Merge pull request #224 from jcwbacker/hayabusa (75befa89) · Commits · aflab / astrogeology / ISIS3

isis/src/base/apps/isis2pds/isis2pds.cpp

+40 −30

Original line number	Diff line number	Diff line
		@@ -38,11 +38,13 @@ void IsisMain() {
		p.SetInputCube("FROM");

		if (ui.GetString("STRETCH") == "LINEAR") {
		if(ui.GetString("BITTYPE") != "32BIT")
		if (ui.GetString("BITTYPE") != "32BIT") {
		p.SetInputRange();
		}
		if(ui.GetString("STRETCH") == "MANUAL")
		}
		if (ui.GetString("STRETCH") == "MANUAL") {
		p.SetInputRange(ui.GetDouble("MINIMUM"), ui.GetDouble("MAXIMUM"));
		}

		double min = -DBL_MAX;
		double max = DBL_MAX;
		@@ -75,13 +77,16 @@ void IsisMain() {
		setRangeAndPixels(ui, p, min, max, NONE);
		}

		if(ui.GetString("ENDIAN") == "MSB")
		if (ui.GetString("ENDIAN") == "MSB") {
		p.SetOutputEndian(Isis::Msb);
		else if(ui.GetString("ENDIAN") == "LSB")
		}
		else if (ui.GetString("ENDIAN") == "LSB") {
		p.SetOutputEndian(Isis::Lsb);
		}

		if(ui.GetString("LABTYPE") == "FIXED")
		if (ui.GetString("LABTYPE") == "FIXED") {
		p.SetExportType(ProcessExportPds::Fixed);
		}

		if (ui.GetBoolean("CHECKSUM")) {
		p.setCanGenerateChecksum(true);
		@@ -130,11 +135,13 @@ void IsisMain() {
		QString outFileName(outFile.expanded());

		if (ui.GetString("STRETCH") == "LINEAR") {
		if(ui.GetString("BITTYPE") != "32BIT")
		if (ui.GetString("BITTYPE") != "32BIT") {
		process.SetInputRange();
		}
		if(ui.GetString("STRETCH") == "MANUAL")
		}
		if (ui.GetString("STRETCH") == "MANUAL") {
		process.SetInputRange(ui.GetDouble("MINIMUM"), ui.GetDouble("MAXIMUM"));
		}

		double min = -DBL_MAX;
		double max = DBL_MAX;
		@@ -167,10 +174,12 @@ void IsisMain() {
		setRangeAndPixels(ui, process, min, max, NONE);
		}

		if(ui.GetString("ENDIAN") == "MSB")
		if (ui.GetString("ENDIAN") == "MSB") {
		process.SetOutputEndian(Isis::Msb);
		else if(ui.GetString("ENDIAN") == "LSB")
		}
		else if (ui.GetString("ENDIAN") == "LSB") {
		process.SetOutputEndian(Isis::Lsb);
		}

		// Records what it did to the print.prt file
		PvlGroup results("DNs Used");
		@@ -184,6 +193,7 @@ void IsisMain() {
		Application::Log(results);

		process.StandardPds4Label();
		// ProcessExportPds4::translateUnits(pdsLabel);//???
		process.WritePds4(outFileName);
		}

isis/src/base/apps/isis2pds/tsts/pds4/Makefile

+10 −1

Original line number	Diff line number	Diff line
		@@ -7,8 +7,17 @@ commands:

		# Remove parts of output that can occur in any order and convert to txt for comparison
		$(SED) 's+\Product_Observational.*>+\Product_Observational>+' \
		$(OUTPUT)/dawnEqui.xml > $(OUTPUT)/dawnEqui.txt;
		$(OUTPUT)/dawnEqui.xml \
		> $(OUTPUT)/tempLabel1.txt;
		$(SED) 's+\modification_date.*>+\modification_date>+' \
		$(OUTPUT)/tempLabel1.txt \
		> $(OUTPUT)/tempLabel2.txt;
		$(SED) 's+\ISIS version.*<+\ISIS version.<+' \
		$(OUTPUT)/tempLabel2.txt \
		> $(OUTPUT)/dawnEqui.txt;

