/*! Calculation of peak, bg areas, bg_subtracted_peak_height for an arbitrary region using the suppeak algorithm as of 03/09 */
//summary method for methods relating to quantitating peaks.
void peak_annotate(SlimCrawPeak peak)
{
set_peak_slope(peak);
//calls set_peak_areas onpeak member variables
set_peak_bg_subtracted_area(peak);
calc_fwhm(peak);
}
void ratchet_back_to_frac_maxval(SlimCrawPeak peak, float frac = 0.01f, float bg_level = 0.0f)
{
float[] chrom = active_chrom;
if (frac > 1)
{
throw new Exception("define the fraction ranging from 0 to 1");
}
float min_level = (peak.raw_height - bg_level) * frac;
for (int i = peak.start_rt_idx; i < peak.peak_rt_idx; i++)
{
if (chrom[i] >= min_level)
{
peak.start_rt_idx = i;
break;
}
}
for (int i = peak.stop_rt_idx; i > peak.peak_rt_idx; i--)
{
if (chrom[i] >= min_level)
{
peak.stop_rt_idx = i;
break;
}
}
}
public void reannotate_peak(SlimCrawPeak peak, int start_idx, int stop_idx)
{
peak.start_rt_idx = start_idx;
peak.stop_rt_idx = stop_idx;
peak.peak_rt_idx = get_peakloc_in_range(start_idx, stop_idx);
set_peak_bg_subtracted_area(peak);
//update this to incorporate other functions
}
public void peak_tweak(SlimCrawPeak peak, CrawPeakMethod m)
{
if (m.extend_to_zero_crossing)
{
extend_to_zero_crossing(peak, m.fraction_to_valley);
}
else if (m.extend_peak_to_lower_bound)
{
extend_to_lower_boundary(peak, m.extend_allowed_asymmetry);
}
}
//ER - USE THIS TO JOIN PEAKS TOGETHER -
///adds the right-hand peak to the left-hand peak
///a version that returns a new peak would be useful too but that is low priority
///based on the determination to merge peaks, join to_glom to changed
void glom_peak(SlimCrawPeak changed, SlimCrawPeak to_glom)
{
if (to_glom.start_rt_idx > changed.start_rt_idx)
{
changed.stop_rt_idx = to_glom.stop_rt_idx;
}
else
{
changed.start_rt_idx = to_glom.start_rt_idx;
}
changed.len = changed.stop_rt_idx - changed.start_rt_idx + 1;
peak_tweak(changed, pf.method);
set_peak_bg_subtracted_area(changed);
}
public CrawdadPeak(SlimCrawPeak crawPeak)
{
TimeIndex = crawPeak.peak_rt_idx;
StartIndex = crawPeak.start_rt_idx;
EndIndex = crawPeak.stop_rt_idx;
Height = crawPeak.peak_height;
// Note: Crawdad had a bug that caused it to return negative areas.
// Using Math::Max() below left in place to protect against that,
// even though the bug is believed to be fixed.
Area = Math.Max(0.0f, crawPeak.peak_area);
BackgroundArea = Math.Max(0.0f, crawPeak.bg_area);
Fwhm = crawPeak.fwhm;
FwhmDegenerate = !crawPeak.fwhm_calculated_ok;
}
public void calc_fwfpcnt(SlimCrawPeak peak)
{
float[] chrom = active_chrom;
float lh_height = chrom[peak.start_rt_idx];
float rh_height = chrom[peak.stop_rt_idx];
float height = peak.raw_height - Math.Min(lh_height, rh_height);
float fpct_max = (float)(peak.raw_height - (height / 100 * 95));
int lh_pt = -1, rh_pt = -1;
float lh_hm, rh_hm;
for (int i = peak.start_rt_idx; i < peak.peak_rt_idx; i++)
{
if (chrom[i] <= fpct_max && chrom[i + 1] >= fpct_max)
{
lh_pt = i;
break;
}
}
for (int i = peak.peak_rt_idx; i < Math.Min(peak.stop_rt_idx, chrom.Length - 2); i++)
{
if (chrom[i] >= fpct_max && chrom[i + 1] <= fpct_max)
{
rh_pt = i;
break;
}
}
if (lh_pt == -1)
{
lh_hm = peak.start_rt_idx;
}
else
{
float frac_delta = (fpct_max - chrom[lh_pt]) / (chrom[lh_pt + 1] - chrom[lh_pt]);
lh_hm = lh_pt + frac_delta;
}
