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NUCLEUSinv update
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1. extended the BAM NMR tomograph import routine to handle data files that do not belong to a *lift*-set (i.e. do not have a z-position defined in the par-file)
2. bug fix: when importing a *LIAG* project where the calibration file is already inverted, and hence, automatically imported, the relaxation time was not used as *Tbulk* time for the sample
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@ThoHiller
ThoHiller committed Jun 27, 2019
1 parent 923fe2d commit 7ab6650
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Showing 14 changed files with 1,103 additions and 1,017 deletions.
4 changes: 2 additions & 2 deletions NUCLEUSinv/NUCLEUSinv.m
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Expand Up @@ -38,8 +38,8 @@
if ~isempty(h0); close(h0); end

%% GUI 'header' info and defaults
myui.version = '0.1.5';
myui.date = '27.03.2019';
myui.version = '0.1.7';
myui.date = '27.06.2019';
myui.author = 'Thomas Hiller';
myui.email = 'thomas.hiller[at]leibniz-liag.de';
myui.fontsize = 10;
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2 changes: 1 addition & 1 deletion NUCLEUSinv/NUCLEUSinv_updateInterface.m
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Expand Up @@ -638,7 +638,7 @@
'String',num2str(data.param.sampVol));
end

% Matlab need some time
% Matlab needs some time
pause(0.001);

end
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4 changes: 2 additions & 2 deletions NUCLEUSmod/NUCLEUSmod.m
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Expand Up @@ -41,8 +41,8 @@
if ~isempty(h0); close(h0); end

%% GUI 'header' info and defaults
myui.version = '0.1.5';
myui.date = '27.03.2019';
myui.version = '0.1.7';
myui.date = '27.06.2019';
myui.author = 'Thomas Hiller';
myui.email = 'thomas.hiller[at]leibniz-liag.de';
myui.fontsize = 10;
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4 changes: 2 additions & 2 deletions doc/nucleus/NUCLEUSinv/NUCLEUSinv.html
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Expand Up @@ -111,8 +111,8 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0038 <span class="keyword">if</span> ~isempty(h0); close(h0); <span class="keyword">end</span>
0039
0040 <span class="comment">%% GUI 'header' info and defaults</span>
0041 myui.version = <span class="string">'0.1.5'</span>;
0042 myui.date = <span class="string">'27.03.2019'</span>;
0041 myui.version = <span class="string">'0.1.7'</span>;
0042 myui.date = <span class="string">'27.06.2019'</span>;
0043 myui.author = <span class="string">'Thomas Hiller'</span>;
0044 myui.email = <span class="string">'thomas.hiller[at]leibniz-liag.de'</span>;
0045 myui.fontsize = 10;
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2 changes: 1 addition & 1 deletion doc/nucleus/NUCLEUSinv/NUCLEUSinv_updateInterface.html
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Expand Up @@ -718,7 +718,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0638 <span class="string">'String'</span>,num2str(data.param.sampVol));
0639 <span class="keyword">end</span>
0640
0641 <span class="comment">% Matlab need some time</span>
0641 <span class="comment">% Matlab needs some time</span>
0642 pause(0.001);
0643
0644 <span class="keyword">end</span>
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4 changes: 2 additions & 2 deletions doc/nucleus/NUCLEUSmod/NUCLEUSmod.html
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Expand Up @@ -117,8 +117,8 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0041 <span class="keyword">if</span> ~isempty(h0); close(h0); <span class="keyword">end</span>
0042
0043 <span class="comment">%% GUI 'header' info and defaults</span>
0044 myui.version = <span class="string">'0.1.5'</span>;
0045 myui.date = <span class="string">'27.03.2019'</span>;
0044 myui.version = <span class="string">'0.1.7'</span>;
0045 myui.date = <span class="string">'27.06.2019'</span>;
0046 myui.author = <span class="string">'Thomas Hiller'</span>;
0047 myui.email = <span class="string">'thomas.hiller[at]leibniz-liag.de'</span>;
0048 myui.fontsize = 10;
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247 changes: 138 additions & 109 deletions doc/nucleus/functions/import/LoadNMRData_bamtom.html
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Expand Up @@ -114,7 +114,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0038 <span class="comment">% load Parameter file</span>
0039 [parData] = <a href="#_sub2" class="code" title="subfunction [data] = LoadParameterFile(datapath,fname)">LoadParameterFile</a>(in.path,[in.name,<span class="string">'.par'</span>]);
