OpenMS  3.0.0
ContinuousWaveletTransformNumIntegration.h
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31 // $Maintainer: Timo Sachsenberg $
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35 
36 #pragma once
37 
38 #include <cmath>
39 
42 
43 
44 #ifdef DEBUG_PEAK_PICKING
45 #include <iostream>
46 #include <fstream>
47 #endif
48 
49 namespace OpenMS
50 {
58  {
59 public:
62 
70 
71 
75  {}
76 
79 
93  template <typename InputPeakIterator>
94  void transform(InputPeakIterator begin_input,
95  InputPeakIterator end_input,
96  float resolution)
97  {
98 #ifdef DEBUG_PEAK_PICKING
99  std::cout << "ContinuousWaveletTransformNumIntegration::transform: start " << begin_input->getMZ() << " until " << (end_input - 1)->getMZ() << std::endl;
100 #endif
101  if (fabs(resolution - 1) < 0.0001)
102  {
103  // resolution = 1 corresponds to the cwt at supporting points which have a distance corresponding to the minimal spacing in [begin_input,end_input)
104  SignedSize n = distance(begin_input, end_input);
105  signal_length_ = n;
106 
107  signal_.clear();
108  signal_.resize(n);
109 
110  // TODO avoid to compute the cwt for the zeros in signal
111 #ifdef DEBUG_PEAK_PICKING
112  std::cout << "---------START TRANSFORM---------- \n";
113 #endif
114  InputPeakIterator help = begin_input;
115  for (int i = 0; i < n; ++i)
116  {
117  signal_[i].setMZ(help->getMZ());
118  signal_[i].setIntensity((Peak1D::IntensityType)integrate_(help, begin_input, end_input));
119  ++help;
120  }
121 #ifdef DEBUG_PEAK_PICKING
122  std::cout << "---------END TRANSFORM----------" << std::endl;
123 #endif
124  // no zeropadding
125  begin_right_padding_ = n;
126  end_left_padding_ = -1;
127  }
128  else
129  {
130  SignedSize n = SignedSize(resolution * distance(begin_input, end_input));
131  double origin = begin_input->getMZ();
132  double spacing = ((end_input - 1)->getMZ() - origin) / (n - 1);
133 
134  std::vector<double> processed_input(n);
135  signal_.clear();
136  signal_.resize(n);
137 
138  InputPeakIterator it_help = begin_input;
139  processed_input[0] = it_help->getIntensity();
140 
141  double x;
142  for (SignedSize k = 1; k < n; ++k)
143  {
144  x = origin + k * spacing;
145  // go to the real data point next to x
146  while (((it_help + 1) < end_input) && ((it_help + 1)->getMZ() < x))
147  {
148  ++it_help;
149  }
150  processed_input[k] = getInterpolatedValue_(x, it_help);
151  }
152 
153  // TODO avoid to compute the cwt for the zeros in signal
154  for (Int i = 0; i < n; ++i)
155  {
156  signal_[i].setMZ(origin + i * spacing);
157  signal_[i].setIntensity((Peak1D::IntensityType)integrate_(processed_input, spacing, i));
158  }
159 
160  begin_right_padding_ = n;
161  end_left_padding_ = -1;
162  }
163  }
164 
175  void init(double scale, double spacing) override;
176 
177 protected:
178 
180  template <typename InputPeakIterator>
181  double integrate_(InputPeakIterator x, InputPeakIterator first, InputPeakIterator last)
182  {
183 #ifdef DEBUG_PEAK_PICKING
184  std::cout << "integrate_" << std::endl;
185 #endif
186 
187  double v = 0.;
188  double middle_spacing = wavelet_.size() * spacing_;
189 
190  double start_pos = ((x->getMZ() - middle_spacing) > first->getMZ()) ? (x->getMZ() - middle_spacing)
191  : first->getMZ();
192  double end_pos = ((x->getMZ() + middle_spacing) < (last - 1)->getMZ()) ? (x->getMZ() + middle_spacing)
193  : (last - 1)->getMZ();
194 
195  InputPeakIterator help = x;
196 
197 #ifdef DEBUG_PEAK_PICKING
198  std::cout << "integrate from middle to start_pos " << help->getMZ() << " until " << start_pos << std::endl;
199 #endif
200 
201  //integrate from middle to start_pos
202  while ((help != first) && ((help - 1)->getMZ() > start_pos))
203  {
204  // search for the corresponding data point of help in the wavelet (take the left most adjacent point)
205  double distance = fabs(x->getMZ() - help->getMZ());
