Merge branch 'dev' of github.com:USGS-Astrogeology/ISIS3 into pep4xmlfix (b6e54010) · Commits · aflab / astrogeology / ISIS3

.gitignore

+1 −0

Original line number	Diff line number	Diff line
		@@ -27,6 +27,7 @@ object_script.*.Debug
		*_plugin_import.cpp
		*.moc
		ui_*.h
		*.html

		# ignore all files created by squish coco
		*csmes

isis/src/base/objs/PvlTranslationTable/PvlTranslationTable.cpp

+1 −1

Original line number	Diff line number	Diff line
		@@ -234,7 +234,7 @@ namespace Isis {
		const PvlKeyword &key = *it;
		// compare the value from the input file to the second value of each Translation in the trans file.
		// ignore cases for input values
		if((QString) key[1] == tmpFValue) {
		if(QString::compare((QString) key[1], tmpFValue, Qt::CaseInsensitive) == 0) {
		return key[0];
		}
		else if((QString) key[1] == "*") {

isis/src/control/apps/cnetbin2pvl/cnetbin2pvl.xml

+14 −14

Original line number	Diff line number	Diff line
		@@ -8,8 +8,8 @@
		<description>
		<p>
		This program converts an Isis3 control network file from binary into a human readable
		utf8 pvl formatted file. The output pvl will be written as the latest Pvl version.
		The most recent Pvl template can be found in the Control data directory under templates/controlnetworks.
		UTF-8 pvl formatted file. The output .pvl will be written as the latest PVL version.
		The most recent PVL template can be found in the Control data directory under templates/controlnetworks.
		</p>
		</description>

		@@ -28,8 +28,8 @@
		Added a basic progress
		</change>
		<change name="Adam Goins" date="2018-01-24">
		Updated Description to reflect utf file format.
		Added link to current Pvl template.
		Updated Description to reflect UTF-8 file format.
		Added link to current PVL template.
		Added user example.
		</change>
		</history>
		@@ -54,10 +54,10 @@
		<type>filename</type>
		<fileMode>output</fileMode>
		<brief>
		Pvl formated control net file
		PVL formatted control net file
		</brief>
		<description>
		A control net file in the Pvl format.
		A control network file in the PVL format.
		</description>
		<filter>
		.cnet .pvl
		@@ -67,14 +67,14 @@
		</groups>
		<examples>
		<example>
		<brief>Converting a binary Control Network to a Pvl network.</brief>
		<description>A binary V0001 Control Network converted to the latest Pvl network.</description>
		<brief>Converting a binary Control Network to a PVL network.</brief>
		<description>A binary V0001 Control Network converted to the latest PVL network.</description>
		<terminalInterface>
		<commandLine>
		from=/usgs/cpkgs/isis3/data/control/testData/unitTest_ControlNetVersioner_ProtoNetwork1_ProtoV0001.net to=PvlNetwork.pvl
		</commandLine>
		<description>
		In this example we are converting a binary V0001 network from the test data area to a Pvl network.
		In this example, we are converting a binary V0001 network from the test data area to a PVL network.
		</description>
		</terminalInterface>
		<inputImages>
		@@ -89,20 +89,20 @@
		</inputImages>
		<outputImages>
		<image src="assets/image/OutputNetwork.png" width="500" height="500">
		<brief>Output Pvl network from cnetbin2pvl</brief>
		<brief>Output PVL network from cnetbin2pvl</brief>
		<description>
		This is the Pvl network that results from running cnetbin2pvl.
		This is the PVL network that results from running cnetbin2pvl.
		</description>
		<thumbnail caption="Output Pvl network that was made from the existing network." src="assets/image/OutputNetwork.png" width="200" height="165"/>
		<thumbnail caption="Output PVL network that was made from the existing network." src="assets/image/OutputNetwork.png" width="200" height="165"/>
		<parameterName>TO</parameterName>
		</image>
		</outputImages>
		<guiInterfaces>
		<guiInterface>
		<image width="500" height="500" src="assets/image/cnetbin2pvlGUI.png">
		<brief>Example Gui</brief>
		<brief>Example GUI</brief>
		<description>
		Screenshot of GUI with parameters filled to convert a binary Control Network to a Pvl network.
		Screenshot of GUI with parameters filled to convert a binary Control Network to a PVL network.
		</description>
		<thumbnail width="200" height="165" caption="Cnetbin2pvl -gui" src="assets/image/cnetbin2pvlGUI.png"/>
		</image>

