Merge branch 'dev' of github.com:USGS-Astrogeology/ISIS3 into rosetta (4c43b092) · Commits · aflab / astrogeology / ISIS3

isis/make/config.linux-x86_64

+3 −0

Original line number	Diff line number	Diff line
		@@ -526,5 +526,8 @@ THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libtbb.so"
		# Add the Boost libraries
		THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libboost.so"

		# Add srtp deps (Qt5WebEngine deps) -- see #5365
		THIRDPARTYLIBS += "$(ISIS3SYSLIB)/libsrtp.so"

		# Plugins
		THIRDPARTYPLUGINS += "$(ISIS3LOCAL)/plugins/"

isis/make/config.linux-x86_64_Fedora25

+4 −1

Original line number	Diff line number	Diff line
		@@ -479,7 +479,6 @@ THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libsuperlu*.so"
		THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libsuitesparseconfig.so"
		THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/liblapack.so"
		THIRDPARTYLIBS += "$(ISIS3SYSLIB)/libblas.so"
		THIRDPARTYLIBS += "$(ISIS3ALTSYSLIB)/libgfortran.so*"
		THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libxerces-c.so"
		THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libgeotiff.so"
		THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libtiff.so"
		@@ -533,5 +532,9 @@ THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libtbb.so"
		# Add the Boost libraries
		THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libboost.so"

		# Add and patch the gfortran's rpath to $ORIGIN (so it can find its quadmath dependency) -- #4610
		PATCHLIBS += "$(ISIS3ALTSYSLIB)/libgfortran.so*"
		THIRDPARTYLIBS += "$(ISIS3SYSLIB)/libquadmath.so"

		# Plugins
		THIRDPARTYPLUGINS += "$(ISIS3LOCAL)/plugins/"

isis/src/base/apps/fits2isis/tsts/default/Makefile

+3 −7

Original line number	Diff line number	Diff line
		@@ -4,10 +4,6 @@ include $(ISISROOT)/make/isismake.tsts

		commands:
		$(APPNAME) from=$(INPUT)/WFPC2u5780205r_c0fx.fits \
		to=$(OUTPUT)/fitsTruth.cub \
		> /dev/null;
		raw2isis from=$(INPUT)/WFPC2u5780205r_c0fx.fits \
		to=$(OUTPUT)/rawTruth.cub \
		SAMPLES=200 LINES=200 BANDS=4 SKIP=23040 \
		BITTYPE=REAL BYTEORDER=MSB \
		> /dev/null;
		to=$(OUTPUT)/fitsTruth.cub > /dev/null;
		catlab from=$(OUTPUT)/fitsTruth.cub \
		to=$(OUTPUT)/fitsTruth.pvl > /dev/null;

isis/src/base/apps/fits2isis/tsts/organization/Makefile

+6 −4

Original line number	Diff line number	Diff line
		@@ -4,8 +4,10 @@ include $(ISISROOT)/make/isismake.tsts

		commands:
		$(APPNAME) from=$(INPUT)/lsb_0034933739_0x53c_sci_1.fit \
		to=$(OUTPUT)/bilTruth.cub organization=bil imagenumber=1\
		> /dev/null;
		to=$(OUTPUT)/bilTruth.cub organization=bil imagenumber=1 > /dev/null;
		catlab from=$(OUTPUT)/bilTruth.cub \
		to=$(OUTPUT)/bilTruth.pvl > /dev/null;
		$(APPNAME) from=$(INPUT)/lsb_0034933739_0x53c_sci_1.fit \
		to=$(OUTPUT)/bsqTruth.cub organization=bsq imagenumber=1 \
		> /dev/null;
		to=$(OUTPUT)/bsqTruth.cub organization=bsq imagenumber=1 > /dev/null;
		catlab from=$(OUTPUT)/bsqTruth.cub \
		to=$(OUTPUT)/bsqTruth.pvl > /dev/null;

isis/src/base/objs/FileName/FileName.cpp

+330 −39

Original line number	Diff line number	Diff line
		@@ -40,41 +40,99 @@ using namespace std;

		namespace Isis {

		/**
		* Constructs an empty FileName object.
		*/
		FileName::FileName() {
		m_d = new Data;
		}


		/**
		* Constructs a FileName object using a char pointer as a file name.
		*
		* @param file char pointer representing new filename
		*/
		FileName::FileName(const char *file) {
		m_d = new Data;
		m_d->setOriginal(file);
		}


		/**
		* Constructs a FileName object using a QString as a file name.
		*
		* @param file Qstring representing new filename
		*/
		FileName::FileName(const QString &file) {
		m_d = new Data;
		m_d->setOriginal(file);
		}


		/**
		* Constructs a copy of a FileName object using another FileName object.
		*
		* @param &other FileName object to copy.
		*/
		FileName::FileName(const FileName &other) : m_d(other.m_d) {
		}


