# HG changeset patch
# User tomwalters
# Date 1281612491 0
# Node ID 0db637cac96b6f5bededdb481a2404b90f9e4a79
# Parent  578ec2d32170a7353870922ce97de712f3f815c0
- Added as-yet-unfinished support for a proper configuraiton file format
- Added a couple of pythin scripts to generate HMM configuration files
- Variable name changes and other cosmetic things
- Added the option for the noise generation to do pink noise (untested)

diff -r 578ec2d32170 -r 0db637cac96b experiments/scripts/cnbh-syllables/feature_generation/nap_profile_features.aimcopycfg
--- a/experiments/scripts/cnbh-syllables/feature_generation/nap_profile_features.aimcopycfg	Thu Aug 12 09:15:49 2010 +0000
+++ b/experiments/scripts/cnbh-syllables/feature_generation/nap_profile_features.aimcopycfg	Thu Aug 12 11:28:11 2010 +0000
@@ -7,10 +7,11 @@
 
 module2.name = GammatoneFilterbank
 module2.id = gt
-module2.child1 = SmoothNAP
+module2.child1 = StandardNAP
+module2.child2 = SmoothNAP
 
 module3.name = SmoothNAP
-module3.id = hcl
+module3.id = nap
 module3.parameters = <<<ENDPARAMS
 nap.lowpass_cutoff = 100.0
 ENDPARAMS
@@ -27,5 +28,5 @@
 module5.id = gaussians
 module5.child1 = SmoothNAPOutput
 
-module6.name = SmoothNAPOutput
-module6.id = htk_out
+moudule6.name = SmoothNAPOutput
+module6.id = htk_out
\ No newline at end of file
diff -r 578ec2d32170 -r 0db637cac96b src/Modules/Features/ModuleGaussians.cc
--- a/src/Modules/Features/ModuleGaussians.cc	Thu Aug 12 09:15:49 2010 +0000
+++ b/src/Modules/Features/ModuleGaussians.cc	Thu Aug 12 11:28:11 2010 +0000
@@ -38,17 +38,17 @@
   module_type_ = "features";
   module_version_ = "$Id$";
 
-  m_iParamNComp = parameters_->DefaultInt("features.gaussians.ncomp", 4);
-  m_fParamVar = parameters_->DefaultFloat("features.gaussians.var", 115.0);
-  m_fParamPosteriorExp =
-    parameters_->DefaultFloat("features.gaussians.posterior_exp", 6.0);
-  m_iParamMaxIt = parameters_->DefaultInt("features.gaussians.maxit", 250);
+  m_iParamNComp = parameters_->DefaultInt("gaussians.ncomp", 4);
+  m_fParamVar = parameters_->DefaultFloat("gaussians.var", 115.0);
+  m_fParamPosteriorExp = parameters_->DefaultFloat("gaussians.posterior_exp",
+                                                   6.0);
+  m_iParamMaxIt = parameters_->DefaultInt("gaussians.maxit", 250);
 
   // The parameters system doesn't support tiny numbers well, to define this
   // variable as a string, then convert it to a float afterwards
-  parameters_->DefaultString("features.gaussians.priors_converged", "1e-7");
-  m_fParamPriorsConverged =
-    parameters_->GetFloat("features.gaussians.priors_converged");
+  parameters_->DefaultString("gaussians.priors_converged", "1e-7");
+  priors_converged_ = parameters_->GetFloat("gaussians.priors_converged");
+  output_positions_ = parameters_->DefaultBool("gaussians.positions", false);
 }
 
 ModuleGaussians::~ModuleGaussians() {
@@ -60,8 +60,9 @@
 
   // Assuming the number of channels is greater than twice the number of
   // Gaussian components, this is ok
+  output_component_count_ = 1; // Energy component
   if (input.channel_count() >= 2 * m_iParamNComp) {
-    output_.Initialize(m_iParamNComp, 1, input.sample_rate());
+    output_component_count_ += (m_iParamNComp - 1);
   } else {
     LOG_ERROR(_T("Too few channels in filterbank to produce sensible "
                  "Gaussian features. Either increase the number of filterbank"
@@ -69,6 +70,12 @@
     return false;
   }
 
+  if (output_positions_) {
+    output_component_count_ += m_iParamNComp;
+  }
+
+  output_.Initialize(output_component_count_, 1, input.sample_rate());
+
   m_iNumChannels = input.channel_count();
   m_pSpectralProfile.resize(m_iNumChannels, 0.0f);
 
