#include <filterresample.h>

Inheritance diagram for pappso::FilterResampleKeepPointInPolygon:

Public Member Functions
	FilterResampleKeepPointInPolygon ()

	FilterResampleKeepPointInPolygon (const SelectionPolygon &selection_polygon, DataKind data_kind)

	FilterResampleKeepPointInPolygon (const SelectionPolygonSpecVector &selection_polygon_specs)

	FilterResampleKeepPointInPolygon (const FilterResampleKeepPointInPolygon &other)

virtual	~FilterResampleKeepPointInPolygon ()

void	newSelectionPolygonSpec (const SelectionPolygonSpec &selection_polygon_spec)

FilterResampleKeepPointInPolygon &	operator= (const FilterResampleKeepPointInPolygon &other)

Trace &	filter (Trace &trace) const override

Trace &	filter (Trace &trace, double dt_value, double rt_value) const

virtual Trace &	filter (Trace &data_points) const=0

Public Member Functions inherited from pappso::FilterInterface
virtual	~FilterInterface ()

Private Attributes
std::vector< SelectionPolygonSpec >	m_selectionPolygonSpecs

double	m_lowestMz = std::numeric_limits<double>::max()

double	m_greatestMz = std::numeric_limits<double>::min()

Detailed Description

Definition at line 105 of file filterresample.h.

Constructor & Destructor Documentation

◆ FilterResampleKeepPointInPolygon() [1/4]

pappso::FilterResampleKeepPointInPolygon::FilterResampleKeepPointInPolygon ( )

Definition at line 242 of file filterresample.cpp.

243 {

244 }

◆ FilterResampleKeepPointInPolygon() [2/4]

pappso::FilterResampleKeepPointInPolygon::FilterResampleKeepPointInPolygon	(	const SelectionPolygon &	selection_polygon,
		DataKind	data_kind
	)

Definition at line 247 of file filterresample.cpp.

 {
   // It is assumed that the selection polygon always has x:MZ and y:DT|RT
   // depending on the spec data kind.
  
   m_selectionPolygonSpecs.push_back(
     SelectionPolygonSpec(selection_polygon, data_kind));
  
   m_lowestMz =
     m_selectionPolygonSpecs.front().selectionPolygon.getBottomMostPoint().y();
   m_greatestMz =
     m_selectionPolygonSpecs.front().selectionPolygon.getTopMostPoint().y();
 }

References m_greatestMz, m_lowestMz, and m_selectionPolygonSpecs.

◆ FilterResampleKeepPointInPolygon() [3/4]

pappso::FilterResampleKeepPointInPolygon::FilterResampleKeepPointInPolygon ( const SelectionPolygonSpecVector & selection_polygon_specs )

Definition at line 263 of file filterresample.cpp.

 {
   qDebug();
  
   m_selectionPolygonSpecs.assign(selection_polygon_specs.begin(),
                                  selection_polygon_specs.end());
  
   for(auto &&item : m_selectionPolygonSpecs)
     {
       m_lowestMz =
         std::min(m_lowestMz, item.selectionPolygon.getBottomMostPoint().y());
  
       m_greatestMz =
         std::max(m_greatestMz, item.selectionPolygon.getTopMostPoint().y());
     }
 }

References m_greatestMz, m_lowestMz, and m_selectionPolygonSpecs.

◆ FilterResampleKeepPointInPolygon() [4/4]

pappso::FilterResampleKeepPointInPolygon::FilterResampleKeepPointInPolygon ( const FilterResampleKeepPointInPolygon & other )

Definition at line 282 of file filterresample.cpp.

 {
   qDebug();
  
   m_selectionPolygonSpecs.assign(other.m_selectionPolygonSpecs.begin(),
                                  other.m_selectionPolygonSpecs.end());
  
   for(auto &&item : m_selectionPolygonSpecs)
     {
       m_lowestMz =
         std::min(m_lowestMz, item.selectionPolygon.getBottomMostPoint().y());
  
       m_greatestMz =
         std::max(m_greatestMz, item.selectionPolygon.getTopMostPoint().y());
     }
 }

References m_greatestMz, m_lowestMz, and m_selectionPolygonSpecs.

◆ ~FilterResampleKeepPointInPolygon()

virtual pappso::FilterResampleKeepPointInPolygon::~FilterResampleKeepPointInPolygon ( )

inlinevirtual

Definition at line 119 of file filterresample.h.

119 {};

Member Function Documentation

◆ filter() [1/3]

virtual Trace& pappso::FilterInterface::filter

◆ filter() [2/3]

Trace& pappso::FilterResampleKeepPointInPolygon::filter ( Trace & trace ) const

overridevirtual

Implements pappso::FilterInterface.

◆ filter() [3/3]

Trace & pappso::FilterResampleKeepPointInPolygon::filter	(	Trace &	trace,
		double	dt_value,
		double	rt_value
	)		const

Definition at line 346 of file filterresample.cpp.

 {
   // Each time a new selection polygon spec is added, the lowest and greatest
   // m/z values are computed. We use these values to remove from the spectrum
   // all the points that are outside of that lowest-gratest range.
  
