void
LeastSquaresFitHistory::execute()
{
if (_x_values.size() != _y_values.size())
mooseError("In LeastSquresFitTimeHistory size of data in x_values and y_values must be equal");
if (_x_values.size() == 0)
mooseError("In LeastSquresFitTimeHistory size of data in x_values and y_values must be > 0");
// Create a copy of _x_values that we can modify.
std::vector<Real> x_values(_x_values.begin(), _x_values.end());
std::vector<Real> y_values(_y_values.begin(), _y_values.end());
for (MooseIndex(_x_values) i = 0; i < _x_values.size(); ++i)
{
x_values[i] = (x_values[i] + _x_shift) * _x_scale;
y_values[i] = (y_values[i] + _y_shift) * _y_scale;
}
PolynomialFit pf(x_values, y_values, _order, true);
pf.generate();
std::vector<Real> coeffs = pf.getCoefficients();
mooseAssert(coeffs.size() == _coeffs.size(),
"Sizes of current coefficients and vector of coefficient vectors must match");
for (MooseIndex(coeffs) i = 0; i < coeffs.size(); ++i)
_coeffs[i]->push_back(coeffs[i]);
_times->push_back(_t);
}
HypreSolver3D::HypreSolver3D(ptrdiff_t N0_, double Lz_,
ptrdiff_t N1_, double Ly_,
ptrdiff_t N2_, double Lx_):
N0(N0_), Lz(Lz_), N1(N1_), Ly(Ly_), N2(N2_), Lx(Lx_)
{
MPI_Comm_rank(MPI_COMM_WORLD, &myid);
MPI_Comm_size(MPI_COMM_WORLD, &num_procs);
N = N0*N1*N2;
dz = Lz/(N0+1);
dy = Ly/(N1+1);
dx = Lx/(N2+1);
h2 = dy*dy;
nx = N2;
ny = N1;
int zp = (int)(N0/num_procs);
int extra = N0-zp*num_procs;
if(myid<extra)
{
z0 = myid*zp + myid;
nz = zp+1;
}
else
{
z0 = myid*zp + extra;
nz = zp;
}
local_size = ny*nx*nz;
ilower = z0*nx*ny;
iupper = ilower+local_size-1;
// Build rhs and init x
HYPRE_IJVectorCreate(MPI_COMM_WORLD, ilower, iupper, &hv_b);
HYPRE_IJVectorSetObjectType(hv_b, HYPRE_PARCSR);
HYPRE_IJVectorCreate(MPI_COMM_WORLD, ilower, iupper, &hv_x);
HYPRE_IJVectorSetObjectType(hv_x, HYPRE_PARCSR);
std::vector<double> rhs_values(local_size, 1.);
std::vector<double> x_values(local_size, 0.);
rows.resize(local_size);
for (int i=0; i<local_size; i++)
rows[i] = ilower + i;
set_x0(&x_values[0]);
set_rhs(&rhs_values[0]);
build_A();
build_solver();
}
/**
Calculation of a derivate with order h.
@param h: order of the derivative.
@param x: coordinate to interpolate to.
*/
double Interpolator1D::operator()(unsigned int h, double x) const {
// This will be the returned value.
// Initialize it to zero.
double y = 0.0;
if (x < x_values(0)) {
if (h == 0)
y = extrap_values(0);
else
y = 0;
} else if (x > x_values(x_values.size() - 1)) {
if (h == 0)
y = extrap_values(1);
else
y = 0;
} else { // if it is within the bounds, interpolate with the polynomial.
unsigned int index;
if (x == x_values(0))
index = 0;
else if (x == x_values.last_v())
index = x_values.size() - 2;
else {
const double* itx = lower_bound(x_values.begin(), x_values.end(), x);
itx--;
index = itx - x_values.begin();
}
y = calcSplineValue(index, h, x);
}
return y;
}
/**
* Interpolates the spline value for the a given abscissas "x"
*/
double Interpolator1D::operator()(double x) const {
// This will be the returned value.
// Initialize it to zero.
double y = 0.0;
if (x < x_values(0))
y = extrap_values(0);
else if (x == x_values(0))
y = y_values(0);
else if (x > x_values(x_values.size() - 1))
y = extrap_values(1);
else { // if it is within the bounds, interpolate with the polynomial.
const double* itx = lower_bound(x_values.begin(), x_values.end(), x);
itx--;
const unsigned int index = itx - x_values.begin();
//Important note!: spline values could be different from
//node values because of discontinuity of the spline at the nodes.