if (rh_pt == -1)
{
rh_hm = peak.stop_rt_idx;
}
else
{
float frac_delta = (chrom[rh_pt] - fpct_max) / (chrom[rh_pt] - chrom[rh_pt + 1]);
rh_hm = rh_pt + frac_delta;
}
peak.fwfpct = rh_hm - lh_hm;
peak.fvalue = peak.peak_rt_idx - lh_hm;
}
public void calc_fwhm(SlimCrawPeak peak)
{
float[] chrom = active_chrom;
float lh_height = chrom[peak.start_rt_idx];
float rh_height = chrom[peak.stop_rt_idx];
float height = peak.raw_height - Math.Min(lh_height, rh_height);
float half_max = (float)(peak.raw_height - (height / 2.0));
int lh_pt = -1, rh_pt = -1;
float lh_hm, rh_hm;
for (int i = peak.start_rt_idx; i < peak.peak_rt_idx; i++)
{
if (chrom[i] <= half_max && chrom[i + 1] >= half_max)
{
lh_pt = i;
break;
}
}
for (int i = peak.peak_rt_idx; i < Math.Min(peak.stop_rt_idx, chrom.Length - 2); i++)
{
if (chrom[i] >= half_max && chrom[i + 1] <= half_max)
{
rh_pt = i;
break;
}
}
peak.fwhm_calculated_ok = (lh_pt > -1 && rh_pt > -1);
if (lh_pt == -1)
{
lh_hm = peak.start_rt_idx;
}
else
{
float frac_delta = (half_max - chrom[lh_pt]) / (chrom[lh_pt + 1] - chrom[lh_pt]);
lh_hm = lh_pt + frac_delta;
}
if (rh_pt == -1)
{
rh_hm = peak.stop_rt_idx;
}
else
{
float frac_delta = (chrom[rh_pt] - half_max) / (chrom[rh_pt] - chrom[rh_pt + 1]);
rh_hm = rh_pt + frac_delta;
}
peak.fwhm = rh_hm - lh_hm;
}
CrawdadPeak GetPeak(int startIndex, int endIndex)
{
startIndex += _widthDataWings;
endIndex += _widthDataWings;
SlimCrawPeak peak = new SlimCrawPeak();
_pPeakFinder.annotator.reannotate_peak(peak, startIndex, endIndex);
_pPeakFinder.annotator.calc_fwhm(peak);
peak.start_rt_idx -= _widthDataWings;
peak.stop_rt_idx -= _widthDataWings;
peak.peak_rt_idx -= _widthDataWings;
return(new CrawdadPeak(peak));
}
protected override void peak_voodoo(int lh_valley, int rh_valley, int peak_loc)
{
SlimCrawPeak peak = new SlimCrawPeak(lh_valley, rh_valley, peak_loc, chrom, chrom_bg_scratch, mz_idx);
annotator.refind_peak_peak(peak);
annotator.peak_tweak(peak, method);
//peak.peak_height = 0.0f;
//note this needs to altered if we do not use the standard of defining the peak area as
//stretching from one end to the other
annotator.set_peak_slope(peak);
annotator.set_peak_bg_subtracted_area(peak);
annotator.calc_fwhm(peak);
annotator.calc_fwfpcnt(peak);
annotator.calc_fwbase(peak);
sps.Add(peak);
}
void extend_to_lower_boundary(SlimCrawPeak peak, float allowed_asymmetry = 1.0f)
{
//1. find lower point
//2. find farther end-point
//3. extend higher point until either: lower point is reached,
//get intensity at either edge...
float intensity_at_lh_bound = pf.chrom[peak.start_rt_idx];
float intensity_at_rh_bound = pf.chrom[peak.stop_rt_idx];
int max_distance = Math.Max(peak.peak_rt_idx - peak.start_rt_idx, peak.stop_rt_idx - peak.peak_rt_idx);
int min_distance = Math.Min(peak.peak_rt_idx - peak.start_rt_idx, peak.stop_rt_idx - peak.peak_rt_idx);
int max_allowed_distance = (int)Math.Round(max_distance * allowed_asymmetry);
int max_delta_from_edge = max_allowed_distance - min_distance;
if (intensity_at_lh_bound < intensity_at_rh_bound)
{
//extend bound rightwards until either max distance is reached, or
int delta = 0;
for (; delta < max_delta_from_edge; delta++)
{
int pos = peak.stop_rt_idx + delta;
if (pf.chrom[pos] <= intensity_at_lh_bound)
{
break;
}
}
peak.stop_rt_idx += delta; //changed peak boundary, what would I need to adjust now...?