		/**
		* Destroys the FileName object.
		*/
		FileName::~FileName() {
		}


		/**
		* Returns the path of the original file name. For *nix operating
		* systems this includes everything up to but not including the
		* last slash "/". For filenames created without any slashes
		* the current working directory will be returned.
		*
		* <pre>
		* for a full file specification of:
		* "/home/me/img/picture.jpg"
		* originalPath() gives:
		* "/home/me/img"
		* </pre>
		*
		* @return QString of the path portion of the original filename.
		*/
		QString FileName::originalPath() const {
		return QFileInfo(m_d->original(false)).path();
		}


		/**
		* Returns the path of the file name. For *nix operating
		* systems this includes everything up to but not including the
		* last slash "/". For filenames created without any slashes
		* the current working directory will be returned.
		*
		* <pre>
		* for a full file specification of:
		* "/home/me/img/picture.jpg"
		* path() gives:
		* "/home/me/img"
		* </pre>
		*
		* @return QString of the path portion of the filename.
		*/
		QString FileName::path() const {
		return QFileInfo(expanded()).path();
		}


		/**
		* Returns a QString of the attributes in a filename, attributes are expected to be of type
		* CubeAttributeInput or CubeAttributeOutput. Filenames without any attributes return an
		* empty QString.
		*
		* <pre>
		* for a full file specification of:
		* "/tmp/Peaks.cub+Bsq"
		* attributes() gives:
		* "Bsq"
		* </pre>
		*
		* @return QString of the attributes specified in the filename.
		*/
		QString FileName::attributes() const {
		QString result;
		QString fileNameWithAttribs = QFileInfo(m_d->original(true)).fileName();
		@@ -87,32 +145,98 @@ namespace Isis {
		return result;
		}


		/**
		* Returns the name of the file without the path and without extensions.
		*
		* <pre>
		* for a full file specification of:
		* "/tmp/Peaks.cub.gz"
		* baseName() gives:
		* "Peaks"
		* </pre>
		*
		* @return QString containing every character excluding the path and all extensions.
		*/
		QString FileName::baseName() const {
		return QFileInfo(m_d->original(false)).completeBaseName();
		}


		/**
		* Returns the name of the file excluding the path and the attributes in the file name.
		*
		* <pre>
		* for a full file specification of:
		* "/tmp/Peaks.cub+Bsq"
		* name() gives:
		* "Peaks.cub"
		* </pre>
		*
		* @return QString containing every character in the file name exluding the path and attributes
		* of the file.
		*/
		QString FileName::name() const {
		return QFileInfo(m_d->original(false)).fileName();
		}


		/**
		* Returns the last extension of the file name.
		*
		* <pre>
		* for a full file specification of:
		* "/tmp/Peaks.cub.gz"
		* extension() gives:
		* "gz"
		* </pre>
		*
		* @return QString containing every character in the file name after the last "." character.
		*/
		QString FileName::extension() const {
		return QFileInfo(m_d->original(false)).suffix();
		}


		/**
		* Returns a QString of the full file name including the file path, excluding the attributes.
		* Any Isis Preferences or environment variables indicated by $, are changed to what they
		* represent.
		*
		* <pre>
		* for a full file specification of:
		* "$ISISROOT/tmp/Peaks.cub+Bsq"
		* expanded() gives:
		* "/usgs/pkgs/isis3/isis/tmp/Peaks.cub"
		* </pre>
		*
		* @return QString
		*/
		QString FileName::expanded() const {
		return m_d->expanded(false);
		}


		/**
		* Returns the full file name including the file path
		*
		* <pre>
		* for a full file specification of:
		* "$ISISROOT/tmp/Peaks.cub+Bsq"
		* original() gives:
		* "$ISISROOT/tmp/Peaks.cub+Bsq"
		* </pre>
		*
		* @return QString containing every character in the file name and the path
		*/
		QString FileName::original() const {
		return m_d->original(true);
		}


		/**
		* Adds a new extension to the file name. If the current extension is the same as the
		* new extension it will return an unchanged FileName object.
		*
		* @param newExtension The new file extension to be added at the end of the file name after all
		* exisiting extensions.
		*
		* @return FileName object with added extension
		*/
		FileName FileName::addExtension(const QString &newExtension) const {
		FileName result = *this;

		@@ -129,7 +253,11 @@ namespace Isis {
		return result;
		}


		/**
		* Removes all extensions in the file name
		*
		* @return FileName object with all extensions removed
		*/
		FileName FileName::removeExtension() const {
		QString attributesStr = attributes();

		@@ -142,7 +270,13 @@ namespace Isis {
		return result;
		}


		/**
		* Sets all current file extensions to a new extension in the file name.
		*
		* @param newExtension The new file extension to replace any current file extensions with
		*
		* @return FileName object with all existing extensions replaced by the new extension
		*/
		FileName FileName::setExtension(const QString &newExtension) const {
		FileName result = *this;

