bio-affy 0.1.0.alpha.1

data/ext/src/read_celfile_generic.c

@@ -0,0 +1,2061 @@
+/*************************************************************
+ **
+ ** file: read_celfile_generic.c
+ **
+ ** Written by B. M. Bolstad <bmb@bmbolstad.com>
+ **
+ ** Aim is to read in Affymetrix CEL files in the
+ ** "Command Console Generic Data" File Format
+ ** This format is sometimes known as the Calvin format
+ **
+ ** As with other file format functionality in affyio
+ ** gzipped files are accepted.
+ **
+ ** The implementation here is based upon openly available 
+ ** file format information. The code here is not dependent or based
+ ** in anyway on that in the Fusion SDK.
+ **
+ **
+ ** History
+ ** Sept 3, 2007 -Initial version
+ ** Sept 9, 2007 - fix compiler warnings
+ ** Oct 11, 2007 - fix missing DatHeader problem
+ ** Feb 11, 2008 - add #include for inttypes.h in situations that stdint.h might not exist
+ ** Feb 13, 2008 - fix problems with generic_get_detailed_header_info(), gzgeneric_get_detailed_header_info()
+ ** May 18, 2009 - Add Ability to extract scan date from CEL file header
+ **
+ *************************************************************/
+#include <R.h>
+#include <Rdefines.h>
+#include <Rmath.h>
+#include <Rinternals.h>
+
+#define HAVE_STDINT_H 1
+#ifdef HAVE_STDINT_H
+#include <stdint.h>
+#elif HAVE_INTTYPES_H
+#include <inttypes.h>
+#endif
+#include <wchar.h>
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <zlib.h>
+
+#include "read_generic.h"
+#include "read_celfile_generic.h"
+#include "read_abatch.h"
+
+int isGenericCelFile(const char *filename){
+
+  FILE *infile;
+  generic_file_header file_header;
+  generic_data_header data_header;
+  
+  if ((infile = fopen(filename, "rb")) == NULL)
+    {
+      error("Unable to open the file %s",filename);
+      return 0;
+    }
+
+  if (!read_generic_file_header(&file_header,infile)){
+    fclose(infile);
+    return 0;
+  }
+
+  if (!read_generic_data_header(&data_header,infile)){
+    Free_generic_data_header(&data_header);
+    fclose(infile);
+    return 0;
+  }
+  
+  if (strcmp(data_header.data_type_id.value, "affymetrix-calvin-intensity") !=0){
+    Free_generic_data_header(&data_header);
+ 
+
+
+   fclose(infile);
+    return 0;
+  }
+  Free_generic_data_header(&data_header);
+  
+  fclose(infile);
+  return 1;
+}
+
+
+
+char *generic_get_header_info(const char *filename, int *dim1, int *dim2){
+
+  FILE *infile;
+  generic_file_header file_header;
+  generic_data_header data_header;
+
+  char *cdfName = 0;
+
+  nvt_triplet *triplet;
+  AffyMIMEtypes cur_mime_type;
+
+  int size;
+
+  wchar_t *wchartemp=0;
+  
+  if ((infile = fopen(filename, "rb")) == NULL)
+    {
+      error("Unable to open the file %s",filename);
+      return 0;
+    }
+  
+  read_generic_file_header(&file_header,infile);
+  read_generic_data_header(&data_header,infile);
+
+  /*  affymetrix-array-type  text/plainText/plain String is HG-U133_Plus_2
+      Now Trying it again. But using exposed function
+      Its a Text/plain string value is HG-U133_Plus_2 with size 14
+      affymetrix-cel-cols  text/x-calvin-integer-32Its a int32_t  value is 1164
+      Now Trying it again. But using exposed function
+      Its a int32_t  value is 1164
+      affymetrix-cel-rows  text/x-calvin-integer-32Its a int32_t  value is 1164
+  */
+
+  triplet =  find_nvt(&data_header,"affymetrix-array-type");
+  
+  cur_mime_type = determine_MIMETYPE(*triplet);
+
+  wchartemp = decode_MIME_value(*triplet,cur_mime_type, wchartemp, &size);
+  cdfName = Calloc(size + 1, char);
+  wcstombs(cdfName, wchartemp, size);
+  Free(wchartemp);
+
+  triplet =  find_nvt(&data_header,"affymetrix-cel-cols");
+  cur_mime_type = determine_MIMETYPE(*triplet);
+  decode_MIME_value(*triplet,cur_mime_type, dim1, &size);
+  
+  triplet =  find_nvt(&data_header,"affymetrix-cel-rows");
+  cur_mime_type = determine_MIMETYPE(*triplet);
+  decode_MIME_value(*triplet,cur_mime_type, dim2, &size);
+  
+  Free_generic_data_header(&data_header);
+  fclose(infile);
+
+  return cdfName;
+ 
+}
+
+
+
+
+void generic_get_detailed_header_info(const char *filename, detailed_header_info *header_info){
+  
+  FILE *infile;
+  generic_file_header file_header;
+  generic_data_header data_header;
+  nvt_triplet *triplet;
+  AffyMIMEtypes cur_mime_type;
+  int size;
+
+  int algorithm_paramsize = 0;
+  float tempfloat;
+
+  wchar_t *wchartemp=0;
+  char *chartemp=0;
+  
+  if ((infile = fopen(filename, "rb")) == NULL)
+    {
+      error("Unable to open the file %s",filename);
+    }
+  
+  read_generic_file_header(&file_header,infile);
+  read_generic_data_header(&data_header,infile);
+  
+  triplet =  find_nvt(&data_header,"affymetrix-array-type");
+
+  cur_mime_type = determine_MIMETYPE(*triplet);
+
+  wchartemp = decode_MIME_value(*triplet,cur_mime_type, wchartemp, &size);
+  header_info->cdfName = Calloc(size + 1, char);
+  wcstombs(header_info->cdfName, wchartemp, size);
+  Free(wchartemp);
+
+  triplet =  find_nvt(&data_header,"affymetrix-cel-cols");
+  cur_mime_type = determine_MIMETYPE(*triplet);
+  decode_MIME_value(*triplet,cur_mime_type, &(header_info->cols), &size);
+  
+  triplet =  find_nvt(&data_header,"affymetrix-cel-rows");
+  cur_mime_type = determine_MIMETYPE(*triplet);
+  decode_MIME_value(*triplet,cur_mime_type, &(header_info->rows), &size);
+  
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-GridULX"); 
+  cur_mime_type = determine_MIMETYPE(*triplet);
+  decode_MIME_value(*triplet,cur_mime_type, &tempfloat, &size);
+  header_info->GridCornerULx = (int)(tempfloat +0.5);
+
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-GridULY"); 
+  cur_mime_type = determine_MIMETYPE(*triplet);
+  decode_MIME_value(*triplet,cur_mime_type, &tempfloat, &size);
+  header_info->GridCornerULy = (int)(tempfloat +0.5);
+  
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-GridURX"); 
+  cur_mime_type = determine_MIMETYPE(*triplet);
+  decode_MIME_value(*triplet,cur_mime_type, &tempfloat, &size);
+  header_info->GridCornerURx = (int)(tempfloat +0.5);
+  
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-GridURY"); 
+  cur_mime_type = determine_MIMETYPE(*triplet);
+  decode_MIME_value(*triplet,cur_mime_type, &tempfloat, &size);
+  header_info->GridCornerURy = (int)(tempfloat +0.5);
+  
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-GridLLX"); 
+  cur_mime_type = determine_MIMETYPE(*triplet);
+  decode_MIME_value(*triplet,cur_mime_type, &tempfloat, &size);
+  header_info->GridCornerLLx = (int)(tempfloat +0.5);
+
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-GridLLY"); 
+  cur_mime_type = determine_MIMETYPE(*triplet);
+  decode_MIME_value(*triplet,cur_mime_type, &tempfloat, &size);
+  header_info->GridCornerLLy = (int)(tempfloat +0.5);
+  
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-GridLRX"); 
+  cur_mime_type = determine_MIMETYPE(*triplet);
+  decode_MIME_value(*triplet,cur_mime_type, &tempfloat, &size);
+  header_info->GridCornerLRx = (int)(tempfloat +0.5);
+  
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-GridLRY"); 
+  cur_mime_type = determine_MIMETYPE(*triplet);
+  decode_MIME_value(*triplet,cur_mime_type, &tempfloat, &size);
+  header_info->GridCornerLRy = (int)(tempfloat +0.5);
+  
+    
+  triplet =  find_nvt(&data_header,"affymetrix-dat-header");
+  
+  if (triplet != NULL){
+    cur_mime_type = determine_MIMETYPE(*triplet);
+    
+    wchartemp = decode_MIME_value(*triplet,cur_mime_type, wchartemp, &size);
+    header_info->DatHeader = Calloc(size + 1, char);
+    wcstombs(header_info->DatHeader, wchartemp, size);
+    Free(wchartemp);
+  } else {
+    header_info->DatHeader = Calloc(2, char);
+  }
+
+ triplet =  find_nvt(&data_header,"affymetrix-scan-date");
+  
+  if (triplet != NULL){
+    cur_mime_type = determine_MIMETYPE(*triplet);
+    
+    wchartemp = decode_MIME_value(*triplet,cur_mime_type, wchartemp, &size);
+    header_info->ScanDate = Calloc(size + 1, char);
+    wcstombs(header_info->ScanDate, wchartemp, size);
+    Free(wchartemp);
+  } else {
+    header_info->ScanDate = Calloc(2, char);
+  }
+
+
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-name");
+  cur_mime_type = determine_MIMETYPE(*triplet);
+
