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FeatureViewerController.m
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FeatureViewerController.m
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//
// FeatureViewerController.m
//
// Created by Grogee on 9/25/10.
// Copyright 2010 __MyCompanyName__. All rights reserved.
//
#import "FeatureViewerController.h"
@implementation FeatureViewerController
@synthesize fw;
@synthesize wfv;
@synthesize dim1;
@synthesize dim2;
@synthesize dim3;
@synthesize Clusters;
@synthesize ClusterOptions;
@synthesize isValidCluster;
//@synthesize filterClustersPredicate;
@synthesize clustersSortDescriptor;
@synthesize clustersSortDescriptors;
@synthesize waveformsFile;
@synthesize activeCluster,selectedCluster,selectedClusters,selectedWaveform;
//@synthesize selectedClusters;
//@synthesize selectedWaveform;
@synthesize featureCycleInterval;
@synthesize releasenotes;
@synthesize rasterView;
@synthesize histView;
@synthesize stimInfo;
@synthesize clusterMenu,waveformsMenu,clusterNotesPanel;
@synthesize filterClustersPredicate;
-(void)awakeFromNib
{
//[self setClusters:[NSMutableArray array]];
dataloaded = NO;
queue = [[[NSOperationQueue alloc] init] retain];
currentBaseName = NULL;
timestamps = NULL;
[self setFilterClustersPredicate:[NSPredicate predicateWithFormat: @"valid==YES"]];
[[NSNotificationCenter defaultCenter] addObserver: self selector:@selector(receiveNotification:)
name:@"showInput" object: nil];
[[NSNotificationCenter defaultCenter] addObserver: self selector:@selector(receiveNotification:)
name:@"highlight" object: nil];
[[NSNotificationCenter defaultCenter] addObserver: self selector:@selector(receiveNotification:)
name:@"performClusterOption" object: nil];
[[NSNotificationCenter defaultCenter] addObserver: self selector:@selector(receiveNotification:)
name:NSUserDefaultsDidChangeNotification object: nil];
//load the nibs
//setup defaults
/*NSUserDefaults *defaults = [NSUserDefaults standardUserDefaults];
NSNumber *fci = [defaults objectForKey:@"featureCycleInterval"];
if(fci == nil )
{
//no default value was found; use 0.5
[defaults registerDefaults:[NSDictionary dictionaryWithObjectsAndKeys:[NSNumber numberWithFloat:0.5], @"featureCycleInterval",nil]];
}*/
//[self setFeatureCycleInterval:[defaults objectForKey:@"featureCycleInterval"]];
[self setFeatureCycleInterval:[NSNumber numberWithFloat:0.5]];
//load the releasenotes
NSString *rn = [[NSBundle mainBundle] pathForResource:@"release_notes" ofType: @"rtf"];
NSAttributedString *reln = [[[NSAttributedString alloc] initWithPath:rn documentAttributes:NULL] autorelease];
[self setReleasenotes: reln];
//set up predicates for filter
NSPredicateEditorRowTemplate *row = [[[NSPredicateEditorRowTemplate alloc] initWithLeftExpressions: [NSArray arrayWithObjects:[NSExpression expressionForKeyPath:@"valid"],[NSExpression expressionForKeyPath: @"active"],nil] rightExpressions:
[NSArray arrayWithObjects:[NSExpression expressionForConstantValue: [NSNumber numberWithInt:1]],[NSExpression expressionForConstantValue:[NSNumber numberWithInt:1]],nil] modifier: NSDirectPredicateModifier operators:
[NSArray arrayWithObjects:[NSNumber numberWithInt: NSEqualToPredicateOperatorType],[NSNumber numberWithInt: NSNotEqualToPredicateOperatorType],nil] options:
NSCaseInsensitivePredicateOption] autorelease];
[filterPredicates setRowTemplates: [NSArray arrayWithObjects:row,nil]];
//load the rasterview window
//setup some usedefaults
/*
NSUserDefaults *defaults = [NSUserDefaults standardUserDefaults];
if( [defaults objectForKey:@"autoLoadWaveforms"] == nil )
{
[defaults setBool:YES forKey:@"autoLoadWaveforms"];
}
*/
shouldShowRaster = NO;
shouldShowWaveforms = NO;
autoLoadWaveforms = YES;
[selectClusterOption removeAllItems];
//create the waveforms menu
waveformsMenu = [[NSMenu alloc] init];
[waveformsMenu addItemWithTitle:@"Find correlated waveforms" action:@selector(correlateWaveforms:) keyEquivalent:@""];
[[self wfv] setMenu:waveformsMenu];
}
-(BOOL) acceptsFirstResponder
{
return YES;
}
-(IBAction) loadFeatureFile: (id)sender
{
/*TODO: Make this a bit more generic; the only thing the user should have to select is the waveformsfile. Everything else
