New Horizons MVIC and LORRI camera and ingest ref#1962,2120,2122 (09ad8b6b) · Commits · aflab / astrogeology / ISIS3

isis/src/base/apps/fits2isis/fits2isis.cpp

+3 −2

Original line number	Diff line number	Diff line
		@@ -24,11 +24,12 @@ void IsisMain() {
		ProcessImportFits pfits;

		pfits.setFitsFile(FileName(ui.GetFileName("FROM")));
		pfits.setProcessFileStructure(0);

		Cube *output = pfits.SetOutputCube("TO");

		// Add instrument group if any keywords were put into it.
		PvlGroup instGrp = pfits.standardInstrumentGroup();
		PvlGroup instGrp = pfits.standardInstrumentGroup(pfits.fitsLabel(0));
		if (instGrp.keywords() > 0) {

		output->label()->findObject("IsisCube") += instGrp;
		@@ -36,7 +37,7 @@ void IsisMain() {

		// Save the input FITS label in the Cube original labels
		Pvl pvl;
		pvl += pfits.fitsLabel();
		pvl += pfits.fitsLabel(0);
		OriginalLabel originals(pvl);
		output->write(originals);

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

+2 −2

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

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

isis/src/base/objs/ProcessImportFits/ProcessImportFits.cpp

+117 −57

Original line number	Diff line number	Diff line
		@@ -23,14 +23,16 @@
		#include "ProcessImportFits.h"

		#include <iostream>
		#include <math.h>

		#include <QDebug>
		#include <QString>
		#include <sstream>

		#include "Preference.h"
		#include "IException.h"
		#include "IString.h"
		#include "LineManager.h"
		#include "Preference.h"
		#include "Pvl.h"
		#include "PvlGroup.h"
		#include "PixelType.h"
		@@ -43,7 +45,8 @@ namespace Isis {
		* Constructor for ProcessImportFits
		*/
		ProcessImportFits::ProcessImportFits() {
		m_fitsLabel = NULL;
		m_fitsLabels = NULL;
		m_headerSizes = NULL;
		}


		@@ -51,35 +54,45 @@ namespace Isis {
		* Destructor for ProcessImportFits
		*/
		ProcessImportFits::~ProcessImportFits() {
		delete m_fitsLabel;
		delete m_fitsLabels;
		delete m_headerSizes;
		m_file.close();
		}


		/**
		* Extract the FITS label from the file
		* Extract all the FITS labels from the file. This includes the main and all extensions
		*
		*/
		void ProcessImportFits::extractFitsLabel() {
		void ProcessImportFits::extractFitsLabels() {

		// The main FITS label starts at the beginning of the file
		// Each FITS keyword in the lable is store in 80 bytes (space padded to 80 if necessary)

		m_fitsLabel = new PvlGroup("FitsLabels");
		m_fitsLabels = new QList< PvlGroup * >;
		m_headerSizes = new QList < int >;

		// Read in the FITS labels and convert to PVL
		// Process each FITS label area. Storing each in its own PvlGroup
		char readBuf[81];
		IString line = "";
		unsigned int place = 0;
		unsigned int place;

		// The main FITS label starts at the beginning of the file
		// FITS extension labels start after the previous data and on a 2080 byte boundry
		// Each FITS keyword in all lables is store in 80 bytes (space padded to 80 if necessary)

		// Start at the beginning of the file for the main FITS label
		m_file.seekg(0, std::ios_base::beg);

		// Read the first label line (80 chars)
		// We are assuming the file pointer is set to the beginning of the first/next label
		while (m_file.read(readBuf, 80) && m_file.gcount() == 80) {

		PvlGroup *fitsLabel = new PvlGroup("FitsLabels");

		// Read the first line
		m_file.seekg(0);
		m_file.read(readBuf, 80);
		readBuf[80] = '\0';
		line = readBuf;
		place += 80;
		place = 80;

		// Process each fits label record (80 bytes) and place keyword, value pairs into PvlKeywords
		// with any associated comments
		while (line.substr(0, 3) != "END") {

		// Check for blank lines
		@@ -117,59 +130,112 @@ namespace Isis {
		}
		}
		}
		m_fitsLabel->addKeyword(label);
		fitsLabel->addKeyword(label);
		}

		// Read the next line
		m_file.seekg(place);
		// Read the next label line
		m_file.read(readBuf, 80);
		readBuf[80] = '\0';
		place += 80;
		line = readBuf;
		place += 80;
		}

		// Save off the PvlGroup and the number of records read from this label
		m_fitsLabels->push_back(fitsLabel);
		m_headerSizes->push_back((int)ceil(place / 2880.0));

		// The file pointer should be pointing at the end of the record that contained "END"
		// Move the file pointer past the padding after the "END"
		std::streamoff jump;
		jump = m_headerSizes->last() * 2880 - place;
		m_file.seekg(jump, std::ios_base::cur);