		$(RM) $(OUTPUT)/dawnEqui.xml > /dev/null;
		$(RM) $(OUTPUT)/tempLabel1.txt > /dev/null;
		$(RM) $(OUTPUT)/tempLabel2.txt > /dev/null;
		$(RM) $(OUTPUT)/dawnEqui.img > /dev/null;

isis/src/base/apps/stats/tsts/default/Makefile

+2 −2

Original line number	Diff line number	Diff line
		@@ -16,6 +16,6 @@ commands:
		> /dev/null;

		$(APPNAME) from=$(INPUT)/isisTruth.cub \
		\| grep -v stats \
		\| grep -v "stats:" \
		\| grep -v Processed \
		>& $(OUTPUT)/output.pvl;

isis/src/base/objs/ProcessExportPds4/ProcessExportPds4.cpp

+254 −119

Original line number	Diff line number	Diff line
		@@ -24,8 +24,10 @@

		#include <QDomDocument>
		#include <QMap>
		#include <QRegularExpression>
		#include <QString>

		#include "Application.h"
		#include "FileName.h"
		#include "IException.h"
		#include "Projection.h"
		@@ -43,6 +45,9 @@ namespace Isis {
		*
		*/
		ProcessExportPds4::ProcessExportPds4() {

		m_lid = "";

		qSetGlobalQHashSeed(1031); // hash seed to force consistent output

		m_domDoc = new QDomDocument("");
		@@ -104,12 +109,19 @@ namespace Isis {


		/**
		* Create a standard PDS label for type IMAGE. The image label will be
		* Creates a PDS4 label. The image label will be
		* stored internally in the class.
		*
		* This method has a similar function to
		* ProcessExportPds::CreateImageLabel. However, it will create
		* images of object type Array_3D_Image, Array_2D_Image, or
		* Array_3D_Spectrum.
		*/
		void ProcessExportPds4::CreateImageLabel() {

		try {
		// <Product_Observational>
		// <Identification_Area>
		identificationArea();
		}
		catch (IException &e) {
		@@ -117,6 +129,8 @@ namespace Isis {
		throw IException(e, IException::Programmer, msg, _FILEINFO_);
		}
		try {
		// <Product_Observational>
		// <Observation_Area>
		standardInstrument();
		}
		catch (IException &e) {
		@@ -124,25 +138,34 @@ namespace Isis {
		throw IException(e, IException::Programmer, msg, _FILEINFO_);
		}
		try {
		// <Product_Observational>
		// <Observation_Area>
		// <Discipline_Area>
		// <disp:Display_Settings>
		displaySettings();
		}
		catch (IException &e) {
		QString msg = "Unable to translate and export display settings.";
		throw IException(e, IException::Programmer, msg, _FILEINFO_);
		}
		// Temporarily removed spectral processing because it needs further work.
		//
		// try {
		// standardBandBin();
		// }
		// catch (IException &e) {
		// QString msg = "Unable to translate and export spectral information.";
		// throw IException(e, IException::Programmer, msg, _FILEINFO_);
		// }

		try {
		// <Product_Observational>
		// <Observation_Area>
		// <Discipline_Area>
		// <sp:Spectral_Characteristics> OR <img:Imaging>
		standardBandBin();
		}
		catch (IException &e) {
		QString msg = "Unable to translate and export spectral information.";
		throw IException(e, IException::Programmer, msg, _FILEINFO_);
		}

		try {
		// <Product_Observational>
		// <Observation_Area>
		// <Discipline_Area>
		// display settings, and cartography handled in this method:
		// <card:Cartography>
		StandardAllMapping();
		}
		catch (IException &e) {
		@@ -150,8 +173,9 @@ namespace Isis {
		throw IException(e, IException::Programmer, msg, _FILEINFO_);
		}
		try {
		// file observation area
		StandardImageImage();
		// <Product_Observational>
		// <File_Area_Observational>
		fileAreaObservational();
		}
		catch (IException &e) {
		QString msg = "Unable to translate and export standard image information.";
		@@ -166,11 +190,13 @@ namespace Isis {
		*/
		void ProcessExportPds4::standardInstrument() {
		Pvl *inputLabel = InputCubes[0]->label();
		FileName transfile;
		FileName translationFileName;

		if (inputLabel->findObject("IsisCube").hasGroup("Instrument")) {

		// Translate the Instrument group
		transfile = "$base/translations/pds4ExportInstrument.trn";
		PvlToXmlTranslationManager instXlator(*inputLabel, transfile.expanded());
		translationFileName = "$base/translations/pds4ExportInstrument.trn";
		PvlToXmlTranslationManager instXlator(*inputLabel, translationFileName.expanded());
		instXlator.Auto(*m_domDoc);