can be derived from that. For this, we would need to get the contents of the directory, using NSFilemanager, then loop through
each feature file to get both the data and the feature names
*/
NSOpenPanel *openPanel = [NSOpenPanel openPanel];
[openPanel setDelegate:[[[OpenPanelDelegate alloc] init]autorelease]];
[openPanel setTitle:@"Choose feature file to load"];
[[openPanel delegate] setExtensions: [NSArray arrayWithObjects:@"fd",@"fet",nil]];
[openPanel setAllowsMultipleSelection:NO];
[openPanel setCanChooseDirectories: YES];
int result = [openPanel runModal];
if( result == NSOKButton )
{
//if we are loading a new dataset, remove everything about the old
if(dataloaded == YES)
{
[dim1 removeAllItems];
[dim2 removeAllItems];
[dim3 removeAllItems];
[[NSNotificationCenter defaultCenter] removeObserver:self name:@"ClusterStateChanged" object: nil];
[[self fw] hideAllClusters];
[self removeAllObjectsFromClusters];
[[[self wfv] window] orderOut:self];
}
NSString *path = [[openPanel URL] path];
[self openFeatureFile: path];
}
}
-(void) openFeatureFile:(NSString*)path
{
NSAutoreleasePool *_pool;
_pool = [[NSAutoreleasePool alloc] init];
//data object to hold the feature data
NSString *directory = [path stringByDeletingLastPathComponent];
NSMutableData *data = [NSMutableData dataWithCapacity:100000*sizeof(float)];
float *tmp_data,*tmp_data2;
int cols=0;
int rows = 0;
int i,j,k;
BOOL anyLoaded = NO;
NSMutableArray *feature_names = [NSMutableArray arrayWithCapacity:16];
NSString *filebase;
//get the group; format: gXXXX
//NSError *xerror = NULL;
//NSString *group = [[NSRegularExpression regularExpressionWithPattern:@"(g[0-9]*)" options: NSRegularExpressionCaseInsensitive: error &xerror] firstMatchInString: path option: 0 range:NSMakeRange(0,[path length])];
NSRange grange = [path rangeOfString:@"waveforms"];
NSString *group = [path substringWithRange:NSMakeRange(grange.location-5, 5)];
if( [[path pathExtension] isEqualToString:@"fd"])
{
NSArray *dir_contents = [[[NSFileManager defaultManager] contentsOfDirectoryAtPath: directory error: nil] pathsMatchingExtensions:[NSArray arrayWithObjects:@"fd",nil]];
if( [dir_contents count] == 0)
{
return;
}
//geth the base path
//TODO: This does not work if there are underscores in the file name
//find the last occurrence of "_"
NSRange range = [[path lastPathComponent] rangeOfString:@"_" options:NSBackwardsSearch];
filebase = [[path lastPathComponent] substringToIndex:range.location];
currentBaseName = [[NSString stringWithString:filebase] retain];
//set the current directory of the process to the the one pointed to by the load dialog
[[NSFileManager defaultManager] changeCurrentDirectoryPath:directory];
//get all feature files, i.e. files ending in .fd from the FD directory
//NSArray *dir_contents = [[[NSFileManager defaultManager] contentsOfDirectoryAtPath:[[path stringByDeletingLastPathComponent] stringByAppendingPathComponent:@"FD"] error: NULL]
// pathsMatchingExtensions:[NSArray arrayWithObjects:@"fd",nil]];
//get waveforms file
NSEnumerator *enumerator = [dir_contents objectEnumerator];
id file;
header H;
//float *tmp_data,*tmp_data2;
//TODO: parallelize this
while(file = [enumerator nextObject] )
{
if(([file hasPrefix:filebase] )) //&& ([[file stringByDeletingPathExtension]))
{
//check if this file contains a valid feature
if( [[file stringByDeletingPathExtension] isEqualToString:filebase] )
{
//skip
continue;
}
const char *filename = [[NSString pathWithComponents: [NSArray arrayWithObjects: directory,file,nil]] cStringUsingEncoding:NSASCIIStringEncoding];
H = *readFeatureHeader(filename, &H);
tmp_data = NSZoneMalloc([self zone], H.rows*H.cols*sizeof(float));
tmp_data2 = NSZoneMalloc([self zone], H.rows*H.cols*sizeof(float));
//the feature file will in general have a channelValidity file; this tells me which channels were used
float *_channelValidity = NSZoneMalloc([self zone],H.numChannels*sizeof(float));
channelValidity = NSZoneMalloc([self zone],H.numChannels*sizeof(uint8_t));
tmp_data = readFeatureData(filename, tmp_data,_channelValidity);
//copy to the global channelValidity variable
for(i=0;i<H.numChannels;i++)
