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2c28332
Push MTD
t-aretz May 4, 2023
54fcc16
Deque for MassTrace
t-aretz May 15, 2023
97ab6d2
Works but not pretty or finished, but works
t-aretz May 15, 2023
314ee53
Sort In Place, no copies, less memory
t-aretz May 15, 2023
3704886
First Steps in queue try
t-aretz May 17, 2023
b3d8a9c
works but not really parallel, why?
t-aretz May 17, 2023
a9dbb3a
Different outcome with different threads and slow
t-aretz May 18, 2023
4f03fd6
gitignore add smaple file
t-aretz May 18, 2023
82a6c42
Another Approach and search_traces function
t-aretz May 18, 2023
fbe1d4f
noch mit bug, fehler noch nicht gefunden
t-aretz May 18, 2023
e4fc8ab
Some changes
t-aretz May 18, 2023
2a9a523
Searches in Funtions, for trying pragma omp tasks
t-aretz May 19, 2023
b5711d4
Intensity Version
t-aretz May 19, 2023
dc98474
Same result with different threads
t-aretz May 20, 2023
0ad144d
Other while loop break
t-aretz May 20, 2023
f9b4c36
Fix small bug, added (add_to_peaks) critical
t-aretz May 21, 2023
17d5809
Deadlock ?
t-aretz May 23, 2023
306f607
with peak_visited right
t-aretz May 23, 2023
5db5572
one thread too many traces, more threads deadlock
t-aretz May 23, 2023
6b5d2cc
Changed Interface
t-aretz May 23, 2023
c434153
more threads lead to memory errors
t-aretz May 23, 2023
6e676a8
Läuft, zu viele Traces noch
t-aretz May 24, 2023
7d5e4e8
klappt
t-aretz May 24, 2023
43c748a
klappt
t-aretz May 24, 2023
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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -31,3 +31,4 @@ cmake-*-build
*.code-workspace
.vs
.clion.*
src/tests/class_tests/openms/data/SA1_subset_verysmall.mzML
86 changes: 79 additions & 7 deletions src/openms/include/OpenMS/FILTERING/DATAREDUCTION/MassTraceDetection.h
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@maxvk79 maxvk79 May 5, 2023 •
edited
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coding convention! in several function names: instead of foo_bar() do fooBar()

double find_offset_(Size peak_index_in_apices_vec, double mass_error_ppm_, const PeakMap& input_exp, const std::vector& apices_vec);

Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,7 @@

#pragma once

#include <boost/dynamic_bitset.hpp>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/KERNEL/MassTrace.h>
Expand Down Expand Up @@ -84,7 +85,12 @@ namespace OpenMS
*/

/// Allows the iterative computation of the intensity-weighted mean of a mass trace's centroid m/z.
void updateIterativeWeightedMeanMZ(const double &, const double &, double &, double &, double &);
void updateIterativeWeightedMeanMZ(const double added_mz,
const double added_int,
double& centroid_mz,
double& prev_counter,
double& prev_denom
);

/** @name Main computation methods
*/
Expand All @@ -97,27 +103,93 @@ namespace OpenMS

/** @name Private methods and members
*/


protected:
void updateMembers_() override;

private:

struct Apex
{
Apex(double intensity, Size scan_idx, Size peak_idx);
double intensity;
Size scan_idx;
Size peak_idx;
Apex(PeakMap& map, const Size scan_idx, const Size peak_idx);
// Default constructors
Apex() = default;
Apex(const Apex& other) = default;
Apex(Apex&& other) = default;

// Move assignment operator
Apex& operator=(Apex&& other)
{
if (this != &other) {
map_ = other.map_;
scan_idx_ = other.scan_idx_;
peak_idx_ = other.peak_idx_;
}
return *this;
}

PeakMap& map_;
Size scan_idx_;
Size peak_idx_;

///get's the corresponding values
double getMZ() const;
double getRT() const;
double getIntensity() const;
};

struct NextIndex
{
/// C'tor: init with number of threads in parallel region
NextIndex(const std::vector<Apex>& data, const Size total_peak_count, const std::vector<Size>& spec_offsets, const double mass_error_ppm);

/// Get the next free apex index which is not in the neighbourhood of a currently processing apex (in another thread)
/// (Internally adds the apex's m/z to a blacklist which prevents other threads from obtaining an apex nearby)
/// This function blocks until the next free apex is not conflicting anymore - i.e. another thread called setApexAsProcessed()
Size getNextFreeIndex();

/// If an apex was processed call this function to remove the apex from the blacklist and increase the current_apex_
/// ... doesn't create a feature
void setApexAsProcessed();
/// ... does create a feature
void setApexAsProcessed(const std::vector<std::pair<Size, Size> >& gathered_idx);

bool isConflictingApex(const Apex a) const;

bool isVisited(const Size scan_idx, const Size peak_idx) const;

void setNumberOfThreads(const Size thread_num);


/// reference for usage
const std::vector<Apex>& data_;
const std::vector<Size>& spec_offsets_;

/// own datastructure
std::vector<bool> peak_visited_;
Size current_Apex_;
std::vector<std::pair<RangeMZ,RangeRT>> lock_list_;
std::vector<double> lock_list_2_;
double mass_error_ppm_;
};

/// internal check for FWHM meta data
bool checkFWHMMetaData_(const PeakMap& work_exp);

/// The internal run method
void run_(const std::vector<Apex>& chrom_apices,
void run_(std::vector<Apex>& chrom_apices,
const Size peak_count,
const PeakMap & work_exp,
const std::vector<Size>& spec_offsets,
std::vector<MassTrace> & found_masstraces,
const Size max_traces = 0);

// Find Offset for Peak
static double findOffset_(const double centroid_mz, const double mass_error_ppm_);
Size calc_right_border_(Size peak_index_in_apices_vec, const PeakMap& input_exp, const std::vector<Apex>& apices_vec);
Size calc_left_border_(Size peak_index_in_apices_vec, const PeakMap& input_exp, const std::vector<Apex>& apices_vec);

// parameter stuff
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@maxvk79 maxvk79 May 5, 2023

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what does stuff mean?

Suggestion: more precise description

double mass_error_ppm_;
double mass_error_da_;
Expand All @@ -133,4 +205,4 @@ namespace OpenMS

bool reestimate_mt_sd_;
};
}
}
9 changes: 9 additions & 0 deletions src/openms/include/OpenMS/KERNEL/MassTrace.h
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Original file line number Diff line number Diff line change
Expand Up @@ -88,6 +88,15 @@ namespace OpenMS
/// Detailed constructor for vector
MassTrace(const std::vector<PeakType>& trace_peaks);

/// Constructor for typr T with move iterator
template <typename InputIterator>
MassTrace(InputIterator begin, InputIterator end) :
trace_peaks_(std::make_move_iterator(begin), std::make_move_iterator(end)),
label_(),
smoothed_intensities_()
{
}

/// Destructor
~MassTrace() = default;

Expand Down
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