+  wchartemp = decode_MIME_value(*triplet,cur_mime_type, wchartemp, &size);
+  header_info->Algorithm = Calloc(size + 1, char);
+  wcstombs(header_info->Algorithm, wchartemp, size);
+  Free(wchartemp);
+  
+
+
+  //  "Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004;AlgVersion:6.0;FixedCellSize:TRUE;FullFeatureWidth:7;FullFeatureHeight:7;IgnoreOutliersInShiftRows:FALSE;FeatureExtraction:TRUE;PoolWidthExtenstion:2;PoolHeightExtension:2;UseSubgrids:FALSE;RandomizePixels:FALSE;ErrorBasis:StdvMean;StdMult:1.00000"
+
+  algorithm_paramsize = 0;
+  
+  header_info->AlgorithmParameters = Calloc(11, char);
+  strncpy(header_info->AlgorithmParameters,"Percentile:",11);
+  algorithm_paramsize+=11;
+
+    
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-Percentile");
+  if (triplet != NULL){
+    cur_mime_type = determine_MIMETYPE(*triplet);
+    
+    chartemp = decode_MIME_value_toASCII(*triplet,cur_mime_type, chartemp, &size);
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + size +1, char);
+    strncpy(&header_info->AlgorithmParameters[algorithm_paramsize], chartemp, size);
+    algorithm_paramsize+= size +1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+    Free(chartemp);
+  } else {
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 1, char);
+    algorithm_paramsize+= 1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+  }
+
+  
+  header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 11, char);
+  strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"CellMargin:",11);
+  algorithm_paramsize+=11;
+
+    
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-CellMargin"); 
+  if (triplet != NULL){
+    cur_mime_type = determine_MIMETYPE(*triplet);
+    
+    chartemp = decode_MIME_value_toASCII(*triplet,cur_mime_type, chartemp, &size);
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + size +1, char);
+    strncpy(&header_info->AlgorithmParameters[algorithm_paramsize], chartemp, size);
+    algorithm_paramsize+= size +1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+    Free(chartemp);
+  } else {
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 1, char);
+    algorithm_paramsize+= 1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+  }
+
+  header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 12, char);
+  strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"OutlierHigh:",12);
+  algorithm_paramsize+=12;
+
+    
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-OutlierHigh");
+  if (triplet != NULL){
+    cur_mime_type = determine_MIMETYPE(*triplet);
+    
+    chartemp = decode_MIME_value_toASCII(*triplet,cur_mime_type, chartemp, &size);
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + size +1, char);
+    strncpy(&header_info->AlgorithmParameters[algorithm_paramsize], chartemp, size);
+    algorithm_paramsize+= size +1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+    Free(chartemp);
+  } else {
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 1, char);
+    algorithm_paramsize+= 1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+  }
+  
+  header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 11, char);
+  strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"OutlierLow:",11);
+  algorithm_paramsize+=11;
+
+    
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-OutlierLow");
+  if (triplet != NULL){
+    cur_mime_type = determine_MIMETYPE(*triplet);
+    
+    chartemp = decode_MIME_value_toASCII(*triplet,cur_mime_type, chartemp, &size);
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + size +1, char);
+    strncpy(&header_info->AlgorithmParameters[algorithm_paramsize], chartemp, size);
+    algorithm_paramsize+= size +1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+    Free(chartemp);
+  } else {
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 1, char);
+    algorithm_paramsize+= 1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+  }
+  
+  header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 11, char);
+  strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"AlgVersion:",11);
+  algorithm_paramsize+=11;
+
+    
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-AlgVersion");
+  if (triplet != NULL){
+    cur_mime_type = determine_MIMETYPE(*triplet);
+    
+    chartemp = decode_MIME_value_toASCII(*triplet,cur_mime_type, chartemp, &size);
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + size +1, char);
+    strncpy(&header_info->AlgorithmParameters[algorithm_paramsize], chartemp, size);
+    algorithm_paramsize+= size +1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+    Free(chartemp);
+  } else {
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 1, char);
+    algorithm_paramsize+= 1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+  }
+
+  header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 14, char);
+  strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FixedCellSize:",14);
+  algorithm_paramsize+=14;
+
+    
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-FixedCellSize");
+  if (triplet != NULL){
+    cur_mime_type = determine_MIMETYPE(*triplet);
+    
+    chartemp = decode_MIME_value_toASCII(*triplet,cur_mime_type, chartemp, &size);
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + size +1, char);
+    strncpy(&header_info->AlgorithmParameters[algorithm_paramsize], chartemp, size);
+    algorithm_paramsize+= size +1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+    Free(chartemp);
+  } else {
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 1, char);
+    algorithm_paramsize+= 1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+  }
+  
+  header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 17, char);
+  strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FullFeatureWidth:",17);
+  algorithm_paramsize+=17;
+
+    
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-FullFeatureWidth");
+  if (triplet != NULL){
+    cur_mime_type = determine_MIMETYPE(*triplet);
+    
+    chartemp = decode_MIME_value_toASCII(*triplet,cur_mime_type, chartemp, &size);
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + size +1, char);
+    strncpy(&header_info->AlgorithmParameters[algorithm_paramsize], chartemp, size);
+    algorithm_paramsize+= size +1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+     Free(chartemp);
+  } else {
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 1, char);
+    algorithm_paramsize+= 1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+  }
+  
+  header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 18, char);
+  strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FullFeatureHeight:",18);
+  algorithm_paramsize+=18;
+
+    
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-FullFeatureHeight");
+  if (triplet != NULL){
+    cur_mime_type = determine_MIMETYPE(*triplet);
+    
+    chartemp = decode_MIME_value_toASCII(*triplet,cur_mime_type, chartemp, &size);
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + size +1, char);
+    strncpy(&header_info->AlgorithmParameters[algorithm_paramsize], chartemp, size);
+    algorithm_paramsize+= size +1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+    Free(chartemp);
+  } else {
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 1, char);
+    algorithm_paramsize+= 1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+  }
+  
+  header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 26, char);
+  strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"IgnoreOutliersInShiftRows:",26);
+  algorithm_paramsize+=26;
+
+    
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-IgnoreOutliersInShiftRows");
+  if (triplet != NULL){
+    cur_mime_type = determine_MIMETYPE(*triplet);
+    
+    chartemp = decode_MIME_value_toASCII(*triplet,cur_mime_type, chartemp, &size);
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + size +1, char);
+    strncpy(&header_info->AlgorithmParameters[algorithm_paramsize], chartemp, size);
+    algorithm_paramsize+= size +1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+    Free(chartemp);
+  } else {
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 1, char);
+    algorithm_paramsize+= 1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+  }