		// NOTE: For now we only handle image data (i.e., keywords BITPIX & NAXIS & NAXISx must exist)
		// Does this look like a label for a FITS image? Stop after the first label that does not
		// because we don't know how to move the file pointer past a non-image data.
		if (fitsLabel->hasKeyword("BITPIX") && fitsLabel->hasKeyword("NAXIS") &&
		fitsLabel->hasKeyword("NAXIS1")) {

		int bytesPerPixel = 0;
		bytesPerPixel = (int)((*fitsLabel)["BITPIX"]);
		bytesPerPixel = fabs(bytesPerPixel);
		bytesPerPixel /= 8;

		unsigned int axis1 = 1;
		axis1 = toInt((*fitsLabel)["NAXIS1"]);

		unsigned int axis2 = 1;
		if (fitsLabel->hasKeyword("NAXIS2")) {
		axis2 = toInt((*fitsLabel)["NAXIS2"]);
		}

		// Save off the number of header records read
		m_headers = (int)((place + 2881) / 2880);
		unsigned int axis3 = 1;
		if (fitsLabel->hasKeyword("NAXIS3")) {
		axis3 = toInt((*fitsLabel)["NAXIS3"]);
		}

		jump = (int)(ceil(bytesPerPixel * axis1 * axis2 * axis3 / 2880.0) * 2880.0);
		m_file.seekg(jump, std::ios_base::cur);
		}
		// Do we have at least on header that looks like it has image data? If so, we can continue,
		// but ignore the rest of the file because we don't know how to skip over a non-image data.
		else if (m_fitsLabels->size() > 1) {
		m_fitsLabels->pop_back();
		m_headerSizes->pop_back();
		break;
		}
		else {
		QString msg = QObject::tr("The FITS file does not contain a section header that looks "
		"like it describes an image [%1]").arg(m_name.toString());
		throw IException(IException::User, msg, _FILEINFO_);
		}
		}
		}


		/**
		* Supplies the FITS label
		* Supplies the requested FITS label
		*
		* @param FITS label after being converted to a PvlGroup
		* @param labelNumber FITS label number. zero (0) is the first/main label
		* @return PvlGroup version of a FITS label corrisponding to requested label number
		*/
		PvlGroup ProcessImportFits::fitsLabel() const {
		if (!m_fitsLabel) {
		PvlGroup ProcessImportFits::fitsLabel(int labelNumber) const {
		if (!m_fitsLabels) {
		QString msg = QObject::tr("The FITS label has not been initialized, call setFitsFile first");
		throw IException(IException::Programmer, msg, _FILEINFO_);
		}
		else if (m_fitsLabels->size() < labelNumber) {
		QString msg = QObject::tr("The requested FITS label number does not exist from file [%1]").arg(m_name.toString());
		throw IException(IException::Programmer, msg, _FILEINFO_);
		}

		return *m_fitsLabel;
		return (m_fitsLabels)[labelNumber];
		}


		/**
		* Return a populated instrument group
		*
		* @param a FITS label after being converted to a PvlGroup
		* @return an instrument group filled with keywords from the FITS label
		*/
		PvlGroup ProcessImportFits::standardInstrumentGroup() const {
		PvlGroup ProcessImportFits::standardInstrumentGroup(PvlGroup fitsLabel) const {

		// NOTE: This needs to be changed over to use translation files

		// Attempt to extract the standard instrument group keywords
		PvlGroup inst("Instrument");
		if (m_fitsLabel->hasKeyword("DATE-OBS")) {
		inst += PvlKeyword("StartTime", (*m_fitsLabel)["DATE-OBS"][0]);
		if (fitsLabel.hasKeyword("DATE-OBS")) {
		inst += PvlKeyword("StartTime", fitsLabel["DATE-OBS"][0]);
		}
		if (m_fitsLabel->hasKeyword("OBJECT")) {
		inst += PvlKeyword("Target", (*m_fitsLabel)["OBJECT"][0]);
		if (fitsLabel.hasKeyword("OBJECT")) {
		inst += PvlKeyword("Target", fitsLabel["OBJECT"][0]);
		}
		if (m_fitsLabel->hasKeyword("INSTRUME")) {
		inst += PvlKeyword("InstrumentId", (*m_fitsLabel)["INSTRUME"][0]);
		if (fitsLabel.hasKeyword("INSTRUME")) {
		inst += PvlKeyword("InstrumentId", fitsLabel["INSTRUME"][0]);
		}
		if (m_fitsLabel->hasKeyword("OBSERVER")) {
		inst += PvlKeyword("SpacecraftName", (*m_fitsLabel)["OBSERVER"][0]);
		if (fitsLabel.hasKeyword("OBSERVER")) {
		inst += PvlKeyword("SpacecraftName", fitsLabel["OBSERVER"][0]);
		}

		return inst;
		@@ -192,32 +258,34 @@ namespace Isis {
		}

		// Get the FITS labels internalized
		extractFitsLabel();
		extractFitsLabels();

