Merge branch 'dev' of github.com:USGS-Astrogeology/ISIS3 into dev (cf339b1e) · Commits · aflab / astrogeology / ISIS3

.gitignore

+2 −1

Original line number	Diff line number	Diff line
		@@ -27,10 +27,11 @@ object_script.*.Debug
		*_plugin_import.cpp
		*.moc
		ui_*.h
		*.html
		*html

		# ignore all files created by squish coco
		*csmes
		*csexe

		print.prt

isis/src/base/objs/ProcessImport/ProcessImport.cpp

+42 −60

Original line number	Diff line number	Diff line
		@@ -1847,11 +1847,6 @@ namespace Isis {
		*/
		void ProcessImport::ProcessBip(void funct(Isis::Buffer &out)) {

		// Figure out the number of bytes to read for a single line
		int readBytes = Isis::SizeOf(p_pixelType);
		readBytes = readBytes * p_ns * p_nb;
		char *in = new char [readBytes];

		// Set up an Isis::EndianSwapper object
		QString tok(Isis::ByteOrderName(p_byteOrder));
		tok = tok.toUpper();
		@@ -1902,6 +1897,11 @@ namespace Isis {
		p_progress->SetMaximumSteps(p_nl);
		p_progress->CheckStatus();

		// Figure out the number of bytes to read for a single line
		int sampleBytes = Isis::SizeOf(p_pixelType) * p_nb + p_dataPreBytes + p_dataPostBytes;
		int readBytes = p_ns * sampleBytes;
		char *in = new char [readBytes];

		// Loop for each line
		for(int line = 0; line < p_nl; line++) {
		// Check the last io
		@@ -1915,16 +1915,6 @@ namespace Isis {
		// Space for storing prefix and suffix data pointers
		vector<char *> tempPre, tempPost;

		// Handle any line prefix bytes
		pos = fin.tellg();
		if (p_saveDataPre) {
		tempPre.push_back(new char[p_dataPreBytes]);
		fin.read(tempPre.back(), p_dataPreBytes);
		}
		else {
		fin.seekg(p_dataPreBytes, ios_base::cur);
		}

		// Check the last io
		if (!fin.good()) {
		QString msg = "Cannot read file [" + p_inFile + "]. Position [" +
		@@ -1960,31 +1950,32 @@ namespace Isis {
		// to special pixels
		int osamp = 0;

		for(int samp = band; samp < p_ns * p_nb; samp += p_nb) {
		for(int samp = 0; samp < p_ns; samp++) {
		int bufferIndex = p_dataPreBytes + Isis::SizeOf(p_pixelType)band + sampsampleBytes;
		switch(p_pixelType) {
		case Isis::UnsignedByte:
		(out)[osamp] = (double)((unsigned char )in)[samp];
		(out)[osamp] = (double)((unsigned char )in)[bufferIndex];
		break;
		case Isis::UnsignedWord:
		(*out)[osamp] =
		(double)swapper.UnsignedShortInt((unsigned short int *)in+samp);
		(double)swapper.UnsignedShortInt(&in[bufferIndex]);
		break;
		case Isis::SignedWord:
		(out)[osamp] = (double)swapper.ShortInt((short int )in+samp);
		(*out)[osamp] = (double)swapper.ShortInt(&in[bufferIndex]);
		break;
		case Isis::SignedInteger:
		(out)[samp] = (double)swapper.Int((int )in+samp);
		(*out)[samp] = (double)swapper.Int(&in[bufferIndex]);
		break;
		case Isis::Real:
		if(p_vax_convert) {
		(out)[osamp]= VAXConversion( (float )in+samp );
		(*out)[osamp]= VAXConversion(&in[bufferIndex]);
		}
		else {
		(out)[osamp] = (double)swapper.Float((float )in+samp);
		(*out)[osamp] = (double)swapper.Float(&in[bufferIndex]);
		}
		break;
		case Isis::Double:
		(out)[osamp] = (double)swapper.Double((double )in+samp);
		(*out)[osamp] = (double)swapper.Double(&in[bufferIndex]);
		break;
		default:
		break;
		@@ -2008,33 +1999,25 @@ namespace Isis {
		funct(*out);
		}