isis/src/control/objs/ControlGraph/ControlGraph.cpp

deleted100644 → 0

+0 −481

Original line number	Diff line number	Diff line
		#include "IsisDebug.h"
		#include "ControlGraph.h"

		#include <iostream>
		#include <utility>

		#include <QHash>
		#include <QMap>
		#include <QString>
		#include <QVector>
		#include <QQueue>
		#include <QPair>

		#include "ControlMeasure.h"
		#include "ControlPoint.h"
		#include "GroupedStatistics.h"
		#include "ControlNet.h"
		#include "IException.h"
		#include "IString.h"



		namespace Isis {

		/**
		* construct a ControlGraph given a ControlNet
		*
		* @param someControlNet ControlNet to construct a ControlGraph from
		*/
		ControlGraph::ControlGraph(ControlNet *someControlNet) {
		cnet = someControlNet;
		cubeIdToIndexHash = NULL;
		cubeIndexToIdHash = NULL;
		graph = NULL;
		graph = new QMap< int, QPair< AdjacentCubeList, GroupedStatistics > >();

		// cubeIdToIndexHash provides a way of assigning unique sequential indices
		// to all of the Cube Serial numbers in the ControlNet, while
		// cubeIndexToIdHash prvides a way to get the Cube Serial numbers back.
		cubeIdToIndexHash = new QHash< QString, int >();
		cubeIndexToIdHash = new QHash< int, QString >();
		cubeIdToIndexHash->reserve(cnet->GetNumPoints() / 5);
		cubeIndexToIdHash->reserve(cnet->GetNumPoints() / 5);

		HashCubesAndPopulateGraph();

		CalculateIslands();

		if (islands->size())
		connected = false;
		else
		connected = true;
		}


		/**
		* copy construct a ControlGraph object
		*
		* @param other The ControlGraph to construct a copy of
		*/
		ControlGraph::ControlGraph(const ControlGraph &other) {
		cnet = other.cnet;

		cubeIdToIndexHash = NULL;
		cubeIndexToIdHash = NULL;
		graph = NULL;
		islands = NULL;

		cubeIdToIndexHash = new QHash< QString, int >(*other.cubeIdToIndexHash);
		cubeIndexToIdHash = new QHash< int, QString >(*other.cubeIndexToIdHash);
		graph = new QMap< int, QPair< AdjacentCubeList, GroupedStatistics > >(
		*other.graph);
		islands = new QVector< QVector< int > >(*other.islands);

		connected = other.connected;
		}


		/**
		* Destruct a ControlGraph
		*/
		ControlGraph::~ControlGraph() {
		cnet = NULL;

		if (cubeIdToIndexHash) {
		delete cubeIdToIndexHash;
		cubeIdToIndexHash = NULL;
		}

		if (cubeIndexToIdHash) {
		delete cubeIndexToIdHash;
		cubeIndexToIdHash = NULL;
		}

		if (graph) {
		delete graph;
		graph = NULL;
		}

		if (islands) {
		delete islands;
		islands = NULL;
		}
		}


		//! Returns true if this ControlGraph is connected or false otherwise
		bool ControlGraph::IsConnected() const {
		return connected;
		}


		/**
		* There can be 0 islands or 2 or more islands. GetIslandCount will never
		* return 1 since 1 island is really just a connected graph (with 0 islands).
		*/
		int ControlGraph::GetIslandCount() const {
		return islands->size();
		}


