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1
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1 /////////////////////////////////////////////////////////
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2 // Cent_adjust version number and modification history
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3 // ImmPort BISC project
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4 // Author: Yu "Max" Qian
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5 // v1.01: Oct 16, 2009
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6 // Line 899 of the main function:
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7 // Changed kmean_term=1 to kmean_term=2
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8 //////////////////////////////////////////////////////////
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9
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10
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11 #include <time.h>
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12 #include <stdio.h>
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13 #include <stdlib.h>
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14 #include <math.h>
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15 #include <string.h>
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16
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17 #define DEBUG 0
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18 #define LINE_LEN 1024
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19 #define FILE_NAME_LEN 128
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20 #define PARA_NAME_LEN 64
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21 #define MAX_VALUE 1000000000
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22 #define CUBE 0
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23
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24
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25 void getctrfileinfo(FILE *f_src_ctr, long *num_clust)
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26 {
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27 int ch='\n';
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28 int prev='\n';
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29 long num_rows=0;
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30
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31 while ((ch = fgetc(f_src_ctr))!= EOF )
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32 {
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33 if (ch == '\n')
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34 {
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35 ++num_rows;
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36 }
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37 prev = ch;
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38 }
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39 if (prev!='\n')
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40 ++num_rows;
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41
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42 *num_clust=num_rows;
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43 //printf("center file has %ld rows\n", *num_clust);
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44 }
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45
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46 /************************************* Read basic info of the source file **************************************/
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47 void getfileinfo(FILE *f_src, long *file_Len, long *num_dm, char *name_string, int *time_ID)
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48 {
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49 char src[LINE_LEN];
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50 char current_name[64];
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51 char prv;
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52
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53 long num_rows=0;
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54 long num_columns=0;
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55 int ch='\n';
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56 int prev='\n';
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57 long time_pos=0;
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58 long i=0;
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59 long j=0;
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60
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61
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62
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63 src[0]='\0';
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64 fgets(src, LINE_LEN, f_src);
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65
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66 name_string[0]='\0';
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67 current_name[0]='\0';
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68 prv='\n';
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69
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70 while ((src[i]==' ') || (src[i]=='\t')) //skip space and tab characters
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71 i++;
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72
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73 while ((src[i]!='\r') && (src[i]!='\n')) //repeat until the end of the line
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74 {
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75 current_name[j]=src[i];
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76
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77 if ((src[i]=='\t') && (prv!='\t')) //a complete word
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78 {
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79 current_name[j]='\0';
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80
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81 /*
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82 * Commented out John Campbell, June 10 2010
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83 * We no longer want to automatically remove Time column.
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84 * This column should have been removed by column selection
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85 if (0!=strcmp(current_name,"Time"))
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86 {
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87 num_columns++; //num_columns does not inlcude the column of Time
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88 time_pos++;
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89 strcat(name_string,current_name);
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90 strcat(name_string,"\t");
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91 }
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92 else
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93 {
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94 *time_ID=time_pos;
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95 }
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96 */
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97
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98 num_columns++;
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99 strcat(name_string,current_name);
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100 strcat(name_string,"\t");
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101
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102 current_name[0]='\0';
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103 j=0;
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104 }
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105
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106 if ((src[i]=='\t') && (prv=='\t')) //a duplicate tab or space
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107 {
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108 current_name[0]='\0';
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109 j=0;
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110 }
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111
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112 if (src[i]!='\t')
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113 j++;
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114
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115
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116 prv=src[i];
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117 i++;
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118 }
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119
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120 if (prv!='\t') //the last one hasn't been retrieved
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121 {
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122 current_name[j]='\0';
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123 /*
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124 * Commented out John Campbell, June 10 2010
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125 * We no longer want to automatically remove Time column.
