Added VAX->IEEE conversion routines to ProcessImport for reading Galileo NIMS qubs. Ref#2368 (33f8d618) · Commits · aflab / astrogeology / ISIS3

isis/src/base/apps/pds2isis/pds2isis.xml

+11 −2

Original line number	Diff line number	Diff line
		<?xml version="1.0" encoding="UTF-8"?>

		<application name="pds2isis" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="http://isis.astrogeology.usgs.gov/Schemas/Application/application.xsd">
		<application name="pds2isis" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
		xsi:noNamespaceSchemaLocation=
		"http://isis.astrogeology.usgs.gov/Schemas/Application/application.xsd">

		<brief>Import PDS or ISIS2 image into ISIS3 cube format</brief>

		@@ -116,6 +118,13 @@
		<change name="Kimberly Oyama" date="2012-11-21">
		Added app tests for BIP and BIL formatted input. References #819.
		</change>
		<change name="Tyler Wilson" data ="2016-02-25">
		Added an app test for opening Galileo NIMS qubes saved in VAX format. Modified the filter
		tag on FROM parameter in this document to also recognize *.qub files. All changes
		relating to converting VAX to IEEE were made in ProcessImport, ProcessImportPds.
		References: #2368.
		</change>

		</history>

		<category>
		@@ -140,7 +149,7 @@
		enter the label file name.
		</description>
		<filter>
		.lbl .img
		.lbl .img *.qub
		</filter>
		</parameter>

isis/src/base/apps/pds2isis/tsts/testNIMSQub/Makefile

0 → 100644

+7 −0

Original line number	Diff line number	Diff line
		APPNAME = pds2isis

		include $(ISISROOT)/make/isismake.tsts

		commands:
		$(APPNAME) from=$(INPUT)/30i001ci.qub \
		to=$(OUTPUT)/30i001ci.cub > /dev/null;

isis/src/base/apps/pds2isis/tsts/testNIMSQub/input/30i001ci.qub

0 → 100644

+309 KiB

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

+317 −2

Original line number	Diff line number	Diff line
		@@ -52,6 +52,7 @@ namespace Isis {
		// Initialize input file information
		p_inFile = "";
		p_pixelType = Isis::None;
		p_suffixPixelType = Isis::None;
		p_ns = p_nl = p_nb = 0;
		p_byteOrder = Isis::NoByteOrder;
		p_fileHeaderBytes = 0;
		@@ -59,7 +60,9 @@ namespace Isis {
		p_dataTrailerBytes = 0;
		p_dataPreBytes = 0;
		p_dataPostBytes = 0;
		p_suffixData = 0;
		p_organization = ProcessImport::BSQ;

		p_base.push_back(0.0);
		p_mult.push_back(1.0);
		// Make all special pixels invalid
		@@ -75,6 +78,8 @@ namespace Isis {
		p_saveDataPre = false;
		p_saveDataPost = false;
		p_saveFileTrailer = false;
		p_vax_convert = false;


		p_fileHeader = NULL;
		p_fileTrailer = NULL;
		@@ -112,6 +117,192 @@ namespace Isis {
		}
		}

		//tjw:



		/**
		* Determines if the VAX encoded pixel value is special or not
		*
		* @param vax A pointer to a VAX pixel
		* @param pix An enumerated value indicating the VAX pixel type
		* @return bool Returns true if the bit pattern for the enumerated
		* type matches that pointed to by vax. Returns false
		* otherwise.
		*/


		bool ProcessImport::IsVAXSpecial(unsigned int *vax, VAXSpecialPixel pix){



		unsigned int VAX_NULL = 0xFFFFFFFF;
		unsigned int VAX_MIN = 0xFFEFFFFF;
		unsigned int VAX_LRS = 0xFFFEFFFF;
		unsigned int VAX_LIS = 0xFFFDFFFF;
		unsigned int VAX_HIS = 0xFFFCFFFF;
		unsigned int VAX_HRS = 0xFFFBFFFF;
		int n;

		unsigned int x;
		memcpy(&x,vax,sizeof(unsigned int));

		switch(pix) {

		case VAX_NULL4:
		n=memcmp(&VAX_NULL,&x,sizeof(unsigned int));
		if (n==0){
		return true;