{
channelValidity[i] = (uint8_t)_channelValidity[i];
}
nchannels = H.numChannels;
nvalidChannels = H.rows;
NSZoneFree([self zone],_channelValidity);
if(tmp_data == NULL)
{
//create an alert
NSAlert *alert = [NSAlert alertWithMessageText:@"Feature file could not be loaded" defaultButton:@"OK" alternateButton:nil otherButton:nil informativeTextWithFormat:@""];
[alert runModal];
NSZoneFree([self zone], tmp_data);
NSZoneFree([self zone], tmp_data2);
continue;
}
//transpose
for(i=0;i<H.rows;i++)
{
for(j=0;j<H.cols;j++)
{
tmp_data2[j*H.rows+i] = tmp_data[i*H.cols+j];
}
}
/*//find max
float max,min;
float l;
vDSP_maxv(tmp_data2,1,&max,H.rows*(H.cols));
//find min
vDSP_minv(tmp_data2,1,&min,H.rows*(H.cols));
l = max-min;
*/
//scale each feature to be between -1 and +1 if autoscale is requested
//note that this is an overall scaling, so it should not distort the relationship
//between dimensions
/*
if( [[NSUserDefaults standardUserDefaults] boolForKey:@"autoScaleAxes"] == YES )
{
for(j=0;j<(H.rows)*(H.cols);j++)
{
tmp_data2[j] = 2*(tmp_data2[j]-min)/l-1;
}
}
*/
[data appendBytes:tmp_data2 length: H.rows*H.cols*sizeof(float)];
NSZoneFree([self zone], tmp_data);
NSZoneFree([self zone], tmp_data2);
cols+=H.rows;
//feature names
//get basename
NSString *fn = [[[[file lastPathComponent] componentsSeparatedByString:@"_"] lastObject] stringByDeletingPathExtension];
for(j=0;j<H.numChannels;j++)
{
if(channelValidity[j]==1)
{
[feature_names addObject: [fn stringByAppendingFormat:@"%d",j+1]];
}
}
//notify that we have indeed loaded something
anyLoaded = YES;
}
//scale individual features
/*need to reshape the data
tmp_data = malloc([data length]);
float *tmp_data2 = [data bytes];
for(i=0;i<H.rows;i++)
{
for(j=0;j<tmp_cols;j++)
{
tmp_data[i*tmp_cols+j] = tmp_data_2[j%H.cols+]
}
}*/
rows = H.cols;
}
if( anyLoaded == NO)
{
return;
}
//need to reshape
tmp_data = NSZoneMalloc([self zone], rows*cols*sizeof(float));
tmp_data2 = (float*)[data bytes];
for(i=0;i<rows;i++)
{
for(k=0;k<cols/H.rows;k++)
{
for(j=0;j<H.rows;j++)
{
tmp_data[i*cols+k*H.rows+j] = tmp_data2[k*rows*H.rows + i*H.rows+j];
}
}
}
//free(temp_data);
}
else if([[[[path lastPathComponent] componentsSeparatedByString:@"."] objectAtIndex:1] isEqualToString:@"fet"])
{
//the file is a .fet file; it will have all the features written in ascii format, one row per line
//the first line contains the number of columns
filebase = [[[path lastPathComponent] componentsSeparatedByString:@"."] objectAtIndex:0];
//NSLog(@"LastComponent: %@",[path lastPathComponent]);
currentBaseName = [[NSString stringWithString:filebase] retain];
NSArray *lines = [[NSString stringWithContentsOfFile:path] componentsSeparatedByString:@"\n"];
cols = [[lines objectAtIndex:0] intValue];
//check if last line is empty
if( [[lines lastObject] isEqualToString:@""] )
{
rows = [lines count]-2;
}
else
{
rows = [lines count]-1;
}
tmp_data = malloc(rows*cols*sizeof(float));
int i,j;
for(i=0;i<rows;i++)
{
NSScanner *tokens = [NSScanner scannerWithString: [lines objectAtIndex:i+1]];
//skip all whitespace characters
[tokens setCharactersToBeSkipped:[NSCharacterSet whitespaceCharacterSet]];
for(j=0;j<cols;j++)
{
[tokens scanFloat:tmp_data+i*cols+j];
}
}
/*
float max,min;
float l;
//find max
vDSP_maxv(tmp_data,1,&max,rows*cols);
//find min
vDSP_minv(tmp_data,1,&min,rows*cols);
l = max-min;
for(j=0;j<rows*cols;j++)
{
tmp_data[j] = 2*(tmp_data[j]-min)/l-1;
}*/
[data appendBytes:tmp_data length:rows*cols*sizeof(float)];
//tmp_data2 = (float*)[data bytes];
//free(tmp_data);
//we don't know what the features are, so just call them by the the column
for(j=0;j<cols;j++)
{
[feature_names addObject: [NSString stringWithFormat:@"feature%d", j]];
}
}
//float *tmp_data = malloc(rows*cols*sizeof(float));
//tmp_data2 = [data bytes];
NSRange range;
range.location = 0;
range.length = rows*cols*sizeof(float);
//scale data
float max,min,l;
if( [[NSUserDefaults standardUserDefaults] integerForKey:@"autoScaleAxes"] == 0 )
{
//find max
vDSP_maxv(tmp_data,1,&max,rows*cols);
//find min
vDSP_minv(tmp_data,1,&min,rows*cols);
l = max-min;
for(j=0;j<rows*cols;j++)
{
tmp_data[j] = 2*(tmp_data[j]-min)/l-1;
}
}
