Problem with varargin and getting output

조회 수: 3(최근 30일)
Lissa Aerts
Lissa Aerts 2021년 3월 21일
답변: Sjoerd 2021년 3월 25일
I do not get any output of AnalogSignals. However, the variable ans is created. I tried writing a script but I read that the varargin should be inside of the function script .. Any tips?
function [Markers,MLabels,VideoFrameRate,AnalogSignals,ALabels,AUnits,AnalogFrameRate,Event,ParameterGroup,CameraInfo]=...
readC3D(FullFileName, varargin)
% ReadC3D: Read 3D video coordinate and analog (FP) data from a C3D file
%
% Input: FullFileName - file (including path) to be read
% (optional) force number of markers
% (optional) subtractAnalogOffset - indices of columns (in order of ALabels)
% Output:
% Markers 3D-marker data [NvideoFrames x Nmarkers*Ndim(=3)]
% MLabels marker column identifiers
% VideoFrameRate Frames/sec
% AnalogSignals Analog signals [Nsignals x NanalogSamples ]
% ALabels anolog column (signal) idenitifiers
% AnalogFrameRate Samples/sec
% Event Event(Nevents).time ..value ..name
% ParameterGroup ParameterGroup(Ngroups).Parameters(Nparameters).data ..etc.
% CameraInfo MarkerRelated CameraInfo [Nmarkers x NvideoFrames]
% ResidualError MarkerRelated ErrorInfo [Nmarkers x NvideoFrames]
%
% AUTHOR(S) AND VERSION-HISTORY
% Ver. 1.0 Creation (Alan Morris, Toronto, October 1998) [originally named "getc3d.m"]
% Ver. 2.0 Revision (Jaap Harlaar, Amsterdam, april 2002)
% Ver. 3.0 Revision (Ajay Seth, Stanford University, August 2007)
% Ver. 3.1 Revision (Sjoerd Bruijn, KU leuven, May 2012. Speedup.)
% Note: removed ability to limit number of markers
% note: assumes scale <0
%==========================================================================
map = '/MATLAB Drive/BIOMECH/C3D Data/'; % map met C3D data
cond = {'Sit_HR_Trial0','Sit_MR_Trial0','Sup_HR_Trial0','Sup_MR_Trial0'}; % Condities van testopstelling (Sit_HR Sit_MR ..)
addpath('/MATLAB Drive/BIOMECH/Functions')
map_out = '/MATLAB Drive/BIOMECH/TRC Caren files/' % map waar je data wilt opslaan
for i = 1:length(cond)
for j = 1
FullFileName = [map, char(cond(i)),num2str(j),'.c3d']
end
end
Markers=[];
MLabels=[];
VideoFrameRate=0;
AnalogSignals=[];
ALabels=[];
AnalogFrameRate=0;
Event=[];
ParameterGroup=[];
CameraInfo=[];
ResidualError=[];
% ###############################################
% ## ##
% ## open the file ##
% ## ##
% ###############################################
ind=findstr(FullFileName,'\');
if ind>0, FileName=FullFileName(ind(length(ind))+1:length(FullFileName)); else FileName=FullFileName; end
fid=fopen(FullFileName,'r','n'); % native format (PC-intel)
if fid==-1,
h=errordlg(['File: ',FileName,' could not be opened'],'application error');
uiwait(h)
return
end
NrecordFirstParameterblock=fread(fid,1,'int8'); % Reading record number of parameter section
key=fread(fid,1,'int8'); % key = 80;
if key~=80,
h=errordlg(['File: ',FileName,' does not comply to the C3D format'],'application error');
uiwait(h)
fclose(fid)
return
end
fseek(fid,512*(NrecordFirstParameterblock-1)+3,'bof'); % jump to processortype - field
proctype=fread(fid,1,'int8')-83; % proctype: 1(INTEL-PC); 2(DEC-VAX); 3(MIPS-SUN/SGI)
if proctype==2,
fclose(fid);
fid=fopen(FullFileName,'r','d'); % DEC VAX D floating point and VAX ordering
end
% ###############################################
% ## ##
% ## read header ##
% ## ##
% ###############################################
%NrecordFirstParameterblock=fread(fid,1,'int8'); % Reading record number of parameter section
%key1=fread(fid,1,'int8'); % key = 80;
fseek(fid,2,'bof');
Nmarkers=fread(fid,1,'int16'); %number of markers
if nargin > 1,
if ~isempty(varargin{1}),
Nmarkersinput = varargin{1};
end
end
NanalogSamplesPerVideoFrame=fread(fid,1,'int16'); %number of analog channels x #analog frames per video frame
StartFrame=fread(fid,1,'int16'); %# of first video frame
EndFrame=fread(fid,1,'int16'); %# of last video frame
MaxInterpolationGap=fread(fid,1,'int16'); %maximum interpolation gap allowed (in frame)
Scale=fread(fid,1,'float32'); %floating-point scale factor to convert 3D-integers to ref system units
if Scale>0
warndlg('Program was written to use scale < 0. Apparently, this is not the case for this file. Reverting back to old readc3d code, will be slow!')
