/
VeecoReader.java
201 lines (169 loc) · 5.76 KB
/
VeecoReader.java
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
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
/*
* #%L
* OME Bio-Formats package for reading and converting biological file formats.
* %%
* Copyright (C) 2005 - 2016 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
* - Glencoe Software, Inc.
* - University of Dundee
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 2 of the
* License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public
* License along with this program. If not, see
* <http://www.gnu.org/licenses/gpl-2.0.html>.
* #L%
*/
package loci.formats.in;
import java.io.IOException;
import java.util.Arrays;
import java.util.Hashtable;
import java.util.Vector;
import loci.common.DataTools;
import loci.common.services.DependencyException;
import loci.common.services.ServiceException;
import loci.common.services.ServiceFactory;
import loci.formats.CoreMetadata;
import loci.formats.FormatException;
import loci.formats.FormatReader;
import loci.formats.FormatTools;
import loci.formats.MetadataTools;
import loci.formats.MissingLibraryException;
import loci.formats.meta.MetadataStore;
import loci.formats.services.NetCDFService;
import ome.xml.model.primitives.PositiveFloat;
/**
* VeecoReader is the file format reader for Veeco HDF files.
*/
public class VeecoReader extends FormatReader {
// -- Fields --
private NetCDFService netcdf;
private Object image;
private boolean unpackEndian = true;
// -- Constructor --
/** Constructs a new Veeco reader. */
public VeecoReader() {
super("Veeco", "hdf");
domains = new String[] {FormatTools.SEM_DOMAIN};
}
// -- IFormatReader API methods --
/**
* @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int)
*/
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
throws FormatException, IOException
{
FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
if (image instanceof byte[][]) {
byte[][] byteImage = (byte[][]) image;
for (int row=h+y-1; row>=y; row--) {
System.arraycopy(byteImage[row], x, buf, (row - y) * w, w);
}
}
else if (image instanceof short[][]) {
short[][] shortImage = (short[][]) image;
int output = 0;
for (int row=h+y-1; row>=y; row--) {
for (int col=x; col<x+w; col++) {
DataTools.unpackBytes(
shortImage[row][col], buf, output, 2, unpackEndian);
output += 2;
}
}
}
return buf;
}
/* @see loci.formats.IFormatReader#close(boolean) */
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) {
if (netcdf != null) netcdf.close();
image = null;
unpackEndian = true;
}
}
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
protected void initFile(String id) throws FormatException, IOException {
super.initFile(id);
CoreMetadata m = core.get(0);
try {
ServiceFactory factory = new ServiceFactory();
netcdf = factory.getInstance(NetCDFService.class);
netcdf.setFile(id);
}
catch (DependencyException e) {
throw new MissingLibraryException(e);
}
Vector<String> variableList = netcdf.getVariableList();
// a single variable containing the image data is expected
if (variableList.size() == 0) {
throw new FormatException("No image data found");
}
String imageName = variableList.get(0);
try {
image = netcdf.getVariableValue(imageName);
}
catch (ServiceException e) {
throw new FormatException("Could not retrieve image data", e);
}
Hashtable<String, Object> attributes =
netcdf.getVariableAttributes(imageName);
for (String attr : attributes.keySet()) {
addGlobalMeta(attr, attributes.get(attr));
}
if (image instanceof byte[][]) {
byte[][] byteImage = (byte[][]) image;
m.sizeX = byteImage[0].length;
m.sizeY = byteImage.length;
m.pixelType = FormatTools.INT8;
}
else if (image instanceof short[][]) {
short[][] shortImage = (short[][]) image;
m.sizeX = shortImage[0].length;
m.sizeY = shortImage.length;
m.pixelType = FormatTools.INT16;
// set the endianness to use when unpacking pixels
// NetCDF may not return the pixels with a constant endianness,
// so this ensures that the reader corrects accordingly (see ticket 12085)
short nativeMin = 0;
short nativeMax = 0;
short swappedMin = 0;
short swappedMax = 0;
for (int y=0; y<shortImage.length; y++) {
for (int x=0; x<shortImage[y].length; x++) {
if (shortImage[y][x] < nativeMin) {
nativeMin = shortImage[y][x];
}
if (shortImage[y][x] > nativeMax) {
nativeMax = shortImage[y][x];
}
short swapped = DataTools.swap(shortImage[y][x]);
if (swapped < swappedMin) {
swappedMin = swapped;
}
if (swapped > swappedMax) {
swappedMax = swapped;
}
}
}
unpackEndian = nativeMin <= swappedMin && nativeMax >= swappedMax;
}
m.sizeZ = 1;
m.sizeC = 1;
m.sizeT = 1;
m.imageCount = m.sizeZ * m.sizeC * m.sizeT;
m.dimensionOrder = "XYCZT";
m.littleEndian = false;
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
}
}