else if( [[NSUserDefaults standardUserDefaults] integerForKey:@"autoScaleAxes"]==1 )
{
//scale each feature individually
for(i=0;i<cols;i++)
{
//find max
vDSP_maxv(tmp_data+i,cols,&max,rows);
//find min
vDSP_minv(tmp_data+i,cols,&min,rows);
//scale the data
l = (max-min);
//vDSP_addv(tmp_data2+i,cols,&min,
//vDSP_vsdiv(tmp_data2+i,cols,&l,tmp_data+i,cols,rows*cols);
for(j=0;j<rows;j++)
{
tmp_data[j*cols+i] = 2*(tmp_data[j*cols+i]-min)/l-1;
}
}
}
/*
//find max
vDSP_maxv(tmp_data,1,&max,rows*cols);
//find min
vDSP_minv(tmp_data,1,&min,rows*cols);
l = max-min;
for(j=0;j<rows*cols;j++)
{
tmp_data[j] = 2*(tmp_data[j]-min)/l-1;
}
*/
[data replaceBytesInRange:range withBytes:tmp_data length: rows*cols*sizeof(float)];
NSZoneFree([self zone], tmp_data);
[fw createVertices:data withRows:rows andColumns:cols];
//[fw loadVertices: [openPanel URL]];
[dim1 addItemsWithObjectValues:feature_names];
[dim2 addItemsWithObjectValues:feature_names];
[dim3 addItemsWithObjectValues:feature_names];
//get time data
//NSLog(@"XYZF: Is this going to work?");
//NSLog(@"Filebase: %@",filebase);
//check for the presence of xml file
if (([self waveformsFile] == NULL ) && (autoLoadWaveforms == YES) )
{
//check for the presence of spk files; first we need to load some info
NSString *xmlFile = [[[path lastPathComponent] componentsSeparatedByString:@"."] objectAtIndex:1];
xmlFile = [directory stringByAppendingPathComponent: [xmlFile stringByAppendingPathExtension:@"xml"]];
if( [[NSFileManager defaultManager] fileExistsAtPath:xmlFile] )
{
//NSDictionary *info = [NSDictionary dictionaryWithContentsOfFile:xmlFile];
//now check for the presence of spk file
NSString *spkFile = [path stringByReplacingOccurrencesOfString:@"fet" withString:@"spk"];
//NSUInteger group = [[path pathExtension] intValue];
if( [[NSFileManager defaultManager] fileExistsAtPath:spkFile] )
{
//we only need to know the number of bits and the number of channels
//NSNumber *nbits = [[info objectForKey:@"acquisitionSystem"] objectForKey:@"nBits"];
//NSNumber *nchannels = [[[[info objectForKey: @"anatomicalDescription"] objectForKey:@"channelGroups"] objectAtIndex:group] count];
//now read the info from the file
//NSData *spikeData = [NSData dataWithContentsOfFile:spkFile];
}
}
//waveforms file usually resides in a directory above the feature file
NSArray *waveformfiles = [[[[NSFileManager defaultManager] contentsOfDirectoryAtPath: [directory stringByDeletingLastPathComponent] error: nil]
pathsMatchingExtensions:[NSArray arrayWithObjects:@"bin",nil]] filteredArrayUsingPredicate:
[NSPredicate predicateWithFormat:@"SELF BEGINSWITH %@", filebase]];
//NSString *waveformsPath = @"";
if( [waveformfiles count] == 1 )
{
[self setWaveformsFile: [[directory stringByDeletingLastPathComponent] stringByAppendingPathComponent: [waveformfiles objectAtIndex:0]]];
const char *waveformsPath = [waveformsFile cStringUsingEncoding: NSASCIIStringEncoding];
nptHeader spikeHeader;
spikeHeader = *getSpikeInfo(waveformsPath, &spikeHeader);
unsigned long long int *times = malloc(rows*sizeof(unsigned long long int));
unsigned int *times_indices = malloc(rows*sizeof(unsigned int));
for(i=0;i<rows;i++)
{
times_indices[i] = i;
}
times = getTimes(waveformsPath, &spikeHeader, times_indices, rows, times);
timestamps = [[NSData dataWithBytes:times length:rows*sizeof(unsigned long long int)] retain];
free(times);
free(times_indices);
}
}
//load feature anems
//NSArray *feature_names = [[NSString stringWithContentsOfFile:@"../../feature_names.txt"] componentsSeparatedByString:@"\n"];
/*NSArray *feature_names;
//open panel
result = [openPanel runModal];
if( result == NSOKButton )
{
feature_names = [[NSString stringWithContentsOfURL :[openPanel URL]] componentsSeparatedByString:@"\n"];
[dim1 addItemsWithObjectValues:feature_names];
[dim2 addItemsWithObjectValues:feature_names];
[dim3 addItemsWithObjectValues:feature_names];
}*/
params.rows = rows;
params.cols = cols;
[dim1 setEditable:NO];
[dim1 selectItemAtIndex:0];
[dim2 setEditable:NO];
[dim2 selectItemAtIndex:1];
[dim3 setEditable:NO];
[dim3 selectItemAtIndex:2];
featureNames = [[NSMutableArray arrayWithArray:feature_names] retain];
