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Merged
dankessler merged 3 commits into from
Jun 19, 2012
Merged

Mc error logging #66

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b889011
adding script copying and logging
mangstad Jun 14, 2012
cbe1859
initial finalized version of mc_Logger
mangstad Jun 14, 2012
8e986d3
added logging to Preprocess_mc_template, FirstLevel_mc_template, and …
mangstad Jun 14, 2012
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35 changes: 17 additions & 18 deletions FirstLevel/FirstLevel_mc_template.m
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Original file line number Diff line number Diff line change
Expand Up @@ -3,32 +3,30 @@
%%% These options are the same between Preprocessing and First level
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% The path to SPM on your system
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
spmpath = '/net/dysthymia/spm8';

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% The folder that contains your subject folders
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Exp = '/net/data4/MAS/';

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% Path where your logfiles will be stored
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
LogTemplate = '[Exp]/Logs';

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Path where your images are located
%%
%% Variables you can use in your template are:
%% Exp = path to your experiment directory
%% iSubject = index for subject
%% Subject = name of subject from SubjDir (using iSubject as index of row)
%% iRun = index of run (listed in Column 3 of SubjDir)
%% Run = name of run from RunDir (using iRun as index of row)
%% * = wildcard (can only be placed in final part of template)
%% Examples:
%% ImageTemplate = '[Exp]/Subjects/[Subject]/func/run_0[iRun]/';
%% ImageTemplate = '[Exp]/Subjects/[Subject]/TASK/func/[Run]/'
%%% Path where your images are located
%%%
%%% Variables you can use in your template are:
%%% Exp = path to your experiment directory
%%% iSubject = index for subject
%%% Subject = name of subject from SubjDir (using iSubject as index of row)
%%% iRun = index of run (listed in Column 3 of SubjDir)
%%% Run = name of run from RunDir (using iRun as index of row)
%%% * = wildcard (can only be placed in final part of template)
%%% Examples:
%%% ImageTemplate = '[Exp]/Subjects/[Subject]/func/run_0[iRun]/';
%%% ImageTemplate = '[Exp]/Subjects/[Subject]/TASK/func/[Run]/'
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

ImageTemplate = '[Exp]/Subjects/[Subject]/TASK/func/[Run]zz/';

% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Expand Down Expand Up @@ -389,6 +387,7 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
end

global mcRoot;
%DEVSTART
mcRoot = fullfile(fileparts(mfilename('fullpath')),'..');
%DEVSTOP
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14 changes: 12 additions & 2 deletions FirstLevel/PreprocessFirstLevel_central.m
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Expand Up @@ -3,7 +3,17 @@
%%% Instead make a copy of PreprocessingFirstLevel_template.m
%%% and edit that to match your data
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
addpath /net/dysthymia/slab/users/sripada/repos/matlabScripts %%%% this is for generate_path_CSS

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% Code to create logfile name
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
LogDirectory = mc_GenPath(struct('Template',LogTemplate,'mode','makedir'));
result = mc_Logger('setup',LogDirectory);
if (~result)
%error with setting up logging
mc_Error('There was an error creating your logfiles.\nDo you have permission to write to %s?',LogDirectory);
end

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% General calculations that apply to both Preprocessing and First Level
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Expand Down Expand Up @@ -38,7 +48,7 @@
Pwra = [nop rep stp];
Pswra = [smp nop rep stp];

addpath(spmpath);
%addpath(spmpath);

@dankessler dankessler Jun 15, 2012

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Just to be clear, this was removed since path adding happens in the template script now, right?

addpath(pwd);
spm('defaults','fmri');
global defaults
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9 changes: 5 additions & 4 deletions FirstLevel/Preprocess_mc_template.m
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Expand Up @@ -4,14 +4,14 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% The path to SPM on your system
%%% The folder that contains your subject folders
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
spmpath = '/net/dysthymia/spm8';
Exp = '/net/data4/MAS/';

@dankessler dankessler Jun 15, 2012

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These are good fixes, but some are going to make pulling in @heffjos pull request that has similar changes to Preprocess_mc_template and similar changes in FirstLevel_mc_template a bit tricky. check out the diff at https://github.com/UMPsychMethodsCore/MethodsCore/pull/43/files#diff-10


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% The folder that contains your subject folders
%%% Path where your logfiles will be stored
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Exp = '/net/data4/MAS/';
LogTemplate = '[Exp]/Logs';


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Expand Down Expand Up @@ -203,6 +203,7 @@
donormalize = 1;
dosmooth = 1;

global mcRoot;
%DEVSTART
mcRoot = fullfile(fileparts(mfilename('fullpath')),'..');
%DEVSTOP
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9 changes: 6 additions & 3 deletions matlabScripts/mc_Error.m
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
function mc_Error(errorString,varargin)
% A utility function to make error handling and logging more compact
% A single call to mc_Error will log the error to the global mc_LogName,
% A single call to mc_Error will log the error to the global mcLog,
% bring up an error dialog box with your error message, and actually throw
% an exception with the Matlab error function.
%
Expand Down Expand Up @@ -37,8 +37,11 @@ function mc_Error(errorString,varargin)
errormsg = errorString;
end

