[Enhancement I] Add multichannel volume (#13)

* add multichannel volume * swap to datainterface * fix import * fix test name * fix intercompatability * fix light sources * fix * ryans suggestion * adjust to use full list * adjust constructor test * reorder kwargs in mock * adjust kwargs order in mock * Implement lists of object references with tests * Adjust constructor test to match * fix outer spec to match altered one * Apply suggestions from code review Co-authored-by: Ryan Ly <[email protected]> * fix outer spec to match altered one (#20) Co-authored-by: CodyCBakerPhD <[email protected]> --------- Co-authored-by: CodyCBakerPhD <[email protected]> Co-authored-by: Ryan Ly <[email protected]>
catalystneuro · Jul 15, 2024 · e5c3892 · e5c3892
1 parent 6e4614a
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Showing 6 changed files with 219 additions and 6 deletions.
diff --git a/spec/ndx-microscopy.extensions.yaml b/spec/ndx-microscopy.extensions.yaml
@@ -247,7 +247,7 @@ groups:
       - frames
       - height
       - width
-      - depth
+      - depths
       shape:
       - null
       - null
@@ -258,3 +258,81 @@ groups:
       doc: Link to VolumetricImagingSpace object containing metadata about the region of physical space this imaging data
         was recorded from.
       target_type: VolumetricImagingSpace
+
+  - neurodata_type_def: MultiChannelMicroscopyVolume
+    neurodata_type_inc: NWBDataInterface
+    doc: Static (not time-varying) volumetric imaging data acquired from multiple optical channels.
+    attributes:
+    - name: description
+      dtype: text
+      doc: Description of the MultiChannelVolume.
+      required: false
+    - name: unit
+      dtype: text
+      doc: Base unit of measurement for working with the data. Actual stored values are
+        not necessarily stored in these units. To access the data in these units,
+        multiply 'data' by 'conversion' and add 'offset'.
+    - name: conversion
+      dtype: float32
+      default_value: 1.0
+      doc: Scalar to multiply each element in data to convert it to the specified 'unit'.
+        If the data are stored in acquisition system units or other units
+        that require a conversion to be interpretable, multiply the data by 'conversion'
+        to convert the data to the specified 'unit'. e.g. if the data acquisition system
+        stores values in this object as signed 16-bit integers (int16 range
+        -32,768 to 32,767) that correspond to a 5V range (-2.5V to 2.5V), and the data
+        acquisition system gain is 8000X, then the 'conversion' multiplier to get from
+        raw data acquisition values to recorded volts is 2.5/32768/8000 = 9.5367e-9.
+      required: false
+    - name: offset
+      dtype: float32
+      default_value: 0.0
+      doc: Scalar to add to the data after scaling by 'conversion' to finalize its coercion
+        to the specified 'unit'. Two common examples of this include (a) data stored in an
+        unsigned type that requires a shift after scaling to re-center the data,
+        and (b) specialized recording devices that naturally cause a scalar offset with
+        respect to the true units.
+      required: false
+    datasets:
+    - name: data
+      doc: Recorded imaging data, shaped by (frame height, frame width, number of depth planes, number of optical
+        channels).
+      dtype: numeric
+      dims:
+      - height
+      - width
+      - depths
+      - optical_channels
+      shape:
+      - null
+      - null
+      - null
+      - null
+    - name: light_sources
+      doc: An ordered list of references to MicroscopyLightSource objects containing metadata about the excitation methods.
+      neurodata_type_inc: VectorData
+      dtype:
+        reftype: object
+        target_type: MicroscopyLightSource
+      dims:
+        - light_sources
+      shape:
+        - null
+    - name: optical_channels
+      doc: An ordered list of references to MicroscopyOpticalChannel objects containing metadata about the indicator and filters used to collect this data. This maps to the last dimension of `data`, i.e., the i-th MicroscopyOpticalChannel contains metadata about the indicator and filters used to collect the volume at `data[:,:,:,i]`.
+      neurodata_type_inc: VectorData
+      dtype:
+        reftype: object
+        target_type: MicroscopyOpticalChannel
+      dims:
+        - optical_channels
+      shape:
+        - null
+    links:
+    - name: microscope
+      doc: Link to a Microscope object containing metadata about the device used to acquire this imaging data.
+      target_type: Microscope
+    - name: imaging_space
+      doc: Link to VolumetricImagingSpace object containing metadata about the region of physical space this imaging data
+        was recorded from.
+      target_type: VolumetricImagingSpace
diff --git a/src/pynwb/ndx_microscopy/__init__.py b/src/pynwb/ndx_microscopy/__init__.py
@@ -30,6 +30,7 @@
 PlanarMicroscopySeries = get_class("PlanarMicroscopySeries", extension_name)
 VariableDepthMicroscopySeries = get_class("VariableDepthMicroscopySeries", extension_name)
 VolumetricMicroscopySeries = get_class("VolumetricMicroscopySeries", extension_name)
+MultiChannelMicroscopyVolume = get_class("MultiChannelMicroscopyVolume", extension_name)
 
