v.db.univar -> db.univar

git-svn-id: https://svn.osgeo.org/grass/grass/trunk@57174 15284696-431f-4ddb-bdfa-cd5b030d7da7

scripts/db.univar/Makefile

@@ -0,0 +1,7 @@
+MODULE_TOPDIR = ../..
+
+PGM=db.univar
+
+include $(MODULE_TOPDIR)/include/Make/Script.make
+
+default: script

scripts/db.univar/db.univar.html

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+<h2>DESCRIPTION</h2>
+
+<em>v.db.univar</em> calculates basic univariate statistics for numeric
+attributes in a data table. It will calculate minimum, maximum, range, mean,
+standard deviation, variance, coefficient of variation, quartiles, median, and
+90th percentile.
+It uses <em>db.select</em> to create list values for statistical calculations.
+
+<em>NOTES</em>
+
+If the database and driver are not specified, the default values set in
+<em>db.connect</em> will be used.
+
+<h2>EXAMPLE</h2>
+
+In this example, random points are sampled from the elevation map
+(North Carolina sample dataset) and univariate statistics performed:
+<div class="code"><pre>
+g.region rast=elevation -p
+v.random output=samples n=100
+v.db.addtable samples column="heights double precision"
+v.what.rast samples raster=elevation colum=heights
+v.db.select samples
+
+v.db.univar samples colum=heights
+</pre></div>
+
+<h2>SEE ALSO</h2>
+
+<em>
+<a href="r.univar.html">r.univar</a>,
+<a href="v.univar.html">v.univar,</a>,
+<a href="db.select.html">db.select</a>,
+<a href="d.vect.thematic.html">d.vect.thematic</a>
+</em>
+
+<h2>AUTHOR</h2>
+ Michael Barton, Arizona State University
+<p>and authors of <em>r.univar.sh</em>
+
+<p><i>Last changed: $Date$</i>

