void defineParams()
{
produces_an_output = true;
get_image_info = false;
XmippMetadataProgram::defineParams();
addUsageLine("Operate with image files headers. By default in Xmipp, geometrical transformations");
addUsageLine("coming in images files headers are ignored. Instead this information is read from");
addUsageLine("the images metadata if exist. With this program geometrical transformations can be");
addUsageLine("extracted to a metadata or assigned to header, also allows print or reset image file headers.");
addParamsLine("[ --print <decompose=0>] : Print the geometrical transformations in image file headers.");
addParamsLine(" : if input is stack and decompose=1 print header of each individual image.");
addParamsLine(" alias -p;");
addParamsLine("or --extract : The output is a selfile with geometrical transformations read from image file headers.");
addParamsLine(" alias -e;");
addParamsLine(" requires -o;");
addParamsLine("or --assign : Write the geometrical transformations from selfile to the image file headers.");
addParamsLine(" alias -a;");
addParamsLine("or --reset : Reset the geometrical transformations in image file headers.");
addParamsLine(" alias -r;");
addParamsLine("or --tree : Print the tree scheme from file containers as hdf5 files.");
addParamsLine(" alias -t;");
addParamsLine("or --sampling_rate <Ts=-1> : Change the sampling rate (in Angstrom units) in the image file header.");
addParamsLine(" : If no value is passed then current value in header is print.");
addParamsLine(" alias -s;");
addParamsLine(" [--round_shifts] :Round shifts to integers");
addExampleLine("Print the header of the images in metadata: ", false);
addExampleLine("xmipp_image_header -i images.sel");
addExampleLine("Extract geometrical transformations from image file headers: ", false);
addExampleLine("xmipp_image_header -i smallStack.stk --extract -o header.doc");
addExampleLine("Assign the geometrical transformations from the metadata to header: ", false);
addExampleLine("xmipp_image_header -i header.doc --assign");
addSeeAlsoLine("transform_geometry");
addKeywords("header, geometric, transformation, print");
}
/**
Writes in the xml file an 'pubmedArticle' node containing the advanced metadata given of an article
@param articleId: id of the article to add to the xml documment
@param abstract: abstract of the article to add
@param keywords: vector with the keywords of the article to add
@param references: vector with the ids of the articles referenced by the article to add
*/
void ExtendedArticlesXMLGenerator::addArticle(int articleId, const string &abstract, const string &articleBody, const vector<string> &keywords, const vector<int> &references)
{
//Add openning tag
addOpenningTag(aXMLFile, "extendedArticle");
//Add nodes
addArticleId(articleId);
addKeywords(keywords);
addAbstract(abstract);
addArticleBody(articleBody);
addReferences(references);
//Add closing tag
addClosingTag(aXMLFile, "extendedArticle");
}
void defineParams()
{
each_image_produces_an_output = true;
addUsageLine("Adjust the grey level value of the pixels to a specified range.");
addKeywords("mask, normalization");
addSeeAlsoLine("transform_normalize");
XmippMetadataProgram::defineParams();
addParamsLine(" --range <min_val> <max_val> : Output minimum and maximum values.");
addParamsLine(" alias -r;");
addParamsLine(" [--noise <sigma=0>] : Variation of the limit range values.");
mask_prm.defineParams(this,INT_MASK, NULL, "Pixels in the mask area are guaranteed to be into the specified range.");