+
+
+
+  header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 18, char);
+  strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FeatureExtraction:",18);
+  algorithm_paramsize+=18;
+
+    
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-FeatureExtraction");
+  if (triplet != NULL){
+    cur_mime_type = determine_MIMETYPE(*triplet);
+    
+    chartemp = decode_MIME_value_toASCII(*triplet,cur_mime_type, chartemp, &size);
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + size +1, char);
+    strncpy(&header_info->AlgorithmParameters[algorithm_paramsize], chartemp, size);
+    algorithm_paramsize+= size +1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+    Free(chartemp);
+  } else {
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 1, char);
+    algorithm_paramsize+= 1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+  }
+
+
+
+  
+  header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 20, char);
+  strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"PoolWidthExtenstion:",20);
+  algorithm_paramsize+=20;
+
+    
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-PoolWidthExtenstion");
+  if (triplet != NULL){
+    cur_mime_type = determine_MIMETYPE(*triplet);
+    
+    chartemp = decode_MIME_value_toASCII(*triplet,cur_mime_type, chartemp, &size);
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + size +1, char);
+    strncpy(&header_info->AlgorithmParameters[algorithm_paramsize], chartemp, size);
+    algorithm_paramsize+= size +1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+    Free(chartemp);
+  } else {
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 1, char);
+    algorithm_paramsize+= 1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+  }
+
+  
+  header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 20, char);
+  strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"PoolHeightExtension:",20);
+  algorithm_paramsize+=20;
+
+    
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-PoolHeightExtension");
+  if (triplet != NULL){
+    cur_mime_type = determine_MIMETYPE(*triplet);
+    
+    chartemp = decode_MIME_value_toASCII(*triplet,cur_mime_type, chartemp, &size);
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + size +1, char);
+    strncpy(&header_info->AlgorithmParameters[algorithm_paramsize], chartemp, size);
+    algorithm_paramsize+= size +1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+    Free(chartemp);
+  } else {
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 1, char);
+    algorithm_paramsize+= 1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+  }
+
+
+  header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 12, char);
+  strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"UseSubgrids:",12);
+  algorithm_paramsize+=12;
+  
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-UseSubgrids");
+  if (triplet != NULL){
+    cur_mime_type = determine_MIMETYPE(*triplet);
+    
+    chartemp = decode_MIME_value_toASCII(*triplet,cur_mime_type, chartemp, &size);
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + size +1, char);
+    strncpy(&header_info->AlgorithmParameters[algorithm_paramsize], chartemp, size);
+    algorithm_paramsize+= size +1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+    Free(chartemp);
+  } else {
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 1, char);
+    algorithm_paramsize+= 1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+  }
+
+
+  header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 16, char);
+  strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"RandomizePixels:",16);
+  algorithm_paramsize+=16;
+    
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-RandomizePixels");
+  if (triplet != NULL){
+    cur_mime_type = determine_MIMETYPE(*triplet);
+    
+    chartemp = decode_MIME_value_toASCII(*triplet,cur_mime_type, chartemp, &size);
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + size +1, char);
+    strncpy(&header_info->AlgorithmParameters[algorithm_paramsize], chartemp, size);
+    algorithm_paramsize+= size +1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+    Free(chartemp);
+  } else {
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 1, char);
+    algorithm_paramsize+= 1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+  }
+
+
+
+  header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 11, char);
+  strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"ErrorBasis:",11);
+  algorithm_paramsize+=11;
+
+    
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-ErrorBasis");
+  if (triplet != NULL){
+    cur_mime_type = determine_MIMETYPE(*triplet);
+    
+    chartemp = decode_MIME_value_toASCII(*triplet,cur_mime_type, chartemp, &size);
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + size +1, char);
+    strncpy(&header_info->AlgorithmParameters[algorithm_paramsize], chartemp, size);
+    algorithm_paramsize+= size +1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+    Free(chartemp);
+  } else {
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 1, char);
+    algorithm_paramsize+= 1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+  }
+
+  
+  header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 8, char);
+  strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"StdMult:",8);
+  algorithm_paramsize+=8;
+
+    
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-StdMult");
+  if (triplet != NULL){
+    cur_mime_type = determine_MIMETYPE(*triplet);
+    
+    chartemp = decode_MIME_value_toASCII(*triplet,cur_mime_type, chartemp, &size);
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + size +1, char);
+    strncpy(&header_info->AlgorithmParameters[algorithm_paramsize], chartemp, size);
+    algorithm_paramsize+= size +1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+    Free(chartemp);
+  } else {
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 1, char);
+    algorithm_paramsize+= 1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+  }
+
+
+  
+  header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 1, char);
+  header_info->AlgorithmParameters[algorithm_paramsize] ='\0';
+  
+
+  Free_generic_data_header(&data_header);
+  fclose(infile);
+
+
+
+}
+
+
+
+
+int check_generic_cel_file(const char *filename, const char *ref_cdfName, int ref_dim_1, int ref_dim_2){
+
+  char *cdfName =0;
+  int dim1, dim2;
+
+
+  FILE *infile;
+  generic_file_header file_header;
+  generic_data_header data_header;
+  
+  nvt_triplet *triplet;
+  AffyMIMEtypes cur_mime_type;
+  
+  int size;
+
+  wchar_t *wchartemp=0;
+  
+
+  if ((infile = fopen(filename, "rb")) == NULL)
+    {
+      error("Unable to open the file %s",filename);
+      return 0;
+    }
+
+  read_generic_file_header(&file_header,infile);
+  read_generic_data_header(&data_header,infile);
+  
+
+   triplet =  find_nvt(&data_header,"affymetrix-array-type");
+  
+  cur_mime_type = determine_MIMETYPE(*triplet);
+
+  wchartemp = decode_MIME_value(*triplet,cur_mime_type, wchartemp, &size);
+  cdfName = Calloc(size + 1, char);
+  wcstombs(cdfName, wchartemp, size);
+  Free(wchartemp);
+
+  triplet =  find_nvt(&data_header,"affymetrix-cel-cols");
+  cur_mime_type = determine_MIMETYPE(*triplet);
+  decode_MIME_value(*triplet,cur_mime_type, &dim1, &size);
+  
+  triplet =  find_nvt(&data_header,"affymetrix-cel-rows");
+  cur_mime_type = determine_MIMETYPE(*triplet);
+  decode_MIME_value(*triplet,cur_mime_type, &dim2, &size);
+  
+  Free_generic_data_header(&data_header);
+  
+  if ((dim1 != ref_dim_1) || (dim2 != ref_dim_2)){
+    error("Cel file %s does not seem to have the correct dimensions",filename);
+  }
+  
+  if (strncasecmp(cdfName,ref_cdfName,strlen(ref_cdfName)) != 0){
+    error("Cel file %s does not seem to be of %s type",filename,ref_cdfName);
+  }
+
+  Free(cdfName);
+
+
+  fclose(infile);
+  return 0;
+}
+
+
+
+
+/***************************************************************
+ **
+ ** static int read_binarycel_file_intensities(const char *filename, double *intensity, int chip_num, int rows, int cols,int chip_dim_rows)
+ **
+ ** 
+ ** This function reads binary cel file intensities into the data matrix
+ **