//register featureview for notification about change in highlight
//feature view only received notification from waveforms view
//[[NSNotificationCenter defaultCenter] addObserver: fw selector:@selector(receiveNotification:)
// name:@"highlight" object: [self wfv]];
[[NSNotificationCenter defaultCenter] addObserver:self selector:@selector(receiveNotification:)
name:@"setFeatures" object:nil];
if( [[NSUserDefaults standardUserDefaults] boolForKey:@"stimInfo"] ==YES)
{
NSString *stimInfoFile = NULL;
NSString *stimInfoDir = directory;
if( waveformsFile != NULL )
{
//attempt to locate a simtinfo object. This should be located two levels above the waveformfile
NSString *stimInfoDir = [waveformsFile stringByDeletingLastPathComponent];
stimInfoFile = [waveformsFile lastPathComponent];
NSRange _r = [stimInfoFile rangeOfString:@"g00"];
stimInfoFile = [stimInfoDir stringByAppendingPathComponent:[[stimInfoFile substringWithRange:NSMakeRange(0, _r.location)] stringByAppendingString:@".ini"]];
if( [[NSFileManager defaultManager] fileExistsAtPath:stimInfoFile] == NO)
{
stimInfoDir = [[waveformsFile stringByDeletingLastPathComponent] stringByDeletingLastPathComponent];
stimInfoFile = [waveformsFile lastPathComponent];
_r = [stimInfoFile rangeOfString:@"g00"];
stimInfoFile = [stimInfoDir stringByAppendingPathComponent:[[stimInfoFile substringWithRange:NSMakeRange(0, _r.location)] stringByAppendingString:@"_stimInfo.mat"]];
}
}
if( [[NSFileManager defaultManager] fileExistsAtPath:stimInfoFile] == NO)
{
stimInfoFile=NULL;
//ask for the file name
NSOpenPanel *panel = [NSOpenPanel openPanel];
[panel setDirectory:stimInfoDir];
[panel setTitle:@"Open stimulus file"];
[panel setAllowedFileTypes: [NSArray arrayWithObjects:@"ini", nil]];
int result = [panel runModal];
if (result == NSOKButton )
{
stimInfoFile = [panel filename];
}
}
if(stimInfoFile != NULL)
{
//load stimInfo
stimInfo = [[[StimInfo alloc] init] retain];
[stimInfo readFromFile:stimInfoFile];
[stimInfo readMonitorSyncs];
[stimInfo readDescriptor];
[stimInfo getFramePoints];
//[stimInfo getTriggerSignalWithThreshold:1500.0];
}
else
{
//pop up a dialog box asking for the necessary values; we can get by creating an approximate raster by getting the duration of each stimulus repetition
}
}
//only reset clusters if data has already been loaded
if( ([self Clusters] != nil) && (dataloaded == YES ) )
{
[self removeAllObjectsFromClusters];
}
dataloaded = YES;
//show window
if( [[[self fw] window] isVisible] == NO )
{
[[[self fw] window] orderFront:self];
}
//create a noise cluster with all points
Cluster *firstCluster = [[Cluster alloc] init];
[firstCluster setClusterId:[NSNumber numberWithInt:0]];
[firstCluster setIndices:[NSMutableIndexSet indexSetWithIndexesInRange:NSMakeRange(0, rows)]];
[firstCluster setNpoints:[NSNumber numberWithUnsignedInt: rows]];
unsigned int *points = malloc(rows*sizeof(unsigned int));
for(i=0;i<rows;i++)
{
points[i] = (unsigned int)i;
}
[firstCluster setPoints:[NSMutableData dataWithBytes:points length:rows*sizeof(unsigned int)]];
free(points);
[firstCluster createName];
[firstCluster makeActive];
//create cluster color
float *_ccolor = malloc(3*sizeof(float));
_ccolor[0] = 1.0f;//use_colors[3*cids[i+1]];
_ccolor[1] = 0.85f;//use_colors[3*cids[i+1]+1];
_ccolor[2] = 0.35f;//use_colors[3*cids[i+1]+2];
[firstCluster setColor: [NSData dataWithBytes:_ccolor length:3*sizeof(float)]];
free(_ccolor);
[selectClusterOption addItemWithTitle:@"Create cluster"];
[selectClusterOption addItemWithTitle:@"Add points to cluster"];
[selectClusterOption addItemWithTitle:@"Delete"];
[selectClusterOption addItemWithTitle:@"Compute ISOmap"];
[clusterMenu addItemWithTitle:@"Create cluster" action:@selector(performClusterOption:) keyEquivalent:@""];
[clusterMenu addItemWithTitle:@"Add points to cluster" action:@selector(performClusterOption:) keyEquivalent:@""];
[clusterMenu addItemWithTitle:@"Remove points from cluster" action:@selector(performClusterOption:) keyEquivalent:@""];
//before we create the cluster, hide all existing clusters
[[self fw] hideAllClusters];
if([ self Clusters] != nil )
{
[self insertObject:firstCluster inClustersAtIndex:0];
}
else
{