//When the spline is discontinuous, the function value is one half
//the value from the left and the value from the right.
if (x == x_values(index))
y = y_values(index);
else if (x == x_values(index + 1))
y = y_values(index + 1);
else
y = calcSplineValue(index, 0, x);
}
return y;
}
double Interpolator1D::calcSplineValue(unsigned int interval, unsigned int h,
double x) const {
double dx = x - x_values(interval);
double t = 1.0;
double y = 0.0;
for (size_t j = h; j < spline_coeffs.numrows(); ++j) {
double m = 1.0;
for (size_t k = j; k > j - h; --k)
m *= double(k);
y += spline_coeffs(j, interval) * m * t;
t *= dx;
}
return y;
}
Vector<double> Interpolator1D::getInterpolationRange() const {
Vector<double> x(2);
x(0) = x_values(0);
x(1) = x_values.last_v();
return x;
}
// Processes the point cloud with OpenCV using the PCL cluster indices
void processClusters( const std::vector<pcl::PointIndices> cluster_indices,
// const sensor_msgs::PointCloud2ConstPtr& pointcloud_msg,
const pcl::PointCloud<pcl::PointXYZRGB>::ConstPtr cloud_transformed,
const pcl::PointCloud<pcl::PointXYZRGB>::ConstPtr& cloud_filtered,
const pcl::PointCloud<pcl::PointXYZRGB>& cloud )
{
// -------------------------------------------------------------------------------------------------------
// Convert image
ROS_INFO_STREAM_NAMED("perception","Converting image to OpenCV format");
try
{
sensor_msgs::ImagePtr image_msg(new sensor_msgs::Image);
// pcl::toROSMsg (*pointcloud_msg, *image_msg);
pcl::toROSMsg (*cloud_transformed, *image_msg);
cv_bridge::CvImagePtr input_bridge = cv_bridge::toCvCopy(image_msg, "rgb8");
full_input_image = input_bridge->image;
}
catch (cv_bridge::Exception& ex)
{
ROS_ERROR_STREAM_NAMED("perception","[calibrate] Failed to convert image");
return;
}
// -------------------------------------------------------------------------------------------------------
// Process Image
// Convert image to gray
cv::cvtColor( full_input_image, full_input_image_gray, CV_BGR2GRAY );
//cv::adaptiveThreshold( full_input_image, full_input_image_gray, 255, CV_ADAPTIVE_THRESH_MEAN_C, CV_THRESH_BINARY,5,10);
// Blur image - reduce noise with a 3x3 kernel
cv::blur( full_input_image_gray, full_input_image_gray, cv::Size(3,3) );
ROS_INFO_STREAM_NAMED("perception","Finished coverting");
// -------------------------------------------------------------------------------------------------------
// Check OpenCV and PCL image height for errors
int image_width = cloud.width;
int image_height = cloud.height;
ROS_DEBUG_STREAM( "PCL Image height " << image_height << " -- width " << image_width << "\n");
int image_width_cv = full_input_image.size.p[1];
int image_height_cv = full_input_image.size.p[0];
ROS_DEBUG_STREAM( "OpenCV Image height " << image_height_cv << " -- width " << image_width_cv << "\n");
if( image_width != image_width_cv || image_height != image_height_cv )
{
ROS_ERROR_STREAM_NAMED("perception","PCL and OpenCV image heights/widths do not match!");
return;
}
// -------------------------------------------------------------------------------------------------------
// GUI Stuff
// First window
const char* opencv_window = "Source";
/*
cv::namedWindow( opencv_window, CV_WINDOW_AUTOSIZE );
cv::imshow( opencv_window, full_input_image_gray );
*/
// while(true) // use this when we want to tweak the image
{
output_image = full_input_image.clone();
// -------------------------------------------------------------------------------------------------------
// Start processing clusters
ROS_INFO_STREAM_NAMED("perception","Finding min/max in x/y axis");
int top_image_overlay_x = 0; // tracks were to copyTo the mini images
// for each cluster, see if it is a block
for(size_t c = 0; c < cluster_indices.size(); ++c)
{
ROS_INFO_STREAM_NAMED("perception","\n\n");
ROS_INFO_STREAM_NAMED("perception","On cluster " << c);
// find the outer dimensions of the cluster
double xmin = 0; double xmax = 0;
