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abfload.m
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function [d,si,h]=abfload(fn,varargin)
% ** function [d,si,h]=abfload(fn,varargin)
% loads and returns data in ABF (Axon Binary File) format.
% Data may have been acquired in the following modes:
% (1) event-driven variable-length (currently only abf versions < 2.0)
% (2) event-driven fixed-length or waveform-fixed length
% (3) gap-free
% Information about scaling, the time base and the number of channels and
% episodes is extracted from the header of the abf file.
%
% OPERATION
% If the second input variable is the char array 'info' as in
% [d,si,h]=abfload('d:\data01.abf','info')
% abfload will not load any data but return detailed information (header
% parameters) on the file in output variable h. d and si will be empty.
% In all other cases abfload will load data. Optional input parameters
% listed below (= all except the file name) must be specified as
% parameter/value pairs, e.g. as in
% d=abfload('d:\data01.abf','start',100,'stop','e');
%
% >>> INPUT VARIABLES >>>
% NAME TYPE, DEFAULT DESCRIPTION
% fn char array abf data file name
% start scalar, 0 only gap-free-data: start of cutout to be
% read (unit: s)
% stop scalar or char, only gap-free-data: end of cutout to be
% 'e' read (unit: sec). May be set to 'e' (end
% of file).
% sweeps 1d-array or char, only episodic data: sweep numbers to be
% 'a' read. By default, all sweeps will be read
% ('a').
% channels cell array names of channels to be read, like
% or char, 'a' {'IN 0','IN 8'} (make sure spelling is
% 100% correct, including blanks). If set
% to 'a', all channels will be read.
% *****************************************
% NOTE: channel order in output variable d
% ignores the order in 'channels', and
% instead always matches the order inherent
% to the abf file, to be retrieved in
% output variable h!
% *****************************************
% chunk scalar, 0.05 only gap-free-data: the elementary chunk
% size (megabytes) to be used for the
% 'discontinuous' mode of reading data
% (fewer channels to be read than exist)
% machineF char array, the 'machineformat' input parameter of the
% 'ieee-le' matlab fopen function. 'ieee-le' is the
% correct option for windows; depending on
% the platform the data were recorded/shall
% be read by abfload 'ieee-be' is the
% alternative.
% doDispInfo logical, true if true, information on the loaded file
% will be put out to console (if false,
% only ínformation on erroneous input will
% be displayed)
% << OUTPUT VARIABLES <<<
% NAME TYPE DESCRIPTION
% d the data read, the format depending on the record-
% ing mode
% 1. GAP-FREE:
% 2d array 2d array of size
% <data pts> by <number of chans>
% Examples of access:
% d(:,2) data from channel 2 at full length
% d(1:100,:) first 100 data points from all channels
% 2. EPISODIC FIXED-LENGTH/WAVEFORM FIXED-LENGTH/HIGH-SPEED OSCILLOSCOPE:
% 3d array 3d array of size
% <data pts per sweep> by <number of chans> by <number
% of sweeps>.
% Examples of access:
% d(:,2,:) a matrix containing all episodes
% (at full length) of the second
% channel in its columns
% d(1:200,:,[1 11]) contains first 200 data points of
% episodes 1 and 11 of all channels
% 3. EPISODIC VARIABLE-LENGTH:
% cell array cell array whose elements correspond to single sweeps.
% Each element is a (regular) array of size
% <data pts per sweep> by <number of chans>
% Examples of access:
% d{1} a 2d-array which contains episode 1
% (all of it, all channels)
% d{2}(1:100,2) a 1d-array containing the first 100
% data points of channel 2 in episode 1
% si scalar the sampling interval in us
% h struct information on file (selected header parameters)
%
% CONTRIBUTORS
% Original version by Harald Hentschke ([email protected])
% Extended to abf version 2.0 by Forrest Collman ([email protected])
% pvpmod.m by Ulrich Egert ([email protected])
% Small patch to avoid error caused by activated HumSilencer by Michael Rabenstein ([email protected])
% -------------------------------------------------------------------------
% PART 1: check of input vars
% -------------------------------------------------------------------------
% --- defaults
% gap-free
start=0.0;
stop='e';
% episodic
sweeps='a';
% general
channels='a';
% the size of data chunks (see above) in Mb. 0.05 Mb is an empirical value
% which works well for abf with 6-16 channels and recording durations of
% 5-30 min
chunk=0.05;
machineF='ieee-le';
doDispInfo=true;
% if first and only optional input argument is string 'info' the user's
% request is to obtain information on the file (header parameters), so set
% flag accordingly
if nargin==2 && ischar(varargin{1}) && strcmp('info',varargin{1})
doLoadData=false;
% if no output argument is requested assume that the user would like to
% obtain some basic information on the file on the command window, so
% leave doDispInfo at its default (true value). Do the same if only one
% output arg is specified (which is most certainly done inadvertently
% because in 'info' mode this will be an empty array). In all other cases
% assume that text output is not required so suppress it
if nargout>1
doDispInfo=false;
end
else
doLoadData=true;
% assign values of optional input parameters if any were given
pvpmod(varargin);
end
% some constants
BLOCKSIZE=512;
% output variables
d=[];
si=[];
h=[];
if ischar(stop)
if ~strcmpi(stop,'e')
error('input parameter ''stop'' must be specified as ''e'' (=end of recording) or as a scalar');
end
end
% check existence of file
if ~exist(fn,'file')
error(['could not find file ' fn]);
end
