Merge pull request #17 from VisLab/main

Updated the tests for the hed_wrappers

hedmat/hed_wrappers/get_schema_obj.m

@@ -8,15 +8,14 @@
 % Returns:
 %     schema_obj - A hedSchema object
 %
-   hedModule = py.importlib.import_module('hed');
-
-   if py.isinstance(schema, hedModule.HedSchema) || ...
-       py.isinstance(schema, hedModule.HedSchemaGroup)
-       schema_obj = schema;
-   elseif ischar(schema)
-       schema_obj = hedModule.schema.load_schema_version(schema);
+   hmod = py.importlib.import_module('hed');
+   if ischar(schema)
+       schema_obj = hmod.load_schema_version(schema);
    elseif iscell(schema)
-       schema_obj = hedModule.schema.load_schema_version(py.list(schema));
+       schema_obj = hmod.load_schema_version(py.list(schema));
+   elseif py.isinstance(schema, hmod.HedSchema) || ...
+       py.isinstance(schema, hmod.HedSchemaGroup)
+       schema_obj = schema;
    else
        schema_obj = py.None;
    end

hedmat/hed_wrappers/get_string_objs.m

@@ -16,9 +16,9 @@
 % To manipulate directly in MATLAB -- convert to a cell array of char
 % using string(cell(hedObjs))
 
-    amod = py.importlib.import_module('hed.tools.analysis');
-    event_manager = amod.event_manager.EventManager(events, schema);
-    tag_manager = amod.hed_tag_manager.HedTagManager(event_manager, ...
+    hmod = py.importlib.import_module('hed');
+    event_manager = hmod.EventManager(events, schema);
+    tag_manager = hmod.HedTagManager(event_manager, ...
         py.list(remove_types));
     hed_string_objs = ...
         tag_manager.get_hed_objs(include_context, replace_defs);

hedmat/hed_wrappers/get_tabular_obj.m

@@ -1,9 +1,10 @@
-function tabular_obj = get_tabular_obj(events, sidecar)
+function tabular_obj = get_tabular_obj(events, sidecar, sampling_rate)
 % Returns a HED TabularInput object representing events or other columnar item.
 % 
 % Parameters:
 %    events - string, struct, or TabularInput for tabular data.
 %    sidecar - Sidecar object, string, or struct or py.None
+%    sampling_rate - optional sampling rate if struct doesn't have onset
 %
 % Returns:
 %     tabular_obj - HEDTools TabularInput object representing tabular data.
@@ -19,7 +20,13 @@
     else
         sidecar_obj = get_sidecar_obj(sidecar);
     end
-    if ischar(events) || isstring(events)
+    if nargin == 1
+        sampling_rate = NaN;
+    end
+    if isstruct(events)
+        events = struct2string(rectify_events(events, sampling_rate));
+        tabular_obj = umod.str_to_tabular(events, sidecar_obj);
+    elseif ischar(events) || isstring(events)
         tabular_obj = umod.str_to_tabular(events, sidecar_obj);
     else
         throw(MException('getTabularInput:Invalid input'))

hedmat/hed_wrappers/validate_bids.m

@@ -8,7 +8,8 @@
 %     issue_string - A string with the validation issues suitable for
 %                   printing (has newlines).
 %
-    py.importlib.import_module('hed');
-    bids = py.hed.tools.BidsDataset(data_root);
+    hed = py.importlib.import_module('hed')
+    % amod = py.importlib.import_module('hed.tools.analysis.annotation_util');
+    bids = hed.get_bids_dataset(data_root);
     issues = bids.validate();
     issue_string = string(py.hed.get_printable_issue_string(issues));

tests/test_hed_wrappers/TestGetHedFactor.m

@@ -16,13 +16,12 @@ function importPythonModules(testCase)
             json_path = fullfile(data_path, filesep, ...
                 'task-FacePerception_events.json'); 
             events_path = fullfile(data_path, filesep, 'sub-002', ...
-                filesep, 'ses-1', filesep, 'EEG', filesep,...
+                filesep, 'ses-1', filesep, 'eeg', filesep,...
                 'sub-002_ses-1_task-FacePerception_run-1_events.tsv'); 
             events = fileread(events_path);
             sidecar = fileread(json_path);
             testCase.tabular_obj = get_tabular_obj(events, sidecar);
-            testCase.schema = ...
-                testCase.hmod.schema.load_schema_version('8.2.0');
+            testCase.schema = testCase.hmod.load_schema_version('8.2.0');
         end
     end
 