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126 * This column should have been removed by column selection
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127 if (0!=strcmp(current_name,"Time"))
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128 {
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129 num_columns++;
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130 strcat(name_string,current_name);
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131 time_pos++;
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132 }
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133 else
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134 {
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135 *time_ID=time_pos;
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136 }
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137 */
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138
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139 num_columns++;
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140 strcat(name_string,current_name);
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141 }
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142
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143 if (DEBUG==1)
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144 {
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145 printf("time_ID is %d\n",*time_ID);
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146 printf("name_string is %s\n",name_string);
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147 }
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148
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149 // # of rows
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150
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151 while ((ch = fgetc(f_src))!= EOF )
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152 {
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153 if (ch == '\n')
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154 {
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155 ++num_rows;
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156 }
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157 prev = ch;
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158 }
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159 if (prev!='\n')
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160 ++num_rows;
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161
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162 *file_Len=num_rows;
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163 *num_dm=num_columns;
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164
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165 //printf("original file size is %ld; number of dimensions is %ld\n", *file_Len, *num_dm);
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166 }
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167
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168
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169
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170 ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
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171 /************************************* Read the source file into uncomp_data **************************************/
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172 void readsource(FILE *f_src, long file_Len, long num_dm, double **uncomp_data, int time_ID)
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173 {
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174 long time_pass=0; //to mark whether the time_ID has been passed
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175 long index=0;
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176
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177 long i=0;
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178 long j=0;
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179 long t=0;
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180
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181 char src[LINE_LEN];
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182 char xc[LINE_LEN/10];
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183
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184 src[0]='\0';
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185 fgets(src,LINE_LEN, f_src); //skip the first line about parameter names
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186
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187 while (!feof(f_src) && (index<file_Len)) //index = 0, 1, ..., file_Len-1
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188 {
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189 src[0]='\0';
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190 fgets(src,LINE_LEN,f_src);
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191 i=0;
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192 time_pass=0;
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193
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194 if (time_ID==-1)
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195 {
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196 for (t=0;t<num_dm;t++) //there is no time_ID
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197 {
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198 xc[0]='\0';
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199 j=0;
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200 while ((src[i]!='\r') && (src[i]!='\n') && (src[i]!=' ') && (src[i]!='\t'))
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201 {
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202 xc[j]=src[i];
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203 i++;
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204 j++;
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205 }
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206
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207 xc[j]='\0';
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208 i++;
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209
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210 uncomp_data[index][t]=atof(xc);
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211 }