% -------------------------------------------------------------------------
% PART 2a: determine abf version
% -------------------------------------------------------------------------
dispif(doDispInfo,['opening ' fn '..']);
[fid,messg]=fopen(fn,'r',machineF);
if fid == -1
error(messg);
end
% on the occasion, determine absolute file size
fseek(fid,0,'eof');
fileSz=ftell(fid);
fseek(fid,0,'bof');
% *** read value of parameter 'fFileSignature' (i.e. abf version) from header ***
sz=4;
[fFileSignature,n]=fread(fid,sz,'uchar=>char');
if n~=sz
fclose(fid);
error('something went wrong reading value(s) for fFileSignature');
end
% rewind
fseek(fid,0,'bof');
% transpose
fFileSignature=fFileSignature';
% one of the first checks must be whether file signature is valid
switch fFileSignature
case 'ABF ' % ** note the blank
% ************************
% abf version < 2.0
% ************************
case 'ABF2'
% ************************
% abf version >= 2.0
% ************************
otherwise
error('unknown or incompatible file signature');
end
% -------------------------------------------------------------------------
% PART 2b: define file information ('header' parameters) of interest
% -------------------------------------------------------------------------
% The list of header parameters created below (variable 'headPar') is
% derived from the abf version 1.8 header section. It is by no means
% exhaustive (i.e. there are many more parameters in abf files) but
% sufficient for proper upload, scaling and arrangement of data acquired
% under many conditons. Further below, these parameters will be made fields
% of struct h. h, which is also an output variable, is then used in PART 3,
% which does the actual job of uploading, scaling and rearranging the data.
% That part of the code relies on h having a certain set of fields
% irrespective of ABF version.
% Unfortunately, in the transition to ABF version 2.0 many of the header
% parameters were moved to different places within the abf file and/or
% given other names or completely restructured. In order for the code to
% work with pre- and post-2.0 data files, all parameters missing in the
% header must be gotten into h. This is accomplished in lines ~288 and
% following:
% if h.fFileVersionNumber>=2
% ...
% Furthermore,
% - h as an output from an ABF version < 2.0 file will not contain new
% parameters introduced into the header like 'nCRCEnable'
% - h will in any case contain a few 'home-made' fields that have
% proven to be useful. Some of them depend on the recording mode. Among
% the more or less self-explanatory ones are
% -- si sampling interval
% -- recChNames the names of all channels, e.g. 'IN 8',...
% -- dataPtsPerChan sample points per channel
% -- dataPts sample points in file
% -- recTime recording start and stop time in seconds from
% midnight (millisecond resolution)
% -- sweepLengthInPts sample points per sweep (one channel)
% -- sweepStartInPts the start times of sweeps in sample points
% (from beginning of recording)
% define header proper depending on ABF version by call to local function
headPar=define_header(fFileSignature);
% define all sections that there are
Sections=define_Sections;
% define a few of these (currently, only the TagInfo section is used for
% all versions of ABF, but that may change in the future)
ProtocolInfo=define_ProtocolInfo;
ADCInfo=define_ADCInfo;
TagInfo=define_TagInfo;
UserListInfo=define_UserListInfo;
EpochPerDACInfo=define_EpochPerDACInfo;
% -------------------------------------------------------------------------
% PART 2c: read parameters of interest
% -------------------------------------------------------------------------
% convert headPar to struct
s=cell2struct(headPar,{'name','offs','numType','value'},2);
numOfParams=size(s,1);
clear tmp headPar;
% convert names in structure to variables and read value from header
for g=1:numOfParams
if fseek(fid, s(g).offs,'bof')~=0
fclose(fid);
error(['something went wrong locating ' s(g).name]);
end
sz=length(s(g).value);
% use dynamic field names
[h.(s(g).name),n]=fread(fid,sz,s(g).numType);
if n~=sz
fclose(fid);
error(['something went wrong reading value(s) for ' s(g).name]);
end
end
% file signature needs to be transposed
h.fFileSignature=h.fFileSignature';
% several header parameters need a fix or version-specific refinement:
if strcmp(h.fFileSignature,'ABF2')
% h.fFileVersionNumber needs to be converted from an array of integers to
% a float
h.fFileVersionNumber=h.fFileVersionNumber(4)+h.fFileVersionNumber(3)*.1...
+h.fFileVersionNumber(2)*.001+h.fFileVersionNumber(1)*.0001;
% convert ms to s
h.lFileStartTime=h.uFileStartTimeMS*.001;
else
% h.fFileVersionNumber is a float32 the value of which is sometimes a
% little less than what it should be (e.g. 1.6499999 instead of 1.65)
h.fFileVersionNumber=.001*round(h.fFileVersionNumber*1000);
% in abf < 2.0 two parameters are needed to obtain the file start time
% with millisecond precision - let's integrate both into parameter
% lFileStartTime (unit: s) so that nFileStartMillisecs will not be needed
h.lFileStartTime=h.lFileStartTime+h.nFileStartMillisecs*.001;
end
if h.fFileVersionNumber>=2
% -----------------------------------------------------------------------
% *** read file information that has moved from the header section to
% other sections in ABF version >= 2.0 and assign selected values to
% fields of 'generic' header variable h ***
% -----------------------------------------------------------------------
% --- read in the Sections
Sects=cell2struct(Sections,{'name'},2);
numOfSections=length(Sections);
offset=76;
% this creates all sections (ADCSection, ProtocolSection, etc.)
