void DataSignal :: WriteSmartPeakInfoToXML (RGTextOutput& text, const RGString& indent, const RGString& bracketTag, const RGString& locationTag) {
int peak;
Endl endLine;
RGString suffix;
// if (HasCrossChannelSignalLink ()) {
if (HasAlleleName () && (!mDoNotCall)) {
peak = (int) floor (Peak () + 0.5);
if (mOffGrid)
suffix = " OL";
text << indent << "<" << bracketTag << ">" << endLine;
text << indent << "\t<mean>" << GetMean () << "</mean>" << endLine;
text << indent << "\t<height>" << peak << "</height>" << endLine;
text << indent << "\t<BPS>" << GetBioID () << "</BPS>" << endLine;
// text << indent << "\t<" << locationTag << ">" << (int) floor (GetApproximateBioID () + 0.5) << "</" << locationTag << ">" << endLine;
text << indent << "\t<" << locationTag << ">" << GetApproximateBioID () << "</" << locationTag << ">" << endLine;
text << indent << "\t<PeakArea>" << TheoreticalArea () << "</PeakArea>" << endLine;
text << indent << "\t<allele>" << GetAlleleName () << suffix << "</allele>" << endLine;
text << indent << "\t<width>" << 4.0 * GetStandardDeviation () << "</width>" << endLine;
text << indent << "\t<fit>" << GetCurveFit () << "</fit>" << endLine;
text << indent << "</" + bracketTag << ">" << endLine;
}
// }
}
bool DataSignal :: ReportSmartNoticeObjects (RGTextOutput& text, const RGString& indent, const RGString& delim) {
if (NumberOfSmartNoticeObjects () > 0) {
int msgLevel = GetHighestMessageLevelWithRestrictionSM ();
RGDListIterator it (*mSmartMessageReporters);
SmartMessageReporter* nextNotice;
text.SetOutputLevel (msgLevel);
if (!text.TestCurrentLevel ()) {
text.ResetOutputLevel ();
return false;
}
Endl endLine;
text << endLine;
text << indent << "Notices for curve with (Mean, Sigma, Peak, 2Content, Fit) = " << delim << delim << delim << delim << delim << delim;
text << GetMean () << delim << GetStandardDeviation () << delim << Peak () << delim << GetScale (2) << delim << Fit << endLine;
while (nextNotice = (SmartMessageReporter*) it ())
text << indent << nextNotice->GetMessage () << nextNotice->GetMessageData () << endLine;
text.ResetOutputLevel ();
text.Write (1, "\n");
}
else
return false;
return true;
}
/** Add a peak to the list
* @param ipeak :: Peak object to add (copy) into this.
*/
void PeaksWorkspace::addPeak(const API::IPeak& ipeak)
{
if (dynamic_cast<const Peak*>(&ipeak))
{
peaks.push_back((const Peak&) ipeak);
}
else
{
peaks.push_back(Peak(ipeak));
}
}
/** Execute the algorithm.
*/
void CreatePeaksWorkspace::exec()
{
MatrixWorkspace_sptr instWS = getProperty("InstrumentWorkspace");
PeaksWorkspace_sptr out(new PeaksWorkspace());
setProperty("OutputWorkspace", out);
int NumberOfPeaks = getProperty("NumberOfPeaks");
if (instWS)
{
out->setInstrument(instWS->getInstrument());
// Create some default peaks
for (int i=0; i < NumberOfPeaks; i++)
{
out->addPeak( Peak(out->getInstrument(), out->getInstrument()->getDetectorIDs(true)[0], 1.0) );
}
}
}
double SuperGaussian :: GetPullupToleranceInBP (double noise) const {
//pullUpToleranceFactor
double P = Peak ();
if (P <= 0.0)