		// If instrument and spacecraft values were translated, create the combined name
		@@ -232,24 +258,68 @@ namespace Isis {
		}

		// Translate the Target name
		try {
		transfile = "$base/translations/pds4ExportTargetFromInstrument.trn";
		PvlToXmlTranslationManager targXlator(*inputLabel, transfile.expanded());
		translationFileName = "$base/translations/pds4ExportTargetFromInstrument.trn";
		PvlToXmlTranslationManager targXlator(*inputLabel, translationFileName.expanded());
		targXlator.Auto(*m_domDoc);

		// move target to just below Observing_System.
		QDomElement targetIdNode = obsAreaNode.firstChildElement("Target_Identification");
		obsAreaNode.insertAfter(targetIdNode, obsAreaNode.firstChildElement("Observing_System"));

		}
		catch (IException &e1) {
		try {
		transfile = "$base/translations/pds4ExportTargetFromMapping.trn";
		PvlToXmlTranslationManager targXlator(*inputLabel, transfile.expanded());
		else if (inputLabel->findObject("IsisCube").hasGroup("Mapping")) {

		translationFileName = "$base/translations/pds4ExportTargetFromMapping.trn";
		PvlToXmlTranslationManager targXlator(*inputLabel, translationFileName.expanded());
		targXlator.Auto(*m_domDoc);

		}
		else {
		throw IException(IException::Unknown, "Unable to find a target in input cube.", _FILEINFO_);
		}
		catch (IException &e2) {
		IException finalError(IException::Unknown, "Unable to find a target in input cube.", _FILEINFO_);
		finalError.append(e1);
		finalError.append(e2);
		throw finalError;
		}


		/**
		* Allows mission specific programs to set logical_identifier
		* required for PDS4 labels. This value is added to the xml file
		* by the identificationArea() method.
		*
		* The input string should be colon separated string with 6
		* identifiers:
		*
		* <ol>
		* <li> urn </li>
		* <li> space_agency (ususally nasa) </li>
		* <li> archiving_organization (usually pds) </li>
		* <li> bundle_id </li>
		* <li> collection_id </li>
		* <li> product_id </li>
		* </ol>
		*
		* Example:
		* urn:esa:psa:em16_tgo_frd:data_raw:frd_raw_sc_d_20150625T133700-20150625T135700
		*
		* @author 2018-05-21 Jeannie Backer
		*
		* @param lid The logical identifier value required for PDS4
		* compliant labels.
		*/
		void ProcessExportPds4::setLogicalId(QString lid) {
		m_lid = lid;
		}


		/**
		* Allows mission specific programs to use specified
		* versions of dictionaries.
		*
		* @author 2018-05-21 Jeannie Backer
		*
		* @param schema The string of schema to be set.
		*/
		void ProcessExportPds4::setSchemaLocation(QString schema) {
		m_schemaLocation = schema;
		}


		@@ -259,10 +329,46 @@ namespace Isis {
		*/
		void ProcessExportPds4::identificationArea() {
		Pvl *inputLabel = InputCubes[0]->label();
		FileName transfile;
		transfile = "$base/translations/pds4ExportIdentificationArea.trn";
		PvlToXmlTranslationManager xlator(*inputLabel, transfile.expanded());
		FileName translationFileName;
		translationFileName = "$base/translations/pds4ExportIdentificationArea.trn";
		PvlToXmlTranslationManager xlator(*inputLabel, translationFileName.expanded());
		xlator.Auto(*m_domDoc);

		if (m_lid.isEmpty()) {
		m_lid = "urn:nasa:pds:TBD:TBD:TBD";
		}

		QDomElement identificationElement;
		QStringList identificationPath;
		identificationPath.append("Product_Observational");
		identificationPath.append("Identification_Area");
		try {
		identificationElement = getElement(identificationPath);
		if( identificationElement.isNull() ) {
		throw IException(IException::Unknown, "", _FILEINFO_);
		}
		}
		catch(IException &e) {
		QString msg = "Could not find Identification_Area element "
		"to add modification history under.";
		throw IException(IException::Programmer, msg, _FILEINFO_);
		}