206  Size index_w_r = (Size) Math::round(distance / spacing_);
207  if (index_w_r >= wavelet_.size())
208  {
209  index_w_r = wavelet_.size() - 1;
210  }
211  double wavelet_right = wavelet_[index_w_r];
212 
213 #ifdef DEBUG_PEAK_PICKING
214  std::cout << "distance x help " << distance << std::endl;
215  std::cout << "distance in wavelet_ " << index_w_r * spacing_ << std::endl;
216  std::cout << "wavelet_right " << wavelet_right << std::endl;
217 #endif
218 
219  // search for the corresponding datapoint for (help-1) in the wavelet (take the left most adjacent point)
220  distance = fabs(x->getMZ() - (help - 1)->getMZ());
221  Size index_w_l = (Size) Math::round(distance / spacing_);
222  if (index_w_l >= wavelet_.size())
223  {
224  index_w_l = wavelet_.size() - 1;
225  }
226  double wavelet_left = wavelet_[index_w_l];
227 
228  // start the interpolation for the true value in the wavelet
229 
230 #ifdef DEBUG_PEAK_PICKING
231  std::cout << " help-1 " << (help - 1)->getMZ() << " distance x, help-1" << distance << std::endl;
232  std::cout << "distance in wavelet_ " << index_w_l * spacing_ << std::endl;
233  std::cout << "wavelet_ at left " << wavelet_left << std::endl;
234 
235  std::cout << " intensity " << fabs((help - 1)->getMZ() - help->getMZ()) / 2. << " * " << (help - 1)->getIntensity() << " * " << wavelet_left << " + " << (help)->getIntensity() << "* " << wavelet_right
236  << std::endl;
237 #endif
238 
239  v += fabs((help - 1)->getMZ() - help->getMZ()) / 2. * ((help - 1)->getIntensity() * wavelet_left + help->getIntensity() * wavelet_right);
240  --help;
241  }
242 
243 
244  //integrate from middle to end_pos
245  help = x;
246 #ifdef DEBUG_PEAK_PICKING
247  std::cout << "integrate from middle to endpos " << (help)->getMZ() << " until " << end_pos << std::endl;
248 #endif
249  while ((help != (last - 1)) && ((help + 1)->getMZ() < end_pos))
250  {
251  // search for the corresponding datapoint for help in the wavelet (take the left most adjacent point)
252  double distance = fabs(x->getMZ() - help->getMZ());
253  Size index_w_l = (Size) Math::round(distance / spacing_);
254  if (index_w_l >= wavelet_.size())
255  {
256  index_w_l = wavelet_.size() - 1;
257  }
258  double wavelet_left = wavelet_[index_w_l];
259 
260 #ifdef DEBUG_PEAK_PICKING
261  std::cout << " help " << (help)->getMZ() << " distance x, help" << distance << std::endl;
262  std::cout << "distance in wavelet_ " << index_w_l * spacing_ << std::endl;
263  std::cout << "wavelet_ at left " << wavelet_left << std::endl;
264 #endif
265 
266  // search for the corresponding datapoint for (help+1) in the wavelet (take the left most adjacent point)
267  distance = fabs(x->getMZ() - (help + 1)->getMZ());
268  Size index_w_r = (Size) Math::round(distance / spacing_);
269  if (index_w_r >= wavelet_.size())
270  {
271  index_w_r = wavelet_.size() - 1;
272  }
273  double wavelet_right = wavelet_[index_w_r];
274 
275 #ifdef DEBUG_PEAK_PICKING
276  std::cout << " help+1 " << (help + 1)->getMZ() << " distance x, help+1" << distance << std::endl;
277  std::cout << "distance in wavelet_ " << index_w_r * spacing_ << std::endl;
278  std::cout << "wavelet_ at right " << wavelet_right << std::endl;
279 #endif
280 
281  v += fabs(help->getMZ() - (help + 1)->getMZ()) / 2. * (help->getIntensity() * wavelet_left + (help + 1)->getIntensity() * wavelet_right);
282  ++help;
283  }
284 
285 
286 #ifdef DEBUG_PEAK_PICKING
287  std::cout << "return" << (v / sqrt(scale_)) << std::endl;
288 #endif
289  return v / sqrt(scale_);
290  }
291 
293  double integrate_(const std::vector<double> & processed_input, double spacing_data, int index);
294 
296  inline double marr_(const double x) const
297  {
298  return (1 - x * x) * exp(-x * x / 2);
299  }
300 
301  };
302 } //namespace OpenMS
OpenMS::ContinuousWaveletTransform
This class is the base class of the continuous wavelet transformation.
