Geografic-Information-System/scripts/r3.in.xyz/r3.in.xyz.py

#!/usr/bin/env python3
############################################################################
#
# MODULE:       r3.in.xyz
# AUTHOR:       M. Hamish Bowman, Dunedin, New Zealand
# PURPOSE:      Run r.in.xyz in a loop for various z-levels and construct
#		a 3D raster. Unlike r.in.xyz, reading from stdin and z-scaling
#		won't work.
#
# COPYRIGHT:    (c) 2011-2012 Hamish Bowman, and the GRASS Development Team
#		Port of r3.in.xyz(.sh) for GRASS 6.4.
#               This program is free software under the GNU General Public
#               License (>=v2). Read the file COPYING that comes with GRASS
#               for details.
#
#		This program is distributed in the hope that it will be useful,
#		but WITHOUT ANY WARRANTY; without even the implied warranty of
#		MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#		GNU General Public License for more details.
#
#############################################################################

# %Module
# % description: Create a 3D raster map from an assemblage of many coordinates using univariate statistics
# % keyword: raster3d
# % keyword: import
# % keyword: voxel
# % keyword: LIDAR
# % keyword: statistics
# % keyword: conversion
# % keyword: aggregation
# % keyword: binning
# %End
# %Flag
# % key: s
# % description: Scan data file for extent then exit
# %End
# %Flag
# % key: g
# % description: In scan mode, print using shell script style
# %End
# %Flag
# % key: i
# % description: Ignore broken lines
# %End
# %Option G_OPT_F_INPUT
# % required: yes
# % description: ASCII file containing input data
# %End
# %Option
# % key: output
# % type: string
# % required: yes
# % multiple: no
# % key_desc: name
# % description: Name for output raster map
# % gisprompt: new,grid3,3d-raster
# %End
# %Option
# % key: method
# % type: string
# % required: no
# % multiple: no
# % options: n,min,max,range,sum,mean,stddev,variance,coeff_var,median,percentile,skewness,trimmean
# % description: Statistic to use for raster values
# % answer: mean
# % guisection: Statistic
# %End
# %Option
# % key: type
# % type: string
# % required: no
# % multiple: no
# % options: float,double
# % description: Storage type for resultant raster map
# % answer: float
# %End
# %Option G_OPT_F_SEP
# % guisection: Input
# %End
# %Option
# % key: x
# % type: integer
# % required: no
# % multiple: no
# % description: Column number of x coordinates in input file (first column is 1)
# % answer: 1
# % guisection: Input
# %End
# %Option
# % key: y
# % type: integer
# % required: no
# % multiple: no
# % description: Column number of y coordinates in input file
# % answer: 2
# % guisection: Input
# %End
# %Option
# % key: z
# % type: integer
# % required: no
# % multiple: no
# % description: Column number of z coordinates in input file
# % answer: 3
# % guisection: Input
# %End
# %Option
# % key: value_column
# % type: integer
# % required: no
# % multiple: no
# % label: Column number of data values in input file
# % description: If not given or set to 0, the data points' z-values are used
# % answer: 0
# % guisection: Input
# %End
# %Option
# % key: vrange
# % type: double
# % required: no
# % key_desc: min,max
# % description: Filter range for value column data (min,max)
# %End
# %option
# % key: vscale
# % type: double
# % required: no
# % multiple: no
# % description: Scaling factor to apply to value column data
# % answer: 1.0
# %end
# %Option
# % key: percent
# % type: integer
# % required: no
# % multiple: no
# % options: 1-100
# % description: Percent of map to keep in memory
# % answer: 100
# %End
# %Option
# % key: pth
# % type: integer
# % required: no
# % multiple: no
# % options: 1-100
# % description: pth percentile of the values
# % guisection: Statistic
# %End
# %Option
# % key: trim
# % type: double
# % required: no
# % multiple: no
# % options: 0-50
# % description: Discard <trim> percent of the smallest and <trim> percent of the largest observations
# % guisection: Statistic
# %End
# %Option
# % key: workers
# % type: integer
# % required: no
# % multiple: no
# % options: 1-256
# % answer: 1
# % description: Number of parallel processes to launch
# %End


import sys
import os
import atexit
from grass.script import core as grass
from grass.exceptions import CalledModuleError


def cleanup():
    grass.run_command('g.remove', flags='f',
                      type="rast", pattern='tmp.r3xyz.%d.*' % os.getpid(),
                      quiet=True)