+ **************************************************************/
+
+int read_genericcel_file_intensities(const char *filename, double *intensity, int chip_num, int rows, int cols,int chip_dim_rows){
+
+  int i=0, j=0;
+  int cur_index;
+  
+  int fread_err=0;
+  
+  FILE *infile;
+
+  generic_file_header my_header;
+  generic_data_header my_data_header;
+  generic_data_group my_data_group;
+
+  generic_data_set my_data_set;
+
+
+  if ((infile = fopen(filename, "rb")) == NULL)
+    {
+      error("Unable to open the file %s\n",filename);
+      return 0;
+    }
+  
+
+  
+  read_generic_file_header(&my_header, infile);
+  read_generic_data_header(&my_data_header, infile);
+  read_generic_data_group(&my_data_group,infile);
+
+  read_generic_data_set(&my_data_set,infile); 
+  read_generic_data_set_rows(&my_data_set,infile); 
+
+  for (i =0; i < my_data_set.nrows; i++){
+    intensity[chip_num*my_data_set.nrows + i] = (double)(((float *)my_data_set.Data[0])[i]);
+  }
+  
+  fclose(infile);
+  Free_generic_data_set(&my_data_set);
+  Free_generic_data_header(&my_data_header);
+  Free_generic_data_group(&my_data_group);
+
+
+
+
+  return(0);
+}
+
+
+
+
+
+int read_genericcel_file_stddev(const char *filename, double *intensity, int chip_num, int rows, int cols,int chip_dim_rows){
+
+  int i=0, j=0;
+  int cur_index;
+  
+  int fread_err=0;
+  
+  FILE *infile;
+
+  generic_file_header my_header;
+  generic_data_header my_data_header;
+  generic_data_group my_data_group;
+
+  generic_data_set my_data_set;
+
+
+  if ((infile = fopen(filename, "rb")) == NULL)
+    {
+      error("Unable to open the file %s\n",filename);
+      return 0;
+    }
+  
+
+  
+  read_generic_file_header(&my_header, infile);
+  read_generic_data_header(&my_data_header, infile);
+  read_generic_data_group(&my_data_group,infile);
+
+  read_generic_data_set(&my_data_set,infile); 
+  fseek(infile, my_data_set.file_pos_last, SEEK_SET); 
+  Free_generic_data_set(&my_data_set);
+ 
+  read_generic_data_set(&my_data_set,infile); 
+  read_generic_data_set_rows(&my_data_set,infile); 
+  for (i =0; i < my_data_set.nrows; i++){
+    intensity[chip_num*my_data_set.nrows + i] = (double)(((float *)my_data_set.Data[0])[i]);
+  }
+  Free_generic_data_set(&my_data_set);
+  Free_generic_data_header(&my_data_header);
+  Free_generic_data_group(&my_data_group);
+
+  fclose(infile);
+
+
+  return(0);
+
+
+
+
+
+}
+
+
+
+int read_genericcel_file_npixels(const char *filename, double *intensity, int chip_num, int rows, int cols,int chip_dim_rows){
+
+  int i=0, j=0;
+  int cur_index;
+  
+  int fread_err=0;
+  
+  FILE *infile;
+
+  generic_file_header my_header;
+  generic_data_header my_data_header;
+  generic_data_group my_data_group;
+
+  generic_data_set my_data_set;
+
+
+  if ((infile = fopen(filename, "rb")) == NULL)
+    {
+      error("Unable to open the file %s\n",filename);
+      return 0;
+    }
+  
+
+  
+  read_generic_file_header(&my_header, infile);
+  read_generic_data_header(&my_data_header, infile);
+  read_generic_data_group(&my_data_group,infile);
+
+  read_generic_data_set(&my_data_set,infile); 
+  fseek(infile, my_data_set.file_pos_last, SEEK_SET); 
+  Free_generic_data_set(&my_data_set);
+ 
+  read_generic_data_set(&my_data_set,infile); 
+  fseek(infile, my_data_set.file_pos_last, SEEK_SET); 
+  Free_generic_data_set(&my_data_set);
+  
+
+  read_generic_data_set(&my_data_set,infile); 
+  read_generic_data_set_rows(&my_data_set,infile); 
+  for (i =0; i < my_data_set.nrows; i++){
+    intensity[chip_num*my_data_set.nrows + i] = (double)(((short *)my_data_set.Data[0])[i]);
+  }
+  Free_generic_data_set(&my_data_set);
+  Free_generic_data_header(&my_data_header);
+  Free_generic_data_group(&my_data_group);
+
+  fclose(infile);
+
+
+  return(0);
+
+
+
+
+}
+
+
+
+
+void generic_get_masks_outliers(const char *filename, int *nmasks, short **masks_x, short **masks_y, int *noutliers, short **outliers_x, short **outliers_y){
+
+
+
+
+  int i=0, j=0;
+  int cur_index;
+  
+  int fread_err=0;
+  
+  FILE *infile;
+
+  generic_file_header my_header;
+  generic_data_header my_data_header;
+  generic_data_group my_data_group;
+
+  generic_data_set my_data_set;
+
+
+  if ((infile = fopen(filename, "rb")) == NULL)
+    {
+      error("Unable to open the file %s\n",filename);
+      
+    }
+  
+
+  
+  read_generic_file_header(&my_header, infile);
+  read_generic_data_header(&my_data_header, infile);
+  read_generic_data_group(&my_data_group,infile);
+
+  /* passing the intensities */
+  read_generic_data_set(&my_data_set,infile); 
+  fseek(infile, my_data_set.file_pos_last, SEEK_SET); 
+  Free_generic_data_set(&my_data_set);
+ 
+  /* passing by the stddev */
+  read_generic_data_set(&my_data_set,infile); 
+  fseek(infile, my_data_set.file_pos_last, SEEK_SET); 
+  Free_generic_data_set(&my_data_set);
+  
+  /* passing by the npixels */
+  read_generic_data_set(&my_data_set,infile); 
+  fseek(infile, my_data_set.file_pos_last, SEEK_SET); 
+  Free_generic_data_set(&my_data_set);
+ 
+  /* Now lets go for the "Outlier" */
+  read_generic_data_set(&my_data_set,infile); 
+   
+  
+  *noutliers = my_data_set.nrows;
+
+  *outliers_x = Calloc(my_data_set.nrows,short); 
+  *outliers_y = Calloc(my_data_set.nrows,short);
+  
+  read_generic_data_set_rows(&my_data_set,infile); 
+  
+  for (i=0; i < my_data_set.nrows; i++){
+    (*outliers_x)[i] = ((short *)my_data_set.Data[0])[i];
+    (*outliers_y)[i] = ((short *)my_data_set.Data[1])[i];
+  }
+  
+  fseek(infile, my_data_set.file_pos_last, SEEK_SET); 
+  Free_generic_data_set(&my_data_set);
+
+  /* Now lets go for the "Mask" */
+  read_generic_data_set(&my_data_set,infile); 
+   
+  *nmasks = my_data_set.nrows;
+
+  *masks_x = Calloc(my_data_set.nrows,short); 
+  *masks_y = Calloc(my_data_set.nrows,short);
+  
+  
+  read_generic_data_set_rows(&my_data_set,infile); 
+  for (i=0; i < my_data_set.nrows; i++){
+    (*outliers_x)[i] = ((short *)my_data_set.Data[0])[i];
+    (*outliers_y)[i] = ((short *)my_data_set.Data[1])[i];
+  }
+  Free_generic_data_set(&my_data_set);
+  Free_generic_data_header(&my_data_header);
+  Free_generic_data_group(&my_data_group);
+
+  fclose(infile);
+  
+}
+
+
+
+
+
+void generic_apply_masks(const char *filename, double *intensity, int chip_num, int rows, int cols,int chip_dim_rows, int rm_mask, int rm_outliers){
+
+
+  int i=0, j=0;
+  int cur_index;
+  
+  short cur_x, cur_y;
+
+
+  int fread_err=0;
+  int nrows;
+  int size;
+
+  FILE *infile;
+
+  generic_file_header my_header;
+  generic_data_header my_data_header;
+  generic_data_group my_data_group;
+
+  generic_data_set my_data_set;
+  nvt_triplet *triplet;
+  AffyMIMEtypes cur_mime_type;
+
+  if ((infile = fopen(filename, "rb")) == NULL)
+    {
+      error("Unable to open the file %s\n",filename);
+      
+    }
+ 
+
+  
+  read_generic_file_header(&my_header, infile);
+  read_generic_data_header(&my_data_header, infile);
+  read_generic_data_group(&my_data_group,infile);
+
+    
+  triplet =  find_nvt(&my_data_header,"affymetrix-cel-rows");
+  cur_mime_type = determine_MIMETYPE(*triplet);
+  decode_MIME_value(*triplet,cur_mime_type, &nrows, &size);
+  
+
+
+  /* passing the intensities */
+  read_generic_data_set(&my_data_set,infile); 
+  fseek(infile, my_data_set.file_pos_last, SEEK_SET); 
+  Free_generic_data_set(&my_data_set);
+ 
+  /* passing by the stddev */
+  read_generic_data_set(&my_data_set,infile); 
+  fseek(infile, my_data_set.file_pos_last, SEEK_SET); 
+  Free_generic_data_set(&my_data_set);
+  
+  /* passing by the npixels */
+  read_generic_data_set(&my_data_set,infile); 
+  fseek(infile, my_data_set.file_pos_last, SEEK_SET); 
+  Free_generic_data_set(&my_data_set);
+ 
+  /* Now lets go for the "Outlier" */
+  read_generic_data_set(&my_data_set,infile); 
+  
+  if (rm_outliers){
+    read_generic_data_set_rows(&my_data_set,infile); 
+    for (i=0; i < my_data_set.nrows; i++){
+      cur_x = ((short *)my_data_set.Data[0])[i];
+      cur_y = ((short *)my_data_set.Data[1])[i];
+      cur_index = (int)cur_x + nrows*(int)cur_y; 
+      intensity[chip_num*rows + cur_index] =  R_NaN;
+    }
+  }
+  
+  fseek(infile, my_data_set.file_pos_last, SEEK_SET); 
+  Free_generic_data_set(&my_data_set);
