Add a new option to add a labels file and a means file.

src/Options.cpp

@@ -10,14 +10,14 @@ using namespace std;
 static void show_help(const char *progname, int exitcode) {
     cerr << "Usage: " << progname << " -m MODEL -w WEIGHTS INPUTS..." << endl
          << endl
-         << R"END(
-Simulate the specified network on the specified inputs.
+         << R"END(Simulate the specified network on the specified inputs.
 
 Options:
 	-h	show this message
-	-m	(required) the model file to simulate
+	-n	(required) the model file to simulate
 	-w	(required) the trained weights
-)END" << endl;
+    -m  means file. Will be substracted from input if available.
+    -l  labels file. Will be used to print prediction labels if available.)END" << endl;
 
     exit(exitcode);
 }
@@ -32,10 +32,12 @@ static void check_file(const char *filename) {
 Options Options::parse(const int argc, char *const argv[]) {
     string model;
     string weights;
+    string means;
+    string labels;
 
     char c;
 
-    while ((c = getopt(argc, argv, "hm:w:")) != -1) {
+    while ((c = getopt(argc, argv, "hm:w:n:l:")) != -1) {
         switch (c) {
             case 'h':
                 show_help(argv[0], 0);
@@ -46,16 +48,27 @@ Options Options::parse(const int argc, char *const argv[]) {
                 weights = optarg;
                 break;
 
-            case 'm':
+            case 'n':
                 check_file(optarg);
                 model = optarg;
                 break;
 
+            case 'm':
+                check_file(optarg);
+                means = optarg;
+                break;
+
+            case 'l':
+                check_file(optarg);
+                labels = optarg;
+                break;
+
             case '?':
                 show_help(argv[0], 1);
                 break;
 
             default:
+                cerr << "Unhandled option: " << c << endl;
                 abort();
         }
     }
@@ -78,23 +91,36 @@ Options Options::parse(const int argc, char *const argv[]) {
         show_help(argv[0], 1);
     }
 
-    return Options(move(model), move(weights), move(inputs));
+    return Options(move(model), move(weights), move(means), move(labels), move(inputs));
 }
 
-Options::Options(string &&model, string &&weights, vector<string> &&inputs) noexcept:
+Options::Options(string &&model, string &&weights, string&& means, string&& labels, vector<string> &&inputs) noexcept:
         modelPath(move(model)),
         weightsPath(move(weights)),
-        inputPaths(move(inputs)) {
+        meansPath(means),
+        labelsPath(labels),
+        inputPaths(move(inputs))
+{
 }
 
-const string &Options::model() const {
+const string& Options::model() const {
     return modelPath;
 }
 
-const string &Options::weights() const {
+const string& Options::weights() const {
     return weightsPath;
 }
 
-const vector<string> &Options::inputs() const {
+const vector<string>& Options::inputs() const {
     return inputPaths;
 }
+
+const string& Options::means() const
+{
+    return meansPath;
+}
+
+const string& Options::labels() const
+{
+    return labelsPath;
+}

src/Options.hpp

@@ -12,17 +12,20 @@ namespace fmri {
     public:
         static Options parse(const int argc, char *const argv[]);
 
-        const string &model() const;
+        const string& model() const;
+        const string& weights() const;
+        const string& means() const;
+        const string& labels() const;
 
-        const string &weights() const;
-
-        const vector<string> &inputs() const;
+        const vector<string>& inputs() const;
 
     private:
         const string modelPath;
         const string weightsPath;
+        const string meansPath;
+        const string labelsPath;
         const vector<string> inputPaths;
 
-        Options(string &&, string &&, vector<string> &&) noexcept;
+        Options(string &&, string &&, string&&, string&&, vector<string> &&) noexcept;
     };
 }

src/Simulator.cpp

@@ -1,5 +1,5 @@
+#include <cassert>
 #include <iostream>
-#include <iterator>
 #include <vector>
 
