Merge branch 'dev' into internal-link-checking

CHANGELOG.md

@@ -17,6 +17,7 @@
 ### Bug fixes
 - Fix bug where namespaces were loaded in "w-" mode. @h-mayorquin [#1795](https://github.com/NeurodataWithoutBorders/pynwb/pull/1795)
 - Fix bug where pynwb version was reported as "unknown" to readthedocs @stephprince [#1810](https://github.com/NeurodataWithoutBorders/pynwb/pull/1810)
+- Fixed bug to allow linking of `TimeSeries.data` by setting the `data` constructor argument to another `TimeSeries`. @oruebel [#1766](https://github.com/NeurodataWithoutBorders/pynwb/pull/1766)
 
 ### Documentation and tutorial enhancements
 - Add RemFile to streaming tutorial. @bendichter [#1761](https://github.com/NeurodataWithoutBorders/pynwb/pull/1761)
@@ -27,8 +28,8 @@
 ## PyNWB 2.5.0 (August 18, 2023)
 
 ### Enhancements and minor changes
-- Add `TimeSeries.get_timestamps()`. @bendichter [#1741](https://github.com/NeurodataWithoutBorders/pynwb/pull/1741)
-- Add `TimeSeries.get_data_in_units()`. @bendichter [#1745](https://github.com/NeurodataWithoutBorders/pynwb/pull/1745)
+- Added `TimeSeries.get_timestamps()`. @bendichter [#1741](https://github.com/NeurodataWithoutBorders/pynwb/pull/1741)
+- Added `TimeSeries.get_data_in_units()`. @bendichter [#1745](https://github.com/NeurodataWithoutBorders/pynwb/pull/1745)
 - Updated `ExternalResources` name change to `HERD`, along with HDMF 3.9.0 being the new minimum. @mavaylon1 [#1754](https://github.com/NeurodataWithoutBorders/pynwb/pull/1754)
 
 ### Documentation and tutorial enhancements
@@ -41,15 +42,15 @@
 ## PyNWB 2.4.0 (July 23, 2023)
 
 ### Enhancements and minor changes
-- Add support for `ExternalResources`. @mavaylon1 [#1684](https://github.com/NeurodataWithoutBorders/pynwb/pull/1684)
-- Update links for making a release. @mavaylon1 [#1720](https://github.com/NeurodataWithoutBorders/pynwb/pull/1720)
+- Added support for `ExternalResources`. @mavaylon1 [#1684](https://github.com/NeurodataWithoutBorders/pynwb/pull/1684)
+- Updated links for making a release. @mavaylon1 [#1720](https://github.com/NeurodataWithoutBorders/pynwb/pull/1720)
 
 ### Bug fixes
 - Fixed sphinx-gallery setting to correctly display index in the docs with sphinx-gallery>=0.11. @oruebel [#1733](https://github.com/NeurodataWithoutBorders/pynwb/pull/1733)
 
 ### Documentation and tutorial enhancements
 - Added thumbnail for Optogentics tutorial. @oruebel [#1729](https://github.com/NeurodataWithoutBorders/pynwb/pull/1729)
-- Update and fix errors in tutorials. @bendichter @oruebel
+- Updated and fixed errors in tutorials. @bendichter @oruebel
 
 ## PyNWB 2.3.3 (June 26, 2023)
 

src/pynwb/io/base.py

@@ -73,6 +73,19 @@ def timestamps_carg(self, builder, manager):
         else:
             return tstamps_builder.data
 
+    @NWBContainerMapper.object_attr("data")
+    def data_attr(self, container, manager):
+        ret = container.fields.get('data')
+        if isinstance(ret, TimeSeries):
+            owner = ret
+            curr = owner.fields.get('data')
+            while isinstance(curr, TimeSeries):
+                owner = curr
+                curr = owner.fields.get('data')
+            data_builder = manager.build(owner)
+            ret = LinkBuilder(data_builder['data'], 'data')
+        return ret
+
     @NWBContainerMapper.constructor_arg("data")
     def data_carg(self, builder, manager):
         # handle case where a TimeSeries is read and missing data
@@ -105,7 +118,10 @@ def unit_carg(self, builder, manager):
                 data_builder = manager.construct(target.parent)
             else:
                 data_builder = target
-        unit_value = data_builder.attributes.get('unit')
+        if isinstance(data_builder, TimeSeries):  # Data linked in another timeseries
+            unit_value = data_builder.unit
+        else:  # DatasetBuilder owned by this timeseries
+            unit_value = data_builder.attributes.get('unit')
         if unit_value is None:
             return timeseries_cls.DEFAULT_UNIT
         return unit_value