		/**
		* @param island A list of all cubes that are on this island are desired
		*
		* @returns A list of CubeSerialNumbers which are located on the given island
		*/
		const QVector< QString > ControlGraph::GetCubesOnIsland(const int &island)
		const {
		if (connected) {
		QString msg = "\n\nGetCubesOnIsland called on connected graph with no "
		"islands!!!\n\n";
		throw IException(IException::Programmer, msg.toStdString(), _FILEINFO_);
		}

		ASSERT(islands->size() != 0);

		if (island < 0 \|\| island >= islands->size()) {
		QString msg = "\n\nA list of cubes was requested from island " +
		QString::number(island) + "\nbut that island does not exist!!!"
		"\n\nThere are " + QString::number(islands->size()) + " islands "
		"numbered from 0 to " + QString::number(islands->size() - 1) + "\n\n";
		throw IException(IException::Programmer, msg.toStdString(), _FILEINFO_);
		}

		QVector< QString > cubeList;
		for (int i = 0; i < (*islands)[island].size(); i++) {
		cubeList.push_back(cubeIndexToIdHash->value((*islands)[island][i]));
		}

		return cubeList;
		}


		/**
		* @returns A list of all CubeSerialNumbers in the given ControlNet
		*/
		const QVector< QString > ControlGraph::GetCubeList() const {
		QVector< QString > cubeList;

		// for each key in the cubeIdToIndexHash add the key to a vector
		QHash< QString, int >::const_iterator i = cubeIdToIndexHash->constBegin();
		while (i != cubeIdToIndexHash->constEnd()) {
		cubeList.push_back(i.key());
		i++;
		}

		return cubeList;
		}


		/**
		* @param CubeSerialNumber The Serial number of the cube to get Statistics on
		*
		* @returns Statistics for all measures associated with the given cube
		*/
		const GroupedStatistics &ControlGraph::GetMeasureStats(const QString &
		CubeSerialNumber) const {
		return graph->find(cubeIdToIndexHash->value(CubeSerialNumber)).value()
		.second;
		}


		/**
		* @param other The ControlGraph on the right side of the =
		*/
		ControlGraph &ControlGraph::operator=(const ControlGraph &other) {
		if (this == &other)
		return *this;

		if (cubeIdToIndexHash) {
		delete cubeIdToIndexHash;
		cubeIdToIndexHash = NULL;
		}
		if (cubeIndexToIdHash) {
		delete cubeIndexToIdHash;
		cubeIndexToIdHash = NULL;
		}
		if (graph) {
		delete graph;
		graph = NULL;
		}
		if (islands) {
		delete islands;
		islands = NULL;
		}

		cnet = other.cnet;
		connected = other.connected;

		cubeIdToIndexHash = new QHash< QString, int >(*other.cubeIdToIndexHash);
		cubeIndexToIdHash = new QHash< int, QString >(*other.cubeIndexToIdHash);
		graph = new QMap< int, QPair< AdjacentCubeList, GroupedStatistics > >(
		*other.graph);
		islands = new QVector< QVector< int > >(*other.islands);

		return *this;
		}


		/**
		* @param someControlNet The ControlNet to create a ControlGraph from
		*/
		void ControlGraph::HashCubesAndPopulateGraph() {
		// index assigned to last hashed cube (-1 means empty hash table)
		int cubeIndex = -1;

		// whats about to happen is this:
		//
		// for all ControlPoints in the given ControlNet
		// for each ControlMeasure (cube) in the ControlPoint
		// for all the other ControlMeasures (other cubes) in the ControlPoint
		// add connection from previous for loops cube to this for loops cube
		//
		// along the way as we encounter new cubes they are hashed. Also, for all
		// the measures encountered be the middle for loop statistics are saved.

		for (int cpIndex = 0; cpIndex < cnet->GetNumPoints(); cpIndex++) {
		if (!(*cnet)[cpIndex]->IsIgnored()) {
		// use a reference for the current ControlPoint for clearity
		const ControlPoint &curCtrlPoint = (cnet)[cpIndex];
		for (int cmIndex = 0; cmIndex < curCtrlPoint.GetNumMeasures(); cmIndex++) {
		// get current cube's serial number and hash if new
		QString curCube = curCtrlPoint[cmIndex]->GetCubeSerialNumber();
		if (!cubeIdToIndexHash->contains(curCube)) {
		cubeIdToIndexHash->insert(curCube, ++cubeIndex);
		cubeIndexToIdHash->insert(cubeIndex, curCube);
		}
		int curCubeIndex = cubeIdToIndexHash->value(curCube);