   // Find the iterator to the most front of the DataPoint vector (mass
   // spectrum).
  
   // Note that the m_lowestMz and m_greatestMz are set during construction of
   // this FilterResampleKeepPointInPolygon filter using the
   // selection polygon specs.
  
   qDebug() << "The lowest and greatest m/z values:" << m_lowestMz << "and"
            << m_greatestMz;
  
   // Start by filtering away all the data points outside of the
   // [m_lowestMz--m_greatestMz] range.
  
   FilterResampleKeepXRange the_filter(m_lowestMz, m_greatestMz);
  
   trace = the_filter.filter(trace);
  
   // Now iterate in all the data points remaining in the trace and for each
   // point craft a "virtual" point using the dt|rt value and the m/z value of
   // the data point (data_point.x).
  
   auto begin_it = trace.begin();
   auto end_it   = trace.end();
  
   qDebug() << "Iterating in the m/z range:" << begin_it->x << "-"
            << std::prev(end_it)->x;
  
   // Start at the end of the range. The iter is outside of the requested range,
   // in fact, as shown using iter-- below.
   auto iter = end_it;
  
   while(iter > begin_it)
     {
       // Immediately go to the last data point of the desired iteration range of
       // the trace that we need to filter.  Remember that end() is not pointing
       // to any vector item, but past the last one.
       iter--;
  
       qDebug() << "Iterating in trace data point with m/z value:" << iter->x;
  
       // Now that we have the m/z value, we can check it, in combination with
       // the value in the selection polygon spec (to make a point) against the
       // various selection polygon specs in our member vector.
  
       double checked_value;
  
       for(auto &&spec : m_selectionPolygonSpecs)
         {
           // qDebug() << "Iterating in selection polygon spec:" <<
           // spec.toString();
  
           if(spec.dataKind == DataKind::dt)
             {
               if(dt_value == -1)
                 qFatal("Programming error.");
  
               checked_value = dt_value;
  
               // qDebug() << "The data kind: dt.";
             }
           else if(spec.dataKind == DataKind::rt)
             {
               checked_value = rt_value;
  
               // qDebug() << "The data kind: rt.";
             }
           else
             qFatal("Programming error.");
  
           // First version doing the whole computation on the basis of the
           // selection polygon's all faces.
           //
           if(!spec.selectionPolygon.contains(QPointF(checked_value, iter->x)))
             iter = trace.erase(iter);
  
 #if 0 
  
           //This code does not work because depending on the orientation of the
             //skewed selection polygon (left bottom to right top or left top to
                 //right bottom or or Or depending on the axes of the
                 //bi-dimensional colormap, requiring transposition or not), the
             //notion of "left line" and of "right line" changes.
  
           // Second version checking that point is right of left vertical line
           // of polygon and left of right vertical line.
  
           // double res = sideofline(XX;YY;xA;yA;xB;yB) =
           // (xB-xA) * (YY-yA) - (yB-yA) * (XX-xA)
  
           // If res == 0, the point is on the line
           // If rest < 0, the point is on the right of the line
           // If rest > 0, the point is on the left of the line
  
           // Left vertical line of the polygon
  
           // Bottom point
           double xA_left =
             spec.selectionPolygon.getPoint(PointSpecs::BOTTOM_LEFT_POINT).x();
           double yA_left =
             spec.selectionPolygon.getPoint(PointSpecs::BOTTOM_LEFT_POINT).y();
  
           // Top point
           double xB_left =
             spec.selectionPolygon.getPoint(PointSpecs::TOP_LEFT_POINT).x();
           double yB_left =
             spec.selectionPolygon.getPoint(PointSpecs::TOP_LEFT_POINT).y();
  
           qDebug() << "The left line goes: (" << xA_left << "," << yA_left
                    << ")->(" << xB_left << "," << yB_left << ")";
  
           if((xB_left - xA_left) * (iter->x - yA_left) -
                (yB_left - yA_left) * (checked_value - xA_left) >
              0)
             {
               // The point is left of the left line. We can remove the point
               // from the mass spectrum.
  
               qDebug() << qSetRealNumberPrecision(10)
                        << "Filtered out point (left of left line):"
                        << checked_value << "-" << iter->x;
  
               iter = trace.erase(iter);
  
               // No need to go on with the analysis, just go to the next (that
               // is, previous, since we iterate backwards) data point.
  
               continue;
             }
           else
             {
               qDebug() << qSetRealNumberPrecision(10)
                        << "Kept point (right of left line):" << checked_value
                        << "-" << iter->x;
             }
  
           // Right vertical line of the polygon
  
           // Bottom point
           double xA_right =
             spec.selectionPolygon.getPoint(PointSpecs::BOTTOM_RIGHT_POINT).x();
           double yA_right =
             spec.selectionPolygon.getPoint(PointSpecs::BOTTOM_RIGHT_POINT).y();
  
