Initial checkin of New Horizons LORRI camera and ingest Ref# 1895, Ref# 1896, Ref# 1897 (4a2f781c) · Commits · aflab / astrogeology / ISIS3

isis/IsisPreferences

+1 −0

Changes for isis/IsisPreferences: 1 added line, 0 removed lines.
Original line number	Diff line number	Diff line
		@@ -175,6 +175,7 @@ Group = DataDirectory
		Mgs = $ISIS3DATA/mgs
		Mro = $ISIS3DATA/mro
		Near = $ISIS3DATA/near
		NewHorizons = $ISIS3DATA/newhorizons
		Odyssey = $ISIS3DATA/odyssey
		Rolo = $ISIS3DATA/rolo
		Smart1 = $ISIS3DATA/smart1

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

+11 −164

Changes for isis/src/base/apps/fits2isis/fits2isis.cpp: 11 added lines, 164 removed lines.
Original line number	Diff line number	Diff line
		@@ -4,7 +4,7 @@
		#include "IException.h"
		#include "IString.h"
		#include "OriginalLabel.h"
		#include "ProcessImport.h"
		#include "ProcessImportFits.h"
		#include "Pvl.h"
		#include "PvlGroup.h"
		#include "PvlKeyword.h"
		@@ -21,179 +21,26 @@ void IsisMain() {

		UserInterface &ui = Application::GetUserInterface();

		QString from = ui.GetFileName("FROM");
		ProcessImportFits pfits;

		// Setup to read headers/labels
		ifstream input;
		input.open(from.toAscii().data(), ios::in \| ios::binary);

		// Check stream open status
		if(!input.is_open()) {
		QString msg = "Cannot open input file [" + from + "]";
		throw IException(IException::Io, msg, _FILEINFO_);
		}

		char reading[81];
		IString line = "";
		unsigned int place = 0;
		PvlGroup labels("OriginalLabels");

		// Load first line
		input.seekg(0);
		input.read(reading, 80);
		reading[80] = '\0';
		line = reading;
		place += 80;

		// Read in and place in PvlKeywords and a PvlGroup
		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());
		// Remove up to beginning of data
		line.TrimHead(" ='");
		line.TrimTail(" ");
		if(label.name() == "COMMENT" \|\| label.name() == "HISTORY") {
		label += line.ToQt();
		}
		else {
		// Access the data without the comment if there is one
		IString value = line.Token("/");
		// Clear to end of data, including single quotes
		value.TrimTail(" '");
		label += value.ToQt();
		line.TrimHead(" ");
		// If the remaining line QString has anything, it is comments.
		if(line.size() > 0) {
		label.addComment(line.ToQt());
		// A possible format for units, other possiblites exist.
		if(line != line.Token("[")) {
		label.setUnits(line.Token("[").Token("]").ToQt());
		}
		}
		}
		labels += label;
		}
		// Load next line
		input.seekg(place);
		input.read(reading, 80);
		reading[80] = '\0';
		place += 80;
		line = reading;
		}

		// Done with stream
		input.close();

		// Its possible they could have this instead of T, in which case we won't even try
		if(labels["SIMPLE"][0] == "F") {
		QString msg = "The file [" + ui.GetFileName("FROM") + "] does not conform to the FITS standards";
		throw IException(IException::User, msg, _FILEINFO_);
		}

		ProcessImport pfits;

		pfits.SetInputFile(ui.GetFileName("FROM"));

		// Header size will be a multiple of 2880
		int multiple = (int)((place + 2881) / 2880);
		pfits.SetFileHeaderBytes(multiple * 2880);
		pfits.SaveFileHeader();

		// Find pixel type, there are several unsupported possiblites
		Isis::PixelType type;
		QString msg = "";
		switch(toInt(labels["BITPIX"][0])) {
		case 8:
		type = Isis::UnsignedByte;
		break;
		case 16:
		type = Isis::SignedWord;
		break;
		case 32:
		msg = "Signed 32 bit integer (int) pixel type is not supported at this time";
		throw IException(IException::User, msg, _FILEINFO_);
		break;
		case 64:
		msg = "Signed 64 bit integer (long) pixel type is not supported at this time";
		throw IException(IException::User, msg, _FILEINFO_);
		break;
		case -32:
		type = Isis::Real;
		break;
		case -64:
		msg = "64 bit floating point (double) pixel type is not supported at this time";
		throw IException(IException::User, msg, _FILEINFO_);
		break;
		default:
		msg = "Unknown pixel type [" + labels["BITPIX"][0] + "] cannot be imported";
		throw IException(IException::User, msg, _FILEINFO_);
		break;
		}

		pfits.SetPixelType(type);

		// It is possible to have a NAXIS value of 0 meaning no data, the file could include
		// xtensions with data, however, those aren't supported as of Oct '09
		if(toInt(labels["NAXIS"][0]) == 2) {
		pfits.SetDimensions(toInt(labels["NAXIS1"][0]), toInt(labels["NAXIS2"][0]), 1);
		}
		else if(toInt(labels["NAXIS"][0]) == 3) {
		pfits.SetDimensions(toInt(labels["NAXIS1"][0]), toInt(labels["NAXIS2"][0]),
		toInt(labels["NAXIS3"][0]));
		}
		else {
		QString msg = "NAXIS count of [" + labels["NAXIS"][0] + "] is not supported at this time";
		throw IException(IException::User, msg, _FILEINFO_);
		}