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212 }
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213 else
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214 {
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215 for (t=0;t<=num_dm;t++) //the time column needs to be skipped, so there are num_dm+1 columns
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216 {
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217 xc[0]='\0';
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218 j=0;
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219 while ((src[i]!='\r') && (src[i]!='\n') && (src[i]!=' ') && (src[i]!='\t'))
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220 {
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221 xc[j]=src[i];
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222 i++;
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223 j++;
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224 }
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225
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226 xc[j]='\0';
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227 i++;
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228
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229 if (t==time_ID)
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230 {
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231 time_pass=1;
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232 continue;
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233 }
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234
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235 if (time_pass)
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236 uncomp_data[index][t-1]=atof(xc);
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237 else
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238 uncomp_data[index][t]=atof(xc);
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239 }
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240 }
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241 index++;
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242 //fprintf(fout_ID,"%s",src);
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243 } //end of while
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244
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245 if (DEBUG == 1)
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246 {
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247 printf("the last line of the source data is:\n");
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248 for (j=0;j<num_dm;j++)
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249 printf("%f ",uncomp_data[index-1][j]);
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250 printf("\n");
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251 }
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252 }
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253
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254 /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
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255 void readcenter(FILE *f_src_ctr, long num_clust, long num_dm, double **cluster_center, long *IDmapping)
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256 {
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257 char src[LINE_LEN];
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258 char xc[LINE_LEN/10];
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259
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260 long i=0;
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261 long j=0;
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262 int m=0;
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263 int t=0;
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264
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265 for (i=0;i<num_clust;i++)
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266 {
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267 src[0]='\0';
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268 fgets(src,LINE_LEN, f_src_ctr);
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269 m=0;
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270 for (j=0;j<num_dm+1;j++)
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271 {
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272 xc[0]='\0';
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273 t=0;
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274 while ((src[m]!='\r') && (src[m]!='\n') && (src[m]!=' ') && (src[m]!='\t'))
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275 {
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276 xc[t]=src[m];
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277 m++;
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278 t++;
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279 }
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280 xc[t]='\0';
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281 m++;
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282 if (j==0)
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283 IDmapping[i]=atoi(xc);
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284 else
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285 cluster_center[i][j-1]=atof(xc);
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286 //printf("cluster_center[%d][%d]=%f\n",i,j,cluster_center[i][j]);
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287 }
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288 }
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289 }
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290
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291
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292 /**************************************** Normalization ******************************************/
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293 void tran(double **orig_data, long clean_Len, long num_dm, long norm_used, double **matrix_to_cluster)
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294 {
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295 long i=0;
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296 long j=0;
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297
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298 double biggest=0;
