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Prepare Osprey compilation - Helge #410

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May 23, 2022
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Prepare Osprey compilation - Helge #410

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8 changes: 4 additions & 4 deletions GUI/Osprey.m
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@
% HISTORY:
% 2019-07-11: First version of the code.
%% Check for available add-ons
[~] = osp_Toolbox_Check ('OspreyGUI',0);
[~,~] = osp_Toolbox_Check ('OspreyGUI',0);
%% Set up Layout
%Here we set up the color layout
%default colormap and fonts
Expand All @@ -30,7 +30,7 @@
logoFcn = @()imread('osprey.png', 'BackgroundColor', gui.colormap.Background);
logoBanner = uiw.utility.loadIcon(logoFcn);
% Here the intro banner is created
gui.d = uiw.dialog.About('Name', 'Osprey','Version','2.0.0','Date', 'April 12, 2022',...
gui.d = uiw.dialog.About('Name', 'Osprey','Version','2.1.0','Date', 'April 12, 2022',...
'Timeout', 3,'CustomText', 'Osprey is provided by Johns Hopkins University.',...
'ContactInfo', 'gabamrs@gmail.com','LogoCData', logoBanner);

Expand Down Expand Up @@ -79,7 +79,7 @@
set(gui.CreateJob,'Callback',{@onCreateJob});
% JobFile input button
gui.LoadJob = uicontrol('Parent', gui.Buttons,'Style','PushButton','String','Load Job file','ForegroundColor', gui.colormap.Foreground,...
'TooltipString', 'Load a Job (.m or .csv-file)');
'TooltipString', 'Load a Job (.m, .json or .csv-file) Osprey Standalone Supports .json and .csv files only');
set(gui.LoadJob,'Units','Normalized','Position',[0.1 0.75 0.8 0.08], 'FontSize', 16, 'FontName', gui.font, 'FontWeight', 'Bold');
set(gui.LoadJob,'Callback',{@onLoadJob});
% MRSCont input button
Expand Down Expand Up @@ -161,7 +161,7 @@ function onCreateJob( ~, ~) %Callback Create Job button

function onLoadJob( ~, ~) %Callback Load Job button
% User wants to quit out of the application
gui.out = uipickfiles('FilterSpec',[ospFolder], 'REFilter', '\.m$|\.csv$','NumFiles',1,'Prompt','Select Osprey job file (.m or .csv-file)');
gui.out = uipickfiles('FilterSpec',[ospFolder], 'REFilter', '\.m$|\.csv$|\.json$','NumFiles',1,'Prompt','Select Osprey job file (.m, .json or .csv-file)');
if iscell(gui.out)
loadJob(gui);
end
Expand Down
22 changes: 11 additions & 11 deletions GUI/OspreyGUI.m
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Expand Up @@ -87,17 +87,17 @@
end
end
diary off

% This is for the compiled GUI
MRSCont.flags.hasSPM = 1;

% Toolbox check
if isfield(MRSCont.flags,'isToolChecked')
[MRSCont.flags.hasSPM,MRSCont.ver.CheckOsp] = osp_Toolbox_Check ('OspreyGUI',MRSCont.flags.isToolChecked);
else
[MRSCont.flags.hasSPM,MRSCont.ver.CheckOsp] = osp_Toolbox_Check ('OspreyGUI',0);
MRSCont.flags.isToolChecked = 1;
end
if MRSCont.flags.hasSPM
load(fullfile(gui.folder.ospFolder,'GUI','SPMpath.mat'),'SPMpath')
gui.folder.spmversion = SPMpath;
end

% Show warning if the version is different
if ~strcmp(MRSCont.ver.Osp,MRSCont.ver.CheckOsp)
Expand Down Expand Up @@ -150,7 +150,7 @@
end

%Setting up remaining values in dependence of the conducted processing steps
if MRSCont.flags.didLoadData %Get variables regarding the loading
if MRSCont.flags.didLoad %Get variables regarding the loading
if ~isempty(MRSCont.raw{1,gui.controls.Selected}.seq)
if strcmp(sprintf('\n'),MRSCont.raw{1,gui.controls.Selected}.seq(end)) %Clean up Sequence Name if needed
gui.load.Names.Seq = MRSCont.raw{1,gui.controls.Selected}.seq(1:end-1);
Expand Down Expand Up @@ -266,7 +266,7 @@
end

end
gui.waitbar.overall = MRSCont.flags.didLoadData+MRSCont.flags.didProcess+MRSCont.flags.didFit+MRSCont.flags.didCoreg+MRSCont.flags.didSeg+MRSCont.flags.didQuantify+MRSCont.flags.didOverview;
gui.waitbar.overall = MRSCont.flags.didLoad+MRSCont.flags.didProcess+MRSCont.flags.didFit+MRSCont.flags.didCoreg+MRSCont.flags.didSeg+MRSCont.flags.didQuantify+MRSCont.flags.didOverview;
gui.waitbar.step = 1/ gui.waitbar.overall;