		}
		break;

		case VAX_LRS4:
		n=memcmp(&VAX_LRS,&x,sizeof(unsigned int));
		if (n==0){

		return true;
		}
		break;

		case VAX_LIS4:
		n=memcmp(&VAX_LIS,&x,sizeof(unsigned int));
		if (n==0) {

		return true;
		}
		break;

		case VAX_HIS4:
		n=memcmp(&VAX_HIS,&x,sizeof(unsigned int));
		if (n==0){

		return true;
		}
		break;

		case VAX_HRS4:
		n=memcmp(&VAX_HRS,&x,sizeof(unsigned int));
		if (n==0){

		return true;
		}
		break;

		case VAX_MIN4:
		n=memcmp(&VAX_MIN,&x,sizeof(unsigned int));
		if (n==0){

		return true;
		}
		break;

		default:
		return false;

		}

		return false;

		}

		//tjw

		/**
		* Conversion routine which translates VAX_REAL to IEEE_REAL
		*
		* @param ibuf Memory buffer of input data to be converted
		* @return double the converted value
		*/


		double ProcessImport::VAXConversion(void *ibuf) {



		float result;
		double dresult;
		bool swap_bytes = false;
		bool swap_words = true;
		int exp_adjust = -1;
		int exp_mask = 0;
		int exp_word = 1;
		int exp_byte;
		Isis::ByteOrder in_order = p_byteOrder;
		Isis::ByteOrder out_order;


		unsigned int oli, ili; //4-byte buffer io ptrs
		unsigned short *osi; //2-byte buffer io ptrs
		char *oci; //1-byte buffer io ptrs

		if ( Isis::IsLsb() ) {

		exp_byte = 1;
		out_order = Isis::Lsb;

		}

		//Byte order = MSB
		else {
		exp_byte = 0;
		out_order = Isis::Msb;
		}

		if (in_order != out_order) {
		swap_bytes =true;

		}

		oli = (unsigned int * ) ibuf;
		ili = (unsigned int * ) ibuf;

		if (IsVAXSpecial(oli,Isis::VAX_NULL4) )
		return Isis::NULL8;

		if (IsVAXSpecial(oli,Isis::VAX_LIS4) )
		return Isis::LOW_INSTR_SAT8;

		if (IsVAXSpecial(oli,Isis::VAX_LRS4) )
		return Isis::LOW_REPR_SAT8;

		if (IsVAXSpecial(oli,Isis::VAX_HIS4) )
		return Isis::HIGH_INSTR_SAT8;

		if (IsVAXSpecial(oli,Isis::VAX_HRS4) )
		return Isis::HIGH_REPR_SAT8;

		if (IsVAXSpecial(oli,Isis::VAX_MIN4) )
		return Isis::VALID_MIN8;

		//test for word swapping
		if (swap_words) {

		oli = (ili <<16) \| (*ili >> 16);
		}

		osi = (unsigned short* ) oli;

		//test for byte swapping

		if (swap_bytes) {
		osi[0] = (osi[0] >> 8 ) \| (osi[0] << 8);
		osi[1] = (osi[1] >> 8 ) \| (osi[1] << 8);
		}

		//Isolate the exponent and do the conversion
		oci = (char *) &osi[exp_word];

		if ( (oci[exp_byte] & EXPONENT_MASK) != exp_mask)
		oci[exp_byte] += exp_adjust;

		result = (float )oli;
		dresult = static_cast<double>(result);
		return dresult;

		}



		/**
		* Sets the pixel type of the input file.
		@@ -134,6 +325,19 @@ namespace Isis {
		}
		};

		void ProcessImport::SetSuffixPixelType(const Isis::PixelType type) {

		if ((type == Isis::Double) \|\| (type == Isis::Real) \|\| (type == Isis::SignedWord) \|\|
		(type == Isis::UnsignedWord) \|\| (type == Isis::UnsignedByte)) {
		p_suffixPixelType = type;
		}
		else {
		QString msg = "Unsupported pixel type [" +
		Isis::PixelTypeName(type) + "]";
		throw IException(IException::Programmer, msg, _FILEINFO_);
		}
		};


