1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
|
/*
* Copyright 2007 - 2018 ETH Zuerich, CISD and SIS.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package ch.systemsx.cisd.hdf5;
import ch.systemsx.cisd.hdf5.exceptions.HDF5SpaceRankMismatch;
import hdf.hdf5lib.exceptions.HDF5JavaException;
/**
* A parameter class to specify the block and slice to read from or write to a multi-dimensional array.
*/
public final class HDF5ArrayBlockParams
{
int[] blockDimensions;
long[] blockIndex;
long[] blockOffset;
long[] boundIndexArray;
IndexMap boundIndexMap;
HDF5ArrayBlockParams()
{
// Only HDF5ArrayBlockParamsBuilder can instantiate this class.
}
int[] getBlockDimensions()
{
return blockDimensions;
}
long[] getOffset(int[] blockDimensions)
{
if (blockOffset == null)
{
if (blockDimensions == null)
{
throw new HDF5JavaException("No block dimensions set");
}
blockOffset = new long[blockDimensions.length];
if (blockIndex != null)
{
if (blockDimensions.length != blockIndex.length)
{
throw new HDF5SpaceRankMismatch(blockDimensions.length, blockIndex.length);
}
for (int i = 0; i < blockOffset.length; ++i)
{
blockOffset[i] = blockIndex[i] * blockDimensions[i];
}
}
}
return blockOffset;
}
long[] getOffset()
{
return getOffset(blockDimensions);
}
long[] getBoundIndexArray()
{
return boundIndexArray;
}
IndexMap getBoundIndexMap()
{
return boundIndexMap;
}
boolean hasBlock()
{
return blockDimensions != null || blockIndex != null || blockOffset != null;
}
boolean hasSlice()
{
return boundIndexArray != null || boundIndexMap != null;
}
//
// Public interface
//
/**
* Sets an array block dimensions.
*
* @param dimensions The block dimensions.
*/
public HDF5ArrayBlockParams block(int... dimensions)
{
this.blockDimensions = dimensions;
return this;
}
/**
* Sets the array block indices.
*
* @param blockIndex The block index in each dimension (offset: multiply with the
* <var>blockDimensions</var> in the according dimension).
*/
public HDF5ArrayBlockParams index(long... blockIndex)
{
this.blockIndex = blockIndex;
return this;
}
/**
* Sets the array block offset.
*
* @param offset The offset in the array to start reading from in each dimension.
*/
public HDF5ArrayBlockParams offset(long... offset)
{
this.blockOffset = offset;
return this;
}
/**
* Sets an array slice. The slice is defined by "bound indices", each of which is fixed to a
* given value. The data block read or written only contains the free (i.e. non-fixed) indices.
*
* @param boundIndices The array containing the values of the bound indices at the respective
* index positions, and -1 at the free index positions. For example an array of
* <code>new long[] { -1, -1, 5, -1, 7, -1 }</code> has 2 and 4 as bound indices and
* binds them to the values 5 and 7, respectively.
*/
public HDF5ArrayBlockParams slice(long... boundIndices)
{
boundIndexArray = boundIndices;
return this;
}
/**
* Sets an array slice. The slice is defined by "bound indices", each of which is fixed to a
* given value. The data block read or written only contains the free (i.e. non-fixed) indices.
*
* @param boundIndices The mapping of indices to index values which should be bound. For example
* a map of <code>new IndexMap().mapTo(2, 5).mapTo(4, 7)</code> has 2 and 4 as bound
* indices and binds them to the values 5 and 7, respectively.
*/
public HDF5ArrayBlockParams slice(IndexMap boundIndices)
{
boundIndexMap = boundIndices;
return this;
}
}
|
