Author: extemporaneousb
Date: 2010-04-21 03:36:54 +0200 (Wed, 21 Apr 2010)
New Revision: 11
Modified:
inst/.Rhistory
inst/h5_files/ex_1.h5
inst/h5_files/makeH5.py
inst/tests.R
src/h5_wrap.c
Log:
Some partially broken code for doing hyperslab selection.
Modified: inst/.Rhistory
===================================================================
--- inst/.Rhistory 2010-04-16 01:09:15 UTC (rev 10)
+++ inst/.Rhistory 2010-04-21 01:36:54 UTC (rev 11)
@@ -1,18 +1,4 @@
-.Call("h5R_get_dataset_str", d)
-.Call("_h5R_get_dataset_str", d)
-.Call("_h5R_get_dataset_str", d)
-1
d = .Call("h5R_get_dataset", g at ePtr, "ds_2")
-.Call("_h5R_get_dataset_str", d)
-.Call("_h5R_get_dataset_str", d)
-1
-d = .Call("h5R_get_dataset", g at ePtr, "ds_2")
-.Call("_h5R_get_dataset_str", d)
-.Call("_h5R_get_dataset_str", d)
-x
-1
-d = .Call("h5R_get_dataset", g at ePtr, "ds_2")
-.Call("_h5R_get_dataset_str", d)
.Call("__h5R_get_dataset_str", d)
d = .Call("h5R_get_dataset", g at ePtr, "ds_2")
.Call("__h5R_get_dataset_str", d)
@@ -34,13 +20,11 @@
.Call("__h5R_get_dataset_str", d)
d = .Call("h5R_get_dataset", g at ePtr, "ds_2")
.Call("__h5R_get_dataset_str", d)
-d = .Call("h5R_get_dataset", g at ePtr, "ds_2")
.Call("__h5R_get_dataset_str", d)
.Call("__h5R_get_dataset_str", d)
.Call("__h5R_get_dataset_str", d)
.Call("__h5R_get_dataset_str", d)
.Call("__h5R_get_dataset_str", d)
-.Call("__h5R_get_dataset_str", d)
d = .Call("h5R_get_dataset", g at ePtr, "ds_2")
.Call("__h5R_get_dataset_str", d)
.Call("__h5R_get_dataset_str", d)
@@ -148,3 +132,19 @@
?drop
d[1,1]
d3[1,1,]
+d
+.Call("h5R_read_slab", d at ePtr, as.integer(0,0), as.integer(5,5))
+4
+.Call("h5R_read_slab", d at ePtr, as.integer(0,0), as.integer(5,5))
+1
+.Call("h5R_read_slab", d at ePtr, as.integer(0,0), as.integer(5,5))
+1
+.Call("h5R_read_slab", d at ePtr, as.integer(0,0), as.integer(5,5))
+1
+d3
+d3[1,,]
+dint
+.Call("h5R_read_slab", dint at ePtr, as.integer(0,0), as.integer(5,5))
+1
+dint[,]
+1
Modified: inst/h5_files/ex_1.h5
===================================================================
(Binary files differ)
Modified: inst/h5_files/makeH5.py
===================================================================
--- inst/h5_files/makeH5.py 2010-04-16 01:09:15 UTC (rev 10)
+++ inst/h5_files/makeH5.py 2010-04-21 01:36:54 UTC (rev 11)
@@ -23,6 +23,8 @@
g.create_dataset("ds_4", data = s.reshape((2, 10)))
+g.create_dataset("ds_5", data = a.reshape(21, 9))
+
f.close()
f = h5py.File("ex_1.h5")
Modified: inst/tests.R
===================================================================
--- inst/tests.R 2010-04-16 01:09:15 UTC (rev 10)
+++ inst/tests.R 2010-04-21 01:36:54 UTC (rev 11)
@@ -8,6 +8,10 @@
## ex_1
f <- H5File(files[1])
g <- getH5Group(f, "group_1")
+
+dint <- getH5Dataset(g, "ds_5")
+.Call("h5R_read_slab", dint at ePtr, as.integer(c(0,0)), as.integer(c(5,5)), as.integer(c(5,5)))
+
d <- getH5Dataset(g, "ds_1")
d[1:10, 1:10]
d[1:10,]
Modified: src/h5_wrap.c
===================================================================
--- src/h5_wrap.c 2010-04-16 01:09:15 UTC (rev 10)
+++ src/h5_wrap.c 2010-04-21 01:36:54 UTC (rev 11)
@@ -178,17 +178,17 @@
void* buf;
switch (INTEGER(h5R_get_type(h5_dataset))[0]) {
- case H5T_INTEGER :
+ case H5T_INTEGER:
PROTECT(dta = allocVector(INTSXP, _h5R_get_nelts(h5_dataset)));
memtype = H5T_NATIVE_INT;
buf = INTEGER(dta);
break;
- case H5T_FLOAT :
+ case H5T_FLOAT:
PROTECT(dta = allocVector(REALSXP, _h5R_get_nelts(h5_dataset)));
memtype = H5T_NATIVE_DOUBLE;
buf = REAL(dta);
break;
- case H5T_STRING :
+ case H5T_STRING:
return _h5R_read_vlen_str(h5_dataset);
default:
error("Unsupported class in h5R_read_dataset.");
@@ -198,6 +198,50 @@
return(dta);
}
+
+SEXP h5R_read_slab(SEXP h5_dataset, SEXP _offsets, SEXP _counts, SEXP _orank) {
+ SEXP dta = R_NilValue;
+ hid_t space, memspace;
+ int ndims, i;
+
+ int* offsets = INTEGER(_offsets);
+ int* counts = INTEGER(_counts);
+ int* orank = INTEGER(_orank);
+
+ hsize_t sel[] = {0, 0};
+
+ int v = 1;
+ for (i = 0; i < length(_orank); i++) {
+ v *= orank[i];
+ }
+
+ switch (INTEGER(h5R_get_type(h5_dataset))[0]) {
+ case H5T_INTEGER:
+ Rprintf("In H5T_INTEGER with v = %d\n", v);
+
+ space = _h5R_get_space(h5_dataset);
+ H5Sselect_hyperslab(space, H5S_SELECT_SET, (hsize_t*) offsets, NULL, NULL, (hsize_t*) counts);
+
+ /* memspace = H5Screate_simple(length(_orank), (hsize_t*) orank, NULL); */
+ /* H5Sselect_hyperslab(memspace, H5S_SELECT_SET, sel, NULL, (hsize_t*) counts, NULL); */
+
+ PROTECT(dta = allocVector(INTSXP, v));
+ Rprintf("About to read dataset, v = %d\n", v);
+ Rprintf("offset: %d, %d\n", offsets[0], offsets[1]);
+ Rprintf("counts: %d, %d\n", counts[0], counts[1]);
+
+ H5Dread(HID(h5_dataset), H5T_NATIVE_INT, H5S_ALL, space, H5P_DEFAULT, (void *) INTEGER(dta));
+ break;
+ default:
+ error("Unsupported class in %s\n", __func__);
+
+ }
+
+ UNPROTECT(1);
+
+ return dta;
+}
+
/**
* I am currently keeping read_attr and read_dataset separate because