		/**
		* Sets the physical size of the input cube. This must be invoked prior to
		@@ -149,9 +353,13 @@ namespace Isis {
		*/
		void ProcessImport::SetDimensions(const int ns, const int nl, const int nb) {
		if (ns > 0 && nl > 0 && nb > 0) {


		p_ns = ns;
		p_nl = nl;
		p_nb = nb;


		}
		else {
		QString msg = "Illegal dimension [" + toString(ns) + ", " +
		@@ -195,6 +403,7 @@ namespace Isis {
		void ProcessImport::SetFileHeaderBytes(const int bytes) {
		if (bytes >= 0) {
		p_fileHeaderBytes = bytes;

		}
		else {
		QString msg = "Illegal file header size [" + toString(bytes) + "]";
		@@ -253,7 +462,9 @@ namespace Isis {
		*/
		void ProcessImport::SetDataHeaderBytes(const int bytes) {
		if (bytes >= 0) {

		p_dataHeaderBytes = bytes;

		}
		else {
		QString msg = "Illegal data header size [" + toString(bytes) + "]";
		@@ -262,6 +473,14 @@ namespace Isis {
		};


		void ProcessImport::SetSuffixOffset(int samples,int lines, int coreBands,int itemBytes){

		p_suffixData = sampleslinescoreBands*itemBytes;


		};


		/**
		* This method sets the number of bytes in the trailer of each
		* datablock of a file. A data trailer is a block of non-image
		@@ -315,6 +534,7 @@ namespace Isis {

		if (bytes >= 0) {
		p_dataPreBytes = bytes;

		}
		else {
		QString msg = "Illegal data prefix size [" + toString(bytes) + "]";
		@@ -345,6 +565,7 @@ namespace Isis {

		if (bytes >= 0) {
		p_dataPostBytes = bytes;

		}
		else {
		QString msg = "Illegal data suffix size [" + toString(bytes) + "]";
		@@ -527,6 +748,7 @@ namespace Isis {
		* This method returns the number of file header bytes
		*/
		int ProcessImport::FileHeaderBytes() const {

		return p_fileHeaderBytes;
		}

		@@ -567,6 +789,7 @@ namespace Isis {
		* This method returns the number of data duffix bytes
		*/
		int ProcessImport::DataSuffixBytes() const {

		return p_dataPostBytes;
		}

		@@ -745,6 +968,26 @@ namespace Isis {
		*/
		void ProcessImport::SetOrganization(const ProcessImport::Interleave org) {
		p_organization = org;

		};


		//tjw:
		/**
		* Sets the VAX flag of the input cube. If true, then the core pixel type of
		* the input cube is VAX, and VAX conversion routines need to be run to
		* convert the pixels to IEEE format.
		*
		* @param vax_convert Flag indicating whether or not to run VAX conersion methods
		*/



		void ProcessImport::SetVAXConvert(const bool vax_convert){


		p_vax_convert = vax_convert;

		};


		@@ -1154,6 +1397,8 @@ namespace Isis {
		* Position[]. Byte count[]"
		*/
		void ProcessImport::ProcessBsq(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;
		@@ -1176,11 +1421,14 @@ namespace Isis {

		// Handle the file header
		streampos pos = fin.tellg();
		//tjw
		if (p_saveFileHeader) {
		p_fileHeader = new char[p_fileHeaderBytes];
		fin.read(p_fileHeader, p_fileHeaderBytes);
		fin.seekg(p_suffixData+p_fileHeaderBytes,ios_base::beg);
		}
		else {
		fin.seekg(p_fileHeaderBytes+p_suffixData, ios_base::beg);
		fin.seekg(p_fileHeaderBytes, ios_base::beg);
		}

		@@ -1219,14 +1467,19 @@ namespace Isis {
		mult = p_mult[0];
		}


		// Handle any data headers (e.g., the data at the beginning of each band)
		pos = fin.tellg();
		if (p_saveDataHeader) {
		p_dataHeader.push_back(new char[p_dataHeaderBytes]);
		fin.read(p_dataHeader.back(), p_dataHeaderBytes);