double ymin = 0; double ymax = 0;
// also remember each min & max's correponding other coordinate (not needed for z)
double xminy = 0; double xmaxy = 0;
double yminx = 0; double ymaxx = 0;
// also remember their corresponding indice
int xmini = 0; int xmaxi = 0;
int ymini = 0; int ymaxi = 0;
// loop through and find all min/max of x/y
for(size_t i = 0; i < cluster_indices[c].indices.size(); i++)
{
int j = cluster_indices[c].indices[i];
// Get RGB from point cloud
pcl::PointXYZRGB p = cloud_transformed->points[j];
double x = p.x;
double y = p.y;
if(i == 0) // initial values
{
xmin = xmax = x;
ymin = ymax = y;
xminy = xmaxy = y;
yminx = ymaxx = x;
xmini = xmaxi = ymini = ymaxi = j; // record the indice corresponding to the min/max
}
else
{
if( x < xmin )
{
xmin = x;
xminy = y;
xmini = j;
}
if( x > xmax )
{
xmax = x;
xmaxy = y;
xmaxi = j;
}
if( y < ymin )
{
ymin = y;
yminx = x;
ymini = j;
}
if( y > ymax )
{
ymax = y;
ymaxx = x;
ymaxi = j;
}
}
}
ROS_DEBUG_STREAM_NAMED("perception","Cluster size - xmin: " << xmin << " xmax: " << xmax << " ymin: " << ymin << " ymax: " << ymax);
ROS_DEBUG_STREAM_NAMED("perception","Cluster size - xmini: " << xmini << " xmaxi: " << xmaxi << " ymini: " << ymini << " ymaxi: " << ymaxi);
// ---------------------------------------------------------------------------------------------
// Check if these dimensions make sense for the block size specified
double xside = xmax-xmin;
double yside = ymax-ymin;
const double tol = 0.01; // 1 cm error tolerance
// In order to be part of the block, xside and yside must be between
// blocksize and blocksize*sqrt(2)
if(xside > block_size-tol &&
xside < block_size*sqrt(2)+tol &&
yside > block_size-tol &&
yside < block_size*sqrt(2)+tol )
{
// -------------------------------------------------------------------------------------------------------
// Get the four farthest corners of the block - use OpenCV only on the region identified by PCL
// Get the pixel coordinates of the xmax and ymax indicies
int px_xmax = 0; int py_xmax = 0;
int px_ymax = 0; int py_ymax = 0;
getXYCoordinates( xmaxi, image_height, image_width, px_xmax, py_xmax);
getXYCoordinates( ymaxi, image_height, image_width, px_ymax, py_ymax);
// Get the pixel coordinates of the xmin and ymin indicies
int px_xmin = 0; int py_xmin = 0;
int px_ymin = 0; int py_ymin = 0;
getXYCoordinates( xmini, image_height, image_width, px_xmin, py_xmin);
getXYCoordinates( ymini, image_height, image_width, px_ymin, py_ymin);
ROS_DEBUG_STREAM_NAMED("perception","px_xmin " << px_xmin << " px_xmax: " << px_xmax << " py_ymin: " << py_ymin << " py_ymax: " << py_ymax );
// -------------------------------------------------------------------------------------------------------
// Change the frame of reference from the robot to the camera
// Create an array of all the x value options
const int x_values_a[] = {px_xmax, px_ymax, px_xmin, px_ymin};
const int y_values_a[] = {py_xmax, py_ymax, py_xmin, py_ymin};
// Turn it into a vector
std::vector<int> x_values (x_values_a, x_values_a + sizeof(x_values_a) / sizeof(x_values_a[0]));
std::vector<int> y_values (y_values_a, y_values_a + sizeof(y_values_a) / sizeof(y_values_a[0]));
// Find the min
int x1 = *std::min_element(x_values.begin(), x_values.end());
int y1 = *std::min_element(y_values.begin(), y_values.end());
// Find the max
int x2 = *std::max_element(x_values.begin(), x_values.end());
int y2 = *std::max_element(y_values.begin(), y_values.end());
ROS_DEBUG_STREAM_NAMED("perception","x1: " << x1 << " y1: " << y1 << " x2: " << x2 << " y2: " << y2);
// -------------------------------------------------------------------------------------------------------
// Expand the ROI by a fudge factor, if possible
const int FUDGE_FACTOR = 5; // pixels
if( x1 > FUDGE_FACTOR)
x1 -= FUDGE_FACTOR;
if( y1 > FUDGE_FACTOR )
y1 -= FUDGE_FACTOR;
if( x2 < image_width - FUDGE_FACTOR )
x2 += FUDGE_FACTOR;