}
if (intensity_at_rh_bound < intensity_at_lh_bound)
{
//extend bound leftwards until either max distance is reached, or
int delta = 0;
for (; delta < max_delta_from_edge; delta++)
{
int pos = peak.start_rt_idx - delta;
if (pf.chrom[pos] <= intensity_at_rh_bound)
{
break;
}
}
peak.start_rt_idx -= delta; //changed peak boundary, what would I need to adjust now...?
}
}
void extend_to_zero_crossing(SlimCrawPeak peak, float perc_towards_valley)
{
////advance until next chrom2d zero crossing from rh_boundary
float c2d_intensity_at_rh_bound = pf.chrom_2d[peak.stop_rt_idx];
float c2d_intensity_at_lh_bound = pf.chrom_2d[peak.start_rt_idx];
float rh_cutoff = c2d_intensity_at_rh_bound * perc_towards_valley;
float lh_cutoff = c2d_intensity_at_lh_bound * perc_towards_valley;
int plus_cross_to_right_idx = crawutils.lower_bound(pf.plus_crosses, peak.stop_rt_idx);
if (plus_cross_to_right_idx == pf.plus_crosses.Count - 1)
{
//TODO -- extend out to last point?
}
else
{
plus_cross_to_right_idx++;
for (int i = peak.stop_rt_idx; i <= pf.plus_crosses[plus_cross_to_right_idx]; i++)
{
if (pf.chrom_2d[i] < rh_cutoff)
{
peak.stop_rt_idx = i - 1;
}
}
}
int minus_cross_to_left_idx = crawutils.lower_bound(pf.minus_crosses, peak.start_rt_idx);
if (minus_cross_to_left_idx == 0)
{
//TODO -- extend out to last point?
}
else
{
for (int i = peak.start_rt_idx; i >= pf.minus_crosses[plus_cross_to_right_idx]; i--)
{
if (pf.chrom_2d[i] < lh_cutoff)
{
peak.stop_rt_idx = i + 1;
}
}
}
}
///returns the leftmost, and rightmost peak index which overlap with this peak
public (int leftmost, int rightmost) find_overlap_bounds_by_peak_rt_idx(SlimCrawPeak p)
{
int lh_peak_idx = crawutils.get_lh_idx(peak_peak_idxs, p.start_rt_idx) + 1;
int rh_peak_idx;
for (rh_peak_idx = lh_peak_idx; rh_peak_idx < peak_peak_idxs.Length; rh_peak_idx++)
{
if (p.stop_rt_idx < peak_peak_idxs[rh_peak_idx])
{
break;
}
}
// TODO comparison between signed and unsigned integer expressions
if (rh_peak_idx == peak_peak_idxs.Length)
{
rh_peak_idx--;
}
return(lh_peak_idx, rh_peak_idx);
}
private void ClearPeaksByHeight(SlimCrawPeak p)
{
bool found = false;
for (int i = 0; i < peaks_by_height.Count; i++)
{
if (peaks_by_height[i].peak_height > p.peak_height)
{
break;
}
if (peaks_by_height[i].peak_height == p.peak_height)
{
peaks_by_height.RemoveAt(i);
found = true;
break;
}
}
if (!found)
{
throw new Exception("peak height must match");
}
}
private void ClearPeaksByStartRtIdx(SlimCrawPeak p)
{
bool found = false;
for (int i = 0; i < peaks_by_rt.Count; i++)
{
if (peaks_by_rt[i].start_rt_idx > p.start_rt_idx)
{
break;
}
if (peaks_by_rt[i].start_rt_idx == p.start_rt_idx)
{
peaks_by_rt.RemoveAt(i);
found = true;
break;
}
}
if (!found)
{
throw new Exception("peak start_rt_idx must match");
}
}
double get_raw_area(SlimCrawPeak peak) => get_area(peak.start_rt_idx, peak.stop_rt_idx);
void extend_to_1d_zero(SlimCrawPeak peak, bool start_at_peak)
{
int delta_to_lh, delta_to_rh;
int lh_start, rh_start;
if (start_at_peak)
{
lh_start = rh_start = peak.peak_rt_idx;
}
else
{
lh_start = peak.start_rt_idx;
rh_start = peak.stop_rt_idx;
}
//find crossing point in the 1st derivative
(List <int> c1d_plus_crosses, List <int> c1d_minus_crosses) = pf.find_cross_points(pf.chrom_1d);
/*ER BUGBUG
* PLACE WHERE PEAKS ARE EXTENDED USING 1st derivative.
