[svn-r3988]

Purpose:
    new features
Description:
    1. add an option to convert HDF4 file without HDF4 specified attributes such as
	HDF4_OBJECT_TYPE, HDF4_REF_NUM etc.
        it can be done by inputting "h4toh5 -na input.hdf"
        The default converter will still keep HDF4 specfied attributes.
    2. Add compression features (gzip) for image too. Now the compressed HDF4 image
       can be supported by using HDF5 gzip. Not sure whether tools can read it. Need to be       tested.
    3. Change SPACEPAD to NULLTERM for HDF4 dimensional name list. We can use variable length HDF5 string to represent these names, however currently H5dump and H5view cannot support variable length HDF5 string. converter will wait for other tools' update.

Solution:
Platforms tested:
     eirene(Red Hat 6.2) and arabica(solaris 2.7)

1 files changed, 197 insertions, 11 deletions

diff --git a/tools/h4toh5/h4toh5image.c b/tools/h4toh5/h4toh5image.c
index 8fbbdc0..47c5363 100644
--- a/tools/h4toh5/h4toh5image.c
+++ b/tools/h4toh5/h4toh5image.c
@@ -44,7 +44,7 @@ Author:  Kent Yang(ymuqun@ncsa.uiuc.edu)
  *-------------------------------------------------------------------------
  */	
 
-int Image_h4_to_h5(int32 file_id,int32 ri_id,hid_t h5_group,hid_t h5_palgroup) {
+int Image_h4_to_h5(int32 file_id,int32 ri_id,hid_t h5_group,hid_t h5_palgroup,int h4_attr) {
 
   int32    istat;
   int32    ngrattrs;
@@ -67,6 +67,16 @@ int Image_h4_to_h5(int32 file_id,int32 ri_id,hid_t h5_group,hid_t h5_palgroup) {
   int32    chunk_dims[2];
   int32    c_flags;
 
+  /* for checking compression */
+
+  sp_info_block_t info_block;
+  int16           special_code;
+  int32           access_id;
+  uint16          ri_ref;
+  int             gzip_level;
+  uint16          temp_tag;
+  uint16*          ptag_out;
+
   /* define varibles for hdf5. */
 
   hid_t    h5ty_id;
@@ -82,8 +92,14 @@ int Image_h4_to_h5(int32 file_id,int32 ri_id,hid_t h5_group,hid_t h5_palgroup) {
   size_t   h4memsize;
   hsize_t   fielddim[1];
   hsize_t  h5dims[2];
+  hsize_t bufsize;
   herr_t   ret;
   hid_t    create_plist;
+  hid_t    write_plist;
+
+
+  temp_tag = DFTAG_NULL;
+  ptag_out = &temp_tag;
 
   /* zeroing out memory.*/
 
@@ -147,13 +163,13 @@ int Image_h4_to_h5(int32 file_id,int32 ri_id,hid_t h5_group,hid_t h5_palgroup) {
   /* change the order of image dimension:
      due to the difference of hdf4 image specification and
      hdf5 image specification. */
-     
   
 
   h5dims[0] = edges[1]-start[1];
   h5dims[1] = edges[0]-start[0];
 
   gr_ref = GRidtoref(ri_id);
+
   if(gr_ref == 0) {
     printf("error in obtaining gr reference number. \n");
     free(image_data);
@@ -196,10 +212,88 @@ int Image_h4_to_h5(int32 file_id,int32 ri_id,hid_t h5_group,hid_t h5_palgroup) {
   /* create property list. */
 
   create_plist = H5Pcreate(H5P_DATASET_CREATE);
+  /* wait until the compression information can be obtained for image,
+     4/28/2001, Kent Yang.*/
+
+  ri_ref = 0;
+  /*
+   ri_ref = get_RIref(file_id,DFTAG_VG,gr_ref,ptag_out);
+
+  if(ri_ref >0 ){
+    if(*ptag_out == DFTAG_RI) printf("okay\n");
+    access_id = Hstartread(file_id,*ptag_out,ri_ref);
+  }
+  */
+  if(ri_ref == 0) 
+    access_id = FAIL;
+  
+
+  /*  if(access_id == FAIL){
+    printf("cannot find RI tag,the compression mode will not be checked");
+    printf(" when RIG is not chunked.\n");
+    }*/
+  
+  if(access_id != FAIL) {
+    istat = Hinquire(access_id,NULL,NULL,NULL,NULL,NULL,NULL,NULL,&special_code);
+    if(istat == FAIL) {
+      printf("failed to inquire information \n ");
+      free(image_data);
+       free(h5cimage_name);
+      H5Pclose(create_plist);
+      return FAIL;	
+    }
 