for i=1:numOfSections
eval([Sects(i).name '=ReadSectionInfo(fid,offset);']);
offset=offset+4+4+8;
end
% --- read in the StringsSection and use some fields (to retrieve
% information on the names of recorded channels and the units as well as
% the recording protocol used)
fseek(fid,StringsSection.uBlockIndex*BLOCKSIZE,'bof');
BigString=fread(fid,StringsSection.uBytes,'char');
% extract path and name of protocol file (excluding drive letter):
% - find the first occurrence of a backslash in BigString
tmpIx1=strfind(lower(char(BigString)'),'\');
% - find '.pro' as this is the file extension of protocol files
tmpIx2=strfind(lower(char(BigString)'),'.pro');
% - extract everything in between and place in field of header struct h
if ~isempty(tmpIx1) && ~isempty(tmpIx2)
h.protocolName=char(BigString(tmpIx1:tmpIx2(1)+3))';
else
h.protocolName='protocol name could not be identified';
end
% this is a hack: determine where either of strings 'clampex',
% 'clampfit', 'axoscope' or patchxpress' begin
progString={'clampex','clampfit','axoscope','patchxpress'};
goodstart=[];
for i=1:numel(progString)
goodstart=cat(1,goodstart,strfind(lower(char(BigString)'),progString{i}));
end
if isempty(goodstart)
error('problems in StringsSection: unrecognized acquisition program');
end
BigString=BigString(goodstart(1):end)';
stringends=find(BigString==0);
stringends=[0 stringends];
Strings=cell(1,length(stringends)-1);
for i=1:length(stringends)-1
Strings{i}=char(BigString(stringends(i)+1:stringends(i+1)-1));
end
h.recChNames=cell(ADCSection.llNumEntries,1);
h.recChUnits=cell(ADCSection.llNumEntries,1);
% --- read in the ADCSection & copy some values to header h
for i=1:ADCSection.llNumEntries
ADCsec(i)=ReadSection(fid,ADCSection.uBlockIndex*BLOCKSIZE+ADCSection.uBytes*(i-1),ADCInfo);
ii=ADCsec(i).nADCNum+1;
h.nADCSamplingSeq(i)=ADCsec(i).nADCNum;
h.recChNames(i)=Strings(ADCsec(i).lADCChannelNameIndex);
unitsIndex=ADCsec(i).lADCUnitsIndex;
if unitsIndex>0
h.recChUnits(i)=Strings(ADCsec(i).lADCUnitsIndex);
else
h.recChUnits(i)={'nil'};
end
h.nTelegraphEnable(ii)=ADCsec(i).nTelegraphEnable;
h.fTelegraphAdditGain(ii)=ADCsec(i).fTelegraphAdditGain;
h.fInstrumentScaleFactor(ii)=ADCsec(i).fInstrumentScaleFactor;
h.fSignalGain(ii)=ADCsec(i).fSignalGain;
h.fADCProgrammableGain(ii)=ADCsec(i).fADCProgrammableGain;
h.fInstrumentOffset(ii)=ADCsec(i).fInstrumentOffset;
h.fSignalOffset(ii)=ADCsec(i).fSignalOffset;
end
% --- read in the protocol section & copy some values to header h
ProtocolSec=ReadSection(fid,ProtocolSection.uBlockIndex*BLOCKSIZE,ProtocolInfo);
h.nOperationMode=ProtocolSec.nOperationMode;
h.fSynchTimeUnit=ProtocolSec.fSynchTimeUnit;
h.lNumSamplesPerEpisode=ProtocolSec.lNumSamplesPerEpisode;
h.nADCNumChannels=ADCSection.llNumEntries;
h.lActualAcqLength=DataSection.llNumEntries;
h.lDataSectionPtr=DataSection.uBlockIndex;
h.nNumPointsIgnored=0;
% in ABF version < 2.0 h.fADCSampleInterval is the sampling interval
% defined as
% 1/(sampling freq*number_of_channels)
% so divide ProtocolSec.fADCSequenceInterval by the number of
% channels
h.fADCSampleInterval=ProtocolSec.fADCSequenceInterval/h.nADCNumChannels;
h.fADCRange=ProtocolSec.fADCRange;
h.lADCResolution=ProtocolSec.lADCResolution;
% --- read in the Epoch section, rearrange values and place in header
% struct h
for i=1:EpochPerDACSection.llNumEntries
EPDsec(i)=ReadSection(fid,EpochPerDACSection.uBlockIndex*BLOCKSIZE+EpochPerDACSection.uBytes*(i-1),EpochPerDACInfo);
end
if EpochPerDACSection.llNumEntries>0
% number of analog output (AO) channels
uniqueAO=unique([EPDsec.nDACNum]);
for k=1:numel(uniqueAO)
% index to elements of EDPsec dealing with current AO channel
ix=[EPDsec.nDACNum]==uniqueAO(k);
% struct DACEpoch contains one element per AO channel; the values of
% its fields represent the values of the different epochs (columns
% labeled A, B and so on in the waveform tab in clampex), the only
% exception being the numeric index of the channel
h.DACEpoch(k).nDACNum=uniqueAO(k);
% compute the 'first/last holding' values, the small additional delay
% after which stimulation waveforms are put out. The unit is sample
% points. ** NOTE: the formula below is based on
% i) code in function ABFH_GetHoldingDuration in abfhwave.cpp,
% presumably a code file belonging to an early version of program
% 'stimfit', and presumably derived from code available back then
% from the company formerly known as Axon Instruments
% ii) heuristics, determined from a number of abf V. 2.00 files from
% different labs in all of which 16/8-channel ADC/DAC systems were
% used.
