-
Notifications
You must be signed in to change notification settings - Fork 242
/
FEIReader.java
164 lines (134 loc) · 4.56 KB
/
FEIReader.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
/*
* #%L
* OME Bio-Formats package for reading and converting biological file formats.
* %%
* Copyright (C) 2005 - 2017 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 loci.common.RandomAccessInputStream;
import loci.formats.CoreMetadata;
import loci.formats.FormatException;
import loci.formats.FormatReader;
import loci.formats.FormatTools;
import loci.formats.MetadataTools;
import loci.formats.meta.MetadataStore;
/**
* FEIReader is the file format reader for FEI and Philips .img files.
*/
public class FEIReader extends FormatReader {
// -- Constants --
public static final String FEI_MAGIC_STRING = "XL";
private static final int INVALID_PIXELS = 112;
// -- Fields --
private int headerSize;
// -- Constructor --
/** Constructs a new FEI reader. */
public FEIReader() {
super("FEI/Philips", "img");
suffixSufficient = false;
domains = new String[] {FormatTools.SEM_DOMAIN};
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
final int blockLen = 2;
if (!FormatTools.validStream(stream, blockLen, false)) return false;
return stream.readString(blockLen).startsWith(FEI_MAGIC_STRING);
}
/**
* @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int)
*/
@Override
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);
in.seek(headerSize);
byte[] segment = new byte[getSizeX() / 2];
byte[] plane = new byte[FormatTools.getPlaneSize(this)];
// interlace frames - there are four rows of two columns
for (int q=0; q<4; q++) {
for (int row=q; row<getSizeY(); row+=4) {
for (int s=0; s<2; s++) {
in.read(segment);
in.skipBytes(INVALID_PIXELS / 2);
for (int col=s; col<getSizeX(); col+=2) {
plane[row*getSizeX() + col] = segment[col / 2];
}
}
}
}
try (RandomAccessInputStream pixels = new RandomAccessInputStream(plane)) {
readPlane(pixels, x, y, w, h, buf);
}
return buf;
}
/* @see loci.formats.IFormatReader#close(boolean) */
@Override
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) {
headerSize = 0;
}
}
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
super.initFile(id);
in = new RandomAccessInputStream(id);
in.order(true);
CoreMetadata m = core.get(0);
LOGGER.info("Reading file header");
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
in.skipBytes(44);
float magnification = in.readFloat();
float kV = in.readFloat() / 1000;
float wd = in.readFloat();
in.skipBytes(12);
float spot = in.readFloat();
addGlobalMeta("Magnification", magnification);
addGlobalMeta("kV", kV);
addGlobalMeta("Working distance", wd);
addGlobalMeta("Spot", spot);
}
in.seek(514);
m.sizeX = in.readShort() - INVALID_PIXELS;
m.sizeY = in.readShort();
in.skipBytes(4);
headerSize = in.readShort();
// always one grayscale plane per file
m.sizeZ = 1;
m.sizeC = 1;
m.sizeT = 1;
m.imageCount = 1;
m.littleEndian = true;
m.pixelType = FormatTools.UINT8;
m.rgb = false;
m.indexed = false;
m.interleaved = false;
m.dimensionOrder = "XYCZT";
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
}
}