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299 double smallest=MAX_VALUE;
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300
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301 double *aver; //average of each column
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302 double *std; //standard deviation of each column
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303
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304 aver=(double*)malloc(sizeof(double)*clean_Len);
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305 memset(aver,0,sizeof(double)*clean_Len);
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306
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307 std=(double*)malloc(sizeof(double)*clean_Len);
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308 memset(std,0,sizeof(double)*clean_Len);
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309
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310 if (norm_used==2) //z-score normalization
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311 {
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312 for (j=0;j<num_dm;j++)
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313 {
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314 aver[j]=0;
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315 for (i=0;i<clean_Len;i++)
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316 aver[j]=aver[j]+orig_data[i][j];
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317 aver[j]=aver[j]/(double)clean_Len;
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318
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319 std[j]=0;
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320 for (i=0;i<clean_Len;i++)
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321 std[j]=std[j]+(orig_data[i][j]-aver[j])*(orig_data[i][j]-aver[j]);
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322 std[j]=sqrt(std[j]/(double)clean_Len);
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323
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324 for (i=0;i<clean_Len;i++)
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325 matrix_to_cluster[i][j]=(orig_data[i][j]-aver[j])/std[j]; //z-score normalization
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326 }
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327 }
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328
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329 if (norm_used==1) //0-1 min-max normalization
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330 {
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331 for (j=0;j<num_dm;j++)
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332 {
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333 biggest=0;
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334 smallest=MAX_VALUE;
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335 for (i=0;i<clean_Len;i++)
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336 {
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337 if (orig_data[i][j]>biggest)
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338 biggest=orig_data[i][j];
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339 if (orig_data[i][j]<smallest)
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340 smallest=orig_data[i][j];
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341 }
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342
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343 for (i=0;i<clean_Len;i++)
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344 {
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345 if (biggest==smallest)
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346 matrix_to_cluster[i][j]=biggest;
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347 else
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348 matrix_to_cluster[i][j]=(orig_data[i][j]-smallest)/(biggest-smallest);
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349 }
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350 }
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351 }
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352
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353 if (norm_used==0) //no normalization
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354 {
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355 for (i=0;i<clean_Len;i++)
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356 for (j=0;j<num_dm;j++)
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357 matrix_to_cluster[i][j]=orig_data[i][j];
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358 }
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359
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360
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361 }
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362
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363 /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
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364 void assign_event(double **Matrix, long k, long dist_used, double kmean_term, long file_Len, long num_dm, long *shortest_id, double **center, int random_init)
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365 {
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366
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367 long i=0;
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368
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369 long j=0;
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370 long t=0;
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371 long random=0;
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372 long random1=0;
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373 long random2=0;
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374 long times=0;
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375 long times_allowed=0;
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376
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377 long *num; //num[i]=t means the ith cluster has t points
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378
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379 double vvv=1.0; // the biggest variation;
