Mercurial > repos > matces > carpet_toolsuite

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