libpappsomspp
Library for mass spectrometry
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Redefines the floor intensity of the Trace. More...
#include <filterlowintensitysignalremoval.h>
Public Member Functions | |
FilterLowIntensitySignalRemoval (double mean, double std_dev, double threshold) | |
FilterLowIntensitySignalRemoval (const QString ¶meters) | |
FilterLowIntensitySignalRemoval (const FilterLowIntensitySignalRemoval &other) | |
virtual | ~FilterLowIntensitySignalRemoval () |
FilterLowIntensitySignalRemoval & | operator= (const FilterLowIntensitySignalRemoval &other) |
Trace & | filter (Trace &data_points) const override |
double | getThreshold () const |
QString | name () const override |
QString | toString () const override |
Return a string with the textual representation of the configuration data. More... | |
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virtual | ~FilterNameInterface () |
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virtual | ~FilterInterface () |
Protected Member Functions | |
void | buildFilterFromString (const QString &strBuildParams) override |
build this filter using a string More... | |
Trace & | nonConstFilter (Trace &data_points) |
std::size_t | detectClusterApices (const Trace &trace) |
Trace::const_iterator | backwardFindApex (const Trace &trace, Trace::const_iterator iter, double distance_threshold) |
Trace::const_iterator | forwardFindApex (const Trace &trace, Trace::const_iterator iter, double distance_threshold) |
Trace | reconstructTrace (const Trace &trace) |
Private Types | |
using | TraceCIter = Trace::const_iterator |
using | ClusterApices = std::vector< TraceCIter > |
using | ApicesSPtr = std::shared_ptr< ClusterApices > |
Private Attributes | |
double | m_threshold |
double | m_noiseMean |
double | m_noiseStdDev |
const std::size_t | m_minIntPointCount = 5 |
const std::size_t | m_minIntStdDevFactor = 2 |
double | m_min |
double | m_max |
double | m_minMean |
double | m_minStdDev |
double | m_noiseLevel |
bool | m_seen_upward_phase = false |
TraceCIter | m_prevApex = static_cast<Trace::const_iterator>(0) |
TraceCIter | m_curApex = static_cast<Trace::const_iterator>(0) |
TraceCIter | m_curIter = static_cast<Trace::const_iterator>(0) |
TraceCIter | m_prevIter = static_cast<Trace::const_iterator>(0) |
std::vector< ApicesSPtr > | m_clusters |
Static Private Attributes | |
static constexpr double | nan = std::numeric_limits<double>::quiet_NaN() |
constexpr static double | INTRA_CLUSTER_INTER_PEAK_DISTANCE = 1.1 |
Redefines the floor intensity of the Trace.
The amplitude of the trace is computed (maxValue - minValue) Its fraction is calculated = amplitude * (percentage / 100) The threshold value is computed as (minValue + fraction)
When the values to be filtered are below that threshold they acquire that threshold value.
When the values to be filtered are above that threshold they remain unchanged.
This effectively re-floors the values to threshold.
Definition at line 71 of file filterlowintensitysignalremoval.h.
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Definition at line 138 of file filterlowintensitysignalremoval.h.
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Definition at line 137 of file filterlowintensitysignalremoval.h.
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Definition at line 129 of file filterlowintensitysignalremoval.h.
pappso::FilterLowIntensitySignalRemoval::FilterLowIntensitySignalRemoval | ( | double | mean, |
double | std_dev, | ||
double | threshold | ||
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Definition at line 52 of file filterlowintensitysignalremoval.cpp.
References m_noiseMean, m_noiseStdDev, and m_threshold.
pappso::FilterLowIntensitySignalRemoval::FilterLowIntensitySignalRemoval | ( | const QString & | parameters | ) |
Definition at line 61 of file filterlowintensitysignalremoval.cpp.
References buildFilterFromString().
pappso::FilterLowIntensitySignalRemoval::FilterLowIntensitySignalRemoval | ( | const FilterLowIntensitySignalRemoval & | other | ) |
Definition at line 68 of file filterlowintensitysignalremoval.cpp.
References m_noiseMean, m_noiseStdDev, and m_threshold.
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Definition at line 77 of file filterlowintensitysignalremoval.cpp.