% The formula may be hardware dependent; it may change (=be
% corrected, should it not be general) in the future.
h.DACEpoch(k).firstHolding=floor(...
8*(h.lNumSamplesPerEpisode/h.nADCNumChannels)/512);
fieldNm=setdiff(fieldnames(EPDsec),'nDACNum','stable');
for fIx=1:numel(fieldNm)
h.DACEpoch(k).(fieldNm{fIx})=[EPDsec(ix).(fieldNm{fIx})];
end
end
else
h.DACEpoch=[];
end
% --- read in the user list section - unclear how to get the values
% (commented code lines below are a first guess)
UserListSec=ReadSection(fid,UserListSection.uBlockIndex*BLOCKSIZE,UserListInfo);
% fseek(fid,UserListSec.lULParamValueListIndex*BLOCKSIZE,'bof');
% nada=fread(fid,100,'uchar=>char')
% --- in contrast to procedures with all other sections do not read the
% sync array section but rather copy the values of its fields to the
% corresponding fields of h
h.lSynchArrayPtr=SynchArraySection.uBlockIndex;
h.lSynchArraySize=SynchArraySection.llNumEntries;
else
% -------------------------------------------------------------------------
% *** here, do the inverse: in ABF version<2 files extract information
% from header variable h and place it in corresponding new section
% variable(s)
% -------------------------------------------------------------------------
TagSection.llNumEntries=h.lNumTagEntries;
TagSection.uBlockIndex=h.lTagSectionPtr;
TagSection.uBytes=64;
end
% -------------------------------------------------------------------------
% PART 2d: groom parameters & perform some plausibility checks
% -------------------------------------------------------------------------
if h.lActualAcqLength<h.nADCNumChannels
fclose(fid);
error('less data points than sampled channels in file');
end
% the numerical value of all recorded channels (numbers 0..15)
recChIdx=h.nADCSamplingSeq(1:h.nADCNumChannels);
% the corresponding indices into loaded data d
recChInd=1:length(recChIdx);
if h.fFileVersionNumber<2
% the channel names, e.g. 'IN 8' (for ABF version 2.0 these have been
% extracted above at this point)
h.recChNames=(reshape(char(h.sADCChannelName),10,16))';
h.recChNames=h.recChNames(recChIdx+1,:);
% same with signal units
h.recChUnits=(reshape(char(h.sADCUnits),8,16))';
h.recChUnits=h.recChUnits(recChIdx+1,:);
% convert to cell arrays
h.recChNames=deblank(cellstr(h.recChNames));
h.recChUnits=deblank(cellstr(h.recChUnits));
end
% check whether requested channels exist
chInd=[];
eflag=0;
if ischar(channels)
if strcmp(channels,'a')
chInd=recChInd;
else
fclose(fid);
error('input parameter ''channels'' must either be a cell array holding channel names or the single character ''a'' (=all channels)');
end
else
% check for requested channels which do not exist
missingChan=setdiff(channels,h.recChNames);
% identify requested channels among available ones
[nil,chInd]=intersect(h.recChNames,channels);
% ** index chInd must be sorted because intersect sorts h.recChNames
% alphanumerically, which needs not necessarily correspond to the order
% inherent in the abf file (e.g. if channels are named 'Lynx1 ... Lynx10
% etc.)