%Version check and updating log file
Expand Down Expand Up @@ -333,7 +333,7 @@
gui.layout.b_load = uicontrol('Parent', gui.layout.p2,'Style','PushButton','String','Load data','Enable','on','ForegroundColor', gui.colormap.Foreground);
set(gui.layout.b_load,'Units','Normalized','Position',[0.1 0.75 0.8 0.08], 'FontSize', 16, 'FontName', gui.font, 'FontWeight', 'Bold','Tag','LoadButton');

if (MRSCont.flags.didLoadData == 1 && isfield(MRSCont, 'raw'))
if (MRSCont.flags.didLoad == 1 && isfield(MRSCont, 'raw'))
sz_raw = size(MRSCont.raw);
if (gui.controls.nDatasets(1) >= sz_raw(end))
gui.layout.b_load.Enable = 'off';
Expand All @@ -346,7 +346,7 @@
set(gui.layout.b_proc,'Units','Normalized','Position',[0.1 0.75 0.8 0.08], 'FontSize', 16, 'FontName', gui.font, 'FontWeight', 'Bold','Tag','ProcButton');
if (MRSCont.flags.didProcess == 1 && isfield(MRSCont, 'raw') && (gui.controls.nDatasets(1) >= length(MRSCont.processed.metab)))
gui.layout.b_proc.Enable = 'off';
else if ~(MRSCont.flags.didLoadData == 1 && isfield(MRSCont, 'raw') && (gui.controls.nDatasets(1) >= sz_raw(end)))
else if ~(MRSCont.flags.didLoad == 1 && isfield(MRSCont, 'raw') && (gui.controls.nDatasets(1) >= sz_raw(end)))
gui.layout.b_proc.Enable = 'off';
end
end
Expand All @@ -364,7 +364,7 @@
% Coregister button
gui.layout.b_coreg = uicontrol('Parent', gui.layout.p2,'Style','PushButton','String','CoRegister','Enable','off','ForegroundColor', gui.colormap.Foreground);
set(gui.layout.b_coreg,'Units','Normalized','Position',[0.1 0.59 0.8 0.08], 'FontSize', 16, 'FontName', gui.font, 'FontWeight', 'Bold','Tag','CoregButton');
if MRSCont.flags.hasSPM == 1 && ~isempty(MRSCont.files_nii) && ~(MRSCont.flags.didCoreg == 1 && isfield(MRSCont, 'coreg') && (gui.controls.nDatasets(1) >= length(MRSCont.coreg.vol_image))) && (MRSCont.flags.didLoadData == 1 && isfield(MRSCont, 'raw') && (gui.controls.nDatasets(1) >= length(MRSCont.raw)))
if MRSCont.flags.hasSPM == 1 && ~isempty(MRSCont.files_nii) && ~(MRSCont.flags.didCoreg == 1 && isfield(MRSCont, 'coreg') && (gui.controls.nDatasets(1) >= length(MRSCont.coreg.vol_image))) && (MRSCont.flags.didLoad == 1 && isfield(MRSCont, 'raw') && (gui.controls.nDatasets(1) >= length(MRSCont.raw)))
if ~(isfield(MRSCont.flags,'addImages') && (MRSCont.flags.addImages == 0) && MRSCont.flags.moved)
gui.layout.b_coreg.Enable = 'on';
end
Expand Down Expand Up @@ -470,7 +470,7 @@
% been completed:
gui.controls.waitbar = waitbar(0,'Start','Name','Loading your MRS Container');
waitbar(0,gui.controls.waitbar,'Loading your raw spectra')
if (MRSCont.flags.didLoadData == 1 && isfield(MRSCont, 'raw') && (gui.controls.nDatasets(1) >= sz_raw(end))) % Was data loaded at all that can be looked at?
if (MRSCont.flags.didLoad == 1 && isfield(MRSCont, 'raw') && (gui.controls.nDatasets(1) >= sz_raw(end))) % Was data loaded at all that can be looked at?
set(gui.layout.tabs, 'Visible','on');
osp_iniLoadWindow(gui);
if MRSCont.flags.isMRSI
Expand Down Expand Up @@ -528,7 +528,7 @@
set(gui.controls.b_save_meanOvTab,'Callback',{@osp_onPrint,gui});
end
gui.layout.tabs.Selection = 1;
if ~MRSCont.flags.didLoadData %Turn of Listbox if data has not been loaded
if ~MRSCont.flags.didLoad %Turn of Listbox if data has not been loaded
gui.layout.ListBox.Enable = 'off';
end
set(gui.layout.tabs, 'Visible','on');
Expand Down
14 changes: 8 additions & 6 deletions GUI/osp_Toolbox_Check.m
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Original file line number Diff line number Diff line change
Expand Up @@ -30,11 +30,13 @@
%
% HISTORY:
% 2020-05-15: First version of the code.
%%
%%% 1. GET SPMPATH AND TOOLBOXES%%%
warning('off','MATLAB:javaclasspath:jarAlreadySpecified');
OspreyVersion = 'Osprey 2.0.0';
%% % 1. SAVE OSPREY VERSION%%%
%%% 1. SAVE OSPREY VERSION%%%
OspreyVersion = 'Osprey 2.1.0';
fprintf(['Timestamp %s ' OspreyVersion ' ' Module '\n'], datestr(now,'mmmm dd, yyyy HH:MM:SS'));
hasSPM = 1; % For the compiled GUI
%% % 2. GET SPMPATH AND TOOLBOXES%%%
warning('off','MATLAB:javaclasspath:jarAlreadySpecified');
addons = matlab.addons.installedAddons;
available = cellstr(table2cell(addons(:,1)));
for tl = 1 : size(addons,1)
Expand Down Expand Up @@ -90,7 +92,7 @@
available(find(cellfun(@(a)~isempty(a)&&a<1,enabled)), :) = [];
end

