Mercurial > hg > calciumsiganalyser

changeset 2:e26a8489c148

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Release 2: the duration of the median filtering window has been added to the plugin setting parameters.
author mathieub <mathieu.barthet@eecs.qmul.ac.uk>
date Wed, 22 Jun 2011 14:34:06 +0100
parents 26c75dbfe61c
children 57cb253812c7
files CHANGELOG CalciumSignalAnalyser.cpp CalciumSignalAnalyser.h CalciumSignalAnalyser.o CalciumSignalAnalyser_plugins.cpp CalciumSignalAnalyser_plugins.o INSTALL.txt README.txt doc/CalciumSignalAnalyserVampPlugin-doc.pdf vamp-calcium-signal-analyser.dylib
diffstat 10 files changed, 128 insertions(+), 69 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CHANGELOG	Wed Jun 22 14:34:06 2011 +0100
@@ -0,0 +1,4 @@
+
+Changes in the Calcium Signal Analyser Vamp plugin 2 since the previous release 1:
+
+- The duration of the median filtering window has been added to the plugin setting parameters.
--- a/CalciumSignalAnalyser.cpp	Mon Jun 20 22:10:14 2011 +0100
+++ b/CalciumSignalAnalyser.cpp	Wed Jun 22 14:34:06 2011 +0100
@@ -3,17 +3,22 @@
 /*
  Calcium Signal Analyser Vamp Plugin
  
- Description: Detects and characterises the transients in noisy signals.
+ Transient detection and characterisation for calcium signals.
  
- Authors: Mathieu Barthet.
- Based on the QM Vamp note onset detector plugin by Christian Landone, 
- Chris Duxbury, and Juan Pablo Bello.
+ Centre for Digital Music, Queen Mary University of London.
+ This file copyright 2010-2011 Mathieu Barthet and QMUL.
  
- Version: 1
+ Based on the QM Vamp note onset detector plugin by Christian 
+ Landone, Chris Duxbury, and Juan Pablo Bello.
  
- Centre for Digital Music, Queen Mary, University of London.
- All rights reserved.
- */
+ This program is free software; you can redistribute it and/or
+ modify it under the terms of the GNU General Public License as
+ published by the Free Software Foundation; either version 2 of the
+ License, or (at your option) any later version.  See the file
+ COPYING included with this distribution for more information.
+  
+ Version: 2
+*/
 
 #include "CalciumSignalAnalyser.h"
 
@@ -38,6 +43,7 @@
 time(0),
 m_sensitivity(50),
 m_delta(0.2),
+m_mfwindur(10),
 processcounter(0)
 {
 #ifdef VERBOSE
@@ -93,7 +99,7 @@
 int
 CalciumSignalAnalyser::getPluginVersion() const
 {
-    return 1;
+    return 2;
 }
 
 string
@@ -130,6 +136,17 @@
     desc.unit = "";
     list.push_back(desc);
 	
+	desc.identifier = "mfwindowduration";
+    desc.name = "Duration of the median filtering window";
+    desc.description = "Sets the duration of the median filtering window";
+    desc.minValue = 2;
+    desc.maxValue = 100;
+    desc.defaultValue = 10;
+    desc.isQuantized = true;
+    desc.quantizeStep = 0.1;
+    desc.unit = "s";
+    list.push_back(desc);
+
     return list;
 }
 
@@ -141,6 +158,9 @@
 	}
 	else if (name == "deltathreshold") {
 		return m_delta;	
+	}
+	else if (name == "mfwindowduration") {
+		return m_mfwindur;	
 	}	
 	
     return 0.0;
@@ -158,6 +178,10 @@
 		if (m_delta == value) return;
         m_delta = value;
 	}
+	else if (name == "mfwindowduration") {
+		if (m_mfwindur == value) return;
+        m_mfwindur = value;
+	}
 }
 
 
@@ -411,13 +435,24 @@
     ppParams.LPACoeffs = aCoeffs;
     ppParams.LPBCoeffs = bCoeffs;
     