		// Handle any line suffix bytes
		pos = fin.tellg();
		if (p_saveDataPost) {
		tempPost.push_back(new char[p_dataPostBytes]);
		fin.read(tempPost.back(), p_dataPostBytes);
		}
		else {
		fin.seekg(p_dataPostBytes, ios_base::cur);
		}

		// Check the last io
		if (!fin.good()) {
		QString msg = "Cannot read file [" + p_inFile + "]. Position [" +
		toString((int)pos) + "]. Byte count [" +
		toString(p_dataPreBytes) + "]" ;
		throw IException(IException::Io, msg, _FILEINFO_);
		}

		} // End band loop

		// Save off the prefix bytes vector
		// Handle record prefix and suffix
		if (p_saveDataPre) {
		for(int samp = 0; samp < p_ns; samp++) {
		char *samplePrefix = new char[p_dataPreBytes];
		memcpy(samplePrefix, &in[samp*sampleBytes], p_dataPreBytes);
		tempPre.push_back(samplePrefix);
		}
		p_dataPre.push_back(tempPre);
		tempPre.clear();
		}

		// Save off the suffix bytes vector
		if (p_saveDataPost) {
		for(int samp = 0; samp < p_ns; samp++) {
		char *sampleSuffix = new char[p_dataPostBytes];
		int suffixIndex = p_dataPreBytes + Isis::SizeOf(p_pixelType)p_nb + sampsampleBytes;
		memcpy(sampleSuffix, &in[suffixIndex], p_dataPostBytes);
		tempPost.push_back(sampleSuffix);
		}
		p_dataPost.push_back(tempPost);
		tempPost.clear();
		}
		@@ -2043,12 +2026,11 @@ namespace Isis {
		if (!fin.good()) {
		QString msg = "Cannot read file [" + p_inFile + "]. Position [" +
		toString((int)pos) + "]. Byte count [" +
		toString(p_fileHeaderBytes) + "]" ;
		toString(p_dataPreBytes) + "]" ;
		throw IException(IException::Io, msg, _FILEINFO_);
		}

		} // End band loop

		// Handle the data trailer
		pos = fin.tellg();
		if (p_saveDataTrailer) {
		p_dataTrailer.push_back(new char[p_dataTrailerBytes]);

isis/src/base/objs/ProcessImport/ProcessImport.h

+13 −2

Original line number	Diff line number	Diff line
		@@ -152,6 +152,17 @@ namespace Isis {
		* @history 2017-05-29 Kristin Berry - Added support for data trailers in BIP files and fixed
		* a typo so that DataTrailerBytes() will return the correct value.
		* References #3888.
		* @history 2018-05-01 Jesse Mapel - Changed data suffix and prefix in BIP files. Previously,
		* data suffixes and prefixes were for each band before/after each line.
		* Now, data suffixes and prefixes are before/after each sample. For a
		* RGB, 3-band image with n samples a line of data was previously
		* \| Header \| R prefix \| G prefix \| B prefix \| R 1 \| G 1 \| B 1\| ...
		* \| R n \| G n \| B n\| R suffix \| G suffix \| B suffix \| Trailer \|. Now
		* it is \| Header \| Prefix 1 \| R 1 \| G 1 \| B 1 \| Suffix 1 \| ...
		* \| Prefix n \| R n \| G n \| B n \| Suffix n \| Trailer \|. This change
		* was made to accomodate Rosetta VIRTIS-m calibrated data files and
		* has no impact on other supported BIP files.
		* Fixes #5398.
		*
		*/
		class ProcessImport : public Isis::Process {

