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comparison carpet-src-1/tools/CARPET/Raw_data.py @ 0:cdd489d98766

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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author matces
date Tue, 07 Jun 2011 16:50:41 -0400
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-1:000000000000 0:cdd489d98766
1 #!/usr/bin/env python
2
3 # Copyright 2009 Matteo Cesaroni, Lucilla Luzi
4 #
5 # This program is free software; ; you can redistribute it and/or modify
6 # it under the terms of the GNU Lesser General Public License as published by
7 # the Free Software Foundation; either version 3 of the License, or (at your
8 # option) any later version.
9 #
10 # This program is distributed in the hope that it will be useful,
11 # but WITHOUT ANY WARRANTY; without even the implied warranty of
12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 # GNU General Public License for more details.
14 .
15
16 import sys
17 from rpy import *
18
19
20 def stop_err(msg):
21 sys.stderr.write(msg)
22 sys.exit()
23
24 def main():
25
26 # Handle input params
27 in_fname = sys.argv[1]
28 out_fname = sys.argv[2]
29 #sys.stdout=open('log.txt','a')
30 try:
31 column = int( sys.argv[3] ) - 1
32 column_x = int( sys.argv[4] ) - 1
33 column_y = int( sys.argv[5] ) - 1
34 except:
35 stop_err( "..Column not specified, your query does not contain a column of numerical data." )
36
37
38 title = sys.argv[6]
39
40 skipped_lines = 0
41 first_invalid_line = 0
42 invalid_value = ''
43
44 riga = []
45 for tuo in range(1,1025):
46 riga.append(int(0))
47 #print riga
48
49 matrice = []
50 for mio in range(1,769):
51 #print mio
52 matrice.append(riga)
53
54 #print matrix
55 matrix1 = array(matrice)
56 #print matrix1
57 for i, line in enumerate( file( in_fname ) ):
58 valid = True
59 line = line.rstrip('\r\n')
60 # Skip comments
61 if line and not line.startswith( '#' ):
62 # Extract values and convert to floats
63 row = []
64 val = 0
65 val_x = 0
66 val_y = 0
67 try:
68 fields = line.split( "\t" )
69 val = fields[column]
70 val_x = (int(fields[column_x])-1)
71 val_y = (int(fields[column_y])-1)
72 matrix1[val_x][val_y]=float(val)
73
74
75 except:
76 valid = False
77 skipped_lines += 1
78 if not first_invalid_line:
79 first_invalid_line = i+1
80 else:
81 try:
82 row.append( float( val ) )
83 except ValueError:
84 valid = False
85 skipped_lines += 1
86 if not first_invalid_line:
87 first_invalid_line = i+1
88 invalid_value = fields[column]
89 else:
90 valid = False
91 skipped_lines += 1
92 if not first_invalid_line:
93 first_invalid_line = i+1
94
95 output_prima=sys.stdout
96 fsock=open('log.txt','w')
97 sys.stdout=fsock
98
99
100 for i in range(768):
101 for j in range(1024):
102 if j<1022:
103 print "%s\t" %matrix1[i][j],
104 if j==1023:
105 print "%s" %matrix1[i][j]
106 sys.stdout=output_prima
107 fsock.close()
108
109 set_default_mode(NO_CONVERSION)
110 if skipped_lines < i:
111 #print "..on columnn %s" %sys.argv[3]
112 a=r.read_table("log.txt")
113 b=r.as_matrix(a)
114 #r.print_(b)
115 #b=r.cbind(a[1],a[1])
116 r.pdf( out_fname, 8, 8 )
117 r.image(z=r.log2(b),col=r.terrain_colors(100000),main=title, xlab="X", ylab="Y")
118 r.dev_off()
119
120 else:
121 print "..all values in column %s are non-numeric." %sys.argv[3]
122
123 if skipped_lines > 0:
124 print "..skipped %d invalid lines starting with line #%d. Value '%s' is not numeric." % ( skipped_lines, first_invalid_line, invalid_value )
125
126 r.quit( save="no" )
127
128 if __name__ == "__main__":
129 main()
130