added support for threading and progress bars to ENVI streaming classes

David Mayerich
1 parent e376212f
Showing 8 changed files with 315 additions and 46 deletions Show diff stats
stim/biomodels/network.h
stim/envi/bil.h
stim/envi/binary.h
stim/envi/bip.h
stim/envi/bsq.h
stim/envi/envi.h
stim/ui/progressbar.h
stim/visualization/obj.h
@@ -42,10 +42,15 @@ class network{
 	/// Stores information about a single capillary (a length of vessel between two branch or end points)
 	//template<typename T>
-	class fiber{
+	class fiber : public std::list< point >{
+
+		using std::list< point >::begin;
+		using std::list< point >::end;
+		using std::list< point >::size;
+
 	public:
-		std::list< point > P;		//geometric point positions
+		//std::list< point > P;		//geometric point positions
 		typename std::list< t_node >::iterator n[2];				//indices to terminal nodes
 		unsigned int id;
@@ -60,9 +65,9 @@ class network{
 			//for each point
 			typename std::list< point >::iterator i;	//create a point iterator
-			for(i = P.begin(); i != P.end(); i++){		//for each point in the fiber
+			for(i = begin(); i != end(); i++){		//for each point in the fiber
-				if(i == P.begin())						//if this is the first point, just store it
+				if(i == begin())						//if this is the first point, just store it
 					p1 = *i;
 				else{									//if this is any other point
 					p0 = p1;							//shift p1->p0
@@ -84,9 +89,9 @@ class network{
 			//for each point
 			typename std::list< point >::iterator i;	//create a point iterator
-			for(i = P.begin(); i != P.end(); i++){		//for each point in the fiber
+			for(i = begin(); i != end(); i++){		//for each point in the fiber
-				if(i == P.begin()){						//if this is the first point, just store it
+				if(i == begin()){						//if this is the first point, just store it
 					p1 = *i;
 					r1 = i->r;
 				}
@@ -116,13 +121,13 @@ class network{
 		std::vector< stim::vec<T> > geometry(){
 			std::vector< stim::vec<T> > result;				//create an array to store the fiber geometry
-			result.resize( P.size() );					//pre-allocate the array
+			result.resize( size() );					//pre-allocate the array
 			typename std::list< point >::iterator p;				//create a list iterator
 			unsigned int pi = 0;						//create an index into the result array
 			//for each geometric point on the fiber centerline
-			for(p = P.begin(); p != P.end(); p++){
+			for(p = begin(); p != end(); p++){
 				result[pi] = *p;
 				pi++;
 			}
@@ -136,7 +141,7 @@ class network{
 			//create an iterator for the point list
 			typename std::list<point>::iterator i;
-			for(i = P.begin(); i != P.end(); i++){
+			for(i = begin(); i != end(); i++){
 				ss<<i->str()<<"  r = "<<i->r<<std::endl;
 			}
@@ -316,7 +321,7 @@ public:
 			for(unsigned int pi = 0; pi < nP; pi++){
 				point p = (point)L[pi];					//move the geometric coordinates into a point structure
 				p.r = R[pi][0];							//store the radius
-				f->P.push_back(p);						//push the point onto the current fiber
+				f->push_back(p);						//push the point onto the current fiber
 			}
 		}
@@ -338,9 +343,9 @@ public:
 			//if the number of outgoing nodes is nonzero
 			if(ni->out.size() != 0)
-				result[vi] = ni->out.front()->P.front();
+				result[vi] = ni->out.front()->front();
 			else if(ni->in.size() != 0)
-				result[vi] = ni->in.front()->P.back();
+				result[vi] = ni->in.front()->back();
 			vi++;										//increment the array index
 		}
@@ -406,9 +411,6 @@ public:
 		}
 		return object;
-
-
-
 	}
 	/// This function returns the information necessary for a simple graph-based physical (ex. fluid) simulation.