@@ -90,16 +97,12 @@
     return;
   }
   // Calculate spectral profile
-  for (int iChannel = 0;
-       iChannel < input.channel_count();
-       ++iChannel) {
-    m_pSpectralProfile[iChannel] = 0.0f;
-    for (int iSample = 0;
-         iSample < input.buffer_length();
-         ++iSample) {
-      m_pSpectralProfile[iChannel] += input[iChannel][iSample];
+  for (int ch = 0; ch < input.channel_count(); ++ch) {
+    m_pSpectralProfile[ch] = 0.0f;
+    for (int i = 0; i < input.buffer_length(); ++i) {
+      m_pSpectralProfile[ch] += input[ch][i];
     }
-    m_pSpectralProfile[iChannel] /= static_cast<float>(input.buffer_length());
+    m_pSpectralProfile[ch] /= static_cast<float>(input.buffer_length());
   }
 
   float spectral_profile_sum = 0.0f;
@@ -107,36 +110,35 @@
     spectral_profile_sum += m_pSpectralProfile[i];
   }
 
+  // Set the last component of the feature vector to be the log energy
   float logsum = log(spectral_profile_sum);
   if (!isinf(logsum)) {
-    output_.set_sample(m_iParamNComp - 1, 0, logsum);
+    output_.set_sample(output_component_count_ - 1, 0, logsum);
   } else {
-    output_.set_sample(m_iParamNComp - 1, 0, -1000.0);
+    output_.set_sample(output_component_count_ - 1, 0, -1000.0);
   }
 
-  for (int iChannel = 0;
-       iChannel < input.channel_count();
-       ++iChannel) {
-    m_pSpectralProfile[iChannel] = pow(m_pSpectralProfile[iChannel], 0.8f);
+  for (int ch = 0; ch < input.channel_count(); ++ch) {
+    m_pSpectralProfile[ch] = pow(m_pSpectralProfile[ch], 0.8);
   }
 
   RubberGMMCore(2, true);
 
-  float fMean1 = m_pMu[0];
-  float fMean2 = m_pMu[1];
+  float mean1 = m_pMu[0];
+  float mean2 = m_pMu[1];
   // LOG_INFO(_T("Orig. mean 0 = %f"), m_pMu[0]);
   // LOG_INFO(_T("Orig. mean 1 = %f"), m_pMu[1]);
   // LOG_INFO(_T("Orig. prob 0 = %f"), m_pA[0]);
   // LOG_INFO(_T("Orig. prob 1 = %f"), m_pA[1]);
 
-  float fA1 = 0.05 * m_pA[0];
-  float fA2 = 1.0 - 0.25 * m_pA[1];
+  float a1 = 0.05 * m_pA[0];
+  float a2 = 1.0 - 0.25 * m_pA[1];
 
   // LOG_INFO(_T("fA1 = %f"), fA1);
   // LOG_INFO(_T("fA2 = %f"), fA2);
 
-  float fGradient = (fMean2 - fMean1) / (fA2 - fA1);
-  float fIntercept = fMean2 - fGradient * fA2;
+  float gradient = (mean2 - mean1) / (a2 - a1);
+  float intercept = mean2 - gradient * a2;
 
   // LOG_INFO(_T("fGradient = %f"), fGradient);
   // LOG_INFO(_T("fIntercept = %f"), fIntercept);
@@ -144,7 +146,7 @@
   for (int i = 0; i < m_iParamNComp; ++i) {
     m_pMu[i] = (static_cast<float>(i)
                 / (static_cast<float>(m_iParamNComp) - 1.0f))
-                * fGradient + fIntercept;
+                * gradient + intercept;
                 // LOG_INFO(_T("mean %d = %f"), i, m_pMu[i]);
   }
 
@@ -154,6 +156,7 @@
 
   RubberGMMCore(m_iParamNComp, false);
 
+  // Amplitudes first
   for (int i = 0; i < m_iParamNComp - 1; ++i) {
     if (!isnan(m_pA[i])) {
       output_.set_sample(i, 0, m_pA[i]);
@@ -162,6 +165,19 @@
     }
   }
 
+  // Then means if required
+  if (output_positions_) {
+    int idx = 0;
+    for (int i = m_iParamNComp - 1; i < 2 * m_iParamNComp - 1; ++i) {
+      if (!isnan(m_pMu[i])) {
+        output_.set_sample(i, 0, m_pMu[idx]);
+      } else {
+        output_.set_sample(i, 0, 0.0f);
+      }
+      ++idx;
+    }
+  }
+
   PushOutput();
 }
 