 #include "Simulator.hpp"
@@ -8,7 +8,7 @@ using namespace caffe;
 using namespace std;
 using namespace fmri;
 
-Simulator::Simulator(const string& model_file, const string& weights_file) :
+Simulator::Simulator(const string& model_file, const string& weights_file, const string& means_file) :
 	net(model_file, TEST)
 {
 	net.CopyTrainedLayersFrom(weights_file);
@@ -21,16 +21,18 @@ Simulator::Simulator(const string& model_file, const string& weights_file) :
 			input_geometry.height, input_geometry.width);
 	/* Forward dimension change to all layers. */
 	net.Reshape();
+
+    if (means_file != "")  {
+        means = processMeans(means_file);
+    }
+
 }
 
-void Simulator::simulate(const string& image_file)
+vector<Simulator::DType> Simulator::simulate(const string& image_file)
 {
 	cv::Mat im = cv::imread(image_file, -1);
 
-	if (im.empty()) {
-		cerr << "Unable to read " << image_file << endl;
-		return;
-	}
+    assert(!im.empty());
 
     auto input = preprocess(im);
     auto channels = getWrappedInputLayer();
@@ -44,10 +46,7 @@ void Simulator::simulate(const string& image_file)
     const DType *end = begin + output_layer->channels();
     vector<DType> result(begin, end);
 
-    // TODO: visualize, rather than just print.
-    for (auto v : result) {
-        cout << v << endl;
-    }
+    return result;
 }
 
 vector<cv::Mat> Simulator::getWrappedInputLayer()
@@ -111,8 +110,36 @@ cv::Mat Simulator::preprocess(cv::Mat original) const
     cv::Mat sample_float;
     resized.convertTo(sample_float, num_channels == 3 ? CV_32FC3 : CV_32FC1);
 
-    // TODO: substract means.
-    // Don't know if necessary yet.
-
+    if (means.empty()) {
         return sample_float;
+    }
+
+    cv::Mat normalized;
+    cv::subtract(sample_float, means, normalized);
+
+    return normalized;
+
+}
+
+cv::Mat Simulator::processMeans(const string &means_file) const
+{
+    BlobProto proto;
+    ReadProtoFromBinaryFileOrDie(means_file, &proto);
+
+    Blob<DType> mean_blob;
+    mean_blob.FromProto(proto);
+
+    assert(mean_blob.channels() == num_channels);
+
+    vector<cv::Mat> channels;
+    float* data = mean_blob.mutable_cpu_data();
+    for (unsigned int i = 0; i < num_channels; ++i) {
+        channels.emplace_back(mean_blob.height(), mean_blob.width(), CV_32FC1, data);
+        data += mean_blob.height() * mean_blob.width();
+    }
+
+    cv::Mat mean;
+    cv::merge(channels, mean);
+
+    return cv::Mat(input_geometry, mean.type(), cv::mean(mean));
 }

src/Simulator.hpp

@@ -17,16 +17,18 @@ namespace fmri {
     public:
         typedef float DType;
 
-        Simulator(const string &model_file, const string &weights_file);
+        Simulator(const string &model_file, const string &weights_file, const string &means_file = "");
 
-        void simulate(const string &input_file);
+        vector<DType> simulate(const string &input_file);
 
     private:
         caffe::Net<DType> net;
         cv::Size input_geometry;
+        cv::Mat means;
         unsigned int num_channels;
 
         vector<cv::Mat> getWrappedInputLayer();
         cv::Mat preprocess(cv::Mat original) const;
+        cv::Mat processMeans(const string &means_file) const;
     };
 }

src/main.cpp

@@ -10,7 +10,7 @@ int main(int argc, char *const argv[]) {
 
     Options options = Options::parse(argc, argv);
 
-    Simulator simulator(options.model(), options.weights());
+    Simulator simulator(options.model(), options.weights(), options.means());
 
     for (const auto &image : options.inputs()) {
         simulator.simulate(image);