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380 double distance=0.0;
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381 double xv=0.0;
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382 double variation=0.0;
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383 double EPS=0.0;
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384 double diff=0.0;
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385 double mean_dx=0;
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386 double mean_dy=0;
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387 double sum_var=0;
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388 double dx=0;
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389 double dy=0;
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390 double sd_x=0;
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391 double sd_y=0;
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392
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393 double *temp_center;
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394 double *shortest_distance;
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395
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396 double **sum;
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397
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398 temp_center = (double *)malloc(sizeof(double)*num_dm);
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399 memset(temp_center,0,sizeof(double)*num_dm);
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400
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401 /* Choosing Centers */
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402 if (random_init)
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403 {
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404 for (i=0;i<k;i++)
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405 {
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406 random1=rand()*rand();
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407 //srand( (unsigned)time( NULL ) );
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408 random2=abs((random1%5)+1);
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409 for (t=0;t<random2;t++)
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410 random2=random2*rand()+rand();
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411
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412 random=abs(random2%file_Len);
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413 //printf("random=%d\n",random);
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414 for (j=0;j<num_dm;j++)
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415 center[i][j]=Matrix[random][j];
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416
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417 }
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418 }
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419
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420 //printf("finish random selection\n");
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421 /* To compute the nearest center for every point */
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422
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423 shortest_distance = (double *)malloc(sizeof(double)*file_Len);
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424 memset(shortest_distance,0,sizeof(double)*file_Len);
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425
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426 num = (long *)malloc(sizeof(long)*k);
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427 memset(num,0,sizeof(long)*k);
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428
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429 sum = (double **)malloc(sizeof(double*)*k);
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430 memset(sum,0,sizeof(double*)*k);
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431 for (i=0;i<k;i++)
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432 {
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433 sum[i] = (double *)malloc(sizeof(double)*num_dm);
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434 memset(sum[i],0,sizeof(double)*num_dm);
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|
|
435 }
|
|
|
436
|
|
|
437 for (i=0;i<k;i++)
|
|
|
438 for (j=0;j<num_dm;j++)
|
|
|
439 sum[i][j]=0.0; //sum[i][j] = k means the sum of the jth dimension of all points in the ith group is k
|
|
|
440
|
|
|
441 //printf("before recursion\n");
|
|
|
442 if (kmean_term>=1)
|
|
|
443 times_allowed = (long)kmean_term;
|
|
|
444 else
|
|
|
445 EPS = kmean_term;
|
|
|
446
|
|
|
447 times=0;
|
|
|
448
|
|
|
449 while (((vvv>EPS) && (kmean_term<1)) || ((times<times_allowed) && (kmean_term>=1)))
|
|
|
450 {
|
|
|
451 for (i=0;i<k;i++)
|
|
|
452 {
|
|
|
453 num[i]=0;
|
|
|
454 for (j=0;j<num_dm;j++)
|
|
|
455 sum[i][j]=0.0;
|
|
|
456 }
|
|
|
457
|
|
|
458 for (i=0;i<file_Len;i++) //for each data point i, we compute the distance between Matrix[i] and center[j]
|
|
|
459 {
|
|
|
460 shortest_distance[i]=MAX_VALUE;
|
|
|
461 for (j=0;j<k;j++) //for each center j
|
|
|
462 {
|
|
|
463
|
|
|
464 distance=0.0;
|
|
|
465
|
|
|
466 if (dist_used==0) //Euclidean distance
|
|
|
467 {
|
|
|
468 for (t=0;t<num_dm;t++) //for each dimension
|
|
|
469 {
|
|
|
470 diff=center[j][t]-Matrix[i][t];
|
|
|
471 if (diff<0)
|
|
|
472 diff=-diff;
|
|
|
473
|
|
|
474 if (CUBE)
|
|
|
475 distance = distance+(diff*diff*diff);
|
|
|
476 else
|
|
|
477 distance = distance+(diff*diff);
|
|
|
478 }
|
|
|
479 }
|
|
|
480 else //pearson correlation
|
|
|
481 {
|
|
|
482 mean_dx=0.0;
|
|
|
483 mean_dy=0.0;
|
|
|
484 sum_var=0.0;
|
|
|
485 dx=0.0;
|
|
|
486 dy=0.0;
|
|
|
487 sd_x=0.0;
|
|
|
488 sd_y=0.0;
|
|
|
489 for (t=0;t<num_dm;t++)
|
|
|
490 {
|
|
|
491 mean_dx+=center[j][t];
|
|
|
492 mean_dy+=Matrix[i][t];
|
|
|
493 }
|
|
|
494 mean_dx=mean_dx/(double)num_dm;
|
|
|
495 mean_dy=mean_dy/(double)num_dm;
|
|
|
496 //printf("mean_dx=%f\n",mean_dx);
|
|
|
497
|
|
|
498 for (t=0;t<num_dm;t++)
|
|
|
499 {
|
|
|
500 dx=center[j][t]-mean_dx;
|
|
|
501 dy=Matrix[i][t]-mean_dy;
|
|
|
502 sum_var+=dx*dy;
|
|
|
503 sd_x+=dx*dx;
|
|
|
504 sd_y+=dy*dy;
|
|
|
505 }
|
|
|
506 if (sqrt(sd_x*sd_y)==0)
|
|
|
507 distance = 1.0;
|
|
|
508 else
|
|
|