@@ -169,12 +185,12 @@
   int iSizeX = m_iNumChannels;
 
   // Normalise the spectral profile
-  float fSpectralProfileTotal = 0.0f;
+  float SpectralProfileTotal = 0.0f;
   for (int iCount = 0; iCount < iSizeX; iCount++) {
-    fSpectralProfileTotal += m_pSpectralProfile[iCount];
+    SpectralProfileTotal += m_pSpectralProfile[iCount];
   }
   for (int iCount = 0; iCount < iSizeX; iCount++) {
-    m_pSpectralProfile[iCount] /= fSpectralProfileTotal;
+    m_pSpectralProfile[iCount] /= SpectralProfileTotal;
   }
 
   if (bDoInit) {
@@ -200,12 +216,12 @@
       pP_mod_X[i] = 0.0f;
     }
 
-    for (int i = 0; i < iNComponents; i++) {
+    for (int c = 0; c < iNComponents; c++) {
       for (int iCount = 0; iCount < iSizeX; iCount++) {
         pP_mod_X[iCount] += 1.0f / sqrt(2.0f * M_PI * m_fParamVar)
                             * exp((-0.5f)
-                            * pow(static_cast<float>(iCount+1) - m_pMu[i], 2)
-                            / m_fParamVar) * m_pA[i];
+                            * pow(static_cast<float>(iCount+1) - m_pMu[c], 2)
+                            / m_fParamVar) * m_pA[c];
       }
     }
 
@@ -251,7 +267,7 @@
     }
     fPrdist /= iNComponents;
 
-    if (fPrdist < m_fParamPriorsConverged) {
+    if (fPrdist < priors_converged_) {
       // LOG_INFO("Converged!");
       break;
     }
diff -r 578ec2d32170 -r 0db637cac96b src/Support/ModuleTree.cc
--- a/src/Support/ModuleTree.cc	Thu Aug 12 09:15:49 2010 +0000
+++ b/src/Support/ModuleTree.cc	Thu Aug 12 11:28:11 2010 +0000
@@ -24,152 +24,7 @@
  *  \version \$Id: $
  */
 
-#include "Support/ModuleFactory.h"
-#include "Support/Module.h"
-#include "Support/ModuleTree.h"
-
 namespace aimc {
-using std::endl;
-ModuleTree::ModuleTree() : root_module_(NULL),
-                           initialized_(false) {
+  ParseConfigFile(string )
   