return (mPullupTolerance + (2.0 * sin (0.5 * acos (Fit)) / 4.47));
double localFit = Fit;
if (localFit < 0.1)
localFit = 0.1;
double localNoise = noise;
double LN = 0.95 * P;
if (localNoise > LN)
localNoise = LN;
double temp1 = 1.0 / localFit;
double temp = 2.0 * (temp1 * temp1 - 1.0) * StandardDeviation * log (P / (P - localNoise));
return (mPullupTolerance + pullUpToleranceFactor * mApproxBioIDPrime * sqrt (temp));
}
void PeakDetectorNaiveImpl::findPeaks(const FrequencyData& fd, peakdata::Scan& result) const
{
result.scanNumber = fd.scanNumber();
result.retentionTime = fd.retentionTime();
result.observationDuration = fd.observationDuration();
result.calibrationParameters = fd.calibrationParameters();
result.peakFamilies.clear();
const double noiseLevel = sqrt(fd.variance());
const double threshold = noiseLevel * noiseFactor_;
for (FrequencyData::const_iterator it=fd.data().begin(); it!=fd.data().end(); ++it)
if (isPeak(it, fd.data(), threshold, detectionRadius_))
{
result.peakFamilies.push_back(PeakFamily());
PeakFamily& peakFamily = result.peakFamilies.back();
peakFamily.peaks.push_back(Peak());
Peak& peak = peakFamily.peaks.back();
peak.frequency = it->x;
peak.intensity = it->y.real();
peak.phase = it->y.imag();
}
}
void DataSignal :: WriteSmartTableArtifactInfoToXML (RGTextOutput& text, RGTextOutput& tempText, const RGString& indent, const RGString& bracketTag, const RGString& locationTag) {
int peak;
Endl endLine;
RGString suffix;
RGString label;
SmartMessageReporter* notice;
int i;
RGString virtualAllele;
SmartMessageReporter* nextNotice;
text.SetOutputLevel (1);
int msgNum;
smAcceptedOLLeft acceptedOLLeft;
smAcceptedOLRight acceptedOLRight;
int reportedMessageLevel = GetHighestMessageLevelWithRestrictionSM ();
//bool hasThreeLoci;
//bool needLocus0;
if ((!DontLook ()) && (NumberOfSmartNoticeObjects () != 0)) {
bool firstNotice = true;
peak = (int) floor (Peak () + 0.5);
virtualAllele = GetVirtualAlleleName ();
text << indent << "<" << bracketTag << ">" << endLine; // Should be <Artifact>
text << indent << "\t<Id>" << GetSignalID () << "</Id>" << endLine;
text << indent << "\t<Level>" << reportedMessageLevel << "</Level>" << endLine;
text << indent << "\t<RFU>" << peak << "</RFU>" << endLine;
text << indent << "\t<" << locationTag << ">" << GetApproximateBioID () << "</" << locationTag << ">" << endLine;
text << indent << "\t<PeakArea>" << TheoreticalArea () << "</PeakArea>" << endLine;
text << indent << "\t<Time>" << GetMean () << "</Time>" << endLine;
text << indent << "\t<Fit>" << GetCurveFit () << "</Fit>" << endLine;
if (!mAllowPeakEdit)
text << indent << "\t<AllowPeakEdit>false</AllowPeakEdit>" << endLine;
RGDListIterator it (*mSmartMessageReporters);
i = 0;
while (notice = (SmartMessageReporter*) it ()) {
if (!notice->GetDisplayOsirisInfo ())
continue;
if (firstNotice) {
label = indent + "\t<Label>";
firstNotice = false;
}
if (i > 0)
label << " ";
label += notice->GetMessage ();
label += notice->GetMessageData ();
i++;
}
if (i > 0) {
label << "</Label>";
text << label << endLine;
}
// Now add list of notices...