isis/src/base/objs/PvlToPvlTranslationManager/PvlToPvlTranslationManager.cpp

+77 −51

Original line number	Diff line number	Diff line
		@@ -40,7 +40,7 @@ namespace Isis {
		* set the input label before translating. This may be done by using
		* SetLabel(Pvl inputLabel) or Auto(Pvl inputLabel, Pvl outputLabel).
		*
		* @param transFile The translation file to be used to tranlate keywords in
		* @param transFile The translation file to be used to translate keywords in
		* the input label.
		*/
		PvlToPvlTranslationManager::PvlToPvlTranslationManager(const QString &transFile)
		@@ -53,8 +53,8 @@ namespace Isis {
		* input label before translating. This may be done by using SetLabel(Pvl
		* inputLabel) or Auto(Pvl inputLabel, Pvl outputLabel).
		*
		* @param transStrm A stream containing the tranlation table to be used to
		* tranlate keywords in the input label.
		* @param transStrm A stream containing the translation table to be used to
		* translate keywords in the input label.
		*/
		PvlToPvlTranslationManager::PvlToPvlTranslationManager(std::istream &transStrm)
		: LabelTranslationManager(transStrm) {
		@@ -66,7 +66,7 @@ namespace Isis {
		*
		* @param inputLabel The Pvl holding the input label.
		*
		* @param transFile The translation file to be used to tranlate keywords in
		* @param transFile The translation file to be used to translate keywords in
		* the input label.
		*/
		PvlToPvlTranslationManager::PvlToPvlTranslationManager(Pvl &inputLabel,
		@@ -81,8 +81,8 @@ namespace Isis {
		*
		* @param inputLabel The Pvl holding the input label.
		*
		* @param transStrm A stream containing the tranlation table to be used to
		* tranlate keywords in the input label.
		* @param transStrm A stream containing the translation table to be used to
		* translate keywords in the input label.
		*/
		PvlToPvlTranslationManager::PvlToPvlTranslationManager(Pvl &inputLabel,
		std::istream &transStrm)
		@@ -103,47 +103,58 @@ namespace Isis {

		/**
		* Returns a translated value. The output name is used to find the input
		* group, keyword, default and tranlations in the translation table. If the
		* keyword does not exist in the input label, the input default if
		* available will be used as the input value. This input value
		* is then used to search all of the translations. If a match is
		* found the translated value is returned.
		* group, keyword, default and translations in the translation table. If the
		* keyword does not exist in the input label and an input default is available,
		* then this default will be used as the input value. This input value is
		* then used to search all of the translations. If a match is found the
		* translated value is returned.
		*
		* @param nName The output name used to identify the input keyword to be
		* translated.
		* @param translationGroupName The name of the PVL translation
		* group used to identify the
		* input/output keywords to be
		* translated. Often, this is the
		* same as the output keyword name.
		*
		* @param findex The index into the input keyword array. Defaults to 0
		*
		* @return string
		*/
		QString PvlToPvlTranslationManager::Translate(QString nName, int findex) {
		QString PvlToPvlTranslationManager::Translate(QString translationGroupName, int findex) {
		const PvlContainer *con;
		int inst = 0;
		PvlKeyword grp;

		while((grp = InputGroup(nName, inst++)).name() != "") {
		while((grp = InputGroup(translationGroupName, inst++)).name() != "") {
		if((con = GetContainer(grp)) != NULL) {
		if(con->hasKeyword(InputKeywordName(nName))) {
		return PvlTranslationTable::Translate(nName,
		(*con)[InputKeywordName(nName)][findex]);
		if(con->hasKeyword(InputKeywordName(translationGroupName))) {
		return PvlTranslationTable::Translate(translationGroupName,
		(*con)[InputKeywordName(translationGroupName)][findex]);
		}
		}
		}

		return PvlTranslationTable::Translate(nName);
		return PvlTranslationTable::Translate(translationGroupName);
		}


