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  • Description of lf_censor
    called by SOURCE CODE 0001 function fit lf censor x y cens varargin 0002 0003 Censored local regression using normal assumption 0004 Must provide x y and cens 0005 All other arguments to locfit can be provided with the 0006 exception of weights 0007 0008 NEED Kaplan Meier Estimate Iterations are fixed 0009 0010 0011 lfc y y 0012 unc find cens 0013 0014 for i 0 3 0015 fit

    Original URL path: http://www.chronux.org/Documentation/chronux/locfit/m/lf_censor.html (2015-03-27)
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  • Description of plx_waves
    npw ts wave plx waves filename ch u 0002 plx waves filename channel unit Read waveform data from a plx file 0003 0004 n npw ts wave plx waves filename channel unit 0005 0006 INPUT 0007 filename if empty string will use File Open dialog 0008 channel 1 based channel number 0009 unit unit number 0 invalid 1 4 valid 0010 OUTPUT 0011 n number of waveforms 0012 npw number of points in each waveform 0013 ts array of timestamps in seconds 0014 wave array of waveforms npw n raw a d values 0015 0016 if nargin 3 0017 disp 3 input arguments are required 0018 return 0019 end 0020 0021 n 0 0022 npw 0 0023 ts 0 0024 wave 0 0025 0026 if isempty filename 0027 fname pathname uigetfile plx Select a plx file 0028 filename strcat pathname fname 0029 end 0030 0031 fid fopen filename r 0032 if fid 1 0033 disp cannot open file 0034 return 0035 end 0036 0037 disp strcat file filename 0038 0039 read file header 0040 header fread fid 64 int32 0041 freq header 35 frequency 0042 ndsp header 36 number of dsp channels 0043 nevents header 37 number of external events 0044 nslow header 38 number of slow channels 0045 npw header 39 number of points in wave 0046 npr header 40 number of points before threshold 0047 tscounts fread fid 5 130 int32 0048 wfcounts fread fid 5 130 int32 0049 evcounts fread fid 1 512 int32 0050 0051 skip variable headers 0052 fseek fid 1020 ndsp 296 nevents 296 nslow cof 0053 0054 record 0 0055 wave zeros npw 1 0056 wf zeros npw 1 0057 0058 read data records 0059 while feof fid 0 0060 type fread fid 1 int16 0061 upperbyte fread fid 1 int16 0062 timestamp

    Original URL path: http://www.chronux.org/Documentation/chronux/dataio/ReadingPLXandDDTfilesinMatlab/plx_waves.html (2015-03-27)
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  • Description of FlyOrient
    angle in the lower half plane CROSS REFERENCE INFORMATION This function calls pca1 PCA1 Perform PCA using covariance This function is called by FindFly FINDFLY SOURCE CODE 0001 function orientation FlyOrient subset frame threshold 0002 0003 FLYORIENT 0004 Usage 0005 orientation FlyOrient subset frame threshold 0006 0007 This function takes in a subset frame around the fly calculated by 0008 FindFly and discards the 3D data by placing points where the pixel intensity 0009 is larger than the user chosen threshold Then Principal Components 0010 Analysis by way fot the pca1 function is performed on the resulting 0011 scatter plot to find the direction of maximum variance this direction 0012 is taken to be the fly s ambiguous orientation 0013 orientation is a vector consisting of two angles complements that comprise 0014 the body axis The first element is an angle in the upper half plane the 0015 second element is an angle in the lower half plane 0016 0017 Written by Dan Valente 0018 11 October 2006 0019 0020 Normalize frame data by pixel of maximum intensity 0021 subset frame subset frame max max subset frame 0022 0023 Put dots where fly is and do PCA on reduced data

    Original URL path: http://www.chronux.org/Documentation/chronux/fly_track/FTrack/functions/FlyOrient.html (2015-03-27)
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  • Description of fig1_1
    Setting ev none means that locfit computes only the parametric fit In this case deg 1 i e linear CROSS REFERENCE INFORMATION This function calls This function is called by runbook SOURCE CODE 0001 Local Regression and Likelihood Figure 1 1 0002 0003 A linear regression and plot for Spencer s mortality 0004 data Unlike the book I use locfit for this 0005 0006 Setting ev none means that locfit

    Original URL path: http://www.chronux.org/Documentation/chronux/locfit/Book/fig1_1.html (2015-03-27)
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  • Description of lfband
    using a single i e global estimate of sigma 2 CROSS REFERENCE INFORMATION This function calls invlink inverse link function for locfit lfmarg computes grid margins from a locfit object used for plotting predict Interpolate a fit produced by locfit This function is called by SOURCE CODE 0001 function lfband fit varargin 0002 0003 adds confidence bands around the plot of a locfit fit 0004 0005 for 2 d fits produces separate surface plots of upper and 0006 lower confidence limits 0007 0008 Bands are based on 95 pointwise coverage using a single 0009 i e global estimate of sigma 2 0010 0011 xfit lfmarg fit 0012 placing band g before varargin ensures that 0013 user provided band has precedence 0014 ypp predict fit xfit band g varargin 0015 yfit ypp 1 0016 se ypp 2 0017 bands ypp 3 0018 0019 data fit data 0020 xdata data x 0021 p size xdata 2 0022 cv 1 96 0023 fali fit fit points family link 0024 cl invlink bands 1 fali 0025 cu invlink bands 2 fali 0026 0027 if p 1 0028 hold on 0029 plot xfit 1 cu 0030 plot xfit 1 cl 0031 hold off 0032 end