it.Reset ();
while (nextNotice = (SmartMessageReporter*) it ()) {
msgNum = Notice::GetNextMessageNumber ();
nextNotice->SetMessageCount (msgNum);
text << indent << "\t<MessageNumber>" << msgNum << "</MessageNumber>" << endLine;
tempText << "\t\t<Message>\n";
tempText << "\t\t\t<MessageNumber>" << msgNum << "</MessageNumber>\n";
tempText << "\t\t\t<Text>" << nextNotice->GetMessage () << nextNotice->GetMessageData () << "</Text>\n";
if (nextNotice->HasViableExportInfo ()) {
if (nextNotice->IsEnabled ())
tempText << "\t\t\t<Hidden>false</Hidden>\n";
else
tempText << "\t\t\t<Hidden>true</Hidden>\n";
if (!nextNotice->IsCritical ())
tempText << "\t\t\t<Critical>false</Critical>\n";
if (nextNotice->IsEnabled ())
tempText << "\t\t\t<Enabled>true</Enabled>\n";
else
tempText << "\t\t\t<Enabled>false</Enabled>\n";
if (!nextNotice->IsEditable ())
tempText << "\t\t\t<Editable>false</Editable>\n";
if (nextNotice->GetDisplayExportInfo ())
tempText << "\t\t\t<DisplayExportInfo>true</DisplayExportInfo>\n";
else
tempText << "\t\t\t<DisplayExportInfo>false</DisplayExportInfo>\n";
if (!nextNotice->GetDisplayOsirisInfo ())
tempText << "\t\t\t<DisplayOsirisInfo>false</DisplayOsirisInfo>\n";
tempText << "\t\t\t<MsgName>" << nextNotice->GetMessageName () << "</MsgName>\n";
//tempText << "\t\t\t<ExportProtocolList>";
//tempText << "\t\t\t" << nextNotice->GetExportProtocolInformation ();
//tempText << "\t\t\t</ExportProtocolList>\n";
}
tempText << "\t\t</Message>\n";
}
// Now add list of alleles
//hasThreeLoci = (mLocus != NULL) && (mLeftLocus != NULL) && (mRightLocus != NULL);
//if (mLocus != NULL) {
// if ((mLeftLocus == NULL) && (mRightLocus == NULL))
// needLocus0 = true;
// else
// needLocus0 = false;
//}
//else
// needLocus0 = false;
//needLocus0 = (!hasThreeLoci) && ((mLocus != mLeftLocus) || (mLocus != mRightLocus));
if (mLocus != NULL) {
//testing
RGString locusName = mLocus->GetLocusName ();
suffix = GetAlleleName (0);
if ((suffix.Length () > 0) || (virtualAllele.Length () > 0)) {
text << indent << "\t<Allele>" << endLine;
if (suffix.Length () > 0)
text << indent << "\t\t<Name>" << suffix << "</Name>" << endLine;
else
text << indent << "\t\t<Name>" << virtualAllele << "</Name>" << endLine;
if (mOffGrid)
suffix = "true";
else if (mAcceptedOffGrid)
suffix = "accepted";
else
suffix = "false";
text << indent << "\t\t<OffLadder>" << suffix << "</OffLadder>" << endLine;
text << indent << "\t\t<BPS>" << GetBioID (0) << "</BPS>" << endLine;
text << indent << "\t\t<Locus>" << mLocus->GetLocusName () << "</Locus>" << endLine;
text << indent << "\t\t<Location>0</Location>" << endLine;
text << indent << "\t</Allele>" << endLine;
}
}
if ((mLeftLocus != NULL) && (mLeftLocus != mLocus)) {
if (mAlleleNameLeft.Length () > 0) {
text << indent << "\t<Allele>" << endLine;
text << indent << "\t\t<Name>" << mAlleleNameLeft << "</Name>" << endLine;
if (mIsOffGridLeft)
suffix = "true";
else if (GetMessageValue (acceptedOLLeft))
suffix = "accepted";
else
suffix = "false";
text << indent << "\t\t<OffLadder>" << suffix << "</OffLadder>" << endLine;
text << indent << "\t\t<BPS>" << GetBioID (-1) << "</BPS>" << endLine;
text << indent << "\t\t<Locus>" << mLeftLocus->GetLocusName () << "</Locus>" << endLine;
text << indent << "\t\t<Location>-1</Location>" << endLine;
text << indent << "\t</Allele>" << endLine;
}
}
if ((mRightLocus != NULL) && (mRightLocus != mLocus)) {
if (mAlleleNameRight.Length () > 0) {
text << indent << "\t<Allele>" << endLine;
text << indent << "\t\t<Name>" << mAlleleNameRight << "</Name>" << endLine;
if (mIsOffGridRight)
suffix = "true";