		QDomElement lidElement = identificationElement.firstChildElement("logical_identifier");
		PvlToXmlTranslationManager::resetElementValue(lidElement, m_lid);

		// Get export history and add <Modification_History> element.
		// These regular expressions match the pipe followed by the date from
		// the Application::Version() return value.
		QRegularExpression versionRegex(" \\\| \\d{4}\\-\\d{2}\\-\\d{2}");
		QString historyDescription = "Created PDS4 output product from ISIS cube with the "
		+ FileName(Application::Name()).baseName()
		+ " application from ISIS version "
		+ Application::Version().remove(versionRegex) + ".";
		// This regular expression matches the time from the Application::DateTime return value.
		QRegularExpression dateRegex("T\\d{2}:\\d{2}:\\d{2}");
		QString historyDate = Application::DateTime().remove(dateRegex);
		addHistory(historyDescription, historyDate);
		}


		@@ -273,9 +379,9 @@ namespace Isis {
		void ProcessExportPds4::displaySettings() {

		Pvl *inputLabel = InputCubes[0]->label();
		FileName transfile;
		transfile = "$base/translations/pds4ExportDisplaySettings.trn";
		PvlToXmlTranslationManager xlator(*inputLabel, transfile.expanded());
		FileName translationFileName;
		translationFileName = "$base/translations/pds4ExportDisplaySettings.trn";
		PvlToXmlTranslationManager xlator(*inputLabel, translationFileName.expanded());
		xlator.Auto(*m_domDoc);

		// Add header info
		@@ -294,14 +400,9 @@ namespace Isis {
		// Spectra
		// Get the input Isis cube label and find the BandBin group if it has one
		Pvl *inputLabel = InputCubes[0]->label();
		if(inputLabel->hasObject("IsisCube") &&
		!(inputLabel->findObject("IsisCube").hasGroup("BandBin"))) return;

		FileName transfile;
		transfile = "$base/translations/pds4ExportBandBin.trn";
		PvlToXmlTranslationManager xlator(*inputLabel, transfile.expanded());
		xlator.Auto(*m_domDoc);
		QString imageObject = imageObjectType(*inputLabel);

		if (imageObject.compare("Array_3D_Spectrum") == 0) {
		// Add header info
		addSchema("PDS4_SP_1100.sch",
		"PDS4_SP_1100.xsd",
		@@ -309,17 +410,32 @@ namespace Isis {
		"http://pds.nasa.gov/pds4/sp/v1");
		}

		QString translationFile = "$base/translations/pds4ExportBandBin";
		translationFile += imageObject.remove(0,9); // remove first 9 characters: Array_2D_ or Array_3D_
		translationFile += ".trn";
		FileName translationFileName(translationFile);

		PvlToXmlTranslationManager xlator(*inputLabel, translationFileName.expanded());
		xlator.Auto(*m_domDoc);

		}


		/**
		* Create and internalize a standard image output label from the input image.
		* @todo determine whether to treat single band as 2d array
		* Create and internalize an image output label from the input
		* image. This method has a similar function to
		* ProcessExportPds::StandardImageImage.
		*/
		void ProcessExportPds4::StandardImageImage() {
		void ProcessExportPds4::fileAreaObservational() {
		Pvl *inputLabel = InputCubes[0]->label();
		FileName transfile;
		QString imageObject = imageObjectType(*inputLabel);

		transfile = "$base/translations/pds4ExportArray3DImage.trn";
		PvlToXmlTranslationManager xlator(*inputLabel, transfile.expanded());
		QString translationFile = "$base/translations/pds4Export";
		translationFile += QString(imageObject).remove('_');
		translationFile += ".trn";
		FileName translationFileName(translationFile);

