retina
Class OIDTimecourseAnalyzer

java.lang.Object
  |
  +--retina.OIDAnalyzer
        |
        +--retina.OIDTimecourseAnalyzer
All Implemented Interfaces:
OIDBaseAnalyzer
Direct Known Subclasses:
OIDTimecourseStimulatedAnalyzer

public class OIDTimecourseAnalyzer
extends OIDAnalyzer

Optical Imaging of the Retina timecourse analyzer for all frames (not only stimulus frames). Divides stimulated area reflectance by non-stimulated area reflectance framewise. Does not work if whole retina stimulated. Analyze a series of OID frames a and show timecourse of stimulated area reflectance relative to non stimulated area for all unique conditions/frames. Copyright (c) 1999-2004, Michael Abramoff. All rights reserved.


Field Summary
protected static java.util.Vector bag
           
protected static java.util.Vector bagAlignment
           
protected  boolean doPP
           
 
Fields inherited from class retina.OIDAnalyzer
functionName, scriptProcessor
 
Constructor Summary
OIDTimecourseAnalyzer()
           
OIDTimecourseAnalyzer(ScriptProcessor scriptProcessor)
           
 
Method Summary
 void analyze(float[][] a, float[][] regestimates, int frameWidth, java.lang.String directory, java.lang.String name)
          Analyze a series of OID frames a.
 void exit(int total, int frameWidth, int frameHeight, java.lang.String directory, java.lang.String name)
          Hook for exit.
 void init(ScriptProcessor scriptProcessor)
           
 boolean prefersRegistration()
           
protected  void process(float[][][] r, float[][][][] regs, java.lang.String name, java.lang.String maskname, java.lang.String[] condNames)
          process r results.
protected  void processAverageResults(float[][] regEstimates, java.lang.String name, int length, int uniqueconds, float[][] sem, float[][] timecourse, float[][] masks, int useMask)
           
protected  void processPDSresults(double[][] pds, double[][] freqs, java.lang.String name)
          Process an array of PDS results and its frequencies.
protected  void windowProcess(float[][][] r, float[][][][] regs, int start, java.lang.String name, java.lang.String maskname, java.lang.String[] condNames)
          Process the r and regs as Zimmerman windowed results, i.e.
 
Methods inherited from class retina.OIDAnalyzer
main, printInfo, printUsage, saveAnalysis, toString
 
Methods inherited from class java.lang.Object
, clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

bag

protected static java.util.Vector bag

bagAlignment

protected static java.util.Vector bagAlignment

doPP

protected boolean doPP
Constructor Detail

OIDTimecourseAnalyzer

public OIDTimecourseAnalyzer()

OIDTimecourseAnalyzer

public OIDTimecourseAnalyzer(ScriptProcessor scriptProcessor)
Method Detail

prefersRegistration

public boolean prefersRegistration()
Overrides:
prefersRegistration in class OIDAnalyzer

init

public void init(ScriptProcessor scriptProcessor)
Overrides:
init in class OIDAnalyzer

analyze

public void analyze(float[][] a,
                    float[][] regestimates,
                    int frameWidth,
                    java.lang.String directory,
                    java.lang.String name)
Description copied from class: OIDAnalyzer
Analyze a series of OID frames a. Default first frame analysis.
Overrides:
analyze in class OIDAnalyzer
Parameters:
a - a float[][] with the reflectance frames.
regEstimates - the estimates of alignment for each frame with a[0].
frameWidth - the width in pixels of the frames in a
directory - the name of the directory where the result should go.
name - the name(s) of the file(s) on which a is based

processPDSresults

protected void processPDSresults(double[][] pds,
                                 double[][] freqs,
                                 java.lang.String name)
Process an array of PDS results and its frequencies.

process

protected void process(float[][][] r,
                       float[][][][] regs,
                       java.lang.String name,
                       java.lang.String maskname,
                       java.lang.String[] condNames)
process r results.

windowProcess

protected void windowProcess(float[][][] r,
                             float[][][][] regs,
                             int start,
                             java.lang.String name,
                             java.lang.String maskname,
                             java.lang.String[] condNames)
Process the r and regs as Zimmerman windowed results, i.e. window a: -3, -2, -1 window b: 0, 1, 2 window c: 3, 4, 5 window d: 6, 7, 8 relative to stimulus onset.
Parameters:
r - a float[condition][frame][cycle] array with the r's for each frame.
regs - a float[][][][] with registration parameters for each frame.
start - the index of the frame when the stimulus is first on.

processAverageResults

protected void processAverageResults(float[][] regEstimates,
                                     java.lang.String name,
                                     int length,
                                     int uniqueconds,
                                     float[][] sem,
                                     float[][] timecourse,
                                     float[][] masks,
                                     int useMask)

exit

public void exit(int total,
                 int frameWidth,
                 int frameHeight,
                 java.lang.String directory,
                 java.lang.String name)
Hook for exit. Called at the end of all file processing (after last call to analyze).
Overrides:
exit in class OIDAnalyzer