libpappsomspp
Library for mass spectrometry
|
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... | |
![]() | |
virtual | ~FilterNameInterface () |
![]() | |
virtual | ~FilterInterface () |
Protected Member Functions | |
void | buildFilterFromString (const QString &strBuildParams) override |
build this filter using a string More... | |
Trace & | nonConstFilter (Trace &data_points) |
Private Types | |
using | IndexIntensity = std::pair< std::size_t, double > |
using | ApexSPtr = std::shared_ptr< IndexIntensity > |
using | Cluster = std::vector< ApexSPtr > |
using | ClusterSPtr = std::shared_ptr< std::vector< ApexSPtr > > |
Private Member Functions | |
std::size_t | detectIsotopicClusters (const Trace &trace) |
Private Attributes | |
const double | nan = std::numeric_limits<double>::quiet_NaN() |
double | m_threshold |
double | m_noiseMean |
double | m_noiseStdDev |
Trace | m_helperTraceCopy |
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 |
IndexIntensity | m_prevApex = std::pair(0, nan) |
IndexIntensity | m_curApex = std::pair(0, nan) |
IndexIntensity | m_cur = std::pair(0, nan) |
IndexIntensity | m_prev = std::pair(0, nan) |
std::vector< ClusterSPtr > | m_isotopicClusters |
Static Private Attributes | |
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.
|
private |
Definition at line 126 of file filterlowintensitysignalremoval.h.
|
private |
Definition at line 127 of file filterlowintensitysignalremoval.h.
|
private |
Definition at line 128 of file filterlowintensitysignalremoval.h.
|
private |
Definition at line 75 of file filterlowintensitysignalremoval.h.
pappso::FilterLowIntensitySignalRemoval::FilterLowIntensitySignalRemoval | ( | double | mean, |
double | std_dev, | ||
double | threshold | ||
) |
Definition at line 51 of file filterlowintensitysignalremoval.cpp.
References m_noiseMean, m_noiseStdDev, and m_threshold.
pappso::FilterLowIntensitySignalRemoval::FilterLowIntensitySignalRemoval | ( | const QString & | parameters | ) |
Definition at line 60 of file filterlowintensitysignalremoval.cpp.
References buildFilterFromString().
pappso::FilterLowIntensitySignalRemoval::FilterLowIntensitySignalRemoval | ( | const FilterLowIntensitySignalRemoval & | other | ) |
Definition at line 67 of file filterlowintensitysignalremoval.cpp.
References m_noiseMean, m_noiseStdDev, and m_threshold.
|
virtual |
Definition at line 76 of file filterlowintensitysignalremoval.cpp.
|
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 97 of file filterlowintensitysignalremoval.cpp.
References m_noiseMean, m_noiseStdDev, m_threshold, and name().
Referenced by FilterLowIntensitySignalRemoval().
|
private |
Definition at line 120 of file filterlowintensitysignalremoval.cpp.
References INTRA_CLUSTER_INTER_PEAK_DISTANCE, m_cur, m_curApex, m_isotopicClusters, m_prev, m_prevApex, m_threshold, nan, and pappso::y.
Referenced by nonConstFilter().
|
overridevirtual |
Implements pappso::FilterInterface.
Definition at line 392 of file filterlowintensitysignalremoval.cpp.
References nonConstFilter().
double pappso::FilterLowIntensitySignalRemoval::getThreshold | ( | ) | const |
Definition at line 447 of file filterlowintensitysignalremoval.cpp.
References m_threshold.
|
overridevirtual |
Implements pappso::FilterNameInterface.
Definition at line 462 of file filterlowintensitysignalremoval.cpp.
Referenced by buildFilterFromString(), and toString().
Definition at line 403 of file filterlowintensitysignalremoval.cpp.
References detectIsotopicClusters(), m_helperTraceCopy, m_isotopicClusters, and pappso::DataPoint::toString().
Referenced by filter().
FilterLowIntensitySignalRemoval & pappso::FilterLowIntensitySignalRemoval::operator= | ( | const FilterLowIntensitySignalRemoval & | other | ) |
Definition at line 82 of file filterlowintensitysignalremoval.cpp.
References m_noiseMean, m_noiseStdDev, and m_threshold.
|
overridevirtual |
Return a string with the textual representation of the configuration data.
Implements pappso::FilterNameInterface.
Definition at line 455 of file filterlowintensitysignalremoval.cpp.
References m_threshold, and name().
|
staticconstexprprivate |
Definition at line 107 of file filterlowintensitysignalremoval.h.
Referenced by detectIsotopicClusters().
|
private |
Definition at line 123 of file filterlowintensitysignalremoval.h.
Referenced by detectIsotopicClusters().
|
private |
Definition at line 122 of file filterlowintensitysignalremoval.h.
Referenced by detectIsotopicClusters().
|
private |
Definition at line 109 of file filterlowintensitysignalremoval.h.
Referenced by nonConstFilter().
|
private |
Definition at line 131 of file filterlowintensitysignalremoval.h.
Referenced by detectIsotopicClusters(), and nonConstFilter().
|
private |
Definition at line 114 of file filterlowintensitysignalremoval.h.
|
private |
Definition at line 113 of file filterlowintensitysignalremoval.h.
|
private |
Definition at line 110 of file filterlowintensitysignalremoval.h.
|
private |
Definition at line 111 of file filterlowintensitysignalremoval.h.
|
private |
Definition at line 115 of file filterlowintensitysignalremoval.h.
|
private |
Definition at line 116 of file filterlowintensitysignalremoval.h.
|
private |
Definition at line 117 of file filterlowintensitysignalremoval.h.
|
private |
Definition at line 104 of file filterlowintensitysignalremoval.h.
Referenced by FilterLowIntensitySignalRemoval(), buildFilterFromString(), and operator=().
|
private |
Definition at line 105 of file filterlowintensitysignalremoval.h.
Referenced by FilterLowIntensitySignalRemoval(), buildFilterFromString(), and operator=().
|
private |
Definition at line 124 of file filterlowintensitysignalremoval.h.
Referenced by detectIsotopicClusters().
|
private |
Definition at line 121 of file filterlowintensitysignalremoval.h.
Referenced by detectIsotopicClusters().
|
private |
Definition at line 119 of file filterlowintensitysignalremoval.h.
|
private |
Definition at line 103 of file filterlowintensitysignalremoval.h.
Referenced by FilterLowIntensitySignalRemoval(), buildFilterFromString(), detectIsotopicClusters(), getThreshold(), operator=(), and toString().
|
private |
Definition at line 101 of file filterlowintensitysignalremoval.h.
Referenced by detectIsotopicClusters().