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us_pseudo_absorbance/us_convert_scan: initialize loading the referenc…
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…e scan from a csv file
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@samo38
samo38 committed Jun 20, 2024
1 parent a284a39 commit 981fe32
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Showing 2 changed files with 160 additions and 14 deletions.
173 changes: 159 additions & 14 deletions programs/us_pseudo_absorbance/us_convert_scan.cpp
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
#include "us_convert_scan.h"
#include "us_load_auc.h"
#include "us_csv_loader.h"
#include <QGuiApplication>

US_ConvertScan::US_ConvertScan() : US_Widgets()
Expand Down Expand Up @@ -89,19 +90,17 @@ US_ConvertScan::US_ConvertScan() : US_Widgets()
align_center(ct_scan_to);

QGridLayout* scan_lyt = new QGridLayout();
scan_lyt->addWidget(lb_scans, 0, 0, 1, 1);
scan_lyt->addWidget(ct_scans, 0, 1, 1, 1);
scan_lyt->addWidget(lb_scans, 0, 0, 1, 1);
scan_lyt->addWidget(ct_scans, 0, 1, 1, 1);
// scan_lyt->addWidget(lb_smooth, 1, 0, 1, 1);
// scan_lyt->addWidget(ct_smooth, 1, 1, 1, 1);
scan_lyt->addWidget(pb_apply, 0, 2, 1, 1);
scan_lyt->addWidget(lb_maxod, 1, 0, 1, 1);
scan_lyt->addWidget(ct_maxod, 1, 1, 1, 2);

scan_lyt->addWidget(lb_scan_from, 2, 0, 1, 1);
scan_lyt->addWidget(ct_scan_from, 2, 1, 1, 2);

scan_lyt->addWidget(lb_scan_to, 3, 0, 1, 1);
scan_lyt->addWidget(ct_scan_to, 3, 1, 1, 2);
scan_lyt->addWidget(pb_apply, 0, 2, 1, 1);
scan_lyt->addWidget(lb_scan_from, 1, 0, 1, 1);
scan_lyt->addWidget(ct_scan_from, 1, 1, 1, 2);
scan_lyt->addWidget(lb_scan_to, 2, 0, 1, 1);
scan_lyt->addWidget(ct_scan_to, 2, 1, 1, 2);
scan_lyt->addWidget(lb_maxod, 3, 0, 1, 1);
scan_lyt->addWidget(ct_maxod, 3, 1, 1, 2);

tb_triple = new QTableWidget();
tb_triple->setRowCount(0);
Expand Down Expand Up @@ -263,6 +262,7 @@ US_ConvertScan::US_ConvertScan() : US_Widgets()

connect(this, &US_ConvertScan::sig_plot, this, &US_ConvertScan::plot_all);
connect(pb_import, &QPushButton::clicked, this, &US_ConvertScan::import_run);
connect(pb_load_ref, &QPushButton::clicked, this, &US_ConvertScan::load_ref_scan);
connect(pb_reset, &QPushButton::clicked, this, &US_ConvertScan::reset);
connect(pb_prev_id, &QPushButton::clicked, this, &US_ConvertScan::prev_id);
connect(pb_next_id, &QPushButton::clicked, this, &US_ConvertScan::next_id);
Expand Down Expand Up @@ -344,6 +344,142 @@ void US_ConvertScan::apply_nscans() {
emit sig_plot();
}

void US_ConvertScan::load_ref_scan() {
QString filter = "text files (*);;csv files (*.csv);;dat files (*.dat)";
QString fpath = QFileDialog::getOpenFileName(this, "Load Reference Scans",
US_Settings::dataDir(), filter);
if (fpath.isEmpty()) {
return;
}

for (int ii = 0; ii < refscan_files.size(); ii++) {
QString file_loaded = refscan_files.at(ii).filename;
if (file_loaded.compare(fpath) == 0) {
QMessageBox::warning(this, "Error!", "The following file has already been uploaded!\n" + fpath);
return;
}
}