    Original URL path: http://www.chronux.org/Documentation/chronux/locfit/m/lfband.html (2015-03-27)
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  • Description of predict
    fitted Fitted values from a locfit object lfband adds confidence bands around the plot of a locfit fit lfplot Plot for one or two dimensions a locfit fit locfit all Smoothing noisy data using Local Regression and Likelihood residuals Residuals or a few other things from a locfit fit scb Simultaneous Confidence Bands SOURCE CODE 0001 function y se predict varargin 0002 0003 Interpolate a fit produced by locfit 0004 0005 predict fit produces the fitted values at locfit s selected points 0006 predict fit x interpolates the fits to points specified by x 0007 0008 Input arguments 0009 fit The locfit fit 0010 x Points to interpolate at May be a matrix with d columns 0011 or cell with d components each a vector In the former 0012 case a fitted value is computed for each row of x 0013 In the latter the components of x are interpreted as 0014 grid margins 0015 Can also specify data evaluate at data points 0016 or fitp extract the fitted points 0017 band value 0018 Type of standard errors to compute Default is band n for none 0019 Other choices are band g use a global s to estimate the resiudal 0020 standard deviation so standard errors are s l x 0021 band l use a local s x so std errors are s x l x 0022 band p prediction errors so s sqrt 1 l x 2 0023 direct 0024 Compute the local fit directly rather than using local 0025 regression at each point specified by the x argument 0026 kappa vector 0027 Vector of constants for simultaneous confidence bands 0028 computed by the kappa0 function 0029 level value 0030 Coverage probability for confidence intervals and bands 0031 Default is 0 95 0032 0033 Output is a vector of

    Original URL path: http://www.chronux.org/Documentation/chronux/locfit/m/predict.html (2015-03-27)
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  • Description of FlyTracker
    filename 0018 FrameRange range of frames to examine 0019 NBackFrames number of frames in static background used only to 0020 find fly in first frame 0021 opt1 neg or pos This multiplies the frame data by a 0022 negative sign neg or not pos FindFly needs the 0023 fly to be a bright spot so the choice of this depends on 0024 the origional image If the original image is RGB chances 0025 are that neg needs to be selected 0026 sqrsize This is half the length of the sides of the square 0027 around the brightest spot to be used in the CM calculation 0028 and the orientation calculation 0029 alpha This is the weighting parameter for the running 0030 background It must be close to 1 for best results 0031 0 9 seems like a good value for this anything less 0032 seems to degrade SNR But for generalities sake it 0033 is still a user input parameter 0034 ellipse parameters of the elliptical area that will be tracked 0035 0036 Output 0037 x y The x and y locations of the fly in each frame 0038 orientation A matrix containing the UHP and LHP body axis orientation 0039 angles for each frame UHP are in the first row LHP are in 0040 the second row See FlyOrient and FindFly for more 0041 details 0042 0043 This function uses the videoReader function to input the video file into a Matlab object 0044 Usage on videoReader and other functions in the videoIO toolbox can be 0045 found in the videoIO documentation 0046 0047 Written by Dan Valente 8 8 07 0048 0049 Please note Video indexes start at frame 0 0050 StartFrame FrameRange 1 0051 EndFrame FrameRange end 0052 NFrames EndFrame StartFrame 1 0053 0054 If NBackFrames is smaller than the number of frames we want to look at 0055 we ll just take a smaller background average using all the frames of 0056 interest 0057 if NBackFrames NFrames 0058 NBackFrames NFrames 0059 end 0060 0061 initialize some variables 0062 x 0063 y 0064 orientUHP 0065 orientLHP 0066 0067 load in video object using videoReader 0068 video videoReader filename 0069 info getinfo video 0070 width info width 0071 height info height 0072 0073 just prevents error if user wants to track to end but enters the 0074 incorrect EndFrame recall frame index starts at 0 0075 if info numFrames EndFrame 0076 EndFrame EndFrame 1 0077 elseif info numFrames EndFrame 0078 EndFrame info numFrames 1 0079 end 0080 0081 seek to StartFrame for initial background calculation 0082 seek video StartFrame 0083 0084 mask ellipse mask 0085 0086 disp Calculating background 0087 background zeros height width 0088 for bframe 1 NBackFrames 0089 img getframe video 0090 current mask double img 1 just take first color matrix and mask out unwanted portions 0091 background background current NBackFrames 0092 next video 0093 end 0094 flipper 256 ones height width mask 0095 if strcmp opt1 neg 1 make sure our fly will be a

    Original URL path: http://www.chronux.org/Documentation/chronux/fly_track/FTrack/functions/FlyTracker.html (2015-03-27)
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  • Description of fig1_2
    function is called by runbook SOURCE CODE 0001 Local Regression and Likelihood Figure 1 2 0002 0003 Spencer s mortality data 15 and 21 point rules 0004 Doesn t use locfit 0005 0006 load spencer 0007 0008 figure Name fig1 2a Spencer mortality data 0009 plot age mortality o 0010 title 15 point rule 0011 xlabel Age Years 0012 ylabel Mortality Rate 0013 hold on 0014 plot age spence15 mortality

    Original URL path: http://www.chronux.org/Documentation/chronux/locfit/Book/fig1_2.html (2015-03-27)
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