Definition: ContinuousWaveletTransform.h:46
OpenMS::ContinuousWaveletTransform::signal_length_
SignedSize signal_length_
Definition: ContinuousWaveletTransform.h:225
OpenMS::ContinuousWaveletTransform::spacing_
double spacing_
Definition: ContinuousWaveletTransform.h:224
OpenMS::ContinuousWaveletTransform::end_left_padding_
SignedSize end_left_padding_
Definition: ContinuousWaveletTransform.h:230
OpenMS::ContinuousWaveletTransformNumIntegration::transform
void transform(InputPeakIterator begin_input, InputPeakIterator end_input, float resolution)
Computes the wavelet transform of a given profile data interval [begin_input,end_input)
Definition: ContinuousWaveletTransformNumIntegration.h:94
OpenMS::Constants::k
const double k
Definition: Constants.h:153
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::ContinuousWaveletTransform::signal_
std::vector< Peak1D > signal_
The transformed signal.
Definition: ContinuousWaveletTransform.h:217
OpenMS::ContinuousWaveletTransform::begin_right_padding_
SignedSize begin_right_padding_
Definition: ContinuousWaveletTransform.h:231
OpenMS::ContinuousWaveletTransform::wavelet_
std::vector< double > wavelet_
The pre-tabulated wavelet used for the transform.
Definition: ContinuousWaveletTransform.h:220
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::ContinuousWaveletTransform::PeakConstIterator
std::vector< Peak1D >::const_iterator PeakConstIterator
Raw data const iterator type.
Definition: ContinuousWaveletTransform.h:50
MathFunctions.h
OpenMS::Math::round
T round(T x)
Rounds the value.
Definition: MathFunctions.h:166
OpenMS::ContinuousWaveletTransformNumIntegration::integrate_
double integrate_(InputPeakIterator x, InputPeakIterator first, InputPeakIterator last)
Computes the convolution of the wavelet and the profile data at position x with resolution = 1.
Definition: ContinuousWaveletTransformNumIntegration.h:181
OpenMS::ContinuousWaveletTransformNumIntegration::~ContinuousWaveletTransformNumIntegration
~ContinuousWaveletTransformNumIntegration() override
Destructor.
Definition: ContinuousWaveletTransformNumIntegration.h:78
OpenMS::SignedSize
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:134
float
OpenMS::ContinuousWaveletTransform::scale_
double scale_
Spacing and scale of the wavelet and length of the signal.
Definition: ContinuousWaveletTransform.h:223
OpenMS::ContinuousWaveletTransformNumIntegration
This class computes the continuous wavelet transformation using a marr wavelet.
Definition: ContinuousWaveletTransformNumIntegration.h:56
OpenMS::ContinuousWaveletTransformNumIntegration::PeakConstIterator
ContinuousWaveletTransform::PeakConstIterator PeakConstIterator
Profile data const iterator type.
Definition: ContinuousWaveletTransformNumIntegration.h:61
OpenMS::ContinuousWaveletTransformNumIntegration::ContinuousWaveletTransformNumIntegration
ContinuousWaveletTransformNumIntegration()
Constructor.
Definition: ContinuousWaveletTransformNumIntegration.h:73
OpenMS::ContinuousWaveletTransformNumIntegration::marr_
double marr_(const double x) const
Computes the Marr wavelet at position x.
Definition: ContinuousWaveletTransformNumIntegration.h:296
ContinuousWaveletTransform.h