tests/integration/hdf5/test_base.py

@@ -46,6 +46,27 @@ def test_timestamps_linking(self):
         tsb = nwbfile.acquisition['b']
         self.assertIs(tsa.timestamps, tsb.timestamps)
 
+    def test_data_linking(self):
+        ''' Test that data get linked to in TimeSeries '''
+        tsa = TimeSeries(name='a', data=np.linspace(0, 1, 1000), timestamps=np.arange(1000.), unit='m')
+        tsb = TimeSeries(name='b', data=tsa, timestamps=np.arange(1000.), unit='m')
+        tsc = TimeSeries(name='c', data=tsb, timestamps=np.arange(1000.), unit='m')
+        nwbfile = NWBFile(identifier='foo',
+                          session_start_time=datetime(2017, 5, 1, 12, 0, 0, tzinfo=tzlocal()),
+                          session_description='bar')
+        nwbfile.add_acquisition(tsa)
+        nwbfile.add_acquisition(tsb)
+        nwbfile.add_acquisition(tsc)
+        with NWBHDF5IO(self.path, 'w') as io:
+            io.write(nwbfile)
+        with NWBHDF5IO(self.path, 'r') as io:
+            nwbfile = io.read()
+        tsa = nwbfile.acquisition['a']
+        tsb = nwbfile.acquisition['b']
+        tsc = nwbfile.acquisition['c']
+        self.assertIs(tsa.data, tsb.data)
+        self.assertIs(tsa.data, tsc.data)
+
 
 class TestImagesIO(AcquisitionH5IOMixin, TestCase):
 

tests/integration/hdf5/test_modular_storage.py

@@ -14,29 +14,35 @@
 class TestTimeSeriesModular(TestCase):
 
     def setUp(self):
-        self.start_time = datetime(1971, 1, 1, 12, tzinfo=tzutc())
+        # File paths
+        self.data_filename = os.path.join(os.getcwd(), 'test_time_series_modular_data.nwb')
+        self.link_filename = os.path.join(os.getcwd(), 'test_time_series_modular_link.nwb')
 
+        # Make the data container file write
+        self.start_time = datetime(1971, 1, 1, 12, tzinfo=tzutc())
         self.data = np.arange(2000).reshape((1000, 2))
         self.timestamps = np.linspace(0, 1, 1000)
-
+        # The container before roundtrip
         self.container = TimeSeries(
             name='data_ts',
             unit='V',
             data=self.data,
             timestamps=self.timestamps
         )
+        self.data_read_io = None          # HDF5IO used for reading the main data file
+        self.read_data_nwbfile = None     # The NWBFile read after roundtrip
+        self.read_data_container = None   # self.container after roundtrip
 
-        self.data_filename = os.path.join(os.getcwd(), 'test_time_series_modular_data.nwb')
-        self.link_filename = os.path.join(os.getcwd(), 'test_time_series_modular_link.nwb')
-
-        self.read_container = None
-        self.link_read_io = None
-        self.data_read_io = None
+        # Variables for the second file which links the main data file
+        self.link_container = None        # The container with the links before write
+        self.read_link_container = None   # The container with the links after roundtrip
+        self.read_link_nwbfile = None     # The NWBFile container containing link_container after roundtrip
+        self.link_read_io = None          # HDF5IO use for reading the read_link_nwbfile
 
     def tearDown(self):
-        if self.read_container:
-            self.read_container.data.file.close()
-            self.read_container.timestamps.file.close()
+        if self.read_link_container:
+            self.read_link_container.data.file.close()
+            self.read_link_container.timestamps.file.close()
         if self.link_read_io:
             self.link_read_io.close()
         if self.data_read_io:
@@ -64,49 +70,83 @@ def roundtripContainer(self):
             data_write_io.write(data_file)
 