chInd=sort(chInd);
if isempty(chInd) || ~isempty(missingChan)
% set error flag to 1
eflag=1;
end
end
if eflag
fclose(fid);
disp('**** available channels:');
disp(h.recChNames);
disp(' ');
disp('**** requested channels:');
disp(channels);
error('at least one of the requested channels does not exist in data file (see above)');
else
dispif(doDispInfo,'**** available channels:');
dispif(doDispInfo,h.recChNames);
end
% gain of telegraphed instruments, if any
if h.fFileVersionNumber>=1.65
addGain=h.nTelegraphEnable.*h.fTelegraphAdditGain;
addGain(addGain==0)=1;
else
addGain=ones(size(h.fTelegraphAdditGain));
end
% determine offset at which data start
switch h.nDataFormat
case 0
dataSz=2; % bytes/point
precision='int16';
case 1
dataSz=4; % bytes/point
precision='float32';
otherwise
fclose(fid);
error('invalid number format');
end
headOffset=h.lDataSectionPtr*BLOCKSIZE+h.nNumPointsIgnored*dataSz;
% h.fADCSampleInterval is the TOTAL sampling interval
h.si=h.fADCSampleInterval*h.nADCNumChannels;
% assign same value to si, which is an output variable
si=h.si;
if ischar(sweeps) && sweeps=='a'
nSweeps=h.lActualEpisodes;
sweeps=1:h.lActualEpisodes;
else
nSweeps=length(sweeps);
end
% determine time unit in synch array section
switch h.fSynchTimeUnit
case 0
% time information in synch array section is in terms of ticks
h.synchArrTimeBase=1;
otherwise
% time information in synch array section is in terms of usec
h.synchArrTimeBase=h.fSynchTimeUnit;
end
% read in the TagSection, do a few computations & write to h.tags
h.tags=[];
for i=1:TagSection.llNumEntries
tmp=ReadSection(fid,TagSection.uBlockIndex*BLOCKSIZE+TagSection.uBytes*(i-1),TagInfo);
% time of tag entry from start of experiment in s (corresponding expisode
% number, if applicable, will be determined later)
h.tags(i).timeSinceRecStart=tmp.lTagTime*h.synchArrTimeBase/1e6;
h.tags(i).comment=char(tmp.sComment)';
end
% -------------------------------------------------------------------------
% PART 3: read data (note: from here on code is generic and abf version
% should not matter)
% -------------------------------------------------------------------------
switch h.nOperationMode
case 1
dispif(doDispInfo,'data were acquired in event-driven variable-length mode');
if h.fFileVersionNumber>=2.0
errordlg('abfload currently does not work with data acquired in event-driven variable-length mode and ABF version 2.0','ABF version issue');
else
if (h.lSynchArrayPtr<=0 || h.lSynchArraySize<=0)
fclose(fid);
error('internal variables ''lSynchArraynnn'' are zero or negative');
end
% the byte offset at which the SynchArraySection starts
h.lSynchArrayPtrByte=BLOCKSIZE*h.lSynchArrayPtr;
% before reading Synch Arr parameters check if file is big enough to hold them
% 4 bytes/long, 2 values per episode (start and length)
if h.lSynchArrayPtrByte+2*4*h.lSynchArraySize<fileSz
fclose(fid);
error('file seems not to contain complete Synch Array Section');
end
if fseek(fid,h.lSynchArrayPtrByte,'bof')~=0
fclose(fid);
error('something went wrong positioning file pointer to Synch Array Section');
end
[synchArr,n]=fread(fid,h.lSynchArraySize*2,'int32');
if n~=h.lSynchArraySize*2
fclose(fid);
error('something went wrong reading synch array section');
end
% make synchArr a h.lSynchArraySize x 2 matrix
synchArr=permute(reshape(synchArr',2,h.lSynchArraySize),[2 1]);
% the length of episodes in sample points
segLengthInPts=synchArr(:,2)/h.synchArrTimeBase;
% the starting ticks of episodes in sample points WITHIN THE DATA FILE
segStartInPts=cumsum([0 (segLengthInPts(1:end-1))']*dataSz)+headOffset;
% start time (synchArr(:,1)) has to be divided by h.nADCNumChannels to get true value
% go to data portion
if fseek(fid,headOffset,'bof')~=0
fclose(fid);
error('something went wrong positioning file pointer (too few data points ?)');
end
% ** load data if requested
if doLoadData
d=cell(1,nSweeps);
for i=1:nSweeps
% if selected sweeps are to be read, seek correct position
if ~isequal(nSweeps,h.lActualEpisodes)
fseek(fid,segStartInPts(sweeps(i)),'bof');
end
[tmpd,n]=fread(fid,segLengthInPts(sweeps(i)),precision);
if n~=segLengthInPts(sweeps(i))
warning(['something went wrong reading episode ' int2str(sweeps(i)) ': ' segLengthInPts(sweeps(i)) ' points should have been read, ' int2str(n) ' points actually read']);
end
h.dataPtsPerChan=n/h.nADCNumChannels;
if rem(n,h.nADCNumChannels)>0
fclose(fid);
error('number of data points in episode not OK');
end
% separate channels..
tmpd=reshape(tmpd,h.nADCNumChannels,h.dataPtsPerChan);
% retain only requested channels
tmpd=tmpd(chInd,:);
tmpd=tmpd';
% if data format is integer, scale appropriately; if it's float, tmpd is fine
if ~h.nDataFormat
for j=1:length(chInd)
ch=recChIdx(chInd(j))+1;
tmpd(:,j)=tmpd(:,j)/(h.fInstrumentScaleFactor(ch)*h.fSignalGain(ch)*h.fADCProgrammableGain(ch)*addGain(ch))...