[self setClusters:[NSMutableArray arrayWithObject:firstCluster]];
}
[_pool drain];
}
-(void)loadStimInfo
{
NSString *stimInfoFile = NULL;
NSString *stimInfoDir;
if( waveformsFile != NULL )
{
//attempt to locate a simtinfo object. This should be located two levels above the waveformfile
NSString *stimInfoDir = [waveformsFile stringByDeletingLastPathComponent];
stimInfoFile = [waveformsFile lastPathComponent];
NSRange _r = [stimInfoFile rangeOfString:@"g00"];
stimInfoFile = [stimInfoDir stringByAppendingPathComponent:[[stimInfoFile substringWithRange:NSMakeRange(0, _r.location)] stringByAppendingString:@".ini"]];
if( [[NSFileManager defaultManager] fileExistsAtPath:stimInfoFile] == NO)
{
stimInfoDir = [[waveformsFile stringByDeletingLastPathComponent] stringByDeletingLastPathComponent];
stimInfoFile = [waveformsFile lastPathComponent];
_r = [stimInfoFile rangeOfString:@"g00"];
stimInfoFile = [stimInfoDir stringByAppendingPathComponent:[[stimInfoFile substringWithRange:NSMakeRange(0, _r.location)] stringByAppendingString:@"stimInfo.mat"]];
}
}
if( [[NSFileManager defaultManager] fileExistsAtPath:stimInfoFile] == NO)
{
stimInfoFile=NULL;
//ask for the file name
NSOpenPanel *panel = [NSOpenPanel openPanel];
if( stimInfoDir != nil)
{
[panel setDirectory:stimInfoDir];
}
[panel setTitle:@"Open stimulus file"];
[panel setAllowedFileTypes: [NSArray arrayWithObjects:@"ini", nil]];
int result = [panel runModal];
if (result == NSOKButton )
{
stimInfoFile = [panel nameFieldStringValue];
}
}
if(stimInfoFile != NULL)
{
//load stimInfo
stimInfo = [[[StimInfo alloc] init] retain];
[stimInfo readFromFile:stimInfoFile];
[stimInfo readMonitorSyncs];
[stimInfo readDescriptor];
[stimInfo getFramePoints];
//[stimInfo getTriggerSignalWithThreshold:1500.0];
}
else
{
//pop up a dialog box asking for the necessary values; we can get by creating an approximate raster by getting the duration of each stimulus repetition
}
}
- (IBAction) loadClusterIds: (id)sender
{
NSOpenPanel *openPanel = [NSOpenPanel openPanel];
//set a delegate for openPanel so that we can control which files can be opened
[openPanel setDelegate:[[[OpenPanelDelegate alloc] init] autorelease]];
//set the basePath to the current basepath so that only cluster files compatible with the currently loaded feature files are allowed
[[openPanel delegate] setBasePath: currentBaseName];
[[openPanel delegate] setExtensions: [NSArray arrayWithObjects: @"clu",@"fv",@"overlap",@"cut",@"clusters",nil]];
int result = [openPanel runModal];
if( result == NSOKButton )
{
[self openClusterFile:[[openPanel URL] path]];
}
}
- (void)openClusterFile:(NSString*)path;
{
NSAutoreleasePool *_pool = [[NSAutoreleasePool alloc] init];
unsigned int i,j;
[[NSNotificationCenter defaultCenter] removeObserver: self name: @"ClusterStateChanged" object: nil];
//remove all the all clusters
//[self removeAllObjectsFromClusters];
//NSString *filename = [[openPanel URL] path];
//get the components of the filename; sometimes we are interested int he last extension, sometimes the second last
NSArray *fileComps = [[path lastPathComponent] componentsSeparatedByString:@"."];
NSUInteger nFileComps = [fileComps count];
NSString *extension = [fileComps objectAtIndex:1];
float *cluster_colors;
NSMutableArray *tempArray;
//check if data is loaded
if(dataloaded==NO)
{
//need to load the data before loading the clusters
//get the basename
NSString *basename = [[[path lastPathComponent] componentsSeparatedByString:@"."] objectAtIndex:0];
NSString *directory = [path stringByDeletingLastPathComponent];
NSString *featurePath = [directory stringByAppendingPathComponent:[NSString stringWithFormat:@"%@_area.fd", basename]];
//set the waveforms file as well
NSString *wfFile = [directory stringByAppendingPathComponent:[NSString stringWithFormat:@"%@.bin", basename]];
if( [[NSFileManager defaultManager] fileExistsAtPath:wfFile] == YES )
{
[self setWaveformsFile:wfFile];
}
//check if the path exists
if( [[NSFileManager defaultManager] fileExistsAtPath:featurePath] == NO )
{
//try the FD directory
featurePath = [[directory stringByAppendingPathComponent:@"FD"] stringByAppendingPathComponent:
[NSString stringWithFormat:@"%@_area.fd", basename]];
