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-rw-r--r--java/src/hdf/hdf5lib/HDFArray.java304
1 files changed, 120 insertions, 184 deletions
diff --git a/java/src/hdf/hdf5lib/HDFArray.java b/java/src/hdf/hdf5lib/HDFArray.java
index 30f0fc8..63e17e8 100644
--- a/java/src/hdf/hdf5lib/HDFArray.java
+++ b/java/src/hdf/hdf5lib/HDFArray.java
@@ -16,6 +16,7 @@ package hdf.hdf5lib;
import hdf.hdf5lib.exceptions.HDF5Exception;
import hdf.hdf5lib.exceptions.HDF5JavaException;
+import java.util.Arrays;
/**
* This is a class for handling multidimensional arrays for HDF.
@@ -394,6 +395,7 @@ public class HDFArray {
throw (ex);
}
_barray = bytes; /* hope that the bytes are correct.... */
+
if (ArrayDescriptor.dims == 1) {
/* special case */
/* 2 data copies here! */
@@ -496,8 +498,62 @@ public class HDFArray {
Object oo = _theArray;
int n = 0; /* the current byte */
+ int m = 0; /* the current array index */
int index = 0;
int i;
+ Object flattenedArray = null;
+ switch (ArrayDescriptor.NT) {
+ case 'J':
+ flattenedArray = (Object) HDFNativeData.byteToLong(_barray);
+ break;
+ case 'S':
+ flattenedArray = (Object) HDFNativeData.byteToShort(_barray);
+ break;
+ case 'I':
+ flattenedArray = (Object) HDFNativeData.byteToInt(_barray);
+ break;
+ case 'F':
+ flattenedArray = (Object) HDFNativeData.byteToFloat(_barray);
+ break;
+ case 'D':
+ flattenedArray = (Object) HDFNativeData.byteToDouble(_barray);
+ break;
+ case 'B':
+ flattenedArray = (Object) _barray;
+ break;
+ case 'L':
+ switch (ArrayDescriptor.className) {
+ case "java.lang.Byte":
+ flattenedArray = (Object) ByteToByteObj(_barray);
+ break;
+ case "java.lang.Short":
+ flattenedArray = (Object) ByteToShort(_barray);
+ break;
+ case "java.lang.Integer":
+ flattenedArray = (Object) ByteToInteger(_barray);
+ break;
+ case "java.lang.Long":
+ flattenedArray = (Object) ByteToLongObj(_barray);
+ break;
+ case "java.lang.Float":
+ flattenedArray = (Object) ByteToFloatObj(_barray);
+ break;
+ case "java.lang.Double":
+ flattenedArray = (Object) ByteToDoubleObj(_barray);
+ break;
+ default:
+ HDF5JavaException ex = new HDF5JavaException(
+ "HDFArray: unsupported Object type: "
+ + ArrayDescriptor.NT);
+ throw (ex);
+ } // end of switch statement for arrays of boxed objects
+ default:
+ HDF5JavaException ex = new HDF5JavaException(
+ "HDFArray: unknown or unsupported type: "
+ + ArrayDescriptor.NT);
+ throw (ex);
+ } // end of switch statement for arrays of primitives
+
while (n < ArrayDescriptor.totalSize) {
oo = ArrayDescriptor.objs[0];
index = n / ArrayDescriptor.bytetoindex[0];
@@ -524,172 +580,58 @@ public class HDFArray {
/* array-ify */
try {
- if (ArrayDescriptor.NT == 'J') {
- long[] arow = HDFNativeData.byteToLong(n,
- ArrayDescriptor.dimlen[ArrayDescriptor.dims],
- _barray);
- java.lang.reflect.Array
- .set(
- ArrayDescriptor.objs[ArrayDescriptor.dims - 2],
- (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]),
- arow);
- n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1];
- ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++;
- }
- else if (ArrayDescriptor.NT == 'I') {
- int[] arow = HDFNativeData.byteToInt(n,
- ArrayDescriptor.dimlen[ArrayDescriptor.dims],
- _barray);
- java.lang.reflect.Array
- .set(
- ArrayDescriptor.objs[ArrayDescriptor.dims - 2],
- (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]),
- arow);
-
- n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1];
- ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++;
- }
- else if (ArrayDescriptor.NT == 'S') {
- short[] arow = HDFNativeData.byteToShort(n,
- ArrayDescriptor.dimlen[ArrayDescriptor.dims],
- _barray);
- java.lang.reflect.Array
- .set(
- ArrayDescriptor.objs[ArrayDescriptor.dims - 2],
- (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]),
- arow);
-
- n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1];
- ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++;
- }
- else if (ArrayDescriptor.NT == 'B') {
- System.arraycopy(_barray, n,
- ArrayDescriptor.objs[ArrayDescriptor.dims - 1], 0,