         # read data file
-        with HDF5IO(self.data_filename, 'r', manager=get_manager()) as self.data_read_io:
-            data_file_obt = self.data_read_io.read()
-
-            # write "link file" with timeseries.data that is an external link to the timeseries in "data file"
-            # also link timeseries.timestamps.data to the timeseries.timestamps in "data file"
-            with HDF5IO(self.link_filename, 'w', manager=get_manager()) as link_write_io:
-                link_file = NWBFile(
-                    session_description='a test file',
-                    identifier='link_file',
-                    session_start_time=self.start_time
-                )
-                self.link_container = TimeSeries(
-                    name='test_mod_ts',
-                    unit='V',
-                    data=data_file_obt.get_acquisition('data_ts'),  # test direct link
-                    timestamps=H5DataIO(
-                        data=data_file_obt.get_acquisition('data_ts').timestamps,
-                        link_data=True  # test with setting link data
-                    )
-                )
-                link_file.add_acquisition(self.link_container)
-                link_write_io.write(link_file)
+        self.data_read_io = HDF5IO(self.data_filename, 'r', manager=get_manager())
+        self.read_data_nwbfile = self.data_read_io.read()
+        self.read_data_container = self.read_data_nwbfile.get_acquisition('data_ts')
 
-        # note that self.link_container contains a link to a dataset that is now closed
+        # write "link file" with timeseries.data that is an external link to the timeseries in "data file"
+        # also link timeseries.timestamps.data to the timeseries.timestamps in "data file"
+        with HDF5IO(self.link_filename, 'w', manager=get_manager()) as link_write_io:
+            link_file = NWBFile(
+                session_description='a test file',
+                identifier='link_file',
+                session_start_time=self.start_time
+            )
+            self.link_container = TimeSeries(
+                name='test_mod_ts',
+                unit='V',
+                data=H5DataIO(
+                    data=self.read_data_container.data,
+                    link_data=True  # test with setting link data
+                ),
+                timestamps=H5DataIO(
+                    data=self.read_data_container.timestamps,
+                    link_data=True  # test with setting link data
+                )
+            )
+            link_file.add_acquisition(self.link_container)
+            link_write_io.write(link_file)
 
         # read the link file
         self.link_read_io = HDF5IO(self.link_filename, 'r', manager=get_manager())
-        self.read_nwbfile = self.link_read_io.read()
-        return self.getContainer(self.read_nwbfile)
+        self.read_link_nwbfile = self.link_read_io.read()
+        return self.getContainer(self.read_link_nwbfile)
 