509 distance = 1.0 - (sum_var/(sqrt(sd_x*sd_y))); // distance ranges from 0 to 2;
|
|
|
510 //printf("distance=%f\n",distance);
|
|
|
511 } //pearson correlation ends
|
|
|
512
|
|
|
513
|
|
|
514 if (distance<shortest_distance[i])
|
|
|
515 {
|
|
|
516 shortest_distance[i]=distance;
|
|
|
517 shortest_id[i]=j;
|
|
|
518 }
|
|
|
519 }//end for j
|
|
|
520 num[shortest_id[i]]=num[shortest_id[i]]+1;
|
|
|
521 for (t=0;t<num_dm;t++)
|
|
|
522 sum[shortest_id[i]][t]=sum[shortest_id[i]][t]+Matrix[i][t];
|
|
|
523 }//end for i
|
|
|
524 /* recompute the centers */
|
|
|
525 //compute_mean(group);
|
|
|
526 vvv=0.0;
|
|
|
527 for (j=0;j<k;j++)
|
|
|
528 {
|
|
|
529 memcpy(temp_center,center[j],sizeof(double)*num_dm);
|
|
|
530 variation=0.0;
|
|
|
531 if (num[j]!=0)
|
|
|
532 {
|
|
|
533 for (t=0;t<num_dm;t++)
|
|
|
534 {
|
|
|
535 center[j][t]=sum[j][t]/(double)num[j];
|
|
|
536 xv=(temp_center[t]-center[j][t]);
|
|
|
537 variation=variation+xv*xv;
|
|
|
538 }
|
|
|
539 }
|
|
|
540
|
|
|
541 if (variation>vvv)
|
|
|
542 vvv=variation; //vvv is the biggest variation among the k clusters;
|
|
|
543 }
|
|
|
544 //compute_variation;
|
|
|
545 times++;
|
|
|
546 } //end for while
|
|
|
547
|
|
|
548
|
|
|
549
|
|
|
550 free(num);
|
|
|
551 for (i=0;i<k;i++)
|
|
|
552 free(sum[i]);
|
|
|
553 free(sum);
|
|
|
554 free(temp_center);
|
|
|
555 free(shortest_distance);
|
|
|
556
|
|
|
557 }
|
|
|
558
|
|
|
559 //////////////////////////////////////////////////////
|
|
|
560 /*************************** Show *****************************/
|
|
|
561 void show(double **Matrix, long *cluster_id, long file_Len, long k, long num_dm, char *name_string, long *IDmapping)
|
|
|
562 {
|
|
|
563 int situ1=0;
|
|
|
564 int situ2=0;
|
|
|
565
|
|
|
566 long i=0;
|
|
|
567 long id=0;
|
|
|
568 long j=0;
|
|
|
569 long info_id=0;
|
|
|
570 long nearest_id=0;
|
|
|
571 long insert=0;
|
|
|
572 long temp=0;
|
|
|
573 long m=0;
|
|
|
574 long n=0;
|
|
|
575 long t=0;
|
|
|
576
|
|
|
577 long *size_c;
|
|
|
578
|
|
|
579
|
|
|
580
|
|
|
581 long **size_mybound_1;
|
|
|
582 long **size_mybound_2;
|
|
|
583 long **size_mybound_3;
|
|
|
584 long **size_mybound_0;
|
|
|
585
|
|
|
586 double interval=0.0;
|
|
|
587
|
|
|
588 double *big;
|
|
|
589 double *small;
|
|
|
590
|
|
|
591
|
|
|
592 double **center;
|
|
|
593 double **mybound;
|
|
|
594
|
|
|
595 long **prof; //prof[i][j]=1 means population i is + at parameter j
|
|
|
596
|
|
|
597 FILE *fpcnt_id; //proportion id
|
|
|
598 //FILE *fcent_id; //center_id, i.e., centers of clusters within the original data
|
|
|
599 FILE *fprof_id; //profile_id
|
|
|
600
|
|
|
601 big=(double *)malloc(sizeof(double)*num_dm);
|
|
|
602 memset(big,0,sizeof(double)*num_dm);
|
|
|
603
|
|
|
604 small=(double *)malloc(sizeof(double)*num_dm);
|
|
|
605 memset(small,0,sizeof(double)*num_dm);
|
|
|
606
|
|
|
607 for (i=0;i<num_dm;i++)
|
|
|
608 {
|
|
|
609 big[i]=0.0;
|
|
|
610 small[i]=(double)MAX_VALUE;
|
|
|
611 }
|
|
|
612
|
|
|
613
|
|
|
614 size_c=(long *)malloc(sizeof(long)*k);
|
|
|
615 memset(size_c,0,sizeof(long)*k);
|
|
|
616
|
|
|
617 center=(double**)malloc(sizeof(double*)*k);
|
|
|
618 memset(center,0,sizeof(double*)*k);
|
|
|
619 for (i=0;i<k;i++)
|
|
|
620 {
|
|
|
621 center[i]=(double*)malloc(sizeof(double)*num_dm);
|
|
|
622 memset(center[i],0,sizeof(double)*num_dm);
|
|
|
623 }
|
|
|
624
|
|
|
625 mybound=(double**)malloc(sizeof(double*)*num_dm);
|
|
|
626 memset(mybound,0,sizeof(double*)*num_dm);
|
|
|
627 for (i=0;i<num_dm;i++) //there are 3 mybounds for 4 categories
|
|
|
628 {
|
|
|
629 mybound[i]=(double*)malloc(sizeof(double)*3);
|
|
|
630 memset(mybound[i],0,sizeof(double)*3);
|
|
|
631 }
|
|
|
632
|
|
|
633 prof=(long **)malloc(sizeof(long*)*k);
|
|
|
634 memset(prof,0,sizeof(long*)*k);
|
|
|
635 for (i=0;i<k;i++)
|
|
|
636 {
|
|
|
637 prof[i]=(long *)malloc(sizeof(long)*num_dm);
|
|
|
638 memset(prof[i],0,sizeof(long)*num_dm);
|
|
|
639 }
|
|
|
640
|
|
|
641
|
|
|
642 for (i=0;i<file_Len;i++)
|
|
|
643 {
|
|
|
644 id=cluster_id[i];
|
|
|
645 for (j=0;j<num_dm;j++)
|
|
|
646 {
|
|
|
647 center[id][j]=center[id][j]+Matrix[i][j];
|
|
|
648 if (big[j]<Matrix[i][j])
|
|
|
649 big[j]=Matrix[i][j];
|
|
|
650 if (small[j]>Matrix[i][j])
|
|
|
651 small[j]=Matrix[i][j];
|
|
|
652 }
|
|
|
653
|
|
|
654 size_c[id]++;
|
|
|
655 }
|
|
|
656
|
|
|
657 for (i=0;i<k;i++)
|
|
|
658 for (j=0;j<num_dm;j++)
|
|
|
659 {
|
|
|
660 if (size_c[i]!=0)
|
|
|
661 center[i][j]=(center[i][j]/(double)(size_c[i]));
|
|
|
662 else
|
|
|
663 center[i][j]=0;
|
|
|
664 }
|
|
|
665
|
|
|
666 for (j=0;j<num_dm;j++)
|
|
|
667 {
|
|
|
668 interval=((big[j]-small[j])/4.0);
|
|
|
669 //printf("interval[%d] is %f\n",j,interval);
|
|
|
670 for (i=0;i<3;i++)
|
|
|
671 mybound[j][i]=small[j]+((double)(i+1)*interval);
|
|
|
672 }
|
|
|
673
|
|
|
674
|
|
|
675 size_mybound_0=(long **)malloc(sizeof(long*)*k);
|
|
|
676 memset(size_mybound_0,0,sizeof(long*)*k);
|
|
|
677
|
|
|
678 for (i=0;i<k;i++)
|
|
|
679 {
|
|
|
680 size_mybound_0[i]=(long*)malloc(sizeof(long)*num_dm);
|
|
|
681 memset(size_mybound_0[i],0,sizeof(long)*num_dm);
|
|
|
682 }
|
|
|
683
|
|
|
684 size_mybound_1=(long **)malloc(sizeof(long*)*k);
|
|
|
685 memset(size_mybound_1,0,sizeof(long*)*k);
|
|
|
686
|
|
|
687 for (i=0;i<k;i++)
|
|
|
688 {
|
|
|
689 size_mybound_1[i]=(long*)malloc(sizeof(long)*num_dm);
|
|
|
690 memset(size_mybound_1[i],0,sizeof(long)*num_dm);
|
|
|
691 }
|
|
|
692
|
|
|
693 size_mybound_2=(long **)malloc(sizeof(long*)*k);
|
|
|
694 memset(size_mybound_2,0,sizeof(long*)*k);
|
|
|
695
|
|
|
696 for (i=0;i<k;i++)
|
|
|
697 {
|
|
|
698 size_mybound_2[i]=(long*)malloc(sizeof(long)*num_dm);
|
|
|
699 memset(size_mybound_2[i],0,sizeof(long)*num_dm);
|
|
|
700 }
|
|
|
701
|
|
|
702 size_mybound_3=(long **)malloc(sizeof(long*)*k);
|
|
|
703 memset(size_mybound_3,0,sizeof(long*)*k);
|
|
|
704
|
|
|
705 for (i=0;i<k;i++)
|
|
|
706 {
|
|
|
707 size_mybound_3[i]=(long*)malloc(sizeof(long)*num_dm);
|
|
|
708 memset(size_mybound_3[i],0,sizeof(long)*num_dm);
|
|
|
709 }
|
|
|
710
|
|
|
711 for (i=0;i<file_Len;i++)
|
|
|
712 for (j=0;j<num_dm;j++)
|
|
|
713 {
|
|
|
714 if (Matrix[i][j]<mybound[j][0])// && ((Matrix[i][j]-small[j])>0)) //the smallest values excluded
|
|
|
715 size_mybound_0[cluster_id[i]][j]++;
|
|
|
716 else
|
|
|
717 {
|
|
|
718 if (Matrix[i][j]<mybound[j][1])
|
|
|
719 size_mybound_1[cluster_id[i]][j]++;
|
|
|
720 else
|
|