+    if(special_code >0){
+      
+      if(HDget_special_info(access_id,&info_block)==FAIL){
+	printf("fail to get special info.\n");
+	free(image_data);
+	free(h5cimage_name);
+	H5Pclose(create_plist);
+	return FAIL;	
+      }
+      /* free(info_block.cdims);*/
+      if(info_block.key == SPECIAL_COMP) {
+   
+	if(c_flags == HDF_NONE){
+	  /* 1. the current HDF5 will not handle compression case itself, 
+	     in order that the converted HDF5 is compressed, we have to
+	     provide a chunking size. currently it is set to h5dim[i].*/
+
+	  printf("okay to sds compress.\n");
+	  
+	    chunk_dims[0] = (hsize_t)(h5dims[0]);
+            chunk_dims[1] =(hsize_t)(h5dims[1]);
+	  
+	  if(H5Pset_chunk(create_plist, 2, chunk_dims)<0) {
+	    printf("failed to set up chunking information for ");
+	    printf("property list.\n");
+	    free(image_data);
+	    free(h5cimage_name);
+	    H5Pclose(create_plist);
+	    return FAIL;	
+	  }
+       
+	  if(H5Pset_deflate(create_plist,GZIP_COMLEVEL)<0){
+	    /*    if(H5Pset_deflate(create_plist,2)<0){*/
+	    printf("fail to set compression method for HDF5 file.\n"); 
+	     free(image_data);
+	    free(h5cimage_name);
+	    H5Pclose(create_plist);
+	    return FAIL;
+	  }
+	}
+
+      }
+      /* free(info_block.cdims);*/
+    }
+
+  }
   if(c_flags == HDF_CHUNK || c_flags == (HDF_CHUNK | HDF_COMP)
      || c_flags == (HDF_CHUNK | HDF_NBIT)  ){
 
+    if(c_def_out.comp.comp_type == COMP_CODE_RLE || c_def_out.comp.comp_type == COMP_CODE_NBIT || c_def_out.comp.comp_type == COMP_CODE_SKPHUFF || c_def_out.comp.comp_type == COMP_CODE_DEFLATE || c_def_out.comp.comp_type == COMP_CODE_JPEG) {
+   
      chunk_dims[0] = c_def_out.chunk_lengths[0]; 
      chunk_dims[1] = c_def_out.chunk_lengths[1];
        
@@ -207,11 +301,40 @@ int Image_h4_to_h5(int32 file_id,int32 ri_id,hid_t h5_group,hid_t h5_palgroup) {
        printf("failed to set up chunking information for ");
        printf("property list.\n");
        free(image_data);
+       free(h5cimage_name);
        H5Pclose(create_plist);
        return FAIL;	
      }
+
+     if(c_def_out.comp.comp_type == COMP_CODE_DEFLATE)
+	gzip_level = c_def_out.comp.cinfo.deflate.level;
+      else gzip_level = GZIP_COMLEVEL;
+	if(H5Pset_deflate(create_plist,gzip_level)<0){
+	  printf("fail to set compression method for HDF5 file.\n"); 
+	   free(image_data);
+	   free(h5cimage_name);
+	   H5Pclose(create_plist);
+	}
+    }
   }
-  if (ncomp == 1) {
+
+  /* HDF4 can support various compression methods including simple RLE, NBIT, Skip Huffman, gzip,Jpeg , HDF5 currently only supports gzip compression. 
+ By default, we will compress HDF5 dataset by using gzip compression if HDF5 file is compressed. */
+
+  
+ write_plist = H5Pcreate(H5P_DATASET_XFER);
+ bufsize = h4memsize *h5dims[1]*ncomp;
+
+  if(H5Pset_buffer(write_plist,bufsize,NULL,NULL)<0) {
+    printf("fail to create data transfer property list.\n");
+    free(image_data);
+    free(h5cimage_name);
+    H5Pclose(create_plist);
+    H5Pclose(write_plist);
+    return FAIL;		
+  }
+
+ if (ncomp == 1) {
 
      h5d_sid = H5Screate_simple(2,h5dims,NULL);
      