QString note = "A Header Instance: cm;220nm;222nm;224nm";
US_CSV_Loader *csv_loader = new US_CSV_Loader(fpath, note, true, this);
int state = csv_loader->exec();
if (state != QDialog::Accepted) return;
double min_r = 5;
double max_r = 8;
QString mesg = tr("Reference scan files should have at least two columns with the following pattern. "
"The preferred data separator is semicolon. "
"The first column is the radial points where header name is (cm). "
"The radial point should be between %1 to %2 cm and equally distanced with 0.001 cm. "
"The rest of the columns are reference profiles at different wavelengths. "
"They should be positive values where the header specifies what wavelength they are for."
"Each wavelength header item should be number followed by (nm). "
"Here is an example:\n\n"
"cm;220nm;222nm;224nm;226nm;230nm\n"
"5.8;1629.81;1712.49;1579.66;1732.45;1632.21\n"
"5.801;1631.89;1713.16;1580.46;1733.07;1632.54\n"
"....\n"
"....\n").arg(min_r).arg(max_r);
US_CSV_Loader::CSV_Data csv_data = csv_loader->data();
if (csv_data.columnCount() < 2 ) {
QMessageBox::warning(this, "Error!", mesg + "\n\nError in the number of columns!");
return;
}
QStringList header = csv_data.header();
QVector<double> wavl;
QVector<QPair<double, int>> wavl_idx;
for (int ii = 0; ii < header.size(); ii++) {
QString name = header.at(ii).trimmed();
if (ii == 0 && name.compare("cm", Qt::CaseSensitive) != 0) {
QMessageBox::warning(this, "Error!", mesg + "\n\nError in the header!");
return;
} else if (ii > 0) {
if (name.endsWith("nm")) {
name.chop(2);
bool ok;
double val = name.toDouble(&ok);
if (!ok) {
QMessageBox::warning(this, "Error!", mesg + "\n\nError in the header!");
return;
}
if (val < 180 || val > 800) {
QMessageBox::warning(this, "Error!", "Error in the header! Wavelengths are out of range. "
"They must be in a range of 180 to 800 nm.");
return;
}
if (wavl.contains(val)) {
QMessageBox::warning(this, "Error!", mesg + "\n\nError in the header! Wavelength redundancy!");
return;
} else {
wavl << val;
wavl_idx << qMakePair(val, ii - 1);
}
} else {
QMessageBox::warning(this, "Error!", mesg + "\n\nError in the header!");
return;
}
}
}
QVector<double> xvalues = csv_data.columnAt(0);
QString mesg_r = mesg + "\n\nError in the radial points!";
if (xvalues.first() < min_r || xvalues.last() > max_r) {
QMessageBox::warning(this, "Error!", mesg_r);
return;
}
for(int ii = 1; ii < xvalues.size(); ii++) {
double r = xvalues.at(ii);
if (r < min_r || r > max_r) {
QMessageBox::warning(this, "Error!", mesg_r);
return;
}
double dr = xvalues.at(ii) - xvalues.at(ii - 1);
if (dr < 0.0008 || dr > 0.003) {
QMessageBox::warning(this, "Error!", mesg_r);
return;
}
}
mesg_r = mesg + "\n\nError in the data values!";
QVector<QVector<double>> yvalues;
for (int ii = 1; ii < csv_data.columnCount(); ii++) {
QVector<double> col = csv_data.columnAt(ii);
foreach (double d, col) {
if (d <= 0) {
QMessageBox::warning(this, "Error!", mesg_r + " Negative and zero values are not allowed!");
return;
}
}
yvalues << col;
}

std::sort(wavl_idx.begin(), wavl_idx.end(),
[](auto a, auto b) { return a.first < b.first;});
RefscanFile reffile;
double min_wvl = 10000;
double max_wvl = 0;
reffile.xvalues << xvalues;
for (int ii = 0; ii < wavl_idx.size(); ii++) {
double wvl = wavl_idx.at(ii).first;
double idx = wavl_idx.at(ii).second;
min_wvl = qMin(min_wvl, wvl);
max_wvl = qMax(max_wvl, wvl);
reffile.wavelength << wvl;
reffile.yvalues << yvalues.at(idx);
}
reffile.min_wvl = min_wvl;
reffile.max_wvl = max_wvl;
reffile.nwvl = reffile.wavelength.size();
reffile.filename = fpath;
reffile.name = tr("Reference %1").arg(refscan_files.size() + 1);

refscan_files << reffile;
set_table();
set_wavl_ctrl();
pb_reset->setEnabled(true);
hasData = true;
le_status->clear();

}

int US_ConvertScan::read_auc(QVector<US_DataIO::RawData>& rawdata,
QVector<QVector<QVector<double>>>& absorbance,
QVector<QVector<QVector<double>>>& refscans,
Expand Down Expand Up @@ -908,7 +1044,7 @@ void US_ConvertScan::save_run() {
void US_ConvertScan::set_table(){
tb_triple->disconnect();
tb_triple->clearContents();
tb_triple->setRowCount(ccw_items.size());
tb_triple->setRowCount(ccw_items.size() + refscan_files.size());

QString runid;
int rcode = 1;
Expand Down Expand Up @@ -960,15 +1096,24 @@ void US_ConvertScan::set_table(){
twi_cc = new QTableWidgetItem(item_cc);
twi_cc->setFlags(twi_cc->flags() & ~Qt::ItemIsEditable);
twi_cc->setFont(font);
tb_triple->setItem(ii, 0, twi_cc);
int II = ccw_items.size() + ii;
tb_triple->setItem(II, 0, twi_cc);

QString item_wvl = tr("%1-%2 (%3)").arg(refscan_files.at(ii).min_wvl)
.arg(refscan_files.at(ii).max_wvl).arg(refscan_files.at(ii).nwvl);
QTableWidgetItem *twi_wvl;
twi_wvl = new QTableWidgetItem(item_wvl);
twi_wvl->setFlags(twi_wvl->flags() & ~Qt::ItemIsEditable);
twi_wvl->setFont(font);
tb_triple->setItem(ii, 1, twi_wvl);
tb_triple->setItem(II, 1, twi_wvl);

QTableWidgetItem *twi_2 = new QTableWidgetItem();
twi_2->setFlags(twi_2->flags() & ~Qt::ItemIsEditable);
tb_triple->setItem(II, 2, twi_2);

QTableWidgetItem *twi_3 = new QTableWidgetItem();
twi_3->setFlags(twi_3->flags() & ~Qt::ItemIsEditable);
tb_triple->setItem(II, 3, twi_3);
}

for (int ii = 0; ii < ccw_items.size(); ii++) {
Expand Down
1 change: 1 addition & 0 deletions programs/us_pseudo_absorbance/us_convert_scan.h
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Original file line number Diff line number Diff line change
Expand Up @@ -47,6 +47,7 @@ private slots:
void lower_scan_range(double);
void upper_scan_range(double);
void plot_ref_state();
void load_ref_scan();

private:

Expand Down

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