		}
		else {
		//cout << p_suffixData << endl;
		fin.seekg(p_dataHeaderBytes, ios_base::cur);


		}

		// Check the last io
		@@ -1277,26 +1530,37 @@ namespace Isis {
		for(int samp = 0; samp < p_ns; samp++) {
		switch(p_pixelType) {
		case Isis::UnsignedByte:
		//cout << "UnsignedByte" << endl;
		(out)[samp] = (double)((unsigned char )in)[samp];
		break;
		case Isis::UnsignedWord:
		//cout << "Unsigned word."<< endl;
		(*out)[samp] =
		(double)swapper.UnsignedShortInt((unsigned short int *)in+samp);
		break;
		case Isis::SignedWord:
		//cout << "Signed Word." << endl;
		(out)[samp] = (double)swapper.ShortInt((short int )in+samp);
		break;
		case Isis::Real:
		//tjw:
		if(p_vax_convert)
		(out)[samp]= VAXConversion( (float )in+samp );
		else
		(out)[samp] = (double)swapper.Float((float )in+samp);

		break;
		case Isis::Double:
		//cout << "Double" << endl;
		(out)[samp] = (double)swapper.Double((double )in+samp);
		break;


		default:
		break;
		}

		// Sets out to isis special pixel or leaves it if valid

		(out)[samp] = TestPixel((out)[samp]);

		if (Isis::IsValidPixel((*out)[samp])) {
		@@ -1395,6 +1659,10 @@ namespace Isis {
		}






		/**
		* Function to process files stored as Band Interleaved by Line
		*
		@@ -1429,6 +1697,21 @@ namespace Isis {

		// Handle the file header
		streampos pos = fin.tellg();



		if (p_saveFileHeader) {
		p_fileHeader = new char[p_fileHeaderBytes];
		fin.read(p_fileHeader, p_fileHeaderBytes);
		fin.seekg(p_suffixData+p_fileHeaderBytes,ios_base::beg);
		}
		else {
		fin.seekg(p_fileHeaderBytes+p_suffixData, ios_base::beg);
		fin.seekg(p_fileHeaderBytes, ios_base::beg);
		}


		#if 0
		if (p_saveFileHeader) {
		p_fileHeader = new char[p_fileHeaderBytes];
		fin.read(p_fileHeader, p_fileHeaderBytes);
		@@ -1436,6 +1719,8 @@ namespace Isis {
		else {
		fin.seekg(p_fileHeaderBytes, ios_base::beg);
		}
		#endif


		// Check the last io
		if (!fin.good()) {
		@@ -1532,6 +1817,10 @@ namespace Isis {
		(out)[samp] = (double)swapper.ShortInt((short int )in+samp);
		break;
		case Isis::Real:
		//tjw:
		if(p_vax_convert)
		(out)[samp]= VAXConversion( (float )in+samp );
		else
		(out)[samp] = (double)swapper.Float((float )in+samp);
		break;
		case Isis::Double:
		@@ -1642,6 +1931,7 @@ 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;
		@@ -1663,15 +1953,33 @@ namespace Isis {
		}

		// Handle the file header

		//tjw
		streampos pos = fin.tellg();
		if (p_saveFileHeader) {
		p_fileHeader = new char[p_fileHeaderBytes];
		fin.read(p_fileHeader, p_fileHeaderBytes);
		fin.seekg(p_suffixData+p_fileHeaderBytes,ios_base::beg);
		}
		else {
		fin.seekg(p_fileHeaderBytes+p_suffixData, ios_base::beg);
		fin.seekg(p_fileHeaderBytes, ios_base::beg);
		}



		#if 0

		if (p_saveFileHeader) {
		p_fileHeader = new char[p_fileHeaderBytes];
		fin.read(p_fileHeader, p_fileHeaderBytes);
		}
		else {
		fin.seekg(p_fileHeaderBytes, ios_base::beg);
		}

