Merge branch 'dev' of github.com:USGS-Astrogeology/ISIS3 into dev (a151dcf3) · Commits · aflab / astrogeology / ISIS3

isis/src/base/apps/isis2std/isis2std.xml

+65 −73

Original line number	Diff line number	Diff line
		@@ -3,22 +3,22 @@
		<application name="isis2std" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="http://isis.astrogeology.usgs.gov/Schemas/Application/application.xsd">

		<brief>
		Exports a cube to a PNG, BMP, GIF, TIFF, JPEG, or JPEG 2000
		Exports a cube to PNG, BMP, TIFF, JPEG, or JPEG 2000
		</brief>

		<description>
		<p>
		This program exports an ISIS cube to one of several popular standard image
		formats. The current supported formats are BMP, GIF, JPEG, JP2, PNG, and TIFF.
		formats. The current supported formats are BMP, JPEG, JP2, PNG, and TIFF.
		</p>
		<p>
		This program uses TrollTech's version of the Qt Library to export BMP,
		GIF and JPEG formatted output images. For these format types, due to limitations of Qt, the
		input file size must not exceed 2 gigabytes and the only valid output bit type is 8BIT.
		This program uses TrollTech's version of the Qt Library to export BMP
		and JPEG formatted output images. For these format types, due to limitations of Qt, the
		input file size must not exceed 2 gigabytes and the only valid output bit type is 8-bit.
		</p>
		<p>
		The JPEG2000 (JP2) and TIFF formats do not depend on the Qt library. These formats do not
		have the 2 GB limitation for input files and the output bit type may be 8BIT, U16BIT or S16BIT.
		have the 2 GB limitation for input files and the output bit type may be 8-bit, U16-bit or S16-bit.
		For these formats, the writing routines output are streamed lines from the cube, and little
		of the image is held in memory at any one time, therefore increasing the processing speed to
		convert the file. It is recommended that large images are exported to JP2 or TIFF format.
		@@ -36,7 +36,7 @@
		<p>
		In addition, if the cube has Mapping labels, the program will produce a world file for use
		in Arc and/or other GIS packages. The file will have an extension that uses the first and
		last letters for the image extention and a "w". For example, .tif produces a world file
		last letters for the image extension and a "w". For example, .tif produces a world file
		extension of .tfw.
		</p>
		<p>
		@@ -118,7 +118,10 @@
		<change name="Jeffrey Covington" date="2015-02-12">
		Changed default compression of TIFF format images to no compression. Added COMPRESSION parameter to
		choose the compression algorithm for TIFF format images. Fixes #1745

		</change>
		<change name="Kaitlyn Lee" date="2018-02-08">
		Removed the option to export as a GIF because Qt does not support GIF
		exports. Fixes #1667.
		</change>
		</history>
		<category>
		@@ -149,7 +152,7 @@
		</brief>
		<description>
		Use this parameter to select the filename and band to export. For
		example, file.cub+5 will select band 5
		example, file.cub+5 will select band 5.
		</description>
		<filter>
		*.cub
		@@ -164,7 +167,7 @@
		</brief>
		<description>
		Use this parameter to select the filename and band to export. For
		example, file.cub+5 will select band 5
		example, file.cub+5 will select band 5.
		</description>
		<filter>
		*.cub
		@@ -179,7 +182,7 @@
		</brief>
		<description>
		Use this parameter to select the filename and band to export. For
		example, file.cub+5 will select band 5
		example, file.cub+5 will select band 5.
		</description>
		<filter>
		*.cub
		@@ -194,7 +197,7 @@
		</brief>
		<description>
		Use this parameter to select the filename and band to export. For
		example, file.cub+5 will select band 5
		example, file.cub+5 will select band 5.
		</description>
		<filter>
		*.cub
		@@ -209,7 +212,7 @@
		</brief>
		<description>
		Use this parameter to select the filename and band to export. For
		example, file.cub+5 will select band 5
		example, file.cub+5 will select band 5.
		</description>
		<filter>
		*.cub
		@@ -303,13 +306,13 @@
		<brief>Format of output image</brief>
		<description>
		This parameter is used to select the output format. It can be one of
		PNG, BMP, JPEG, TIF, GIF, or JP2. Note that not all formats may be
		PNG, BMP, JPEG, TIF, or JP2. Note that not all formats may be
		available. It will depend on your installation of the Qt libraries.
		<p>
		In addition, if the cube has Mapping labels, the program will produce
		a world file for use in Arc and/or other GIS packages. The file will
		have an extension that uses the first and last letters for the image
		extention and a "w". For example, .tif produces a world file extension of .tfw.
		extension and a "w". For example, .tif produces a world file extension of .tfw.
		</p>
		</description>