end
NrecordDataBlock=fread(fid,1,'int16'); %starting record number for 3D point and analog data
NanalogFramesPerVideoFrame=fread(fid,1,'int16');
if NanalogFramesPerVideoFrame > 0,
NanalogChannels=NanalogSamplesPerVideoFrame/NanalogFramesPerVideoFrame;
else
NanalogChannels=0;
end
VideoFrameRate=fread(fid,1,'float32');
AnalogFrameRate=VideoFrameRate*NanalogFramesPerVideoFrame;
% ###############################################
% ## ##
% ## read events ##
% ## ##
% ###############################################
fseek(fid,298,'bof');
EventIndicator=fread(fid,1,'int16');
if EventIndicator==12345,
Nevents=fread(fid,1,'int16');
fseek(fid,2,'cof'); % skip one position/2 bytes
if Nevents>0,
for i=1:Nevents,
Event(i).time=fread(fid,1,'float');
end
fseek(fid,188*2,'bof');
for i=1:Nevents,
Event(i).value=fread(fid,1,'int8');
end
fseek(fid,198*2,'bof');
for i=1:Nevents,
Event(i).name=cellstr(char(fread(fid,4,'char')'));
end
end
end
% ###############################################
% ## ##
% ## read 1st parameter block ##
% ## ##
% ###############################################
fseek(fid,512*(NrecordFirstParameterblock-1),'bof');
dat1=fread(fid,1,'int8');
key2=fread(fid,1,'int8'); % key = 80;
NparameterRecords=fread(fid,1,'int8');
proctype=fread(fid,1,'int8')-83; % proctype: 1(INTEL-PC); 2(DEC-VAX); 3(MIPS-SUN/SGI)
Ncharacters=fread(fid,1,'int8'); % characters in group/parameter name
GroupNumber=fread(fid,1,'int8'); % id number -ve=group / +ve=parameter
while Ncharacters > 0 % The end of the parameter record is indicated by <0 characters for group/parameter name
if GroupNumber<0 % Group data
GroupNumber=abs(GroupNumber);
GroupName=fread(fid,[1,Ncharacters],'char');
ParameterGroup(GroupNumber).name=cellstr(char(GroupName)); %group name
offset=fread(fid,1,'int16'); %offset in bytes
deschars=fread(fid,1,'int8'); %description characters
GroupDescription=fread(fid,[1,deschars],'char');
ParameterGroup(GroupNumber).description=cellstr(char(GroupDescription)); %group description
ParameterNumberIndex(GroupNumber)=0;
fseek(fid,offset-3-deschars,'cof');
else % parameter data
clear dimension;
ParameterNumberIndex(GroupNumber)=ParameterNumberIndex(GroupNumber)+1;
ParameterNumber=ParameterNumberIndex(GroupNumber); % index all parameters within a group
ParameterName=fread(fid,[1,Ncharacters],'char'); % name of parameter
% read parameter name
if size(ParameterName)>0
ParameterGroup(GroupNumber).Parameter(ParameterNumber).name=cellstr(char(ParameterName)); %save parameter name
end
% read offset
offset=fread(fid,1,'int16'); %offset of parameters in bytes
filepos=ftell(fid); %present file position
nextrec=filepos+offset(1)-2; %position of beginning of next record
% read type
type=fread(fid,1,'int8'); % type of data: -1=char/1=byte/2=integer*2/4=real*4
ParameterGroup(GroupNumber).Parameter(ParameterNumber).datatype=type;
% read number of dimensions
dimnum=fread(fid,1,'int8');
if dimnum==0
datalength=abs(type); %length of data record
else
mult=1;
for j=1:dimnum
dimension(j)=fread(fid,1,'uint8');
mult=mult*dimension(j);
ParameterGroup(GroupNumber).Parameter(ParameterNumber).dim(j)=dimension(j); %save parameter dimension data
end
datalength=abs(type)*mult; %length of data record for multi-dimensional array
end
if type==-1 %datatype=='char'
wordlength=dimension(1); %length of character word
if dimnum==2 & datalength>0 %& parameter(idnumber,index,2).dim>0
for j=1:dimension(2)
data=fread(fid,[1,wordlength],'char'); %character word data record for 2-D array