@@ -35,6 +35,8 @@ protected:
 		return R[1];
 	}
+	using binary<T>::thread_data;
+
 public:
 	using binary<T>::open;
@@ -318,12 +320,17 @@ public:
 			}//loop for YZ line end  
 			target.write(reinterpret_cast<const char*>(c), L);   //write the corrected data into destination	
+
+			thread_data = (double)k / Y() * 100;
 		}//loop for Y slice end		
 		free(a);
 		free(b);
 		free(c);
 		target.close();
+
+		thread_data = 100;
+
 		return true;	
 	}
@@ -366,11 +373,14 @@ public:
 				}								
 			}
 			target.write(reinterpret_cast<const char*>(c), L);   //write normalized data into destination
+
+			thread_data = (double)j / Y() * 100;
 		}
 		free(b);
 		free(c);
 		target.close();
+		thread_data = 100;
 		return true;
 	}
@@ -390,9 +400,13 @@ public:
 		for ( unsigned i = 0; i < Z(); i++)
 		{			
 				band_index(p, i);
-				target.write(reinterpret_cast<const char*>(p), S);   //write a band data into target file	
+				target.write(reinterpret_cast<const char*>(p), S);   //write a band data into target file
+
+				thread_data = (double)i / Z() * 100;	//store the progress for the current operation	
 		}
+		thread_data = 100;							//set the current progress to 100%
+
 		free(p);
 		target.close();
 		return true;
@@ -421,11 +435,15 @@ public:
 				unsigned ks = k * X();
 				for ( unsigned j = 0; j < X(); j++)
 					q[k + j * Z()] = p[ks + j];
+
+				thread_data = (double)(i * Z() + k) / (Z() * Y()) * 100;	//store the progress for the current operation	
 			}
 			target.write(reinterpret_cast<const char*>(q), S);   //write a band data into target file	
 		}
+		thread_data = 100;
+
 		free(p);
 		free(q);
@@ -28,7 +28,7 @@ protected:
 	unsigned int header;	//header size (in bytes)
 	unsigned char* mask;	//pointer to a character array: 0 = background, 1 = foreground (or valid data)
-
+	unsigned int thread_data;		//unsigned integer used to pass data to threads during processing
 	/// Private initialization function used to set default parameters in the data structure.
@@ -36,6 +36,8 @@ protected:
 		memset(R, 0, sizeof(unsigned int) * D);		//initialize the resolution to zero
 		header = 0;									//initialize the header size to zero
 		mask = NULL;
+
+		thread_data = 0;
 	}
 	/// Private helper function that returns the size of the file on disk using system functions.
@@ -95,6 +97,14 @@ protected:
 public:
+	unsigned int get_thread_data(){
+		return thread_data;
+	}
+
+	void reset_thread_data(){
+		thread_data = 0;
+	}
+
 	/// Open a binary file for streaming.
 	/// @param filename is the name of the binary file
@@ -37,6 +37,8 @@ protected:
 		return R[0];
 	}
+	using binary<T>::thread_data;
+
 public:
 	using binary<T>::open;
@@ -327,6 +329,8 @@ public:
 			}//loop for YZ line end  
 			target.write(reinterpret_cast<const char*>(c), L);   //write the corrected data into destination	
+
+			thread_data = (double)k / Y() * 100;
 		}//loop for Y slice end
@@ -335,6 +339,8 @@ public:
 		free(b);
 		free(c);
 		target.close();
+
+		thread_data = 100;
 		return true;	
 	}
@@ -379,12 +385,15 @@ public:
 				}								
 			}
 			target.write(reinterpret_cast<const char*>(c), L);   //write normalized data into destination
+
+			thread_data = (double) j / Y() * 100;
 		}
 		free(b);
 		free(c);
 		target.close();
+		thread_data = 100;
 		return true;
 	}
@@ -434,10 +443,13 @@ public:
 				unsigned ks = k * X();
 				for ( unsigned j = 0; j < X(); j++)
 					q[ks + j] = p[k + j * Z()];
+
+				thread_data = (double)(i * Z() + k) / (Y() * Z()) * 100;
 			}
 			target.write(reinterpret_cast<const char*>(q), S);   //write a band data into target file	
 		}
+		thread_data = 100;
 		free(p);
 		free(q);
@@ -882,6 +894,8 @@ public:
 		//close the output file
 		target.close();
 		free(spectrum);
+
+		return true;
 	}
 	bool unsift(std::string outfile, unsigned char* mask, unsigned int samples, unsigned int lines){
@@ -42,6 +42,8 @@ protected:
 		return R[2];
 	}
+	using binary<T>::thread_data;
+
 public:
 	using binary<T>::open;
@@ -259,6 +261,8 @@ public:
 			}
 			target.write(reinterpret_cast<const char*>(c), S);   //write the corrected data into destination
+
+			thread_data = (double)cii / B * 100;
 		}	
@@ -268,6 +272,8 @@ public:
 		free(b);
 		free(c);
 		target.close();
+
+		thread_data = 100;
 		return true;
 	}
@@ -304,13 +310,18 @@ public:
 					c[i] = c[i] / b[i];
 			}
 			target.write(reinterpret_cast<const char*>(c), S);   //write normalized data into destination
+
+			thread_data = (double)j / B * 100;
 		}
+		
+
 		//header.save(headername);         //save the new header file
 		free(b);