-	//TO-DO: the duration of the median filtering window could be another adjustable parameter 
-	//of the plugin since the optimal duration may vary according to signals. It should not be 
-	//set up in samples but in seconds instead to maintain the same behavior for different signal 
-	//sample frequencies.
-	
-	ppParams.WinT.post = 8; //works well with calcium data (15 samples at 3 Hz --> W = 5 s --> M = 2.5 s)
-    ppParams.WinT.pre = 7;
+	int NWin;
+	float samples = m_inputSampleRate*m_mfwindur;
+	if (samples < 4){
+		NWin = 4; //minimal possible length of the window in samples
+#ifdef VERBOSE
+		cout << "WARNING: CalciumSignalAnalyser::getRemainingFeatures:"
+		<< "The duration of the median filtering window is too small considering the"
+		<< "sample frequency of the signal. Duration of "<< NWin/m_inputSampleRate
+		<< " s used instead."
+		<< endl;
+#endif
+	}else{
+		NWin = floor(m_inputSampleRate*m_mfwindur);
+		if (NWin%2 != 0) NWin--;
+	}	
+		
+	ppParams.WinT.post = NWin/2;
+    ppParams.WinT.pre = NWin/2 - 1;
     		
 	ppParams.QuadThresh.a = (100 - m_sensitivity) / 1000.0;
     ppParams.QuadThresh.b = 0;
--- a/CalciumSignalAnalyser.h	Mon Jun 20 22:10:14 2011 +0100
+++ b/CalciumSignalAnalyser.h	Wed Jun 22 14:34:06 2011 +0100
@@ -1,20 +1,24 @@
 /* -*- c-basic-offset: 4 indent-tabs-mode: nil -*-  vi:set ts=8 sts=4 sw=4: */
 
 /*
- Header file for the Calcium Signal Analyser Vamp Plugin
+ Calcium Signal Analyser Vamp Plugin
  
- Description: Detects and characterises the transients in noisy signals.
+ Transient detection and characterisation for calcium signals.
  
- Authors: Mathieu Barthet.
- Based on the QM Vamp note onset detector plugin by Christian Landone, 
- Chris Duxbury, and Juan Pablo Bello.
+ Centre for Digital Music, Queen Mary University of London.
+ This file copyright 2010-2011 Mathieu Barthet and QMUL.
  
- Version: 1
+ Based on the QM Vamp note onset detector plugin by Christian 
+ Landone, Chris Duxbury, and Juan Pablo Bello.
  
- Centre for Digital Music, Queen Mary, University of London.
- All rights reserved.
+ This program is free software; you can redistribute it and/or
+ modify it under the terms of the GNU General Public License as
+ published by the Free Software Foundation; either version 2 of the
+ License, or (at your option) any later version.  See the file
+ COPYING included with this distribution for more information.
  
-*/
+ Version: 2
+ */
 
 #ifndef _CALCIUM_SIGNAL_ANALSYER_PLUGIN_H_
 #define _CALCIUM_SIGNAL_ANALSYER_PLUGIN_H_
@@ -72,6 +76,7 @@
 	
     float m_sensitivity;
 	float m_delta;
+	float m_mfwindur;
 	
 	int processcounter;
 };
Binary file CalciumSignalAnalyser.o has changed
--- a/CalciumSignalAnalyser_plugins.cpp	Mon Jun 20 22:10:14 2011 +0100
+++ b/CalciumSignalAnalyser_plugins.cpp	Wed Jun 22 14:34:06 2011 +0100
@@ -1,17 +1,22 @@
 /*
-Calcium Signal Analyser Vamp Plugin
-
-Description: Detects and characterises the transients in noisy signals.
+ Calcium Signal Analyser Vamp Plugin
  