		/**
		* Translate the requested output name to output values using the input name
		* and values or default value
		* and values or default value.
		*
		* @param nName The output name used to identify the input keyword to be
		* translated.
		* Note: This is a protected method used when automatically
		* translating
		*
		* @see Auto().
		*
		* @param translationGroupName The name of the PVL translation
		* group used to identify the
		* input/output keywords to be
		* translated. Often, this is the
		* same as the output keyword name.
		*
		* @return PvlKeyword
		*/
		PvlKeyword PvlToPvlTranslationManager::DoTranslation(const QString nName) {
		PvlKeyword PvlToPvlTranslationManager::DoTranslation(const QString translationGroupName) {
		const PvlContainer *con = NULL;
		PvlKeyword key;

		@@ -151,9 +162,9 @@ namespace Isis {
		PvlGroup transGroup;
		PvlKeyword grp;

		while((grp = InputGroup(nName, inst++)).name() != "") {
		while((grp = InputGroup(translationGroupName, inst++)).name() != "") {
		if((con = GetContainer(grp)) != NULL) {
		transGroup = TranslationTable().findGroup(nName);
		transGroup = TranslationTable().findGroup(translationGroupName);
		Pvl::ConstPvlKeywordIterator it = transGroup.findKeyword("InputKey",
		transGroup.begin(),
		transGroup.end());
		@@ -162,10 +173,10 @@ namespace Isis {
		while(it != transGroup.end()) {
		const PvlKeyword &result = *it;
		if(con->hasKeyword(result[0])) {
		key.setName(OutputName(nName));
		key.setName(OutputName(translationGroupName));

		for(int v = 0; v < (*con)[(result[0])].size(); v++) {
		key.addValue(PvlTranslationTable::Translate(nName,
		key.addValue(PvlTranslationTable::Translate(translationGroupName,
		(*con)[result[0]][v]),
		(*con)[result[0]].unit(v));
		}
		@@ -177,8 +188,8 @@ namespace Isis {
		}
		}

		return PvlKeyword(OutputName(nName),
		PvlTranslationTable::Translate(nName, ""));
		return PvlKeyword(OutputName(translationGroupName),
		PvlTranslationTable::Translate(translationGroupName, ""));
		}


		@@ -222,16 +233,20 @@ namespace Isis {
		/**
		* Returns the ith input value associated with the output name argument.
		*
		* @param nName The output name used to identify the input keyword.
		* @param translationGroupName The name of the PVL translation
		* group used to identify the
		* input/output keywords to be
		* translated. Often, this is the
		* same as the output keyword name.
		*
		* @param findex The index into the input keyword array. Defaults to 0
		*
		* @throws IException::Programmer
		*/
		const PvlKeyword &PvlToPvlTranslationManager::InputKeyword(const QString nName) const {
		const PvlKeyword &PvlToPvlTranslationManager::InputKeyword(const QString translationGroupName) const {

		int instanceNumber = 0;
		PvlKeyword inputGroupKeyword = InputGroup(nName, instanceNumber);
		PvlKeyword inputGroupKeyword = InputGroup(translationGroupName, instanceNumber);
		bool anInputGroupFound = false;

		while(inputGroupKeyword.name() != "") {
		@@ -239,31 +254,31 @@ namespace Isis {
		if(containingGroup != NULL) {
		anInputGroupFound = true;

		if(containingGroup->hasKeyword(InputKeywordName(nName))) {
		return containingGroup->findKeyword(InputKeywordName(nName));
		if(containingGroup->hasKeyword(InputKeywordName(translationGroupName))) {
		return containingGroup->findKeyword(InputKeywordName(translationGroupName));
		}
		}

		instanceNumber ++;
		inputGroupKeyword = InputGroup(nName, instanceNumber);
		inputGroupKeyword = InputGroup(translationGroupName, instanceNumber);
		}

		if(anInputGroupFound) {
		QString msg = "Unable to find input keyword [" + InputKeywordName(nName) +
		"] for output name [" + nName + "] in file [" + TranslationTable().fileName() + "]";
		QString msg = "Unable to find input keyword [" + InputKeywordName(translationGroupName) +
		"] for output name [" + translationGroupName + "] in file [" + TranslationTable().fileName() + "]";
		throw IException(IException::Programmer, msg, _FILEINFO_);
		}
		else {
		QString container = "";

		for(int i = 0; i < InputGroup(nName).size(); i++) {
		for(int i = 0; i < InputGroup(translationGroupName).size(); i++) {
		if(i > 0) container += ",";

		container += InputGroup(nName)[i];
		container += InputGroup(translationGroupName)[i];
		}