else if (GetMessageValue (acceptedOLRight))
suffix = "accepted";
else
suffix = "false";
text << indent << "\t\t<OffLadder>" << suffix << "</OffLadder>" << endLine;
text << indent << "\t\t<BPS>" << GetBioID (1) << "</BPS>" << endLine;
text << indent << "\t\t<Locus>" << mRightLocus->GetLocusName () << "</Locus>" << endLine;
text << indent << "\t\t<Location>1</Location>" << endLine;
text << indent << "\t</Allele>" << endLine;
}
}
text << indent << "</" + bracketTag << ">" << endLine;
}
text.ResetOutputLevel ();
}
void DataSignal :: WriteSmartArtifactInfoToXML (RGTextOutput& text, const RGString& indent, const RGString& bracketTag, const RGString& locationTag) {
int peak;
Endl endLine;
RGString suffix;
RGString label;
SmartMessageReporter* notice;
int i;
RGString virtualAllele;
int reportedMessageLevel;
reportedMessageLevel = GetHighestMessageLevelWithRestrictionSM ();
bool thisIsFirstNotice = true;
if ((!DontLook ()) && (NumberOfSmartNoticeObjects () != 0)) {
peak = (int) floor (Peak () + 0.5);
if (mOffGrid)
suffix = " OL";
virtualAllele = GetVirtualAlleleName ();
RGDListIterator it (*mSmartMessageReporters);
i = 0;
while (notice = (SmartMessageReporter*) it ()) {
if (!notice->GetDisplayOsirisInfo ())
continue;
if (thisIsFirstNotice) {
text << indent << "<" << bracketTag << ">" << endLine;
text << indent << "\t<level>" << reportedMessageLevel << "</level>" << endLine;
text << indent << "\t<mean>" << GetMean () << "</mean>" << endLine;
text << indent << "\t<height>" << peak << "</height>" << endLine;
// text << indent << "\t<" << locationTag << ">" << (int) floor (GetApproximateBioID () + 0.5) << "</" << locationTag << ">" << endLine;
text << indent << "\t<" << locationTag << ">" << GetApproximateBioID () << "</" << locationTag << ">" << endLine;
text << indent << "\t<PeakArea>" << TheoreticalArea () << "</PeakArea>" << endLine;
if (virtualAllele.Length () > 0)
text << indent << "\t<equivAllele>" << virtualAllele << suffix << "</equivAllele>" << endLine;
text << indent << "\t<width>" << 4.0 * GetStandardDeviation () << "</width>" << endLine;
text << indent << "\t<fit>" << GetCurveFit () << "</fit>" << endLine;
label = indent + "\t<label>";
thisIsFirstNotice = false;
}
if (i > 0)
label << " ";
label += notice->GetMessage ();
label += notice->GetMessageData ();
i++;
}
RGString temp = GetVirtualAlleleName () + suffix;
if (temp.Length () > 0) {
if (i > 0)
label << " ";
label += "Allele " + temp;
}
if (i > 0) {
label << "</label>";
text << label << endLine;
text << indent << "</" + bracketTag << ">" << endLine;
}
/*if ((signalLink != NULL) && (!signalLink->xmlArtifactInfoWritten)) {
signalLink->xmlArtifactInfoWritten = true;
peak = signalLink->height;
text << indent << "<" << bracketTag << ">" << endLine;
text << indent << "\t<mean>" << signalLink->mean << "</mean>" << endLine;
text << indent << "\t<height>" << peak << "</height>" << endLine;
text << indent << "\t<" << locationTag << ">" << signalLink->bioID << "</" << locationTag << ">" << endLine;
text << indent << "\t<fit>" << GetCurveFit () << "</fit>" << endLine;
label = indent + "\t<label>";
mNoticeObjectIterator.Reset ();
i = 0;
while (notice = (Notice*) mNoticeObjectIterator ()) {
if (i > 0)
label << " ";
label += notice->GetLabel ();
i++;
}
if (temp.Length () > 0) {
if (i > 0)
label << " ";
label += "Allele " + temp;
}
label << "</label>";
text << label << endLine;
text << indent << "</" + bracketTag << ">" << endLine;
}*/
}
}
bool Star::AutoFind(const usImage& image, int extraEdgeAllowance, int searchRegion)
{
if (!image.Subframe.IsEmpty())
{