		PvlToXmlTranslationManager xlator(*inputLabel, translationFileName.expanded());
		xlator.Auto(*m_domDoc);

		QDomElement rootElement = m_domDoc->documentElement();
		@@ -350,15 +466,14 @@ namespace Isis {
		}

		if (!fileAreaObservationalElement.isNull()) {
		QDomElement array3DImageElement =
		fileAreaObservationalElement.firstChildElement("Array_3D_Image");

		if (!array3DImageElement.isNull()) {
		QDomElement arrayImageElement =
		fileAreaObservationalElement.firstChildElement(imageObject);
		if (!arrayImageElement.isNull()) {

		// reorder axis elements.
		// Translation order: elements, axis_name, sequence_number
		// Correct order: axis_name, elements, sequence_number
		QDomElement axisArrayElement = array3DImageElement.firstChildElement("Axis_Array");
		QDomElement axisArrayElement = arrayImageElement.firstChildElement("Axis_Array");
		while( !axisArrayElement.isNull() ) {
		QDomElement axisNameElement = axisArrayElement.firstChildElement("axis_name");
		axisArrayElement.insertBefore(axisNameElement,
		@@ -367,8 +482,8 @@ namespace Isis {
		}

		QDomElement elementArrayElement = m_domDoc->createElement("Element_Array");
		array3DImageElement.insertBefore(elementArrayElement,
		array3DImageElement.firstChildElement("Axis_Array"));
		arrayImageElement.insertBefore(elementArrayElement,
		arrayImageElement.firstChildElement("Axis_Array"));

		QDomElement dataTypeElement = m_domDoc->createElement("data_type");
		PvlToXmlTranslationManager::setElementValue(dataTypeElement,
		@@ -389,6 +504,26 @@ namespace Isis {
		}


		QString ProcessExportPds4::imageObjectType(Pvl &inputLabel) {
		// not sure how to easily determine whether an isis3 cube should be
		// exported as spectral. for now, we will only export image arrays
		#if 0
		if (inputLabel.findObject("IsisCube").hasGroup("BandBin")) {
		return "Array_3D_Spectrum";
		}
		#endif

		int bands = (int) inputLabel.findObject("IsisCube")
		.findObject("Core")
		.findGroup("Dimensions")
		.findKeyword("Bands");
		if (bands > 1) {
		return "Array_3D_Image";
		}
		return "Array_2D_Image";
		}


		/**
		* Adds necessary information to the xml header for a pds4 class.
		*

isis/src/base/objs/ProcessExportPds4/ProcessExportPds4.h

+9 −3

Original line number	Diff line number	Diff line
		@@ -98,22 +98,28 @@ namespace Isis {
		void WritePds4(QString outFile);
		QDomElement getElement(QStringList xmlPath, QDomElement parent=QDomElement());
		void addHistory(QString description, QString date = "tbd", QString version = "1.0");
		void setLogicalId(QString lid);
		void setSchemaLocation(QString schema);

		static void translateUnits(QDomDocument &label,
		QString transMapFile = "$base/translations/pds4ExportUnits.pvl");

		protected:
		void addSchema(QString sch, QString xsd, QString xmlns, QString xmlnsURI) ;
		protected:
		// void addSchema(QString sch, QString xsd, QString xmlns, QString xmlnsURI) ;
		void identificationArea();
		void standardInstrument();
		void standardBandBin();
		void displaySettings();
		void fileAreaObservational();
		QString imageObjectType(Pvl &inputLabel);
		QString PDS4PixelType(PixelType pixelType, ByteOrder endianType);
		static QMap<QString, QString> createUnitMap(Pvl configPvl);
		static void translateChildUnits(QDomElement parent, QMap<QString, QString> transMap);

		QDomDocument *m_domDoc; //!< XML label
		QString m_schemaLocation; //!< QString with all schema locations required
		QDomDocument *m_domDoc; //!< XML label.
		QString m_schemaLocation; //!< QString with all schema locations required.
		QString m_lid; //!< QString with specified logical identifier.

		};
		}