ParameterGroup(GroupNumber).Parameter(ParameterNumber).data(j)=cellstr(char(data));
end
elseif dimnum==1 & datalength>0
data=fread(fid,[1,wordlength],'char'); %numerical data record of 1-D array
ParameterGroup(GroupNumber).Parameter(ParameterNumber).data=cellstr(char(data));
end
elseif type==1 %1-byte for boolean
Nparameters=datalength/abs(type);
data=fread(fid,Nparameters,'int8');
ParameterGroup(GroupNumber).Parameter(ParameterNumber).data=data;
elseif type==2 & datalength>0 %integer
Nparameters=datalength/abs(type);
data=fread(fid,Nparameters,'int16');
if dimnum>1
ParameterGroup(GroupNumber).Parameter(ParameterNumber).data=reshape(data,dimension);
else
ParameterGroup(GroupNumber).Parameter(ParameterNumber).data=data;
end
elseif type==4 & datalength>0
Nparameters=datalength/abs(type);
data=fread(fid,Nparameters,'float');
if dimnum>1
ParameterGroup(GroupNumber).Parameter(ParameterNumber).data=reshape(data,dimension);
else
ParameterGroup(GroupNumber).Parameter(ParameterNumber).data=data;
end
else
% error
end
deschars=fread(fid,1,'int8'); %description characters
if deschars>0
description=fread(fid,[1,deschars],'char');
ParameterGroup(GroupNumber).Parameter(ParameterNumber).description=cellstr(char(description));
end
%moving ahead to next record
fseek(fid,nextrec,'bof');
end
% check group/parameter characters and idnumber to see if more records present
Ncharacters=fread(fid,1,'int8'); % characters in next group/parameter name
GroupNumber=fread(fid,1,'int8'); % id number -ve=group / +ve=parameter
end
% ###############################################
% ## ##
% ## read data block ##
% ## ##
% ###############################################
% Get the coordinate and analog data
fseek(fid,(NrecordDataBlock-1)*512,'bof');
NvideoFrames=EndFrame - StartFrame + 1;
h = waitbar(0,[FileName,' is loading...']);
% Original marker structure is annoying to work with and to output to file
% so changing here so that it is listed three coordinates at a time
% in order of the marker labels. -aseth
if Scale<0
reps = [int2str(4*Nmarkers),'*float32'];
if Nmarkers>0
tmpMKR = fread(fid,inf,reps,4*NanalogFramesPerVideoFrame*NanalogChannels); % note four bytes per analog channel data skipped
% Reshape/resize/reorder data
% First do the markers
tmpMKR = reshape(tmpMKR,Nmarkers*4,length(tmpMKR)./(4*Nmarkers)) ; % go from one long column to a 4xNMxNVF matrix
Markers = tmpMKR';
Markers(:,4:4:end)=[];% trim off the residual/camera contribution stuff%
else
Markers=ones(0,3)*nan;
end
waitbar(0.3,h)
% Get camera contribution/residual
if Nmarkers>0
a = fix(tmpMKR(4:4:end,:));
highbyte=fix(a/256);
lowbyte=a-highbyte*256;
CameraInfo=highbyte;
ResidualError=lowbyte*abs(Scale);
else
CameraInfo=nan;
ResidualError=nan;
end
waitbar(0.6,h)
if NanalogChannels > 0
% Read in analog data as repeated blocks
fseek(fid,(NrecordDataBlock-1)*512+4*4*Nmarkers,'bof');
reps = [int2str(NanalogFramesPerVideoFrame*NanalogChannels),'*float32'];
tmpANL = fread(fid,inf,reps,4*4*Nmarkers); % note: four bytes per 3d data skipped
% Reshape the analog data
AnalogSignals = reshape(tmpANL,NanalogChannels,length(tmpANL)/NanalogChannels)';
else
AnalogSignals = 0;
end
waitbar(1,h)
else
for i=1:NvideoFrames
for j=1:Nmarkers
Markers(i,3*j-2:3*j)=fread(fid,3,'int16')'.*Scale;
ResidualError(i,j)=fread(fid,1,'int8');
CameraInfo(i,j)=fread(fid,1,'int8');
end
waitbar(i/NvideoFrames,h)
for j=1:NanalogFramesPerVideoFrame,
AnalogSignals(j+NanalogFramesPerVideoFrame*(i-1),1:NanalogChannels)=...