+
+  /* Now lets go for the "Mask" */
+  read_generic_data_set(&my_data_set,infile); 
+  if (rm_mask){
+    read_generic_data_set_rows(&my_data_set,infile); 
+    for (i=0; i < my_data_set.nrows; i++){
+      cur_x = ((short *)my_data_set.Data[0])[i];
+      cur_y = ((short *)my_data_set.Data[1])[i];
+      cur_index = (int)cur_x + nrows*(int)cur_y; 
+      intensity[chip_num*rows + cur_index] =  R_NaN;
+    }
+  }
+  Free_generic_data_set(&my_data_set);
+  Free_generic_data_header(&my_data_header);
+  Free_generic_data_group(&my_data_group);
+
+  fclose(infile);
+  
+}
+
+/*******************************************************************************************************
+ *******************************************************************************************************
+ **
+ ** Code below supports gzipped command console format CEL files
+ **
+ *******************************************************************************************************
+ *******************************************************************************************************/
+
+
+int isgzGenericCelFile(const char *filename){
+
+  gzFile *infile;
+  generic_file_header file_header;
+  generic_data_header data_header;
+  
+  if ((infile = gzopen(filename, "rb")) == NULL)
+    {
+      error("Unable to open the file %s",filename);
+      return 0;
+    }
+
+  if (!gzread_generic_file_header(&file_header,infile)){
+    gzclose(infile);
+    return 0;
+  }
+
+  if (!gzread_generic_data_header(&data_header,infile)){
+    Free_generic_data_header(&data_header);
+    gzclose(infile);
+    return 0;
+  }
+  
+  if (strcmp(data_header.data_type_id.value, "affymetrix-calvin-intensity") !=0){
+    Free_generic_data_header(&data_header);
+ 
+
+
+   gzclose(infile);
+    return 0;
+  }
+  Free_generic_data_header(&data_header);
+  
+  gzclose(infile);
+  return 1;
+}
+
+
+
+char *gzgeneric_get_header_info(const char *filename, int *dim1, int *dim2){
+
+  gzFile *infile;
+  generic_file_header file_header;
+  generic_data_header data_header;
+
+  char *cdfName = 0;
+
+  nvt_triplet *triplet;
+  AffyMIMEtypes cur_mime_type;
+
+  int size;
+
+  wchar_t *wchartemp=0;
+  
+  if ((infile = gzopen(filename, "rb")) == NULL)
+    {
+      error("Unable to open the file %s",filename);
+      return 0;
+    }
+  
+  gzread_generic_file_header(&file_header,infile);
+  gzread_generic_data_header(&data_header,infile);
+
+  /*  affymetrix-array-type  text/plainText/plain String is HG-U133_Plus_2
+      Now Trying it again. But using exposed function
+      Its a Text/plain string value is HG-U133_Plus_2 with size 14
+      affymetrix-cel-cols  text/x-calvin-integer-32Its a int32_t  value is 1164
+      Now Trying it again. But using exposed function
+      Its a int32_t  value is 1164
+      affymetrix-cel-rows  text/x-calvin-integer-32Its a int32_t  value is 1164
+  */
+
+  triplet =  find_nvt(&data_header,"affymetrix-array-type");
+  
+  cur_mime_type = determine_MIMETYPE(*triplet);
+
+  wchartemp = decode_MIME_value(*triplet,cur_mime_type, wchartemp, &size);
+  cdfName = Calloc(size + 1, char);
+  wcstombs(cdfName, wchartemp, size);
+  Free(wchartemp);
+
+  triplet =  find_nvt(&data_header,"affymetrix-cel-cols");
+  cur_mime_type = determine_MIMETYPE(*triplet);
+  decode_MIME_value(*triplet,cur_mime_type, dim1, &size);
+  
+  triplet =  find_nvt(&data_header,"affymetrix-cel-rows");
+  cur_mime_type = determine_MIMETYPE(*triplet);
+  decode_MIME_value(*triplet,cur_mime_type, dim2, &size);
+  
+  Free_generic_data_header(&data_header);
+  gzclose(infile);
+
+  return cdfName;
+ 
+}
+
+
+
+
+void gzgeneric_get_detailed_header_info(const char *filename, detailed_header_info *header_info){
+  
+  gzFile *infile;
+  generic_file_header file_header;
+  generic_data_header data_header;
+  nvt_triplet *triplet;
+  AffyMIMEtypes cur_mime_type;
+  int size;
+
+  int algorithm_paramsize = 0;
+  float tempfloat;
+
+  wchar_t *wchartemp = 0;
+  char *chartemp = 0;
+  
+  if ((infile = gzopen(filename, "rb")) == NULL)
+    {
+      error("Unable to open the file %s",filename);
+    }
+  
+  gzread_generic_file_header(&file_header,infile);
+  gzread_generic_data_header(&data_header,infile);
+  
+  triplet =  find_nvt(&data_header,"affymetrix-array-type");
+
+  cur_mime_type = determine_MIMETYPE(*triplet);
+
+  wchartemp = decode_MIME_value(*triplet,cur_mime_type, wchartemp, &size);
+  header_info->cdfName = Calloc(size + 1, char);
+  wcstombs(header_info->cdfName, wchartemp, size);
+  Free(wchartemp);
+
+  triplet =  find_nvt(&data_header,"affymetrix-cel-cols");
+  cur_mime_type = determine_MIMETYPE(*triplet);
+  decode_MIME_value(*triplet,cur_mime_type, &(header_info->cols), &size);
+  
+  triplet =  find_nvt(&data_header,"affymetrix-cel-rows");
+  cur_mime_type = determine_MIMETYPE(*triplet);
+  decode_MIME_value(*triplet,cur_mime_type, &(header_info->rows), &size);
+  
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-GridULX"); 
+  cur_mime_type = determine_MIMETYPE(*triplet);
+  decode_MIME_value(*triplet,cur_mime_type, &tempfloat, &size);
+  header_info->GridCornerULx = (int)(tempfloat +0.5);
+
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-GridULY"); 
+  cur_mime_type = determine_MIMETYPE(*triplet);
+  decode_MIME_value(*triplet,cur_mime_type, &tempfloat, &size);
+  header_info->GridCornerULy = (int)(tempfloat +0.5);
+  
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-GridURX"); 
+  cur_mime_type = determine_MIMETYPE(*triplet);
+  decode_MIME_value(*triplet,cur_mime_type, &tempfloat, &size);
+  header_info->GridCornerURx = (int)(tempfloat +0.5);
+  
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-GridURY"); 
+  cur_mime_type = determine_MIMETYPE(*triplet);
+  decode_MIME_value(*triplet,cur_mime_type, &tempfloat, &size);
+  header_info->GridCornerURy = (int)(tempfloat +0.5);
+  
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-GridLLX"); 
+  cur_mime_type = determine_MIMETYPE(*triplet);
+  decode_MIME_value(*triplet,cur_mime_type, &tempfloat, &size);
+  header_info->GridCornerLLx = (int)(tempfloat +0.5);
+
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-GridLLY"); 
+  cur_mime_type = determine_MIMETYPE(*triplet);
+  decode_MIME_value(*triplet,cur_mime_type, &tempfloat, &size);
+  header_info->GridCornerLLy = (int)(tempfloat +0.5);
+  
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-GridLRX"); 
+  cur_mime_type = determine_MIMETYPE(*triplet);
+  decode_MIME_value(*triplet,cur_mime_type, &tempfloat, &size);
+  header_info->GridCornerLRx = (int)(tempfloat +0.5);
+  
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-GridLRY"); 
+  cur_mime_type = determine_MIMETYPE(*triplet);
+  decode_MIME_value(*triplet,cur_mime_type, &tempfloat, &size);
+  header_info->GridCornerLRy = (int)(tempfloat +0.5);
+  
+    
+  triplet =  find_nvt(&data_header,"affymetrix-dat-header");
+  if (triplet != NULL){
+    cur_mime_type = determine_MIMETYPE(*triplet);
+    
+    wchartemp = decode_MIME_value(*triplet,cur_mime_type, wchartemp, &size);
+    header_info->DatHeader = Calloc(size + 1, char);
+    wcstombs(header_info->DatHeader, wchartemp, size);
+    Free(wchartemp);
+  } else {
+    header_info->DatHeader = Calloc(2, char);
+  }
+
+  triplet =  find_nvt(&data_header,"affymetrix-scan-date");
+  
+  if (triplet != NULL){
+    cur_mime_type = determine_MIMETYPE(*triplet);
+    
+    wchartemp = decode_MIME_value(*triplet,cur_mime_type, wchartemp, &size);
+    header_info->ScanDate = Calloc(size + 1, char);
+    wcstombs(header_info->ScanDate, wchartemp, size);
+    Free(wchartemp);
+  } else {
+    header_info->ScanDate = Calloc(2, char);
+  }
+
+
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-name");
+  cur_mime_type = determine_MIMETYPE(*triplet);
+
+  wchartemp = decode_MIME_value(*triplet,cur_mime_type, wchartemp, &size);
+  header_info->Algorithm = Calloc(size + 1, char);
+  wcstombs(header_info->Algorithm, wchartemp, size);
+  Free(wchartemp);
+  
+
+
+  //  "Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004;AlgVersion:6.0;FixedCellSize:TRUE;FullFeatureWidth:7;FullFeatureHeight:7;IgnoreOutliersInShiftRows:FALSE;FeatureExtraction:TRUE;PoolWidthExtenstion:2;PoolHeightExtension:2;UseSubgrids:FALSE;RandomizePixels:FALSE;ErrorBasis:StdvMean;StdMult:1.00000"