Debug.AddLine("Autofind called on subframe, returning error");
return false; // not found
}
wxBusyCursor busy;
Debug.AddLine(wxString::Format("Star::AutoFind called with edgeAllowance = %d searchRegion = %d", extraEdgeAllowance, searchRegion));
// run a 3x3 median first to eliminate hot pixels
usImage smoothed;
smoothed.CopyFrom(image);
Median3(smoothed);
// convert to floating point
FloatImg conv(smoothed);
// downsample the source image
const int downsample = 1;
if (downsample > 1)
{
FloatImg tmp;
Downsample(tmp, conv, downsample);
conv.Swap(tmp);
}
// run the PSF convolution
{
FloatImg tmp;
psf_conv(tmp, conv);
conv.Swap(tmp);
}
enum { CONV_RADIUS = 4 };
int dw = conv.Size.GetWidth(); // width of the downsampled image
int dh = conv.Size.GetHeight(); // height of the downsampled image
wxRect convRect(CONV_RADIUS, CONV_RADIUS, dw - 2 * CONV_RADIUS, dh - 2 * CONV_RADIUS); // region containing valid data
SaveImage(conv, "PHD2_AutoFind.fit");
enum { TOP_N = 100 }; // keep track of the brightest stars
std::set<Peak> stars; // sorted by ascending intensity
double global_mean, global_stdev;
GetStats(&global_mean, &global_stdev, conv, convRect);
Debug.AddLine("AutoFind: global mean = %.1f, stdev %.1f", global_mean, global_stdev);
const double threshold = 0.1;
Debug.AddLine("AutoFind: using threshold = %.1f", threshold);
// find each local maximum
int srch = 4;
for (int y = convRect.GetTop() + srch; y <= convRect.GetBottom() - srch; y++)
{
for (int x = convRect.GetLeft() + srch; x <= convRect.GetRight() - srch; x++)
{
float val = conv.px[dw * y + x];
bool ismax = false;
if (val > 0.0)
{
ismax = true;
for (int j = -srch; j <= srch; j++)
{
for (int i = -srch; i <= srch; i++)
{
if (i == 0 && j == 0)
continue;
if (conv.px[dw * (y + j) + (x + i)] > val)
{
ismax = false;
break;
}
}
}
}
if (!ismax)
continue;
// compare local maximum to mean value of surrounding pixels
const int local = 7;
double local_mean, local_stdev;
wxRect localRect(x - local, y - local, 2 * local + 1, 2 * local + 1);
localRect.Intersect(convRect);
GetStats(&local_mean, &local_stdev, conv, localRect);
// this is our measure of star intensity
double h = (val - local_mean) / global_stdev;
if (h < threshold)
{
// Debug.AddLine(wxString::Format("AG: local max REJECT [%d, %d] PSF %.1f SNR %.1f", imgx, imgy, val, SNR));
continue;
}
// coordinates on the original image
int imgx = x * downsample + downsample / 2;
int imgy = y * downsample + downsample / 2;
stars.insert(Peak(imgx, imgy, h));
if (stars.size() > TOP_N)
stars.erase(stars.begin());
}
}
for (std::set<Peak>::const_reverse_iterator it = stars.rbegin(); it != stars.rend(); ++it)
Debug.AddLine("AutoFind: local max [%d, %d] %.1f", it->x, it->y, it->val);
// merge stars that are very close into a single star
{
const int minlimitsq = 5 * 5;
repeat:
for (std::set<Peak>::const_iterator a = stars.begin(); a != stars.end(); ++a)
{
std::set<Peak>::const_iterator b = a;
++b;
for (; b != stars.end(); ++b)
{
int dx = a->x - b->x;
int dy = a->y - b->y;
int d2 = dx * dx + dy * dy;
if (d2 < minlimitsq)
{
// very close, treat as single star
Debug.AddLine("AutoFind: merge [%d, %d] %.1f - [%d, %d] %.1f", a->x, a->y, a->val, b->x, b->y, b->val);
// erase the dimmer one
stars.erase(a);
goto repeat;
}
}
}
}
// exclude stars that would fit within a single searchRegion box
{
// build a list of stars to be excluded
std::set<int> to_erase;
const int extra = 5; // extra safety margin
const int fullw = searchRegion + extra;
for (std::set<Peak>::const_iterator a = stars.begin(); a != stars.end(); ++a)
{
std::set<Peak>::const_iterator b = a;
++b;
