This repository has been archived by the owner on Jan 6, 2021. It is now read-only.
-
Notifications
You must be signed in to change notification settings - Fork 4
/
minimum_writer.cpp
149 lines (131 loc) · 4.87 KB
/
minimum_writer.cpp
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
/*
* #%L
* BSD implementations of Bio-Formats readers and writers
* %%
* Copyright (C) 2005 - 2016 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
* - Glencoe Software, Inc.
* - University of Dundee
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
// A C++ version of the Bio-Formats MinimumWriter example.
// For the original Java version, see:
// components/formats-bsd/utils/MinimumWriter.java
// for JVM initialization
#include "javaTools.h"
// for Bio-Formats C++ bindings
#include "formats-api-5.3.4.h"
#include "formats-bsd-5.3.4.h"
#include "ome-xml-5.4.0.h"
using jace::JNIException;
using jace::proxy::java::io::IOException;
using jace::proxy::java::lang::Boolean;
using jace::proxy::java::lang::Integer;
using jace::proxy::loci::formats::FormatException;
using jace::proxy::loci::formats::FormatTools;
using jace::proxy::loci::formats::ImageWriter;
using jace::proxy::loci::formats::meta::IMetadata;
using jace::proxy::loci::formats::services::OMEXMLServiceImpl;
using jace::proxy::ome::xml::model::enums::DimensionOrder;
using jace::proxy::ome::xml::model::enums::PixelType;
using jace::proxy::ome::xml::model::primitives::PositiveInteger;
#include <iostream>
using std::cout;
using std::endl;
#include <exception>
using std::exception;
#include <string>
using std::string;
// for rand
#include <stdio.h>
#include <stdlib.h>
// -- Methods --
/*
* Demonstrates the minimum amount of metadata
* necessary to write out an image plane.
*/
bool minWrite(int argc, const char *argv[]) {
if (argc < 2) {
cout << "Please specify an output file name." << endl;
return -1;
}
string id = argv[1];
// create blank 512x512 image
cout << "Creating random image..." << endl;
int w = 512, h = 512;
int pixelType = FormatTools::UINT16();
//byte[] img = new byte[w * h * FormatTools.getBytesPerPixel(pixelType)];
int planeSize = w * h * FormatTools::getBytesPerPixel(pixelType);
ByteArray img(planeSize); // pre-allocate buffer
// fill with random data
for (int i=0; i<planeSize; i++) img[i] = rand();
// create metadata object with minimum required metadata fields
cout << "Populating metadata..." << endl;
OMEXMLServiceImpl service;
IMetadata meta = service.createOMEXMLMetadata();
meta.createRoot();
meta.setImageID("Image:0", 0);
meta.setPixelsID("Pixels:0", 0);
meta.setPixelsBinDataBigEndian(Boolean(1), 0, 0);
meta.setPixelsDimensionOrder(DimensionOrder::XYZCT(), 0);
meta.setPixelsType(
PixelType::fromString(FormatTools::getPixelTypeString(pixelType)), 0);
meta.setPixelsSizeX(PositiveInteger(Integer(w)), 0);
meta.setPixelsSizeY(PositiveInteger(Integer(h)), 0);
meta.setPixelsSizeZ(PositiveInteger(Integer(1)), 0);
meta.setPixelsSizeC(PositiveInteger(Integer(1)), 0);
meta.setPixelsSizeT(PositiveInteger(Integer(1)), 0);
meta.setChannelID("Channel:0:0", 0, 0);
meta.setChannelSamplesPerPixel(Integer(1), 0, 0);
// write image plane to disk
cout << "Writing image to '" << id << "'..." << endl;
ImageWriter writer;
writer.setMetadataRetrieve(meta);
writer.setId(id);
writer.saveBytes(0, img);
writer.close();
cout << "Done." << endl;
}
int main(int argc, const char *argv[]) {
try {
JavaTools::createJVM();
minWrite(argc, argv);
}
catch (FormatException& fe) {
fe.printStackTrace();
return -2;
}
catch (IOException& ioe) {
ioe.printStackTrace();
return -3;
}
catch (JNIException& jniException) {
cout << "An unexpected JNI error occurred. " << jniException.what() << endl;
return -4;
}
catch (exception& e) {
cout << "An unexpected C++ error occurred. " << e.what() << endl;
return -5;
}
}