if( [[NSFileManager defaultManager] fileExistsAtPath:featurePath] == NO )
{
//file could not be automatically located; popup a dialog to ask for it
[self loadFeatureFile:self];
}
else {
//we found the feature file, so open it
[self openFeatureFile:featurePath];
}
}
else
{
[self openFeatureFile:featurePath];
}
}
//create a data object to hold the channels
unsigned int *_chs = malloc(nvalidChannels*sizeof(unsigned int));
j = 0;
for(i=0;i<nchannels;i++)
{
if(channelValidity[i]==1)
{
_chs[j] = i;
j+=1;
}
}
if( [[fileComps lastObject] isEqualToString:@"fv"] )
{
tempArray = [NSKeyedUnarchiver unarchiveObjectWithFile:path];
//get cluster colors
//NSMutableData *_cluster_colors = [NSMutableData dataWithCapacity:params.rows*3*sizeof(float)];
cluster_colors = NSZoneMalloc([self zone], params.rows*3*sizeof(float));
id _cluster;
NSEnumerator *_clustersEnumerator = [tempArray objectEnumerator];
while( _cluster = [_clustersEnumerator nextObject] )
{
unsigned int *_points = (unsigned int*)[[_cluster points] bytes];
unsigned int _npoints = [[_cluster npoints] intValue];
float *_color = (float*)[[_cluster color] bytes];
for(i=0;i<_npoints;i++)
{
cluster_colors[3*_points[i]] = _color[0];
cluster_colors[3*_points[i]+1] = _color[1];
cluster_colors[3*_points[i]+2] = _color[2];
}
}
[tempArray makeObjectsPerformSelector:@selector(makeValid)];
}
else
{
if( [[fileComps lastObject] isEqualToString:@"cut"] || [[fileComps objectAtIndex:nFileComps-2] isEqualToString:@"clu"] )
{
int offset = 1;
if( [[fileComps lastObject] isEqualToString:@"cut"] )
{
offset = 0;
}
//char *fname = [path cStringUsingEncoding:NSASCIIStringEncoding];
//TODO: Check if there is also an overlap present; if so, load it as well
/*
header H;
H = *readFeatureHeader("../../test2.hdf5", &H);
int rows = H.rows;
*/
int *cids = NSZoneMalloc([self zone], (rows+1)*sizeof(int));
//cids = readClusterIds(fname, cids);
NSArray *lines = [[NSString stringWithContentsOfFile:path encoding: NSASCIIStringEncoding error: NULL] componentsSeparatedByCharactersInSet:[NSCharacterSet newlineCharacterSet]];
//iteratae through lines
NSEnumerator *lines_enum = [lines objectEnumerator];
id line;
NSNumberFormatter *formatter = [[[NSNumberFormatter alloc] init] autorelease];
int cidx = 0;
while ( (line = [lines_enum nextObject] ) )
{
NSNumber *q = [formatter numberFromString:line];
//if line is not a string, q is nil
if( q )
{
cids[cidx] = [q intValue];
cidx+=1;
}
}
//find the maximum cluster number
//TODO: this is quick and dirty; should try and speed this up
int maxCluster = 0;
int i;
for(i=0;i<rows;i++)
{
if( cids[i+offset] > maxCluster )
{
maxCluster = cids[i+offset];
}
}
//since we are using 0-based indexing, the number of clusters is maxCluster+1
maxCluster+=1;
tempArray = [NSMutableArray arrayWithCapacity:maxCluster];
//count the number of points in each cluster
unsigned int *npoints;
npoints = calloc(maxCluster,sizeof(unsigned int));
cluster_colors = NSZoneMalloc([self zone],rows*3*sizeof(float));
for(i=0;i<rows;i++)
{
if( cids[i+offset] >= 0 )
{
npoints[cids[i+offset]]+=1;
}
}
for(i=0;i<maxCluster;i++)
{
Cluster *cluster = [[Cluster alloc] init];
cluster.clusterId = [NSNumber numberWithUnsignedInt:i];
//cluster.name = [NSString stringWithFormat: @"%d",i];
cluster.npoints = [NSNumber numberWithUnsignedInt: npoints[i]];
//cluster.name = [[[[cluster clusterId] stringValue] stringByAppendingString:@": "] stringByAppendingString:[[cluster npoints] stringValue]];
[cluster createName];
cluster.indices = [NSMutableIndexSet indexSet];
cluster.valid = 1;
[cluster setChannels: [NSData dataWithBytes: _chs length:nvalidChannels*sizeof(unsigned int)]];
//set color
float color[3];
color[0] = ((float)rand())/RAND_MAX;
color[1] = ((float)rand())/RAND_MAX;
color[2] = ((float)rand())/RAND_MAX;
cluster.color = [NSData dataWithBytes: color length:3*sizeof(float)];
unsigned int *points = malloc(npoints[i]*sizeof(unsigned int));
int j,k = 0;
//use a binary mask to indicate cluster membership
//uint8 *_mask = calloc(rows,sizeof(uint8));
for(j=0;j<rows;j++)
{
if(cids[j+offset]==i)
{
points[k] = (unsigned int)j;
//mask[j] = 1;
k+=1;
//set the colors at the same time