*h.fADCRange/h.lADCResolution+h.fInstrumentOffset(ch)-h.fSignalOffset(ch);
end
end
% now place in cell array, an element consisting of one sweep with channels in columns
d{i}=tmpd;
end
end
end
case {2,4,5}
if h.nOperationMode==2
dispif(doDispInfo,'data were acquired in event-driven fixed-length mode');
elseif h.nOperationMode==4
dispif(doDispInfo,'data were acquired in high-speed oscilloscope mode');
else
dispif(doDispInfo,'data were acquired in waveform fixed-length mode');
end
% extract timing information on sweeps
if (h.lSynchArrayPtr<=0 || h.lSynchArraySize<=0)
fclose(fid);
error('internal variables ''lSynchArraynnn'' are zero or negative');
end
% the byte offset at which the SynchArraySection starts
h.lSynchArrayPtrByte=BLOCKSIZE*h.lSynchArrayPtr;
% before reading Synch Arr parameters check if file is big enough to hold them
% 4 bytes/long, 2 values per episode (start and length)
if h.lSynchArrayPtrByte+2*4*h.lSynchArraySize>fileSz
fclose(fid);
error('file seems not to contain complete Synch Array Section');
end
if fseek(fid,h.lSynchArrayPtrByte,'bof')~=0
fclose(fid);
error('something went wrong positioning file pointer to Synch Array Section');
end
[synchArr,n]=fread(fid,h.lSynchArraySize*2,'int32');
if n~=h.lSynchArraySize*2
fclose(fid);
error('something went wrong reading synch array section');
end
% make synchArr a h.lSynchArraySize x 2 matrix
synchArr=permute(reshape(synchArr',2,h.lSynchArraySize),[2 1]);
if numel(unique(synchArr(:,2)))>1
fclose(fid);
error('sweeps of unequal length in file recorded in fixed-length mode');
end
% the length of sweeps in sample points (**note: parameter lLength of
% the ABF synch section is expressed in samples (ticks) whereas
% parameter lStart is given in synchArrTimeBase units)
h.sweepLengthInPts=synchArr(1,2)/h.nADCNumChannels;
% the starting ticks of episodes in sample points (t0=1=beginning of
% recording)
h.sweepStartInPts=synchArr(:,1)*(h.synchArrTimeBase/h.fADCSampleInterval/h.nADCNumChannels);
% recording start and stop times in seconds from midnight
h.recTime=h.lFileStartTime;
h.recTime=h.recTime+[0 (1e-6*(h.sweepStartInPts(end)+h.sweepLengthInPts))*h.fADCSampleInterval*h.nADCNumChannels];
% determine first point and number of points to be read
startPt=0;
h.dataPts=h.lActualAcqLength;
h.dataPtsPerChan=h.dataPts/h.nADCNumChannels;
if rem(h.dataPts,h.nADCNumChannels)>0 || rem(h.dataPtsPerChan,h.lActualEpisodes)>0
fclose(fid);
error('number of data points not OK');
end
% temporary helper var
dataPtsPerSweep=h.sweepLengthInPts*h.nADCNumChannels;
if fseek(fid,startPt*dataSz+headOffset,'bof')~=0
fclose(fid);
error('something went wrong positioning file pointer (too few data points ?)');
end
% the starting ticks of episodes in sample points WITHIN THE DATA FILE
selectedSegStartInPts=((sweeps-1)*dataPtsPerSweep)*dataSz+headOffset;
% ** load data if requested
if doLoadData
% preallocate d
d=zeros(h.sweepLengthInPts,length(chInd),nSweeps);
for i=1:nSweeps
status=fseek(fid,selectedSegStartInPts(i),'bof');
if status==-1
fclose(fid);
error(['something went wrong reading episode ' int2str(sweeps(i)) '; file pointer beyond file limits (check sweeps)']);
end
[tmpd,n]=fread(fid,dataPtsPerSweep,precision);
if n~=dataPtsPerSweep
fclose(fid);
error(['something went wrong reading episode ' int2str(sweeps(i)) ': ' dataPtsPerSweep ' points should have been read, ' int2str(n) ' points actually read']);
end
h.dataPtsPerChan=n/h.nADCNumChannels;
if rem(n,h.nADCNumChannels)>0
fclose(fid);
error('number of data points in episode not OK');
end
% separate channels..
tmpd=reshape(tmpd,h.nADCNumChannels,h.dataPtsPerChan);
% retain only requested channels
tmpd=tmpd(chInd,:);
tmpd=tmpd';
% if data format is integer, scale appropriately; if it's float, d is fine
if ~h.nDataFormat
for j=1:length(chInd)
ch=recChIdx(chInd(j))+1;
tmpd(:,j)=tmpd(:,j)/(h.fInstrumentScaleFactor(ch)*h.fSignalGain(ch)*h.fADCProgrammableGain(ch)*addGain(ch))...
*h.fADCRange/h.lADCResolution+h.fInstrumentOffset(ch)-h.fSignalOffset(ch);
end
end
% now fill 3d array
d(:,:,i)=tmpd;
end
end
case 3
dispif(doDispInfo,'data were acquired in gap-free mode');
% from start, stop, headOffset and h.fADCSampleInterval calculate first point to be read
% and - unless stop is given as 'e' - number of points
startPt=floor(1e6*start*(1/h.fADCSampleInterval));
% this corrects undesired shifts in the reading frame due to rounding errors in the previous calculation
startPt=floor(startPt/h.nADCNumChannels)*h.nADCNumChannels;
% if stop is a char array, it can only be 'e' at this point (other values would have
% been caught above)
if ischar(stop)
h.dataPtsPerChan=h.lActualAcqLength/h.nADCNumChannels-floor(1e6*start/h.si);
h.dataPts=h.dataPtsPerChan*h.nADCNumChannels;
else
h.dataPtsPerChan=floor(1e6*(stop-start)*(1/h.si));
h.dataPts=h.dataPtsPerChan*h.nADCNumChannels;
if h.dataPts<=0
fclose(fid);
error('start is larger than or equal to stop');
end
end
if rem(h.dataPts,h.nADCNumChannels)>0
fclose(fid);
error('number of data points not OK');
end
tmp=1e-6*h.lActualAcqLength*h.fADCSampleInterval;
dispif(doDispInfo,['total length of recording: ' num2str(tmp,'%5.1f') ' s ~ ' num2str(tmp/60,'%3.0f') ' min']);
dispif(doDispInfo,['sampling interval: ' num2str(h.si,'%5.0f') ' µs']);
% 8 bytes per data point expressed in Mb
dispif(doDispInfo,['memory requirement for complete upload in matlab: '...
