verion 0.5.3

Author: wiheto

CHANGELOG.md

@@ -1,6 +1,24 @@
 # Changelog
 
-## Version 0.5.2 (In development)
+## Version 0.5.3
+
+### Improvements
+Improved tenetobids loading of temporal network files (reshaped correctly).
+
+Event files in tenetobids
+
+get_aux_file new name of get_confound_files.
+
+## Fixes
+Force order of columns for TemporalNetwork (fixes #73)
+
+Fixing problems regarding documentation and testing
+
+## Changes
+Changed numpy requirement to 1.20.1
+
+
+## Version 0.5.2 
 
 ### 0.5.2 Improvements
 
@@ -10,7 +28,7 @@ Improved sidecar checking.
 
 Added is_jsonable to utils.
 
-~~Check_packages added (credit to @jolespin). Modified somewhat as importing to globals within wrapper was not working. This was accepted then removed.~~
+~~Check_packages added (credit to @jolespin). Modified somewhat as importing to globals within wrapper was not working. This was accepted to main branch then removed.~~
 
 Session in TenetoBids now included, if present.
 

teneto/_version.py

@@ -1 +1 @@
-__version__ = "0.5.2-dev-c"
+__version__ = "0.5.3"

teneto/classes/bids.py

@@ -170,6 +170,7 @@ def run(self, run_func, input_params, output_desc=None, output_pipeline_name=Non
                 run_func, output_pipeline_name, self.exist_ok)
 
         input_files = self.get_selected_files(run_func.split('.')[-1])
+
         if not input_files:
             raise ValueError('No input files')
         if troubleshoot:
@@ -182,11 +183,12 @@ def run(self, run_func, input_params, output_desc=None, output_pipeline_name=Non
         for f in input_files:
             f_entities = f.get_entities()
             if get_confounds == 1:
-                input_params['confounds'] = self.get_confounds(f)
+                input_params['confounds'] = self.get_aux_file(f, filetype='confounds')
             data, sidecar = self.load_file(f)
-            self.troubleshoot('Input file name', {'f': f,
-                                            'f_entities': f_entities,
-                                            'sidecar': sidecar})
+            if troubleshoot:
+                self.troubleshoot('Input file name', {'f': f,
+                                                    'f_entities': f_entities,
+                                                    'sidecar': sidecar})
             if 'sidecar' in dict(funcparams):
                 input_params['sidecar'] = sidecar
             if data is None:
@@ -393,32 +395,39 @@ def update_bids_filter(self, filter_addons):
         """
         self.bids_filter.update(filter_addons)
 
-    def get_confounds(self, bidsfile, confound_filters=None):
-        """Tries to automatically get the confounds file of an input file, and loads it
+    def get_aux_file(self, bidsfile, filetype='confounds'):
+        """Tries to automatically get auxiliary data for input files, and loads it
 
         Paramters
         ==========
         bidsfile : BIDSDataFile or BIDSImageFile
             The BIDS file that the confound file is gong to be matched.
+        filetype : string
+            Can be confounds, events. 
+            Specified if you want to get the confound or events data.
         """
-        if confound_filters is None:
-            confound_filters = {}
+        if filetype == 'confounds':
+            suffix = 'regressors'
+        elif filetype == 'events': 
+            suffix = 'events'
+        else:
+            raise ValueError('unknown file type')
         # Get the entities of the filename
         file_entities = bidsfile.get_entities()
         # Ensure that the extension and suffix are correct
-        file_entities['suffix'] = 'regressors'
+        file_entities['suffix'] = suffix
         file_entities['extension'] = '.tsv'
         if 'desc' in file_entities:
             file_entities.pop('desc')
-        confoundsfile = self.BIDSLayout.get(**file_entities)
-        if len(confoundsfile) == 0:
-            raise ValueError('Non confounds found')
-        elif len(confoundsfile) > 1:
-            raise ValueError('More than one confounds file found')
-        # Load the confounds file
-        confounds = load_tabular_file(
-            confoundsfile[0].dirname + '/' + confoundsfile[0].filename, index_col=False)
-        return confounds
+        auxfile = self.BIDSLayout.get(**file_entities)
+        if len(auxfile) == 0:
+            raise ValueError('Non auxiliary file (type: ' + filetype + ') found')
+        elif len(auxfile) > 1:
+            raise ValueError('More than one auxiliary file (type: ' + filetype + ') found')
+        # Load the aux file
+        aux = load_tabular_file(
+            auxfile[0].dirname + '/' + auxfile[0].filename, index_col=False)
+        return aux
 
     def load_data(self, bids_filter=None):
         """Returns data, default is the input data.
@@ -484,3 +493,13 @@ def troubleshoot(self, stepname, status):
             print(status[step])
             print('++++++++')
         print('******** TROUBLESHOOT STEP: ' + stepname + ', end ********')
+
+    def load_events(self):
+        """
+        Loads event data for selected files
+        """
+        input_files = self.get_selected_files()
+        events = {}
+        for f in input_files:
+            events[f.filename] = self.get_aux_file(f, filetype='events')
+        return events

teneto/data/testdata/dummybids/sub-001/func/sub-001_task-a_run-1_events.tsv

@@ -0,0 +1,4 @@
+onset	duration	trial_type	value
+1	2	stim-a	1
+3	2	stim-b	2
+4	3	stim-a	1