@@ -219,6 +342,8 @@ int Image_h4_to_h5(int32 file_id,int32 ri_id,hid_t h5_group,hid_t h5_palgroup) {
        printf("error in creating space for dataset. \n");
        free(image_data);
        free(h5cimage_name);
+       H5Pclose(create_plist);
+        H5Pclose(write_plist);
        return FAIL;
      }
 
@@ -229,15 +354,17 @@ int Image_h4_to_h5(int32 file_id,int32 ri_id,hid_t h5_group,hid_t h5_palgroup) {
        free(image_data);
        free(h5cimage_name);
        H5Pclose(create_plist);
+        H5Pclose(write_plist);
        return FAIL;
      }
 
-     if (H5Dwrite(h5dset,h5memtype,h5d_sid,h5d_sid,H5P_DEFAULT,
+     if (H5Dwrite(h5dset,h5memtype,h5d_sid,h5d_sid,write_plist,
 		  image_data)<0) {
         printf("error writing data for hdf5 dataset converted from images.\n");
 	free(image_data);
 	free(h5cimage_name);
         H5Pclose(create_plist);
+	 H5Pclose(write_plist);
         return FAIL;
      }
 	
@@ -251,6 +378,7 @@ int Image_h4_to_h5(int32 file_id,int32 ri_id,hid_t h5_group,hid_t h5_palgroup) {
        free(image_data);
        free(h5cimage_name);
        H5Pclose(create_plist);
+        H5Pclose(write_plist);
        return FAIL;
      }
 
@@ -260,6 +388,7 @@ int Image_h4_to_h5(int32 file_id,int32 ri_id,hid_t h5_group,hid_t h5_palgroup) {
        free(image_data);
        free(h5cimage_name);
        H5Pclose(create_plist);
+        H5Pclose(write_plist);
        return FAIL;
      }
     
@@ -275,6 +404,7 @@ int Image_h4_to_h5(int32 file_id,int32 ri_id,hid_t h5_group,hid_t h5_palgroup) {
        free(image_data);
        free(h5cimage_name);
        H5Pclose(create_plist);
+        H5Pclose(write_plist);
        return FAIL;
      }
 
@@ -284,6 +414,7 @@ int Image_h4_to_h5(int32 file_id,int32 ri_id,hid_t h5_group,hid_t h5_palgroup) {
        free(image_data);
        free(h5cimage_name);
        H5Pclose(create_plist);
+        H5Pclose(write_plist);
        return FAIL;
      }
 
@@ -293,6 +424,7 @@ int Image_h4_to_h5(int32 file_id,int32 ri_id,hid_t h5_group,hid_t h5_palgroup) {
        free(image_data);
        free(h5cimage_name);
        H5Pclose(create_plist);
+        H5Pclose(write_plist);
        return FAIL;
      }
 
@@ -302,6 +434,7 @@ int Image_h4_to_h5(int32 file_id,int32 ri_id,hid_t h5_group,hid_t h5_palgroup) {
        free(image_data);
        free(h5cimage_name);
        H5Pclose(create_plist);
+        H5Pclose(write_plist);
        return FAIL;
      }
 
@@ -311,6 +444,7 @@ int Image_h4_to_h5(int32 file_id,int32 ri_id,hid_t h5_group,hid_t h5_palgroup) {
        free(image_data);
        free(h5cimage_name);
        H5Pclose(create_plist);
+        H5Pclose(write_plist);
        return FAIL;
      }
      
@@ -320,6 +454,7 @@ int Image_h4_to_h5(int32 file_id,int32 ri_id,hid_t h5_group,hid_t h5_palgroup) {
        free(image_data);
        free(h5cimage_name);
        H5Pclose(create_plist);
+        H5Pclose(write_plist);
        return FAIL;
      }
      }
@@ -330,6 +465,7 @@ int Image_h4_to_h5(int32 file_id,int32 ri_id,hid_t h5_group,hid_t h5_palgroup) {
        free(image_data);
        free(h5cimage_name);
        H5Pclose(create_plist);
+        H5Pclose(write_plist);
        return FAIL;
      }
 
@@ -340,15 +476,17 @@ int Image_h4_to_h5(int32 file_id,int32 ri_id,hid_t h5_group,hid_t h5_palgroup) {
        free(image_data);
        free(h5cimage_name);
        H5Pclose(create_plist);
+        H5Pclose(write_plist);
        return FAIL;
      }
 
