[H5r-commits] r18 - inst src

[noreply at r-forge.r-project.org]

Author: extemporaneousb
Date: 2010-04-30 19:04:56 +0200 (Fri, 30 Apr 2010)
New Revision: 18

Modified:
   inst/testSlab.R
   src/h5_wrap.c
Log:
Added support for String hyperslab selection.



Modified: inst/testSlab.R
===================================================================
--- inst/testSlab.R	2010-04-30 00:14:37 UTC (rev 17)
+++ inst/testSlab.R	2010-04-30 17:04:56 UTC (rev 18)
@@ -54,3 +54,18 @@
 d3[1,1,1]
 d3[1,,]
 d3[,,1]
+
+
+dStr <- getH5Dataset(g, "ds_2", inMemory = FALSE)
+dStrM <- getH5Dataset(g, "ds_2", inMemory = TRUE)
+all(dStr[1:2] == dStrM[1:2])
+all(dStr[1:2] == dStrM[1:2])
+
+
+dStr <- getH5Dataset(g, "ds_4", inMemory = FALSE)
+dStrM <- getH5Dataset(g, "ds_4", inMemory = TRUE)
+all(dStr[1:2,] == dStrM[1:2,])
+all(dStr[,1:2] == dStrM[,1:2])
+
+x = replicate(1000000, dStr[,1:5])
+

Modified: src/h5_wrap.c
===================================================================
--- src/h5_wrap.c	2010-04-30 00:14:37 UTC (rev 17)
+++ src/h5_wrap.c	2010-04-30 17:04:56 UTC (rev 18)
@@ -206,7 +206,7 @@
     /** I'm surprised I have to do this, but it seems to be necessary. **/
     hsize_t* _h_offsets = (hsize_t*) Calloc(length(_counts), hsize_t);
     hsize_t* _h_counts  = (hsize_t*) Calloc(length(_counts), hsize_t);
-    
+
     int v = 1;
     for (i = 0; i < length(_counts); i++) {
     	v *= counts[i];
@@ -214,6 +214,10 @@
 	_h_counts[i]  = counts[i];
     }
 
+    space = _h5R_get_space(h5_dataset);
+    H5Sselect_hyperslab(space, H5S_SELECT_SET, _h_offsets, NULL, _h_counts, NULL);
+    memspace = H5Screate_simple(length(_counts), _h_counts, NULL);
+
     switch (INTEGER(h5R_get_type(h5_dataset))[0]) {
     case H5T_INTEGER: 
 	PROTECT(dta = allocVector(INTSXP, v));
@@ -226,17 +230,31 @@
 	buf = REAL(dta);
 	break;
     case H5T_STRING:
-	error("String slab selection not yet supported.\n");
+	buf = (char **) Calloc(v, char*);
+	memtype = H5Tcopy (H5T_C_S1);
+	H5Tset_size (memtype, H5T_VARIABLE);   
+	break;
     default:
 	error("Unsupported class in %s\n", __func__);
     }
     
-    space = _h5R_get_space(h5_dataset);
-    H5Sselect_hyperslab(space, H5S_SELECT_SET, _h_offsets, NULL, _h_counts, NULL);
-    memspace = H5Screate_simple(length(_counts), _h_counts, NULL);
-    H5Dread(HID(h5_dataset), memtype, memspace, space, 
-	    H5P_DEFAULT, buf);
+    H5Dread(HID(h5_dataset), memtype, memspace, space, H5P_DEFAULT, buf);
 
+    /** There requires a little more with strings. **/
+    if (H5T_STRING == INTEGER(h5R_get_type(h5_dataset))[0]) {
+	PROTECT(dta = allocVector(STRSXP, v));
+	for (i = 0; i < v; i++)
+	    if (((char **) buf)[i]) {
+		SET_STRING_ELT(dta, i, mkChar(  ((char **) buf)[i] )); 
+	    }
+
+	H5Dvlen_reclaim (memtype, memspace, H5P_DEFAULT, buf);
+	
+	H5Tclose(memtype);
+	Free(buf);
+    }
+
+
     /** clean up. **/
     Free(_h_offsets);
     Free(_h_counts);