if( y2 < image_height - FUDGE_FACTOR )
y2 += FUDGE_FACTOR;
ROS_DEBUG_STREAM_NAMED("perception","After Fudge Factor - x1: " << x1 << " y1: " << y1 << " x2: " << x2 << " y2: " << y2);
// -------------------------------------------------------------------------------------------------------
// Create ROI parameters
// (x1,y1)----------------------
// | |
// | ROI |
// | |
// |_____________________(x2,y2)|
// Create Region of Interest
int roi_width = x2 - x1;
int roi_height = y2 - y1;
cv::Rect region_of_interest = cv::Rect( x1, y1, roi_width, roi_height );
ROS_DEBUG_STREAM_NAMED("perception","ROI: x " << x1 << " -- y " << y1 << " -- height " << roi_height << " -- width " << roi_width );
// -------------------------------------------------------------------------------------------------------
// Find paramters of the block in pixel coordiantes
int block_center_x = x1 + 0.5*roi_width;
int block_center_y = y1 + 0.5*roi_height;
int block_center_z = block_size / 2; // TODO: make this better
const cv::Point block_center = cv::Point( block_center_x, block_center_y );
// -------------------------------------------------------------------------------------------------------
// Create a sub image of just the block
cv::Point a1 = cv::Point(x1, y1);
cv::Point a2 = cv::Point(x2, y2);
cv::rectangle( output_image, a1, a2, cv::Scalar(0, 255, 255), 1, 8);
// Crop image (doesn't actually copy the data)
cropped_image = full_input_image_gray(region_of_interest);
// -------------------------------------------------------------------------------------------------------
// Detect edges using canny
ROS_INFO_STREAM_NAMED("perception","Detecting edges using canny");
// Find edges
cv::Mat canny_output;
cv::Canny( cropped_image, canny_output, canny_threshold, canny_threshold*2, 3 );
// Get mini window stats
const int mini_width = canny_output.size.p[1];
const int mini_height = canny_output.size.p[0];
const cv::Size mini_size = canny_output.size();
const cv::Point mini_center = cv::Point( mini_width/2, mini_height/2 );
// Find contours
vector<vector<cv::Point> > contours;
vector<cv::Vec4i> hierarchy;
cv::findContours( canny_output, contours, hierarchy, CV_RETR_TREE, CV_CHAIN_APPROX_SIMPLE, cv::Point(0, 0) );
ROS_INFO_STREAM_NAMED("perception","Contours");
// Draw contours
cv::Mat drawing = cv::Mat::zeros( mini_size, CV_8UC3 );
ROS_INFO_STREAM_NAMED("perception","Drawing contours");
// Find the largest contour for getting the angle
double max_contour_length = 0;
int max_contour_length_i;
for( size_t i = 0; i< contours.size(); i++ )
{
double contour_length = cv::arcLength( contours[i], false );
if( contour_length > max_contour_length )
{
max_contour_length = contour_length;
max_contour_length_i = i;
}
//ROS_DEBUG_STREAM_NAMED("perception","Contour length = " << contour_length << " of index " << max_contour_length_i);
cv::Scalar color = cv::Scalar( (30 + i*10) % 255, (30 + i*10) % 255, (30 + i*10) % 255);
cv::drawContours( drawing, contours, (int)i, color, 1, 8, hierarchy, 0, cv::Point() );
//drawContours( image, contours, contourIdx, color, thickness, lineType, hierarchy, maxLevel, offset )
}
// -------------------------------------------------------------------------------------------------------
// Copy largest contour to main image
cv::Scalar color = cv::Scalar( 0, 255, 0 );
cv::drawContours( output_image, contours, (int)max_contour_length_i, color, 1, 8, hierarchy, 0, a1 );
//drawContours( image, contours, contourIdx, color, thickness, lineType, hierarchy, maxLevel, offset )
// -------------------------------------------------------------------------------------------------------
// Copy largest contour to seperate image
cv::Mat hough_input = cv::Mat::zeros( mini_size, CV_8UC1 );
cv::Mat hough_input_color;
cv::Scalar hough_color = cv::Scalar( 200 );
cv::drawContours( hough_input, contours, (int)max_contour_length_i, hough_color, 1, 8, hierarchy, 0 );
