[C++ API] Creating OME-TIFF with multiple series
Posted: Wed Feb 03, 2016 12:34 pmHi,
I'm a OME-TIFF beginner. And I want to create a OME-TIFF with multiple images, these images don't form something like planes, so I thought I use series for that.
I adapted the shipped example `metadata-formatwriter.org` but always get a debug assertion deep down in the library guts:
The adapted example code is attached, my changes were:
Did I understand the documentation right?
I'm using bioformats 5.1.7 with a C++11 compiler.
Thanks in advance,
Thomas
Here is the full code of the example:
I'm a OME-TIFF beginner. And I want to create a OME-TIFF with multiple images, these images don't form something like planes, so I thought I use series for that.
I adapted the shipped example `metadata-formatwriter.org` but always get a debug assertion deep down in the library guts:
- Code: Select all
Image count: 2
Plane count: 1
PixelBuffer PixelType is uint16
VariantPixelBuffer PixelType is uint16
Wrote 786432 uint16 pixels
Plane count: 1
PixelBuffer PixelType is uint16
VariantPixelBuffer PixelType is uint16
Wrote 786432 uint16 pixels
Caught exception: vector::_M_range_check: __n (which is 1) >= this->size() (which is 0)
The adapted example code is attached, my changes were:
- Code: Select all
$diff -Nur metadata-formatwriter-orig.cpp metadata-formatwriter.cpp
--- metadata-formatwriter-orig.cpp 2016-01-31 00:18:14.795891269 +0100
+++ metadata-formatwriter.cpp 2016-02-03 13:25:59.402170072 +0100
@@ -91,6 +91,7 @@
core->bitsPerPixel = 12U;
core->dimensionOrder = DimensionOrder::XYZTC;
seriesList.push_back(core);
+ seriesList.push_back(core);
fillMetadata(*meta, seriesList);
@@ -104,7 +105,7 @@
std::ostream& stream)
{
// Total number of images (series)
- dimension_size_type ic = 1;
+ dimension_size_type ic = 2;
stream << "Image count: " << ic << '\n';
// Loop over images
Did I understand the documentation right?
I'm using bioformats 5.1.7 with a C++11 compiler.
Thanks in advance,
Thomas
Here is the full code of the example:
- Code: Select all
/*
* #%L
* OME-BIOFORMATS C++ library for image IO.
* Copyright © 2015 Open Microscopy Environment:
* - Massachusetts Institute of Technology
* - National Institutes of Health
* - University of Dundee
* - Board of Regents of the University of Wisconsin-Madison
* - Glencoe Software, Inc.
* %%
* 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.
*
* The views and conclusions contained in the software and documentation are
* those of the authors and should not be interpreted as representing official
* policies, either expressed or implied, of any organization.
* #L%
*/
#include <iostream>
#include <ome/bioformats/CoreMetadata.h>
#include <ome/bioformats/MetadataTools.h>
#include <ome/bioformats/VariantPixelBuffer.h>
#include <ome/bioformats/out/OMETIFFWriter.h>
#include <ome/xml/meta/OMEXMLMetadata.h>
#include <ome/compat/memory.h>
#include <ome/common/filesystem.h>
using boost::filesystem::path;
using ome::compat::make_shared;
using ome::compat::shared_ptr;
using ome::bioformats::dimension_size_type;
using ome::bioformats::fillMetadata;
using ome::bioformats::CoreMetadata;
using ome::bioformats::DIM_SPATIAL_X;
using ome::bioformats::DIM_SPATIAL_Y;
using ome::bioformats::DIM_SUBCHANNEL;
using ome::bioformats::FormatWriter;
using ome::bioformats::MetadataMap;
using ome::bioformats::out::OMETIFFWriter;
using ome::bioformats::PixelBuffer;
using ome::bioformats::PixelBufferBase;
using ome::bioformats::PixelProperties;
using ome::bioformats::VariantPixelBuffer;
using ome::xml::model::enums::PixelType;
using ome::xml::model::enums::DimensionOrder;
namespace
{
/* write-example-start */
shared_ptr< ::ome::xml::meta::OMEXMLMetadata>
createMetadata()
{
// OME-XML metadata store.
shared_ptr< ::ome::xml::meta::OMEXMLMetadata> meta(make_shared< ::ome::xml::meta::OMEXMLMetadata>());
// Create simple CoreMetadata and use this to set up the OME-XML
// metadata. This is purely for convenience in this example; a
// real writer would typically set up the OME-XML metadata from an
// existing MetadataRetrieve instance or by hand.