		QMap < int, QPair< AdjacentCubeList, GroupedStatistics >
		>::iterator graphIterator = graph->find(curCubeIndex);

		// look for adjacent cubes
		for (int cmIndex2 = 0; cmIndex2 < curCtrlPoint.GetNumMeasures(); cmIndex2++) {
		if (cmIndex2 != cmIndex) {
		// get adjacent cube's serial number and hash if new
		QString adjacentCube = curCtrlPoint[cmIndex2]->GetCubeSerialNumber();
		if (!cubeIdToIndexHash->contains(adjacentCube)) {
		cubeIdToIndexHash->insert(adjacentCube, ++cubeIndex);
		cubeIndexToIdHash->insert(cubeIndex, adjacentCube);
		}
		int adjCubeIndex = cubeIdToIndexHash->value(adjacentCube);

		// add a connection from the current cube to the adjacent cube
		if (graphIterator != graph->end()) {
		graphIterator.value().first.AddConnection(adjCubeIndex, cpIndex,
		cmIndex2);
		}
		else {
		AdjacentCubeList newCubeList(adjCubeIndex, cpIndex, cmIndex2);
		GroupedStatistics cmStats;
		graph->insert(curCubeIndex, qMakePair(newCubeList, cmStats));
		}
		}
		} // of for all measures in cp

		// save off statistics
		if (graphIterator != graph->end()) {
		QVector< QString > dataNames(cnet->GetPoint(cpIndex)->
		GetMeasure(cmIndex)->GetMeasureDataNames());

		for (int i = 0; i < dataNames.size(); i++)
		graphIterator.value().second.AddStatistic(dataNames[i],
		cnet->GetPoint(cpIndex)->GetMeasure(cmIndex)->
		GetMeasureData(dataNames[i]));
		} // of saving statistics
		} // of for all measures in cp
		} // of if not an igrored point
		} // of for all ControlPoints in net
		} // of HashCubesAndPopulateGraph


		/**
		* Determines whether or not islands exist and calculates what they are if
		* present
		*/
		void ControlGraph::CalculateIslands() {
		// assume subgraphs exist! (check assumption at the very end of the method)

		// A search list has a value for every cube, which defaults to false.
		// A breadth-first search is used to test connectivity and works by setting
		// each cubes cooresponding search list value to true as it is visited.
		// At the end of the first round the true entries make up the first
		// subgragh. As they are added to the first subgraph they are removed from
		// the search list. The remaining false entries must have the breadth-first
		// search done on them to determine the next subgraph(s). This process
		// continues until all entries in the search list are true (until all cubes
		// have been visited)
		QMap< int, bool > searchList;
		for (int i = 0; i < graph->size(); i++)
		searchList.insert(i, false);

		// For each subgraph keep a list of the cubes in the subgraph. This is
		// represented by a 2d vector where the inner vectors are cubes within a
		// subgraph and the outer vector is a list of subgraphs
		islands = new QVector< QVector< int > >();

		// keeps track of which itteration of the breadth-first search we are on and
		// thus also which subgraph we are currently populating
		int subgraphIndex = -1;

		while (searchList.size()) {
		// create a new subgraph
		subgraphIndex++;
		islands->push_back(QVector< int >());

		// The queue used for breadth-first searching
		QQueue< int > q;

		// visit the first cube
		searchList.begin().value() = true;
		q.enqueue(searchList.begin().key());

		// visit all cubes possible using the breadth-first approach
		while (q.size()) {
		int curVertex(q.dequeue());
		QVector< int > adjacentVertices = graph->find(curVertex).value().first
		.GetAdjacentCubes();

		for (int i = 0; i < adjacentVertices.size(); i++) {
		const int &curNeighbor = adjacentVertices[i];