num2str(round(8*h.lActualAcqLength/2^20)) ' MB']);
% recording start and stop times in seconds from midnight
h.recTime=h.lFileStartTime;
h.recTime=[h.recTime h.recTime+tmp];
if fseek(fid,startPt*dataSz+headOffset,'bof')~=0
fclose(fid);
error('something went wrong positioning file pointer (too few data points ?)');
end
if doLoadData
% *** decide on the most efficient way to read data:
% (i) all (of one or several) channels requested: read, done
% (ii) one (of many) channels requested: use the 'skip' feature of
% fread (which for up to 16 channels is slower than scenario iii below)
% (iii) more than one but not all (of several) channels requested:
% 'discontinuous' mode of reading data. Read a reasonable chunk of data
% (all channels), separate channels, discard non-requested ones (if
% any), place data in preallocated array, repeat until done. This is
% faster than reading the data in one big lump, separating channels and
% discarding the ones not requested
if length(chInd)==1 && h.nADCNumChannels>16
% --- situation (ii)
% jump to proper reading frame position in file
if fseek(fid,(chInd-1)*dataSz,'cof')~=0
fclose(fid);
error('something went wrong positioning file pointer (too few data points ?)');
end
% read, skipping h.nADCNumChannels-1 data points after each read
[d,n]=fread(fid,h.dataPtsPerChan,precision,dataSz*(h.nADCNumChannels-1));
if n~=h.dataPtsPerChan
fclose(fid);
error(['something went wrong reading file (' int2str(h.dataPtsPerChan) ' points should have been read, ' int2str(n) ' points actually read']);
end
elseif length(chInd)/h.nADCNumChannels<1
% --- situation (iii)
% prepare chunkwise upload:
% preallocate d
d=nan(h.dataPtsPerChan,length(chInd));
% the number of data points corresponding to the maximal chunk size,
% rounded off such that from each channel the same number of points is
% read (do not forget that each data point will by default be made a
% double of 8 bytes, no matter what the original data format is)
chunkPtsPerChan=floor(chunk*2^20/8/h.nADCNumChannels);
chunkPts=chunkPtsPerChan*h.nADCNumChannels;
% the number of those chunks..
nChunk=floor(h.dataPts/chunkPts);
% ..and the remainder
restPts=h.dataPts-nChunk*chunkPts;
restPtsPerChan=restPts/h.nADCNumChannels;
% chunkwise row indices into d
dix=(1:chunkPtsPerChan:h.dataPtsPerChan)';
dix(:,2)=dix(:,1)+chunkPtsPerChan-1;
dix(end,2)=h.dataPtsPerChan;
if nChunk
dispif(doDispInfo,['reading file in ' int2str(nChunk) ' chunks of ~' num2str(chunk) ' Mb']);
end
% do it: if no remainder exists loop through all rows of dix,
% otherwise spare last row for the lines below (starting with
% 'if restPts')
for ci=1:size(dix,1)-(restPts>0)
[tmpd,n]=fread(fid,chunkPts,precision);
if n~=chunkPts
fclose(fid);
error(['something went wrong reading chunk #' int2str(ci) ' (' ...
int2str(chunkPts) ' points should have been read, ' int2str(n) ' points actually read']);
end
% separate channels..
tmpd=reshape(tmpd,h.nADCNumChannels,chunkPtsPerChan);
d(dix(ci,1):dix(ci,2),:)=tmpd(chInd,:)';
end
% collect the rest, if any
if restPts
[tmpd,n]=fread(fid,restPts,precision);
if n~=restPts
fclose(fid);
error(['something went wrong reading last chunk (' ...
int2str(restPts) ' points should have been read, ' int2str(n) ' points actually read']);
end
% separate channels..
tmpd=reshape(tmpd,h.nADCNumChannels,restPtsPerChan);
d(dix(end,1):dix(end,2),:)=tmpd(chInd,:)';
end
else
% --- situation (i)
[d,n]=fread(fid,h.dataPts,precision);
if n~=h.dataPts
fclose(fid);
error(['something went wrong reading file (' int2str(h.dataPts) ' points should have been read, ' int2str(n) ' points actually read']);
end
% separate channels..
d=reshape(d,h.nADCNumChannels,h.dataPtsPerChan);
d=d';
end
% if data format is integer, scale appropriately; if it's float, d is fine
if ~h.nDataFormat
for j=1:length(chInd)
ch=recChIdx(chInd(j))+1;
d(:,j)=d(:,j)/(h.fInstrumentScaleFactor(ch)*h.fSignalGain(ch)*h.fADCProgrammableGain(ch)*addGain(ch))...