|
721 {
|
|
|
722 if (Matrix[i][j]<mybound[j][2])
|
|
|
723 size_mybound_2[cluster_id[i]][j]++;
|
|
|
724 else
|
|
|
725 //if (Matrix[i][j]!=big[j]) //the biggest values excluded
|
|
|
726 size_mybound_3[cluster_id[i]][j]++;
|
|
|
727 }
|
|
|
728
|
|
|
729 }
|
|
|
730 }
|
|
|
731
|
|
|
732 fprof_id=fopen("profile.txt","w");
|
|
|
733 fprintf(fprof_id,"Population_ID\t");
|
|
|
734 fprintf(fprof_id,"%s\n",name_string);
|
|
|
735
|
|
|
736 for (i=0;i<k;i++)
|
|
|
737 {
|
|
|
738 fprintf(fprof_id,"%ld\t",IDmapping[i]);
|
|
|
739 for (j=0;j<num_dm;j++)
|
|
|
740 {
|
|
|
741
|
|
|
742 if (size_mybound_0[i][j]>size_mybound_1[i][j])
|
|
|
743 situ1=0;
|
|
|
744 else
|
|
|
745 situ1=1;
|
|
|
746 if (size_mybound_2[i][j]>size_mybound_3[i][j])
|
|
|
747 situ2=2;
|
|
|
748 else
|
|
|
749 situ2=3;
|
|
|
750
|
|
|
751 if ((situ1==0) && (situ2==2))
|
|
|
752 {
|
|
|
753 if (size_mybound_0[i][j]>size_mybound_2[i][j])
|
|
|
754 prof[i][j]=0;
|
|
|
755 else
|
|
|
756 prof[i][j]=2;
|
|
|
757 }
|
|
|
758 if ((situ1==0) && (situ2==3))
|
|
|
759 {
|
|
|
760 if (size_mybound_0[i][j]>size_mybound_3[i][j])
|
|
|
761 prof[i][j]=0;
|
|
|
762 else
|
|
|
763 prof[i][j]=3;
|
|
|
764 }
|
|
|
765 if ((situ1==1) && (situ2==2))
|
|
|
766 {
|
|
|
767 if (size_mybound_1[i][j]>size_mybound_2[i][j])
|
|
|
768 prof[i][j]=1;
|
|
|
769 else
|
|
|
770 prof[i][j]=2;
|
|
|
771 }
|
|
|
772 if ((situ1==1) && (situ2==3))
|
|
|
773 {
|
|
|
774 if (size_mybound_1[i][j]>size_mybound_3[i][j])
|
|
|
775 prof[i][j]=1;
|
|
|
776 else
|
|
|
777 prof[i][j]=3;
|
|
|
778 }
|
|
|
779
|
|
|
780 //begin to output profile
|
|
|
781 if (j==num_dm-1)
|
|
|
782 {
|
|
|
783 if (prof[i][j]==0)
|
|
|
784 fprintf(fprof_id,"1\n");
|
|
|
785 if (prof[i][j]==1)
|
|
|
786 fprintf(fprof_id,"2\n");
|
|
|
787 if (prof[i][j]==2)
|
|
|
788 fprintf(fprof_id,"3\n");
|
|
|
789 if (prof[i][j]==3)
|
|
|
790 fprintf(fprof_id,"4\n");
|
|
|
791 }
|
|
|
792 else
|
|
|
793 {
|
|
|
794 if (prof[i][j]==0)
|
|
|
795 fprintf(fprof_id,"1\t");
|
|
|
796 if (prof[i][j]==1)
|
|
|
797 fprintf(fprof_id,"2\t");
|
|
|
798 if (prof[i][j]==2)
|
|
|
799 fprintf(fprof_id,"3\t");
|
|
|
800 if (prof[i][j]==3)
|
|
|
801 fprintf(fprof_id,"4\t");
|
|
|
802 }
|
|
|
803 }
|
|
|
804 }
|
|
|
805 fclose(fprof_id);
|
|
|
806
|
|
|
807 ///////////////////////////////////////////////////////////
|
|
|
808
|
|
|
809
|
|
|
810 fpcnt_id=fopen("percentage.txt","w");
|
|
|
811 fprintf(fpcnt_id,"Population_ID\tPercentage\n");
|
|
|
812
|
|
|
813 for (t=0;t<k;t++)
|
|
|
814 {
|
|
|
815 fprintf(fpcnt_id,"%ld\t%.2f\n",IDmapping[t],(double)size_c[t]*100.0/(double)file_Len);
|
|
|
816 }
|
|
|
817 fclose(fpcnt_id);
|
|
|
818
|
|
|
819 free(big);
|
|
|
820 free(small);
|
|
|
821 free(size_c);
|
|
|
822
|
|
|
823 for (i=0;i<k;i++)
|
|
|
824 {
|
|
|
825 free(center[i]);
|
|
|
826 free(prof[i]);
|
|
|
827 free(size_mybound_0[i]);
|
|
|
828 free(size_mybound_1[i]);
|
|
|
829 free(size_mybound_2[i]);
|
|
|
830 free(size_mybound_3[i]);
|
|
|
831 }
|
|
|
832 free(center);
|
|
|
833 free(prof);
|
|
|
834 free(size_mybound_0);
|
|
|
835 free(size_mybound_1);
|
|
|
836 free(size_mybound_2);
|
|
|
837 free(size_mybound_3);
|
|
|
838
|
|
|
839 for (i=0;i<num_dm;i++)
|
|
|
840 free(mybound[i]);
|
|
|
841 free(mybound);
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842
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843 }
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844 /******************************************************** Main Function **************************************************/
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845 int main (int argc, char **argv)
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846 {
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847 //inputs
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848 FILE *f_src; //source file pointer
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849 FILE *f_src_ctr; //source center file
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850 //outputs
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851 FILE *f_cid; //cluster-id file pointer
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852 FILE *f_mfi; //added April 16, 2009
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853
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854
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855 char name_string[LINE_LEN]; //for name use
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856
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857 int time_id=-1;
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858
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859 long file_Len=0;
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860 long num_clust=0;
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861 long num_dm=0;
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862 long norm_used=0;
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863 long dist_used=0;
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864 long i=0;
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865 long j=0;
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866
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867 long *cluster_id;
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868 long *IDmapping; //this is to keep the original populationID of the center.txt
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869
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870 double kmean_term=0;
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871
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872 double **cluster_center;
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873 double **orig_data;
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874 double **normalized_data;
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875
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876 /*
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877 _strtime( tmpbuf );
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878 printf( "Starting time:\t\t\t\t%s\n", tmpbuf );
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879 _strdate( tmpbuf );
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880 printf( "Starting date:\t\t\t\t%s\n", tmpbuf );
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881 */
