Added ability to save extra FITS labels (with no image data) upon ingestion... (5a1c430a) · Commits · aflab / astrogeology / ISIS3

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

+2 −2

Original line number	Diff line number	Diff line
		@@ -44,7 +44,7 @@ void IsisMain() {
		Cube *output = pfits.SetOutputCube("TO");

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

		output->label()->findObject("IsisCube") += instGrp;
		@@ -52,7 +52,7 @@ void IsisMain() {

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

isis/src/base/apps/fits2isis/fits2isis.xml

+6 −3

Original line number	Diff line number	Diff line
		@@ -15,7 +15,7 @@

		<history>
		<change name="Mackenzie Boyd" date="2009-10-27">
		Original version
		Original version.
		</change>
		<change name="Stuart Sides" date="2014-08-29">
		Added the ability to read image extensions.
		@@ -24,6 +24,9 @@
		Added the ability to set the organization of the input file to BIL, BSQ, or BIP.
		Added tests for these new options.
		</change>
		<change name="Jeannie Backer and Kaj Williams" date="2017-07-07">
		Modified to reflect ProcessImportFits method name change from fitsLabel to fitsImageLabel.
		</change>
		</history>

		<seeAlso>

isis/src/base/objs/ProcessExportPds/ProcessExportPds.h

+3 −1

Original line number	Diff line number	Diff line
		@@ -41,6 +41,8 @@ namespace Isis {
		* functionality is added to deal with the new start byte values for the
		* tables.
		*
		* @ingroup HighLevelCubeIO
		*
		* @author 2006-09-05 Stuart Sides
		*
		* @internal

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

+173 −87

Original line number	Diff line number	Diff line
		@@ -22,11 +22,11 @@

		#include "ProcessImportFits.h"

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

		#include <QDebug>
		#include <QString>

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

		#include "IException.h"
		@@ -45,7 +45,8 @@ namespace Isis {
		* Constructor for ProcessImportFits
		*/
		ProcessImportFits::ProcessImportFits() {
		m_fitsLabels = NULL;
		m_fitsImageLabels = NULL;
		m_extraFitsLabels = NULL;
		m_headerSizes = NULL;
		m_dataStarts = NULL;
		}
		@@ -55,7 +56,8 @@ namespace Isis {
		* Destructor for ProcessImportFits
		*/
		ProcessImportFits::~ProcessImportFits() {
		delete m_fitsLabels;
		delete m_fitsImageLabels;
		delete m_extraFitsLabels;
		delete m_headerSizes;
		delete m_dataStarts;
		m_file.close();
		@@ -63,24 +65,26 @@ namespace Isis {


		/**
		* Extract all the FITS labels from the file. This includes the labels for the main and each
		* extensions
		* Extract all the FITS labels from the file. This includes the image labels for the main
		* and each extensions as well as any extras.
		*
		*/
		void ProcessImportFits::extractFitsLabels() {

		m_fitsLabels = new QList< PvlGroup * >;
		m_fitsImageLabels = new QList< PvlGroup * >;
		m_extraFitsLabels = new QList< PvlGroup * >;
		m_headerSizes = new QList < int >;
		m_dataStarts = new QList < int >;

		// Process each FITS label area. Storing each in its own PvlGroup
		// Process each FITS label area, storing each in its own PvlGroup.
		char readBuf[81];
		IString line = "";
		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)
		// The main FITS label starts at the beginning of the file.
		// FITS extension labels start after the previous data and on a 2880 byte boundry
		// Each FITS keyword in all lables is stored 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);
		@@ -96,13 +100,18 @@ namespace Isis {
		place = 80;

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

		// Check for blank lines
		if (line.substr(0, 1) != " " && line.substr(0, 1) != "/") {
		// Name of keyword
		PvlKeyword label(line.Token(" =").ToQt()); // Stop on spaces OR equal sign
		if (QString::compare(label.name(), "OBJECT", Qt::CaseInsensitive) == 0) {
		label.setName("TARGET");
		label.addComment("NOTE: This keyword name was changed from 'OBJECT' in the original "
		"fit header file.");
		}
		// Remove up to beginning of data
		line.TrimHead(" =");
		line.TrimTail(" ");
		@@ -145,8 +154,8 @@ namespace Isis {
		}