- ArrayDescriptor.dimlen[ArrayDescriptor.dims]);
- n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1];
- }
- else if (ArrayDescriptor.NT == 'F') {
- float arow[] = HDFNativeData.byteToFloat(n,
- ArrayDescriptor.dimlen[ArrayDescriptor.dims],
- _barray);
- java.lang.reflect.Array
- .set(
- ArrayDescriptor.objs[ArrayDescriptor.dims - 2],
- (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]),
- arow);
-
- n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1];
- ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++;
- }
- else if (ArrayDescriptor.NT == 'D') {
- double[] arow = HDFNativeData.byteToDouble(n,
- ArrayDescriptor.dimlen[ArrayDescriptor.dims],
- _barray);
- java.lang.reflect.Array
- .set(
- ArrayDescriptor.objs[ArrayDescriptor.dims - 2],
- (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]),
- arow);
-
- n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1];
- ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++;
- }
- else if (ArrayDescriptor.NT == 'L') {
- if (ArrayDescriptor.className.equals("java.lang.Byte")) {
- Byte I[] = ByteToByteObj(n,
- ArrayDescriptor.dimlen[ArrayDescriptor.dims],
- _barray);
- java.lang.reflect.Array
- .set(
- ArrayDescriptor.objs[ArrayDescriptor.dims - 2],
- (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]),
- I);
-
- n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1];
- ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++;
- }
- else if (ArrayDescriptor.className
- .equals("java.lang.Integer")) {
- Integer I[] = ByteToInteger(n,
- ArrayDescriptor.dimlen[ArrayDescriptor.dims],
- _barray);
- java.lang.reflect.Array
- .set(
- ArrayDescriptor.objs[ArrayDescriptor.dims - 2],
- (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]),
- I);
-
- n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1];
- ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++;
- }
- else if (ArrayDescriptor.className
- .equals("java.lang.Short")) {
- Short I[] = ByteToShort(n,
- ArrayDescriptor.dimlen[ArrayDescriptor.dims],
- _barray);
- java.lang.reflect.Array
- .set(
- ArrayDescriptor.objs[ArrayDescriptor.dims - 2],
- (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]),
- I);
-
- n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1];
- ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++;
- }
- else if (ArrayDescriptor.className
- .equals("java.lang.Float")) {
- Float I[] = ByteToFloatObj(n,
- ArrayDescriptor.dimlen[ArrayDescriptor.dims],
- _barray);
- java.lang.reflect.Array
- .set(
- ArrayDescriptor.objs[ArrayDescriptor.dims - 2],
- (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]),
- I);
-
- n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1];
- ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++;
- }
- else if (ArrayDescriptor.className
- .equals("java.lang.Double")) {
- Double I[] = ByteToDoubleObj(n,
- ArrayDescriptor.dimlen[ArrayDescriptor.dims],
- _barray);
- java.lang.reflect.Array
- .set(
- ArrayDescriptor.objs[ArrayDescriptor.dims - 2],
- (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]),
- I);
-
- n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1];
- ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++;
- }
- else if (ArrayDescriptor.className.equals("java.lang.Long")) {
- Long I[] = ByteToLongObj(n,
- ArrayDescriptor.dimlen[ArrayDescriptor.dims],
- _barray);
- java.lang.reflect.Array
- .set(
- ArrayDescriptor.objs[ArrayDescriptor.dims - 2],
- (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]),
- I);
-
- n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1];
- ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++;
- }
- else {
- HDF5JavaException ex = new HDF5JavaException(
- "HDFArray: unsupported Object type: "
- + ArrayDescriptor.NT);
- throw (ex);
- }
- }
- else {
- HDF5JavaException ex = new HDF5JavaException(
- "HDFArray: unknown or unsupported type: "
- + ArrayDescriptor.NT);
- throw (ex);
- }
+
+ Object arow = null;
+ int mm = m + ArrayDescriptor.dimlen[ArrayDescriptor.dims];
