Merge pull request #101 from xoltar/betti-save

Allow optional output file argument with --betti
rivetTDA · Jul 28, 2017 · 6ce3c9a · 6ce3c9a
2 parents 109dc51 + 338416b
commit 6ce3c9a
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Showing 5 changed files with 64 additions and 29 deletions.
diff --git a/console.cpp b/console.cpp
@@ -50,6 +50,7 @@ static const char USAGE[] =
       rivet_console --version
       rivet_console <input_file> --identify
       rivet_console <input_file> --betti [-H <dimension>] [-V <verbosity>] [-x <xbins>] [-y <ybins>]
+      rivet_console <input_file> <output_file> --betti [-H <dimension>] [-V <verbosity>] [-x <xbins>] [-y <ybins>]
       rivet_console <precomputed_file> --bounds
       rivet_console <precomputed_file> --barcodes <line_file>
       rivet_console <input_file> <output_file> [-H <dimension>] [-V <verbosity>] [-x <xbins>] [-y <ybins>] [-f <format>] [--binary]
@@ -362,7 +363,7 @@ int main(int argc, char* argv[])
             std::clog << "Wrote arrangement to " << params.outputFile << std::endl;
         }
     });
-    computation.template_points_ready.connect([&points_message, &binary, &betti_only, &verbosity](TemplatePointsMessage message) {
+    computation.template_points_ready.connect([&points_message, &binary, &betti_only, &verbosity, &params](TemplatePointsMessage message) {
         points_message.reset(new TemplatePointsMessage(message));
 
         if (binary) {
@@ -397,8 +398,27 @@ int main(int argc, char* argv[])
             print_dims(message, std::cout);
             std::cout << std::endl;
             print_betti(message, std::cout);
-            std::cout.flush();
+
+            //if an output file has been specified, then save the Betti numbers in an arrangement file (with no barcode templates)
+            if (!params.outputFile.empty()) {
+                std::ofstream file(params.outputFile);
+                if (file.is_open()) {
+                    std::vector<exact> emptyvec;
+                    std::shared_ptr<Arrangement> temp_arrangement = std::make_shared<Arrangement>(emptyvec, emptyvec, verbosity);
+                    std::shared_ptr<ArrangementMessage> temp_am = std::make_shared<ArrangementMessage>(*temp_arrangement);
+                    if (verbosity > 0) {
+                        debug() << "Writing file:" << params.outputFile;
+                    }
+                    write_boost_file(params, *points_message, *temp_am);
+                } else {
+                    std::stringstream ss;
+                    ss << "Error: Unable to write file:" << params.outputFile;
+                    throw std::runtime_error(ss.str());
+                }
+            }
+
             //TODO: this seems a little abrupt...
+            std::cout.flush();
             exit(0);
         }
     });
@@ -413,19 +433,21 @@ int main(int argc, char* argv[])
     }
     std::unique_ptr<ComputationResult> result;
 
+    std::unique_ptr<InputData> input;
+
+    std::shared_ptr<Arrangement> arrangement;
+
     if (barcodes || bounds) {
         result = load_from_precomputed(params.fileName);
         if (barcodes) {
             if (!slices.empty()) {
                 process_barcode_queries(slices, *result);
-                return 0;
             }
         } else {
             process_bounds(*result);
         }
     } else {
 
-        std::unique_ptr<InputData> input;
         try {
             input = inputManager.start(progress);
         } catch (const std::exception& e) {
@@ -441,31 +463,34 @@ int main(int argc, char* argv[])
         if (params.verbosity >= 2) {
             debug() << "Computation complete; augmented arrangement ready.";
         }
-        auto arrangement = result->arrangement;
+        arrangement = result->arrangement;
         if (params.verbosity >= 4) {
             arrangement->print_stats();
         }
 
