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Fix saveNSx to be able to load the saved file #50

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Fix saveNSx to be able to load the saved file #50

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32 changes: 25 additions & 7 deletions NPMK/NSx Utilities/saveNSx.m
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Original file line number Diff line number Diff line change
Expand Up @@ -9,18 +9,36 @@ function saveNSx(NSx,varargin)
% All arguments below are optional:
% Filename: A complete filepath for the output file.
% Default: CurrentFilename-Modified.NSx
% Filespec: Save the file using the filespec specified e.g. 2.3 or 3.0
% Default: same as the filespec loaded

%saveNSx version = '1.0.0.0';
%saveNSx version = '1.0.0.1';

% Version History
%
% 1.0.0.1:
% - Added ability to save to a specific filespec
%

%%
% Verify FilePath and establish overwrite paramaters
if not(isempty(varargin))
FilePath = varargin{1};
else
FilePath = [fullfile(NSx.MetaTags.FilePath,NSx.MetaTags.Filename) '-modified' NSx.MetaTags.FileExt];
% [File,Path] = uiputfile;
% FilePath = [fullfile(Path,NSx.MetaTags.Filename(1:end)),'-modified', NSx.MetaTags.FileExt];
FilePath = [fullfile(NSx.MetaTags.FilePath,NSx.MetaTags.Filename) '-modified' NSx.MetaTags.FileExt];
if length(varargin) >= 1
if not(isempty(varargin{1}))
FilePath = varargin{1};
end
end

% save to a specific filespec
if length(varargin) >= 2
if (varargin{2} == 2.3)
NSx.MetaTags.FileTypeID(1:8) = 'NEURALCD';
NSx.MetaTags.FileSpec(1:3) = '2.3';
end
if (varargin{2} == 3.0)
NSx.MetaTags.FileTypeID(1:8) = 'BRSMPGRP';
NSx.MetaTags.FileSpec(1:3) = '3.0';
end
end