 __all__ = [
     "Microscope",
@@ -42,4 +43,5 @@
     "PlanarMicroscopySeries",
     "VariableDepthMicroscopySeries",
     "VolumetricMicroscopySeries",
+    "MultiChannelMicroscopyVolume",
 ]
diff --git a/src/pynwb/ndx_microscopy/testing/__init__.py b/src/pynwb/ndx_microscopy/testing/__init__.py
@@ -2,6 +2,7 @@
     mock_Microscope,
     mock_MicroscopyLightSource,
     mock_MicroscopyOpticalChannel,
+    mock_MultiChannelMicroscopyVolume,
     mock_PlanarImagingSpace,
     mock_PlanarMicroscopySeries,
     mock_VariableDepthMicroscopySeries,
@@ -18,4 +19,5 @@
     "mock_PlanarMicroscopySeries",
     "mock_VariableDepthMicroscopySeries",
     "mock_VolumetricMicroscopySeries",
+    "mock_MultiChannelMicroscopyVolume",
 ]
diff --git a/src/pynwb/ndx_microscopy/testing/_mock.py b/src/pynwb/ndx_microscopy/testing/_mock.py
@@ -1,7 +1,8 @@
 import warnings
-from typing import Optional, Tuple
+from typing import List, Optional, Tuple
 
 import numpy as np
+import pynwb.base
 from pynwb.testing.mock.utils import name_generator
 
 import ndx_microscopy
@@ -286,3 +287,34 @@ def mock_VolumetricMicroscopySeries(
         timestamps=series_timestamps,
     )
     return volumetric_microscopy_series
+
+
+def mock_MultiChannelMicroscopyVolume(
+    *,
+    microscope: ndx_microscopy.Microscope,
+    imaging_space: ndx_microscopy.VolumetricImagingSpace,
+    light_sources: pynwb.base.VectorData,
+    optical_channels: pynwb.base.VectorData,
+    name: Optional[str] = None,
+    description: str = "This is a mock instance of a MultiChannelMicroscopyVolume type to be used for rapid testing.",
+    data: Optional[np.ndarray] = None,
+    unit: str = "n.a.",
+    conversion: float = 1.0,
+    offset: float = 0.0,
+) -> ndx_microscopy.MultiChannelMicroscopyVolume:
+    series_name = name or name_generator("MultiChannelMicroscopyVolume")
+    imaging_data = data if data is not None else np.ones(shape=(10, 20, 7, 3))
+
+    volumetric_microscopy_series = ndx_microscopy.MultiChannelMicroscopyVolume(
+        name=series_name,
+        description=description,
+        microscope=microscope,
+        imaging_space=imaging_space,
+        light_sources=light_sources,
+        optical_channels=optical_channels,
+        data=imaging_data,
+        unit=unit,
+        conversion=conversion,
+        offset=offset,
+    )
+    return volumetric_microscopy_series
diff --git a/src/pynwb/tests/test_constructors.py b/src/pynwb/tests/test_constructors.py
@@ -2,10 +2,12 @@
 