+
+  algorithm_paramsize = 0;
+  
+  header_info->AlgorithmParameters = Calloc(11, char);
+  strncpy(header_info->AlgorithmParameters,"Percentile:",11);
+  algorithm_paramsize+=11;
+
+    
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-Percentile");
+  if (triplet != NULL){
+    cur_mime_type = determine_MIMETYPE(*triplet);
+    
+    chartemp = decode_MIME_value_toASCII(*triplet,cur_mime_type, chartemp, &size);
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + size +1, char);
+    strncpy(&header_info->AlgorithmParameters[algorithm_paramsize], chartemp, size);
+    algorithm_paramsize+= size +1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+    Free(chartemp);
+  } else {
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 1, char);
+    algorithm_paramsize+= 1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+  }
+
+  
+  header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 11, char);
+  strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"CellMargin:",11);
+  algorithm_paramsize+=11;
+
+    
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-CellMargin"); 
+  if (triplet != NULL){
+    cur_mime_type = determine_MIMETYPE(*triplet);
+    
+    chartemp = decode_MIME_value_toASCII(*triplet,cur_mime_type, chartemp, &size);
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + size +1, char);
+    strncpy(&header_info->AlgorithmParameters[algorithm_paramsize], chartemp, size);
+    algorithm_paramsize+= size +1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+    Free(chartemp);
+  } else {
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 1, char);
+    algorithm_paramsize+= 1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+  }
+
+  header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 12, char);
+  strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"OutlierHigh:",12);
+  algorithm_paramsize+=12;
+
+    
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-OutlierHigh");
+  if (triplet != NULL){
+    cur_mime_type = determine_MIMETYPE(*triplet);
+    
+    chartemp = decode_MIME_value_toASCII(*triplet,cur_mime_type, chartemp, &size);
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + size +1, char);
+    strncpy(&header_info->AlgorithmParameters[algorithm_paramsize], chartemp, size);
+    algorithm_paramsize+= size +1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+    Free(chartemp);
+  } else {
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 1, char);
+    algorithm_paramsize+= 1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+  }
+  
+  header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 11, char);
+  strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"OutlierLow:",11);
+  algorithm_paramsize+=11;
+
+    
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-OutlierLow");
+  if (triplet != NULL){
+    cur_mime_type = determine_MIMETYPE(*triplet);
+    
+    chartemp = decode_MIME_value_toASCII(*triplet,cur_mime_type, chartemp, &size);
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + size +1, char);
+    strncpy(&header_info->AlgorithmParameters[algorithm_paramsize], chartemp, size);
+    algorithm_paramsize+= size +1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+    Free(chartemp);
+  } else {
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 1, char);
+    algorithm_paramsize+= 1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+  }
+  
+  header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 11, char);
+  strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"AlgVersion:",11);
+  algorithm_paramsize+=11;
+
+    
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-AlgVersion");
+  if (triplet != NULL){
+    cur_mime_type = determine_MIMETYPE(*triplet);
+    
+    chartemp = decode_MIME_value_toASCII(*triplet,cur_mime_type, chartemp, &size);
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + size +1, char);
+    strncpy(&header_info->AlgorithmParameters[algorithm_paramsize], chartemp, size);
+    algorithm_paramsize+= size +1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+    Free(chartemp);
+  } else {
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 1, char);
+    algorithm_paramsize+= 1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+  }
+
+  header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 14, char);
+  strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FixedCellSize:",14);
+  algorithm_paramsize+=14;
+
+    
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-FixedCellSize");
+  if (triplet != NULL){
+    cur_mime_type = determine_MIMETYPE(*triplet);
+    
+    chartemp = decode_MIME_value_toASCII(*triplet,cur_mime_type, chartemp, &size);
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + size +1, char);
+    strncpy(&header_info->AlgorithmParameters[algorithm_paramsize], chartemp, size);
+    algorithm_paramsize+= size +1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+    Free(chartemp);
+  } else {
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 1, char);
+    algorithm_paramsize+= 1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+  }
+  
+  header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 17, char);
+  strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FullFeatureWidth:",17);
+  algorithm_paramsize+=17;
+
+    
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-FullFeatureWidth");
+  if (triplet != NULL){
+    cur_mime_type = determine_MIMETYPE(*triplet);
+    
+    chartemp = decode_MIME_value_toASCII(*triplet,cur_mime_type, chartemp, &size);
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + size +1, char);
+    strncpy(&header_info->AlgorithmParameters[algorithm_paramsize], chartemp, size);
+    algorithm_paramsize+= size +1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+     Free(chartemp);
+  } else {
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 1, char);
+    algorithm_paramsize+= 1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+  }
+  
+  header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 18, char);
+  strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FullFeatureHeight:",18);
+  algorithm_paramsize+=18;
+
+    
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-FullFeatureHeight");
+  if (triplet != NULL){
+    cur_mime_type = determine_MIMETYPE(*triplet);
+    
+    chartemp = decode_MIME_value_toASCII(*triplet,cur_mime_type, chartemp, &size);
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + size +1, char);
+    strncpy(&header_info->AlgorithmParameters[algorithm_paramsize], chartemp, size);
+    algorithm_paramsize+= size +1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+    Free(chartemp);
+  } else {
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 1, char);
+    algorithm_paramsize+= 1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+  }
+  
+  header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 26, char);
+  strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"IgnoreOutliersInShiftRows:",26);
+  algorithm_paramsize+=26;
+
+    
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-IgnoreOutliersInShiftRows");
+  if (triplet != NULL){
+    cur_mime_type = determine_MIMETYPE(*triplet);
+    
+    chartemp = decode_MIME_value_toASCII(*triplet,cur_mime_type, chartemp, &size);
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + size +1, char);
+    strncpy(&header_info->AlgorithmParameters[algorithm_paramsize], chartemp, size);
+    algorithm_paramsize+= size +1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+    Free(chartemp);
+  } else {
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 1, char);
+    algorithm_paramsize+= 1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+  }
+
+
+
+  header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 18, char);
+  strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FeatureExtraction:",18);
+  algorithm_paramsize+=18;
+
+    
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-FeatureExtraction");
+  if (triplet != NULL){
+    cur_mime_type = determine_MIMETYPE(*triplet);
+    
+    chartemp = decode_MIME_value_toASCII(*triplet,cur_mime_type, chartemp, &size);