-     if (H5Dwrite(h5dset,h5_cmemtype,h5d_sid,h5d_sid,H5P_DEFAULT,
+     if (H5Dwrite(h5dset,h5_cmemtype,h5d_sid,h5d_sid,write_plist,
 		  (void *)image_data)<0) {
         printf("error writing data\n");
 	free(image_data);
 	free(h5cimage_name);
         H5Pclose(create_plist);
+	 H5Pclose(write_plist);
 	return FAIL;
      } 
      ret   = H5Tclose(h5_ctype);
@@ -374,6 +512,7 @@ int Image_h4_to_h5(int32 file_id,int32 ri_id,hid_t h5_group,hid_t h5_palgroup) {
     free(image_data);
     free(h5cimage_name);
     H5Pclose(create_plist);
+     H5Pclose(write_plist);
     H5Sclose(h5d_sid); 
     H5Dclose(h5dset);
     return FAIL;
@@ -384,6 +523,7 @@ int Image_h4_to_h5(int32 file_id,int32 ri_id,hid_t h5_group,hid_t h5_palgroup) {
     free(h5cimage_name);
     free(image_data);
     H5Pclose(create_plist);
+     H5Pclose(write_plist);
     H5Sclose(h5d_sid); 
     H5Dclose(h5dset);
     return FAIL;
@@ -394,6 +534,7 @@ int Image_h4_to_h5(int32 file_id,int32 ri_id,hid_t h5_group,hid_t h5_palgroup) {
     free(h5cimage_name);
     free(image_data);
     H5Pclose(create_plist);
+     H5Pclose(write_plist);
     H5Sclose(h5d_sid); 
     H5Dclose(h5dset);
     return FAIL;
@@ -408,6 +549,7 @@ int Image_h4_to_h5(int32 file_id,int32 ri_id,hid_t h5_group,hid_t h5_palgroup) {
     printf(" cannot obtain attributes. \n");
      free(image_data);
     H5Pclose(create_plist);
+     H5Pclose(write_plist);
     H5Sclose(h5d_sid); 
     H5Dclose(h5dset);
     return FAIL;
@@ -416,7 +558,8 @@ int Image_h4_to_h5(int32 file_id,int32 ri_id,hid_t h5_group,hid_t h5_palgroup) {
   /*  deal with h5dset predefined and user-defined attributes. 
       Obtain the name and data type and the total number of attributes.  
       Data attribute at hdf4 is only one-dimensional array. */
-	
+
+ 
   if (ncomp == 1 && h4size == 1)
      strcpy(grlabel,RAST8LABEL);
   else if(ncomp == 3 && h4size == 1)
@@ -430,6 +573,7 @@ int Image_h4_to_h5(int32 file_id,int32 ri_id,hid_t h5_group,hid_t h5_palgroup) {
   if(h4_transpredattrs(h5dset,HDF4_OBJECT_TYPE,grlabel)==FAIL){
     printf("error in getting hdf4 image type attribute \n");
     H5Pclose(create_plist);
+     H5Pclose(write_plist);
     H5Sclose(h5d_sid); 
     H5Dclose(h5dset);
     free(h5cimage_name);
@@ -437,19 +581,22 @@ int Image_h4_to_h5(int32 file_id,int32 ri_id,hid_t h5_group,hid_t h5_palgroup) {
     return FAIL;
   }
 
+  if(h4_attr!=0) {
   if(h4_transpredattrs(h5dset,HDF4_OBJECT_NAME,image_name)==FAIL){
     printf("error in getting hdf4 image name attribute. \n");
     H5Pclose(create_plist);
+     H5Pclose(write_plist);
     H5Sclose(h5d_sid); 
     H5Dclose(h5dset);
     free(h5cimage_name);
     free(image_data);
     return FAIL;
   }
-
+  }
   if(h4_transpredattrs(h5dset,HDF4_IMAGE_CLASS,image_class)==FAIL){
     printf("error in getting hdf4 image class attribute. \n");
     H5Pclose(create_plist);
+     H5Pclose(write_plist);
     H5Sclose(h5d_sid); 
     H5Dclose(h5dset);
     free(h5cimage_name);
@@ -457,11 +604,14 @@ int Image_h4_to_h5(int32 file_id,int32 ri_id,hid_t h5_group,hid_t h5_palgroup) {
     return FAIL;
   }
 