		ASSERT(searchList.find(curNeighbor) != searchList.end());

		if (!searchList.find(curNeighbor).value()) {
		searchList.find(curNeighbor).value() = true;
		q.enqueue(curNeighbor);
		}
		}
		} // end of breadth-first search

		// add all true entries to the current subgraph
		QMap< int, bool >::iterator i = searchList.begin();
		while (i != searchList.end()) {
		if (i.value()) {
		(*islands)[subgraphIndex].push_back(i.key());
		}
		i++;
		}

		// remove all the true entries from the search list
		for (int i = 0; i < (*islands)[subgraphIndex].size(); i++) {
		searchList.remove((*islands)[subgraphIndex][i]);
		}
		}

		// if there was only ever one subgraph created then the initial assumption
		// was wrong! There are no islands at all - this is a connected graph!
		if (subgraphIndex == 0) {
		islands->clear();
		}
		}


		/**
		* Construct a new AdjacentCubeList given one initial adjacent connection.
		* An adjacent connection means both an adjacent vertex as well as the edge
		* that connects it. The cubeIndex is the vertex. The edge is a
		* ControlPoint - ControlMeasure combo.
		*
		* @param cubeIndex First adjacent cube
		* @param cpIndex ControlPoint Index
		* @param cmIndex ControlMeasure Index
		*/
		ControlGraph::AdjacentCubeList::AdjacentCubeList(const int &cubeIndex,
		const int &cpIndex, const int &cmIndex) {
		connections = NULL;

		QVector< QPair< int, int > > firstEdge;
		firstEdge.push_back(qMakePair(cpIndex, cmIndex));
		connections = new QMap< int, QVector< QPair< int, int > > >();
		connections->insert(cubeIndex, firstEdge);
		}


		/**
		* copy construct an AdjacentCubeList
		*
		* @param other The AdjacentCubeList to construct a copy of
		*/
		ControlGraph::AdjacentCubeList::AdjacentCubeList(const AdjacentCubeList &
		other) {
		connections = NULL;
		connections = new QMap< int, QVector< QPair< int, int > > >(
		*other.connections);
		}


		//! destruct an AdjacentCubeList
		ControlGraph::AdjacentCubeList::~AdjacentCubeList() {
		if (connections) {
		delete connections;
		connections = NULL;
		}
		}


		/**
		* @returns A list of adjacent cubes!
		*/
		const QVector< int > ControlGraph::AdjacentCubeList::GetAdjacentCubes() const {
		// vector of adjacent cubes to be returned
		QVector< int > adjacentCubes;

		if (!connections)
		return adjacentCubes;

		QMap< int, QVector< QPair< int, int > > >::const_iterator i =
		connections->constBegin();
		while (i != connections->constEnd()) {
		adjacentCubes.push_back(i.key());
		i++;
		}

		return adjacentCubes;
		}


		/**
		* Adds a connection to an AdjacentCubeList. A connection consists of a new
		* vertex as well as the edge that connects it. The vertex is the cube index
		* and the edge is the ControlPoint - ControlMeasure combo.
		*
		* @param cubeIndex Adjacent cube
		* @param cpIndex ControlPoint index
		* @param cmIndex ControlMeasure index
		*/
		void ControlGraph::AdjacentCubeList::AddConnection(const int &cubeIndex,
		const int &cpIndex, const int &cmIndex) {
		QMap< int, QVector< QPair< int, int > > >::iterator i =
		connections->find(cubeIndex);

		// if the cube already exists in our list then just add another edge to it.
		// otherwise we need to add the cube as well.
		if (i != connections->end()) {
		i.value().push_back(qMakePair(cpIndex, cmIndex));
		}
		else {
		QVector< QPair< int, int > > firstEdge;
		firstEdge.push_back(qMakePair(cpIndex, cmIndex));
		connections->insert(cubeIndex, firstEdge);
		}
		}