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + size +1, char);
+    strncpy(&header_info->AlgorithmParameters[algorithm_paramsize], chartemp, size);
+    algorithm_paramsize+= size +1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+    Free(chartemp);
+  } else {
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 1, char);
+    algorithm_paramsize+= 1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+  }
+
+
+
+  
+  header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 20, char);
+  strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"PoolWidthExtenstion:",20);
+  algorithm_paramsize+=20;
+
+    
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-PoolWidthExtenstion");
+  if (triplet != NULL){
+    cur_mime_type = determine_MIMETYPE(*triplet);
+    
+    chartemp = decode_MIME_value_toASCII(*triplet,cur_mime_type, chartemp, &size);
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + size +1, char);
+    strncpy(&header_info->AlgorithmParameters[algorithm_paramsize], chartemp, size);
+    algorithm_paramsize+= size +1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+    Free(chartemp);
+  } else {
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 1, char);
+    algorithm_paramsize+= 1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+  }
+
+  
+  header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 20, char);
+  strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"PoolHeightExtension:",20);
+  algorithm_paramsize+=20;
+
+    
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-PoolHeightExtension");
+  if (triplet != NULL){
+    cur_mime_type = determine_MIMETYPE(*triplet);
+    
+    chartemp = decode_MIME_value_toASCII(*triplet,cur_mime_type, chartemp, &size);
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + size +1, char);
+    strncpy(&header_info->AlgorithmParameters[algorithm_paramsize], chartemp, size);
+    algorithm_paramsize+= size +1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+    Free(chartemp);
+  } else {
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 1, char);
+    algorithm_paramsize+= 1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+  }
+
+
+  header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 12, char);
+  strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"UseSubgrids:",12);
+  algorithm_paramsize+=12;
+  
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-UseSubgrids");
+  if (triplet != NULL){
+    cur_mime_type = determine_MIMETYPE(*triplet);
+    
+    chartemp = decode_MIME_value_toASCII(*triplet,cur_mime_type, chartemp, &size);
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + size +1, char);
+    strncpy(&header_info->AlgorithmParameters[algorithm_paramsize], chartemp, size);
+    algorithm_paramsize+= size +1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+    Free(chartemp);
+  } else {
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 1, char);
+    algorithm_paramsize+= 1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+  }
+
+
+  header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 16, char);
+  strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"RandomizePixels:",16);
+  algorithm_paramsize+=16;
+    
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-RandomizePixels");
+  if (triplet != NULL){
+    cur_mime_type = determine_MIMETYPE(*triplet);
+    
+    chartemp = decode_MIME_value_toASCII(*triplet,cur_mime_type, chartemp, &size);
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + size +1, char);
+    strncpy(&header_info->AlgorithmParameters[algorithm_paramsize], chartemp, size);
+    algorithm_paramsize+= size +1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+    Free(chartemp);
+  } else {
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 1, char);
+    algorithm_paramsize+= 1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+  }
+
+
+
+  header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 11, char);
+  strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"ErrorBasis:",11);
+  algorithm_paramsize+=11;
+
+    
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-ErrorBasis");
+  if (triplet != NULL){
+    cur_mime_type = determine_MIMETYPE(*triplet);
+    
+    chartemp = decode_MIME_value_toASCII(*triplet,cur_mime_type, chartemp, &size);
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + size +1, char);
+    strncpy(&header_info->AlgorithmParameters[algorithm_paramsize], chartemp, size);
+    algorithm_paramsize+= size +1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+    Free(chartemp);
+  } else {
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 1, char);
+    algorithm_paramsize+= 1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+  }
+
+  
+  header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 8, char);
+  strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"StdMult:",8);
+  algorithm_paramsize+=8;
+
+    
+  triplet =  find_nvt(&data_header,"affymetrix-algorithm-param-StdMult");
+  if (triplet != NULL){
+    cur_mime_type = determine_MIMETYPE(*triplet);
+    
+    chartemp = decode_MIME_value_toASCII(*triplet,cur_mime_type, chartemp, &size);
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + size +1, char);
+    strncpy(&header_info->AlgorithmParameters[algorithm_paramsize], chartemp, size);
+    algorithm_paramsize+= size +1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+    Free(chartemp);
+  } else {
+    header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 1, char);
+    algorithm_paramsize+= 1;
+    header_info->AlgorithmParameters[algorithm_paramsize-1]=';';
+  }
+
+
+  
+  header_info->AlgorithmParameters = Realloc(header_info->AlgorithmParameters, algorithm_paramsize + 1, char);
+  header_info->AlgorithmParameters[algorithm_paramsize] ='\0';
+
+  Free_generic_data_header(&data_header);
+  gzclose(infile);
+}
+
+
+
+
+
+
+
+
+int check_gzgeneric_cel_file(const char *filename, const char *ref_cdfName, int ref_dim_1, int ref_dim_2){
+
+  char *cdfName =0;
+  int dim1, dim2;
+
+
+  gzFile *infile;
+  generic_file_header file_header;
+  generic_data_header data_header;
+  
+  nvt_triplet *triplet;
+  AffyMIMEtypes cur_mime_type;
+  
+  int size;
+
+  wchar_t *wchartemp=0;
+  
+
+  if ((infile = gzopen(filename, "rb")) == NULL)
+    {
+      error("Unable to open the file %s",filename);
+      return 0;
+    }
+
+  gzread_generic_file_header(&file_header,infile);
+  gzread_generic_data_header(&data_header,infile);
+  
+
+  triplet =  find_nvt(&data_header,"affymetrix-array-type");
+  
+  cur_mime_type = determine_MIMETYPE(*triplet);
+
+  wchartemp = decode_MIME_value(*triplet,cur_mime_type, wchartemp, &size);
+  cdfName = Calloc(size + 1, char);
+  wcstombs(cdfName, wchartemp, size);
+  Free(wchartemp);
+
+  triplet =  find_nvt(&data_header,"affymetrix-cel-cols");
+  cur_mime_type = determine_MIMETYPE(*triplet);
+  decode_MIME_value(*triplet,cur_mime_type, &dim1, &size);
+  
+  triplet =  find_nvt(&data_header,"affymetrix-cel-rows");
+  cur_mime_type = determine_MIMETYPE(*triplet);
+  decode_MIME_value(*triplet,cur_mime_type, &dim2, &size);
+  
+  Free_generic_data_header(&data_header);
+  
+  if ((dim1 != ref_dim_1) || (dim2 != ref_dim_2)){
+    error("Cel file %s does not seem to have the correct dimensions",filename);
+  }
+  
+  if (strncasecmp(cdfName,ref_cdfName,strlen(ref_cdfName)) != 0){
+    error("Cel file %s does not seem to be of %s type",filename,ref_cdfName);
+  }
+
+  Free(cdfName);
+
+
+  gzclose(infile);
+  return 0;
+}
+
+
+
+
+
+
+int gzread_genericcel_file_intensities(const char *filename, double *intensity, int chip_num, int rows, int cols,int chip_dim_rows){
+
+  int i=0, j=0;
+  int cur_index;
+  
+  int fread_err=0;
+  
+  gzFile *infile;
+
+  generic_file_header my_header;
+  generic_data_header my_data_header;
+  generic_data_group my_data_group;
+
+  generic_data_set my_data_set;
+
+
+  if ((infile = gzopen(filename, "rb")) == NULL)
+    {
+      error("Unable to open the file %s\n",filename);
+      return 0;
+    }
+  
+
+  
+  gzread_generic_file_header(&my_header, infile);
+  gzread_generic_data_header(&my_data_header, infile);
+  gzread_generic_data_group(&my_data_group,infile);