		#endif

		// Check the last io
		if (!fin.good()) {
		QString msg = "Cannot read file [" + p_inFile + "]. Position [" +
		@@ -1754,6 +2062,7 @@ namespace Isis {
		// Swap the bytes if necessary and convert any out of bounds pixels
		// to special pixels
		int osamp = 0;

		for(int samp = band; samp < p_ns * p_nb; samp += p_nb) {
		switch(p_pixelType) {
		case Isis::UnsignedByte:
		@@ -1767,10 +2076,14 @@ namespace Isis {
		(out)[osamp] = (double)swapper.ShortInt((short int )in+samp);
		break;
		case Isis::Real:
		//tjw:
		if(p_vax_convert)
		(out)[osamp]= VAXConversion( (float )in+samp );
		else
		(out)[osamp] = (double)swapper.Float((float )in+samp);
		break;
		case Isis::Double:
		(out)[samp] = (double)swapper.Double((double )in+samp);
		(out)[osamp] = (double)swapper.Double((double )in+samp);
		break;
		default:
		break;
		@@ -2088,3 +2401,5 @@ namespace Isis {

		}

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

+57 −0

Original line number	Diff line number	Diff line
		@@ -145,8 +145,34 @@ namespace Isis {
		* child classes. Added virtual keyword
		* to destructor. References #2215.
		*
		* @history 2016-02-23 Tyler Wilson - Added VAXConversion(...) and IsVAXSpecial(...) routines
		* for importing Galileo NIMS qubs which were originally saved in VAX format.
		* References #2368.
		*
		*/


		// VAX conversion
		#define EXPONENT_MASK ((char) 0x7F)




		//Data type for Galileo: NIMS data
		enum VAXDataType{
		VAX_REAL,
		VAX_INT
		};

		enum VAXSpecialPixel {
		VAX_MIN4,
		VAX_NULL4,
		VAX_LRS4,
		VAX_LIS4,
		VAX_HIS4,
		VAX_HRS4
		};

		class ProcessImport : public Isis::Process {
		public:
		ProcessImport();
		@@ -167,9 +193,17 @@ namespace Isis {
		* Returns the pixel type
		* @return The pixel type of input data
		*/

		void SetSuffixPixelType(const Isis::PixelType type);

		Isis::PixelType PixelType() {
		return p_pixelType;
		}

		Isis::PixelType SuffixPixelType() {
		return p_suffixPixelType;
		}

		void SetDimensions(const int ns, const int nl, const int nb);

		/**
		@@ -206,6 +240,14 @@ namespace Isis {
		return p_byteOrder;
		}


		//tjw: VAX_REAL -> IEEE_REAL

		bool IsVAXSpecial(unsigned int *vax,VAXSpecialPixel pix);
		double VAXConversion(void *ibuf);
		void SetSuffixOffset(int samples,int lines, int coreBands,int itemBytes);


		void SetFileHeaderBytes(const int bytes);
		void SetFileTrailerBytes(const int bytes);
		void SetDataHeaderBytes(const int bytes);
		@@ -252,6 +294,11 @@ namespace Isis {
		all bands is followed by the second pixel for
		all bands.*/
		};

		//tjw
		void SetVAXConvert(const bool vax_flag);


		void SetOrganization(const ProcessImport::Interleave org);
		Interleave Organization() const;

		@@ -280,9 +327,15 @@ namespace Isis {
		private:
		QString p_inFile; //!< Input file name
		Isis::PixelType p_pixelType; //!< Pixel type of input data
		Isis::PixelType p_suffixPixelType;
		int p_ns; //!< Number of samples
		int p_nl; //!< Number of lines
		int p_nb; //!< Number of bands
		int p_suffixData; //!< Number of bytes past the file header bytes
		//!< where the suffix data bands are stored
		//!


		Isis::ByteOrder p_byteOrder; //!< Byte order of data
		int p_fileHeaderBytes; /**< The number of bytes of non-image data at
		the beginning of a file. This does not
		@@ -381,6 +434,10 @@ namespace Isis {
		data. All pixels between this value and the min
		will be converted to the Isis LIS value.*/

		bool p_vax_convert; /**< A boolean flag which is set to true if we
		are converting a VAX formatted real number. */


		void ProcessBsq(void funct(Isis::Buffer &out) = NULL);
		void ProcessBil(void funct(Isis::Buffer &out) = NULL);
		void ProcessBip(void funct(Isis::Buffer &out) = NULL);