Merge pull request #70 from RNA-FRETools/MASH-FRET-1.3.1

Mash fret 1.3.1 - Fix post-release bugs

Author: pflanzenhueter

MASH-FRET/.release_version.json

@@ -1,4 +1,4 @@
 {
-"tag" : "1.2.2",
-"prev_commit_hash" : "e6bd182"
+"tag" : "1.3.0",
+"prev_commit_hash" : "1aa5eac8"
 }

MASH-FRET/source/mod-trace-processing/_callbacks/pushbutton_expProj_Callback.m

@@ -32,18 +32,22 @@ function pushbutton_expProj_Callback(obj, evd, h_fig)
 else
     if ~isempty(p.proj{proj}.proj_file)
         projName = p.proj{proj}.proj_file;
-        [pName,projName,o] = fileparts(projName);
+        [pname,projName,o] = fileparts(projName);
+        if ~isempty(pname)
+            pname = what(pname); % get absolute path
+            pname = pname.path;
+        end
 
     elseif ~isempty(p.proj{proj}.exp_parameters{1,2})
-        pName = pwd;
+        pname = pwd;
         projName = getCorrName(p.proj{proj}.exp_parameters{1,2}, [], ...
             h_fig);
     else
-        pName = pwd;
+        pname = pwd;
         projName = 'project';
     end
 
-    defName = [pName filesep projName '.mash'];
+    defName = [pname filesep projName '.mash'];
     [fname,pname,o] = uiputfile(...
         {'*.mash;', 'MASH project(*.mash)'; ...
          '*.*', 'All Files (*.*)'}, 'Export MASH project', defName);

MASH-FRET/source/mod-trace-processing/management/downCompatibilityTP.m

@@ -103,7 +103,8 @@
     % added by MH, 15.1.2020: recover param for photobleaching-based gamma 
     % calculation, change "show cuttoff" to default laser for pb detection 
     % and insert default tolerance (= 3)
-    if size(p_proj.prm{n}{6},2)>=3 && size(p_proj.prm{n}{6}{3},2)<8
+    if size(p_proj.prm{n}{6},2)>=3 && size(p_proj.prm{n}{6}{3},2)>0 && ...
+            size(p_proj.prm{n}{6}{3},2)<8
         ldon = ones(nFRET,1);
         for i = 1:nFRET
             ldon(i,1) = find(exc==chanExc(p_proj.FRET(i,1)));

MASH-FRET/source/mod-trace-processing/plot/plotData.m

@@ -14,7 +14,7 @@ function plotData(mol, p, axes, prm, plotDscr)
 nExc = p.proj{proj}.nb_excitations;
 chanExc = p.proj{proj}.chanExc;
 
-incl = p.proj{proj}.bool_intensities(:,mol);
+incl = ~~p.proj{proj}.bool_intensities(:,mol)';
 I = p.proj{proj}.intensities_denoise(incl,((mol-1)*nChan+1):mol*nChan,:);
 if plotDscr
     discrI = p.proj{proj}.intensities_DTA(incl, ...

MASH-FRET/source/mod_histogram_analysis/_callbacks/pushbutton_thm_saveProj_Callback.m

@@ -28,8 +28,12 @@ function pushbutton_thm_saveProj_Callback(obj, evd, h_fig)
     else
         projName = 'project.mash';
     end
-    [pName, projName,o] = fileparts(projName);
-    defName = [pName filesep projName '.mash'];
+    [pname, projName,o] = fileparts(projName);
+    if ~isempty(pname)
+        pname = what(pname); % get absolute path
+        pname = pname.path;
+    end
+    defName = [pname filesep projName '.mash'];
     [fname,pname,o] = uiputfile(...
         {'*.mash;', 'MASH project(*.mash)'; ...
          '*.*', 'All Files (*.*)'}, 'Export MASH project', defName);

MASH-FRET/source/mod_simulation/molecules/ud_S_moleculesPan.m

@@ -58,11 +58,11 @@ function ud_S_moleculesPan(h_fig)
 % set state configuration
 set(h.edit_nbStates, 'String', num2str(p.nbStates));
 state = get(h.popupmenu_states, 'Value');
-set(h.popupmenu_states, 'Value', state, 'String', ...
-    cellstr(num2str((1:p.nbStates)'))');
 if state > p.nbStates
     state = p.nbStates;
 end
+set(h.popupmenu_states, 'Value', state, 'String', ...
+    cellstr(num2str((1:p.nbStates)'))');
 if p.impPrm && isfield(p.molPrm, 'stateVal')
     set([h.edit_nbStates h.popupmenu_states h.edit_stateVal ...
         h.edit_simFRETw], 'Enable', 'off');

MASH-FRET/source/mod_transition_analysis/_callbacks/pushbutton_TDPsaveProj_Callback.m

@@ -27,8 +27,12 @@ function pushbutton_TDPsaveProj_Callback(obj, evd, h_fig)
     else
         projName = 'project.mash';
     end
-    [pName, projName,o] = fileparts(projName);
-    defName = [pName filesep projName '.mash'];
+    [pname, projName,o] = fileparts(projName);
+    if ~isempty(pname)
+        pname = what(pname); % get absolute path
+        pname = pname.path;
+    end
+    defName = [pname filesep projName '.mash'];
     [fname,pname,o] = uiputfile(...
         {'*.mash;','MASH project(*.mash)';'*.*', 'All Files (*.*)'},...
         'Export MASH project',defName);

MASH-FRET/source/mod_video_processing/coordinates/updateSF.m

@@ -99,9 +99,20 @@
             % check for correct compilation of mex file for method Schmied2012
             if exist('forloop','file')~=3
                 h = guidata(h_fig);
-                if ~h.mute_actions
+                if h.mute_actions
                     disp(cat(2,'This spotfinder method can not be used:',...
                     ' problem with mex compilation.'));
+%                     disp('MASH-FRET will proceed to file compilation...');
+%                     try
+%                         mex(which('forloop.c'));
+%                     catch err
+%                         if strcmp(err.identifier,...
+%                                 'MATLAB:mex:NoCompilerFound_link_Win64')
+%                             disp()
+%                         else
+%                             throw(err);
+%                         end
+%                     end
                 else
                     setContPan(cat(2,'This spotfinder method can not be ',...
                         'used: problem with mex compilation.'),'error',...

MASH-FRET/source/mod_video_processing/ud_VP_nChan.m

@@ -93,7 +93,8 @@
 if size(p.itg_impMolPrm{1},1)<nC
     for c = 1:nC
         if c>size(p.itg_impMolPrm{1},1)
-            p.itg_impMolPrm{1}(c,1:2) = p.itg_impMolPrm{1}(c-1,1:2) + 2;
+            p.itg_impMolPrm{1} = ...
+                cat(1,p.itg_impMolPrm{1},p.itg_impMolPrm{1}(end,1:2)+2);
         end
     end
 end

MASH-FRET/source/project/checkField.m

@@ -116,6 +116,9 @@
 
 %% check video entries
 % check movie file >> set movie dimensions and reading infos
+if ~isempty(s.movie_file)
+    s.movie_file = which(s.movie_file); % get absolute path
+end
 if ~isempty(s.movie_file) && exist(s.movie_file, 'file')
     s.is_movie = 1;