		// 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));
		m_fitsImageLabels->append(fitsLabel);
		m_headerSizes->append((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" (i.e., points to start of data)
		@@ -154,14 +163,15 @@ namespace Isis {
		jump = m_headerSizes->last() * 2880 - place;
		m_file.seekg(jump, std::ios_base::cur);

		m_dataStarts->push_back(m_file.tellg());
		m_dataStarts->append(m_file.tellg());

		// 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 extension.
		if (fitsLabel->hasKeyword("BITPIX") && fitsLabel->hasKeyword("NAXIS") &&
		fitsLabel->hasKeyword("NAXIS1")) {
		if (fitsLabel->hasKeyword("BITPIX") && fitsLabel->hasKeyword("NAXIS")) {

		// This section can only handle image data
		// (i.e., keywords BITPIX & NAXIS & NAXISx must exist).
		if((int)fitsLabel->findKeyword("NAXIS") > 0) {
		int bytesPerPixel = 0;
		bytesPerPixel = (int)((*fitsLabel)["BITPIX"]);
		bytesPerPixel = std::abs(bytesPerPixel);
		@@ -183,56 +193,120 @@ namespace Isis {
		jump = (int)(ceil(bytesPerPixel * axis1 * axis2 * axis3 / 2880.0) * 2880.0);
		m_file.seekg(jump, std::ios_base::cur);
		}
		else {
		// Note: this will allow us to read extra label sections that have 0 axes,
		// but has image-related info (so BITPIX and NAXIS keywords exist). This
		// includes informational labels, as seen at the beginning of hayabusa2
		// images in this case, there is NO DATA, so no jump should be needed to
		// get to the next section.
		PvlGroup *extraLabelGroup = m_fitsImageLabels->last();
		extraLabelGroup->setName("FitsExtras");
		m_extraFitsLabels->append(extraLabelGroup);

		m_fitsImageLabels->removeLast();
		m_headerSizes->removeLast();
		m_dataStarts->removeLast();
		}
		}
		// 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();
		m_dataStarts->pop_back();
		else if (m_fitsImageLabels->size() > 1) {
		m_fitsImageLabels->removeLast();
		m_headerSizes->removeLast();
		m_dataStarts->removeLast();
		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());
		QString msg = QObject::tr("The FITS file does not contain a section header that appears "
		"to describe an image [%1].").arg(m_name.toString());
		throw IException(IException::User, msg, _FILEINFO_);
		}
		}
		}


		/**
		* Supplies the extra FITS label corresponding to the given index. Zero
		* returns the first label in the FITS header that has no data. To access
		* image labels, call fitsImageLabel().
		*
		* @see fitsImageLabel()
		*
		* @param labelNumber The index to the extra FITS header label.
		*
		* @return PvlGroup version of a FITS label corresponding to requested label number.
		*/
		PvlGroup ProcessImportFits::extraFitsLabel(int labelNumber) const {
		if (labelNumber >= m_extraFitsLabels->size()) {
		QString msg = QObject::tr("The requested label number [%1], from file [%2] is "
		"past the last extra group found in this FITS file. "
		"Extra label count is [%3]").arg(labelNumber).
		arg(m_name.expanded()).arg(m_extraFitsLabels->size()-1);
		throw IException(IException::User, msg, _FILEINFO_);
		}

		if (!m_extraFitsLabels) {
		QString msg = QObject::tr("The FITS label has not been initialized, "
		"call setFitsFile() first.");
		throw IException(IException::Programmer, msg, _FILEINFO_);
		}
		else if (m_extraFitsLabels->size() < labelNumber) {
		QString msg = QObject::tr("The requested FITS label number "
		"was not found in file [%1].").arg(m_name.toString());
		throw IException(IException::Programmer, msg, _FILEINFO_);
		}