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882
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883 if (argc!=3)
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884 {
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885 printf("usage: cent_adjust input_center input_data_file\n");
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886 exit(0);
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887 }
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888
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889
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890 f_src_ctr=fopen(argv[1],"r");
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891
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892 //read source data
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893 f_src=fopen(argv[2],"r");
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894
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895 getfileinfo(f_src, &file_Len, &num_dm, name_string, &time_id); //get the filelength, number of dimensions, and num/name of parameters
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896
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897 rewind(f_src); //reset data file pointer
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898
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899 orig_data = (double **)malloc(sizeof(double*)*file_Len);
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900 memset(orig_data,0,sizeof(double*)*file_Len);
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901 for (i=0;i<file_Len;i++)
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902 {
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903 orig_data[i]=(double *)malloc(sizeof(double)*num_dm);
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904 memset(orig_data[i],0,sizeof(double)*num_dm);
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905 }
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906
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907 readsource(f_src, file_Len, num_dm, orig_data, time_id); //read the data;
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908
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909 fclose(f_src);
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910 /////////////////////////////////////////////////////////////////////////////
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|
911 getctrfileinfo(f_src_ctr, &num_clust); //get how many populations
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912 norm_used=0;
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|
|
913 dist_used=0;
|
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|
914 kmean_term=2; //modified on Oct 16, 2009: changed kmean_term=1 to kmean_term=2
|
|
|
915
|
|
|
916 rewind(f_src_ctr); //reset center file pointer
|
|
|
917
|
|
|
918 //read population center
|
|
|
919 cluster_center=(double **)malloc(sizeof(double*)*num_clust);
|
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|
920 memset(cluster_center,0,sizeof(double*)*num_clust);
|
|
|
921 for (i=0;i<num_clust;i++)
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922 {
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|
|
923 cluster_center[i]=(double*)malloc(sizeof(double)*num_dm);
|
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|
924 memset(cluster_center[i],0,sizeof(double)*num_dm);
|
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|
925 }
|
|
|
926 for (i=0;i<num_clust;i++)
|
|
|
927 for (j=0;j<num_dm;j++)
|
|
|
928 cluster_center[i][j]=0;
|
|
|
929
|
|
|
930 IDmapping=(long *)malloc(sizeof(long)*num_clust);
|
|
|
931 memset(IDmapping,0,sizeof(long)*num_clust);
|
|
|
932
|
|
|
933 readcenter(f_src_ctr,num_clust,num_dm,cluster_center,IDmapping); //read population center
|
|
|
934 fclose(f_src_ctr);
|
|
|
935
|
|
|
936 /////////////////////////////////////////////////////////////////////////////
|
|
|
937 normalized_data=(double **)malloc(sizeof(double*)*file_Len);
|
|
|
938 memset(normalized_data,0,sizeof(double*)*file_Len);
|
|
|
939 for (i=0;i<file_Len;i++)
|
|
|
940 {
|
|
|
941 normalized_data[i]=(double *)malloc(sizeof(double)*num_dm);
|
|
|
942 memset(normalized_data[i],0,sizeof(double)*num_dm);
|
|
|
943 }
|
|
|
944
|
|
|
945 tran(orig_data, file_Len, num_dm, norm_used, normalized_data);
|
|
|
946 /************************************************* Compute number of clusters *************************************************/
|
|
|
947
|
|
|
948 cluster_id=(long*)malloc(sizeof(long)*file_Len);
|
|
|
949 memset(cluster_id,0,sizeof(long)*file_Len);
|
|
|
950
|
|
|
951 assign_event(normalized_data,num_clust,dist_used,kmean_term,file_Len,num_dm,cluster_id,cluster_center,0);
|
|
|
952
|
|
|
953
|
|
|
954 //show(orig_data,cluster_id,file_Len,num_clust,num_dm,show_data,num_disp,name_string);
|
|
|
955 show(orig_data, cluster_id, file_Len, num_clust, num_dm, name_string, IDmapping);
|
|
|
956
|
|
|
957 f_cid=fopen("population_id.txt","w");
|
|
|
958
|
|
|
959 for (i=0;i<file_Len;i++)
|
|
|
960 fprintf(f_cid,"%ld\n",IDmapping[cluster_id[i]]);
|
|
|
961
|
|
|
962
|
|
|
963 fclose(f_cid);
|
|
|
964
|
|
|
965 //added April 16, 2009
|
|
|
966 f_mfi=fopen("MFI.txt","w");
|
|
|
967
|
|
|
968 for (i=0;i<num_clust;i++)
|
|
|
969 {
|
|
|
970 fprintf(f_mfi,"%ld\t",IDmapping[i]);
|
|
|
971
|
|
|
972 for (j=0;j<num_dm;j++)
|
|
|
973 {
|
|
|
974 if (j==num_dm-1)
|
|
|
975 fprintf(f_mfi,"%.0f\n",cluster_center[i][j]);
|
|
|
976 else
|
|
|
977 fprintf(f_mfi,"%.0f\t",cluster_center[i][j]);
|
|
|
978 }
|
|
|
979 }
|
|
|
980 fclose(f_mfi);
|
|
|
981
|
|
|
982 //ended April 16, 2009
|
|
|
983
|
|
|
984 for (i=0;i<num_clust;i++)
|
|
|
985 free(cluster_center[i]);
|
|
|
986 free(cluster_center);
|
|
|
987
|
|
|
988
|
|
|
989 /********************************************** Release memory ******************************************/
|
|
|
990
|
|
|
991 for (i=0;i<file_Len;i++)
|
|
|
992 {
|
|
|
993 free(orig_data[i]);
|
|
|
994 free(normalized_data[i]);
|
|
|
995 }
|
|
|
996
|
|
|
997 free(orig_data);
|
|
|
998 free(normalized_data);
|
|
|
999 free(cluster_id);
|
|
|
1000 free(IDmapping);
|
|
|
1001
|
|
|
1002 /*
|
|
|
1003 _strtime( tmpbuf );
|
|
|
1004 printf( "Ending time:\t\t\t\t%s\n", tmpbuf );
|
|
|
1005 _strdate( tmpbuf );
|
|
|
1006 printf( "Ending date:\t\t\t\t%s\n", tmpbuf );
|
|
|
1007 */
|
|
|
1008
|
|
|
1009 }
|