		QString msg = "Unable to find input group [" + container +
		"] for output name [" + nName + "] in file [" + TranslationTable().fileName() + "]";
		"] for output name [" + translationGroupName + "] in file [" + TranslationTable().fileName() + "]";
		throw IException(IException::Programmer, msg, _FILEINFO_);
		}
		}
		@@ -273,21 +288,25 @@ namespace Isis {
		* Indicates if the input keyword corresponding to the output name exists in
		* the label
		*
		* @param nName The output name used to identify the input keyword.
		* @param translationGroupName The name of the PVL translation
		* group used to identify the
		* input/output keywords to be
		* translated. Often, this is the
		* same as the output keyword name.
		*/
		bool PvlToPvlTranslationManager::InputHasKeyword(const QString nName) {
		bool PvlToPvlTranslationManager::InputHasKeyword(const QString translationGroupName) {

		// Set the current position in the input label pvl
		// by finding the input group corresponding to the output group
		const PvlContainer *con;
		int inst = 0;
		//while ((con = GetContainer(InputGroup(nName, inst++))) != NULL) {
		//if ((con = GetContainer (InputGroup(nName))) != NULL) {
		//while ((con = GetContainer(InputGroup(translationGroupName, inst++))) != NULL) {
		//if ((con = GetContainer (InputGroup(translationGroupName))) != NULL) {

		PvlKeyword grp;
		while((grp = InputGroup(nName, inst++)).name() != "") {
		while((grp = InputGroup(translationGroupName, inst++)).name() != "") {
		if((con = GetContainer(grp)) != NULL) {
		if(con->hasKeyword(InputKeywordName(nName))) return true;
		if(con->hasKeyword(InputKeywordName(translationGroupName))) return true;
		}
		}

		@@ -335,10 +354,17 @@ namespace Isis {

		/**
		* Create the requsted container and any containers above it and
		* return a reference to the container
		* list is an PvlKeyword with an array of container types an their names
		* return a reference to the container. List is a PvlKeyword
		* with an array of container types and their names.
		*
		* @param translationGroupName The name of the PVL translation
		* group used to identify the
		* input/output keywords to be
		* translated. Often, this is the
		* same as the output keyword name.
		* @param pvl Pvl
		*/
		PvlContainer *PvlToPvlTranslationManager::CreateContainer(const QString nName, Pvl &pvl) {
		return LabelTranslationManager::CreateContainer(nName, pvl);
		PvlContainer *PvlToPvlTranslationManager::CreateContainer(const QString translationGroupName, Pvl &pvl) {
		return LabelTranslationManager::CreateContainer(translationGroupName, pvl);
		}
		} // end namespace isis