		return (m_extraFitsLabels)[labelNumber];
		}


		/**
		* Supplies the requested FITS label
		* Supplies the FITS image label corresponding to the given index. Zero
		* returns the first label that precedes actual image data. Extra labels that
		* have no data can be accessed by calling extraFitsLabel().
		*
		* @see extraFitsLabel()
		*
		* @param labelNumber FITS label number. zero (0) is the first/main label
		* @return PvlGroup version of a FITS label corrisponding to requested label number
		* @param labelNumber The index to the FITS header image label.
		*
		* @return PvlGroup version of a FITS label corresponding to requested label number.
		*/
		PvlGroup ProcessImportFits::fitsLabel(int labelNumber) const {
		PvlGroup ProcessImportFits::fitsImageLabel(int labelNumber) const {

		if (labelNumber >= m_fitsLabels->size()) {
		if (labelNumber >= m_fitsImageLabels->size()) {
		QString msg = QObject::tr("The requested label number [%1], from file [%2] is "
		"past the last image in this FITS file. Image count is [%3]").arg(labelNumber).
		arg(m_name.expanded()).arg(m_fitsLabels->size()-1);
		"past the last image group found in this FITS file. "
		"Image label count is [%3]").arg(labelNumber).
		arg(m_name.expanded()).arg(m_fitsImageLabels->size()-1);
		throw IException(IException::User, msg, _FILEINFO_);
		}

		if (!m_fitsLabels) {
		QString msg = QObject::tr("The FITS label has not been initialized, call setFitsFile first");
		if (!m_fitsImageLabels) {
		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());
		else if (m_fitsImageLabels->size() < labelNumber) {
		QString msg = QObject::tr("The requested FITS label number "
		"was not found in file [%1].").arg(m_name.toString());
		throw IException(IException::Programmer, msg, _FILEINFO_);
		}

		return (m_fitsLabels)[labelNumber];
		return (m_fitsImageLabels)[labelNumber];
		}


		/**
		* Return a populated instrument group
		* Return a PVL instrument group populated with expected default values.
		*
		* NOTE: These values are not appropriate for all missions. See specific
		* mission documentation to verify that these are the keywords needed.
		*
		* @param a FITS label after being converted to a PvlGroup
		* @return an instrument group filled with keywords from the FITS label
		* @param fitsLabel A PVL group containing keywords from the FITS label.
		*
		* @return PvlGroup An ISIS cube instrument group filled with keywords from
		* the given FITS label.
		*/
		PvlGroup ProcessImportFits::standardInstrumentGroup(PvlGroup fitsLabel) const {

		@@ -243,8 +317,8 @@ namespace Isis {
		if (fitsLabel.hasKeyword("DATE-OBS")) {
		inst += PvlKeyword("StartTime", fitsLabel["DATE-OBS"][0]);
		}
		if (fitsLabel.hasKeyword("OBJECT")) {
		inst += PvlKeyword("Target", fitsLabel["OBJECT"][0]);
		if (fitsLabel.hasKeyword("TARGET")) {
		inst += PvlKeyword("Target", fitsLabel["TARGET"][0]);
		}
		if (fitsLabel.hasKeyword("INSTRUME")) {
		inst += PvlKeyword("InstrumentId", fitsLabel["INSTRUME"][0]);
		@@ -258,9 +332,10 @@ namespace Isis {


		/**
		* Opens a FITS file and reads the FITS labels
		* Opens a FITS image file with header and reads the FITS labels. Note:
		* This method does not handle detached label files.
		*
		* @param fitsFile Name of the FITS file to open
		* @param fitsFile Name of the FITS file to open.
		*/
		void ProcessImportFits::setFitsFile(FileName fitsFile) {
		m_name = fitsFile;
		@@ -270,7 +345,8 @@ namespace Isis {
		m_file.open(fitsFile.expanded().toLocal8Bit().constData(), std::ios::in \| std::ios::binary);

		if (!m_file.is_open()) {
		QString msg = QObject::tr("Unable to open FITS formatted file [%1]").arg(fitsFile.toString());
		QString msg = QObject::tr("Unable to open FITS formatted file [%1].")
		.arg(fitsFile.toString());
		throw IException(IException::User, msg, _FILEINFO_);
		}

		@@ -278,9 +354,10 @@ namespace Isis {
		extractFitsLabels();