 import pytest
 
+import pynwb
 from ndx_microscopy.testing import (
     mock_Microscope,
     mock_MicroscopyLightSource,
     mock_MicroscopyOpticalChannel,
+    mock_MultiChannelMicroscopyVolume,
     mock_PlanarImagingSpace,
     mock_PlanarMicroscopySeries,
     mock_VariableDepthMicroscopySeries,
@@ -71,5 +73,30 @@ def test_constructor_volumetric_microscopy_series():
     )
 
 
+def test_constructor_multi_channel_microscopy_volume():
+    microscope = mock_Microscope()
+    imaging_space = mock_VolumetricImagingSpace(microscope=microscope)
+    light_sources = [mock_MicroscopyLightSource()]
+    optical_channels = [mock_MicroscopyOpticalChannel()]
+
+    light_sources_used_by_volume = pynwb.base.VectorData(
+        name="light_sources", description="Light sources used by this MultiChannelVolume.", data=light_sources
+    )
+    optical_channels_used_by_volume = pynwb.base.VectorData(
+        name="optical_channels",
+        description=(
+            "Optical channels ordered to correspond to the third axis (e.g., [0, 0, :, 0]) "
+            "of the data for this MultiChannelVolume."
+        ),
+        data=optical_channels,
+    )
+    mock_MultiChannelMicroscopyVolume(
+        microscope=microscope,
+        imaging_space=imaging_space,
+        light_sources=light_sources_used_by_volume,
+        optical_channels=optical_channels_used_by_volume,
+    )
+
+
 if __name__ == "__main__":
     pytest.main()  # Required since not a typical package structure
diff --git a/src/pynwb/tests/test_roundtrip.py b/src/pynwb/tests/test_roundtrip.py
@@ -8,6 +8,7 @@
     mock_Microscope,
     mock_MicroscopyLightSource,
     mock_MicroscopyOpticalChannel,
+    mock_MultiChannelMicroscopyVolume,
     mock_PlanarImagingSpace,
     mock_PlanarMicroscopySeries,
     mock_VariableDepthMicroscopySeries,
@@ -20,7 +21,7 @@ class TestPlanarMicroscopySeriesSimpleRoundtrip(pynwb_TestCase):
     """Simple roundtrip test for PlanarMicroscopySeries."""
 
     def setUp(self):
-        self.nwbfile_path = "test.nwb"
+        self.nwbfile_path = "test_planar_microscopy_series_roundtrip.nwb"
 
     def tearDown(self):
         pynwb.testing.remove_test_file(self.nwbfile_path)
@@ -68,7 +69,7 @@ class TestVolumetricMicroscopySeriesSimpleRoundtrip(pynwb_TestCase):
     """Simple roundtrip test for VolumetricMicroscopySeries."""
 
     def setUp(self):
-        self.nwbfile_path = "test.nwb"
+        self.nwbfile_path = "test_volumetric_microscopy_series_roundtrip.nwb"
 
     def tearDown(self):
         pynwb.testing.remove_test_file(self.nwbfile_path)
@@ -118,7 +119,7 @@ class TestVariableDepthMicroscopySeriesSimpleRoundtrip(pynwb_TestCase):
     """Simple roundtrip test for VariableDepthMicroscopySeries."""
 
     def setUp(self):
-        self.nwbfile_path = "test.nwb"
+        self.nwbfile_path = "test_variable_depth_microscopy_series_roundtrip.nwb"
 
     def tearDown(self):
         pynwb.testing.remove_test_file(self.nwbfile_path)
@@ -133,7 +134,7 @@ def test_roundtrip(self):
         nwbfile.add_device(devices=light_source)
 
         imaging_space = mock_PlanarImagingSpace(name="PlanarImagingSpace", microscope=microscope)
-        nwbfile.add_lab_meta_data(lab_meta_data=imaging_space)  # Would prefer .add_imaging_spacec()
+        nwbfile.add_lab_meta_data(lab_meta_data=imaging_space)  # Would prefer .add_imaging_space()
 