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Definition at line 388 of file filterlowintensitysignalremoval.cpp.
Referenced by reconstructTrace().
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overrideprotectedvirtual |
build this filter using a string
strBuildParams | a string coding the filter and its parameters "filterName|param1;param2;param3" |
Implements pappso::FilterNameInterface.
Definition at line 98 of file filterlowintensitysignalremoval.cpp.
References m_noiseMean, m_noiseStdDev, m_threshold, and name().
Referenced by FilterLowIntensitySignalRemoval().
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Definition at line 121 of file filterlowintensitysignalremoval.cpp.
References INTRA_CLUSTER_INTER_PEAK_DISTANCE, m_clusters, m_curApex, m_curIter, m_prevApex, m_prevIter, and m_threshold.
Referenced by nonConstFilter().
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Implements pappso::FilterInterface.
Definition at line 598 of file filterlowintensitysignalremoval.cpp.
References nonConstFilter().
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Definition at line 457 of file filterlowintensitysignalremoval.cpp.
Referenced by reconstructTrace().
double pappso::FilterLowIntensitySignalRemoval::getThreshold | ( | ) | const |
Definition at line 641 of file filterlowintensitysignalremoval.cpp.
References m_threshold.
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Implements pappso::FilterNameInterface.
Definition at line 656 of file filterlowintensitysignalremoval.cpp.
Referenced by buildFilterFromString(), and toString().
Definition at line 609 of file filterlowintensitysignalremoval.cpp.
References detectClusterApices(), and reconstructTrace().
Referenced by filter().
FilterLowIntensitySignalRemoval & pappso::FilterLowIntensitySignalRemoval::operator= | ( | const FilterLowIntensitySignalRemoval & | other | ) |
Definition at line 83 of file filterlowintensitysignalremoval.cpp.
References m_noiseMean, m_noiseStdDev, and m_threshold.
Definition at line 526 of file filterlowintensitysignalremoval.cpp.
References backwardFindApex(), forwardFindApex(), INTRA_CLUSTER_INTER_PEAK_DISTANCE, m_clusters, and pappso::MapTrace::toTrace().
Referenced by nonConstFilter().
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Return a string with the textual representation of the configuration data.
Implements pappso::FilterNameInterface.
Definition at line 649 of file filterlowintensitysignalremoval.cpp.
References m_threshold, and name().
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Definition at line 116 of file filterlowintensitysignalremoval.h.
Referenced by detectClusterApices(), and reconstructTrace().
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Definition at line 141 of file filterlowintensitysignalremoval.h.
Referenced by detectClusterApices(), and reconstructTrace().
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Definition at line 133 of file filterlowintensitysignalremoval.h.
Referenced by detectClusterApices().
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Definition at line 134 of file filterlowintensitysignalremoval.h.
Referenced by detectClusterApices().
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Definition at line 122 of file filterlowintensitysignalremoval.h.
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Definition at line 121 of file filterlowintensitysignalremoval.h.
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Definition at line 118 of file filterlowintensitysignalremoval.h.
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Definition at line 119 of file filterlowintensitysignalremoval.h.
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Definition at line 123 of file filterlowintensitysignalremoval.h.
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Definition at line 124 of file filterlowintensitysignalremoval.h.
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Definition at line 125 of file filterlowintensitysignalremoval.h.
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Definition at line 113 of file filterlowintensitysignalremoval.h.
Referenced by FilterLowIntensitySignalRemoval(), buildFilterFromString(), and operator=().
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Definition at line 114 of file filterlowintensitysignalremoval.h.
Referenced by FilterLowIntensitySignalRemoval(), buildFilterFromString(), and operator=().
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Definition at line 132 of file filterlowintensitysignalremoval.h.
Referenced by detectClusterApices().
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Definition at line 135 of file filterlowintensitysignalremoval.h.
Referenced by detectClusterApices().
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Definition at line 127 of file filterlowintensitysignalremoval.h.
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Definition at line 112 of file filterlowintensitysignalremoval.h.
Referenced by FilterLowIntensitySignalRemoval(), buildFilterFromString(), detectClusterApices(), getThreshold(), operator=(), and toString().
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Definition at line 110 of file filterlowintensitysignalremoval.h.