bioformats  5.1.8
MetadataTools.h
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3  * OME-BIOFORMATS C++ library for image IO.
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37 
38 #include <string>
39 
40 #include <ome/bioformats/FormatReader.h>
41 #include <ome/bioformats/MetadataMap.h>
42 #include <ome/bioformats/Types.h>
43 
44 #include <ome/common/filesystem.h>
45 
46 #include <ome/xml/meta/Metadata.h>
47 #include <ome/xml/meta/MetadataRoot.h>
48 #include <ome/xml/meta/OMEXMLMetadata.h>
49 
50 #include <ome/xml/model/enums/DimensionOrder.h>
51 
52 #ifndef OME_BIOFORMATS_METADATATOOLS_H
53 #define OME_BIOFORMATS_METADATATOOLS_H
54 
55 namespace ome
56 {
57  namespace bioformats
58  {
59 
60  // Use overloaded functions for creating identifiers since
61  // pre-C++11 compilers don't support the C99 stdarg interface.
62 
70  std::string
71  createID(std::string const& type,
73 
82  std::string
83  createID(std::string const& type,
85  dimension_size_type idx2);
86 
96  std::string
97  createID(std::string const& type,
100  dimension_size_type idx3);
101 
112  std::string
113  createID(std::string const& type,
114  dimension_size_type idx1,
115  dimension_size_type idx2,
116  dimension_size_type idx3,
117  dimension_size_type idx4);
118 
125  ome::compat::shared_ptr< ::ome::xml::meta::OMEXMLMetadata>
127 
134  ome::compat::shared_ptr< ::ome::xml::meta::OMEXMLMetadata>
135  createOMEXMLMetadata(const boost::filesystem::path& file);
136 
143  ome::compat::shared_ptr< ::ome::xml::meta::OMEXMLMetadata>
144  createOMEXMLMetadata(const std::string& text);
145 
152  ome::compat::shared_ptr< ::ome::xml::meta::OMEXMLMetadata>
153  createOMEXMLMetadata(std::istream& stream);
154 
163  ome::compat::shared_ptr< ::ome::xml::meta::OMEXMLMetadata>
164  createOMEXMLMetadata(const FormatReader& reader,
165  bool doPlane = false,
166  bool doImageName = true);
167 
168 
175  ome::compat::shared_ptr< ::ome::xml::meta::MetadataRoot>
176  createOMEXMLRoot(const std::string& document);
177 
186  ome::compat::shared_ptr< ::ome::xml::meta::OMEXMLMetadata>
187  getOMEXMLMetadata(ome::compat::shared_ptr< ::ome::xml::meta::MetadataRetrieve>& retrieve);
188 
200  std::string
202  bool validate = true);
203 
210  bool
211  validateOMEXML(const std::string& document);
212 
227  bool
229  bool correct);
230 
241  void
243  const FormatReader& reader,
244  bool doPlane = false,
245  bool doImageName = true);
246 
256  void
258  const std::vector<ome::compat::shared_ptr<CoreMetadata> > seriesList,
259  bool doPlane = false);
260 
269  void
271  const FormatReader& reader);
272 
281  void
283  const FormatReader& reader);
284 
294  void
296  const CoreMetadata& seriesMetadata,
297  dimension_size_type series);
298 
308  void
310  dimension_size_type series,
311  bool resolve = true);
312 
320  Modulo
321  getModuloAlongZ(const ::ome::xml::meta::OMEXMLMetadata& omexml,
322  dimension_size_type image);
323 
331  Modulo
332  getModuloAlongT(const ::ome::xml::meta::OMEXMLMetadata& omexml,
333  dimension_size_type image);
334 
342  Modulo
343  getModuloAlongC(const ::ome::xml::meta::OMEXMLMetadata& omexml,
344  dimension_size_type image);
345 
354  Modulo
355  getModulo(const ::ome::xml::meta::OMEXMLMetadata& omexml,
356  const std::string& tag,
357  dimension_size_type image);
358 
366  void
368  dimension_size_type series = 0U);
369 
375  void
377 
386  void
388  dimension_size_type image,
389  dimension_size_type sizeC);
390 
397  MetadataMap
399 
406  void
408  const MetadataMap& metadata);
409 
415  bool
417 
423  std::string
424  getModelVersion();
425 
432  std::string
434 
441  std::string
442  getModelVersion(const std::string& document);
443 
450  std::string
451  transformToLatestModelVersion(const std::string& document);
452 
463  void
464  defaultCreationDateEnabled(bool enabled);
465 
480  void
482  dimension_size_type series,
483  const boost::filesystem::path& id);
484 
499  createDimensionOrder(const std::string& order);
500 
512  pixelSize(const ::ome::xml::meta::MetadataRetrieve& meta,
513  dimension_size_type series);
514 
525  pixelSize(const ::ome::xml::meta::MetadataRetrieve& meta);
526 
527 
539  significantPixelSize(const ::ome::xml::meta::MetadataRetrieve& meta,
540  dimension_size_type series);
541 
552  significantPixelSize(const ::ome::xml::meta::MetadataRetrieve& meta);
553 
554  }
555 }
556 
557 #endif // OME_BIOFORMATS_METADATATOOLS_H
558 
559 /*
560  * Local Variables:
561  * mode:C++
562  * End:
563  */
Modulo getModuloAlongC(const ::ome::xml::meta::OMEXMLMetadata &omexml, dimension_size_type image)
Get ModuloAlongC annotation from OME-XML metadata.
Definition: MetadataTools.cpp:704
bool validateModel(::ome::xml::meta::Metadata &meta, bool correct)
Validate a metadata store.