		// Check to make sure it is a FITS file we can handle
		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.").
		PvlGroup label = fitsImageLabel(0);
		if (label.hasKeyword("SIMPLE") && label["SIMPLE"][0] == "F") {
		QString msg = QObject::tr("The file [%1] cannot be processed. "
		"It is an unsupported format.").
		arg(fitsFile.toString());
		throw IException(IException::User, msg, _FILEINFO_);
		}
		@@ -290,29 +367,29 @@ namespace Isis {


		/**
		* Sets the Process file structure parameters based on the FITS labels of choice. NOTE: The
		* (DataPrefixBytes + DataSuffixByte) / PixelSize is subtracted from the number of samples before
		* the output file is created.
		* Sets the Process file structure parameters based on the given image label index.
		*
		* NOTE: The (DataPrefixBytes + DataSuffixByte) / PixelSize is subtracted from the number of
		* samples before the output file is created.
		*
		* @param labelNumber FITS label number. Zero indicates the first/main label, one indicates the
		* first extension, etc...
		* @param labelNumber FITS image index. Zero indicates the first image label, one indicates
		* the first image extension, etc...
		*
		*/
		void ProcessImportFits::setProcessFileStructure(int labelNumber) {

		if (labelNumber >= m_fitsLabels->size()) {
		if (labelNumber >= m_fitsImageLabels->size()) {
		QString msg = QObject::tr("The requested label number [%1], from file [%2] is "
		"past the last image in this FITS file [%3]").arg(labelNumber).
		arg(InputFile()).arg(m_fitsLabels->size()-1);
		"past the last image in this FITS file [%3].").arg(labelNumber).
		arg(InputFile()).arg(m_fitsImageLabels->size()-1);
		throw IException(IException::User, msg, _FILEINFO_);
		}

		PvlGroup label = (m_fitsLabels)[labelNumber];
		PvlGroup label = (m_fitsImageLabels)[labelNumber];

		// Set the ProcessImport to skip over all the previous images and their labels and the label for
		// this image. Don't save this info (think memory)
		SetFileHeaderBytes((*m_dataStarts)[labelNumber]);
		//SaveFileHeader();

		// Find pixel type. NOTE: There are several unsupported possiblites
		Isis::PixelType type;
		@@ -331,14 +408,14 @@ namespace Isis {
		type = Isis::Real;
		break;
		case 64:
		msg = "Signed 64 bit integer (long) pixel type is not supported at this time";
		msg = "Signed 64-bit integer (long) pixel type is not supported for FITS imports.";
		throw IException(IException::User, msg, _FILEINFO_);
		break;
		case -64:
		type = Isis::Double;
		break;
		default:
		msg = "Unknown pixel type [" + label["BITPIX"][0] + "] is not supported for imported";
		msg = "Unknown pixel type [" + label["BITPIX"][0] + "] is not supported for FITS imports.";
		throw IException(IException::User, msg, _FILEINFO_);
		break;
		}
		@@ -354,38 +431,47 @@ namespace Isis {
		// the number of samples.
		if (Organization() == BSQ) {
		if (toInt(label["NAXIS"][0]) == 2) {
		SetDimensions(toInt(label["NAXIS1"][0]) - (DataPrefixBytes()+DataSuffixBytes())/SizeOf(type),
		SetDimensions(toInt(label["NAXIS1"][0])
		- (DataPrefixBytes()+DataSuffixBytes())/SizeOf(type),
		toInt(label["NAXIS2"][0]), 1);
		}
		else if (toInt(label["NAXIS"][0]) == 3) {
		SetDimensions(toInt(label["NAXIS1"][0]) - (DataPrefixBytes()+DataSuffixBytes())/SizeOf(type),
		SetDimensions(toInt(label["NAXIS1"][0])
		- (DataPrefixBytes()+DataSuffixBytes())/SizeOf(type),
		toInt(label["NAXIS2"][0]), toInt(label["NAXIS3"][0]));
		}
		else {
		QString msg = "NAXIS count of [" + label["NAXIS"][0] + "] is not supported at this time";
		QString msg = "NAXIS count of ["
		+ label["NAXIS"][0]
		+ "] is not supported for FITS imports.";
		throw IException(IException::User, msg, _FILEINFO_);
		}
		}
		else if (Organization() == BIL) {
		if (toInt(label["NAXIS"][0]) == 2) {
		SetDimensions(toInt(label["NAXIS1"][0]) - (DataPrefixBytes()+DataSuffixBytes())/SizeOf(type),
		SetDimensions(toInt(label["NAXIS1"][0])
		- (DataPrefixBytes()+DataSuffixBytes())/SizeOf(type),
		1, toInt(label["NAXIS2"][0]));
		}
		else if (toInt(label["NAXIS"][0]) == 3) {
		SetDimensions(toInt(label["NAXIS1"][0]) - (DataPrefixBytes()+DataSuffixBytes())/SizeOf(type),
		SetDimensions(toInt(label["NAXIS1"][0])
		- (DataPrefixBytes()+DataSuffixBytes())/SizeOf(type),
		toInt(label["NAXIS3"][0]), toInt(label["NAXIS2"][0]));
		}
		else {
		QString msg = "NAXIS count of [" + label["NAXIS"][0] + "] is not supported at this time";
		QString msg = "NAXIS count of ["
		+ label["NAXIS"][0]
		+ "] is not supported for FITS imports.";
		throw IException(IException::User, msg, _FILEINFO_);
		}
		}
		else if (Organization() == BIP) {
		QString msg = "BIP (Band interleaved by pixel) organization is not supported at this time.";
		QString msg = "BIP (Band Interleaved by Pixel) "
		"organization is not supported for FITS imports.";
		throw IException(IException::User, msg, _FILEINFO_);
		}
		else {
		QString msg = "Unknown organization is not supported.";
		QString msg = "Unknown organization is not supported for FITS imports.";
		throw IException(IException::User, msg, _FILEINFO_);
		}

