Merge branch '_TMP_RELEASE_BRANCH_' into niak-cog

Author: poquirion

.gitignore

@@ -2,8 +2,5 @@
 BCT/
 *.swp
 *.pyc
-<<<<<<< HEAD
 *.asv
-=======
-jsonlab*/
->>>>>>> master
+psom_gb_vars_local.m

Dockerfile

@@ -1,4 +1,4 @@
-FROM simexp/octave:4.2.1_ubuntu_16
+FROM simexp/octave:4.2.1_cross_u16
 MAINTAINER Pierre-Olivier Quirion <[email protected]>
 
 ENV PSOM_VERSION 2.3.1
@@ -55,8 +55,10 @@ ADD util/bin/niak_jupyter /usr/local/bin/niak_jupyter
 ADD util/lib/psom_gb_vars_local.jupyter /usr/local/lib/psom_gb_vars_local.jupyter
 ADD util/lib/jupyter_notebook_config.py /usr/local/lib/jupyter_notebook_config.py
 EXPOSE 8080
+
+
 # To run with jupyter
-# docker run -it --rm  -v /niak_sandbox:$PWD --user $UID -p 8080:6666 simexp/niak:beta niak_jupyter
+# docker run -it --rm  -v /niak_sandbox:$PWD --user $UID -p 8080:6666 simexp/niak-cog niak_jupyter
 
 
 # Command to run octave as GUI

circle.yml

@@ -9,16 +9,19 @@ machine:
 
 dependencies:
   cache_directories:
-    - "data_test_niak_mnc1"
-    - "~/docker"
+    - "~/cache"
   override:
-    - if [[ -e ~/docker/niak_u16_o4.tar ]]; then docker load -i ~/docker/niak_u16_o4.tar; fi
-    - docker pull simexp/niak_dependency:u16_o4
-    - mkdir -p ~/docker; docker save simexp/niak_dependency:u16_o4 > ~/docker/niak_u16_o4.tar
+    - if [[ -e ~/cache/niak_o4_cross_u16.tar ]]; then docker load -i ~/cache/niak_o4_cross_u16.tar; fi
+    - docker pull simexp/niak_dependency:o4_cross_u16
+    - mkdir -p ~/cache
+    - ls ~/cache
+    - docker save -o ~/cache/niak_o4_cross_u16.tar simexp/niak_dependency:o4_cross_u16
+    - if [[ -e ~/cache/data_test_niak_mnc1 ]]; then cp ~/cache/data_test_niak_mnc1 . ; fi
+    - find ~/cache -type f -not -name "*data_test_niak_mnc1*" -not -name "*niak_o4_cross_u16*" -exec rm {} \; # delete old cache crap!
 
 test:
   override:
-    - docker run -it -v $PWD:$PWD simexp/niak_dependency:u16_o4 /bin/bash -lic "cd $PWD; octave --eval \"addpath(genpath(pwd));[pipe,opt,status] = niak_test_all(struct(),struct('psom',struct('mode_pipeline_manager','session','mode','background','max_queued',6,'flag_pause',false))); exit(status)\"":
+    - docker run -it -v $PWD:$PWD simexp/niak_dependency:o4_cross_u16 /bin/bash -lic "cd $PWD; octave --eval \"addpath(genpath(pwd));[pipe,opt,status] = niak_test_all(struct(),struct('psom',struct('mode_pipeline_manager','session','mode','background','max_queued',6,'flag_pause',false))); exit(status)\"":
        timeout: 21600
 
 #deployment:

commands/misc/niak_gb_vars.m

@@ -133,10 +133,10 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 %% NIAK version
-GB_NIAK.version = 'v1.1.0';
+GB_NIAK.version = 'v1.1.3';
 
 %% Target for tests
-GB_NIAK.target_test = 'ai';
+GB_NIAK.target_test = 'aj';
 
 %% In which path is NIAK ?
 str_read_vol = which('niak_read_vol');

commands/misc/niak_version.m

@@ -51,8 +51,8 @@
 %%%%%%%%%%%%%%%%%
 %%     SVN     %%
 %%%%%%%%%%%%%%%%%
-
-    versions.svn = psom_version_svn();
+% SVN not used anymore 
+%    versions.svn = psom_version_svn();
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %%     Release number     %%