%add future code to call mc_Logger with loglevel Error

global mcLog
if (~isempty(mcLog))
%call logging function
mc_Logger('log',errormsg,1);
end
errordlg(errormsg);
error(errormsg);

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114 changes: 114 additions & 0 deletions matlabScripts/mc_Logger.m
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Original file line number Diff line number Diff line change
@@ -0,0 +1,114 @@
function result = mc_Logger(cmd,argument,loglevel)
% A utility function to setup script copies and log messages to a log file
% FORMAT [result] = mc_Logger(cmd,cmdstring[,loglevel]);
%
% cmd this command tells mc_Logger what mode to run in.
% Current options are:
% 'setup' - create a timestamped copy of the
% original calling script (usually the
% _mc_template script) and create a log
% file in the given directory. In this
% mode cmdstring should contain the log
% directory and loglevel is not needed.
% 'log' - write cmdstring to the log file.
%
% cmdstring in 'setup' mode this should be the log file directory
% to use. In 'log' mode this should be the string that
% will be written to the log file.
%
% loglevel This optional argument should only be used in 'log'
% mode. If given, it sets the level of importance for the
% current cmdstring. Current possible values are:
% 1 - ERROR
% 2 - WARNING
% 3 - STATUS
% If not given, it defaults to 1 (ERROR).
%

result = 0;
global mcLog;
global mcRoot;
switch(lower(cmd))
case 'setup'
%create copy of template script and create log file
[st i] = dbstack('-completenames');
callingscript = st(end).file;
[p f e ans] = fileparts(callingscript);
rightnow = now;
scriptcopy = fullfile(cmdstring,[f '_' datestr(rightnow,'yyyy-mm-dd_HHMMSSFFF') e]);
scriptlog = fullfile(cmdstring,[f '_' datestr(rightnow,'yyyy-mm-dd_HHMMSSFFF') '.log']);

headertxt = '';
lines = 0;
if (exist(fullfile(mcRoot,'.local/mc_releasetag')))
if (exist(fullfile(mcRoot,'.local/CurrentVersionSHA')))
%prepend both release and SHA to template copy
headertxt = sprintf('''This script was run on %s using the Methods Core release and SHA listed below''',datestr(rightnow,'mm/dd/yyyy HH:MM:SS'));
shellcommand = sprintf('echo %s | cat - %s %s %s > %s',headertxt,fullfile(mcRoot,'.local/mc_releasetag'),fullfile(mcRoot,'.local/CurrentVersionSHA'),callingscript,scriptcopy);
lines = 3;
else
%prepend just release to template copy
headertxt = sprintf('''This script was run on %s using the Methods Core release listed below''',datestr(rightnow,'mm/dd/yyyy HH:MM:SS'));
shellcommand = sprintf('echo %s | cat - %s %s > %s',headertxt,fullfile(mcRoot,'.local/mc_releasetag'),callingscript,scriptcopy);
lines = 2;
end
else
if (exist(fullfile(mcRoot,'.local/CurrentVersionSHA')))
%prepend just SHA to template copy
headertxt = sprintf('''This script was run on %s using the Methods Core SHA listed below''',datestr(rightnow,'mm/dd/yyyy HH:MM:SS'));
shellcommand = sprintf('echo %s | cat - %s %s > %s',headertxt,fullfile(mcRoot,'.local/CurrentVersionSHA'),callingscript,scriptcopy);
lines = 2;
else
%neither release nor SHA exist, just make template copy
headertxt = sprintf('''This script was run on %s''',datestr(rightnow,'mm/dd/yyyy HH:MM:SS'));
shellcommand = sprintf('echo %s | cat - %s > %s',headertxt,callingscript,scriptcopy);
lines = 1;
end
end
[status r] = system(shellcommand);
if (status ~= 0)
mc_Error(r);
end
shellcommand = sprintf('sed -i ''%s,%s s/^/%%/'' %s',num2str(1),num2str(lines),scriptcopy);
[status r] = system(shellcommand);
if (status ~= 0)
mc_Error(r);
end

mcLog = scriptlog;
result = 1;
case 'log'
if (~exist(loglevel,'var') || isempty(loglevel))
loglevel = 1;
end
switch(loglevel)
case 1
loglevelstr = 'ERROR: ';
case 2
loglevelstr = 'WARNING: ';
case 3
loglevelstr = 'STATUS: ';
otherwise
loglevelstr = 'UNKNOWN: ';
end
%log cmdstring to log file
if (isempty(mcLog))
%no log file defined
%just return so that scripts using mc_Error but not mcLog global
%can still function without errors
return;
end
if (exist('cmdstring')~=1 || isempty(cmdstring))
%function called but we didn't get anything to log
return;
end
fid = fopen(mcLog,'a');
if (fid == -1)
%could not open file for some reason
mc_Error('Could not open logfile %s for writing.',mcLog);
end
fprintf(fid,'%s\t%s\n',loglevelstr,cmdstring);
result = 1;
end

return;