-}
-  
-bool ModuleTree::LoadConfigFile(const string &filename) {
-  config_.Load(filename.c_str());
-  return ConstructTree();
-}
-
-bool ModuleTree::LoadConfigText(const string &config) {
-  config_.Parse(config.c_str());
-  return ConstructTree();
-}
-
-bool ModuleTree::ConstructTree() {
-  // Make two passes over the configuration file.
-  // The first pass creates all the named modules with their parameters.
-  bool done = false;
-  bool error = false;
-  int module_number = 1;
-  LOG_INFO("Parsing tree...");
-  while (!done) {  
-    char module_name_var[Parameters::MaxParamNameLength];
-    char module_id_var[Parameters::MaxParamNameLength];
-    char module_parameters_var[Parameters::MaxParamNameLength];
-    sprintf(module_name_var, "module%d.name", module_number);
-    sprintf(module_id_var, "module%d.id", module_number);
-    sprintf(module_parameters_var, "module%d.parameters", module_number);
-    if (config_.IsSet(module_name_var)) {
-      string module_name(config_.GetString(module_name_var));
-      LOG_INFO("Module number %d, name %s", module_number, module_name.c_str());
-      if (config_.IsSet(module_id_var)) {
-        const char* id = config_.GetString(module_id_var);
-        const char* parameters = config_.DefaultString(module_parameters_var, "");
-        linked_ptr<Parameters> params(new Parameters);
-        parameters_[module_name] = params;
-        parameters_[module_name]->Parse(parameters);
-        linked_ptr<Module> module(ModuleFactory::Create(id, parameters_[module_name].get()));
-        if (module.get() != NULL) {
-          module->set_instance_name(module_name);
-          modules_[module_name] = module;
-        } else {
-          LOG_ERROR("Module name: %s of type %s not created", module_name.c_str(), id);
-          done = true;
-          error = true;
-        }
-        if (module_number == 1) {
-          root_module_ = module.get();
-        }
-      } else {
-        LOG_ERROR("id field missing for module named %s", module_name.c_str());
-        error = true;
-        done = true;
-      }
-    } else {
-      done = true;
-    }
-    ++module_number;
-  }
-  // The second pass connects up all the modules into a tree.
-  char module_child_var[Parameters::MaxParamNameLength];
-  char module_name_var[Parameters::MaxParamNameLength];
-  LOG_INFO("A total of %d modules", modules_.size());
-  for (unsigned int i = 1; i < modules_.size() + 1; ++i) {
-    int child_number = 1;
-    done = false;
-    sprintf(module_name_var, "module%d.name", i);
-    if (config_.IsSet(module_name_var)) {
-      string module_name(config_.GetString(module_name_var));
-      while (!done) {
-        sprintf(module_child_var, "module%d.child%d", i, child_number);
-        LOG_INFO("Trying %s", module_child_var);
-        if (config_.IsSet(module_child_var)) {
-          string child(config_.GetString(module_child_var));
-          if ((modules_.find(module_name) != modules_.end())
-              && (modules_.find(child) != modules_.end())) {
-            modules_[module_name]->AddTarget(modules_[child].get());
-          } else {
-            LOG_ERROR("Module name not found");
-          }
-        } else {
-          done = true;
-        }
-        ++child_number;
-      }
-    } else {
-      LOG_ERROR("field missing for entry %s", module_name_var);
-      error = true;
-      break;
-    }
-  }
-  return !error;
-}
-
-bool ModuleTree::Initialize(Parameters *global_parameters) {
-  if (root_module_ == NULL) {
-    return false;
-  }
-  // Dummy signal bank for the root module.
-  s_.Initialize(1, 1, 1);
-  initialized_ = root_module_->Initialize(s_, global_parameters);
-  return initialized_;
-}
-
-void ModuleTree::Reset() {
-  if (root_module_ == NULL) {
-    return;
-  }
-  root_module_->Reset();
-}
-
-void ModuleTree::PrintConfiguration(ostream &out) {
-  if (root_module_ == NULL) {
-    return;
-  }
-  root_module_->PrintTargets(out);
-  root_module_->PrintConfiguration(out);
-}
-
-void ModuleTree::Process() {
-  if (root_module_ == NULL) {
-    return;
-  }
-  if (!initialized_) {
-    LOG_ERROR(_T("Module tree not initialized."));
-    return;
-  }
-  while (!root_module_->done()) {
-    root_module_->Process(s_);
-  }
-}
-
-void ModuleTree::MakeDotGraph(ostream &out) {
-  if (root_module_ == NULL) {
-    return;
-  }
-  out << "digraph G {" << endl;
-  root_module_->PrintTargetsForDot(out);
-  out << "}" << endl;
-}
-
-}  // namespace aimc
+}  // namespace aimc
\ No newline at end of file
diff -r 578ec2d32170 -r 0db637cac96b src/Support/ModuleTree.h
--- a/src/Support/ModuleTree.h	Thu Aug 12 09:15:49 2010 +0000
+++ b/src/Support/ModuleTree.h	Thu Aug 12 11:28:11 2010 +0000
@@ -24,47 +24,20 @@
  *  \version \$Id: $
  */
 
-#include <iostream>
-#include <map>
 #include <string>
 
-#include "Support/Common.h"
-#include "Support/Module.h"
-#include "Support/Parameters.h"
-#include "Support/SignalBank.h"
-#include "Support/linked_ptr.h"
-
 namespace aimc {
 using std::string;
-using std::map;
-using std::ostream;
-
 class ModuleTree {
  public:
-  ModuleTree();
-  bool LoadConfigFile(const string &filename);
-  bool LoadConfigText(const string &config_text);
-  string GetFullConfig();
-  bool Initialize(Parameters *global_parameters);
-  void Reset();
-  void PrintConfiguration(ostream &out);
-  void Process();
-  void MakeDotGraph(ostream &out);
-  void set_output_filename_prefix(const string &prefix) {
-    output_filename_prefix_ = prefix;
-  };
+  bool ParseConfigFile(const string &filename);
+  bool ParseConfigText(const string &config_text);
+  void set_output_filename_prefix(const string &prefix);
   string output_filename_prefix() {
     return output_filename_prefix_;
-  };
+  }
  private:
-  bool ConstructTree();
-  Parameters config_;
-  SignalBank s_;
   string output_filename_prefix_;
-  map<string, linked_ptr<Module> > modules_;
-  Module *root_module_;
-  map<string, linked_ptr<Parameters> > parameters_;
-  bool initialized_;
   DISALLOW_COPY_AND_ASSIGN(ModuleTree);
 };
 }  // namespace aimc
\ No newline at end of file