		// Base and multiplier
		if(labels.hasKeyword("BZERO")) {
		pfits.SetBase(toDouble(labels["BZERO"][0]));
		}
		if(labels.hasKeyword("BSCALE")) {
		pfits.SetMultiplier(toDouble(labels["BSCALE"][0]));
		}

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

		// Limited section of standardized keywords that could exist
		bool instGrp = false;
		PvlGroup inst("Instrument");
		if(labels.hasKeyword("DATE-OBS")) {
		instGrp = true;
		inst += PvlKeyword("StartTime", labels["DATE-OBS"][0]);
		}
		if(labels.hasKeyword("OBJECT")) {
		instGrp = true;
		inst += PvlKeyword("Target", labels["OBJECT"][0]);
		}
		if(labels.hasKeyword("INSTRUME")) {
		instGrp = true;
		inst += PvlKeyword("InstrumentId", labels["INSTRUME"][0]);
		}
		if(labels.hasKeyword("OBSERVER")) {
		instGrp = true;
		inst += PvlKeyword("SpacecraftName", labels["OBSERVER"][0]);
		}
		pfits.setFitsFile(FileName(ui.GetFileName("FROM")));

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

		// Add instrument group if any relevant data exists
		Pvl *lbls = output->label();
		if(instGrp) {
		lbls->findObject("IsisCube") += inst;
		// Add instrument group if any keywords were put into it.
		PvlGroup instGrp = pfits.standardInstrumentGroup();
		if (instGrp.keywords() > 0) {

		output->label()->findObject("IsisCube") += instGrp;
		}

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

		// Process...
		// Convert the image data
		pfits.StartProcess();
		pfits.EndProcess();
		}

isis/src/base/objs/Preference/TestPreferences

+1 −0

Changes for isis/src/base/objs/Preference/TestPreferences: 1 added line, 0 removed lines.
Original line number	Diff line number	Diff line
		@@ -176,6 +176,7 @@ Group = DataDirectory
		Messenger = $ISIS3DATA/messenger
		Mgs = $ISIS3DATA/mgs
		Mro = $ISIS3DATA/mro
		NewHorizons = $ISIS3DATA/newhorizons
		Near = $ISIS3DATA/near
		Odyssey = $ISIS3DATA/odyssey
		Rolo = $ISIS3DATA/rolo

isis/src/base/objs/ProcessImportFits/Makefile

0 → 100644

+7 −0

Changes for isis/src/base/objs/ProcessImportFits/Makefile: 7 added lines, 0 removed lines.
Original line number	Diff line number	Diff line
		ifeq ($(ISISROOT), $(BLANK))
		.SILENT:
		error:
		echo "Please set ISISROOT";
		else
		include $(ISISROOT)/make/isismake.objs
		endif
		No newline at end of file

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

0 → 100644

+295 −0

Changes for isis/src/base/objs/ProcessImportFits/ProcessImportFits.cpp: 295 added lines, 0 removed lines.
Original line number	Diff line number	Diff line
		/**
		* @file
		* $Revision: 1.4 $
		* $Date: 2009/12/17 21:13:17 $
		*
		* Unless noted otherwise, the portions of Isis written by the USGS are public
		* domain. See individual third-party library and package descriptions for
		* intellectual property information,user agreements, and related information.
		*
		* Although Isis has been used by the USGS, no warranty, expressed or implied,
		* is made by the USGS as to the accuracy and functioning of such software
		* and related material nor shall the fact of distribution constitute any such
		* warranty, and no responsibility is assumed by the USGS in connection
		* therewith.
		*
		* For additional information, launch
		* $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see
		* the Privacy & Disclaimers page on the Isis website,
		* http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on
		* http://www.usgs.gov/privacy.html.
		*/

		#include "ProcessImportFits.h"

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

		#include "Preference.h"
		#include "IException.h"
		#include "IString.h"
		#include "LineManager.h"
		#include "Pvl.h"
		#include "PvlGroup.h"
		#include "PixelType.h"
		#include "SpecialPixel.h"
		#include "UserInterface.h"

		namespace Isis {

		/**
		* Constructor for ProcessImportFits
		*/
		ProcessImportFits::ProcessImportFits() {
		m_fitsLabel = NULL;
		}


		/**
		* Destructor for ProcessImportFits
		*/
		ProcessImportFits::~ProcessImportFits() {
		delete m_fitsLabel;
		m_file.close();
		}


		/**
		* Extract the FITS label from the file
		*
		*/
		void ProcessImportFits::extractFitsLabel() {

		// 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");

		// Read in the FITS labels and convert to PVL
		char readBuf[81];
		IString line = "";
		unsigned int place = 0;