* crossing points in chrom_1d are found above.
* so you would need to limit the 'walk' out to the 1st derivative crossing point.
* The other option is to investigate what I was doing in the function below, local minimum.
* (perhaps walk out to the point where either the 1st deriv hits zero or the intensity falls below some factor of the peak
* intensity, like 0.05?.
*
* -- it may be best later on, after peak_tweak or whatever the heck it is is called, to trim peaks back, rather than rejecting them... hmmm..
*/
//extend left hand
if (!(lh_start < c1d_plus_crosses[0]))
{
int lh_it = crawutils.lower_bound(c1d_plus_crosses, lh_start);
lh_it--;
int leftmost_c1d_plus_cross = c1d_plus_crosses[lh_it];
//since the cross is defined as going left-to-right, nudge to the other side
leftmost_c1d_plus_cross++;
delta_to_lh = lh_start - leftmost_c1d_plus_cross;
}
else
{
delta_to_lh = 0;
}
//extend right hand
if (!(rh_start > c1d_plus_crosses.Last()))
{
int rh_it = crawutils.lower_bound(c1d_plus_crosses, rh_start);
if (rh_it == c1d_plus_crosses.Count - 1)
{
}
else
{
//rh_it++;
}
int rightmost_c1d_plus_cross = c1d_plus_crosses[rh_it];
delta_to_rh = rightmost_c1d_plus_cross - rh_start;
}
else
{
delta_to_rh = 0;
}
//for now, extend boundaries by delta_to_lh, delta_to_rh - note that we can also use those to enforce some peak asymmetry
if (start_at_peak)
{
peak.start_rt_idx = peak.peak_rt_idx - delta_to_lh;
peak.stop_rt_idx = peak.peak_rt_idx + delta_to_rh;
}
else
{
peak.start_rt_idx -= delta_to_lh;
peak.stop_rt_idx += delta_to_rh;
}
}
void extend_to_1d_zero_local_minimum(SlimCrawPeak peak, bool start_at_peak)
{
int delta_to_lh, delta_to_rh;
int lh_start, rh_start;
if (start_at_peak)
{
lh_start = rh_start = peak.peak_rt_idx;
}
else
{
lh_start = peak.start_rt_idx;
rh_start = peak.stop_rt_idx;
}
//find crossing point in the 1st derivative
(List <int> c1d_plus_crosses, List <int> c1d_minus_crosses) = pf.find_cross_points(pf.chrom_1d);
//extend left hand
int peak_intensity = (int)active_chrom[peak.peak_rt_idx];
int last_minimum_intensity = peak_intensity;
if (!(lh_start < c1d_plus_crosses[0]))
{
int lh_it = crawutils.lower_bound(c1d_plus_crosses, lh_start);
if (lh_it == c1d_plus_crosses.Count)
{
throw new Exception("makes no sense");
}
//walk leftwards
do
{
if (lh_it == 0)
{
break;
}
int this_valley_intensity = (int)active_chrom[c1d_plus_crosses[lh_it]];
if (this_valley_intensity > last_minimum_intensity)
{
//the last valley was the local minimum
lh_it++;
break;
}
last_minimum_intensity = this_valley_intensity;
lh_it--;
} while (lh_it != 0);
int leftmost_c1d_plus_cross = c1d_plus_crosses[lh_it];
//since the cross is defined as going left-to-right, nudge to the other side
leftmost_c1d_plus_cross++;
delta_to_lh = lh_start - leftmost_c1d_plus_cross;
}
else
{
delta_to_lh = 0;
}
//extend right hand
last_minimum_intensity = peak_intensity;
if (!(rh_start > c1d_minus_crosses.Last()))
{
int rh_it = crawutils.lower_bound(c1d_minus_crosses, rh_start);
do
{
if (rh_it == c1d_minus_crosses.Count)
{
rh_it--;
break;
}
int this_valley_intensity = (int)active_chrom[c1d_minus_crosses[rh_it]];
