New version of load_spm_pattern.m with improved 'single' flag handling.

Revamped versions of unit_spm scripts

core/io/load_spm_pattern.m

@@ -117,7 +117,7 @@
 
 %% Create a volume structure
 vol = spm_vol(filenames);
-tmp_data = []; %#ok<NASGU>
+
 
     %%%%%%%%%%%%%%%%%%%%%%
     %sylvains contribution
@@ -132,8 +132,12 @@
 end;
 
 % allocate all at once to avoid reshaping iteratively
-tmp_data = zeros(mSize, total_m);
-
+tmp_data = []; %#ok<NASGU>  This is necessary as the command is now wrapped in an if/else
+if args.single
+    tmp_data = zeros(mSize, total_m,'single');
+else
+    tmp_data = zeros(mSize, total_m);
+end
 total_m = 0;
     %% end contribution
 for h = 1:nFiles % start looping thru the files being used.

tests/spm_test_omnibus.m

@@ -35,6 +35,9 @@
 % DEFAULTS
 % Before we get started we need to setup a single default.
 defaults.fextension = '.nii';
+defaults.single = 'false';
+global single
+
 
 args = propval(varargin,defaults);
 
@@ -44,6 +47,12 @@
     fextension=defaults.fextension;
 end
 
+if (isfield(args,'single'))
+    single = args.single;
+else
+    single = defaults.single;
+end
+
 %% Load up errs and warns so that they you know... work
 errs = {};
 warns = {};
@@ -54,19 +63,19 @@
 %% Run Functional Tests One by One and populate errs/warns.
 
 % run basic spm ana test
-[errs{end+1} warns{end+1}] = unit_spm_ana('fextension',fextension);
+[errs{end+1} warns{end+1}] = unit_spm_ana('fextension',fextension,'single',single);
 
 % run the tutorial comparison
-[errs{end+1} warns{end+1}] = unit_spm_afni_tutcompare('fextension',fextension);
+[errs{end+1} warns{end+1}] = unit_spm_afni_tutcompare('fextension',fextension,'single',single);
 
 % run afni compare
-[errs{end+1} warns{end+1}] = unit_spm_ana_afnicompare('fextension',fextension);
+[errs{end+1} warns{end+1}] = unit_spm_ana_afnicompare('fextension',fextension,'single',single);
 
 % haxby data compare
-[errs{end+1} warns{end+1}] = unit_spm_ana_haxby_dat_compare('fextension',fextension);
+[errs{end+1} warns{end+1}] = unit_spm_ana_haxby_dat_compare('fextension',fextension,'single',single);
 
 %cell array tests
-[errs{end+1} warns{end+1}] = unit_spm_cellarrayfilename_load('fextension',fextension);
+[errs{end+1} warns{end+1}] = unit_spm_cellarrayfilename_load('fextension',fextension,'single',single);
 
 
 end

tests/unit_spm_afni_tutcompare.m

@@ -32,8 +32,10 @@
 % The afni data used in this test was created from the corresponding SPM
 % test data using the afni 3dcopy command with no flags or special
 % commands.
-
 defaults.fextension = '';
+defaults.single = false;
+global single
+
 
 args = propval(varargin,defaults);
 
@@ -43,6 +45,13 @@
     fextension=defaults.fextension;
 end
 
+if (isfield(args,'single'))
+    single = args.single;
+else
+    single = defaults.single;
+    disp('The tutorials have no support for the single command');
+end
+
 errs = {};
 warns = {};
 

tests/unit_spm_ana.m

@@ -47,6 +47,9 @@
 % DEFAULTS
 % Before we get started we need to setup a single default.
 defaults.fextension = '';
+defaults.single = false;
+global single
+
 
 args = propval(varargin,defaults);
 
@@ -56,6 +59,12 @@
     fextension=defaults.fextension;
 end
 
+if (isfield(args,'single'))
+    single = args.single;
+else
+    single = defaults.single;
+end
+
 errs = {};
 warns = {};
 
@@ -185,15 +194,15 @@
 
   % load the pattern the first time
 %  temp_subj_001=load_spm_pattern(temp_subj_001, 'ana_brain','spm_ana_mask',raw_source_filenames{n},'beta_defaults','true');
-  temp_subj_001=load_spm_pattern(temp_subj_001, 'ana_brain','spm_ana_mask',raw_source_filenames{n});
+  temp_subj_001=load_spm_pattern(temp_subj_001, 'ana_brain','spm_ana_mask',raw_source_filenames{n},'single',single);
   %and write it back out.
   write_to_spm(temp_subj_001,'pattern','ana_brain','output_filename',['testwork/utest_' num2str(n) '_' ],'padding',base_padding,'fextension',fextension);
 
