MVAPACK Master Script - Revision history

Mjeppesen at 20:47, 23 March 2022

2022-03-23T20:47:27Z

← Older revision		Revision as of 20:47, 23 March 2022
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	<br />''<nowiki>%% phase correction method objective can be decided</nowiki>''		<br />''<nowiki>%% phase correction method objective can be decided</nowiki>''
	<br /><nowiki>display('Automatic phasing will be performed, you can choose an objective function. Your options are "@simplex_minimum", "@simplex_entropy", "@simplex_whiten", or "@simplex_integral". (Refer to manual)')</nowiki>		<br /><nowiki>display('Automatic phasing will be performed, you can choose an objective function. Your options are "@simplex_minimum", "@simplex_entropy", "@simplex_whiten", or "@simplex_integral". (Refer to manual)')</nowiki>
	<br /><nowiki>phaseobjective = ('Which objective do you choose? ', "s");</nowiki>		<br /><nowiki>phaseobjective = input('Which objective do you choose? ', "s");</nowiki>
	<br /><nowiki>[S.data, S.phc0, S.phc1] = autophase(S.data, F.parms, phaseobjective);</nowiki>		<br /><nowiki>[S.data, S.phc0, S.phc1] = autophase(S.data, F.parms, phaseobjective);</nowiki>
	<br /><nowiki>[S.data, S.phc0, S.phc1] = autophase(S.data, F.parms, phaseobjective);</nowiki>		<br /><nowiki>[S.data, S.phc0, S.phc1] = autophase(S.data, F.parms, phaseobjective);</nowiki>

Mjeppesen: /* The Script */

2022-03-23T20:14:34Z

The Script

← Older revision		Revision as of 20:14, 23 March 2022
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	<br /><nowiki>end</nowiki>		<br /><nowiki>end</nowiki>
	<br /><nowiki>checkforexistence = exist('F.dirs')</nowiki>		<br /><nowiki>checkforexistence = exist('F.dirs')</nowiki>
	<br /><nowiki>if ~checkforexistence</nowiki>		<br /><nowiki>if checkforexistence</nowiki>
	<br /><nowiki> error('There is no NMR data here, seems you have the wrong filepath.')</nowiki>		<br /><nowiki> error('There is no NMR data here, seems you have the wrong filepath.')</nowiki>
	<br /><nowiki>end</nowiki>		<br /><nowiki>end</nowiki>

Mjeppesen at 21:40, 15 February 2022

2022-02-15T21:40:48Z

← Older revision		Revision as of 21:40, 15 February 2022
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	<br /><nowiki>count = 1;</nowiki>		<br /><nowiki>count = 1;</nowiki>
	<br /><nowiki>sizeoffileglob = numel(F.fileglob);</nowiki>		<br /><nowiki>sizeoffileglob = numel(F.fileglob);</nowiki>
			<br /><nowiki>currentdir = pwd;</nowiki>
	<br /><nowiki>for i = [1:sizeoffileglob]</nowiki>		<br /><nowiki>for i = [1:sizeoffileglob]</nowiki>
	<br /><nowiki> if isfolder(F.fileglob{i})</nowiki>		<br /><nowiki> if isfolder(F.fileglob{i})</nowiki>
	<br /><nowiki> ~~if (fexist~~([F.fileglob{1}, '/ser']) \|\| ~~fexist~~(~~[F.fileglob{1},~~ '/fid']))</nowiki>		<br /><nowiki> cd(F.fileglob{i});</nowiki>
			<br /><nowiki> if (stat('ser') \|\| stat('fid'))</nowiki>
	<br /><nowiki> continue;</nowiki>		<br /><nowiki> continue;</nowiki>
	<br /><nowiki> end</nowiki>		<br /><nowiki> end</nowiki>
			<br /><nowiki> cd(currentdir);</nowiki>
	<br /><nowiki> F.dirs{count++} = F.fileglob{i};</nowiki>		<br /><nowiki> F.dirs{count++} = F.fileglob{i};</nowiki>
	<br /><nowiki> end</nowiki>		<br /><nowiki> end</nowiki>

Mjeppesen at 04:19, 19 January 2022

2022-01-19T04:19:50Z

Mjeppesen at 04:18, 19 January 2022

2022-01-19T04:18:23Z

← Older revision		Revision as of 04:18, 19 January 2022
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	==The Script==		==The Script==

