[Enhancement III] Swap to um for depth (#18)

* add multichannel volume

* swap to datainterface

* fix import

* fix test name

* fix intercompatability

* fix light sources

* fix

* add plane segmentation stuff

* fix autogenerated arg

* variable depth volume

* swap to um

* 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

* Update spec/ndx-microscopy.extensions.yaml

* Update spec/ndx-microscopy.extensions.yaml

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* alessandras comments and tests

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* fix import

* fix import

* fix import

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* debug

* debugs

* debugs

* debugs

* debugs

* debugs

* debugs

* debugs

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* Update README.md

---------

Co-authored-by: CodyCBakerPhD <codycbakerphd@gmail.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

README.md

@@ -63,8 +63,7 @@ classDiagram
         --------------------------------------
         data : numeric, frame x height x width
         --> unit : text
-        depth_per_frame : numeric, length of frames
-        -- > unit : text, default="micrometers"
+        depth_per_frame_in_um : numeric, length of frames
 
         --------------------------------------
         links

spec/ndx-microscopy.extensions.yaml

@@ -308,8 +308,8 @@ groups:
     doc: Volumetric imaging data acquired over an irregular number and amount of depths; for instance, when using an
       electrically tunable lens.
     datasets:
-    - name: depth_per_frame_in_mm
-      doc: Depth of each frame in the data array.
+    - name: depth_per_frame_in_um
+      doc: Depth in micrometers of each frame in the data array.
         These values offset the 'z' value of the `origin_coordinates` of the linked `imaging_space` object.
       dtype: numeric
       dims:
@@ -471,9 +471,8 @@ groups:
       - null
       - null
       - null
-    - name: depth_per_frame_in_mm
-      doc: Depth of each frame in the data array.
-        These values offset the 'z' value of the `origin_coordinates` of the linked `imaging_space` object.
+    - name: depth_per_frame_in_um
+      doc: Depth in micrometers of each frame in the data array.
       dtype: numeric
       dims:
       - depths

src/pynwb/ndx_microscopy/testing/_mock.py

@@ -223,7 +223,7 @@ def mock_VariableDepthMicroscopySeries(
     name: Optional[str] = None,
     description: str = "This is a mock instance of a PlanarMicroscopySeries type to be used for rapid testing.",
     data: Optional[np.ndarray] = None,
-    depth_per_frame_in_mm: Optional[np.ndarray] = None,
+    depth_per_frame_in_um: Optional[np.ndarray] = None,
     unit: str = "a.u.",
     conversion: float = 1.0,
     offset: float = 0.0,
@@ -233,10 +233,11 @@ def mock_VariableDepthMicroscopySeries(
 ) -> ndx_microscopy.VariableDepthMicroscopySeries:
     series_name = name or name_generator("VariableDepthMicroscopySeries")
     series_data = data if data is not None else np.ones(shape=(15, 5, 5))
-    series_depth_per_frame_in_mm = (
-        depth_per_frame_in_mm
-        if depth_per_frame_in_mm is not None
-        else np.linspace(start=0.0, stop=1.0, num=series_data.shape[0])
+
+    depth_per_frame_in_um = (
+        depth_per_frame_in_um
+        if depth_per_frame_in_um is not None
+        else np.linspace(start=0.0, stop=30.0, num=series_data.shape[0])
     )
 
     if timestamps is None:
@@ -265,7 +266,7 @@ def mock_VariableDepthMicroscopySeries(
         imaging_space=imaging_space,
         optical_channel=optical_channel,
         data=series_data,
-        depth_per_frame_in_mm=series_depth_per_frame_in_mm,
+        depth_per_frame_in_um=depth_per_frame_in_um,
         unit=unit,
         conversion=conversion,
         offset=offset,
@@ -371,18 +372,19 @@ def mock_VariableDepthMultiChannelMicroscopyVolume(
     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,
-    depth_per_frame_in_mm: Optional[np.ndarray] = None,
+    depth_per_frame_in_um: Optional[np.ndarray] = None,
     unit: str = "n.a.",
     conversion: float = 1.0,
     offset: float = 0.0,
 ) -> ndx_microscopy.VariableDepthMultiChannelMicroscopyVolume:
     series_name = name or name_generator("MultiChannelMicroscopyVolume")
 
     series_data = data if data is not None else np.ones(shape=(15, 5, 5))
-    volume_depth_per_frame_in_mm = (
-        depth_per_frame_in_mm
-        if depth_per_frame_in_mm is not None
-        else np.linspace(start=0.0, stop=1.0, num=series_data.shape[0])
+
+    volume_depth_per_frame_in_um = (
+        depth_per_frame_in_um
+        if depth_per_frame_in_um is not None
+        else np.linspace(start=0.0, stop=30.0, num=series_data.shape[0])
     )
 
     imaging_data = data if data is not None else np.ones(shape=(10, 20, 7, 3))
@@ -394,7 +396,7 @@ def mock_VariableDepthMultiChannelMicroscopyVolume(
         light_sources=light_sources,
         optical_channels=optical_channels,
         data=imaging_data,
-        depth_per_frame_in_mm=volume_depth_per_frame_in_mm,
+        depth_per_frame_in_um=volume_depth_per_frame_in_um,
         unit=unit,
         conversion=conversion,
         offset=offset,