isis/src/base/objs/PvlToPvlTranslationManager/PvlToPvlTranslationManager.h

+27 −31

Original line number	Diff line number	Diff line
		@@ -44,42 +44,38 @@ namespace Isis {
		* @author 2003-05-29 Stuart Sides
		*
		* @internal
		* @history 2003-09-03 Stuart Sides - Modified to work with new isis label
		* format
		* @history 2003-09-25 Stuart Sides - Added the Translate member
		* @history 2005-02-15 Elizabeth Ribelin - Modified file to support Doxygen
		* documentation
		* @history 2006-08-09 Brendan George - Modified to support Optional keyword
		* translation
		* @history 2003-09-03 Stuart Sides - Modified to work with new isis label format.
		* @history 2003-09-25 Stuart Sides - Added the Translate member.
		* @history 2005-02-15 Elizabeth Ribelin - Modified file to support Doxygen documentation.
		* @history 2006-08-09 Brendan George - Modified to support Optional keyword translation.
		* @history 2006-10-01 Stuart Sides - Fixed bug with Optional keyword.
		* Non-optional keywords were being reported
		* instantly.
		* Non-optional keywords were being reported instantly.
		* @history 2006-11-16 Brendan George - Changed instances of "Foreign" to "Input"
		* and "Native" to "Output"
		* and "Native" to "Output".
		* @history 2007-06-22 Stuart Sides - Added ability to have more than one input location
		* keyword for a translation. The first one found
		* which contains the input keyword is used.
		* keyword for a translation. The first one found which contains
		* the input keyword is used.
		* @history 2008-05-09 Steven Lambright - Added ability to change input label without
		* re-reading the translation file.
		* @history 2008-07-10 Noah Hilt - Changed while loops to continue searching
		* other groups if a group has been found, but the keyword does not
		* exist in that group.
		* @history 2008-07-10 Steven Lambright - Changed to use new accessors
		* @history 2008-07-10 Noah Hilt - Changed while loops to continue searching other groups
		* if a group has been found, but the keyword does not exist in
		* that group.
		* @history 2008-07-10 Steven Lambright - Changed to use new accessors.
		* @history 2010-01-04 Steven Lambright - Added InputKeyword method and removed
		* InputSize, InputUnits, InputValue.
		* Renamed private Translate method to
		* DoTranslation to remove ambiguity
		* with a parent method, instead of
		* using a dummy parameter.
		* @history 2017-01-11 Jeannie Backer - Moved several methods to a generic
		* parent class, LabelTranslationManager. Fixes #4584.
		* InputSize, InputUnits, InputValue. Renamed private Translate() method
		* to DoTranslation() to remove ambiguity with a parent method,
		* instead of using a dummy parameter.
		* @history 2017-01-11 Jeannie Backer - Moved several methods to a generic parent class,
		* LabelTranslationManager. Fixes #4584.
		* @history 2017-06-13 Adam Paquette - Changed PvlTranslationManager file name to
		* PvlToPvlTranslationManager. Fixes #4901.
		* @history 2018-01-10 Christopher Combs - Changed ProcessDataFilePointer call to reflect
		* changes made to voy2isis. Fixes #4345, #4421.
		* @history 2018-04-16 Jeannie Backer - Fixed indentation of history comments and
		* brought code closer to coding standards.
		* @todo 2005-02-15 Stuart Sides - add coded example and implementation example
		* to class documentation, and finish
		* documentation
		* documentation.
		*/
		class PvlToPvlTranslationManager : public LabelTranslationManager {
		public:
		@@ -97,24 +93,24 @@ namespace Isis {

		// Attempt to translate the requested output name to output value
		// using the input name and value/default value
		virtual QString Translate(QString nName, int findex = 0);
		virtual QString Translate(QString translationGroupName, int findex = 0);

		// Translate all translation table groups which contain "Auto"
		void Auto(Pvl &outputLabel);
		void Auto(Pvl &inputLabel, Pvl &outputLabel);

		// Return the ith input value associated with a output name
		virtual const PvlKeyword &InputKeyword(const QString nName) const;
		virtual const PvlKeyword &InputKeyword(const QString translationGroupName) const;

		// Return true if the input lable contains the translated group and key names
		virtual bool InputHasKeyword(const QString nName);
		virtual bool InputHasKeyword(const QString translationGroupName);

		void SetLabel(Pvl &inputLabel);

		protected:
		virtual PvlKeyword DoTranslation(const QString nName);
		virtual PvlKeyword DoTranslation(const QString translationGroupName);
		virtual const PvlContainer *GetContainer(const PvlKeyword &inputGroup) const;
		virtual PvlContainer *CreateContainer(const QString nName, Pvl &pvl);
		virtual PvlContainer *CreateContainer(const QString translationGroupName, Pvl &pvl);
		private:
		Pvl p_fLabel; //!< A Pvl object for the input label file
		};