cluster_colors[3*j] = color[0];
cluster_colors[3*j+1] = color[1];
cluster_colors[3*j+2] = color[2];
[[cluster indices] addIndex: (NSUInteger)j];
}
}
cluster.points = [NSMutableData dataWithBytes:points length:npoints[i]*sizeof(unsigned int)];
//cluster.mask = [NSMutableData dataWithBytes: _mask length: rows*sizeof(uint8)];
//free(_mask);
free(points);
//compute ISIs; this step can run on a separate thread
[cluster computeISIs:timestamps];
[cluster setIsTemplate:0];
[cluster setActive: 1];
[tempArray addObject:cluster];
}
NSZoneFree([self zone], cids);
free(npoints);
//free(cluster_colors);
//tell the view to change the colors
}
else if ([[fileComps lastObject] isEqualToString:@"overlap"])
{
const char *fname = [path cStringUsingEncoding:NSASCIIStringEncoding];
uint64_t nelm = getFileSize(fname)/sizeof(uint64_t);
unsigned ncols = nelm/2;
uint64_t *overlaps = NSZoneMalloc([self zone], nelm*sizeof(uint64_t));
overlaps = readOverlapFile(fname, overlaps, nelm);
//since the overlaps are assumed to ordered according to clusters, with cluster ids in the first column, we can easily get
//the maximum numbers of clusters
unsigned int maxCluster = overlaps[ncols-2]+1;
unsigned i;
cluster_colors = NSZoneMalloc([self zone], 3*ncols*sizeof(float));
tempArray = [NSMutableArray arrayWithCapacity:maxCluster];
//NSLog(@"maxCluster: %d", maxCluster);
for(i=0;i<maxCluster;i++)
{
Cluster *cluster = [[Cluster alloc] init];
cluster.clusterId = [NSNumber numberWithUnsignedInt:i];
//cluster.name = [NSString stringWithFormat: @"%d",i];
cluster.npoints = [NSNumber numberWithUnsignedInt: 0];
//cluster.name = [[[[cluster clusterId] stringValue] stringByAppendingString:@": "] stringByAppendingString:[[cluster npoints] stringValue]];
[cluster createName];
cluster.indices = [NSMutableIndexSet indexSet];
cluster.valid = 1;
//set color
float color[3];
color[0] = ((float)rand())/RAND_MAX;
color[1] = ((float)rand())/RAND_MAX;
color[2] = ((float)rand())/RAND_MAX;
cluster.color = [NSData dataWithBytes: color length:3*sizeof(float)];
cluster.points = [NSMutableData dataWithCapacity:1000*sizeof(unsigned long)];
//cluster.mask = [NSMutableData dataWithBytes: _mask length: rows*sizeof(uint8)];
//free(_mask);
//compute ISIs; this step can run on a separate thread
//[cluster computeISIs:timestamps];
[cluster setIsTemplate:0];
[cluster setActive: 1];
//TODO: for some reason, the update doesn't work properly so I had to disable it
//[cluster updateDescription];
[tempArray addObject:cluster];
}
//now loop through the overlap matrix, adding points to the clusters as we go along
unsigned int cid,wfidx,npoints;
cid = maxCluster+1;
Cluster *cluster;
float *color;
for(i=0;i<ncols;i++)
{
wfidx = overlaps[ncols+i];
if( overlaps[i] != cid )
{
cid = overlaps[i];
cluster = [tempArray objectAtIndex:cid];
}
//set the colors
color = (float*)[[cluster color] bytes];
cluster_colors[3*i] = color[0];
cluster_colors[3*i+1] = color[1];
cluster_colors[3*i+2] = color[2];
[[cluster points] appendBytes:&wfidx length:sizeof(unsigned int)];
[[cluster indices] addIndex:wfidx];
npoints = [[cluster npoints] unsignedIntValue];
//increment the number of points
[cluster setNpoints:[NSNumber numberWithUnsignedInt:npoints+1]];
}
//free overlaps since we don't need it
NSZoneFree([self zone], overlaps);
[tempArray makeObjectsPerformSelector:@selector(createName)];
}
else if ([[fileComps lastObject] isEqualToString:@"clusters"])
{
unsigned int* cids;
readMClustClusters([path cStringUsingEncoding:NSASCIIStringEncoding], cids);
}
else
{
//unknown extension
NSAlert *alert = [NSAlert alertWithMessageText:@"Unknown extension" defaultButton:@"OK" alternateButton:nil otherButton:nil informativeTextWithFormat:nil];
[alert runModal];
}
}
free(_chs);
//turn off the first cluster, since it's usually the noise cluster
if(tempArray != nil )
{
[[tempArray objectAtIndex:0] makeInactive];
}
if( dataloaded == YES )
{
//only do this if data has been loaded
[fw setClusterColors: cluster_colors forIndices: NULL length: 1];
}
//since colors are now ccopied, we can free it
NSZoneFree([self zone],cluster_colors);
if( ([self Clusters] != nil) && (dataloaded == YES ) )
{
[self removeAllObjectsFromClusters];