commands/read_write/niak_grab_bids.m

@@ -17,12 +17,10 @@
 %    
 %   FUNC_HINT
 %       (string) A hint to pick one out of many fmri input for exemple 
-%       if the fmri study includes "sub-XX_task-rest-somthing_bold.nii.gz" 
-%       and "sub-XX_task-rest-a_thing_bold.nii.gz" and the something flavor 
-%       needs to be selected, FUNC_HINT = 'something', would do the trick.
-%       Note that FUNC_HINT needs to be a string somewhere between 
-%       "task-rest" and the extention (.nii or .mnc)
-%
+%       if the fmri study includes "sub-XX_task-rest-a_hint_bold.nii.gz"
+%       and "sub-XX_task-rest-a_thing_bold.nii.gz" and the "hint" flavor
+%       needs to be selected, FUNC_HINT = 'hint', would do the trick.
+%       
 %   ANAT_HINT
 %       (string) A hint to pick one out of many anat input. I only one file
 %       is present it will be used by default. If no hint is give an on file
@@ -194,8 +192,7 @@
 
             anat_path = strcat(session_path, filesep, 'anat');
             fmri_path = strcat(session_path, filesep, 'func');
-            fmri_regex = [ "(", subject_dir ".*task-", task_type ,".*", func_hint, ".*(nii|mnc).*)"];
-%            fmri_regex = [ "(", subject_dir ".*)"];
+            fmri_regex = [ "(", subject_dir ".*", func_hint, ".*(nii|mnc).*)"];
             anat_regex = ['(', subject_dir, '.*', anat_hint, '.*(nii|mnc).*)'] ;
             list_anat_dir = dir(anat_path) ;
             list_fmri_dir = dir(fmri_path) ;

commands/read_write/niak_read_hdr_nifti.m

@@ -78,12 +78,15 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 %% Opening the file
-list_formats = {'native','ieee-le','ieee-be'};
+list_formats = {'ieee-le','ieee-be'};
 fid = -1;
 tag_OK = 0;
 num_f = 1;
 
 while ((tag_OK == 0)||(fid < 0))&&(num_f <= length(list_formats))
+    if fid > 0 
+       fclose(fid)
+    end
     fid = fopen(file_name,'r',list_formats{num_f});
     if ~(fid<0)
         fseek(fid,0,'bof');

commands/read_write/niak_read_vol.m

@@ -233,6 +233,7 @@
 
                 [succ,msg] = system(instr_unzip);
                 if succ ~= 0
+                    fprintf(1,"can't run: %s\n", instr_unzip)
                     error(cat(2,'niak:read: ',msg,'. There was a problem unzipping the file. Please check that the command ''',GB_NIAK.unzip,''' works, or change this command using the variable GB_NIAK_UNZIP in the file NIAK_GB_VARS'));
                 end
 
@@ -282,4 +283,4 @@
         end
     end
 
-end
+end

commands/read_write/niak_write_nifti.m

@@ -122,23 +122,23 @@
 switch hdr.info.precision
     case 'uint8'
         hdr.details.datatype = 2;
-        hdr.details.bitpix = int16(8);
+        hdr.details.bitpix = 8;
         vol = uint8(vol);
     case 'int16' 
         hdr.details.datatype = 4;
-        hdr.details.bitpix = int16(16);
+        hdr.details.bitpix = 16;
         vol = int16(vol);
     case 'int32'
         hdr.details.datatype = 8;
-        hdr.details.bitpix = int16(32);
+        hdr.details.bitpix = 32;
         vol = int32(vol);
     case {'float32','float'}
         hdr.details.datatype = 16;
-        hdr.details.bitpix = int16(32);        
+        hdr.details.bitpix = 32;
     	vol = single(vol);
     case 'double'
         hdr.details.datatype = 64;
-        hdr.details.bitpix = int16(64);
+        hdr.details.bitpix = 64;
         vol = double(vol);
 end
 
@@ -318,7 +318,7 @@
 fbytes = ftell(fid);
 
 if ~isequal(fbytes,348),
-    msg = sprintf('For some reason, the header size is not 348 bytes. That should not be the case...');
+    msg = sprintf('For some reason, the header size is %i not 348 bytes. That should not be the case...', fbytes);
     warning(msg);
 end
 

extensions/niak_test/niak_test_connectome_demoniak.m

@@ -107,8 +107,10 @@
     out_c = [path_test.result 'report_test_regression_connectome_demoniak.csv'];
     opt_c.base_source = opt_demo.folder_out;
     opt_c.base_target = path_test.reference;
-    opt_c.black_list_source = [opt_demo.folder_out 'logs' filesep];
-    opt_c.black_list_target = [path_test.reference 'logs' filesep];
+    opt_c.black_list_source{1} = [opt_demo.folder_out 'logs' filesep];
+    opt_c.black_list_target{1} = [path_test.reference 'logs' filesep];
+    opt_c.black_list_source{2} = [opt_demo.folder_out 'pipe_parameters.mat' ];
+     opt_c.black_list_target{2} = [path_test.reference 'pipe_parameters.mat' ];
     pipeline = psom_add_job(pipeline,'test_connectome','niak_test_cmp_files',in_c,out_c,opt_c,false);
     pipeline.test_connectome.dep = list_jobs;
 end