if (this_valley_intensity > last_minimum_intensity)
{
//the last valley was the local minimum
rh_it--;
break;
}
last_minimum_intensity = this_valley_intensity;
rh_it++;
} while (rh_it != c1d_plus_crosses.Count);
int rightmost_c1d_minus_cross = c1d_minus_crosses[rh_it];
delta_to_rh = rightmost_c1d_minus_cross - rh_start;
}
else
{
delta_to_rh = 0;
}
//for now, extend boundaries by delta_to_lh, delta_to_rh - note that we can also use those to enforce some peak asymmetry
if (start_at_peak)
{
peak.start_rt_idx = peak.peak_rt_idx - delta_to_lh;
peak.stop_rt_idx = peak.peak_rt_idx + delta_to_rh;
}
else
{
peak.start_rt_idx -= delta_to_lh;
peak.stop_rt_idx += delta_to_rh;
}
}
///merge peaks based on adjacent peaks with similar slope patterns
///merges peaks by:
///start with the heighest peak -
///find nearest peak
IList <SlimCrawPeak> merge_peaks_list_based(List <SlimCrawPeak> in_peaks)
{
if (!pf.method.merge_peaks_list_based)
{
return(new List <SlimCrawPeak>(in_peaks));
}
List <SlimCrawPeak> peaks_by_height = new List <SlimCrawPeak>(in_peaks);
//TODO -- switch to using priority queues - not enough time to test at the moment
in_peaks.Sort(crawutils.CompByStartRTIdx);
peaks_by_height.Sort((x, y) => x.peak_height.CompareTo(y.peak_height));
peak_lists plist_struct = new peak_lists(peaks_by_height, in_peaks);
//delete the rts iterators
List <SlimCrawPeak> peaks_to_clear = new List <SlimCrawPeak>();
List <int> rts_its = new List <int>();
List <SlimCrawPeak> out_peaks = new List <SlimCrawPeak>();
while (plist_struct.peaks_by_height.Count > 1)
{
SlimCrawPeak highest_p_ptr = plist_struct.peaks_by_height[plist_struct.peaks_by_height.Count - 1];
int lookup = crawutils.lower_bound(plist_struct.peaks_by_rt, highest_p_ptr, crawutils.CompByStartRTIdx);
if (lookup == plist_struct.peaks_by_rt.Count)
{
throw new Exception("should always find an exact RT peak match");
}
SlimCrawPeak candidate = plist_struct.peaks_by_rt[lookup];
if (!(candidate.start_rt_idx == highest_p_ptr.start_rt_idx))
{
throw new Exception("should have always find an exact match");
}
bool comp_lh, comp_rh;
bool merge_lh, merge_rh;
comp_lh = comp_rh = true;
merge_lh = merge_rh = false;
if (lookup == 0)
{
comp_lh = false;
}
if (lookup == (plist_struct.peaks_by_rt.Count - 1))
{
comp_rh = false;
}
///you can merge with up to two adjacent peaks
rts_its.Add(lookup);
peaks_to_clear.Add(plist_struct.peaks_by_rt[lookup]);
if (comp_lh)
{
SlimCrawPeak leftCandidate = plist_struct.peaks_by_rt[lookup - 1];
if (susceptible_to_merge(leftCandidate, candidate))
{
merge_lh = true;
rts_its.Add(lookup - 1);
peaks_to_clear.Add(leftCandidate);
}
}
if (comp_rh)
{
SlimCrawPeak rightCandidate = plist_struct.peaks_by_rt[lookup + 1];
if (susceptible_to_merge(candidate, rightCandidate))
{
merge_rh = true;
rts_its.Add(lookup + 1);
peaks_to_clear.Add(rightCandidate);
}
}
if (merge_lh)
{
glom_peak(candidate, plist_struct.peaks_by_rt[lookup - 1]);
}
if (merge_rh)
{
glom_peak(candidate, plist_struct.peaks_by_rt[lookup + 1]);
}
//TODO inefficient..., we need to copy the peak after it is glommed, otherwise it is out of order in these cases...