		@@ -336,17 +339,6 @@
		<item>COMPRESSION</item>
		</exclusions>
		</option>
		<option value="GIF">
		<brief>Output image will be GIF</brief>
		<description>
		The output image is in GIF (Graphics Interchange Format) format. The default
		extension for this format is "gif."
		</description>
		<exclusions>
		<item>BITTYPE</item>
		<item>COMPRESSION</item>
		</exclusions>
		</option>
		<option value="TIFF">
		<brief>Output image will be TIFF</brief>
		<description>
		@@ -400,7 +392,7 @@
		<brief>Bit type of output file</brief>
		<description>
		This parameter allows the userPackBits is also known as Macintosh RLE. to set the bit type of the output image.
		Some FORMAT values will only allow 8BIT outputs.
		Some FORMAT values will only allow 8-bit outputs.
		16 bit signed (-32767=black, 32768=white)
		</description>
		<list>
		@@ -693,7 +685,7 @@
		</brief>
		<description>
		This example creates an output TIFF format file from 3 bands of an ISIS cube, designated
		red, green, and blue using a linear stretch and 8 bit output type. A histogram is created
		red, green, and blue using a linear stretch and 8-bit output type. A histogram is created
		from the input values. Using this histogram, we determine the minimum value to be any DN
		in the bottom 0.2% of the data. These DNs will be set to black in the output. Similarly,
		the maximum value is any DN in the top 99.8% of the data and these DNs will be set to white.
		@@ -715,7 +707,7 @@
		<description>
		This image show the graphical user interface for this program.
		</description>
		<thumbnail height="200" width="142" src="assets/thumbs/isis2stdGUI.jpg" caption="isis2std with RGB input and 8BIT output"/>
		<thumbnail height="200" width="142" src="assets/thumbs/isis2stdGUI.jpg" caption="isis2std with RGB input and 8-bit output"/>
		</image>
		</guiInterface>
		</guiInterfaces>
		@@ -768,7 +760,7 @@
		Output image.
		</brief>
		<description>
		The 8 bit output image, in TIFF format, created using the input red, green, and blue channels.
		The 8-bit output image, in TIFF format, created using the input red, green, and blue channels.
		</description>
		<thumbnail height="150" width="200" src="assets/thumbs/rgbTIFFoutput.jpg" caption="The color output image."/>
		<parameterName>TO</parameterName>

isis/src/tgo/apps/tgocassisstitch/tgocassisstitch.cpp

+19 −21

Original line number	Diff line number	Diff line
		@@ -117,6 +117,10 @@ QMap<QString, FileName> sortFramelets(FileName frameletListFile) {
		*
		* @param frameletList A list of the framelet cubes to stitch together
		* @param frameFileName The file name of the output frame cube
		*
		* @internal
		* @history 2018-02-15 Adam Goins - Modified stitchFrame to store the Archive
		* group for ingested framelets. Fixes #5333.
		*/
		void stitchFrame(QList<FileName> frameletList, FileName frameFileName) {
		// Create the frame cube based on the first framelet cube
		@@ -130,22 +134,13 @@ void stitchFrame(QList<FileName> frameletList, FileName frameFileName) {
		frameCube.create( frameFileName.expanded() );