for (; b != stars.end(); ++b)
{
int dx = abs(a->x - b->x);
int dy = abs(a->y - b->y);
if (dx <= fullw && dy <= fullw)
{
// stars closer than search region, exclude them both
// but do not let a very dim star eliminate a very bright star
if (b->val / a->val >= 5.0)
{
Debug.AddLine("AutoFind: close dim-bright [%d, %d] %.1f - [%d, %d] %.1f", a->x, a->y, a->val, b->x, b->y, b->val);
}
else
{
Debug.AddLine("AutoFind: too close [%d, %d] %.1f - [%d, %d] %.1f", a->x, a->y, a->val, b->x, b->y, b->val);
to_erase.insert(std::distance(stars.begin(), a));
to_erase.insert(std::distance(stars.begin(), b));
}
}
}
}
RemoveItems(stars, to_erase);
}
// exclude stars too close to the edge
{
enum { MIN_EDGE_DIST = 40 };
int edgeDist = MIN_EDGE_DIST + extraEdgeAllowance;
std::set<Peak>::iterator it = stars.begin();
while (it != stars.end())
{
std::set<Peak>::iterator next = it;
++next;
if (it->x <= edgeDist || it->x >= image.Size.GetWidth() - edgeDist ||
it->y <= edgeDist || it->y >= image.Size.GetHeight() - edgeDist)
{
Debug.AddLine("AutoFind: too close to edge [%d, %d] %.1f", it->x, it->y, it->val);
stars.erase(it);
}
it = next;
}
}
// At first I tried running Star::Find on the survivors to find the best
// star. This had the unfortunate effect of locating hot pixels which
// the psf convolution so nicely avoids. So, don't do that! -ag
// find the brightest non-saturated star. If no non-saturated stars, settle for a saturated star.
bool allowSaturated = false;
while (true)
{
Debug.AddLine("AutoSelect: finding best star allowSaturated = %d", allowSaturated);
for (std::set<Peak>::reverse_iterator it = stars.rbegin(); it != stars.rend(); ++it)
{
Star tmp;
tmp.Find(&image, searchRegion, it->x, it->y, FIND_CENTROID);
if (tmp.WasFound())
{
if (tmp.GetError() == STAR_SATURATED && !allowSaturated)
{
Debug.AddLine("Autofind: star saturated [%d, %d] %.1f Mass %.f SNR %.1f", it->x, it->y, it->val, tmp.Mass, tmp.SNR);
continue;
}
SetXY(it->x, it->y);
Debug.AddLine("Autofind returns star at [%d, %d] %.1f Mass %.f SNR %.1f", it->x, it->y, it->val, tmp.Mass, tmp.SNR);
return true;
}
}
if (allowSaturated)
break; // no stars found
Debug.AddLine("AutoFind: could not find a non-saturated star!");
allowSaturated = true;
}
Debug.AddLine("Autofind: no star found");
return false;
}
bool Star::AutoFind(const usImage& image, int extraEdgeAllowance, int searchRegion)
{
if (!image.Subframe.IsEmpty())
{
Debug.AddLine("Autofind called on subframe, returning error");
return false; // not found
}
wxBusyCursor busy;
Debug.Write(wxString::Format("Star::AutoFind called with edgeAllowance = %d searchRegion = %d\n", extraEdgeAllowance, searchRegion));
// run a 3x3 median first to eliminate hot pixels
usImage smoothed;
smoothed.CopyFrom(image);
Median3(smoothed);
// convert to floating point
FloatImg conv(smoothed);
// downsample the source image
const int downsample = 1;
if (downsample > 1)
{
FloatImg tmp;
Downsample(tmp, conv, downsample);
conv.Swap(tmp);
}
// run the PSF convolution
{
FloatImg tmp;
psf_conv(tmp, conv);
conv.Swap(tmp);
}
enum { CONV_RADIUS = 4 };
int dw = conv.Size.GetWidth(); // width of the downsampled image
int dh = conv.Size.GetHeight(); // height of the downsampled image
wxRect convRect(CONV_RADIUS, CONV_RADIUS, dw - 2 * CONV_RADIUS, dh - 2 * CONV_RADIUS); // region containing valid data
SaveImage(conv, "PHD2_AutoFind.fit");
enum { TOP_N = 100 }; // keep track of the brightest stars
std::set<Peak> stars; // sorted by ascending intensity
double global_mean, global_stdev;
GetStats(&global_mean, &global_stdev, conv, convRect);