+  if(h4_attr !=0){
+ 
   gr_ref = GRidtoref(ri_id);
 
   if(gr_ref == 0) {
     printf("error in obtaining reference number of GR.\n");
     H5Pclose(create_plist);
+     H5Pclose(write_plist);
     H5Sclose(h5d_sid); 
     H5Dclose(h5dset);
     free(h5cimage_name);
@@ -472,18 +622,20 @@ int Image_h4_to_h5(int32 file_id,int32 ri_id,hid_t h5_group,hid_t h5_palgroup) {
   if(h4_transnumattr(h5dset,HDF4_REF_NUM,gr_ref)==FAIL) {
     printf("error in getting hdf4 image number attribute.\n");
     H5Pclose(create_plist);
+     H5Pclose(write_plist);
     H5Sclose(h5d_sid); 
     H5Dclose(h5dset);
     free(h5cimage_name);
     free(image_data);
     return FAIL;
   }
-  
+  }
   /* deal with palette. */
 
-  if(gr_palette(file_id,ri_id,h5dset,h5_palgroup)== FAIL) {
+  if(gr_palette(file_id,ri_id,h5dset,h5_palgroup,h4_attr)== FAIL) {
     printf("error in translating palette into h5 dataset.\n");
     H5Pclose(create_plist);
+     H5Pclose(write_plist);
     H5Sclose(h5d_sid); 
     H5Dclose(h5dset);
     free(h5cimage_name);
@@ -492,6 +644,7 @@ int Image_h4_to_h5(int32 file_id,int32 ri_id,hid_t h5_group,hid_t h5_palgroup) {
   }
  
   ret   = H5Pclose(create_plist);
+   ret  = H5Pclose(write_plist);
   ret   = H5Sclose(h5d_sid); 
   ret   = H5Dclose(h5dset);
   istat = GRendaccess(ri_id);
@@ -518,7 +671,7 @@ int Image_h4_to_h5(int32 file_id,int32 ri_id,hid_t h5_group,hid_t h5_palgroup) {
  *-------------------------------------------------------------------------
  */	
 
-int gr_palette(int32 file_id,int32 ri_id,hid_t h5dset,hid_t h5_palgroup) {
+int gr_palette(int32 file_id,int32 ri_id,hid_t h5dset,hid_t h5_palgroup,int h4_attr) {
 
   int32      pal_id;
   uint16     pal_ref;
@@ -595,7 +748,7 @@ int gr_palette(int32 file_id,int32 ri_id,hid_t h5dset,hid_t h5_palgroup) {
 	return FAIL;
       }
 
-      pal_stat = Palette_h4_to_h5(file_id,pal_id,h5_palgroup,h5pal_name);
+      pal_stat = Palette_h4_to_h5(file_id,pal_id,h5_palgroup,h5pal_name,h4_attr);
 
       if(pal_stat == FAIL) {
         printf("error occurring in transferring palette into dataset. \n");
@@ -859,3 +1012,36 @@ int create_pal_objref(hid_t h5dset,hid_t h5_palgroup,char *h5pal_name){
     H5Aclose(attribID);
     return SUCCEED;
 }
+
+
+uint16 get_RIref(int32 file_id,uint16 tag,int32 gr_ref,uint16* ptag_out){
+
+  DFdi di;
+  int32 found,GroupID;
+  int ri_ref = 0;
+  
+  if((GroupID = DFdiread(file_id,tag,(uint16)gr_ref))<0){
+    printf("cannot find gr_ref\n");
+    return ri_ref;
+  }
+
+  found = 0;
+  di.tag = DFTAG_NULL;
+  di.ref = 0;
+  while((found == 0) &&(DFdiget(GroupID,&di.tag,&di.ref)==0)){
+    if(di.tag == DFTAG_CI ||di.tag == DFTAG_RI || di.tag == DFTAG_CI8 ||
+       di.tag == DFTAG_RI8)
+      found = 1;
+  }
+
+  *ptag_out = di.tag;
+  ri_ref = di.ref;
+  ri_ref = 1;
+  if(!found) {
+    printf("cannot find ri_ref\n");
+    return 0;
+  }
+  DFdifree(GroupID);
+  return ri_ref;
+
+}