Definition: MetadataTools.cpp:358
void removeChannels(::ome::xml::meta::OMEXMLMetadata &omexml, dimension_size_type image, dimension_size_type sizeC)
Remove all but the specified number of valid Channel elements from OME-XML metadata.
Definition: MetadataTools.cpp:865
std::string createID(std::string const &type, dimension_size_type idx)
Create an object identifier for a given object type and index.
Definition: MetadataTools.cpp:177
void removeBinData(::ome::xml::meta::OMEXMLMetadata &omexml)
Remove all BinData elements from OME-XML metadata.
Definition: MetadataTools.cpp:834
DOM Document wrapper.
Definition: Document.h:83
ome::compat::shared_ptr< ::ome::xml::meta::OMEXMLMetadata > getOMEXMLMetadata(ome::compat::shared_ptr< ::ome::xml::meta::MetadataRetrieve > &retrieve)
Get OME-XML metadata from metadata.
Definition: MetadataTools.cpp:318
ome::xml::model::enums::DimensionOrder createDimensionOrder(const std::string &order)
Create a valid DimensionOrder from string.
Definition: MetadataTools.cpp:1136
Metadata storage interface.
Definition: MetadataStore.h:140
DimensionOrder enumeration.
Definition: DimensionOrder.h:69
Boost.Filesystem compatibility.
storage_size_type pixelSize(const ::ome::xml::meta::MetadataRetrieve &meta, dimension_size_type series)
Get the total size of pixel data in a series.
Definition: MetadataTools.cpp:1166
MetadataMap getOriginalMetadata(::ome::xml::meta::OMEXMLMetadata &omexml)
Get original metadata from OME-XML metadata StructuredAnnotations.
Definition: MetadataTools.cpp:892
Modulo getModuloAlongZ(const ::ome::xml::meta::OMEXMLMetadata &omexml, dimension_size_type image)
Get ModuloAlongZ annotation from OME-XML metadata.
Definition: MetadataTools.cpp:690
Open Microscopy Environment C++ implementation.
Definition: CoreMetadata.cpp:40
std::string getModelVersion()
Get the currently-supported OME Data Model version.
Definition: MetadataTools.cpp:1029
void verifyMinimum(::ome::xml::meta::MetadataRetrieve &retrieve, dimension_size_type series)
Verify correctness of minimal amount of metadata in a series.
Definition: MetadataTools.cpp:786
void addMetadataOnly(::ome::xml::meta::OMEXMLMetadata &omexml, dimension_size_type series, bool resolve)
Add a MetadataOnly element to Pixels for the specified series.
Definition: MetadataTools.cpp:666
void setDefaultCreationDate(::ome::xml::meta::MetadataStore &store, dimension_size_type series, const boost::filesystem::path &id)
Set the creation data for a series.
Definition: MetadataTools.cpp:1122
A metadata store implementation for constructing and manipulating OME-XML DOMs for the current versio...
Definition: OMEXMLMetadata.h:67
Modulo getModuloAlongT(const ::ome::xml::meta::OMEXMLMetadata &omexml, dimension_size_type image)
Get ModuloAlongT annotation from OME-XML metadata.
Definition: MetadataTools.cpp:697
void fillPixels(::ome::xml::meta::MetadataStore &store, const FormatReader &reader)
Fill an OME-XML metadata store Pixels element from reader core metadata.
Definition: MetadataTools.cpp:602
std::string transformToLatestModelVersion(const std::string &document)
Transform an OME-XML document to the latest model version.
Definition: MetadataTools.cpp:1103
void fillMetadata(::ome::xml::meta::MetadataStore &store, const FormatReader &reader, bool doPlane, bool doImageName)
Fill OME-XML metadata store from reader core metadata.
Definition: MetadataTools.cpp:479
std::string getOMEXML(::ome::xml::meta::OMEXMLMetadata &omexml, bool validate)
Get OME-XML document from OME-XML metadata.
Definition: MetadataTools.cpp:340
bool validateOMEXML(const std::string &document)
Validate an OME-XML document.
Definition: MetadataTools.cpp:352
ome::compat::shared_ptr< ::ome::xml::meta::MetadataRoot > createOMEXMLRoot(const std::string &document)
Create OME-XML metadata root from XML document.
Definition: MetadataTools.cpp:309
uint64_t storage_size_type
Size type for storage size.
Definition: Types.h:65
Metadata retrieval interface.
Definition: MetadataRetrieve.h:126
bool defaultCreationDateEnabled()
Check if default creation date is enabled.
Definition: MetadataTools.cpp:1110
ome::compat::shared_ptr< ::ome::xml::meta::OMEXMLMetadata > createOMEXMLMetadata(ome::common::xml::dom::Document &document)
Create OME-XML metadata from DOM Document.
Definition: MetadataTools.cpp:223
storage_size_type significantPixelSize(const ::ome::xml::meta::MetadataRetrieve &meta, dimension_size_type series)
Get the total significant size of pixel data in a series.
Definition: MetadataTools.cpp:1201
Abstract class for metadata storage and retrieval.
Definition: Metadata.h:61
std::size_t dimension_size_type
Size type for image dimensions.
Definition: Types.h:59
void fillOriginalMetadata(::ome::xml::meta::OMEXMLMetadata &omexml, const MetadataMap &metadata)
Create OriginalMetadataAnnotations from MetadataMap.
Definition: MetadataTools.cpp:974
void fillAllPixels(::ome::xml::meta::MetadataStore &store, const FormatReader &reader)
Fill all OME-XML metadata store Pixels elements from reader core metadata.
Definition: MetadataTools.cpp:589
Modulo getModulo(const ::ome::xml::meta::OMEXMLMetadata &omexml, const std::string &tag, dimension_size_type image)
Get Modulo annotation from OME-XML metadata.
Definition: MetadataTools.cpp:711