addExampleLine("Adjust an image in the range [-1, 1]:", false);
addExampleLine("xmipp_transform_range_adjust -i image.xmp -o image_adjust.xmp --range -1 1");
addExampleLine("Adjust images in a stack applying a circular mask:", false);
addExampleLine("xmipp_transform_range_adjust -i images.stk -o image_adjust.stk --range -1 1 --mask circular -32");
addExampleLine("Adjust a selection file in the range [-100, 100] with sigma noise 10:", false);
addExampleLine("xmipp_transform_range_adjust -i selection.sel --oroot images/im_adjust:spi -o selection_adjust.sel --range -100 100 --noise 10");
}
//parse
void data::parse(){
cout << "parse" << endl;
//prep the particiapnt xml file
participantXML.pushTag("Document");
//iterate through all keywords in the XML file and generate a list of all the keywords used and their frequencies
//add keyword to keyword list if it is not already in the list
//go to first row with data in it
XML.pushTag("Document");
// XML.pushTag("Worksheet");
// XML.pushTag("Table");
int numRows = XML.getNumTags("Row");
for (int rCnt = 1;rCnt < numRows ;rCnt++){
XML.pushTag("Row",rCnt);
//now i need to iterate through all the cells of the row and look for the one with the correct index of 86
// int numCells = XML.getNumTags("Cell");
// bool collectKeywords = false;
// for (int cCnt = 0;cCnt< numCells;cCnt++){
// if(XML.getAttribute("Cell", "ss:Index", 0, cCnt) == 86){
// collectKeywords = true;
//}
//get all keywords in cells starting at cell 86
// if(collectKeywords){
// XML.pushTag("Cell",cCnt);//col with keywords
// string kws = XML.getValue("Field_85","");//this should return the keywords that need to be split at the return
addKeywords(XML.getValue("Field_85",""));
addKeywords(XML.getValue("Field_86",""));
addKeywords(XML.getValue("Field_87",""));
addKeywords(XML.getValue("Field_88",""));
XML.popTag();
// }
// }
// XML.popTag();
}
//keyword list has been generated, let's see it!
/*cout << endl << endl << "KEYWORD LIST: " << endl;
for (int kCnt = 0; kCnt<keywords.size(); kCnt++){
//cout << keywords[kCnt].first << ", "<< keywords[kCnt].second << endl;
}*/
//sort the list
struct sort_pred {
bool operator()(const std::pair<string,int> &left, const std::pair<string,int> &right) {
return left.second > right.second;
}
};
std::sort(keywords.begin(), keywords.end(), sort_pred());
//std::sort(keywords.begin(), keywords.end(), boost::bind(&std::pair<string, int>::second, _1) < boost::bind(&std::pair<string, int>::second, _2));
//now return the sorted list...
cout << endl << endl << "KEYWORD LIST: " << endl;
for (int kCnt = 0; kCnt<keywords.size(); kCnt++){
cout << keywords[kCnt].first << ", "<< keywords[kCnt].second << endl;
}
}
bool QgsLayerMetadata::readMetadataXml( const QDomElement &metadataElement )
{
QDomNode mnl;
QDomElement mne;
// set identifier
mnl = metadataElement.namedItem( QStringLiteral( "identifier" ) );
mIdentifier = mnl.toElement().text();
// set parent identifier
mnl = metadataElement.namedItem( QStringLiteral( "parentidentifier" ) );
mParentIdentifier = mnl.toElement().text();
// set language
mnl = metadataElement.namedItem( QStringLiteral( "language" ) );
mLanguage = mnl.toElement().text();
// set type
mnl = metadataElement.namedItem( QStringLiteral( "type" ) );
mType = mnl.toElement().text();
// set title
mnl = metadataElement.namedItem( QStringLiteral( "title" ) );
mTitle = mnl.toElement().text();
// set abstract
mnl = metadataElement.namedItem( QStringLiteral( "abstract" ) );
mAbstract = mnl.toElement().text();
// set keywords
