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//# --------------------------------------------------------------------
//# LineFinder.h: this defines utility functions of line finding
//# --------------------------------------------------------------------
//# Copyright (C) 2015
//# National Astronomical Observatory of Japan
//#
//# This library is free software; you can redistribute it and/or modify it
//# under the terms of the GNU Library General Public License as published by
//# the Free Software Foundation; either version 2 of the License, or (at your
//# option) any later version.
//#
//# This library is distributed in the hope that it will be useful, but WITHOUT
//# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
//# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Library General Public
//# License for more details.
//#
//# You should have received a copy of the GNU Library General Public License
//# along with this library; if not, write to the Free Software Foundation,
//# Inc., 675 Massachusetts Ave, Cambridge, MA 02139, USA.
//#
//# Correspondence concerning AIPS++ should be addressed as follows:
//# Internet email: casa-feedback@nrao.edu.
//# Postal address: AIPS++ Project Office
//# National Radio Astronomy Observatory
//# 520 Edgemont Road
//# Charlottesville, VA 22903-2475 USA
//#
//# $Id$
namespace casa { //# NAMESPACE CASA - BEGIN
namespace linefinder {
/*
* Find spectral lines of a spectrum using a threshold based on median
* absolute deviation (MAD).
* The median of lower 80% of MAD values are used to define the
* threshold of line channels.
*
* @param[in] num_data : the number of elements in data and mask vector.
* @param[in] data : a float vector of data to detect lines. should be aligned.
* @param[in] mask : a boolean vector which indecates if the corresponding elements
* in data should be used in line detection.
* Note mask is modified in the function. Edge channels are masked.
* @param[in] threshold: a multiplication factor to define threshold.
* @param[in] max_iteration : the maximum number of iteration to detect line,
* and eliminate the line channels to redefine MAD array.
* @param[in] minwidth : minimum line width (in channel) to detect as lines
* @param[in] maxwidth : maximum line width (in channel) to detect as lines
* @param[in] avg_limit : maximum width of channel binning to run line detection.
* @param[in] edge : the number of elements at the begining and end of data array
* that should be ignored in line detection.
* @return a list of line channel ranges
*
* [overview of line detection algorithm]
* 1. Median absolute deviation of each data element is calculated and
* defined as MAD array.
* 2. Calculate median of MAD array. Only lower 80% of valid elements
* (mask=true and not in lines) are used to calculate the value.
* 3. Compare each element of MAD array and the product of
* threshold and median of MAD. Elements that exceeds
* the threshold value are detected as channels.
* 4. Line range modifications,e.g., extend line ranges for wing component,
* merge overlapping lines, and check if line meets maxwidth and
* minwidth criteria.
* 5. Go to step 1 and repeat line detection by removing line channels
* from MAD calculations. stop iteration either if loop reaches
* max_iteration, no lines found in the bin level, no new line channel
* is detected, or MAD threshold increased compared to the previous
* iteration.
* 6. bin data with 4 times coarser width and repeat line detection again
* untill bin width reaches to avg_limit.
* Merge line ranges detected in the current bin level to previous result.
*/
std::list<std::pair<size_t, size_t>> MADLineFinder(size_t const num_data,
float const data[/*num_data*/], bool mask[/*num_data*/],
float const threshold, uint8_t max_iteration, size_t const minwidth,
size_t const maxwidth, size_t const avg_limit,
std::pair<size_t, size_t> edge);
/*
Create a boolean mask vector from ranges.
mask : a boolean vector that stores output mask. see below for
the values set to each elements of mask.
ranges : a list of start and end idices pairs to set value in mask.