Expand Down
84 changes: 42 additions & 42 deletions NPMK/openNEV.m
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Original file line number Diff line number Diff line change
Expand Up @@ -4,15 +4,15 @@
%
% Opens an .nev file for reading, returns all file information in a NEV
% structure. Works with File Spec 2.1 & 2.2 & 2.3 & 3.0.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Use OUTPUT = openNEV(fname, 'noread', 'report', 'noparse', 'nowarning',
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Use OUTPUT = openNEV(fname, 'noread', 'report', 'noparse', 'nowarning',
% 'nosave', 'nomat', 'uV', 'overwrite', 'direct').
%
%
% NOTE: All input arguments are optional. Input arguments may be in any order.
%
% fname: Name of the file to be opened. If the fname is omitted
% the user will be prompted to select a file using an open
% file user interface.
% the user will be prompted to select a file using an open
% file user interface.
% DEFAULT: Will open Open File UI.
%
% 'noread': Will not read the spike waveforms if user passes this argument.
Expand Down Expand Up @@ -70,24 +70,24 @@
% 'direct': Use this if you are using a CerePlex Direct system
% without the typical strobe mode. This will treat the 16th
% bit of the digital input as a strobe signal and report
% the remaining 15 bits as the digital input value.
% the remaining 15 bits as the digital input value.
%
% OUTPUT: Contains the NEV structure.
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% USAGE EXAMPLE:
%
% USAGE EXAMPLE:
%
% openNEV('report','read');
%
% In the example above, the file dialogue will prompt for a file. A
% report of the file contents will be shown. The digital data will not be
% parsed. The data needs to be in the proper format (refer below). The
% parsed. The data needs to be in the proper format (refer below). The
% spike waveforms are in raw units and not in uV.
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% DIGITAL PARAMETERS/MARKERS FORMAT:
%
% In order for this function to parse your experimental parameters they
% In order for this function to parse your experimental parameters they
% need to be in the following format:
%
% *ParamLabel:Parameter1=value1;Parameter2=value2;Parameter3=value3;#
Expand All @@ -97,11 +97,11 @@
%
% *Stimulation:StimCount=5;Duration=10;#
%
% In the first example, the parameter is of type "ExpParameter". The
% parameters are, "Intensity, Duration, Trials, and PageSement." The
% In the first example, the parameter is of type "ExpParameter". The
% parameters are, "Intensity, Duration, Trials, and PageSement." The
% values of those parameters are, "1.02, 400, 1, and 14," respectively.
% The second example is of type "Stimulation". The name of the parameters
% are "StimCount" and "Duration" and the values are "5" and "10"
% are "StimCount" and "Duration" and the values are "5" and "10"
% respectively.
% -----------------------------------------------------------------------
% It can also read single value markers that follow the following format.
Expand All @@ -110,7 +110,7 @@
%
% EXAMPLES: *WaitSeconds=10;# OR *JuiceStatus=ON;#
%
% The above line is a "Marker". The marker value is 10 in the first
% The above line is a "Marker". The marker value is 10 in the first
% and it's ON in the second example.
% -----------------------------------------------------------------------
% Moreover, the marker could be a single value:
Expand All @@ -126,9 +126,9 @@
% with a semi-colon ';'.
%
% NOTE:
% Every line requires a pound-sign '#' at the very end.
% Every line requires a pound-sign '#' at the very end.
% Every line requires a star sign '*' at the very beginning. If you
% use LabVIEW SendtoCerebus.vi by Kian Torab then there is no need for
% use LabVIEW SendtoCerebus.vi by Kian Torab then there is no need for
% a '*' in the beginning.
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Expand All @@ -139,7 +139,7 @@
% Version History
%
% 4.4.0.0:
% - Major performance boost in reading NEV files when tracking data is
% - Major performance boost in reading NEV files when tracking data is
% stored in the file.
%
% 4.4.0.2:
Expand Down Expand Up @@ -214,7 +214,7 @@
% 6.0.0.0: January 27, 2020
% - Added support for 64-bit timestamps in NEV and NSx.
% - Removed dependency on MATLAB R2016b by removing function 'contains'.
%
%
% 6.1.0.0: April 16, 2020
% - Some bug fixes. (David Kluger)
%
Expand Down Expand Up @@ -335,13 +335,13 @@
%% Defining and validating variables
if ~exist('fileFullPath', 'var')
if exist('getFile.m', 'file') == 2
[fileName pathName] = getFile('*.nev;*.nevm', 'Choose a NEV file...');
[fileName pathName] = getFile('*.nev*', 'Choose a NEV file...');
else
[fileName pathName] = uigetfile;
end
fileFullPath = [pathName fileName];
if fileFullPath==0;
clear variables;
if fileFullPath==0;
clear variables;
if nargout
varargout{1} = [];
end
Expand Down Expand Up @@ -389,7 +389,7 @@
end