0040 <span class="comment">% check if T1 or T2 data</span>
0041 <span class="keyword">if</span> strcmp(parData.measurementType,<span class="string">'CPMG_Lift'</span>)
0041 <span class="keyword">if</span> ~isempty(strfind(parData.measurementType,<span class="string">'CPMG'</span>))
0042 T1T2flag = <span class="string">'T2'</span>;
0043 <span class="keyword">else</span>
0044 T1T2flag = <span class="string">'T1'</span>;
Expand All @@ -131,116 +131,145 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0055
0056 <span class="comment">% read all 'nslices' measurements</span>
0057 nslices = parData.nSlices;
0058
0059 nmrData = cell(1,nslices);
0060 <span class="keyword">for</span> i = 1:nslices
0061 <span class="comment">% find data file</span>
0062 file = dir(fullfile(in.path,[<span class="string">'*'</span>,sprintf(<span class="string">'%03d'</span>,i),<span class="string">'.csv'</span>]));
0063
0064 <span class="comment">% read the data file</span>
0065 data = <a href="#_sub1" class="code" title="subfunction [data] = LoadDataFile(datapath,fname,flag)">LoadDataFile</a>(in.path,file.name,T1T2flag);
0066
0067 <span class="comment">% save the NMR data</span>
0068 nmrData{i}.flag = data.flag;
0069 nmrData{i}.T1IRfac = 1;
0070 nmrData{i}.time = data.time;
0071 nmrData{i}.signal = data.signal;
0072 nmrData{i}.raw = data.raw;
0073 nmrData{i}.phase = data.phase;
0074 nmrData{i}.phase_bam = data.phase_bam;
0075 clear data
0076
0077 <span class="comment">% get file statistics</span>
0078 nmrData{i}.datfile = file.name;
0079 nmrData{i}.date = file.date;
0080 nmrData{i}.datenum = file.datenum;
0081 nmrData{i}.bytes = file.bytes;
0082 <span class="keyword">end</span>
0083 <span class="keyword">end</span>
0084
0085 <span class="comment">% save data to output struct</span>
0086 out.parData = parData;
0087 out.nmrData = nmrData;
0088
0089 <span class="keyword">end</span>
0090
0091 <span class="comment">%% load NMR data file</span>
0092 <a name="_sub1" href="#_subfunctions" class="code">function [data] = LoadDataFile(datapath,fname,flag)</a>
0093
0094 d = importdata(fullfile(datapath,fname),<span class="string">'\t'</span>,3);
0095
0096 <span class="comment">% phase</span>
0097 tmpstr = d.textdata{2,1};
0098 colonstr = strfind(tmpstr,<span class="string">':'</span>);
0099 data.phase_bam = str2double(tmpstr(colonstr+1:end-4));
0100 <span class="comment">% to compare the BAM TOM phase with the NUCLEUS fit phase shift and flip</span>
0101 <span class="comment">% the phase value</span>
0102 data.phase_bam = -1*(data.phase_bam + pi);
0103
0104 <span class="comment">% standard data</span>
0105 data.flag = flag;
0106 data.time = d.data(:,1);
0107 <span class="keyword">switch</span> flag
0108 <span class="keyword">case</span> <span class="string">'T1'</span>
0109 data.signal = d.data(:,2);
0110 <span class="keyword">case</span> <span class="string">'T2'</span>
0111 data.signal = complex(d.data(:,2),d.data(:,3));
0112 [data.signal,data.phase] = <a href="rotateT2phase.html" class="code" title="function [s_rot,alpha] = rotateT2phase(s)">rotateT2phase</a>(data.signal);
0113 <span class="keyword">end</span>
0114
0115 <span class="comment">% save raw data</span>
0116 data.raw.time = data.time;
0117 data.raw.signal = data.signal;
0118
0119 <span class="keyword">end</span>
0120
0121 <span class="comment">%% load parameter file</span>
0122 <a name="_sub2" href="#_subfunctions" class="code">function [data] = LoadParameterFile(datapath,fname)</a>
0123
0124 fid = fopen(fullfile(datapath,fname));
0125 d = textscan(fid,<span class="string">'%s'</span>,<span class="string">'Delimiter'</span>,<span class="string">'\n'</span>);
0126 fclose(fid);
0127
0128 <span class="keyword">for</span> i = 1:size(d{1},1)
0129 str = char(d{1}(i));
0130 <span class="keyword">if</span> ~isempty(str) &amp;&amp; ~strcmp(str(1),<span class="string">'#'</span>)
0131 str = <a href="fixParameterString.html" class="code" title="function str = fixParameterString(str)">fixParameterString</a>(str);
0132 <span class="keyword">if</span> ~isempty(strfind(str,<span class="string">'coilName'</span>)) || ~isempty(strfind(str,<span class="string">'measurementType'</span>))
0133 streq = strfind(str,<span class="string">'='</span>);
0134 newstr = [str(1:streq(1)),<span class="string">''''</span>,strtrim(str(streq(1)+1:end)),<span class="string">''''</span>];
0135 str = newstr;
0136 <span class="keyword">end</span>
0137 eval([<span class="string">'data.'</span>,str,<span class="string">';'</span>]);