std::vector<shared_ptr<CoreMetadata> > seriesList;
shared_ptr<CoreMetadata> core(make_shared<CoreMetadata>());
core->sizeX = 512U;
core->sizeY = 512U;
core->sizeC.clear(); // defaults to 1 channel with 1 subchannel; clear this
core->sizeC.push_back(3U); // replace with single RGB channel
core->pixelType = ome::xml::model::enums::PixelType::UINT16;
core->interleaved = false;
core->bitsPerPixel = 12U;
core->dimensionOrder = DimensionOrder::XYZTC;
seriesList.push_back(core);
seriesList.push_back(core);
fillMetadata(*meta, seriesList);
return meta;
}
/* write-example-end */
/* pixel-example-start */
void
writePixelData(FormatWriter& writer,
std::ostream& stream)
{
// Total number of images (series)
dimension_size_type ic = 2;
stream << "Image count: " << ic << '\n';
// Loop over images
for (dimension_size_type i = 0 ; i < ic; ++i)
{
// Change the current series to this index
writer.setSeries(i);
// Total number of planes.
dimension_size_type pc = 1;
stream << "\tPlane count: " << pc << '\n';
// Loop over planes (for this image index)
for (dimension_size_type p = 0 ; p < pc; ++p)
{
// Pixel buffer; size 512 × 512 with 3 subchannels of type
// uint16_t. It uses the native endianness and has a
// storage order of XYZTC without interleaving
// (subchannels are planar).
shared_ptr<PixelBuffer<PixelProperties<PixelType::UINT16>::std_type> >
buffer(make_shared<PixelBuffer<PixelProperties<PixelType::UINT16>::std_type> >
(boost::extents[512][512][1][1][1][3][1][1][1],
PixelType::UINT16, ome::bioformats::ENDIAN_NATIVE,
PixelBufferBase::make_storage_order(DimensionOrder::XYZTC, false)));
// Fill each subchannel with a different intensity ramp in
// the 12-bit range. In a real program, the pixel data
// would typically be obtained from data acquisition or
// another image.
for (dimension_size_type x = 0; x < 512; ++x)
for (dimension_size_type y = 0; y < 512; ++y)
{
PixelBufferBase::indices_type idx;
std::fill(idx.begin(), idx.end(), 0);
idx[DIM_SPATIAL_X] = x;
idx[DIM_SPATIAL_Y] = y;
idx[DIM_SUBCHANNEL] = 0;
buffer->at(idx) = (static_cast<float>(x) / 512.0f) * 4096.0f;
idx[DIM_SUBCHANNEL] = 1;
buffer->at(idx) = (static_cast<float>(y) / 512.0f) * 4096.0f;
idx[DIM_SUBCHANNEL] = 2;
buffer->at(idx) = (static_cast<float>(x+y) / 1024.0f) * 4096.0f;
}
VariantPixelBuffer vbuffer(buffer);
stream << "PixelBuffer PixelType is " << buffer->pixelType() << '\n';
stream << "VariantPixelBuffer PixelType is " << vbuffer.pixelType() << '\n';
stream << std::flush;
// Write the the entire pixel buffer to the plane.
writer.saveBytes(p, vbuffer);
stream << "Wrote " << buffer->num_elements() << ' ' << buffer->pixelType() << " pixels\n";
}
}
}
/* pixel-example-end */
}
int
main(int argc, char *argv[])
{
try
{
if (argc > 1)
{
// Portable path
path filename(argv[1]);
/* writer-example-start */
// Create metadata for the file to be written.
shared_ptr< ::ome::xml::meta::MetadataRetrieve> meta(createMetadata());
// Create TIFF writer
shared_ptr<FormatWriter> writer(make_shared<OMETIFFWriter>());
// Set writer options before opening a file
writer->setMetadataRetrieve(meta);
writer->setInterleaved(false);
// Open the file
writer->setId(filename);
// Write pixel data
writePixelData(*writer, std::cout);
// Explicitly close writer
writer->close();
/* writer-example-end */
}
else
{
std::cerr << "Usage: " << argv[0] << " ome-xml.xml\n";
std::exit(1);
}
}
catch (const std::exception& e)
{
std::cerr << "Caught exception: " << e.what() << '\n';
std::exit(1);
}
catch (...)
{
std::cerr << "Caught unknown exception\n";
std::exit(1);
}
}