fread(fid,NanalogChannels,'int16')';
end
end
end
close(h) % waitbar
fclose(fid);
I = 1; J = 1;
while ~strcmp(ParameterGroup(I).name, 'POINT');
I = I+1;
end
while ~strcmp(ParameterGroup(I).Parameter(J).name, 'LABELS');
J = J+1;
end
MLabels = ParameterGroup(I).Parameter(J).data;
% Get details about analog data
I = 1; J = 1;
while ~strcmp(ParameterGroup(I).name, 'ANALOG');
I = I+1;
end
for J = 1:length(ParameterGroup(I).Parameter),
category = upper(ParameterGroup(I).Parameter(J).name);
switch category{1}
case 'GEN_SCALE'
gen_scale = ParameterGroup(I).Parameter(J).data;
case 'SCALE'
scales = ParameterGroup(I).Parameter(J).data;
case 'OFFSET'
offsets = ParameterGroup(I).Parameter(J).data;
case 'LABELS'
ALabels = ParameterGroup(I).Parameter(J).data;
case 'UNITS'
AUnits = ParameterGroup(I).Parameter(J).data;
end
end
% number of analog frames and individual signals
[nAF, nAS] = size(AnalogSignals);
% Apply the appropriate scaling and offsets to convert analog voltage to
% appropriate units
if ~isempty(offsets)
if nAS
offsets = offsets(1:nAS);
scales = scales(1:nAS);
AnalogSignals = (AnalogSignals-ones(nAF, 1)*offsets').*(ones(nAF, 1)*scales')*gen_scale;
end
if nargin > 2,
if ~isempty(varargin{2}),
offInds = varargin{2};
offSignals = AnalogSignals(:,offInds);
% super smooth and rectify the data
offSignals = abs(smooth(offSignals, 10, AnalogFrameRate));
dOffSignals = deriv(offSignals,1/AnalogFrameRate);
% Use a 2% threshold
thresh = 0.02*max(dOffSignals);
for I = 1:length(offInds),
% find the starting index where data begins
startInd = min(find(dOffSignals(:,I) >= thresh(I)));
background = mean(AnalogSignals(1:startInd,offInds(I)));
AnalogSignals(:,offInds(I)) = AnalogSignals(:,offInds(I))-background;
end
end
end
else
AnalogSignals=[];
end
% ======================
% end readc3D.m
  댓글 수: 1
Walter Roberson
Walter Roberson 2021년 3월 21일
How are you calling the function ?

댓글을 달려면 로그인하십시오.

답변(2개)

Prudhvi Peddagoni
Prudhvi Peddagoni 2021년 3월 25일
Hi,
You can keep breakpoints at certain lines of the code and execute it. That way you can debug the code and see what data each variable holds at that line.
Hope this helps.

Sjoerd
Sjoerd 2021년 3월 25일
Hi Lissa,
I would move the following code to outside of teh function (in general, don't have paths and filenames inside functions!!)
map = '/MATLAB Drive/BIOMECH/C3D Data/'; % map met C3D data
cond = {'Sit_HR_Trial0','Sit_MR_Trial0','Sup_HR_Trial0','Sup_MR_Trial0'}; % Condities van testopstelling (Sit_HR Sit_MR ..)
addpath('/MATLAB Drive/BIOMECH/Functions')
map_out = '/MATLAB Drive/BIOMECH/TRC Caren files/' % map waar je data wilt opslaan
for i = 1:length(cond)
for j = 1
FullFileName = [map, char(cond(i)),num2str(j),'.c3d']
end
end
outside of the function. Then you want this last part to load the C3d file, per condition, so taht would be:
for i = 1:length(cond)
for j = 1
FullFileName = [map, char(cond(i)),num2str(j),'.c3d']
[Markers,MLabels,VideoFrameRate,AnalogSignals,ALabels,AUnits,AnalogFrameRate,Event,ParameterGroup,CameraInfo]=...
readC3D(FullFileName)
% and then do you calculations here.
end
end
which would load each of your files, do calculations, and then move on to the next one.
As a personn that did some editting (and knows how the function works) you can also contact me directly. You should be able to find my email adress online.

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