scripts/db.univar/db.univar.py

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+#!/usr/bin/env python
+
+############################################################################
+#
+# MODULE:	db.univar (formerly called v.univar.sh)
+# AUTHOR(S):	Michael Barton, Arizona State University
+#               Converted to Python by Glynn Clements
+#               Sync'ed to r.univar by Markus Metz
+# PURPOSE:	Calculates univariate statistics from a GRASS vector map attribute column.
+#               Based on r.univar.sh by Markus Neteler
+# COPYRIGHT:	(C) 2005, 2007, 2008 by the GRASS Development Team
+#
+#		This program is free software under the GNU General Public
+#		License (>=v2). Read the file COPYING that comes with GRASS
+#		for details.
+#
+#############################################################################
+
+#%module
+#% description: Calculates univariate statistics on selected table column.
+#% keywords: database
+#% keywords: statistics
+#% keywords: attribute table
+#%end
+#%option G_OPT_DB_TABLE
+#% key: table
+#% required: yes
+#%end
+#%option G_OPT_DB_COLUMN
+#% description: Name of attribute column on which to calculate statistics (must be numeric)
+#% required: yes
+#%end
+#%option G_OPT_DB_DATABASE
+#%end
+#%option G_OPT_DB_DRIVER
+#% options: dbf,odbc,ogr,sqlite,pg
+#%end
+#%option G_OPT_DB_WHERE
+#%end
+#%option
+#% key: percentile
+#% type: double
+#% description: Percentile to calculate (requires extended statistics flag)
+#% required : no
+#% answer: 90
+#% options: 0-100
+#% multiple: yes
+#%end
+#%flag
+#% key: e
+#% description: Extended statistics (quartiles and 90th percentile)
+#%end
+#%flag
+#% key: g
+#% description: Print stats in shell script style
+#%end
+
+import sys
+import os
+import atexit
+import math
+from grass.script import core as grass
+
+def cleanup():
+    for ext in ['', '.sort']:
+        grass.try_remove(tmp + ext)
+
+def sortfile(infile, outfile):
+    inf = file(infile, 'r')
+    outf = file(outfile, 'w')
+
+    if grass.find_program('sort'):
+        grass.run_command('sort', flags = 'n', stdin = inf, stdout = outf)
+    else:
+        # FIXME: we need a large-file sorting function
+        grass.warning(_("'sort' not found: sorting in memory"))
+        lines = inf.readlines()
+        for i in range(len(lines)):
+            lines[i] = float(lines[i].rstrip('\r\n'))
+        lines.sort()
+        for line in lines:
+            outf.write(str(line) + '\n')
+
+    inf.close()
+    outf.close()
+
+def main():
+    global tmp
+    tmp = grass.tempfile()
+
+    extend = flags['e']
+    shellstyle = flags['g']
+    table = options['table']
+    column = options['column']
+    database = options['database']
+    driver = options['driver']
+    where = options['where']
+    perc = options['percentile']
+
+    if perc and len(perc) > 0:
+        extend = True 
+
+    perc = [float(p) for p in perc.split(',')]
+
+    if not shellstyle:
+        grass.message(_("Calculation for column <%s> of table <%s>...") % (column, table))
+        grass.message(_("Reading column values..."))
+
+    sql = "SELECT %s FROM %s" % (column, table)
+    if where:
+        sql += " WHERE " + where
+
+    if not database:
+        database = None
+
+    if not driver:
+        driver = None
+
+    tmpf = file(tmp, 'w')
+    grass.run_command('db.select', flags = 'c', table = table,
+        database = database, driver = driver, sql = sql,
+        stdout = tmpf)
+    tmpf.close()
+
+    # check if result is empty
+    tmpf = file(tmp)
+    if tmpf.read(1) == '':
+        grass.fatal(_("Table <%s> contains no data.") % table)
+        tmpf.close()
+
+    # calculate statistics
+    if not shellstyle:
+        grass.message(_("Calculating statistics..."))
+
+    N = 0
+    sum = 0.0
+    sum2 = 0.0
+    sum3 = 0.0
+    minv = 1e300
+    maxv = -1e300
+
+    tmpf = file(tmp)
+    for line in tmpf:
+	if len(line.rstrip('\r\n')) == 0:
+	    continue
+        x = float(line.rstrip('\r\n'))
+        N += 1
+        sum += x
+        sum2 += x * x
+        sum3 += abs(x)
+        maxv = max(maxv, x)
+        minv = min(minv, x)
+    tmpf.close()
+
+    if N <= 0:
+        grass.fatal(_("No non-null values found"))
+
+    if not shellstyle:
+        print ""
+        print "Number of values: %d" % N
+        print "Minimum: %g" % minv
+        print "Maximum: %g" % maxv
+        print "Range: %g" % (maxv - minv)
+        print "-----"
+        print "Mean: %g" % (sum/N)
+        print "Arithmetic mean of absolute values: %g" % (sum3/N)
+        print "Variance: %g" % ((sum2 - sum*sum/N)/N)
+        print "Standard deviation: %g" % (math.sqrt((sum2 - sum*sum/N)/N))
+        print "Coefficient of variation: %g" % ((math.sqrt((sum2 - sum*sum/N)/N))/(math.sqrt(sum*sum)/N))
+        print "Sum: %g" % sum
+        print "-----"
+    else:
+        print "n=%d" % N
+        print "min=%.15g" % minv
+        print "max=%.15g" % maxv
+        print "range=%.15g" % (maxv - minv)
+        print "mean=%.15g" % (sum/N)
+        print "mean_abs=%.15g" % (sum3/N)
+        print "variance=%.15g" % ((sum2 - sum*sum/N)/N)
+        print "stddev=%.15g" % (math.sqrt((sum2 - sum*sum/N)/N))
+        print "coeff_var=%.15g" % ((math.sqrt((sum2 - sum*sum/N)/N))/(math.sqrt(sum*sum)/N))
+        print "sum=%.15g" % sum
+
+    if not extend:
+        return
+
+    # preparations:
+    sortfile(tmp, tmp + ".sort")
+
+    number = N
+    odd = N % 2
+    eostr = ['even','odd'][odd]
+
+    q25pos = round(N * 0.25)
+    if q25pos == 0:
+	q25pos = 1
+    q50apos = round(N * 0.50)
+    if q50apos == 0:
+	q50apos = 1
+    q50bpos = q50apos + (1 - odd)
+    q75pos = round(N * 0.75)
+    if q75pos == 0:
+	q75pos = 1
+
+    ppos = {}
+    pval = {}
+    for i in range(len(perc)):
+        ppos[i] = round(N * perc[i] / 100)
+	if ppos[i] == 0:
+	    ppos[i] = 1
+        pval[i] = 0
+
+    inf = file(tmp + ".sort")
+    l = 1
+    for line in inf:
+        if l == q25pos:
+            q25 = float(line.rstrip('\r\n'))
+        if l == q50apos:
+            q50a = float(line.rstrip('\r\n'))
+        if l == q50bpos:
+            q50b = float(line.rstrip('\r\n'))
+        if l == q75pos:
+            q75 = float(line.rstrip('\r\n'))
+        for i in range(len(ppos)):
+            if l == ppos[i]:
+                pval[i] = float(line.rstrip('\r\n'))
+        l += 1
+
+    q50 = (q50a + q50b) / 2
+
+    if not shellstyle:
+        print "1st Quartile: %g" % q25
+        print "Median (%s N): %g" % (eostr, q50)
+        print "3rd Quartile: %g" % q75
+        for i in range(len(perc)):
+            if perc[i] == int(perc[i]): # integer
+                if int(perc[i]) % 10 == 1 and int(perc[i]) != 11:
+                    print "%dst Percentile: %g" % (int(perc[i]), pval[i])
+                elif int(perc[i]) % 10 == 2 and int(perc[i]) != 12:
+                    print "%dnd Percentile: %g" % (int(perc[i]), pval[i])
+                elif int(perc[i]) % 10 == 3 and int(perc[i]) != 13:
+                    print "%drd Percentile: %g" % (int(perc[i]), pval[i])
+                else:
+                    print "%dth Percentile: %g" % (int(perc[i]), pval[i])
+            else:
+                print "%.15g Percentile: %g" % (perc[i], pval[i])
+    else:
+        print "first_quartile=%g" % q25
+        print "median=%g" % q50
+        print "third_quartile=%g" % q75
+        for i in range(len(perc)):
+            percstr = "%.15g" % perc[i]
+            percstr = percstr.replace('.','_')
+            print "percentile_%s=%g" % (percstr, pval[i])
+
+if __name__ == "__main__":
+    options, flags = grass.parser()
+    atexit.register(cleanup)
+    main()