 		free(c);
 		target.close();
+		thread_data = 100;					//make sure that the progress bar is full
 		return true;
 	}
@@ -349,23 +360,26 @@ public:
 		std::ofstream target(outname.c_str(), std::ios::binary);
 		std::string headername = outname + ".hdr";
-		T * p;			//pointer to the current spectrum
-		p = (T*)malloc(L);
-		
-		for ( unsigned i = 0; i < Y(); i++)
+		unsigned int xz_bytes = X() * Z() * sizeof(T);
+		T * xz_slice;						//pointer to the current spectrum
+		xz_slice = (T*)malloc(xz_bytes);
+
+		for ( unsigned y = 0; y < Y(); y++)									//for each y position
 		{
-			file.seekg(X() * i * sizeof(T), std::ios::beg);
-			for ( unsigned j = 0; j < Z(); j++ )
+			file.seekg(y * X() * sizeof(T), std::ios::beg);					//seek to the beginning of the xz slice
+			for ( unsigned z = 0; z < Z(); z++ )							//for each band
 			{
-				file.read((char *)(p + j * X()), sizeof(T) * X());
-				file.seekg(jump, std::ios::cur);    //go to the next band	
+				file.read((char *)(xz_slice + z * X()), sizeof(T) * X());	//read a line
+				file.seekg(jump, std::ios::cur);							//seek to the next band
+
+				thread_data = (double)(y * Z() + z) / (Z() * Y()) * 100;	//update the progress counter	
 			}					
-			target.write(reinterpret_cast<const char*>(p), L);   //write XZ slice data into target file	
+			target.write(reinterpret_cast<const char*>(xz_slice), xz_bytes);   //write the generated XZ slice to the target file	
 		}
-		//header.interleave = rts::envi_header::BIL;  //change the type of file in header file
-		//header.save(headername);
-		free(p);
+		thread_data = 100;
+		
+		free(xz_slice);
 		target.close();
 		return true;
 	}
@@ -23,6 +23,78 @@ public:
 	envi_header header;
+	/// Returns the progress of the current processing operation as a percentage
+	void reset_progress(){
+
+		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
+			if(header.data_type ==envi_header::float32)
+				((bsq<float>*)file)->reset_thread_data();
+			else if(header.data_type == envi_header::float64)
+				((bsq<double>*)file)->reset_thread_data();
+			else
+				std::cout<<"ERROR: unidentified data type"<<std::endl;
+		}
+
+		else if(header.interleave == envi_header::BIL){		//if the infile is bil file
+			if(header.data_type ==envi_header::float32)
+				((bil<float>*)file)->reset_thread_data();
+			else if(header.data_type == envi_header::float64)
+				((bil<double>*)file)->reset_thread_data();
+			else
+				std::cout<<"ERROR: unidentified data type"<<std::endl;
+		}
+
+		else if(header.interleave == envi_header::BIP){		//if the infile is bip file
+			if(header.data_type ==envi_header::float32)
+				((bip<float>*)file)->reset_thread_data();
+			else if(header.data_type == envi_header::float64)
+				((bip<double>*)file)->reset_thread_data();
+			else
+				std::cout<<"ERROR: unidentified data type"<<std::endl;
+		}
+
+		else{
+			std::cout<<"ERROR: unidentified file type"<<std::endl;
+			exit(1);
+		}
+	}
+
+	/// Returns the progress of the current processing operation as a percentage
+	unsigned int progress(){
+
+		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
+			if(header.data_type ==envi_header::float32)
+				return ((bsq<float>*)file)->get_thread_data();
+			else if(header.data_type == envi_header::float64)
+				return ((bsq<double>*)file)->get_thread_data();
+			else
+				std::cout<<"ERROR: unidentified data type"<<std::endl;
+		}
+
+		else if(header.interleave == envi_header::BIL){		//if the infile is bil file
+			if(header.data_type ==envi_header::float32)
+				return ((bil<float>*)file)->get_thread_data();
+			else if(header.data_type == envi_header::float64)
+				return ((bil<double>*)file)->get_thread_data();
+			else
+				std::cout<<"ERROR: unidentified data type"<<std::endl;
+		}
+
+		else if(header.interleave == envi_header::BIP){		//if the infile is bip file
+			if(header.data_type ==envi_header::float32)
+				return ((bip<float>*)file)->get_thread_data();
+			else if(header.data_type == envi_header::float64)
+				return ((bip<double>*)file)->get_thread_data();
+			else
+				std::cout<<"ERROR: unidentified data type"<<std::endl;
+		}
+
+		else{
+			std::cout<<"ERROR: unidentified file type"<<std::endl;
+		}
+		return 0;
+	}
+
 	/// Allocate memory for a new ENVI file based on the current interleave format (BIP, BIL, BSQ) and data type.
 	bool allocate(){
@@ -469,9 +541,8 @@ public:
 		else{
 			std::cout << "ERROR: unidentified file type" << std::endl;
-			exit(1);
 		}
-
+		return 0;
 	}
 	/// Compute the ratio of two baseline-corrected peaks. The result is stored in a pre-allocated array.