%%% 2. CHECK AVAILABILTY %%%
%%% 3. CHECK AVAILABILTY %%%
switch Module
case 'OspreyGUI'
ModuleString = 'fully run \bfOsprey';
Expand Down Expand Up @@ -130,7 +132,7 @@
missingSpecific = setdiff(neededSpecific,available);
missing = setdiff(neededGlobal,available);

%%% 3. CREATE WARNING MESSAGES %%%
%%% 4. CREATE WARNING MESSAGES %%%
if ~ToolChecked
warningMsg = cellstr({});
warning_count = 1;
Expand Down
6 changes: 5 additions & 1 deletion GUI/osp_onGit.m
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Expand Up @@ -23,5 +23,9 @@ function osp_onGit( ~, ~)
% 2020-01-16: First version of the code.
%%% 1. Visit websites %%%

web('https://github.com/schorschinho/osprey', '-browser'); %Github Link
try
web('https://github.com/schorschinho/osprey', '-browser'); %Github Link
catch
system('open "https://github.com/schorschinho/osprey"'); %for compiled Osprey
end
end
6 changes: 4 additions & 2 deletions GUI/osp_onPub.m
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Expand Up @@ -23,7 +23,9 @@ function osp_onPub( ~, ~)
% 2020-01-16: First version of the code.
%%% 1. Visit websites %%%

try

web('https://www.ncbi.nlm.nih.gov/sites/myncbi/1lo2w1io3qTgqH/collections/59221405/public/', '-browser'); %HERCULES paper will create a pubmed collection for referencing all papers

web('https://www.ncbi.nlm.nih.gov/sites/myncbi/1lo2w1io3qTgqH/collections/59221405/public/', '-browser'); %HERCULES paper will create a pubmed collection for referencing all papers
catch
system('open "https://www.ncbi.nlm.nih.gov/sites/myncbi/1lo2w1io3qTgqH/collections/59221405/public/"'); % for the compiled version of Osprey
end
3 changes: 1 addition & 2 deletions coreg/OspreyCoreg.m
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Expand Up @@ -36,8 +36,7 @@

warning('off','all');
% Checking for version, toolbox, and previously run modules
osp_CheckRunPreviousModule(MRSCont, 'OspreyCoreg');
[~,MRSCont.ver.CheckOsp ] = osp_Toolbox_Check ('OspreyCoreg',MRSCont.flags.isGUI);
[~,MRSCont.ver.CheckOsp ] = osp_CheckRunPreviousModule(MRSCont, 'OspreyCoreg');


% Set up saving location
Expand Down
3 changes: 1 addition & 2 deletions fit/OspreyFit.m
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Expand Up @@ -39,8 +39,7 @@

% ----- Load fit settings and fit the metabolite data -----
% Checking for version, toolbox, and previously run modules
osp_CheckRunPreviousModule(MRSCont, 'OspreyFit');
[~,MRSCont.ver.CheckOsp ] = osp_Toolbox_Check('OspreyFit',MRSCont.flags.isGUI);
[~,MRSCont.ver.CheckOsp ] = osp_CheckRunPreviousModule(MRSCont, 'OspreyFit');
% Start timer
MRSCont.runtime.Fit = 0;

Expand Down
Binary file modified job/CreateOspreyJob.mlapp
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