QDomNodeList keywords = metadataElement.elementsByTagName( QStringLiteral( "keywords" ) );
mKeywords.clear();
for ( int i = 0; i < keywords.size(); i++ )
{
QStringList keywordsList;
mnl = keywords.at( i );
mne = mnl.toElement();
QDomNodeList el = mne.elementsByTagName( QStringLiteral( "keyword" ) );
for ( int j = 0; j < el.size(); j++ )
{
keywordsList.append( el.at( j ).toElement().text() );
}
addKeywords( mne.attribute( QStringLiteral( "vocabulary" ) ), keywordsList );
}
// set fees
mnl = metadataElement.namedItem( QStringLiteral( "fees" ) );
mFees = mnl.toElement().text();
// constraints
QDomNodeList constraintsList = metadataElement.elementsByTagName( QStringLiteral( "constraints" ) );
mConstraints.clear();
for ( int i = 0; i < constraintsList.size(); i++ )
{
mnl = constraintsList.at( i );
mne = mnl.toElement();
addConstraint( QgsLayerMetadata::Constraint( mne.text(), mne.attribute( QStringLiteral( "type" ) ) ) );
}
// rights
QDomNodeList rightsNodeList = metadataElement.elementsByTagName( QStringLiteral( "rights" ) );
QStringList rightsList;
for ( int i = 0; i < rightsNodeList.size(); i++ )
{
mnl = rightsNodeList.at( i );
mne = mnl.toElement();
rightsList.append( mne.text() );
}
setRights( rightsList );
// licenses
QDomNodeList licensesNodeList = metadataElement.elementsByTagName( QStringLiteral( "license" ) );
QStringList licensesList;
for ( int i = 0; i < licensesNodeList.size(); i++ )
{
mnl = licensesNodeList.at( i );
mne = mnl.toElement();
licensesList.append( mne.text() );
}
setLicenses( licensesList );
// encoding
mnl = metadataElement.namedItem( QStringLiteral( "encoding" ) );
mEncoding = mnl.toElement().text();
// crs
mnl = metadataElement.namedItem( QStringLiteral( "crs" ) );
if ( !mCrs.readXml( mnl ) )
mCrs = QgsCoordinateReferenceSystem();
// extent
mnl = metadataElement.namedItem( QStringLiteral( "extent" ) );
QgsLayerMetadata::Extent metadataExtent;
// spatial extent
QDomNodeList spatialList = mnl.toElement().elementsByTagName( QStringLiteral( "spatial" ) );
QList< QgsLayerMetadata::SpatialExtent > metadataSpatialExtents;
for ( int i = 0; i < spatialList.size(); i++ )
{
mnl = spatialList.at( i );
mne = mnl.toElement();
QgsLayerMetadata::SpatialExtent se = QgsLayerMetadata::SpatialExtent();
se.extentCrs = QgsCoordinateReferenceSystem( mne.attribute( QStringLiteral( "crs" ) ) );
se.bounds = QgsBox3d();
se.bounds.setXMinimum( mne.attribute( QStringLiteral( "minx" ) ).toDouble() );
se.bounds.setYMinimum( mne.attribute( QStringLiteral( "miny" ) ).toDouble() );
se.bounds.setZMinimum( mne.attribute( QStringLiteral( "minz" ) ).toDouble() );
se.bounds.setXMaximum( mne.attribute( QStringLiteral( "maxx" ) ).toDouble() );
se.bounds.setYMaximum( mne.attribute( QStringLiteral( "maxy" ) ).toDouble() );
se.bounds.setZMaximum( mne.attribute( QStringLiteral( "maxz" ) ).toDouble() );
metadataSpatialExtents.append( se );
}
metadataExtent.setSpatialExtents( metadataSpatialExtents );
// temporal extent
mnl = metadataElement.namedItem( QStringLiteral( "extent" ) );
QDomNodeList temporalList = mnl.toElement().elementsByTagName( QStringLiteral( "temporal" ) );
QList<QgsDateTimeRange> metadataDates;
for ( int j = 0; j < temporalList.size(); j++ )
{
mnl = temporalList.at( j );
QDomNodeList instantList = mnl.toElement().elementsByTagName( QStringLiteral( "instant" ) );
for ( int i = 0; i < instantList.size(); i++ )
{
mnl = instantList.at( i );
QDateTime d = QDateTime().fromString( mnl.toElement().text(), Qt::ISODate );
QgsDateTimeRange date = QgsDateTimeRange( d, d );