*h.fADCRange/h.lADCResolution+h.fInstrumentOffset(ch)-h.fSignalOffset(ch);
end
end
end
otherwise
warning('unknown recording mode -- returning empty matrix');
d=[];
h.si=[];
end
fclose(fid);
% finally, possibly add information on episode number to tags
%Modified by MR to avoid error caused by activated HumSilencer
if ~isempty(h.tags) && isfield(h,'sweepStartInPts')
for i=1:numel(h.tags)
if h.tags(i).timeSinceRecStart > 0 %Comments added during recording
tmp=find(h.tags(i).timeSinceRecStart>=h.sweepStartInPts/1e6*h.si);
h.tags(i).episodeIndex=tmp(end);
elseif h.tags(i).timeSinceRecStart == 0 %HumSilencer comment at timeSinceRecStart = 0
h.tags(i).episodeIndex = 0; %Will be added to episode 0
end
end
end
% ########################################################################
% LOCAL FUNCTIONS
% ########################################################################
function headPar=define_header(fileSig)
switch fileSig
case 'ABF ' % ** note the blank
% ************************
% abf version < 2.0
% ************************
%
% temporary initializing var
tmp=repmat(-1,1,16);
% define vital header parameters and initialize them with -1: set up a
% cell array (and convert it to a struct later on, which is more
% convenient)
% column order is
% name, position in header in bytes, type, value)
headPar={
'fFileSignature',0,'*char',[-1 -1 -1 -1];
'fFileVersionNumber',4,'float32',-1;
'nOperationMode',8,'int16',-1;
'lActualAcqLength',10,'int32',-1;
'nNumPointsIgnored',14,'int16',-1;
'lActualEpisodes',16,'int32',-1;
'lFileStartTime',24,'int32',-1;
'lDataSectionPtr',40,'int32',-1;
'lTagSectionPtr',44,'int32',-1;
'lNumTagEntries',48,'int32',-1;
'lSynchArrayPtr',92,'int32',-1;
'lSynchArraySize',96,'int32',-1;
'nDataFormat',100,'int16',-1;
'nADCNumChannels', 120, 'int16', -1;
'fADCSampleInterval',122,'float', -1;
'fSynchTimeUnit',130,'float',-1;
'lNumSamplesPerEpisode',138,'int32',-1;
'lPreTriggerSamples',142,'int32',-1;
'lEpisodesPerRun',146,'int32',-1;
'fADCRange', 244, 'float', -1;
'lADCResolution', 252, 'int32', -1;
'nFileStartMillisecs', 366, 'int16', -1;
'nADCPtoLChannelMap', 378, 'int16', tmp;
'nADCSamplingSeq', 410, 'int16', tmp;
'sADCChannelName',442, 'uchar', repmat(tmp,1,10);
'sADCUnits',602, 'uchar', repmat(tmp,1,8);
'fADCProgrammableGain', 730, 'float', tmp;
'fInstrumentScaleFactor', 922, 'float', tmp;
'fInstrumentOffset', 986, 'float', tmp;
'fSignalGain', 1050, 'float', tmp;
'fSignalOffset', 1114, 'float', tmp;
'nTelegraphEnable',4512,'int16',tmp;
'fTelegraphAdditGain',4576,'float',tmp
};
case 'ABF2'
% ************************
% abf version >= 2.0
% ************************
headPar={
'fFileSignature',0,'*char',[-1 -1 -1 -1];
'fFileVersionNumber',4,'bit8=>int',[-1 -1 -1 -1];
'uFileInfoSize',8,'uint32',-1;
'lActualEpisodes',12,'uint32',-1;
'uFileStartDate',16','uint32',-1;
'uFileStartTimeMS',20,'uint32',-1;
'uStopwatchTime',24,'uint32',-1;
'nFileType',28,'int16',-1;
'nDataFormat',30,'int16',-1;
'nSimultaneousScan',32,'int16',-1;
'nCRCEnable',34,'int16',-1;
'uFileCRC',36,'uint32',-1;
'FileGUID',40,'uint32',-1;
'uCreatorVersion',56,'uint32',-1;
'uCreatorNameIndex',60,'uint32',-1;
'uModifierVersion',64,'uint32',-1;
'uModifierNameIndex',68,'uint32',-1;
'uProtocolPathIndex',72,'uint32',-1;
};
end
function Sections=define_Sections
Sections={'ProtocolSection';
'ADCSection';
'DACSection';
'EpochSection';
'ADCPerDACSection';
'EpochPerDACSection';
'UserListSection';
'StatsRegionSection';
'MathSection';
'StringsSection';
'DataSection';
'TagSection';
'ScopeSection';
'DeltaSection';
'VoiceTagSection';
'SynchArraySection';
'AnnotationSection';
'StatsSection';
};
function ProtocolInfo=define_ProtocolInfo
ProtocolInfo={
'nOperationMode','int16',1;
'fADCSequenceInterval','float',1;
'bEnableFileCompression','bit1',1;
'sUnused1','char',3;
'uFileCompressionRatio','uint32',1;
'fSynchTimeUnit','float',1;
'fSecondsPerRun','float',1;
'lNumSamplesPerEpisode','int32',1;
'lPreTriggerSamples','int32',1;
'lEpisodesPerRun','int32',1;
'lRunsPerTrial','int32',1;
'lNumberOfTrials','int32',1;
'nAveragingMode','int16',1;
'nUndoRunCount','int16',1;
'nFirstEpisodeInRun','int16',1;
'fTriggerThreshold','float',1;
'nTriggerSource','int16',1;
'nTriggerAction','int16',1;
'nTriggerPolarity','int16',1;
'fScopeOutputInterval','float',1;
'fEpisodeStartToStart','float',1;
'fRunStartToStart','float',1;
'lAverageCount','int32',1;
'fTrialStartToStart','float',1;
'nAutoTriggerStrategy','int16',1;
'fFirstRunDelayS','float',1;
'nChannelStatsStrategy','int16',1;
'lSamplesPerTrace','int32',1;