+ switch (ArrayDescriptor.NT) {
+ case 'B':
+ arow = (Object) Arrays.copyOfRange((byte[]) flattenedArray, m, mm);
+ break;
+ case 'S':
+ arow = (Object) Arrays.copyOfRange((short[]) flattenedArray, m, mm);
+ break;
+ case 'I':
+ arow = (Object) Arrays.copyOfRange((int[]) flattenedArray, m, mm);
+ break;
+ case 'J':
+ arow = (Object) Arrays.copyOfRange((long[]) flattenedArray, m, mm);
+ break;
+ case 'F':
+ arow = (Object) Arrays.copyOfRange((float[]) flattenedArray, m, mm);
+ break;
+ case 'D':
+ arow = (Object) Arrays.copyOfRange((double[]) flattenedArray, m, mm);
+ break;
+ case 'L':
+ switch (ArrayDescriptor.className) {
+ case "java.lang.Byte":
+ arow = (Object) Arrays.copyOfRange((Byte[])flattenedArray, m, mm);
+ break;
+ case "java.lang.Short":
+ arow = (Object) Arrays.copyOfRange((Short[])flattenedArray, m, mm);
+ break;
+ case "java.lang.Integer":
+ arow = (Object) Arrays.copyOfRange((Integer[])flattenedArray, m, mm);
+ break;
+ case "java.lang.Long":
+ arow = (Object) Arrays.copyOfRange((Long[])flattenedArray, m, mm);
+ break;
+ case "java.lang.Float":
+ arow = (Object) Arrays.copyOfRange((Float[])flattenedArray, m, mm);
+ break;
+ case "java.lang.Double":
+ arow = (Object) Arrays.copyOfRange((Double[])flattenedArray, m, mm);
+ break;
+ } // end of switch statement for arrays of boxed numerics
+ } // end of switch statement for arrays of primitives
+
+ java.lang.reflect.Array.set(
+ ArrayDescriptor.objs[ArrayDescriptor.dims - 2],
+ (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]),
+ arow);
+ n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1];
+ ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++;
+ m = mm;
}
catch (OutOfMemoryError err) {
HDF5JavaException ex = new HDF5JavaException(
@@ -717,25 +659,15 @@ public class HDFArray {
+ (ArrayDescriptor.dimlen[i] - 1) + "?"));
}
}
- if (ArrayDescriptor.NT != 'B') {
- if (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1] != ArrayDescriptor.dimlen[ArrayDescriptor.dims - 1]) {
- throw new java.lang.InternalError(new String(
- "HDFArray::arrayify Panic didn't complete all data: currentindex["
- + i + "] = " + ArrayDescriptor.currentindex[i]
- + " (should be " + (ArrayDescriptor.dimlen[i])
- + "?"));
- }
- }
- else {
- if (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1] != (ArrayDescriptor.dimlen[ArrayDescriptor.dims - 1] - 1)) {
- throw new java.lang.InternalError(new String(
- "HDFArray::arrayify Panic didn't complete all data: currentindex["
- + i + "] = " + ArrayDescriptor.currentindex[i]
- + " (should be "
- + (ArrayDescriptor.dimlen[i] - 1) + "?"));
- }
+ if (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1] != ArrayDescriptor.dimlen[ArrayDescriptor.dims - 1]) {
+ throw new java.lang.InternalError(new String(
+ "HDFArray::arrayify Panic didn't complete all data: currentindex["
+ + i + "] = " + ArrayDescriptor.currentindex[i]
+ + " (should be " + (ArrayDescriptor.dimlen[i])
+ + "?"));
}
+
return _theArray;
}
@@ -944,6 +876,7 @@ class ArrayDescriptor {
static int[] currentindex = null;
static int[] bytetoindex = null;
static int totalSize = 0;
+ static int totalElements = 0;
static Object[] objs = null;
static char NT = ' '; /* must be B,S,I,L,F,D, else error */
static int NTsize = 0;
@@ -1052,6 +985,7 @@ class ArrayDescriptor {
dimlen[0] = 1;
dimstart[0] = 0;
currentindex[0] = 0;
+ int elements = 1;
int i;
for (i = 1; i <= dims; i++) {
dimlen[i] = java.lang.reflect.Array.getLength((Object) o);
@@ -1059,7 +993,9 @@ class ArrayDescriptor {
objs[i] = o;
dimstart[i] = 0;
currentindex[i] = 0;
+ elements *= dimlen[i];
}
+ totalElements = elements;
int j;
int dd;
@@ -1083,7 +1019,7 @@ class ArrayDescriptor {
System.out.println("Class: " + theClass);
System.out.println("NT: " + NT + " NTsize: " + NTsize);
System.out.println("Array has " + dims + " dimensions (" + totalSize
- + " bytes)");
+ + " bytes, " + totalElements + " elements)");
int i;
for (i = 0; i <= dims; i++) {
Class tc = objs[i].getClass();
generated by cgit v0.12 at 2024-11-01 15:57:57 (GMT)