		// Check to make sure it is a FITS file we can handle
		PvlGroup label = fitsLabel();
		PvlGroup label = fitsLabel(0);
		if (label["SIMPLE"][0] == "F") {
		QString msg = QObject::tr("The file [%1] can not be processed. It is an unsupported format.").
		arg(fitsFile.toString());
		throw IException(IException::User, msg, _FILEINFO_);
		}

		setProcessFileStructure(label);

		m_file.close();
		}


		/**
		* Sets all the Process file structure parameters. Mostly based on the FITS labels
		* Sets the Process file structure parameters based on the FITS labels of choice
		*
		* @param labelNumber FITS label number. zero (0) is the first/main label
		*
		*/
		void ProcessImportFits::setProcessFileStructure(PvlGroup label) {
		void ProcessImportFits::setProcessFileStructure(int labelNumber) {

		PvlGroup label = (m_fitsLabels)[labelNumber];

		SetFileHeaderBytes(m_headers * 2880);
		SetFileHeaderBytes((m_headerSizes)[labelNumber] 2880);
		SaveFileHeader();

		// Find pixel type, there are several unsupported possiblites
		// Find pixel type. NOTE: There are several unsupported possiblites
		Isis::PixelType type;
		QString msg = "";
		switch (toInt(label["BITPIX"][0])) {
		@@ -268,28 +336,20 @@ namespace Isis {
		if (label.hasKeyword("BZERO")) {
		SetBase(toDouble(label["BZERO"][0]));
		}
		else {
		SetBase(0.0);
		}
		if (label.hasKeyword("BSCALE")) {
		SetMultiplier(toDouble(label["BSCALE"][0]));
		}
		else {
		SetMultiplier(1.0);
		}

		// Byte order
		SetByteOrder(Isis::Msb);

		}






		} // end namespace Isis

isis/src/base/objs/ProcessImportFits/ProcessImportFits.h

+12 −9

Original line number	Diff line number	Diff line
		@@ -22,8 +22,11 @@
		* http://www.usgs.gov/privacy.html.
		*/


		#include "ProcessImport.h"

		template <typename T> class QList;

		namespace Isis {
		/**
		* @brief Import a FITS file
		@@ -37,7 +40,7 @@ namespace Isis {
		* @author 2013-10-08 Stuart Sides
		*
		* @internal
		*
		* @history 2014-06-06 Stuart Sides - Added ability to read and process the FITS extension
		*/

		class ProcessImportFits : public ProcessImport {
		@@ -46,16 +49,16 @@ namespace Isis {
		ProcessImportFits();
		~ProcessImportFits();

		PvlGroup standardInstrumentGroup() const;
		PvlGroup fitsLabel() const;
		PvlGroup standardInstrumentGroup(PvlGroup fitsLabel) const;
		PvlGroup fitsLabel(int labelNumber) const;
		void setFitsFile(FileName fitsFile);
		void setProcessFileStructure(int labelNumber);

		private:
		void extractFitsLabel();
		void setProcessFileStructure(PvlGroup label);
		void extractFitsLabels();

		//! Holds the PvlGroup with the converted FITS labels
		PvlGroup *m_fitsLabel;
		//! Holds the PvlGroups with the converted FITS labels from the main and all extensions
		QList<PvlGroup > m_fitsLabels;

		//! The name of the input FITS file
		FileName m_name;
		@@ -63,8 +66,8 @@ namespace Isis {
		//! The stream used to read the FITS file
		std::ifstream m_file;

		//! The number of 2880 byte header records before the first data
		int m_headers;
		//! The number of 2880 byte header records before each data section
		QList<int> *m_headerSizes;
		};
		};

isis/src/base/objs/SpiceRotation/SpiceRotation.cpp

+2 −6

Original line number	Diff line number	Diff line
		@@ -1531,13 +1531,9 @@ namespace Isis {

		// Don't read type 5 ck here
		if (ic[2] == 5) break;
		if (ic[2] != 3) {
		QString msg = "Time fetching method only works on type 3 and 5 ck";
		throw IException(IException::Programmer, msg, _FILEINFO_);
		}

		//
		// Check times for type 3 ck segment if spacecraft matches
		if (ic[0] == spCode) {
		if (ic[0] == spCode && ic[2] == 3) {
		sct2e_c((int) spCode / 1000, dc[0], &segStartEt);
		sct2e_c((int) spCode / 1000, dc[1], &segStopEt);
		NaifStatus::CheckErrors();