         optical_channel = mock_MicroscopyOpticalChannel(name="MicroscopyOpticalChannel")
         nwbfile.add_lab_meta_data(lab_meta_data=optical_channel)
@@ -162,3 +163,74 @@ def test_roundtrip(self):
             self.assertContainerEqual(
                 variable_depth_microscopy_series, read_nwbfile.acquisition["VariableDepthMicroscopySeries"]
             )
+
+
+class TestMultiChannelMicroscopyVolumeSimpleRoundtrip(pynwb_TestCase):
+    """Simple roundtrip test for MultiChannelMicroscopyVolume."""
+
+    def setUp(self):
+        self.nwbfile_path = "test_multi_channel_microscopy_volume_roundtrip.nwb"
+
+    def tearDown(self):
+        pynwb.testing.remove_test_file(self.nwbfile_path)
+
+    def test_roundtrip(self):
+        nwbfile = mock_NWBFile()
+
+        microscope = mock_Microscope(name="Microscope")
+        nwbfile.add_device(devices=microscope)
+
+        imaging_space = mock_VolumetricImagingSpace(name="VolumetricImagingSpace", microscope=microscope)
+        nwbfile.add_lab_meta_data(lab_meta_data=imaging_space)  # Would prefer .add_imaging_space()
+
+        light_sources = list()
+        light_source_0 = mock_MicroscopyLightSource(name="LightSource")
+        nwbfile.add_device(devices=light_source_0)
+        light_sources.append(light_source_0)
+
+        optical_channels = list()
+        optical_channel_0 = mock_MicroscopyOpticalChannel(name="MicroscopyOpticalChannel")
+        nwbfile.add_lab_meta_data(lab_meta_data=optical_channel_0)
+        optical_channels.append(optical_channel_0)
+
+        # TODO: It might be more convenient in Python to have a custom constructor that takes in a list of
+        # light sources and optical channels and does the VectorData wrapping internally
+        light_sources_used_by_volume = pynwb.base.VectorData(
+            name="light_sources", description="Light sources used by this MultiChannelVolume.", data=light_sources
+        )
+        optical_channels_used_by_volume = pynwb.base.VectorData(
+            name="optical_channels",
+            description=(
+                "Optical channels ordered to correspond to the third axis (e.g., [0, 0, :, 0]) "
+                "of the data for this MultiChannelVolume."
+            ),
+            data=optical_channels,
+        )
+        multi_channel_microscopy_volume = mock_MultiChannelMicroscopyVolume(
+            name="MultiChannelMicroscopyVolume",
+            microscope=microscope,
+            imaging_space=imaging_space,
+            light_sources=light_sources_used_by_volume,
+            optical_channels=optical_channels_used_by_volume,
+        )
+        nwbfile.add_acquisition(nwbdata=multi_channel_microscopy_volume)
+
+        with pynwb.NWBHDF5IO(path=self.nwbfile_path, mode="w") as io:
+            io.write(nwbfile)
+
+        with pynwb.NWBHDF5IO(path=self.nwbfile_path, mode="r", load_namespaces=True) as io:
+            read_nwbfile = io.read()
+
+            self.assertContainerEqual(microscope, read_nwbfile.devices["Microscope"])
+            self.assertContainerEqual(light_source_0, read_nwbfile.devices["LightSource"])
+
+            self.assertContainerEqual(imaging_space, read_nwbfile.lab_meta_data["VolumetricImagingSpace"])
+            self.assertContainerEqual(optical_channel_0, read_nwbfile.lab_meta_data["MicroscopyOpticalChannel"])
+
+            self.assertContainerEqual(
+                multi_channel_microscopy_volume, read_nwbfile.acquisition["MultiChannelMicroscopyVolume"]
+            )
+
+
+if __name__ == "__main__":
+    pytest.main()  # Required since not a typical package structure