-        //if an output file has been specified, then save the arrangement
-        if (!params.outputFile.empty()) {
-            std::ofstream file(params.outputFile);
-            if (file.is_open()) {
-                if (verbosity > 0) {
-                    debug() << "Writing file:" << params.outputFile;
-                }
-                if (params.outputFormat == "R0") {
-                    FileWriter fw(params, *input, *(arrangement), result->template_points);
-                    fw.write_augmented_arrangement(file);
-                } else if (params.outputFormat == "R1") {
-                    write_boost_file(params, *points_message, *arrangement_message);
-                } else {
-                    throw std::runtime_error("Unsupported output format: " + params.outputFormat);
-                }
+    }
+    //if an output file has been specified, then save the arrangement
+    if (!params.outputFile.empty()) {
+        std::ofstream file(params.outputFile);
+        if (file.is_open()) {
+            if (arrangement == nullptr) {
+                arrangement.reset(new Arrangement());
+            }
+            if (verbosity > 0) {
+                debug() << "Writing file:" << params.outputFile;
+            }
+            if (params.outputFormat == "R0") {
+                FileWriter fw(params, *input, *(arrangement), result->template_points);
+                fw.write_augmented_arrangement(file);
+            } else if (params.outputFormat == "R1") {
+                write_boost_file(params, *points_message, *arrangement_message);
             } else {
-                std::stringstream ss;
-                ss << "Error: Unable to write file:" << params.outputFile;
-                throw std::runtime_error(ss.str());
+                throw std::runtime_error("Unsupported output format: " + params.outputFormat);
             }
+        } else {
+            std::stringstream ss;
+            ss << "Error: Unable to write file:" << params.outputFile;
+            throw std::runtime_error(ss.str());
         }
     }
     if (params.verbosity > 2) {

diff --git a/dcel/arrangement_message.cpp b/dcel/arrangement_message.cpp
@@ -530,3 +530,8 @@ Arrangement ArrangementMessage::to_arrangement() const
 //    std::clog << "All anchors identical in to_arrangement" << std::endl;
     return arrangement;
 }
+
+bool ArrangementMessage::is_empty() const
+{
+    return ( x_exact.empty() && y_exact.empty() );
+}
diff --git a/dcel/arrangement_message.h b/dcel/arrangement_message.h
@@ -51,6 +51,8 @@ class ArrangementMessage {
 
     Arrangement to_arrangement() const;
 
+    bool is_empty() const;
+
 private:
     friend class boost::serialization::access;
 

diff --git a/interface/progressdialog.cpp b/interface/progressdialog.cpp
@@ -81,15 +81,18 @@ void ProgressDialog::updateProgress(unsigned current)
 void ProgressDialog::setComputationFinished()
 {
     computation_finished = true;
-    close();
+    QThread::msleep(200); //seems to prevent ProgressDialog from sticking around after it is supposed to have been closed
+    done(0);
 }
 
 void ProgressDialog::closeEvent(QCloseEvent* event)
 {
     if (!computation_finished)
         event->ignore();
-    else
+    else {
         event->accept();
+        QWidget::closeEvent(event);
+    }
 }
 
 QLabel* ProgressDialog::getLabel(unsigned i)

diff --git a/visualizationwindow.cpp b/visualizationwindow.cpp
@@ -166,6 +166,10 @@ void VisualizationWindow::augmented_arrangement_ready(std::shared_ptr<Arrangemen
     //receive the arrangement
     this->arrangement = arrangement;
 
+    if(arrangement->is_empty()) { //e.g. the arrangement contains only Betti numbers and no barcode templates
+        return;
+    }
+
     //TESTING: print arrangement info and verify consistency
     //    arrangement->print_stats();
     //    arrangement->test_consistency();
@@ -286,12 +290,8 @@ void VisualizationWindow::update_persistence_diagram()
         BarcodeTemplate dbc = arrangement->get_barcode_template(angle_precise, offset_precise);
         barcode = dbc.rescale(angle_precise, offset_precise, template_points->template_points, grades);
 
-        qDebug() << "Unshifted barcode:";
-        barcode->print();
-
         //shift the barcode so that "zero" is where the selected line crosses the bottom or left side of the viewing window
     	double ll_corner = rivet::numeric::project_to_line(angle_precise, offset_precise, grades.x[0], grades.y[0]); //lower-left corner of line selection window
-    	qDebug() << "ll_corner: " << ll_corner;
     	barcode = barcode->shift(-1*ll_corner);
 
         //TESTING