		// Setup the label for the new cube
		PvlGroup archGroup = firstFrameletCube.group("Archive");
		PvlGroup kernGroup = firstFrameletCube.group("Kernels");
		PvlGroup instGroup = firstFrameletCube.group("Instrument");
		PvlGroup bandBinGroup("BandBin");
		if ( instGroup.hasKeyword("Filter") ) {
		instGroup["Filter"].setValue("FULLCCD");
		}
		if ( archGroup.hasKeyword("ProductId") ) {
		archGroup.deleteKeyword("ProductId");
		}
		if ( archGroup.hasKeyword("FileName") ) {
		archGroup.deleteKeyword("FileName");
		}
		if ( archGroup.hasKeyword("Window_Count") ) {
		archGroup.deleteKeyword("Window_Count");
		}

		bandBinGroup += PvlKeyword("FilterName", "FULLCCD");

		// Setup Stitch group keywords
		@@ -203,6 +198,10 @@ void stitchFrame(QList<FileName> frameletList, FileName frameFileName) {
		stitchGroup["FilterWidths"] += frameletBandBin["Width"];
		stitchGroup["FilterIkCodes"] += frameletBandBin["NaifIkCode"];

		PvlGroup archiveGroup = frameletCube->group("Archive");
		archiveGroup.setName("Archive" + QString(frameletBandBin["FilterName"]));
		frameCube.putGroup(archiveGroup);

		AlphaCube frameletAlphaCube(*frameletCube);
		stitchGroup["FilterStartSamples"] += toString(frameletAlphaCube.AlphaSample(0.0));
		stitchGroup["FilterSamples"] += toString(frameletAlphaCube.BetaSamples());
		@@ -226,7 +225,6 @@ void stitchFrame(QList<FileName> frameletList, FileName frameFileName) {
		// Finalize the frame cube label
		frameCube.putGroup(instGroup);
		frameCube.putGroup(kernGroup);
		frameCube.putGroup(archGroup);
		frameCube.putGroup(bandBinGroup);
		frameCube.putGroup(stitchGroup);
		}

isis/src/tgo/apps/tgocassisstitch/tgocassisstitch.xml

+3 −0

Original line number	Diff line number	Diff line
		@@ -26,6 +26,9 @@
		Backward Compatibility Issue: Changed name from stitch to tgocassisstitch and
		changed output parameter name "TO" to "OUTPUTPREFIX."
		</change>
		<change name="Adam Goins" date="2018-02-15">
		Modified stitchFrame to store the Archive group for ingested framelets. Fixes #5333.
		</change>
		</history>

		<category>

isis/src/tgo/apps/tgocassisunstitch/tgocassisunstitch.cpp

+53 −27

Original line number	Diff line number	Diff line
		@@ -30,6 +30,10 @@ using namespace Isis;
		*
		* @internal
		* @history 2017-09-15 Kristin Berry - Original Version
		*
		* @history 2018-02-15 Adam Goins - Modified unstitch to parse the archive group
		* from the stitched frame. Changed "Name" to "FilterName"
		* in bandBin group.
		*/
		struct FilterInfo : public PushFrameCameraCcdLayout::FrameletInfo {
		FilterInfo() : FrameletInfo(), m_wavelength(0), m_width(0) { }
		@@ -75,13 +79,14 @@ void IsisMain() {
		PvlKeyword filterLines = inputLabel->findKeyword("FilterLines", PvlObject::Traverse);
		PvlKeyword filterWavelength = inputLabel->findKeyword("FilterCenters", PvlObject::Traverse);
		PvlKeyword filterWidth = inputLabel->findKeyword("FilterWidths", PvlObject::Traverse);

		for (int i = 0; i < filterKey.size(); i++) {
		g_frameletInfoList.append(FilterInfo(filterIkCodes[i].toInt(),
		filterKey[i],
		filterStartSamples[i].toInt(),
		filterStartSamples[i].toDouble(),
		filterStartLines[i].toDouble(),
		filterSamples[i].toInt(),
		filterLines[i].toInt(),
		filterSamples[i].toDouble(),
		filterLines[i].toDouble(),
		filterWavelength[i].toDouble(),
		filterWidth[i].toDouble()));
		}
		@@ -151,16 +156,29 @@ void IsisMain() {
		for (int i = 0; i < g_outputCubes.size(); i++) {
		progress.CheckStatus();
		for (int j = 0; j < inputLabel->findObject("IsisCube").groups(); j++) {
		g_outputCubes[i]->putGroup(inputLabel->findObject("IsisCube").group(j));
		PvlGroup group = inputLabel->findObject("IsisCube").group(j);