-Authors: Mathieu Barthet.
-Based on the QM Vamp note onset detector plugin by Christian Landone, 
-Chris Duxbury, and Juan Pablo Bello.
-
-Version: 1
-
-Centre for Digital Music, Queen Mary University of London.
-All rights reserved.
-*/
+ Transient detection and characterisation for calcium signals.
+ 
+ Centre for Digital Music, Queen Mary University of London.
+ This file copyright 2010-2011 Mathieu Barthet and QMUL.
+ 
+ Based on the QM Vamp note onset detector plugin by Christian 
+ Landone, Chris Duxbury, and Juan Pablo Bello.
+ 
+ This program is free software; you can redistribute it and/or
+ modify it under the terms of the GNU General Public License as
+ published by the Free Software Foundation; either version 2 of the
+ License, or (at your option) any later version.  See the file
+ COPYING included with this distribution for more information.
+ 
+ Version: 2
+ */
 
 #include <vamp/vamp.h>
 #include <vamp-sdk/PluginAdapter.h>
Binary file CalciumSignalAnalyser_plugins.o has changed
--- a/INSTALL.txt	Mon Jun 20 22:10:14 2011 +0100
+++ b/INSTALL.txt	Wed Jun 22 14:34:06 2011 +0100
@@ -9,35 +9,39 @@
 REQUIRED	QM DSP Library		https://code.soundsoftware.ac.uk/projects/qm-dsp
 
 
-To install (by compiling from source)
-=====================================
+To install by compiling from source
+===================================
 
-First download and install the required libraries following the associated instructions 
-(they may require to install other dependencies).
+First download and install the required libraries following their installation 
+instructions (they may require other dependencies). When compiling the plugin, the 
+default location of the required libraries should be:
 
-You can edit the Makefile of the Calcium Signal Analyser Vamp plugin depending your 
-operating system and various options. The directories of the required libraries can be 
-specified. By default, the required libraries are assumed to be installed at the same 
-directory tree level as the plugin.
+../vamp-plugin-sdk, and
+../qm-dsp
 
-To build on a Unix-like system, run
+If you want to install the libraries elsewhere, you can edit the Makefile and specify 
+their location by setting the variables VAMP_SDK_DIR and QM_DSP_DIR.
+
+Edit the Makefile to select the appropriate options for your operating system.
+
+Then to build on a Unix-like system, run:
 
 $ make
 
 Then install the plugin as follows depending on your operating system:
 
-    Win 32  -> Copy vamp-calciumsignalanalyser.dll, vamp-calciumsignalanalyser.cat and
-               vamp-calciumsignalanalyser.n3 to C:\Program Files\Vamp Plugins\
+    Win 32  -> Copy vamp-calciumsignalanalyser.dll, vamp-calciumsignalanalyser.cat (optional) and
+               vamp-calciumsignalanalyser.n3 (optional) to C:\Program Files\Vamp Plugins\
 
-    Win 64  -> Copy vamp-calciumsignalanalyser.dll, vamp-calciumsignalanalyser.cat and
-               vamp-calciumsignalanalyser.n3 to C:\Program Files\Vamp Plugins (x86)\
+    Win 64  -> Copy vamp-calciumsignalanalyser.dll, vamp-calciumsignalanalyser.cat (optional) and
+               vamp-calciumsignalanalyser.n3 (optional) to C:\Program Files\Vamp Plugins (x86)\
 
-    OS/X    -> Copy vamp-calciumsignalanalyser.dylib, vamp-calciumsignalanalyser.cat and
-               vamp-calciumsignalanalyser.n3 to $HOME/Library/Audio/Plug-Ins/Vamp/
+    OS/X    -> Copy vamp-calciumsignalanalyser.dylib, vamp-calciumsignalanalyser.cat (optional) and
+               vamp-calciumsignalanalyser.n3 (optional) to $HOME/Library/Audio/Plug-Ins/Vamp/
                or /Library/Audio/Plug-Ins/Vamp/
 