%% Validating existance of parseCommand
if strcmpi(Flags.ParseData, 'parse')
if strcmpi(Flags.ParseData, 'parse')
if exist('parseCommand.m', 'file') ~= 2
disp('This version of openNEV requires function parseCommand.m to be placed in path.');
clear variables;
Expand All @@ -407,7 +407,7 @@
if exist(matPath, 'file') == 2 && strcmpi(Flags.NoMAT, 'yesmat') && strcmpi(Flags.WarningStat, 'warning')
disp('MAT file corresponding to selected NEV file already exists. Loading MAT instead...');
load(matPath);
NEV.MetaTags.FilePath = fileFullPath;
NEV.MetaTags.FilePath = fileFullPath;
if isempty(NEV.Data.Spikes.Waveform) && strcmpi(Flags.ReadData, 'read') && strcmpi(Flags.WarningStat, 'warning')
disp('The MAT file does not waveforms. Loading NEV instead...');
else
Expand Down Expand Up @@ -498,7 +498,7 @@
NEV.ElectrodesInfo(ElectrodeID).ConnectorBank = char(ExtendedHeader(11)+64);
NEV.ElectrodesInfo(ElectrodeID).ConnectorPin = ExtendedHeader(12);
df = typecast(ExtendedHeader(13:14),'int16');
% This is a workaround for the DigitalFactor overflow in NEV
% This is a workaround for the DigitalFactor overflow in NEV
% files. Remove once Central is updated
if df == 21516
NEV.ElectrodesInfo(ElectrodeID).DigitalFactor = 152592.547;
Expand Down Expand Up @@ -529,8 +529,8 @@
Mode = ExtendedHeader(25);
NEV.IOLabels{Mode+1} = char(ExtendedHeader(9:24).');
clear Mode;
case 'NSASEXEV' %% Not implemented in the Cerebus firmware.
%% Needs to be updated once implemented into the
case 'NSASEXEV' %% Not implemented in the Cerebus firmware.
%% Needs to be updated once implemented into the
%% firmware by Blackrock Microsystems.
NEV.NSAS.Freq = typecast(ExtendedHeader(9:10),'uint16');
NEV.NSAS.DigInputConf = char(ExtendedHeader(11));
Expand Down Expand Up @@ -566,7 +566,7 @@
disp(['PacketID ' PacketID ' is invalid.']);
disp('Please make sure this version of openNEV is compatible with your current NSP firmware.')
fclose(FID);
clear variables;
clear variables;
if nargout
varargout{1} = [];
end
Expand Down Expand Up @@ -682,7 +682,7 @@
NEV.Data.Spikes.TimeStamp = Timestamp(neuralIndices);
NEV.Data.Spikes.Electrode = PacketIDs(neuralIndices);
clear PacketIDs;
NEV.Data.Spikes.Unit = tempClassOrReason(neuralIndices);
NEV.Data.Spikes.Unit = tempClassOrReason(neuralIndices);
%clear neuralIndices;
NEV.Data.SerialDigitalIO.InsertionReason = tempClassOrReason(digserIndices);
clear tempClassOrReason;
Expand All @@ -698,7 +698,7 @@
logEventPacketIDIndices,...
reconfigPacketIDIndices,...
recEventPacketIDIndices];

if ~isempty(allExtraDataPacketIndices) % if there is any extra packets
fseek(FID, Trackers.fExtendedHeader, 'bof');
fseek(FID, (Trackers.readPackets(1)-1) * Trackers.countPacketBytes, 'cof');
Expand All @@ -715,7 +715,7 @@
NEV.Data.Comments.TimeStampStarted = tempTimeStampStarted(orderOfTS); clear tempTimeStampStarted;
tempText = char(tRawData(timeStampBytes+9:Trackers.countPacketBytes, commentIndices).');
NEV.Data.Comments.Text = tempText(orderOfTS,:); clear tempText;

% Transferring NeuroMotive Events to its own structure
neuroMotiveEvents = find(NEV.Data.Comments.CharSet == 255);
NEV.Data.TrackingEvents.TimeStamp = NEV.Data.Comments.TimeStamp(neuroMotiveEvents);
Expand All @@ -737,12 +737,12 @@
NEV.Data.Comments.TimeStampStartedSec = double(NEV.Data.Comments.TimeStampStarted)/double(NEV.MetaTags.TimeRes);
NEV.Data.Comments.Text(neuroMotiveEvents,:) = [];
colorFlag(neuroMotiveEvents) = [];

% Figuring out the text color of the comments that had color
NEV.Data.Comments.Color = dec2hex(NEV.Data.Comments.TimeStampStarted);
NEV.Data.Comments.Color(colorFlag == 1,:) = repmat('0', size(NEV.Data.Comments.Color(colorFlag == 1,:)));
NEV.Data.Comments.TimeStampStarted(colorFlag == 0) = NEV.Data.Comments.TimeStamp(colorFlag == 0);
NEV.Data.Comments.TimeStampStarted(colorFlag == 0) = NEV.Data.Comments.TimeStamp(colorFlag == 0);

clear commentIndices;
end
if ~isempty(videoSyncPacketIDIndices)
Expand Down Expand Up @@ -770,10 +770,10 @@
tmp.NodeCount = typecast(tmp.NodeCount(:), 'uint16').';
tmp.MarkerCount = tRawData(timeStampBytes+9:timeStampBytes+10, trackingPacketIDIndices);
tmp.MarkerCount = typecast(tmp.MarkerCount(:), 'uint16').';