metadataDates << date;
}
QDomNodeList periodList = mnl.toElement().elementsByTagName( QStringLiteral( "period" ) );
for ( int i = 0; i < periodList.size(); i++ )
{
QDomNode begin = periodList.at( i ).namedItem( QStringLiteral( "start" ) );
QDomNode end = periodList.at( i ).namedItem( QStringLiteral( "end" ) );
QDateTime beginDate = QDateTime().fromString( begin.toElement().text(), Qt::ISODate );
QDateTime endDate = QDateTime().fromString( end.toElement().text(), Qt::ISODate );
QgsDateTimeRange date = QgsDateTimeRange( beginDate, endDate );
metadataDates << date;
}
}
metadataExtent.setTemporalExtents( metadataDates );
setExtent( metadataExtent );
// contact
QDomNodeList contactsList = metadataElement.elementsByTagName( QStringLiteral( "contact" ) );
mContacts.clear();
for ( int i = 0; i < contactsList.size(); i++ )
{
mnl = contactsList.at( i );
mne = mnl.toElement();
QgsLayerMetadata::Contact oneContact;
oneContact.name = mne.namedItem( QStringLiteral( "name" ) ).toElement().text();
oneContact.organization = mne.namedItem( QStringLiteral( "organization" ) ).toElement().text();
oneContact.position = mne.namedItem( QStringLiteral( "position" ) ).toElement().text();
oneContact.voice = mne.namedItem( QStringLiteral( "voice" ) ).toElement().text();
oneContact.fax = mne.namedItem( QStringLiteral( "fax" ) ).toElement().text();
oneContact.email = mne.namedItem( QStringLiteral( "email" ) ).toElement().text();
oneContact.role = mne.namedItem( QStringLiteral( "role" ) ).toElement().text();
QList< QgsLayerMetadata::Address > addresses;
QDomNodeList addressList = mne.elementsByTagName( QStringLiteral( "contactAddress" ) );
for ( int j = 0; j < addressList.size(); j++ )
{
QDomElement addressElement = addressList.at( j ).toElement();
QgsLayerMetadata::Address oneAddress;
oneAddress.address = addressElement.namedItem( QStringLiteral( "address" ) ).toElement().text();
oneAddress.administrativeArea = addressElement.namedItem( QStringLiteral( "administrativearea" ) ).toElement().text();
oneAddress.city = addressElement.namedItem( QStringLiteral( "city" ) ).toElement().text();
oneAddress.country = addressElement.namedItem( QStringLiteral( "country" ) ).toElement().text();
oneAddress.postalCode = addressElement.namedItem( QStringLiteral( "postalcode" ) ).toElement().text();
oneAddress.type = addressElement.namedItem( QStringLiteral( "type" ) ).toElement().text();
addresses << oneAddress;
}
oneContact.addresses = addresses;
addContact( oneContact );
}
// links
mnl = metadataElement.namedItem( QStringLiteral( "links" ) );
mne = mnl.toElement();
mLinks.clear();
QDomNodeList el = mne.elementsByTagName( QStringLiteral( "link" ) );
for ( int i = 0; i < el.size(); i++ )
{
mne = el.at( i ).toElement();
QgsLayerMetadata::Link oneLink;
oneLink.name = mne.attribute( QStringLiteral( "name" ) );
oneLink.type = mne.attribute( QStringLiteral( "type" ) );
oneLink.url = mne.attribute( QStringLiteral( "url" ) );
oneLink.description = mne.attribute( QStringLiteral( "description" ) );
oneLink.format = mne.attribute( QStringLiteral( "format" ) );
oneLink.mimeType = mne.attribute( QStringLiteral( "mimeType" ) );
oneLink.size = mne.attribute( QStringLiteral( "size" ) );
addLink( oneLink );
}
// history
QDomNodeList historyNodeList = metadataElement.elementsByTagName( QStringLiteral( "history" ) );
QStringList historyList;
for ( int i = 0; i < historyNodeList.size(); i++ )
{
mnl = historyNodeList.at( i );
mne = mnl.toElement();
historyList.append( mne.text() );
}
setHistory( historyList );
return true;
}
