderr.decode())
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# Output piped stdout if required
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if output == '-stdout':
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return stdout
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else:
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return None
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def extract_pts(las_in, cp_in, survey_date, beach, args=None, verbose=True):
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"""Extract elevations from a las surface based on x and y coordinates.
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Requires lastools in system path.
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Args:
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las_in: bytes from stdout, or path to main input data
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cp_in: point coordinates with columns: id, x, y, z (csv)
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survey_date: survey date string, e.g. '19700101'
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beach: beach name
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args: list of additional arguments, formatted for lastools
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verbose: show all warnings and messages from lastools (boolean)
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Returns:
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Dataframe containing input coordinates with extracted elevations
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Examples:
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# Extract elevations from 'points.las', using control points from 'cp.csv'
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# Specify control point format as: id, x, y, z ('-parse', 'sxyz')
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# Only use points classified as 'ground' ('-keep_class', '2')
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extract_pts('points.las', 'cp.csv', survey_date='20001231', beach='manly',
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args=['-parse', 'sxyz', '-keep_class', '2'])
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"""
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# Assemble lastools arguments
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if args:
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args = ['-cp', cp_in] + args
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else:
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args = ['-cp', cp_in]
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las_data = call_lastools(
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'lascontrol', input=las_in, output='-stdout', args=args, verbose=False)
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# Load result into pandas dataframe
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df = pd.read_csv(io.BytesIO(las_data))
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# Tidy up dataframe
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df = df.drop(columns=['diff'])
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df['lidar_z'] = pd.to_numeric(df['lidar_z'], errors='coerce')
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df['Beach'] = beach
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df = df[[
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'Beach', 'ProfileNum', 'Easting', 'Northing', 'Chainage', 'lidar_z'
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]]
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# Rename columns
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new_names = {
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'ProfileNum': 'Profile',
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'lidar_z': 'Elevation_{}'.format(survey_date),
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}
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df = df.rename(columns=new_names)
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return df
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def update_survey_output(df, output_dir):
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"""Update survey profile output csv files with current survey.
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Args:
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df: dataframe containing current survey elevations
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output_dir: directory where csv files are saved
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Returns:
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None
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"""
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# Merge current survey with existing data
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profiles = df['Profile'].unique()
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for profile in profiles:
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csv_name = os.path.join(output_dir, profile + '.csv')
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# Extract survey data for current profile
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current_profile = df[df['Profile'] == profile]
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try:
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# Load existing results
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master = pd.read_csv(csv_name)
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except FileNotFoundError:
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master = current_profile.copy()
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# Add (or update) current survey
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current_survey_col = df.columns[-1]
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master[current_survey_col] = current_profile[current_survey_col]
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# Export updated results
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master.to_csv(csv_name)
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