     def test_roundtrip(self):
-        self.read_container = self.roundtripContainer()
-
-        # make sure we get a completely new object
-        self.assertIsNotNone(str(self.container))  # added as a test to make sure printing works
+        # Roundtrip the container
+        self.read_link_container = self.roundtripContainer()
+
+        # 1. Make sure our containers are set correctly for the test
+        # 1.1:  Make sure the container we read is not identical to the container we used for writing
+        self.assertNotEqual(id(self.link_container), id(self.read_link_container))
+        self.assertNotEqual(id(self.container), id(self.read_data_container))
+        # 1.2: Make sure the container we read is indeed the correct container we should use for testing
+        self.assertIs(self.read_link_nwbfile.objects[self.link_container.object_id], self.read_link_container)
+        self.assertIs(self.read_data_nwbfile.objects[self.container.object_id], self.read_data_container)
+        # 1.3: Make sure the object_ids of the container we wrote and read are the same
+        self.assertEqual(self.read_link_container.object_id, self.link_container.object_id)
+        self.assertEqual(self.read_data_container.object_id, self.container.object_id)
+        # 1.4: Make sure the object_ids between the source data and link data container are different
+        self.assertNotEqual(self.read_link_container.object_id, self.read_data_container.object_id)
+
+        # Test that printing works for the source data and linked data container
+        self.assertIsNotNone(str(self.container))
+        self.assertIsNotNone(str(self.read_data_container))
         self.assertIsNotNone(str(self.link_container))
-        self.assertIsNotNone(str(self.read_container))
-        self.assertFalse(self.link_container.timestamps.valid)
-        self.assertTrue(self.read_container.timestamps.id.valid)
-        self.assertNotEqual(id(self.link_container), id(self.read_container))
-        self.assertIs(self.read_nwbfile.objects[self.link_container.object_id], self.read_container)
-        self.assertContainerEqual(self.read_container, self.container, ignore_name=True, ignore_hdmf_attrs=True)
-        self.assertEqual(self.read_container.object_id, self.link_container.object_id)
+        self.assertIsNotNone(str(self.read_link_container))
+
+        # Test that timestamps and data are valid after write
+        self.assertTrue(self.read_link_container.timestamps.id.valid)
+        self.assertTrue(self.read_link_container.data.id.valid)
+        self.assertTrue(self.read_data_container.timestamps.id.valid)
+        self.assertTrue(self.read_data_container.data.id.valid)
+
+        # Make sure the data in the read data container and linked data container match the original container
+        self.assertContainerEqual(self.read_link_container, self.container, ignore_name=True, ignore_hdmf_attrs=True)
+        self.assertContainerEqual(self.read_data_container, self.container, ignore_name=True, ignore_hdmf_attrs=True)
+
+        # Make sure the timestamps and data are linked correctly. I.e., the filename of the h5py dataset should
+        # match between the data file and the file with links even-though they have been read from different files
+        self.assertEqual(
+            self.read_data_container.data.file.filename,  # Path where the source data is stored
+            self.read_link_container.data.file.filename   # Path where the linked h5py dataset points to
+        )
+        self.assertEqual(
+            self.read_data_container.timestamps.file.filename,  # Path where the source data is stored
+            self.read_link_container.timestamps.file.filename   # Path where the linked h5py dataset points to
+        )
+
+        # validate both the source data and linked data file via the pynwb validator
         self.validate()
 
     def test_link_root(self):
@@ -159,3 +199,55 @@ def validate(self):
 
     def getContainer(self, nwbfile):
         return nwbfile.get_acquisition('test_mod_ts')
+
+
+class TestTimeSeriesModularLinkViaTimeSeries(TestTimeSeriesModular):
+    """
+    Same as TestTimeSeriesModular but creating links by setting TimeSeries.data
+    and TimeSeries.timestamps to the other TimeSeries on construction, rather than
+    using H5DataIO.
+    """
+    def setUp(self):
+        super().setUp()
+        self.skipTest("This behavior is currently broken. See issue .")
+
+    def roundtripContainer(self):
+        # create and write data file
+        data_file = NWBFile(
+            session_description='a test file',
+            identifier='data_file',
+            session_start_time=self.start_time
+        )
+        data_file.add_acquisition(self.container)
+
+        with HDF5IO(self.data_filename, 'w', manager=get_manager()) as data_write_io:
+            data_write_io.write(data_file)
+
+        # read data file
+        self.data_read_io = HDF5IO(self.data_filename, 'r', manager=get_manager())
+        self.read_data_nwbfile = self.data_read_io.read()
+        self.read_data_container = self.read_data_nwbfile.get_acquisition('data_ts')
+
+        # write "link file" with timeseries.data that is an external link to the timeseries in "data file"
+        # also link timeseries.timestamps.data to the timeseries.timestamps in "data file"
+        with HDF5IO(self.link_filename, 'w', manager=get_manager()) as link_write_io:
+            link_file = NWBFile(
+                session_description='a test file',
+                identifier='link_file',
+                session_start_time=self.start_time
+            )
+            self.link_container = TimeSeries(
+                name='test_mod_ts',
+                unit='V',
+                data=self.read_data_container,       # <--- This is the main difference to TestTimeSeriesModular
+                timestamps=self.read_data_container  # <--- This is the main difference to TestTimeSeriesModular
+            )
+            link_file.add_acquisition(self.link_container)
+            link_write_io.write(link_file)
+
+        # note that self.link_container contains a link to a dataset that is now closed
+
+        # read the link file
+        self.link_read_io = HDF5IO(self.link_filename, 'r', manager=get_manager())
+        self.read_link_nwbfile = self.link_read_io.read()
+        return self.getContainer(self.read_link_nwbfile)