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

		// Process each fits label record (80 bytes) and place keyword, value pairs into PvlKeywords
		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
		// Remove up to beginning of data
		line.TrimHead(" =");
		line.TrimTail(" ");
		if (label.name() == "COMMENT" \|\| label.name() == "HISTORY") {
		label += line.ToQt();
		}
		else {
		// Check for a quoted value
		if (line.substr(0,1) == "'") {
		line.TrimHead("'");
		label += line.Token("'").TrimHead(" ").TrimTail(" ").ToQt();
		line.TrimHead(" '");
		}
		else {
		// Access any remaining data without the trailing comment if there is one
		IString value = line.Token("/");
		// Clear to end of data
		value.TrimTail(" ");
		label += value.ToQt();
		line.TrimHead(" ");
		}
		// If the line still has anything in it, treat it is as a comment.
		if (line.size() > 0) {
		line.TrimHead(" /");
		label.addComment(line.ToQt());
		// A possible format for units, other possiblites exist.
		if (line != line.Token("[")) {
		label.setUnits(line.Token("[").Token("]").ToQt());
		}
		}
		}
		m_fitsLabel->addKeyword(label);
		}

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

		// Save off the number of header records read
		m_headers = (int)((place + 2881) / 2880);

		}


		/**
		* Supplies the FITS label
		*
		* @param FITS label after being converted to a PvlGroup
		*/
		PvlGroup ProcessImportFits::fitsLabel() const {
		if (!m_fitsLabel) {
		QString msg = QObject::tr("The FITS label has not been initialized, call setFitsFile first");
		throw IException(IException::Programmer, msg, _FILEINFO_);
		}

		return *m_fitsLabel;
		}


		/**
		* Return a populated instrument group
		*
		*/
		PvlGroup ProcessImportFits::standardInstrumentGroup() 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 (m_fitsLabel->hasKeyword("OBJECT")) {
		inst += PvlKeyword("Target", (*m_fitsLabel)["OBJECT"][0]);
		}
		if (m_fitsLabel->hasKeyword("INSTRUME")) {
		inst += PvlKeyword("InstrumentId", (*m_fitsLabel)["INSTRUME"][0]);
		}
		if (m_fitsLabel->hasKeyword("OBSERVER")) {
		inst += PvlKeyword("SpacecraftName", (*m_fitsLabel)["OBSERVER"][0]);
		}

		return inst;
		}


		/**
		* Opens a FITS file and reads the FITS labels
		*
		* @param fitsFile Name of the FITS file to open
		*/
		void ProcessImportFits::setFitsFile(FileName fitsFile) {
		SetInputFile(fitsFile.toString()); // Make sure the file exists

		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());
		throw IException(IException::User, msg, _FILEINFO_);
		}

		// Get the FITS labels internalized
		extractFitsLabel();

		// Check to make sure it is a FITS file we can handle
		PvlGroup label = fitsLabel();
		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
		*
		*/
		void ProcessImportFits::setProcessFileStructure(PvlGroup label) {

		SetFileHeaderBytes(m_headers * 2880);
		SaveFileHeader();

		// Find pixel type, there are several unsupported possiblites
		Isis::PixelType type;
		QString msg = "";
		switch (toInt(label["BITPIX"][0])) {
		case 8:
		type = Isis::UnsignedByte;
		break;
		case 16:
		type = Isis::SignedWord;
		break;
		case 32:
		msg = "Signed 32 bit integer (int) pixel type is not supported at this time";
		throw IException(IException::User, msg, _FILEINFO_);
		break;
		case 64:
		msg = "Signed 64 bit integer (long) pixel type is not supported at this time";
		throw IException(IException::User, msg, _FILEINFO_);
		break;
		case -32:
		type = Isis::Real;
		break;
		case -64:
		msg = "64 bit floating point (double) pixel type is not supported at this time";
		throw IException(IException::User, msg, _FILEINFO_);
		break;
		default:
		msg = "Unknown pixel type [" + label["BITPIX"][0] + "] is not supported for imported";
		throw IException(IException::User, msg, _FILEINFO_);
		break;
		}

		SetPixelType(type);

		// It is possible to have a NAXIS value of 0 meaning no data, the file could include
		// xtensions with data, however, those aren't supported yet
		if (toInt(label["NAXIS"][0]) == 2) {
		SetDimensions(toInt(label["NAXIS1"][0]), toInt(label["NAXIS2"][0]), 1);
		}
		else if (toInt(label["NAXIS"][0]) == 3) {
		SetDimensions(toInt(label["NAXIS1"][0]), toInt(label["NAXIS2"][0]),
		toInt(label["NAXIS3"][0]));
		}
		else {
		QString msg = "NAXIS count of [" + label["NAXIS"][0] + "] is not supported at this time";
		throw IException(IException::User, msg, _FILEINFO_);
		}

		// Base and multiplier
		if (label.hasKeyword("BZERO")) {
		SetBase(toDouble(label["BZERO"][0]));
		}
		if (label.hasKeyword("BSCALE")) {
		SetMultiplier(toDouble(label["BSCALE"][0]));
		}

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

		}






		} // end namespace Isis