		/**
		* @param other The AdjacentCubeList on the right side of the =
		*/
		ControlGraph::AdjacentCubeList &ControlGraph::AdjacentCubeList::operator=(
		const AdjacentCubeList &other) {
		if (connections) {
		delete connections;
		connections = NULL;
		}

		connections = new QMap< int, QVector< QPair< int, int > > >(
		*other.connections);

		return *this;
		}
		}

isis/src/control/objs/ControlGraph/ControlGraph.h

deleted100644 → 0

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Original line number	Diff line number	Diff line
		#ifndef ControlGraph_h
		#define ControlGraph_h

		/**
		* @file
		* 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.
		*/


		template< class A, class B > class QHash;
		template< class A, class B > class QMap;
		template< class A, class B > struct QPair;
		template< class A> class QVector;
		class QString;

		namespace Isis {
		class ControlNet;
		class GroupedStatistics;

		/**
		* @brief Control Network statistics and connectivity
		*
		* This class is used to store statistics on a Control Network
		*
		* This class is include safe meaning that includers of this class will only
		* get this class.
		*
		* @ingroup ControlGraph
		*
		* @author 2009-09-23 Eric Hyer
		*
		* @see ControlNet ControlPoint ControlMeasure GroupedStatistics
		*
		* @internal
		* @history 2009-09-23 Eric Hyer Original version
		* @history 2009-10-15 Eric Hyer Added GetCubeList Method
		* @history 2010-10-26 Tracie Sucharski Added missing includes to cpp after
		* removing includes from ControlNet.h.
		* @history 2016-08-28 Kelvin Rodriguez Qpair now properly forward declared as a struct to
		* squash warnings in clang
		*/
		class ControlGraph {
		public:
		ControlGraph(ControlNet *someControlNet);
		ControlGraph(const ControlGraph &other);
		~ControlGraph();

		bool IsConnected() const;
		int GetIslandCount() const;
		const QVector< QString > GetCubesOnIsland(const int &island) const;
		const QVector< QString > GetCubeList() const;
		const GroupedStatistics &GetMeasureStats(const QString &
		CubeSerialNumber) const;

		ControlGraph &operator=(const ControlGraph &other);

		private:
		// nested class forward declaration
		class AdjacentCubeList;

		void HashCubesAndPopulateGraph();
		void CalculateIslands();

		//! ControlNet to make a graph from
		ControlNet *cnet;

		//! Used to get an index from a cube serial number
		QHash< QString, int > * cubeIdToIndexHash;

		//! Used to get a cube serial number from an index
		QHash< int, QString > * cubeIndexToIdHash;

		/**
		* THE GRAPH!! It is a map of cube indices to a pair. The first pair
		* element is a list that contains not only all the cubes which are
		* adjacent to it (as indices also), but also the edges that make these
		* these connections. The second pair element contains statistics on
		* this cube.
		*/
		QMap< int, QPair< AdjacentCubeList, GroupedStatistics > > * graph;

		/**
		* Stores the state of the graphs connectivity so that connectivity must
		* only be calculated once.
		*/
		bool connected;

		//! Stores a list of islands which are themselves a list of cube indices
		QVector< QVector< int > > * islands;

		/**
		* @brief Control Graph nested class
		*
		* This class is used to store adjacent cube connections for ControlGraph
		*
		* @ingroup ControlGraph
		*
		* @author 2009-09-18 Eric Hyer
		*
		* @see ControlGraph
		*
		* @internal
		*
		*/
		class AdjacentCubeList {
		public:
		AdjacentCubeList(const int &cubeIndex, const int &cpIndex, const int
		& cmIndex);
		AdjacentCubeList(const AdjacentCubeList &other);
		~AdjacentCubeList();

		const QVector< int > GetAdjacentCubes() const;
		void AddConnection(const int &cubeIndex, const int &cpIndex, const
		int &cmIndex);
		AdjacentCubeList &operator=(const AdjacentCubeList &other);

		private:
		//! stores all edges or connections for an adjacent cube
		QMap< int, QVector< QPair< int, int > > > * connections;
		};
		};
		};

		#endif