-#ifndef RTS_PROGRESSBAR_H
-#define RTS_PROGRESSBAR_H
-
+#ifndef RTS_PROGRESSBAR_H
+#define RTS_PROGRESSBAR_H
+
 #include <iostream>
 #include <sstream>
 using namespace std;
-static void rtsProgressBar(int percent)
+static void rtsProgressBar(unsigned int percent)
 {
+	//std::cout<<percent<<std::endl;
 	stringstream bar;
 	static int x = 0;
 	string slash[4];
@@ -25,9 +26,10 @@ static void rtsProgressBar(int percent)
 	bar<<"]";
 	cout << "\r"; // carriage return back to beginning of line
 	cout << bar.str() << " " << slash[x] << " " << percent << " %"; // print the bars and percentage
+	cout.flush();
 	x++; // increment to make the slash appear to rotate
 	if(x == 4)
 	x = 0; // reset slash animation
-}
-
-#endif
+}
+
+#endif
@@ -169,6 +169,25 @@ protected:
 		}
+		//returns a vector containing the vertex indices for the geometry
+		void get_v(std::vector<unsigned>& v){
+			v.resize(size());							//resize the vector to match the number of vertices
+			for(unsigned int i = 0; i<size(); i++)		//for each vertex
+				v[i] = at(i)[0];						//copy the vertex index
+		}
+
+		void get_vt(std::vector<unsigned>& vt){
+			vt.resize(size());							//resize the vector to match the number of vertices
+			for(unsigned int i = 0; i<size(); i++)		//for each vertex
+				vt[i] = at(i)[1];						//copy the vertex index
+		}
+
+		void get_vn(std::vector<unsigned>& vn){
+			vn.resize(size());							//resize the vector to match the number of vertices
+			for(unsigned int i = 0; i<size(); i++)		//for each vertex
+				vn[i] = at(i)[2];						//copy the vertex index
+		}
+
 		std::string str(){
 			std::stringstream ss;
@@ -293,6 +312,13 @@ protected:
 		return OBJ_INVALID;
 	}
+	//private method returns the vertex indices for a line
+	std::vector<unsigned> get_l_v(unsigned l){
+
+
+
+	}
+
 public:
 	/// Constructor loads a Wavefront OBJ file
 	obj(std::string filename){
@@ -511,12 +537,70 @@ public:
 	}
 	/// Retrieve the vertex stored in index i
+	/// @param vi is the desired vertex index
+	stim::vec<T> getV(unsigned int vi){
+		stim::vec<T> v = V[vi];
+		return v;
+	}
-	/// @param i is the desired vertex index
-	stim::vec<T> getV(unsigned int i){
+	/// Retrieve the vertex texture coordinate at index i
+	/// @param vti is the desired index
+	stim::vec<T> getVT(unsigned int vti){
+		stim::vec<T> vt = VT[vti];
+		return vt;
+	}
-		stim::vec<T> v = V[i];
-		return v;
+	/// Retrieve the vertex normal at index i
+	/// @param vni is the desired index
+	stim::vec<T> getVN(unsigned int vni){
+		stim::vec<T> vn = VN[vni];
+		return vn;
+	}
+
+
+	/// Retrieve a vertex stored at a list of given indices
+	/// @param vi is an array containing a series of indices
+	std::vector< stim::vec<T> > getV( std::vector<unsigned> vi ){
+
+		std::vector< stim::vec<T> > v;
+		v.resize(vi.size());							//pre-allocate an array of vertices
+
+		std::cout<<"stim::obj::getV: "<<v.size()<<std::endl;
+
+		for(unsigned i = 0; i < vi.size(); i++)
+			v[i] = V[vi[i] - 1];
+
+		return v;										//return the array of vertices
+	}
+
+	/// Retrieve a vertex stored at a list of given indices
+	/// @param vi is an array containing a series of indices
+	std::vector< stim::vec<T> > getVT( std::vector<unsigned> vti ){
+
+		std::vector< stim::vec<T> > vt;
+		vt.resize(vti.size());							//pre-allocate an array of vertices
+
+		std::cout<<"stim::obj::getV: "<<vt.size()<<std::endl;
+
+		for(unsigned i = 0; i < vti.size(); i++)
+			vt[i] = VT[vti[i] - 1];
+
+		return vt;										//return the array of vertices
+	}
+
+	/// Retrieve a vertex stored at a list of given indices