           // Top point
           double xB_right =
             spec.selectionPolygon.getPoint(PointSpecs::TOP_RIGHT_POINT).x();
           double yB_right =
             spec.selectionPolygon.getPoint(PointSpecs::TOP_RIGHT_POINT).y();
  
           qDebug() << "The right line goes: (" << xA_right << "," << yA_right
                    << ")->(" << xB_right << "," << yB_right << ")";
  
           if((xB_right - xA_right) * (iter->x - yA_right) -
                (yB_right - yA_right) * (checked_value - xA_right) <
              0)
             {
               qDebug() << qSetRealNumberPrecision(10)
                        << "Filtered out point (right of right line):"
                        << checked_value << "-" << iter->x;
  
               // The point is right of the right line. We can remove the point
               // from the mass spectrum.
               iter = trace.erase(iter);
  
               // Here, continue is implicit.
               // No need to go on with the analysis, just go to the next (that
               // is, previous, since we iterate backwards) data point.
               // continue;
             }
           else
             {
               if(iter->x >= 449 && iter->x <= 450 && checked_value > 19.5 &&
                  checked_value < 20)
                 qDebug()
                   << qSetRealNumberPrecision(10)
                   << "SHOULD NOT Definitively kept point (left of right line):"
                   << checked_value << "-" << iter->x;
               else
                 qDebug()
                   << qSetRealNumberPrecision(10)
                   << "MIGHT Definitively kept point (left of right line):"
                   << checked_value << "-" << iter->x;
             }
 #endif
         }
       // End of
       // for(auto &&spec : m_selectionPolygonSpecs)
     }
   // End of
   // while(iter > begin_it)
  
   return trace;
 }

References pappso::BOTTOM_LEFT_POINT, pappso::BOTTOM_RIGHT_POINT, pappso::dt, pappso::FilterResampleKeepXRange::filter(), m_greatestMz, m_lowestMz, m_selectionPolygonSpecs, pappso::rt, pappso::TOP_LEFT_POINT, and pappso::TOP_RIGHT_POINT.

◆ newSelectionPolygonSpec()

void pappso::FilterResampleKeepPointInPolygon::newSelectionPolygonSpec ( const SelectionPolygonSpec & selection_polygon_spec )

Definition at line 302 of file filterresample.cpp.

 {
   // It is assumed that the selection polygon always has x:MZ and y:DT|RT
   // depending on the spec data kind.
  
   m_selectionPolygonSpecs.push_back(selection_polygon_spec);
  
   m_lowestMz = std::min(
     m_lowestMz,
     m_selectionPolygonSpecs.back().selectionPolygon.getBottomMostPoint().y());
  
   m_greatestMz = std::max(
     m_greatestMz,
     m_selectionPolygonSpecs.back().selectionPolygon.getTopMostPoint().y());
 }

References m_greatestMz, m_lowestMz, and m_selectionPolygonSpecs.

◆ operator=()

FilterResampleKeepPointInPolygon & pappso::FilterResampleKeepPointInPolygon::operator= ( const FilterResampleKeepPointInPolygon & other )

Definition at line 321 of file filterresample.cpp.

 {
   if(this == &other)
     return *this;
  
   m_selectionPolygonSpecs.assign(other.m_selectionPolygonSpecs.begin(),
                                  other.m_selectionPolygonSpecs.end());
  
   m_lowestMz   = other.m_lowestMz;
   m_greatestMz = other.m_greatestMz;
  
   return *this;
 }

References m_greatestMz, m_lowestMz, and m_selectionPolygonSpecs.

Member Data Documentation

◆ m_greatestMz

double pappso::FilterResampleKeepPointInPolygon::m_greatestMz = std::numeric_limits<double>::min()

private

Definition at line 135 of file filterresample.h.

Referenced by FilterResampleKeepPointInPolygon(), filter(), newSelectionPolygonSpec(), and operator=().

◆ m_lowestMz

double pappso::FilterResampleKeepPointInPolygon::m_lowestMz = std::numeric_limits<double>::max()

private

Definition at line 134 of file filterresample.h.

Referenced by FilterResampleKeepPointInPolygon(), filter(), newSelectionPolygonSpec(), and operator=().

◆ m_selectionPolygonSpecs

std::vector<SelectionPolygonSpec> pappso::FilterResampleKeepPointInPolygon::m_selectionPolygonSpecs

private

Definition at line 133 of file filterresample.h.

Referenced by FilterResampleKeepPointInPolygon(), filter(), newSelectionPolygonSpec(), and operator=().

The documentation for this class was generated from the following files:

pappsomspp/processing/filters/filterresample.h
pappsomspp/processing/filters/filterresample.cpp

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ FilterResampleKeepPointInPolygon() [1/4]

◆ FilterResampleKeepPointInPolygon() [2/4]

◆ FilterResampleKeepPointInPolygon() [3/4]

◆ FilterResampleKeepPointInPolygon() [4/4]

◆ ~FilterResampleKeepPointInPolygon()

Member Function Documentation

◆ filter() [1/3]

◆ filter() [2/3]

◆ filter() [3/3]

◆ newSelectionPolygonSpec()

◆ operator=()

Member Data Documentation

◆ m_greatestMz

◆ m_lowestMz

◆ m_selectionPolygonSpecs