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

+22 −20

Original line number	Diff line number	Diff line
		@@ -29,11 +29,11 @@ template <typename T> class QList;

		namespace Isis {
		/**
		* @brief Import a FITS file
		* @brief Import a FITS file.
		*
		* This class allows a programmer to develop application programs which import Fits cubes and
		* mangles the the FITS label into appropriate ISIS labels. The entire FITS label is converted
		* to an ISIS PVL, allowing the programmer to interagate it with existing ISIS tools.
		* This class allows a programmer to develop application programs which import FITS cubes and
		* mangles the FITS label into appropriate ISIS labels. The entire FITS label is converted
		* to an ISIS PVL, allowing the programmer to interrogate it with existing ISIS tools.
		*
		* @ingroup HighLevelCubeIO
		*
		@@ -45,7 +45,11 @@ namespace Isis {
		* @history 2015-06-02 Kristin Berry - Added error for use of unsupported BIP organization.
		* @history 2016-04-20 Jeannie Backer - Merged Janet Barret's changes to handle SignedInteger
		* imports. Brought code closer to coding standards.
		*
		* @history 2017-07-07 Jeannie Backer and Kaj Williams - Modified extractFitsLabels() to
		* handle labels with extra image information but no image data. Changed
		* fitsLabel() method name to fitsImageLabel(). Added extraFitsLabel().
		* Brought code closer to coding standards. Improved documentation
		* and error messages.
		*/

		class ProcessImportFits : public ProcessImport {
		@@ -55,27 +59,25 @@ namespace Isis {
		virtual ~ProcessImportFits();

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

		private:
		void extractFitsLabels();

		//! 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;

		//! The stream used to read the FITS file
		std::ifstream m_file;

		//! The number/count of 2880 byte header records for each header section
		QList<int> *m_headerSizes;

		//! The starting byte of the data for each image
		QList<int> *m_dataStarts;
		QList<PvlGroup > m_fitsImageLabels; /**< Holds the PvlGroups with the converted FITS image
		labels from the main and all extensions.*/
		QList<PvlGroup > m_extraFitsLabels; /**< Holds the PvlGroups with the converted extra FITS
		labels from the main and all extensions. This
		included label that contain BITPIX and NAXIS
		keyword but are not followed by image data.*/
		FileName m_name; /*< The name of the input FITS file./
		std::ifstream m_file; /*< The stream used to read the FITS file./
		QList<int> m_headerSizes; /*< The number, or count, of 2880 byte header records
		for each image header section.*/
		QList<int> m_dataStarts; /< The starting byte of the data for each image./
		};
		};