+
+  gzread_generic_data_set(&my_data_set,infile); 
+  gzread_generic_data_set_rows(&my_data_set,infile); 
+
+  for (i =0; i < my_data_set.nrows; i++){
+    intensity[chip_num*my_data_set.nrows + i] = (double)(((float *)my_data_set.Data[0])[i]);
+  }
+  
+  gzclose(infile);
+  Free_generic_data_set(&my_data_set);
+  Free_generic_data_header(&my_data_header);
+  Free_generic_data_group(&my_data_group);
+
+
+
+
+  return(0);
+}
+
+
+
+
+
+
+int gzread_genericcel_file_stddev(const char *filename, double *intensity, int chip_num, int rows, int cols,int chip_dim_rows){
+
+  int i=0, j=0;
+  int cur_index;
+  
+  int fread_err=0;
+  
+  gzFile *infile;
+
+  generic_file_header my_header;
+  generic_data_header my_data_header;
+  generic_data_group my_data_group;
+
+  generic_data_set my_data_set;
+
+
+  if ((infile = gzopen(filename, "rb")) == NULL)
+    {
+      error("Unable to open the file %s\n",filename);
+      return 0;
+    }
+  
+
+  
+  gzread_generic_file_header(&my_header, infile);
+  gzread_generic_data_header(&my_data_header, infile);
+  gzread_generic_data_group(&my_data_group,infile);
+
+  gzread_generic_data_set(&my_data_set,infile); 
+  gzseek(infile, my_data_set.file_pos_last, SEEK_SET); 
+  Free_generic_data_set(&my_data_set);
+ 
+  gzread_generic_data_set(&my_data_set,infile); 
+  gzread_generic_data_set_rows(&my_data_set,infile); 
+  for (i =0; i < my_data_set.nrows; i++){
+    intensity[chip_num*my_data_set.nrows + i] = (double)(((float *)my_data_set.Data[0])[i]);
+  }
+  Free_generic_data_set(&my_data_set);
+  Free_generic_data_header(&my_data_header);
+  Free_generic_data_group(&my_data_group);
+
+  gzclose(infile);
+
+
+  return(0);
+
+
+
+
+
+}
+
+
+
+int gzread_genericcel_file_npixels(const char *filename, double *intensity, int chip_num, int rows, int cols,int chip_dim_rows){
+
+  int i=0, j=0;
+  int cur_index;
+  
+  int fread_err=0;
+  
+  gzFile *infile;
+
+  generic_file_header my_header;
+  generic_data_header my_data_header;
+  generic_data_group my_data_group;
+
+  generic_data_set my_data_set;
+
+
+  if ((infile = gzopen(filename, "rb")) == NULL)
+    {
+      error("Unable to open the file %s\n",filename);
+      return 0;
+    }
+  
+
+  
+  gzread_generic_file_header(&my_header, infile);
+  gzread_generic_data_header(&my_data_header, infile);
+  gzread_generic_data_group(&my_data_group,infile);
+
+  gzread_generic_data_set(&my_data_set,infile); 
+  gzseek(infile, my_data_set.file_pos_last, SEEK_SET); 
+  Free_generic_data_set(&my_data_set);
+ 
+  gzread_generic_data_set(&my_data_set,infile); 
+  gzseek(infile, my_data_set.file_pos_last, SEEK_SET); 
+  Free_generic_data_set(&my_data_set);
+  
+
+  gzread_generic_data_set(&my_data_set,infile); 
+  gzread_generic_data_set_rows(&my_data_set,infile); 
+  for (i =0; i < my_data_set.nrows; i++){
+    intensity[chip_num*my_data_set.nrows + i] = (double)(((short *)my_data_set.Data[0])[i]);
+  }
+  Free_generic_data_set(&my_data_set);
+  Free_generic_data_header(&my_data_header);
+  Free_generic_data_group(&my_data_group);
+
+  gzclose(infile);
+
+
+  return(0);
+
+
+
+
+}
+
+
+
+
+
+
+
+void gzgeneric_get_masks_outliers(const char *filename, int *nmasks, short **masks_x, short **masks_y, int *noutliers, short **outliers_x, short **outliers_y){
+
+
+
+
+  int i=0, j=0;
+  int cur_index;
+  
+  int fread_err=0;
+  
+  gzFile *infile;
+
+  generic_file_header my_header;
+  generic_data_header my_data_header;
+  generic_data_group my_data_group;
+
+  generic_data_set my_data_set;
+
+
+  if ((infile = gzopen(filename, "rb")) == NULL)
+    {
+      error("Unable to open the file %s\n",filename);
+      
+    }
+  
+
+  
+  gzread_generic_file_header(&my_header, infile);
+  gzread_generic_data_header(&my_data_header, infile);
+  gzread_generic_data_group(&my_data_group,infile);
+
+  /* passing the intensities */
+  gzread_generic_data_set(&my_data_set,infile); 
+  gzseek(infile, my_data_set.file_pos_last, SEEK_SET); 
+  Free_generic_data_set(&my_data_set);
+ 
+  /* passing by the stddev */
+  gzread_generic_data_set(&my_data_set,infile); 
+  gzseek(infile, my_data_set.file_pos_last, SEEK_SET); 
+  Free_generic_data_set(&my_data_set);
+  
+  /* passing by the npixels */
+  gzread_generic_data_set(&my_data_set,infile); 
+  gzseek(infile, my_data_set.file_pos_last, SEEK_SET); 
+  Free_generic_data_set(&my_data_set);
+ 
+  /* Now lets go for the "Outlier" */
+  gzread_generic_data_set(&my_data_set,infile); 
+   
+  
+  *noutliers = my_data_set.nrows;
+
+  *outliers_x = Calloc(my_data_set.nrows,short); 
+  *outliers_y = Calloc(my_data_set.nrows,short);
+  
+  gzread_generic_data_set_rows(&my_data_set,infile); 
+  
+  for (i=0; i < my_data_set.nrows; i++){
+    (*outliers_x)[i] = ((short *)my_data_set.Data[0])[i];
+    (*outliers_y)[i] = ((short *)my_data_set.Data[1])[i];
+  }
+  
+  gzseek(infile, my_data_set.file_pos_last, SEEK_SET); 
+  Free_generic_data_set(&my_data_set);
+
+  /* Now lets go for the "Mask" */
+  gzread_generic_data_set(&my_data_set,infile); 
+   
+  *nmasks = my_data_set.nrows;
+
+  *masks_x = Calloc(my_data_set.nrows,short); 
+  *masks_y = Calloc(my_data_set.nrows,short);
+  
+  
+  gzread_generic_data_set_rows(&my_data_set,infile); 
+  for (i=0; i < my_data_set.nrows; i++){
+    (*outliers_x)[i] = ((short *)my_data_set.Data[0])[i];
+    (*outliers_y)[i] = ((short *)my_data_set.Data[1])[i];
+  }
+  Free_generic_data_set(&my_data_set);
+  Free_generic_data_header(&my_data_header);
+  Free_generic_data_group(&my_data_group);
+
+  gzclose(infile);
+  
+}
+
+
+
+
+
+void gzgeneric_apply_masks(const char *filename, double *intensity, int chip_num, int rows, int cols,int chip_dim_rows, int rm_mask, int rm_outliers){
+
+
+  int i=0, j=0;
+  int cur_index;
+  
+  short cur_x, cur_y;
+
+
+  int fread_err=0;
+  int nrows;
+  int size;
+
+  gzFile *infile;
+
+  generic_file_header my_header;
+  generic_data_header my_data_header;
+  generic_data_group my_data_group;
+
+  generic_data_set my_data_set;
+  nvt_triplet *triplet;
+  AffyMIMEtypes cur_mime_type;
+
+  if ((infile = gzopen(filename, "rb")) == NULL)
+    {
+      error("Unable to open the file %s\n",filename);
+      
+    }
+ 
+
+  
+  gzread_generic_file_header(&my_header, infile);
+  gzread_generic_data_header(&my_data_header, infile);
+  gzread_generic_data_group(&my_data_group,infile);
+
+    
+  triplet =  find_nvt(&my_data_header,"affymetrix-cel-rows");
+  cur_mime_type = determine_MIMETYPE(*triplet);
+  decode_MIME_value(*triplet,cur_mime_type, &nrows, &size);
+  
+
+
+  /* passing the intensities */
+  gzread_generic_data_set(&my_data_set,infile); 
+  gzseek(infile, my_data_set.file_pos_last, SEEK_SET); 
+  Free_generic_data_set(&my_data_set);
+ 
+  /* passing by the stddev */
+  gzread_generic_data_set(&my_data_set,infile); 
+  gzseek(infile, my_data_set.file_pos_last, SEEK_SET); 
+  Free_generic_data_set(&my_data_set);
+  
+  /* passing by the npixels */
+  gzread_generic_data_set(&my_data_set,infile); 
+  gzseek(infile, my_data_set.file_pos_last, SEEK_SET); 
+  Free_generic_data_set(&my_data_set);
+ 
+  /* Now lets go for the "Outlier" */
+  gzread_generic_data_set(&my_data_set,infile); 
+  
+  if (rm_outliers){
+    gzread_generic_data_set_rows(&my_data_set,infile); 
+    for (i=0; i < my_data_set.nrows; i++){
+      cur_x = ((short *)my_data_set.Data[0])[i];
+      cur_y = ((short *)my_data_set.Data[1])[i];
+      cur_index = (int)cur_x + nrows*(int)cur_y; 
+      intensity[chip_num*rows + cur_index] =  R_NaN;
+    }
+  }
+  
+  gzseek(infile, my_data_set.file_pos_last, SEEK_SET); 
+  Free_generic_data_set(&my_data_set);
+
+  /* Now lets go for the "Mask" */
+  gzread_generic_data_set(&my_data_set,infile); 
+  if (rm_mask){
+    gzread_generic_data_set_rows(&my_data_set,infile); 
+    for (i=0; i < my_data_set.nrows; i++){
+      cur_x = ((short *)my_data_set.Data[0])[i];
+      cur_y = ((short *)my_data_set.Data[1])[i];
+      cur_index = (int)cur_x + nrows*(int)cur_y; 
+      intensity[chip_num*rows + cur_index] =  R_NaN;
+    }
+  }
+  Free_generic_data_set(&my_data_set);
+  Free_generic_data_header(&my_data_header);
+  Free_generic_data_group(&my_data_group);
+  
+  gzclose(infile);
+  
+}
+
+
+