		// The stitched frame has ArchiveRED, ArchiveNIR, ArchivePAN, and ArchiveBLU.
		// We won't add the archive group unless
		if ( group.name().contains("Archive") &&
		group.name() != "Archive" + g_frameletInfoList[i].m_filterName ) {
		continue;
		}

		g_outputCubes[i]->putGroup(group);

		}
		// Update the labels
		Pvl *frameletLabel = g_outputCubes[i]->label();
		frameletLabel->findGroup("Instrument", PvlObject::Traverse).addKeyword(PvlKeyword("Filter",
		g_frameletInfoList[i].m_filterName), PvlObject::Replace);

		// Sets the name from ArchiveRED (or NIR, BLU, PAN) to just "Archive" in the unstitched cube.
		frameletLabel->findGroup("Archive" + g_frameletInfoList[i].m_filterName, PvlObject::Traverse).setName("Archive");

		PvlGroup &bandBin = frameletLabel->findGroup("BandBin", PvlObject::Traverse);

		bandBin.addKeyword(PvlKeyword("Name", g_frameletInfoList[i].m_filterName),
		bandBin.addKeyword(PvlKeyword("FilterName", g_frameletInfoList[i].m_filterName),
		PvlObject::Replace);
		bandBin.addKeyword(PvlKeyword("Center", toString(g_frameletInfoList[i].m_wavelength)));
		bandBin.addKeyword(PvlKeyword("Width", toString(g_frameletInfoList[i].m_width)));
		@@ -209,21 +227,29 @@ void IsisMain() {
		* Separates each of the framelets of the input cube into their own separate output cube.
		*
		* @param in A reference to the input Buffer to process.
		* @internal
		* @history 2018-02-09 Adam Goins - Modified the second operand of the if() statement
		* from in.Line() < [...] to inLine() <= [...] to write all lines
		* up to and including the last line. Fixes an error where the last lines
		* written would be a line of null pixel DN's.
		*
		* @history 2018-02-14 Adam Goins - Modified the copying of the data in the buffer to include
		* the sample offset (m_startSample) for a cube.
		*/
		void unstitchFullFrame(Buffer &in) {
		for (int i=0; i < g_frameletInfoList.size(); i++) {

		if (in.Line() >= g_frameletInfoList[i].m_startLine
		&& in.Line() < (g_frameletInfoList[i].m_startLine + g_frameletInfoList[i].m_lines)) {
		&& in.Line() <= (g_frameletInfoList[i].m_startLine + g_frameletInfoList[i].m_lines)) {
		int outputCubeLineNumber = (in.Line()-1) % g_frameletInfoList[i].m_startLine + 1;
		LineManager mgr(*g_outputCubes[i]);
		mgr.SetLine(outputCubeLineNumber, 1);

		for (int j = 0; j < mgr.size(); j++) {
		mgr[j] = in[j];
		mgr[j] = in[j + g_frameletInfoList[i].m_startSample];
		}
		g_outputCubes[i]->write(mgr);
		return;
		}
		}
		}

isis/src/tgo/apps/tgocassisunstitch/tgocassisunstitch.xml

+16 −9

Original line number	Diff line number	Diff line
		@@ -23,6 +23,13 @@
		but containing other '.'s in the string to not strip off everything after the last period. For example, if the
		user inputs CAS-MCO-2016-11-22T16:10:43.505 as the OUTPUTPREFIX, now the 505 will now be retained.
		</change>
		<change name="Adam Goins" date="2018-02-15">
		Updated the application to include the sample offsets when processing lines from the stitched
		frame into output cubes.
		</change>
		<change name="Adam Goins" date="2018-02-15">
		Modified unstitchFrame to parse the Archive group for each framelet.
		</change>

		</history>