initial port of r3.in.xyz from grass6 addons; raw and completely untested

git-svn-id: https://svn.osgeo.org/grass/grass/trunk@52143 15284696-431f-4ddb-bdfa-cd5b030d7da7

scripts/r3.in.xyz/Makefile

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+MODULE_TOPDIR = ../..
+
+PGM = r3.in.xyz
+
+include $(MODULE_TOPDIR)/include/Make/Script.make
+
+default: script

scripts/r3.in.xyz/r3.in.xyz.html

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+<h2>DESCRIPTION</h2>
+
+<em>r3.in.xyz</em> imports sparse XYZ data from an ASCII file into
+a 3D raster map (voxels). It does this by running the <em>r.in.xyz</em>
+module multiple times for different z-ranges and then assembling the
+slices with <em>r.to.rast3</em>.
+<p>
+See the <a href="r.in.xyz.html">r.in.xyz</a> help page for general
+parameter usage and tips.
+<p>
+The map is created using the rows, columns, and depths set by
+current region settings. Be sure to check and adjust these with
+the <em>g.region</em> module before performing the import.
+
+
+<h2>NOTES</h2>
+
+The 2D and 3D horizontal region resolutions must match. See the
+EXAMPLES section below.
+<p>
+Unlike <em>r.in.xyz</em>, reading from stdin and z-scaling are not
+possible.
+<p>
+To enable parallel processing support, set the <b>workers=</b> option
+to match the number of CPUs or CPU-cores avaiable on your system.
+<p>
+Points falling exactly on a vertical bound will belong to the depth
+band below them, except for points exactly on the top bound, which will
+belong to the top-most slice.
+<p>
+The script is expected to be nearly as efficient as if it was fully
+written in C.
+
+
+<h2>EXAMPLE</h2>
+
+Using the Serpent Mound dataset. (see the
+ <a href="http://grass.osgeo.org/wiki/LIDAR">GRASS LiDAR wiki page</a>)
+
+<div class="code"><pre>
+  #scan dataset for extent:
+  r3.in.xyz -s in=Serpent_Mound_Model_LAS_Data.txt out=dummy \
+     x=1 y=2 z=3 fs=space
+
+  # set the 2D and 3D regions:
+  g.region n=4323641.57 s=4320942.61 w=289020.90 e=290106.02 res=1 -a
+  g.region b=166 t=216 res3=1 tbres=5 -3 -p
+
+  r3.in.xyz in=Serpent_Mound_Model_LAS_Data.txt out=serpent3D \
+     method=mean x=1 y=2 z=3 fs=space type=float
+</pre></div>
+
+
+<h2>BUGS</h2>
+
+<em>r.to.rast3</em> always creates a <tt>double</tt> output map
+regardless of input.
+
+
+<h2>SEE ALSO</h2>
+
+<em>
+<a href="g.region.html">g.region</a><br>
+<a href="r.in.xyz.html">r.in.xyz</a><br>
+<a href="r.to.rast3.html">r.to.rast3</a><br>
+</em>
+
+
+<h2>AUTHOR</h2>
+
+Hamish Bowman<br>
+<i>Dunedin, New Zealand</i>
+
+<p>
+<i>Last changed: $Date$</i>

scripts/r3.in.xyz/r3.in.xyz.py

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+#!/usr/bin/env python
+############################################################################
+#
+# 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
+#% keywords: raster3d, import, voxel, LiDAR
+#%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
+#% key: input
+#% type: string
+#% required: yes
+#% multiple: no
+#% key_desc: name
+#% description: ASCII file containing input data
+#% gisprompt: old_file,file,input
+#%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      
+#% key: fs    
+#% type: string
+#% required: no
+#% multiple: no
+#% key_desc: character
+#% description: Field separator
+#% answer: |  
+#% 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 data values in input file
+#% answer: 3  
+#% guisection: Input
+#%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
+from grass.script import core as grass
+
+
+def cleanup():
+    # FIXME for pid and regex
+    grass.run_command('g.mremove', flags = 'f', rast = 'tmp.r3xyz.$$.*', quiet = True)
+
+
+def main():
+    infile = options['input']
+    output = options['output']
+    method = options['method']
+    dtype = options['type']
+    fs = options['fs']
+    x = options['x']
+    y = options['y']   
+    z = options['z']
+    percent = options['percent']
+    pth = options['pth']
+    trim = options['trim']
+    workers = options['workers']
+    scan_only = flags['s']
+    shell_style = flags['g']
+    ignore_broken = flags['i']
+
+    if workers is 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)
+
+    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', fs = fs, x = x, y = y, z = z)
+	sys.exit()
+
+    addl_opts = []
+    if pth:
+        addl_opts.append("pth = '%s'" % pth)
+    if trim:
+        addl_opts.append("trim = '%s'" % trim)
+    if ignore_broken:
+        addl_opts.append("flags = 'i'")
+
+    if dtype is '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.error(_("The 2D and 3D region settings are different. Can not continue."))
+
+    grass.verbose(_("Region bottom=%.15g  top=%.15g  vertical_cell_res=%.15g  (depths %d)"),
+       % (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 the finished process infos.
+    proc = {}
+
+    for i in range(1, 1 + depths):
+        i_str = '%05d' % i
+	tmp_layer_name = 'tmp.r3xyz.%d.%s' % (os.getpid(), i_str)
+
+        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 layerimport  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, depths, zrange_min, zrange_max))
+
+	proc[i] = grass.start_command('r.in.xyz', input = infile, output = tmp_layer_name,
+				      fs = fs, method = method, x = x, y = y, z = z,
+				      percent = percent, type = dtype,
+				      zrange = '%.15g,%.15g' % (zrange_min, zrange_max),
+				      addl_opts)
+
+	if i % workers is 0:
+	    # wait for the ones launched so far to finish
+	    for p_i in range(1, 1 + depths)[:i]:
+		if not proc[p_i].stdout.closed:
+		    pout[p_i] = proc[p_i].communicate()[0]
+		if proc[p_i].wait() is not 0:
+		    grass.error(_("Trouble importing data. Aborting."))
+
+
+    # wait for jobs to finish, collect any stray output
+    for p_i in range(1, 1 + depths)[:i]:
+	if not proc[p_i].stdout.closed:
+	    pout[p_i] = proc[p_i].communicate()[0]
+	if proc[p_i].wait() is not 0:
+	    grass.error(_("Trouble importing data. Aborting."))
+
+    del proc
+
+    grass.verbose(_("Assembling 3D cube ..."))
+
+    #input order: lower most strata first
+    slices = grass.read_command('g.mlist', type = 'rast', sep = ',',
+				pattern = 'tmp.r3xyz.%d.*' % os.getpid())
+
+    if grass.run_command('r.to.rast3', input = slices, output = output) is 0:
+	grass.message(_("Done. 3D raster map <%s> created.") % output)
+
+
+if __name__ == "__main__":
+    options, flags = grass.parser()
+    atexit.register(cleanup)
+    main()
+
+