def main():
    infile = options['input']
    output = options['output']
    method = options['method']
    dtype = options['type']
    fs = options['separator']
    x = options['x']
    y = options['y']
    z = options['z']
    value_column = options['value_column']
    vrange = options['vrange']
    vscale = options['vscale']
    percent = options['percent']
    pth = options['pth']
    trim = options['trim']
    workers = int(options['workers'])
    scan_only = flags['s']
    shell_style = flags['g']
    ignore_broken = flags['i']

    if workers == 1 and "WORKERS" in os.environ:
        workers = int(os.environ["WORKERS"])

    if not os.path.exists(infile):
        grass.fatal(_("Unable to read input file <%s>") % infile)

    addl_opts = {}
    if pth:
        addl_opts['pth'] = '%s' % pth
    if trim:
        addl_opts['trim'] = '%s' % trim
    if value_column:
        addl_opts['value_column'] = '%s' % value_column
    if vrange:
        addl_opts['vrange'] = '%s' % vrange
    if vscale:
        addl_opts['vscale'] = '%s' % vscale
    if ignore_broken:
        addl_opts['flags'] = 'i'

    if scan_only or shell_style:
        if shell_style:
            doShell = 'g'
        else:
            doShell = ''
        grass.run_command('r.in.xyz', flags='s' + doShell, input=infile,
                          output='dummy', sep=fs, x=x, y=y, z=z,
                          **addl_opts)
        sys.exit()

    if dtype == 'float':
        data_type = 'FCELL'
    else:
        data_type = 'DCELL'

    region = grass.region(region3d=True)

    if region['nsres'] != region['nsres3'] or region['ewres'] != region['ewres3']:
        grass.run_command('g.region', flags='3p')
        grass.fatal(_("The 2D and 3D region settings are different. Can not continue."))

    grass.verbose(_("Region bottom=%.15g  top=%.15g  vertical_cell_res=%.15g  (%d depths)")
                  % (region['b'], region['t'], region['tbres'], region['depths']))

    grass.verbose(_("Creating slices ..."))

    # to avoid a point which falls exactly on a top bound from being
    # considered twice, we shrink the
    # For the top slice we keep it though, as someone scanning the bounds
    # may have set the bounds exactly to the data extent (a bad idea, but
    # it happens..)
    eps = 1.0e-15

    # if there are thousands of depths hopefully this array doesn't get too
    # large and so we don't have to worry much about storing/looping through
    # all the finished process infos.
    proc = {}
    pout = {}

    depths = list(range(1, 1 + region['depths']))

    for i in depths:
        tmp_layer_name = 'tmp.r3xyz.%d.%s' % (os.getpid(), '%05d' % i)

        zrange_min = region['b'] + (region['tbres'] * (i - 1))

        if i < region['depths']:
            zrange_max = region['b'] + (region['tbres'] * i) - eps
        else:
            zrange_max = region['b'] + (region['tbres'] * i)

        # spawn depth layer import job in the background
        #grass.debug("slice %d, <%s>  %% %d" % (band, image[band], band % workers))
        grass.message(_("Processing horizontal slice %d of %d [%.15g,%.15g) ...")
                      % (i, region['depths'], zrange_min, zrange_max))

        proc[i] = grass.start_command('r.in.xyz', input=infile, output=tmp_layer_name,
                                      sep=fs, method=method, x=x, y=y, z=z,
                                      percent=percent, type=data_type,
                                      zrange='%.15g,%.15g' % (zrange_min, zrange_max),
                                      **addl_opts)

        grass.debug("i=%d, %%=%d  (workers=%d)" % (i, i % workers, workers))
        # print sys.getsizeof(proc)  # sizeof(proc array)  [not so big]

        if i % workers == 0:
            # wait for the ones launched so far to finish
            for p_i in depths[:i]:
                pout[p_i] = proc[p_i].communicate()[0]
                if proc[p_i].wait() != 0:
                    grass.fatal(_("Trouble importing data. Aborting."))

    # wait for jSobs to finish, collect any stray output
    for i in depths:
        pout[i] = proc[i].communicate()[0]
        if proc[i].wait() != 0:
            grass.fatal(_("Trouble importing data. Aborting."))

    del proc

    grass.verbose(_("Assembling 3D cube ..."))

    # input order: lower most strata first
    slices = grass.read_command('g.list', type='raster', sep=',',
                                pattern='tmp.r3xyz.%d.*' % os.getpid()).rstrip(os.linesep)
    grass.debug(slices)

    try:
        grass.run_command('r.to.rast3', input=slices, output=output)
    except CalledModuleError:
        grass.message(_("Done. 3D raster map <%s> created.") % output)


if __name__ == "__main__":
    options, flags = grass.parser()
    atexit.register(cleanup)
    main()