hypnogram

.gitignore

@@ -1 +1,2 @@
 build/*
+*~

pn-tds-tools/pn_tds_biosignalscsv_hypnogram.m

@@ -0,0 +1,118 @@
+function [T] = pn_tds_biosignalscsv_hypnogram(varargin)
+%reads varargins of a function and gives back the parsed parameters Compumedics dpsg files and converts in matlab struct
+%
+% cli:
+%   cwlVersion: v1.0-extended
+%   class: matlabfunction
+%   baseCommand: [column_names] = pn_tds_biosignalscsv_hypnogram(varargin)
+%
+%   inputs:
+%     data:
+%       type: csv
+%       inputBinding:
+%         prefix: data
+%       doc: "A csv created with pn_tds_biosignal2csv"
+%     debug:
+%       type: int?
+%       inputBinding:
+%         prefix: debug
+%       doc: "if set to 1 debug information is provided. Default 0"
+%     hypnogram:
+%       type: edf
+%       inputBinding:
+%         prefix: hypnogram
+%       doc: "the corresponding hypnogram in edf-format"
+%   outputs:
+%     table.csv:
+%       type: file
+%       doc: "A csv extended by the number of epoch and the sleep stage"
+%
+%   s:author:
+%     - class: s:Person
+%       s:identifier:  https://orcid.org/0000-0002-7238-5339
+%       s:email: mailto:dagmar.krefting@htw-berlin.de
+%       s:name: Dagmar Krefting
+%
+%   s:dateCreated: "2018-12-08"
+%   s:license: https://spdx.org/licenses/Apache-2.0
+%
+%   s:keywords: edam:topic_3063, edam:topic_2082
+%     doc: 3063: medical informatics, 2082: matrix
+%   s:programmingLanguage: matlab
+%
+%   $namespaces:
+%     s: https://schema.org/
+%     edam: http://edamontology.org/
+%
+%   $schemas:
+%     - https://schema.org/docs/schema_org_rdfa.html
+%     - http://edamontology.org/EDAM_1.18.owl
+%
+%
+% Notes
+% It is based on the montage identifiers eeg, eog,
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% 0. Parse Inputs
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%% required input
+myinput.data = NaN;
+myinput.hypnogram = NaN;
+myinput.debug = 0;
+
+try
+    myinput = mt_parameterparser('myinputstruct',myinput,'varargins',varargin);
+catch ME
+    disp(ME)
+    return
+end
+
+if (myinput.debug)
+    myinput
+end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% 1. Load file and construct the column names
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+% Load csv file
+d = readtable(myinput.data);
+
+% read hypnogram
+[h,sh,s] = sn_edfScan2matScan('data',myinput.hypnogram);
+hypnogram = s{1};
+
+%expand to 30 values (one epoch is 30 seconds
+hypnofull = repmat(hypnogram,1,30);
+hypnofull = reshape(hypnofull',30*length(hypnogram),1);
+
+% create epoch index 
+epoch_index = (1:length(hypnogram))';
+%expand to 30 values
+epoch_index = repmat(epoch_index,1,30);
+epoch_index = reshape(epoch_index',30*length(hypnogram),1);
+
+%create a table with epochs and sleepstage
+T = array2table([epoch_index,hypnofull],'Variablenames',{'epoch';'sleepstage'});
+
+%correct for different table heights
+minheight = min(height(d),height(T));
+
+%cut tables
+T = T(1:minheight,:);
+d = d(1:minheight,:);
+
+%concatenate both tables
+T = [T d];
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% 2. Create table and write csv
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+[pathstr,basename,ext] = fileparts(myinput.data);
+
+tablename = [basename '_hypno.csv'];
+writetable(T,tablename);
+
+