cv::cvtColor(hough_input, hough_input_color, CV_GRAY2BGR);
// -------------------------------------------------------------------------------------------------------
// Hough Transform
cv::Mat hough_drawing = cv::Mat::zeros( mini_size, CV_8UC3 );
std::vector<cv::Vec4i> lines;
ROS_DEBUG_STREAM_NAMED("perception","hough_rho " << hough_rho << " hough_theta " << hough_theta <<
" theta_converted " << (1/hough_theta)*CV_PI/180 << " hough_threshold " <<
hough_threshold << " hough_minLineLength " << hough_minLineLength <<
" hough_maxLineGap " << hough_maxLineGap );
cv::HoughLinesP(hough_input, lines, hough_rho, (1/hough_theta)*CV_PI/180, hough_threshold, hough_minLineLength, hough_maxLineGap);
ROS_WARN_STREAM_NAMED("perception","Found " << lines.size() << " lines");
std::vector<double> line_angles;
// Copy detected lines to the drawing image
for( size_t i = 0; i < lines.size(); i++ )
{
cv::Vec4i line = lines[i];
cv::line( hough_drawing, cv::Point(line[0], line[1]), cv::Point(line[2], line[3]),
cv::Scalar(255,255,255), 1, CV_AA);
// Error check
if(line[3] - line[1] == 0 && line[2] - line[0] == 0)
{
ROS_ERROR_STREAM_NAMED("perception","Line is actually two points at the origin, unable to calculate. TODO: handle better?");
continue;
}
// Find angle
double line_angle = atan2(line[3] - line[1], line[2] - line[0]); //in radian, degrees: * 180.0 / CV_PI;
// Reverse angle direction if negative
if( line_angle < 0 )
{
line_angle += CV_PI;
}
line_angles.push_back(line_angle);
ROS_DEBUG_STREAM_NAMED("perception","Hough Line angle: " << line_angle * 180.0 / CV_PI;);
}
double block_angle = 0; // the overall result of the block's angle
// Everything is based on the first angle
if( line_angles.size() == 0 ) // make sure we have at least 1 angle
{
ROS_ERROR_STREAM_NAMED("perception","No lines were found for this cluster, unable to calculate block angle");
}
else
{
calculateBlockAngle( line_angles, block_angle );
}
// -------------------------------------------------------------------------------------------------------
// Draw chosen angle
ROS_INFO_STREAM_NAMED("perception","Using block angle " << block_angle*180.0/CV_PI);
// Draw chosen angle on mini image
cv::Mat angle_drawing = cv::Mat::zeros( mini_size, CV_8UC3 );
int line_length = 0.5*double(mini_width); // have the line go 1/4 across the screen
int new_x = mini_center.x + line_length*cos( block_angle );
int new_y = mini_center.y + line_length*sin( block_angle );
ROS_INFO_STREAM("Origin (" << mini_center.x << "," << mini_center.y << ") New (" << new_x << "," << new_y <<
") length " << line_length << " angle " << block_angle <<
" mini width " << mini_width << " mini height " << mini_height);
cv::Point angle_point = cv::Point(new_x, new_y);
cv::line( angle_drawing, mini_center, angle_point, cv::Scalar(255,255,255), 1, CV_AA);
// Draw chosen angle on contours image
cv::line( hough_drawing, mini_center, angle_point, cv::Scalar(255,0, 255), 1, CV_AA);
// Draw chosen angle on main image
line_length = 0.75 * double(mini_width); // have the line go 1/2 across the box
new_x = block_center_x + line_length*cos( block_angle );
new_y = block_center_y + line_length*sin( block_angle );
ROS_INFO_STREAM_NAMED("perception",block_center_x << ", " << block_center_y << ", " << new_x << ", " << new_y);
angle_point = cv::Point(new_x, new_y);
cv::line( output_image, block_center, angle_point, cv::Scalar(255,0,255), 2, CV_AA);
// -------------------------------------------------------------------------------------------------------
// Get world coordinates
// Find the block's center point
double world_x1 = xmin+(xside)/2.0;
double world_y1 = ymin+(yside)/2.0;
double world_z1 = table_height + block_size / 2;
// Convert pixel coordiantes back to world coordinates
double world_x2 = cloud_transformed->at(new_x, new_y).x;
double world_y2 = cloud_transformed->at(new_x, new_y).y;
double world_z2 = world_z1; // is this even necessary?