0138 <span class="keyword">end</span>
0139 <span class="keyword">end</span>
0140 data.all = d;
0141
0058 ncsvfiles = numel(dir(fullfile(in.path,<span class="string">'*.csv'</span>)));
0059
0060 <span class="keyword">if</span> nslices == ncsvfiles
0061
0062 nmrData = cell(1,nslices);
0063 <span class="keyword">for</span> i = 1:nslices
0064 <span class="comment">% find data file</span>
0065 file = dir(fullfile(in.path,[<span class="string">'*'</span>,sprintf(<span class="string">'%03d'</span>,i),<span class="string">'.csv'</span>]));
0066
0067 <span class="comment">% read the data file</span>
0068 data = <a href="#_sub1" class="code" title="subfunction [data] = LoadDataFile(datapath,fname,flag)">LoadDataFile</a>(in.path,file.name,T1T2flag);
0069
0070 <span class="comment">% save the NMR data</span>
0071 nmrData{i}.flag = data.flag;
0072 nmrData{i}.T1IRfac = 1;
0073 nmrData{i}.time = data.time;
0074 nmrData{i}.signal = data.signal;
0075 nmrData{i}.raw = data.raw;
0076 nmrData{i}.phase = data.phase;
0077 nmrData{i}.phase_bam = data.phase_bam;
0078 clear data
0079
0080 <span class="comment">% get file statistics</span>
0081 nmrData{i}.datfile = file.name;
0082 nmrData{i}.date = file.date;
0083 nmrData{i}.datenum = file.datenum;
0084 nmrData{i}.bytes = file.bytes;
0085 <span class="keyword">end</span>
0086
0087 <span class="keyword">else</span>
0088
0089 files = dir(fullfile(in.path,<span class="string">'*.csv'</span>));
0090 nmrData = cell(1,ncsvfiles);
0091 <span class="keyword">for</span> i = 1:ncsvfiles
0092 <span class="comment">% read the data file</span>
0093 data = <a href="#_sub1" class="code" title="subfunction [data] = LoadDataFile(datapath,fname,flag)">LoadDataFile</a>(in.path,files(i).name,T1T2flag);
0094
0095 <span class="comment">% save the NMR data</span>
0096 nmrData{i}.flag = data.flag;
0097 nmrData{i}.T1IRfac = 1;
0098 nmrData{i}.time = data.time;
0099 nmrData{i}.signal = data.signal;
0100 nmrData{i}.raw = data.raw;
0101 nmrData{i}.phase = data.phase;
0102 nmrData{i}.phase_bam = data.phase_bam;
0103 clear data
0104
0105 <span class="comment">% get file statistics</span>
0106 nmrData{i}.datfile = files(i).name;
0107 nmrData{i}.date = files(i).date;
0108 nmrData{i}.datenum = files(i).datenum;
0109 nmrData{i}.bytes = files(i).bytes;
0110 <span class="keyword">end</span>
0111 <span class="keyword">end</span>
0112 <span class="keyword">end</span>
0113
0114 <span class="comment">% save data to output struct</span>
0115 out.parData = parData;
0116 out.nmrData = nmrData;
0117
0118 <span class="keyword">end</span>
0119
0120 <span class="comment">%% load NMR data file</span>
0121 <a name="_sub1" href="#_subfunctions" class="code">function [data] = LoadDataFile(datapath,fname,flag)</a>
0122
0123 d = importdata(fullfile(datapath,fname),<span class="string">'\t'</span>,3);
0124
0125 <span class="comment">% phase</span>
0126 tmpstr = d.textdata{2,1};
0127 colonstr = strfind(tmpstr,<span class="string">':'</span>);
0128 data.phase_bam = str2double(tmpstr(colonstr+1:end-4));
0129 <span class="comment">% to compare the BAM TOM phase with the NUCLEUS fit phase shift and flip</span>
0130 <span class="comment">% the phase value</span>
0131 data.phase_bam = -1*(data.phase_bam + pi);
0132
0133 <span class="comment">% standard data</span>
0134 data.flag = flag;
0135 data.time = d.data(:,1);
0136 <span class="keyword">switch</span> flag
0137 <span class="keyword">case</span> <span class="string">'T1'</span>
0138 data.signal = d.data(:,2);
0139 <span class="keyword">case</span> <span class="string">'T2'</span>
0140 data.signal = complex(d.data(:,2),d.data(:,3));
0141 [data.signal,data.phase] = <a href="rotateT2phase.html" class="code" title="function [s_rot,alpha] = rotateT2phase(s)">rotateT2phase</a>(data.signal);
0142 <span class="keyword">end</span>
0143
0144 <span class="comment">%------------- END OF CODE --------------</span>
0145
0146 <span class="comment">%% License:</span>
0147 <span class="comment">% MIT License</span>
0148 <span class="comment">%</span>
0149 <span class="comment">% Copyright (c) 2019 Thomas Hiller</span>
0150 <span class="comment">%</span>
0151 <span class="comment">% Permission is hereby granted, free of charge, to any person obtaining a copy</span>
0152 <span class="comment">% of this software and associated documentation files (the &quot;Software&quot;), to deal</span>
0153 <span class="comment">% in the Software without restriction, including without limitation the rights</span>
0154 <span class="comment">% to use, copy, modify, merge, publish, distribute, sublicense, and/or sell</span>