	~~<br /><nowiki>%%NMRMasterProcessing 1-18-2022 Micah Jeppesen</nowiki>~~
	<br /><nowiki>#Get Files</nowiki>		<br /><nowiki>#Get Files</nowiki>
	<br /><nowiki>display('Using typical unix filename syntax (i.e. ./* or ../your/file/is/here/* or ???). This will only use directories.')</nowiki>		<br /><nowiki>display('Using typical unix filename syntax (i.e. ./* or ../your/file/is/here/* or ???). This will only use directories.')</nowiki>

Mjeppesen at 04:17, 19 January 2022

2022-01-19T04:17:58Z

Show changes

Mjeppesen at 02:24, 19 January 2022

2022-01-19T02:24:00Z

← Older revision		Revision as of 02:24, 19 January 2022
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	==The Script==		==The Script==
	<~~nowiki~~>		<syntaxhighlight lang="matlab">
	#Get Files		#Get Files
	display('Using typical unix filename syntax (i.e. ./* or ../your/file/is/here/* or ???). This will only use directories.')		display('Using typical unix filename syntax (i.e. ./* or ../your/file/is/here/* or ???). This will only use directories.')
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	display('To this point, the important data is extracted and binned as "X.bindata" and can be analyzed');		display('To this point, the important data is extracted and binned as "X.bindata" and can be analyzed');
	</~~nowiki~~>		</syntaxhighlight>

Mjeppesen at 02:21, 19 January 2022

2022-01-19T02:21:04Z

Show changes

Mjeppesen at 02:18, 19 January 2022

2022-01-19T02:18:46Z

Show changes

Mjeppesen at 02:12, 19 January 2022

2022-01-19T02:12:57Z

← Older revision		Revision as of 02:12, 19 January 2022
Line 5:		Line 5:

	==The Script==		==The Script==
			<nowiki>
	#Get Files		#Get Files
	display('Using typical unix filename syntax (i.e. ./* or ../your/file/is/here/* or ???). This will only use directories.')		display('Using typical unix filename syntax (i.e. ./* or ../your/file/is/here/* or ???). This will only use directories.')
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	display('To this point, the important data is extracted and binned as "X.bindata" and can be analyzed');		display('To this point, the important data is extracted and binned as "X.bindata" and can be analyzed');
			</nowiki>