// Get angle from two world coordinates...
double world_theta = abs( atan2(world_y2 - world_y1, world_x2 - world_x1) );
// Attempt to make all angles point in same direction
makeAnglesUniform( world_theta );
// -------------------------------------------------------------------------------------------------------
// GUI Stuff
// Copy the cluster image to the main image in the top left corner
if( top_image_overlay_x + mini_width < image_width )
{
const int common_height = 42;
cv::Rect small_roi_row0 = cv::Rect(top_image_overlay_x, common_height*0, mini_width, mini_height);
cv::Rect small_roi_row1 = cv::Rect(top_image_overlay_x, common_height*1, mini_width, mini_height);
cv::Rect small_roi_row2 = cv::Rect(top_image_overlay_x, common_height*2, mini_width, mini_height);
cv::Rect small_roi_row3 = cv::Rect(top_image_overlay_x, common_height*3, mini_width, mini_height);
drawing.copyTo( output_image(small_roi_row0) );
hough_input_color.copyTo( output_image(small_roi_row1) );
hough_drawing.copyTo( output_image(small_roi_row2) );
angle_drawing.copyTo( output_image(small_roi_row3) );
top_image_overlay_x += mini_width;
}
// figure out the position and the orientation of the block
//double angle = atan(block_size/((xside+yside)/2));
//double angle = atan( (xmaxy - xminy) / (xmax - xmin ) );
// Then add it to our set
//addBlock( xmin+(xside)/2.0, ymin+(yside)/2.0, zmax - block_size/2.0, angle);
//ROS_INFO_STREAM_NAMED("perception","FOUND -> xside: " << xside << " yside: " << yside << " angle: " << block_angle);
addBlock( world_x1, world_y1, world_z1, world_theta );
//addBlock( block_center_x, block_center_y, block_center_z, block_angle);
}
else
{
RcppExport SEXP treePhaser(SEXP Rsignal, SEXP RkeyFlow, SEXP RflowCycle,
SEXP Rcf, SEXP Rie, SEXP Rdr, SEXP Rbasecaller, SEXP RdiagonalStates,
SEXP RmodelFile, SEXP RmodelThreshold, SEXP Rxval, SEXP Ryval)
{
SEXP ret = R_NilValue;
char *exceptionMesg = NULL;
try {
Rcpp::NumericMatrix signal(Rsignal);
Rcpp::IntegerVector keyFlow(RkeyFlow);
string flowCycle = Rcpp::as<string>(RflowCycle);
Rcpp::NumericVector cf_vec(Rcf);
Rcpp::NumericVector ie_vec(Rie);
Rcpp::NumericVector dr_vec(Rdr);
string basecaller = Rcpp::as<string>(Rbasecaller);
unsigned int diagonalStates = Rcpp::as<int>(RdiagonalStates);
// Recalibration Variables
string model_file = Rcpp::as<string>(RmodelFile);
int model_threshold = Rcpp::as<int>(RmodelThreshold);
Rcpp::IntegerVector x_values(Rxval);
Rcpp::IntegerVector y_values(Ryval);
RecalibrationModel recalModel;
if (model_file.length() > 0) {
recalModel.InitializeModel(model_file, model_threshold);
}
ion::FlowOrder flow_order(flowCycle, flowCycle.length());
unsigned int nFlow = signal.cols();
unsigned int nRead = signal.rows();
if(basecaller != "treephaser-swan" && basecaller != "treephaser-solve" && basecaller != "dp-treephaser" && basecaller != "treephaser-adaptive") {
std::string exception = "base value for basecaller supplied: " + basecaller;
exceptionMesg = strdup(exception.c_str());
} else if (flowCycle.length() < nFlow) {
std::string exception = "Flow cycle is shorter than number of flows to solve";
exceptionMesg = strdup(exception.c_str());
} else {
// Prepare objects for holding and passing back results
Rcpp::NumericMatrix predicted_out(nRead,nFlow);
Rcpp::NumericMatrix residual_out(nRead,nFlow);
Rcpp::NumericMatrix norm_additive_out(nRead,nFlow);
Rcpp::NumericMatrix norm_multipl_out(nRead,nFlow);
std::vector< std::string> seq_out(nRead);
// Set up key flow vector
int nKeyFlow = keyFlow.size();
vector <int> keyVec(nKeyFlow);
for(int iFlow=0; iFlow < nKeyFlow; iFlow++)
keyVec[iFlow] = keyFlow(iFlow);
// Iterate over all reads
vector <float> sigVec(nFlow);
BasecallerRead read;
DPTreephaser dpTreephaser(flow_order);
dpTreephaser.SetStateProgression((diagonalStates>0));
// In contrast to pipeline, we always use droop here.