0155 <span class="comment">% copies of the Software, and to permit persons to whom the Software is</span>
0156 <span class="comment">% furnished to do so, subject to the following conditions:</span>
0157 <span class="comment">%</span>
0158 <span class="comment">% The above copyright notice and this permission notice shall be included in all</span>
0159 <span class="comment">% copies or substantial portions of the Software.</span>
0160 <span class="comment">%</span>
0161 <span class="comment">% THE SOFTWARE IS PROVIDED &quot;AS IS&quot;, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR</span>
0162 <span class="comment">% IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,</span>
0163 <span class="comment">% FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE</span>
0164 <span class="comment">% AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER</span>
0165 <span class="comment">% LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,</span>
0166 <span class="comment">% OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE</span>
0167 <span class="comment">% SOFTWARE.</span></pre></div>
0144 <span class="comment">% save raw data</span>
0145 data.raw.time = data.time;
0146 data.raw.signal = data.signal;
0147
0148 <span class="keyword">end</span>
0149
0150 <span class="comment">%% load parameter file</span>
0151 <a name="_sub2" href="#_subfunctions" class="code">function [data] = LoadParameterFile(datapath,fname)</a>
0152
0153 fid = fopen(fullfile(datapath,fname));
0154 d = textscan(fid,<span class="string">'%s'</span>,<span class="string">'Delimiter'</span>,<span class="string">'\n'</span>);
0155 fclose(fid);
0156
0157 <span class="keyword">for</span> i = 1:size(d{1},1)
0158 str = char(d{1}(i));
0159 <span class="keyword">if</span> ~isempty(str) &amp;&amp; ~strcmp(str(1),<span class="string">'#'</span>)
0160 str = <a href="fixParameterString.html" class="code" title="function str = fixParameterString(str)">fixParameterString</a>(str);
0161 <span class="keyword">if</span> ~isempty(strfind(str,<span class="string">'coilName'</span>)) || ~isempty(strfind(str,<span class="string">'measurementType'</span>))
0162 streq = strfind(str,<span class="string">'='</span>);
0163 newstr = [str(1:streq(1)),<span class="string">''''</span>,strtrim(str(streq(1)+1:end)),<span class="string">''''</span>];
0164 str = newstr;
0165 <span class="keyword">end</span>
0166 eval([<span class="string">'data.'</span>,str,<span class="string">';'</span>]);
0167 <span class="keyword">end</span>
0168 <span class="keyword">end</span>
0169 data.all = d;
0170
0171 <span class="keyword">end</span>
0172
0173 <span class="comment">%------------- END OF CODE --------------</span>
0174
0175 <span class="comment">%% License:</span>
0176 <span class="comment">% MIT License</span>
0177 <span class="comment">%</span>
0178 <span class="comment">% Copyright (c) 2019 Thomas Hiller</span>
0179 <span class="comment">%</span>
0180 <span class="comment">% Permission is hereby granted, free of charge, to any person obtaining a copy</span>
0181 <span class="comment">% of this software and associated documentation files (the &quot;Software&quot;), to deal</span>
0182 <span class="comment">% in the Software without restriction, including without limitation the rights</span>
0183 <span class="comment">% to use, copy, modify, merge, publish, distribute, sublicense, and/or sell</span>
0184 <span class="comment">% copies of the Software, and to permit persons to whom the Software is</span>
0185 <span class="comment">% furnished to do so, subject to the following conditions:</span>
0186 <span class="comment">%</span>
0187 <span class="comment">% The above copyright notice and this permission notice shall be included in all</span>
0188 <span class="comment">% copies or substantial portions of the Software.</span>
0189 <span class="comment">%</span>
0190 <span class="comment">% THE SOFTWARE IS PROVIDED &quot;AS IS&quot;, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR</span>
0191 <span class="comment">% IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,</span>
0192 <span class="comment">% FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE</span>
0193 <span class="comment">% AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER</span>
0194 <span class="comment">% LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,</span>
0195 <span class="comment">% OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE</span>
0196 <span class="comment">% SOFTWARE.</span></pre></div>
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