← Older revision		Revision as of 04:19, 19 January 2022
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	<br /><nowiki>F.fileglob = glob(filepath); %% Number of ? is the number of digits of the file name</nowiki>		<br /><nowiki>F.fileglob = glob(filepath); %% Number of ? is the number of digits of the file name</nowiki>
	<br /><nowiki></nowiki>		<br /><nowiki></nowiki>
	<br /><nowiki>%% We only use directories here</nowiki>		<br />''<nowiki>%% We only use directories here</nowiki>''
	<br /><nowiki>count = 1;</nowiki>		<br /><nowiki>count = 1;</nowiki>
	<br /><nowiki>sizeoffileglob = numel(F.fileglob);</nowiki>		<br /><nowiki>sizeoffileglob = numel(F.fileglob);</nowiki>
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	<br /><nowiki></nowiki>		<br /><nowiki></nowiki>
	<br /><nowiki>#Extract Data</nowiki>		<br /><nowiki>#Extract Data</nowiki>
	<br /><nowiki>%% This could be loadnmr or loaddmx - default should be loadnmr</nowiki>		<br />''<nowiki>%% This could be loadnmr or loaddmx - default should be loadnmr</nowiki>''
	<br /><nowiki>display('With "@loadnmr" and "@loaddmx" as your choices. Refer to the manual for these functions.');</nowiki>		<br /><nowiki>display('With "@loadnmr" and "@loaddmx" as your choices. Refer to the manual for these functions.');</nowiki>
	<br /><nowiki>loadingfunc = input('Which would you like to use? ', "s");</nowiki>		<br /><nowiki>loadingfunc = input('Which would you like to use? ', "s");</nowiki>
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	<br /><nowiki></nowiki>		<br /><nowiki></nowiki>
	<br /><nowiki>#Phase and extract real</nowiki>		<br /><nowiki>#Phase and extract real</nowiki>
	<br /><nowiki>%% phase correction method objective can be decided</nowiki>		<br />''<nowiki>%% phase correction method objective can be decided</nowiki>''
	<br /><nowiki>display('Automatic phasing will be performed, you can choose an objective function. Your options are "@simplex_minimum", "@simplex_entropy", "@simplex_whiten", or "@simplex_integral". (Refer to manual)')</nowiki>		<br /><nowiki>display('Automatic phasing will be performed, you can choose an objective function. Your options are "@simplex_minimum", "@simplex_entropy", "@simplex_whiten", or "@simplex_integral". (Refer to manual)')</nowiki>
	<br /><nowiki>phaseobjective = ('Which objective do you choose? ', "s");</nowiki>		<br /><nowiki>phaseobjective = ('Which objective do you choose? ', "s");</nowiki>
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	<br /><nowiki></nowiki>		<br /><nowiki></nowiki>
	<br /><nowiki>#Alignment and Referencing</nowiki>		<br /><nowiki>#Alignment and Referencing</nowiki>
	<br /><nowiki>%% an if could be used to decide if icosshift or cosshift here**</nowiki>		<br />''<nowiki>%% an if could be used to decide if icosshift or cosshift here**</nowiki>''
	<br /><nowiki>display('With "@coshift" and "@icoshift" as your options.')</nowiki>		<br /><nowiki>display('With "@coshift" and "@icoshift" as your options.')</nowiki>
	<br /><nowiki>alignmentoption = input('Which alignment method would you like to use? ',"s");</nowiki>		<br /><nowiki>alignmentoption = input('Which alignment method would you like to use? ',"s");</nowiki>
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	<br /><nowiki>plot(X.ppm, X.data);</nowiki>		<br /><nowiki>plot(X.ppm, X.data);</nowiki>
	<br /><nowiki></nowiki>		<br /><nowiki></nowiki>
	<br /><nowiki>%% an automatic referencing method could be used instead of this (no automatic method currently available)</nowiki>		<br />''<nowiki>%% an automatic referencing method could be used instead of this (no automatic method currently available)</nowiki>''
	<br /><nowiki>adjust_zero = 1</nowiki>		<br /><nowiki>adjust_zero = 1</nowiki>
	<br /><nowiki>zero_adjustment = 0</nowiki>		<br /><nowiki>zero_adjustment = 0</nowiki>
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	<br /><nowiki> end</nowiki>		<br /><nowiki> end</nowiki>
	<br /><nowiki></nowiki>		<br /><nowiki></nowiki>
	<br /><nowiki>%% this can be selected as the manual removal method - otherwise ROI methods could be used?**</nowiki>		<br />''<nowiki>%% this can be selected as the manual removal method - otherwise ROI methods could be used?**</nowiki>''
	<br /><nowiki> remove_var = 1;</nowiki>		<br /><nowiki> remove_var = 1;</nowiki>
	<br /><nowiki> while remove_var</nowiki>		<br /><nowiki> while remove_var</nowiki>
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	<br /><nowiki> end</nowiki>		<br /><nowiki> end</nowiki>
	<br /><nowiki></nowiki>		<br /><nowiki></nowiki>
	<br /><nowiki>%% binning can be done a number of ways we default to adaptive binning***</nowiki>		<br />''<nowiki>%% binning can be done a number of ways we default to adaptive binning***</nowiki>''
	<br /><nowiki>display('There are multiple ways of binning, this walkthrough uses binadapt.')</nowiki>		<br /><nowiki>display('There are multiple ways of binning, this walkthrough uses binadapt.')</nowiki>
	<br /><nowiki>[X.bindata, X.binppm] = binadapt(X.data, X.ppm, F.parms);</nowiki>		<br /><nowiki>[X.bindata, X.binppm] = binadapt(X.data, X.ppm, F.parms);</nowiki>
	<br /><nowiki>%% normalization has multiple options these need to be considered ***</nowiki>		<br />''<nowiki>%% normalization has multiple options these need to be considered ***</nowiki>''
	<br /><nowiki>X.bindata = histmatch(X.bindata);</nowiki>		<br /><nowiki>X.bindata = histmatch(X.bindata);</nowiki>
	<br /><nowiki></nowiki>		<br /><nowiki></nowiki>
	<br /><nowiki>display('To this point, the important data is extracted and binned as "X.bindata" and can be analyzed');</nowiki>		<br /><nowiki>display('To this point, the important data is extracted and binned as "X.bindata" and can be analyzed');</nowiki>
	<br /><nowiki></nowiki>		<br /><nowiki></nowiki>