// To have the same behavior of treephaser-swan as in the pipeline, supply dr=0
bool per_read_phasing = true;
if (cf_vec.size() == 1) {
per_read_phasing = false;
dpTreephaser.SetModelParameters((double)cf_vec(0), (double)ie_vec(0), (double)dr_vec(0));
}
// Main loop iterating over reads and solving them
for(unsigned int iRead=0; iRead < nRead; iRead++) {
// Set phasing parameters for this read
if (per_read_phasing)
dpTreephaser.SetModelParameters((double)cf_vec(iRead), (double)ie_vec(iRead), (double)dr_vec(iRead));
// And load recalibration model
if (recalModel.is_enabled()) {
int my_x = (int)x_values(iRead);
int my_y = (int)y_values(iRead);
const vector<vector<vector<float> > > * aPtr = 0;
const vector<vector<vector<float> > > * bPtr = 0;
aPtr = recalModel.getAs(my_x, my_y);
bPtr = recalModel.getBs(my_x, my_y);
if (aPtr == 0 or bPtr == 0) {
cout << "Error finding a recalibration model for x: " << x_values(iRead) << " y: " << y_values(iRead);
cout << endl;
}
dpTreephaser.SetAsBs(aPtr, bPtr);
}
for(unsigned int iFlow=0; iFlow < nFlow; iFlow++)
sigVec[iFlow] = (float) signal(iRead,iFlow);
// Interface to just solve without any normalization
if (basecaller == "treephaser-solve") { // Interface to just solve without any normalization
read.SetData(sigVec, (int)nFlow);
}
else {
read.SetDataAndKeyNormalize(&(sigVec[0]), (int)nFlow, &(keyVec[0]), nKeyFlow-1);
}
// Execute the iterative solving-normalization routine
if (basecaller == "dp-treephaser") {
dpTreephaser.NormalizeAndSolve_GainNorm(read, nFlow);
}
else if (basecaller == "treephaser-solve") {
dpTreephaser.Solve(read, nFlow);
}
else if (basecaller == "treephaser-adaptive") {
dpTreephaser.NormalizeAndSolve_Adaptive(read, nFlow); // Adaptive normalization
}
else {
dpTreephaser.NormalizeAndSolve_SWnorm(read, nFlow); // sliding window adaptive normalization
}
seq_out[iRead].assign(read.sequence.begin(), read.sequence.end());
for(unsigned int iFlow=0; iFlow < nFlow; iFlow++) {
predicted_out(iRead,iFlow) = (double) read.prediction[iFlow];
residual_out(iRead,iFlow) = (double) read.normalized_measurements[iFlow] - read.prediction[iFlow];
norm_multipl_out(iRead,iFlow) = (double) read.multiplicative_correction.at(iFlow);
norm_additive_out(iRead,iFlow) = (double) read.additive_correction.at(iFlow);
}
}
// Store results
ret = Rcpp::List::create(Rcpp::Named("seq") = seq_out,
Rcpp::Named("predicted") = predicted_out,
Rcpp::Named("residual") = residual_out,
Rcpp::Named("norm_additive") = norm_additive_out,
Rcpp::Named("norm_multipl") = norm_multipl_out);
}
} catch(std::exception& ex) {
forward_exception_to_r(ex);
} catch(...) {
::Rf_error("c++ exception (unknown reason)");
}
if(exceptionMesg != NULL)
Rf_error(exceptionMesg);
return ret;
}
RcppExport SEXP treePhaserSim(SEXP Rsequence, SEXP RflowCycle, SEXP Rcf, SEXP Rie, SEXP Rdr,
SEXP Rmaxflows, SEXP RgetStates, SEXP RdiagonalStates,
SEXP RmodelFile, SEXP RmodelThreshold, SEXP Rxval, SEXP Ryval)
{
SEXP ret = R_NilValue;
char *exceptionMesg = NULL;
try {
Rcpp::StringVector sequences(Rsequence);
string flowCycle = Rcpp::as<string>(RflowCycle);
Rcpp::NumericMatrix cf_vec(Rcf);
Rcpp::NumericMatrix ie_vec(Rie);
Rcpp::NumericMatrix dr_vec(Rdr);
unsigned int max_flows = Rcpp::as<int>(Rmaxflows);
