From 166aca9f4c33bc5642047ceafd5c6bae0d888187 Mon Sep 17 00:00:00 2001

From: "Robert D. Vincent" <robert.d.vincent@mcgill.ca>

Date: Wed, 7 Oct 2015 22:06:38 +0000

Subject: [PATCH] Fix endian issues with label data.

---

 libsrc2/m2util.c | 83 ++++++++++++++++++++++++++++++++++++++++++++------------

 libsrc2/volume.c |  4 +--

 2 files changed, 66 insertions(+), 21 deletions(-)

diff --git a/libsrc2/m2util.c b/libsrc2/m2util.c

index a9367dc..5711208 100644

--- a/libsrc2/m2util.c

+++ b/libsrc2/m2util.c

@@ -1343,33 +1343,80 @@ void miinit ( void )

                 mi2_dbl_to_int ),"H5Tregister")

 }

-/** HDF5 type conversion function for converting an arbitrary integer type to

-* an arbitrary enumerated type.  The beauty part of this is that it is

-* not necessary to actually perform any real conversion!

-*/

-static herr_t mi2_null_conv ( hid_t src_id,

-                              hid_t dst_id,

-                              H5T_cdata_t *cdata,

-                              size_t nelements,

-                              size_t buf_stride,

-                              size_t bkg_stride,

-                              void *buf_ptr,

-                              void *bkg_ptr,

-                              hid_t dset_xfer_plist )

+/** HDF5 type conversion function for converting among integer types.

+ * This handles byte-swapping for enumerated types where needed.

+ */

+static herr_t mi2_int_to_int ( hid_t src_id,

+			       hid_t dst_id,

+			       H5T_cdata_t *cdata,

+			       size_t nelements,

+			       size_t buf_stride,

+			       size_t bkg_stride,

+			       void *buf_ptr,

+			       void *bkg_ptr,

+			       hid_t dset_xfer_plist )

 {

+  unsigned char *dst_ptr;

+  size_t dst_cnt;

+  size_t dst_sz;

+

   switch ( cdata->command ) {

   case H5T_CONV_INIT:

     break;

   case H5T_CONV_CONV:

+    dst_ptr = ( unsigned char * ) buf_ptr;

+    dst_sz = H5Tget_size( dst_id );

+

+    if (dst_sz != H5Tget_size( src_id )) {

+      return -1;		/* Can't change size for now. */

+    }

+    if ( H5Tget_order ( dst_id ) == H5Tget_order ( src_id ) ) {

+      return 0;			/* Nothing to do. */

+    }

+

+    /* The logic of HDF5 seems to be that if a stride is specified,

+    * both the source and destination pointers should advance by that

+    * amount.  This seems wrong to me, but I've examined the HDF5 sources

+    * and that's what their own type converters do.

+    */

+    if ( buf_stride == 0 ) {

+      dst_cnt = dst_sz;

+    } else {

+      dst_cnt = buf_stride;

+    }

+

+    switch ( dst_sz ) {

+    case 8:

+      while ( nelements-- > 0 ) {

+	miswap8 ( dst_ptr );

+	dst_ptr += dst_cnt;

+      }

+      break;

+    case 4:

+      while ( nelements-- > 0 ) {

+	miswap4 ( dst_ptr );

+	dst_ptr += dst_cnt;

+      }

+      break;

+    case 2:

+      while ( nelements-- > 0 ) {

+	miswap2 ( dst_ptr );

+	dst_ptr += dst_cnt;

+      }

+      break;

+    case 1:

+      break;

+    default:

+      return (-1);

+    }

     break;

+

   case H5T_CONV_FREE:

     break;

   default:

-    /* Unknown command */

-    return ( -1 );

+    return (-1);                /* Unknown command. */

   }

-

   return ( 0 );

 }

@@ -1380,9 +1427,9 @@ in order to facilitate conversions from the integer to the enumerated type.

 void miinit_enum ( hid_t type_id )

 {

   H5Tregister ( H5T_PERS_SOFT, "i2e", H5T_NATIVE_INT, type_id,

-                mi2_null_conv );

+                mi2_int_to_int );

   H5Tregister ( H5T_PERS_SOFT, "e2i", type_id, H5T_NATIVE_INT,

-                mi2_null_conv );

+                mi2_int_to_int );

   H5Tregister ( H5T_PERS_SOFT, "d2e", H5T_NATIVE_DOUBLE, type_id,

                 mi2_dbl_to_int );

   H5Tregister ( H5T_PERS_SOFT, "e2d", type_id, H5T_NATIVE_DOUBLE,

diff --git a/libsrc2/volume.c b/libsrc2/volume.c

index b951d14..be8b7d1 100644

--- a/libsrc2/volume.c

+++ b/libsrc2/volume.c

@@ -1449,11 +1449,9 @@ int miopen_volume(const char *filename, int mode, mihandle_t *volume)

     break;

   case H5T_ENUM:

-    handle->mtype_id = H5Tcopy(handle->ftype_id);

+    handle->mtype_id = H5Tget_native_type(handle->ftype_id, H5T_DIR_ASCEND);

     miinit_enum(handle->ftype_id);

     miinit_enum(handle->mtype_id);

-    /* Set native order ---> is not allowed after order is set */

-    //H5Tset_order(handle->mtype_id, H5Tget_order(H5T_NATIVE_INT));

     break;

   default:

-- 

2.6.3