		@@ -153,24 +287,44 @@ namespace Isis {
		return result;
		}


		/**
		* Checks to see if a file name is versioned by date or numerically. Returns true if file is
		* versioned by date or numerically; returns false otherwise.
		*
		* @return Boolean
		*/
		bool FileName::isVersioned() const {
		validateVersioningState();

		return isNumericallyVersioned() \|\| isDateVersioned();
		}


		/**
		* Checks if the file name is versioned numerically. Returns true if the file is versioned
		* numerically; returns false otherwise.
		*
		* @return Boolean
		*/
		bool FileName::isNumericallyVersioned() const {
		return FileName(expanded()).name().contains("?");
		}


		/**
		* Checks if the file name is versioned by date. Returns true if the file is versioned
		* by date; returns false otherwise.
		*
		* @return Boolean
		*/
		bool FileName::isDateVersioned() const {
		return FileName(expanded()).name().contains(QRegExp("\\{.*\\}"));
		}


		/**
		* Searches the directory specified in the file name for the highest version of the file name.
		* Returns a FileName object with the file name changed to reflect the highest version.
		*
		* @return FileName object
		*/
		FileName FileName::highestVersion() const {
		validateVersioningState();

		@@ -197,7 +351,15 @@ namespace Isis {
		return result;
		}


		/**
		* Updates the file name to be the latest version. If the file is versioned by date the
		* newest version will be the current date. If the file is versioned numerically, the newest
		* version will be the current version plus one.
		*
		* @return FileName object with the new version file name.
		*
		* @throws Isis::IException::Unknown
		*/
		FileName FileName::newVersion() const {
		validateVersioningState();

		@@ -238,7 +400,16 @@ namespace Isis {
		return result;
		}


		/**
		* Returns a FileName object of the same file name but versioned numerically by the
		* number passed in as a parameter.
		*
		* @param versionNumber number to version the new FileName object
		*
		* @return FileName object with the new version file name.
		*
		* @throws Isis::IException::Unknown
		*/
		FileName FileName::version(long versionNumber) const {
		QString file = FileName(expanded()).name();

		@@ -269,24 +440,56 @@ namespace Isis {
		return FileName(originalPath() + "/" + file);
		}


		/**
		* Returns a FileName object of the same file name but versioned by the
		* date passed in as a parameter.
		*
		* @param versionDate QDate to version the new FileName object
		*
		* @return FileName object with the new version file name.
		*
		*/
		FileName FileName::version(QDate versionDate) const {
		QString newName = versionDate.toString(fileNameQDatePattern());

		return FileName(originalPath() + "/" + newName);
		}


		/**
		* Returns true if the file exists; false otherwise.
		* If the file is a symlink that points to a nonexistent file, false is returned.
		*
		* @return Boolean
		*/
		bool FileName::fileExists() const {
		return QFileInfo(expanded()).exists();
		}


		/**
		* Returns the path of the file's parent directory as a QDir object
		*
		* <pre>
		* for a full file specification of:
		* "/tmp/Peaks.cub+Bsq"
		* dir() gives:
		* "/tmp/"
		* </pre>
		*
		* @return QDir
		*/
		QDir FileName::dir() const {
		return QFileInfo(expanded()).dir();
		}


		/**
		* Creates a temporary file and returns a FileName object created using the temporary file.
		*
		* @param templateFileName the file name used to create the temporary file.
		*
		* @return FileName object created using the temporary file
		*
		* @throws Isis::IException::Io
		*/
		FileName FileName::createTempFile(FileName templateFileName) {
		QString preppedFileName = QString("%1/%2XXXXXX.%3").arg(templateFileName.path())
		.arg(templateFileName.baseName()).arg(templateFileName.extension());
		@@ -310,18 +513,45 @@ namespace Isis {
		return result;
		}


		/**
		* Returns a QString of the full file name including the file path, excluding the attributes
		* with any Isis Preferences or environment variables indicated by $, changed to what they
		* represent.
		*
		* <pre>
		* for a full file specification of:
		* "$ISISROOT/tmp/Peaks.cub+Bsq"
		* toString() gives:
		* "/usgs/pkgs/isis3/isis/tmp/Peaks.cub"
		* </pre>
		*
		* @return QString
		*/
		QString FileName::toString() const {
		return expanded();
		}


		/**
		* Clears the current contents of the FileName object and reinitializes it with
		* the argument.
		*
		* @param rhs FileName to replace the current contents of the object.
		*
		* @return void
		*/
		FileName &FileName::operator=(const FileName &rhs) {
		m_d = rhs.m_d;
		return *this;
		}