unsigned int get_states = Rcpp::as<int>(RgetStates);
unsigned int diagonalStates = Rcpp::as<int>(RdiagonalStates);
// Recalibration Variables
string model_file = Rcpp::as<string>(RmodelFile);
int model_threshold = Rcpp::as<int>(RmodelThreshold);
Rcpp::IntegerVector x_values(Rxval);
Rcpp::IntegerVector y_values(Ryval);
RecalibrationModel recalModel;
if (model_file.length() > 0) {
recalModel.InitializeModel(model_file, model_threshold);
}
ion::FlowOrder flow_order(flowCycle, flowCycle.length());
unsigned int nFlow = flow_order.num_flows();
unsigned int nRead = sequences.size();
max_flows = min(max_flows, nFlow);
// Prepare objects for holding and passing back results
Rcpp::NumericMatrix predicted_out(nRead,nFlow);
vector<vector<float> > query_states;
vector<int> hp_lengths;
// Iterate over all sequences
BasecallerRead read;
DPTreephaser dpTreephaser(flow_order);
bool per_read_phasing = true;
if (cf_vec.ncol() == 1) {
per_read_phasing = false;
dpTreephaser.SetModelParameters((double)cf_vec(0,0), (double)ie_vec(0,0), (double)dr_vec(0,0));
}
dpTreephaser.SetStateProgression((diagonalStates>0));
unsigned int max_length = (2*flow_order.num_flows());
for(unsigned int iRead=0; iRead<nRead; iRead++) {
string mySequence = Rcpp::as<std::string>(sequences(iRead));
read.sequence.clear();
read.sequence.reserve(2*flow_order.num_flows());
for(unsigned int iBase=0; iBase<mySequence.length() and iBase<max_length; ++iBase){
read.sequence.push_back(mySequence.at(iBase));
}
// Set phasing parameters for this read
if (per_read_phasing)
dpTreephaser.SetModelParameters((double)cf_vec(0,iRead), (double)ie_vec(0,iRead), (double)dr_vec(0,iRead));
// If you bothered specifying a recalibration model you probably want its effect on the predictions...
if (recalModel.is_enabled()) {
int my_x = (int)x_values(iRead);
int my_y = (int)y_values(iRead);
const vector<vector<vector<float> > > * aPtr = 0;
const vector<vector<vector<float> > > * bPtr = 0;
aPtr = recalModel.getAs(my_x, my_y);
bPtr = recalModel.getBs(my_x, my_y);
if (aPtr == 0 or bPtr == 0) {
cout << "Error finding a recalibration model for x: " << x_values(iRead) << " y: " << y_values(iRead);
cout << endl;
}
dpTreephaser.SetAsBs(aPtr, bPtr);
}
if (nRead == 1 and get_states > 0)
dpTreephaser.QueryAllStates(read, query_states, hp_lengths, max_flows);
else
dpTreephaser.Simulate(read, max_flows);
for(unsigned int iFlow=0; iFlow<nFlow and iFlow<max_flows; ++iFlow){
predicted_out(iRead,iFlow) = (double) read.prediction.at(iFlow);
}
}
// Store results
if (nRead == 1 and get_states > 0) {
Rcpp::NumericMatrix states(hp_lengths.size(), nFlow);
Rcpp::NumericVector HPlengths(hp_lengths.size());
for (unsigned int iHP=0; iHP<hp_lengths.size(); iHP++){
HPlengths(iHP) = (double)hp_lengths[iHP];
for (unsigned int iFlow=0; iFlow<nFlow; iFlow++)
states(iHP, iFlow) = (double)query_states.at(iHP).at(iFlow);
}
ret = Rcpp::List::create(Rcpp::Named("sig") = predicted_out,
Rcpp::Named("states") = states,
Rcpp::Named("HPlengths") = HPlengths);
} else {
ret = Rcpp::List::create(Rcpp::Named("sig") = predicted_out);
}
} catch(std::exception& ex) {
forward_exception_to_r(ex);
} catch(...) {
::Rf_error("c++ exception (unknown reason)");
}
if(exceptionMesg != NULL)
Rf_error(exceptionMesg);
return ret;
}