Debug.Write(wxString::Format("AutoFind: global mean = %.1f, stdev %.1f\n", global_mean, global_stdev));
const double threshold = 0.1;
Debug.Write(wxString::Format("AutoFind: using threshold = %.1f\n", threshold));
// find each local maximum
int srch = 4;
for (int y = convRect.GetTop() + srch; y <= convRect.GetBottom() - srch; y++)
{
for (int x = convRect.GetLeft() + srch; x <= convRect.GetRight() - srch; x++)
{
float val = conv.px[dw * y + x];
bool ismax = false;
if (val > 0.0)
{
ismax = true;
for (int j = -srch; j <= srch; j++)
{
for (int i = -srch; i <= srch; i++)
{
if (i == 0 && j == 0)
continue;
if (conv.px[dw * (y + j) + (x + i)] > val)
{
ismax = false;
break;
}
}
}
}
if (!ismax)
continue;
// compare local maximum to mean value of surrounding pixels
const int local = 7;
double local_mean, local_stdev;
wxRect localRect(x - local, y - local, 2 * local + 1, 2 * local + 1);
localRect.Intersect(convRect);
GetStats(&local_mean, &local_stdev, conv, localRect);
// this is our measure of star intensity
double h = (val - local_mean) / global_stdev;
if (h < threshold)
{
// Debug.Write(wxString::Format("AG: local max REJECT [%d, %d] PSF %.1f SNR %.1f\n", imgx, imgy, val, SNR));
continue;
}
// coordinates on the original image
int imgx = x * downsample + downsample / 2;
int imgy = y * downsample + downsample / 2;
stars.insert(Peak(imgx, imgy, h));
if (stars.size() > TOP_N)
stars.erase(stars.begin());
}
}
for (std::set<Peak>::const_reverse_iterator it = stars.rbegin(); it != stars.rend(); ++it)
Debug.Write(wxString::Format("AutoFind: local max [%d, %d] %.1f\n", it->x, it->y, it->val));
// merge stars that are very close into a single star
{
const int minlimitsq = 5 * 5;
repeat:
for (std::set<Peak>::const_iterator a = stars.begin(); a != stars.end(); ++a)
{
std::set<Peak>::const_iterator b = a;
++b;
for (; b != stars.end(); ++b)
{
int dx = a->x - b->x;
int dy = a->y - b->y;
int d2 = dx * dx + dy * dy;
if (d2 < minlimitsq)
{
// very close, treat as single star
Debug.Write(wxString::Format("AutoFind: merge [%d, %d] %.1f - [%d, %d] %.1f\n", a->x, a->y, a->val, b->x, b->y, b->val));
// erase the dimmer one
stars.erase(a);
goto repeat;
}
}
}
}
// exclude stars that would fit within a single searchRegion box
{
// build a list of stars to be excluded
std::set<int> to_erase;
const int extra = 5; // extra safety margin
const int fullw = searchRegion + extra;
for (std::set<Peak>::const_iterator a = stars.begin(); a != stars.end(); ++a)
{
std::set<Peak>::const_iterator b = a;
++b;
for (; b != stars.end(); ++b)
{
int dx = abs(a->x - b->x);
int dy = abs(a->y - b->y);
if (dx <= fullw && dy <= fullw)
{
// stars closer than search region, exclude them both
// but do not let a very dim star eliminate a very bright star
if (b->val / a->val >= 5.0)
{
Debug.Write(wxString::Format("AutoFind: close dim-bright [%d, %d] %.1f - [%d, %d] %.1f\n", a->x, a->y, a->val, b->x, b->y, b->val));
}
else
{
Debug.Write(wxString::Format("AutoFind: too close [%d, %d] %.1f - [%d, %d] %.1f\n", a->x, a->y, a->val, b->x, b->y, b->val));
to_erase.insert(std::distance(stars.begin(), a));
to_erase.insert(std::distance(stars.begin(), b));
}
}
}
}
RemoveItems(stars, to_erase);
}
// exclude stars too close to the edge
{
enum { MIN_EDGE_DIST = 40 };
int edgeDist = MIN_EDGE_DIST + extraEdgeAllowance;
std::set<Peak>::iterator it = stars.begin();
while (it != stars.end())
{
std::set<Peak>::iterator next = it;
++next;
if (it->x <= edgeDist || it->x >= image.Size.GetWidth() - edgeDist ||
it->y <= edgeDist || it->y >= image.Size.GetHeight() - edgeDist)
{