tmp.rigidBodyPoints = tRawData(timeStampBytes+11:NEV.MetaTags.PacketBytes, trackingPacketIDIndices);
tmp.rigidBodyPoints = reshape(typecast(tmp.rigidBodyPoints(:), 'uint16'), size(tmp.rigidBodyPoints, 1)/2, size(tmp.rigidBodyPoints, 2));

if (isfield(NEV, 'ObjTrackInfo'))
for IDX = 1:size(NEV.ObjTrackInfo,2)
emptyChar = find(NEV.ObjTrackInfo(IDX).TrackableName == 0, 1);
Expand Down Expand Up @@ -851,7 +851,7 @@
NEV.Data.Spikes.WaveformUnit = Flags.waveformUnits;
NEV.Data.Spikes.Waveform = fread(FID, [(Trackers.countPacketBytes-hOffset)/2 Trackers.readPackets(2)], ...
[num2str((Trackers.countPacketBytes-hOffset)/2) '*int16=>int16'], hOffset);
NEV.Data.Spikes.Waveform(:, [digserIndices allExtraDataPacketIndices]) = [];
NEV.Data.Spikes.Waveform(:, [digserIndices allExtraDataPacketIndices]) = [];

clear allExtraDataPacketIndices;
if strcmpi(Flags.waveformUnits, 'uv')
Expand Down Expand Up @@ -925,7 +925,7 @@
DShighUniqueBin = dec2bin(NEV.Data.SerialDigitalIO.UnparsedData(uniqueDShighs));
DShighUniqueDec = bin2dec(DShighUniqueBin(:,2:16));
% Removing the non-strobed-high values from SerialDigitalIO
extraMembers = setxor(uniqueDShighs, 1:length(NEV.Data.SerialDigitalIO.UnparsedData));
extraMembers = setxor(uniqueDShighs, 1:length(NEV.Data.SerialDigitalIO.UnparsedData));
NEV.Data.SerialDigitalIO.TimeStamp(extraMembers) = [];
NEV.Data.SerialDigitalIO.TimeStampSec(extraMembers) = [];
NEV.Data.SerialDigitalIO.UnparsedData = DShighUniqueDec;
Expand Down Expand Up @@ -956,7 +956,7 @@
disp(['Data Duration (min) = ' num2str(round(NEV.MetaTags.DataDuration/NEV.MetaTags.SampleRes/60))]);
disp(['Packet Counts = ' num2str(Trackers.countDataPacket)]);
disp(' ');
disp( '*** BASIC HEADER ***********************');
disp( '*** BASIC HEADER ***********************');
disp(['Sample Resolution = ' num2str(NEV.MetaTags.SampleRes)]);
disp(['Date and Time = ' NEV.MetaTags.DateTime]);
disp(['Comment = ' NEV.MetaTags.Comment(1:64) ]);
Expand All @@ -969,19 +969,19 @@
%% Saving the NEV structure as a MAT file for easy access
if strcmpi(Flags.SaveFile, 'save')
if exist(matPath, 'file') == 2 && strcmpi(Flags.Overwrite, 'nooverwrite')
if strcmpi(Flags.WarningStat, 'warning')
if strcmpi(Flags.WarningStat, 'warning')
disp(['File ' matPath ' already exists.']);
overWrite = input('Would you like to overwrite (Y/N)? ', 's');
else
overWrite = 'n';
end
if strcmpi(overWrite, 'y')
if strcmpi(Flags.WarningStat, 'warning')
if strcmpi(Flags.WarningStat, 'warning')
disp('Saving MAT file. This may take a few seconds...');
end
save(matPath, 'NEV', '-v7.3');
else
if strcmpi(Flags.WarningStat, 'warning')
if strcmpi(Flags.WarningStat, 'warning')
disp('File was not overwritten.');
end
end
Expand All @@ -990,7 +990,7 @@
disp(['File ' matPath ' already exists.']);
disp('Overwriting the old MAT file. This may take a few seconds...');
end
save(matPath, 'NEV', '-v7.3');
save(matPath, 'NEV', '-v7.3');
else
if strcmpi(Flags.WarningStat, 'warning')
disp('Saving MAT file. This may take a few seconds...');
Expand Down
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