   % this happens due to the way files are saves the dest name
   % would be valid if they weren't individual files.
   %
   % what does this comment mean???
-  temp_subj_002=load_spm_pattern(temp_subj_002, 'ana_brain','spm_ana_mask',['testwork/utest_' num2str(n) '_' fextension]); 
+  temp_subj_002=load_spm_pattern(temp_subj_002, 'ana_brain','spm_ana_mask',['testwork/utest_' num2str(n) '_' fextension],'single',single);
   data1 = get_mat(temp_subj_001,'pattern','ana_brain');
 
   data2 = get_mat(temp_subj_002,'pattern','ana_brain');
@@ -235,7 +244,7 @@
     index=num2str(i);
   raw_filenames{i} = ['haxby8_r' index fextension];
 end
-subj = load_spm_pattern(subj,'epi','VT_category-selective',raw_filenames);
+subj = load_spm_pattern(subj,'epi','VT_category-selective',raw_filenames,'single',single);
 %keyboard;
 write_to_spm(subj,'pattern','epi','output_filename','testwork/utest2_','padding',base_padding,'fextension',fextension);
 

tests/unit_spm_ana_afnicompare.m

@@ -38,6 +38,9 @@
 % DEFAULTS
 % Before we get started we need to setup a single default.
 defaults.fextension = '';
+defaults.single = 'false';
+global single
+
 
 args = propval(varargin,defaults);
 
@@ -47,6 +50,12 @@
     fextension=defaults.fextension;
 end
 
+if (isfield(args,'single'))
+    single = args.single;
+else
+    single = defaults.single;
+end
+
 errs = {};
 warns = {};
 
@@ -155,9 +164,9 @@
 
 
     % load the pattern the first time
-    temp_subj_001=load_spm_pattern(temp_subj_001, 'ana_brain','spm_ana_mask',spm_file_names{n});
-
-    temp_subj_001=load_afni_pattern(temp_subj_001, 'afni_brain','spm_ana_mask',afni_file_names{n});
+    temp_subj_001=load_spm_pattern(temp_subj_001, 'ana_brain','spm_ana_mask',spm_file_names{n},'single',single);
+    %temp_subj_001=load_spm_pattern(temp_subj_001, 'ana_brain','spm_ana_mask',spm_file_names{n});
+    temp_subj_001=load_afni_pattern(temp_subj_001, 'afni_brain','spm_ana_mask',afni_file_names{n},'single',single);
 
     data1 = get_mat(temp_subj_001,'pattern','ana_brain');
 

tests/unit_spm_ana_haxby_dat_compare.m

@@ -20,6 +20,9 @@
 % DEFAULTS
 % Before we get started we need to setup a single default.
 defaults.fextension = '';
+defaults.single = 'false';
+global single
+
 
 args = propval(varargin,defaults);
 
@@ -29,6 +32,12 @@
     fextension=defaults.fextension;
 end
 
+if (isfield(args,'single'))
+    single = args.single;
+else
+    single = defaults.single;
+end
+
 errs = [];
 warns = [];
 
@@ -47,16 +56,16 @@
 
 write_to_spm(working_subj,'pattern','epi_z_anova_1','new_header','true','pathname','testwork','output_filename','anova_out','fextension',fextension);
 
-working_subj=load_spm_pattern(working_subj,'epi_anova_compare','VT_category-selective',['testwork/anova_out' fextension]);
+working_subj=load_spm_pattern(working_subj,'epi_anova_compare','VT_category-selective',['testwork/anova_out' fextension],'single',single);
 
 
 
 mainpat = get_mat(working_subj,'pattern','epi_z_anova_1');
 
 comparepat = get_mat(working_subj,'pattern','epi_anova_compare');
-
+keyboard;
 if ~isequal(mainpat,comparepat)
-    errs(end+1) = 'data does not compare properly, arbitrary header writeout failed.';
+    errs{end+1} = 'data does not compare properly, arbitrary header writeout failed.  This is normal for the single true flag.';
 end