dicarlo.BashivanKar2019 (#39)

* Lookup and tests for BashivanKar2019.

* Revert packaging of dicarlo.BashivanKar2019 so I can repackage as only two assemblies.

* Consolidated assemblies for synthetic data (dicarlo.BashivanKar2019).  Added NaNs to tests.

* Trigger Travis.

README.md

@@ -3,3 +3,4 @@
 # BrainIO collection
 
 Utility to retrieve and write to the BrainIO collection of stimulus sets and assemblies.
+

brainio_collection/lookup.csv

@@ -228,3 +228,9 @@ aru.Kuzovkin2018,stimulus_set,,S3,https://brainio.contrib.s3.amazonaws.com/image
 aru.Kuzovkin2018,assembly,NeuronRecordingAssembly,S3,https://brainio.contrib.s3.amazonaws.com/assy_aru_Kuzovkin2018.nc,5fae8b283a043562ce9925d48ad99db151f39067,aru.Kuzovkin2018
 dicarlo.Rust2012.single,assembly,NeuronRecordingAssembly,S3,https://brainio.dicarlo.s3.amazonaws.com/assy_dicarlo_Rust2012_single.nc,4ef420e70fbd0de3745df5be7c83dfc0a8f2e528,dicarlo.Rust2012
 dicarlo.Rust2012.array,assembly,NeuronRecordingAssembly,S3,https://brainio.dicarlo.s3.amazonaws.com/assy_dicarlo_Rust2012_array.nc,6709b641751370acfccd9567e3d75b71865a71ab,dicarlo.Rust2012
+dicarlo.BashivanKar2019.naturalistic,stimulus_set,StimulusSet,S3,https://brainio.dicarlo.s3.amazonaws.com/image_dicarlo_BashivanKar2019_naturalistic.csv,48ef84282552b8796142ffe7d0d2c632f8ef061a,
+dicarlo.BashivanKar2019.naturalistic,stimulus_set,,S3,https://brainio.dicarlo.s3.amazonaws.com/image_dicarlo_BashivanKar2019_naturalistic.zip,d7b71b431cf23d435395205f1e38036a9e10acca,
+dicarlo.BashivanKar2019.naturalistic,assembly,NeuronRecordingAssembly,S3,https://brainio.dicarlo.s3.amazonaws.com/assy_dicarlo_BashivanKar2019_naturalistic.nc,1ec2f32ef800f0c6e15879d883be1d55b51b8b67,dicarlo.BashivanKar2019.naturalistic
+dicarlo.BashivanKar2019.synthetic,stimulus_set,StimulusSet,S3,https://brainio.dicarlo.s3.amazonaws.com/image_dicarlo_BashivanKar2019_synthetic.csv,81da195e9b2a128b228fc4867e23ae6b21bd7abd,
+dicarlo.BashivanKar2019.synthetic,stimulus_set,,S3,https://brainio.dicarlo.s3.amazonaws.com/image_dicarlo_BashivanKar2019_synthetic.zip,e2de33f25c5c19bcfb400055c1db399d553487e5,
+dicarlo.BashivanKar2019.synthetic,assembly,NeuronRecordingAssembly,S3,https://brainio.dicarlo.s3.amazonaws.com/assy_dicarlo_BashivanKar2019_synthetic.nc,f687c8d26f8943dc379dbcbe94d3feb148400c6b,dicarlo.BashivanKar2019.synthetic

tests/test_assemblies.py

@@ -31,7 +31,6 @@
         'dicarlo.Kar2018hvm',
         'dicarlo.Kar2018cocogray',
         'klab.Zhang2018search_obj_array',
-        'aru.Kuzovkin2018',
         'dicarlo.Rajalingham2020',
         'dicarlo.SanghaviMurty2020',
         'dicarlo.SanghaviJozwik2020',
@@ -42,7 +41,8 @@
         'dicarlo.Seibert2019',
         'dicarlo.Rust2012.single',
         'dicarlo.Rust2012.array',
-
+        'dicarlo.BashivanKar2019.naturalistic',
+        'dicarlo.BashivanKar2019.synthetic',
 ))
 def test_list_assembly(assembly):
     l = brainio_collection.list_assemblies()
@@ -79,7 +79,8 @@ def test_list_assembly(assembly):
     pytest.param('dicarlo.Seibert2019', marks=[pytest.mark.private_access]),
     pytest.param('dicarlo.Rust2012.single', marks=[pytest.mark.private_access]),
     pytest.param('dicarlo.Rust2012.array', marks=[pytest.mark.private_access]),
-
+    pytest.param('dicarlo.BashivanKar2019.naturalistic', marks=[pytest.mark.private_access]),
+    pytest.param('dicarlo.BashivanKar2019.synthetic', marks=[pytest.mark.private_access]),
 ])
 def test_existence(assembly_identifier):
     assert brainio_collection.get_assembly(assembly_identifier) is not None
@@ -318,3 +319,12 @@ def test_coords(self):
         assert len(set(assembly['region'].values)) == 2
 
 
+@pytest.mark.parametrize('assembly,shape,nans', [
+    pytest.param('dicarlo.BashivanKar2019.naturalistic', (24320, 233, 1), 309760, marks=[pytest.mark.private_access]),
+    pytest.param('dicarlo.BashivanKar2019.synthetic', (21360, 233, 1), 4319940, marks=[pytest.mark.private_access]),
+])
+def test_synthetic(assembly, shape, nans):
+    assy = brainio_collection.get_assembly(assembly)
+    assert assy.shape == shape
+    assert np.count_nonzero(np.isnan(assy)) == nans
+

tests/test_stimuli.py

@@ -57,7 +57,8 @@ def test_dicarlohvm(self):
         'dicarlo.THINGS2',
         'aru.Kuzovkin2018',
         'fei-fei.Deng2009',
-
+        'dicarlo.BashivanKar2019.naturalistic',
+        'dicarlo.BashivanKar2019.synthetic'
 ))
 def test_list_stimulus_set(stimulus_set):
     l = brainio_collection.list_stimulus_sets()