tests/test_hed_wrappers/TestGetSchemaObj.m

@@ -11,13 +11,21 @@ function importPythonModules(testCase)
     end
 
     methods (Test)
+        function testAlreadySchema(testCase)
+            schema = testCase.hmod.load_schema_version('8.2.0');
+            schema1 = get_schema_obj(schema);
+            testCase.assertTrue(py.isinstance(schema, ...
+                testCase.hmod.HedSchema))
+            testCase.assertTrue(py.isinstance(schema1, ...
+                testCase.hmod.HedSchema))
+        end
 
         function testSimpleVersion(testCase)
             % Test single version
             version = '8.2.0';
             schema = get_schema_obj(version);
             assertTrue(testCase, py.isinstance(schema, ...
-                       testCase.hmod.schema.HedSchema), ...
+                       testCase.hmod.HedSchema), ...
                        'The object is not an instance of HedSchema.');
             version = char(schema.version);
             testCase.verifyEqual(version, '8.2.0', ...
@@ -29,7 +37,7 @@ function testMultipleVersions(testCase)
             version = {'ts:8.2.0', 'score_1.1.0'};
             schema = get_schema_obj(version);
             assertTrue(testCase, py.isinstance(schema, ...
-                       testCase.hmod.schema.HedSchemaGroup), ...
+                       testCase.hmod.HedSchemaGroup), ...
                        'The object is not an instance of HedSchemaGroup.');
             versions = cell(schema.get_schema_versions());
             testCase.verifyEqual(char(versions{1}), 'ts:8.2.0', ...

tests/test_hed_wrappers/TestGetStringObjs.m

@@ -19,13 +19,12 @@ function importPythonModules(testCase)
             json_path = fullfile(data_path, filesep, ...
                 'task-FacePerception_events.json');
             events_path = fullfile(data_path, filesep, 'sub-002', ...
-                filesep, 'ses-1', filesep, 'EEG', filesep,...
+                filesep, 'ses-1', filesep, 'eeg', filesep,...
                 'sub-002_ses-1_task-FacePerception_run-1_events.tsv');
             events = fileread(events_path);
             sidecar = fileread(json_path);
             testCase.tabular_obj = get_tabular_obj(events, sidecar);
-            testCase.schema = ...
-                testCase.hmod.schema.load_schema_version('8.2.0');
+            testCase.schema = testCase.hmod.load_schema_version('8.2.0');
         end
     end
 

tests/test_hed_wrappers/TestGetTabularObj.m

@@ -16,7 +16,7 @@ function importPythonModules(testCase)
             testCase.json_path = fullfile(data_path, filesep, ...
                 'task-FacePerception_events.json'); 
             testCase.events_path = fullfile(data_path, filesep, 'sub-002', ...
-                filesep, 'ses-1', filesep, 'EEG', filesep,...
+                filesep, 'ses-1', filesep, 'eeg', filesep,...
                 'sub-002_ses-1_task-FacePerception_run-1_events.tsv'); 
         end
     end

tests/test_hed_wrappers/TestValidateBids.m

@@ -1,13 +1,11 @@
 classdef TestValidateBids < matlab.unittest.TestCase
 
     properties
-        hmod
         data_root
     end
 
     methods (TestClassSetup)
         function importPythonModules(testCase)
-            testCase.hmod = py.importlib.import_module('hed');
             [cur_dir, ~, ~] = fileparts(mfilename("fullpath"));
             testCase.data_root = fullfile(cur_dir, filesep, '..', ...
                 filesep, '..', filesep, 'data', filesep, ...

tests/test_hed_wrappers/TestValidateEvents.m

@@ -23,7 +23,7 @@ function importPythonModules(testCase)
             testCase.bad_sidecar = testCase.hmod.Sidecar(bpath); 
             epath = fullfile(data_path, ...
                 filesep, 'eeg_ds003645s_hed_demo', filesep, 'sub-002', ...
-                filesep, 'ses-1', filesep, 'EEG', filesep,...
+                filesep, 'ses-1', filesep, 'eeg', filesep,...
                 'sub-002_ses-1_task-FacePerception_run-1_events.tsv'); 
             testCase.event_string = fileread(epath);