FeatureViewerController.h

//
//  FeatureViewerController.h
//
//  Created by Grogee on 9/25/10.
//  Copyright 2010 __MyCompanyName__. All rights reserved.
//

#import <Cocoa/Cocoa.h>
#import <Accelerate/Accelerate.h>
#import <AGL/agl.h>

#import "FeatureView.h"
#import "WaveformsView.h"
#import "Cluster.h"
#import "readFeature.h"
#import "nptLoadingEngine.h"
#import "OpenPanelDelegate.h"
#import "utils.h"
#import "ProgressPanel.h"
#import "HistogramView.h"
#import "fileReaders.h"
#import "computeFeatures.h"
#import "RasterView.h"
#import "StimInfo.h"
#import "fileWriters.h"

@interface FeatureViewerController : NSController {
    
    NSMutableArray *Clusters;
    NSMutableArray *ClusterOptions;
    //menu object for performing cluster options
    NSMenu *clusterOptionsMenu;
    Cluster *activeCluster,*selectedCluster;
    NSArray *clusterModel;
    NSPredicate *isValidCluster, *filterClustersPredicate;
	NSIndexSet *selectedClusters;
    NSMutableArray *clustersSortDescriptors;
    NSSortDescriptor *clustersSortDescriptor;
    NSData *vertex_data;
    NSData *timestamps;
	NSMutableArray *featureNames;
	uint8_t *channelValidity;
    header params;
    BOOL dataloaded,autoLoadWaveforms, shouldShowRaster, shouldShowWaveforms;
	NSInteger nchannels,nvalidChannels;
    //name of current cluster set
    NSString *currentBaseName;
    NSString *waveformsFile;
    NSOperationQueue *queue;
    NSTimer *archiveTimer, *cycleTimer;
	NSNumber *featureCycleInterval;
	NSString *selectedWaveform;
	NSAttributedString *releaseNotes;
    StimInfo *stimInfo;
    
    NSMenu *waveformsMenu;
    
    IBOutlet FeatureView *fw;
    IBOutlet WaveformsView *wfv;
    IBOutlet NSComboBox *dim1;
    IBOutlet NSComboBox *dim2;
    IBOutlet NSComboBox *dim3;
    IBOutlet NSButton *allActive;
    IBOutlet NSPanel *filterClustersPanel;
    IBOutlet NSPopUpButton *selectClusterOption;  
    IBOutlet ProgressPanel *progressPanel;
    IBOutlet HistogramView *histView;
	IBOutlet RasterView *rasterView;
	IBOutlet NSPanel *inputPanel;
	IBOutlet NSPanel *cyclePanel;
	IBOutlet NSArrayController *clusterController;
	IBOutlet NSPredicateEditor *filterPredicates;
    IBOutlet NSMenu *clusterMenu;
    IBOutlet NSPanel *clusterNotesPanel;
    
    
    
}
-(void)insertObject:(Cluster *)p inClustersAtIndex:(NSUInteger)index;
-(void)removeObjectFromClustersAtIndex:(NSUInteger)index;
-(void)removeAllObjectsFromClusters;
-(void)setClusters:(NSMutableArray *)a;
-(NSArray*)Clusters;


-(void)setClusterOptions:(NSMutableArray *)a;
-(NSArray*)ClusterOptions;
-(void)insertObject:(NSString *)p inClusterOptionsAtIndex:(NSUInteger)index;
-(void)removeObjectFromClusterOptionsAtIndex:(NSUInteger)index;
-(id)objectInClustersAtIndex: (NSUInteger)index;

-(void)addClusterOption:(NSString*)option;

-(void)ClusterStateChanged:(NSNotification*)notification;
-(void)mergeCluster: (Cluster *)cluster1 withCluster: (Cluster*)cluster2;
-(void)deleteCluster: (Cluster *)cluster;
-(void)loadWaveforms: (Cluster*)cluster;
-(void)readClusterModel:(NSString*)path;
-(void)performComputation:(NSString*)operationTitle usingSelector:(SEL)operationSelector;
-(void)archiveClusters;
-(void) openFeatureFile:(NSString*)path;
-(void) openWaveformsFile: (NSString*)path;
-(void) openClusterFile:(NSString *)path;
-(void) setAvailableFeatures:(NSArray*)channels;
-(void) receiveNotification:(NSNotification*)notification;
//This might go away
-(void) computeFeature:(NSData*)waveforms withNumberOfSpikes: (NSUInteger)nwaves andChannels:(NSUInteger)channels andTimepoints:(NSUInteger)timepoints;
-(void)addPointsToCluster:(Cluster*)cluster;
//
-(void)loadStimInfo;
- (IBAction) loadFeatureFile: (id)sender;
- (IBAction) loadClusterIds: (id)sender;

//- (IBAction) loadWaveforms: (id)sender;
- (IBAction) changeDim1: (id)sender;
- (IBAction) changeDim2: (id)sender;
- (IBAction) changeDim3: (id)sender;
- (IBAction) changeAllClusters: (id)sender;
- (IBAction) performClusterOption: (id)sender;
- (IBAction) saveClusters:(id)sender;
-(IBAction)saveTemplates:(id)sender;
- (IBAction) cycleDims: (id)sender;
- (IBAction) clusterThumbClicked: (id)sender;
//- (IBAction) chooseWaveforms: (id)sender;
- (IBAction) changeCycleInterval: (id)sender;
- (IBAction)saveFeatureSpace:(id)sender;
-(void)cycleDimensionsUsingTimer:(NSTimer*)timer;


//@property (assign) IBOutlet NSWindow *window;
@property (assign) IBOutlet FeatureView *fw;
@property (assign) IBOutlet WaveformsView *wfv;
@property (assign) IBOutlet NSComboBox *dim1;
@property (assign) IBOutlet NSComboBox *dim2;
@property (assign) IBOutlet NSComboBox *dim3;
@property (assign) IBOutlet HistogramView *histView;
@property (assign) IBOutlet RasterView *rasterView;
@property (assign) IBOutlet NSMenu *clusterMenu;
@property (assign) IBOutlet NSPanel *clusterNotesPanel;

@property (retain,readwrite) NSMutableArray *Clusters;
@property (retain,readwrite) NSMutableArray *ClusterOptions;
@property (retain, readwrite) NSPredicate *isValidCluster;
@property (retain, readwrite) NSPredicate *filterClustersPredicate;
@property (retain, readwrite) NSSortDescriptor *clustersSortDescriptor;
@property (retain, readwrite) NSMutableArray *clustersSortDescriptors;
@property (retain, readwrite) NSString *waveformsFile;
@property (assign,readwrite) Cluster *activeCluster, *selectedCluster;
@property (assign,readwrite) NSIndexSet *selectedClusters;
@property (retain,readwrite) NSString *selectedWaveform;
@property (retain,readwrite) NSNumber *featureCycleInterval;
@property (retain,readwrite) NSAttributedString *releasenotes;
@property (retain,readwrite) StimInfo *stimInfo;
@property (retain,readwrite) NSMenu *waveformsMenu;
@end