Debug.Write(wxString::Format("AutoFind: too close to edge [%d, %d] %.1f\n", it->x, it->y, it->val));
stars.erase(it);
}
it = next;
}
}
// At first I tried running Star::Find on the survivors to find the best
// star. This had the unfortunate effect of locating hot pixels which
// the psf convolution so nicely avoids. So, don't do that! -ag
// try to identify the saturation point
// first, find the peak pixel overall
unsigned short maxVal = 0;
for (unsigned int i = 0; i < image.NPixels; i++)
if (image.ImageData[i] > maxVal)
maxVal = image.ImageData[i];
// next see if any of the stars has a flat-top
bool foundSaturated = false;
for (std::set<Peak>::reverse_iterator it = stars.rbegin(); it != stars.rend(); ++it)
{
Star tmp;
tmp.Find(&image, searchRegion, it->x, it->y, FIND_CENTROID);
if (tmp.WasFound() && tmp.GetError() == STAR_SATURATED)
{
if ((maxVal - tmp.PeakVal) * 255U > maxVal)
{
// false positive saturation, flat top but below maxVal
Debug.Write(wxString::Format("AutoSelect: false positive saturation peak = %hu, max = %hu\n", tmp.PeakVal, maxVal));
}
else
{
// a saturated star was found
foundSaturated = true;
break;
}
}
}
unsigned int sat_level; // saturation level, including pedestal
if (foundSaturated)
{
// use the peak overall pixel value as the saturation limit
Debug.Write(wxString::Format("AutoSelect: using saturation level peakVal = %hu\n", maxVal));
sat_level = maxVal; // includes pedestal
}
else
{
// no staurated stars found, can't make any assumption about whether the max val is saturated
Debug.Write(wxString::Format("AutoSelect: using saturation level from BPP %u and pedestal %hu\n",
image.BitsPerPixel, image.Pedestal));
sat_level = ((1U << image.BitsPerPixel) - 1) + image.Pedestal;
if (sat_level > 65535)
sat_level = 65535;
}
unsigned int diff = sat_level > image.Pedestal ? sat_level - image.Pedestal : 0U;
// "near-saturation" threshold at 90% saturation
unsigned short sat_thresh = (unsigned short)((unsigned int) image.Pedestal + 9 * diff / 10);
Debug.Write(wxString::Format("AutoSelect: BPP = %u, saturation at %u, pedestal %hu, thresh = %hu\n",
image.BitsPerPixel, sat_level, image.Pedestal, sat_thresh));
// Final star selection
// pass 1: find brightest star with peak value < 90% saturation AND SNR > 6
// this pass will reject saturated and nearly-saturated stars
// pass 2: find brightest non-saturated star
// pass 3: find brightest star, even if saturated
for (int pass = 1; pass <= 3; pass++)
{
Debug.Write(wxString::Format("AutoSelect: finding best star pass %d\n", pass));
for (std::set<Peak>::reverse_iterator it = stars.rbegin(); it != stars.rend(); ++it)
{
Star tmp;
tmp.Find(&image, searchRegion, it->x, it->y, FIND_CENTROID);
if (tmp.WasFound())
{
if (pass == 1)
{
if (tmp.PeakVal > sat_thresh)
{
Debug.Write(wxString::Format("Autofind: near-saturated [%d, %d] %.1f Mass %.f SNR %.1f Peak %hu\n", it->x, it->y, it->val, tmp.Mass, tmp.SNR, tmp.PeakVal));
continue;
}
if (tmp.GetError() == STAR_SATURATED || tmp.SNR < 6.0)
continue;
}
else if (pass == 2)
{
if (tmp.GetError() == STAR_SATURATED)
{
Debug.Write(wxString::Format("Autofind: star saturated [%d, %d] %.1f Mass %.f SNR %.1f\n", it->x, it->y, it->val, tmp.Mass, tmp.SNR));
continue;
}
}
// star accepted
SetXY(it->x, it->y);
Debug.Write(wxString::Format("Autofind returns star at [%d, %d] %.1f Mass %.f SNR %.1f\n", it->x, it->y, it->val, tmp.Mass, tmp.SNR));
return true;
}
}
if (pass == 1)
Debug.Write("AutoFind: could not find a star on Pass 1\n");
else if (pass == 2)
Debug.Write("AutoFind: could not find a non-saturated star!\n");
}
Debug.Write("Autofind: no star found\n");
return false;
}