		/**
		* Compares equality of two FileName objects. Returns true if the two objects are equal
		* and false otherwise.
		*
		* @param rhs FileName to compare the current FileName object to.
		*
		* @return Boolean
		*/
		bool FileName::operator==(const FileName &rhs) {
		QString expandedOfThis = expanded();
		QString canonicalOfThis = QFileInfo(expandedOfThis).canonicalFilePath();
		@@ -342,12 +572,24 @@ namespace Isis {
		return equal;
		}


		/**
		* Compares equality of two FileName objects. Returns false if the two objects are equal
		* and true otherwise.
		*
		* @param rhs FileName to compare the current FileName object to.
		*
		* @return Boolean
		*/
		bool FileName::operator!=(const FileName &rhs) {
		return !(*this == rhs);
		}


		/**
		* This looks through the directory of the file and checks for the highest version date of
		* the file that is versioned date.
		*
		* @return QDate
		*/
		QDate FileName::highestVersionDate() const {
		QString fileQDatePattern = fileNameQDatePattern();

		@@ -405,7 +647,12 @@ namespace Isis {
		return result;
		}


		/**
		* This looks through the directory of the file and checks for the highest version number of
		* the file that is versioned numerically.
		*
		* @return long
		*/
		long FileName::highestVersionNum() const {
		QString file = FileName(expanded()).name();
		int result = 0;
		@@ -441,7 +688,10 @@ namespace Isis {
		return result;
		}


		/**
		* This verifies the class invariant when using versioning - that the FileName is in an acceptable
		* state to find file version numbers.
		*/
		void FileName::validateVersioningState() const {
		QString file = QFileInfo(expanded()).fileName();

		@@ -484,6 +734,12 @@ namespace Isis {
		}
		}

		/**
		* This changes the files format. Specifically quotes everything not in {} with single quotes
		* and removes the {} from the file name.
		*
		* @return QString
		*/
		QString FileName::fileNameQDatePattern() const {
		// We need to quote everything not in {} with single quotes.
		QString file = FileName(expanded()).name();
		@@ -508,7 +764,12 @@ namespace Isis {
		return file;
		}


		/**
		* This returns a QPair of the text (before, after) a version number in a file. Before being
		* the text before the version number and after being the text after the version number.
		*
		* @return QPair
		*/
		QPair<QString, QString> FileName::splitNameAroundVersionNum() const {
		QString file = FileName(expanded()).name();
		QString before;
		@@ -525,7 +786,9 @@ namespace Isis {
		return QPair<QString, QString>(before, after);
		}


		/**
		* Data constructor, creates a new Data object.
		*/
		FileName::Data::Data() {
		m_originalFileNameString = NULL;
		m_expandedFileNameString = NULL;
		@@ -534,7 +797,11 @@ namespace Isis {
		m_expandedFileNameString = new QString;
		}


		/**
		* Data copy constructor, creates a copy of a Data object.
		*
		* @param &other Data object to copy
		*/
		FileName::Data::Data(const Data &other) : QSharedData(other) {
		m_originalFileNameString = NULL;
		m_expandedFileNameString = NULL;
		@@ -543,7 +810,9 @@ namespace Isis {
		m_expandedFileNameString = new QString(*other.m_expandedFileNameString);
		}


		/**
		* Destroys the Data object.
		*/
		FileName::Data::~Data() {
		delete m_originalFileNameString;
		m_originalFileNameString = NULL;
		@@ -552,7 +821,15 @@ namespace Isis {
		m_expandedFileNameString = NULL;
		}


		/**
		* Returns the original file name, stored in m_originalFileNameString. Boolean
		* parameter includeAttributes determines if the returned file name has the variables
		* included.
		*
		* @param includeAttributes boolean to represent whether the attricubtes should be included.
		*
		* @return Qstring
		*/
		QString FileName::Data::original(bool includeAttributes) const {
		QString result = *m_originalFileNameString;

		@@ -567,7 +844,13 @@ namespace Isis {
		return result;
		}


		/**
		* Sets the original file name, stored in m_originalFileNameString. QString parameter
		* is the new file name to store in m_originalFileNameString. The expanded verison is also
		* set and stored in m_expandedFileNameString when this method is called.
		*
		* @param originalStr the new file name
		*/
		void FileName::Data::setOriginal(const QString &originalStr) {
		*m_originalFileNameString = originalStr;

		@@ -633,7 +916,15 @@ namespace Isis {
		*m_expandedFileNameString = expandedStr;
		}


		/**
		* Returns the expanded file name, stored in m_expandedFileNameString. Boolean
		* parameter includeAttributes determines if the returned file name has the variables
		* included.
		*
		* @param includeAttributes boolean to represent whether the attricubtes should be included.
		*
		* @return Qstring
		*/
		QString FileName::Data::expanded(bool includeAttributes) const {
		QString result = *m_expandedFileNameString;