-    Linux   -> Copy vamp-calciumsignalanalyser.so, vamp-calciumsignalanalyser.cat and
-               vamp-calciumsignalanalyser.n3 to $HOME/vamp/ or /usr/local/lib/vamp/
+    Linux   -> Copy vamp-calciumsignalanalyser.so, vamp-calciumsignalanalyser.cat (optional) and
+               vamp-calciumsignalanalyser.n3 (optional) to $HOME/vamp/ or /usr/local/lib/vamp/
                or /usr/lib/vamp/
 
 
--- a/README.txt	Mon Jun 20 22:10:14 2011 +0100
+++ b/README.txt	Wed Jun 22 14:34:06 2011 +0100
@@ -6,19 +6,26 @@
 characterization of transients in noisy signals. It is adapted for
 the analysis of calcium signals measured using confocal microscopy.
 
+Copyright
+=========
+
+This code is Copyright (c) 2010-2011 Mathieu Barthet, Queen Mary 
+University of London.
+
+The plugin is based on the QM Vamp note onset detector developed 
+by Christian Landone, Chris Duxbury, and Juan Pablo Bello.
+
 The Vamp architecture is a feature extraction system developed at 
 Queen Mary University of London (see more information at: 
 http://www.vamp-plugins.org/).
 
-This code is Copyright (c) 2010-2011 Mathieu Barthet, Queen Mary 
-University of London. The plugin is based on the QM Vamp note onset 
-detector developed by Christian Landone, Chris Duxbury, and Juan 
-Pablo Bello.
-
 About This Release
 ==================
 
-This is release 1.
+This is release 2.
+
+Changes between releases are reported in the CHANGELOG file provided
+with the distribution.
 
 License
 =======
@@ -40,18 +47,18 @@
 
 Installation depends on your operating system.
 
-    Win 32  -> Copy vamp-calciumsignalanalyser.dll, vamp-calciumsignalanalyser.cat and
-               vamp-calciumsignalanalyser.n3 to C:\Program Files\Vamp Plugins\
+    Win 32  -> Copy vamp-calciumsignalanalyser.dll, vamp-calciumsignalanalyser.cat (optional) and
+               vamp-calciumsignalanalyser.n3 (optional) to C:\Program Files\Vamp Plugins\
 
-    Win 64  -> Copy vamp-calciumsignalanalyser.dll, vamp-calciumsignalanalyser.cat and
-               vamp-calciumsignalanalyser.n3 to C:\Program Files\Vamp Plugins (x86)\
+    Win 64  -> Copy vamp-calciumsignalanalyser.dll, vamp-calciumsignalanalyser.cat (optional) and
+               vamp-calciumsignalanalyser.n3 (optional) to C:\Program Files\Vamp Plugins (x86)\
 
-    OS/X    -> Copy vamp-calciumsignalanalyser.dylib, vamp-calciumsignalanalyser.cat and
-               vamp-calciumsignalanalyser.n3 to $HOME/Library/Audio/Plug-Ins/Vamp/
+    OS/X    -> Copy vamp-calciumsignalanalyser.dylib, vamp-calciumsignalanalyser.cat (optional) and
+               vamp-calciumsignalanalyser.n3 (optional) to $HOME/Library/Audio/Plug-Ins/Vamp/
                or /Library/Audio/Plug-Ins/Vamp/
 
-    Linux   -> Copy vamp-calciumsignalanalyser.so, vamp-calciumsignalanalyser.cat and
-               vamp-calciumsignalanalyser.n3 to $HOME/vamp/ or /usr/local/lib/vamp/
+    Linux   -> Copy vamp-calciumsignalanalyser.so, vamp-calciumsignalanalyser.cat (optional) and
+               vamp-calciumsignalanalyser.n3 (optional) to $HOME/vamp/ or /usr/local/lib/vamp/
                or /usr/lib/vamp/
 
 Documentation
@@ -60,7 +67,6 @@
 Additional information on the plugin are given in the plugin documentation 
 which can be found in the /doc directory of this distribution.
 
-
 Credits and references
 ======================
 
Binary file doc/CalciumSignalAnalyserVampPlugin-doc.pdf has changed
Binary file vamp-calcium-signal-analyser.dylib has changed