plist_struct.resort_peaks();
//delete this peak from both vectors
//delete each merged_peak from both vectors
out_peaks.Add(candidate);
foreach (SlimCrawPeak peak in peaks_to_clear)
{
plist_struct.clear_peak(peak);
}
rts_its.Clear();
peaks_to_clear.Clear();
}
if (plist_struct.peaks_by_height.Count > 0)
{
out_peaks.Add(plist_struct.peaks_by_height[0]);
}
return(out_peaks);
}
public static int CompByPeakRTIdx(SlimCrawPeak x, SlimCrawPeak y) => x.peak_rt_idx.CompareTo(y.peak_rt_idx);
///merge peaks if lhs heuristics about slopes apply
bool susceptible_to_merge(SlimCrawPeak lhs, SlimCrawPeak rhs)
{
if (Math.Abs(lhs.stop_rt_idx - rhs.start_rt_idx) > 1)
{
return(false);
}
float max_height = Math.Max(lhs.peak_height, rhs.peak_height);
float max_len = Math.Max(lhs.len, rhs.len);
float one_peak_slope_constraint = (pf.method.one_peak_slope_merge_constraint * max_height) / max_len;
//TODO calcs for mean_peak_slope_constraint in the line below do not make sense
float mean_peak_slope_constraint = (pf.method.mean_slope_merge_constraint * max_height) / max_len;
//opposite slopes are not a valid assumption, when merging two shoulders next to each other
if ((lhs.bgslope * rhs.bgslope) < 0)
{
//at least one peak must have a high slope...
if (one_peak_slope_constraint != 0 &&
((Math.Abs(lhs.bgslope) >= one_peak_slope_constraint) ||
(Math.Abs(rhs.bgslope) >= one_peak_slope_constraint)))
{
return(true);
}
if (mean_peak_slope_constraint != 0 &&
((lhs.bgslope + rhs.bgslope) / 2.0) >= mean_peak_slope_constraint)
{
return(true);
}
}
/* HACK BELOW - not configured with options */
else if (lhs.raw_height < rhs.raw_height)
{
if (lhs.bgslope > 0)
{
if (lhs.height_norm_slope() > 1)
{
return(true);
}
}
}
else if (lhs.raw_height > rhs.raw_height)
{
if (rhs.bgslope < 0)
{
if (rhs.height_norm_slope() < 1)
{
return(true);
}
}
}
else
{
float peak_to_peak_slope = (rhs.peak_height - lhs.peak_height) / (rhs.peak_rt_idx - lhs.peak_rt_idx);
if (rhs.height_norm_slope() > 1)
{
if (peak_to_peak_slope * rhs.bgslope > 1)
{
return(true);
}
}
else if (lhs.height_norm_slope() > 1)
{
if (peak_to_peak_slope * lhs.bgslope > 1)
{
return(true);
}
}
}
return(false);
}
public static int CompByStartRTIdx(SlimCrawPeak x, SlimCrawPeak y) => x.start_rt_idx.CompareTo(y.start_rt_idx);
public void clear_peak(SlimCrawPeak p)
{
ClearPeaksByHeight(p);
ClearPeaksByStartRtIdx(p);
}
public void set_peak_bg_subtracted_area(SlimCrawPeak peak)
{
get_all_areas(peak.start_rt_idx, peak.stop_rt_idx, peak.peak_rt_idx,
ref peak.raw_area, ref peak.bg_area, ref peak.peak_area, ref peak.peak_height, ref peak.raw_height);
}
public void set_peak_slope(SlimCrawPeak peak)
{
float slope = calculate_slope(peak.start_rt_idx, peak.stop_rt_idx);
peak.bgslope = slope;
}
///not implemented yet -- plan is to check the similarity of peaks by a correlation after normalizing for size
bool susceptible_to_merge_by_shape(SlimCrawPeak _1, SlimCrawPeak _2)
{
return(false); //ie not done yet
}
public void refind_peak_peak(SlimCrawPeak peak)
{
peak.peak_rt_idx = get_peakloc_in_range(peak.start_rt_idx, peak.stop_rt_idx);
}