+	/// @param vi is an array containing a series of indices
+	std::vector< stim::vec<T> > getVN( std::vector<unsigned> vni ){
+
+		std::vector< stim::vec<T> > vn;
+		vn.resize(vni.size());							//pre-allocate an array of vertices
+
+		std::cout<<"stim::obj::getV: "<<vn.size()<<std::endl;
+
+		for(unsigned i = 0; i < vni.size(); i++)
+			vn[i] = VN[vni[i] - 1];
+
+		return vn;										//return the array of vertices
 	}
 	stim::vec<T> centroid(){
@@ -585,7 +669,7 @@ public:
 	/// Returns the vertex indices for the specified line
 	/// @param i is the index of the line
-	std::vector< unsigned int > getL_Vi(unsigned int i){
+	/*std::vector< unsigned int > getL_Vi(unsigned int i){
 		unsigned int nP = L[i].size();
@@ -602,12 +686,12 @@ public:
 		}
 		return l;
-	}
+	}*/
 	/// Returns a vector containing the list of texture coordinates associated with each point of a line.
 	/// @param i is the index of the desired line
-	std::vector< stim::vec<T> > getL_VT(unsigned int i){
+	/*std::vector< stim::vec<T> > getL_VT(unsigned int i){
 		//get the number of points in the specified line
 		unsigned int nP = L[i].size();
@@ -633,7 +717,7 @@ public:
 		}
 		return l;
-	}
+	}*/
 	/// Add an array of vertices to the vertex list
 	unsigned int addV(std::vector< stim::vec<T> > vertices){
@@ -674,9 +758,63 @@ public:
 		//push the new geometry to the line list
 		L.push_back(new_line);
+	}
+
+	/// Fills three std::vector structures with the indices representing a line
+	/// @param l is the line index
+	/// @param vi is a vertex index array that will be filled
+	void getLinei(unsigned l, std::vector<unsigned>& vi){
+		L[l-1].get_v(vi);
+	}
+	/// Fills three std::vector structures with the indices representing a line
+	/// @param l is the line index
+	/// @param vi is a vertex index array that will be filled
+	/// @param vti is a vertex texture coordinate index array that will be filled
+	void getLinei(unsigned l, std::vector<unsigned>& vi, std::vector<unsigned>& vti){
+		getLinei(l, vi);
+		L[l-1].get_vt(vti);
 	}
+	/// Fills three std::vector structures with the indices representing a line
+	/// @param l is the line index
+	/// @param vi is a vertex index array that will be filled
+	/// @param vti is a vertex texture coordinate index array that will be filled
+	/// @param vni is a vertex normal index array that will be filled
+	void getLinei(unsigned l, std::vector<unsigned>& vi, std::vector<unsigned>& vti, std::vector<unsigned>& vni){
+		getLinei(l, vi, vti);
+		L[l-1].get_vn(vni);
+	}
+
+	/// Returns a list of points corresponding to the vertices of a line
+	void getLine(unsigned l, std::vector< stim::vec<T> > v){
+
+		std::vector<unsigned> vi;			//create a vector to store indices to vertices
+		getLinei(l, vi);					//get the indices for the line vertices
+		v = getV(vi);						//get the vertices corresponding to the indices
+	}
+
+	void getLine(unsigned l, std::vector< stim::vec<T> > v, std::vector< stim::vec<T> > vt){
+
+		std::vector<unsigned> vi, vti;
+		getLinei(l, vi, vti);					//get the indices for the line vertices
+		v = getV(vi);						//get the vertices corresponding to the indices
+		vt = getVT(vti);
+	}
+
+	void getLine(unsigned l, std::vector< stim::vec<T> > v, 
+							 std::vector< stim::vec<T> > vt, 
+							 std::vector< stim::vec<T> > vn){
+
+		std::vector<unsigned> vi, vti, vni;
+		getLinei(l, vi, vti, vni);					//get the indices for the line vertices
+		v = getV(vi);						//get the vertices corresponding to the indices
+		vt = getVT(vti);
+		vn = getVN(vni);
+
+	}
+
+
 };