Revert changes to retinotopy.yaml (#409)

rly · web-flow · commit feddcbf9111f · 2020-02-07T17:49:06.000-08:00
* Revert changes to retinotopy.yaml in NWB 2.1.0

* Specify shape, and clarify docs, dtype, and dims

* Make sign_map and focal_depth_image optional
diff --git a/core/nwb.retinotopy.yaml b/core/nwb.retinotopy.yaml
@@ -5,114 +5,230 @@ groups:
   doc: 'Intrinsic signal optical imaging or widefield imaging for measuring retinotopy.
     Stores orthogonal maps (e.g., altitude/azimuth; radius/theta) of responses to
     specific stimuli and a combined polarity map from which to identify visual areas.
-    NOTE: for data consistency, all images and arrays are stored in the format [row][column]
+    This group does not store the raw responses imaged during retinotopic mapping or the
+    stimuli presented, but rather the resulting phase and power maps after applying a Fourier
+    transform on the averaged responses.
+    Note: for data consistency, all images and arrays are stored in the format [row][column]
     and [row, col], which equates to [y][x]. Field of view and dimension arrays may
     appear backward (i.e., y before x).'
   datasets:
   - name: axis_1_phase_map
-    neurodata_type_inc: AxisMap
+    dtype: float32
+    dims:
+    - num_rows
+    - num_cols
+    shape:
+    - null
+    - null
     doc: Phase response to stimulus on the first measured axis.
+    attributes:
+    - name: dimension
+      dtype: int32
+      dims:
+      - num_rows, num_cols
+      shape:
+      - 2
+      doc: 'Number of rows and columns in the image. NOTE: row, column representation
+        is equivalent to height, width.'
+    - name: field_of_view
+      dtype: float32
+      dims:
+      - height, width
+      shape:
+      - 2
+      doc: Size of viewing area, in meters.
+    - name: unit
+      dtype: text
+      doc: Unit that axis data is stored in (e.g., degrees).
   - name: axis_1_power_map
-    neurodata_type_inc: AxisMap
+    dtype: float32
+    dims:
+    - num_rows
+    - num_cols
+    shape:
+    - null
+    - null
     doc: Power response on the first measured axis. Response is scaled so 0.0 is no
       power in the response and 1.0 is maximum relative power.
     quantity: '?'
+    attributes:
+    - name: dimension
+      dtype: int32
+      dims:
+      - num_rows, num_cols
+      shape:
+      - 2
+      doc: 'Number of rows and columns in the image. NOTE: row, column representation
+        is equivalent to height, width.'
+    - name: field_of_view
+      dtype: float32
+      dims:
+      - height, width
+      shape:
+      - 2
+      doc: Size of viewing area, in meters.
+    - name: unit
+      dtype: text
+      doc: Unit that axis data is stored in (e.g., degrees).
   - name: axis_2_phase_map
-    neurodata_type_inc: AxisMap
+    dtype: float32
+    dims:
+    - num_rows
+    - num_cols
+    shape:
+    - null
+    - null
     doc: Phase response to stimulus on the second measured axis.
+    attributes:
+    - name: dimension
+      dtype: int32
+      dims:
+      - num_rows, num_cols
+      shape:
+      - 2
+      doc: 'Number of rows and columns in the image. NOTE: row, column representation
+        is equivalent to height, width.'
+    - name: field_of_view
+      dtype: float32
+      dims:
+      - height, width
+      shape:
+      - 2
+      doc: Size of viewing area, in meters.
+    - name: unit
+      dtype: text
+      doc: Unit that axis data is stored in (e.g., degrees).
   - name: axis_2_power_map
-    neurodata_type_inc: AxisMap
+    dtype: float32
+    dims:
+    - num_rows
+    - num_cols
+    shape:
+    - null
+    - null
+    doc: Power response on the second measured axis. Response is scaled so 0.0 is
+      no power in the response and 1.0 is maximum relative power.
     quantity: '?'
-    doc: Power response to stimulus on the second measured axis.
-  - name: sign_map
-    neurodata_type_inc: RetinotopyMap
-    doc: Sine of the angle between the direction of the gradient in axis_1 and axis_2.
+    attributes:
+    - name: dimension
+      dtype: int32
+      dims:
+      - num_rows, num_cols
+      shape:
+      - 2
+      doc: 'Number of rows and columns in the image. NOTE: row, column representation
+        is equivalent to height, width.'
+    - name: field_of_view
+      dtype: float32
+      dims:
+      - height, width
+      shape:
+      - 2
+      doc: Size of viewing area, in meters.
+    - name: unit
+      dtype: text
+      doc: Unit that axis data is stored in (e.g., degrees).
   - name: axis_descriptions
     dtype: text
     dims:
-    - num_axes
+    - axis_1, axis_2
     shape:
     - 2
     doc: Two-element array describing the contents of the two response axis fields.
-      Description should be something like ['altitude', 'azimuth'] or '['radius', 'theta'].
+      Description should be something like ['altitude', 'azimuth'] or '['radius',
+      'theta'].
   - name: focal_depth_image
-    neurodata_type_inc: RetinotopyImage
+    dtype: uint16
+    dims:
+    - num_rows
+    - num_cols
+    shape:
+    - null
+    - null
     doc: 'Gray-scale image taken with same settings/parameters (e.g., focal depth,
       wavelength) as data collection. Array format: [rows][columns].'
+    quantity: '?'
     attributes:
+    - name: bits_per_pixel
+      dtype: int32
+      doc: Number of bits used to represent each value. This is necessary to determine
+        maximum (white) pixel value.
+    - name: dimension
+      dtype: int32
+      dims:
+      - num_rows, num_cols
+      shape:
+      - 2
+      doc: 'Number of rows and columns in the image. NOTE: row, column representation
+        is equivalent to height, width.'
+    - name: field_of_view
+      dtype: float32
+      dims:
+      - height, width
+      shape:
+      - 2
+      doc: Size of viewing area, in meters.
     - name: focal_depth
       dtype: float32
       doc: Focal depth offset, in meters.
-  - name: vasculature_image
-    neurodata_type_inc: RetinotopyImage
-    doc: 'Gray-scale anatomical image of cortical surface. Array structure: [rows][columns]'
-
-datasets:
-- neurodata_type_def: RetinotopyMap
-  neurodata_type_inc: NWBData
-  dtype: float32
-  dims:
-  - num_rows
-  - num_cols
-  shape:
-  - null
-  - null
-  doc: 'Abstract two-dimensional map of responses. Array structure: [num_rows][num_columns]'
-  attributes:
-  - name: dimension
-    dtype: int32
-    dims:
-    - row_col
-    shape:
-    - 2
-    doc: 'Number of rows and columns in the image. NOTE: row, column representation
-      is equivalent to height, width.'
-  - name: field_of_view
+    - name: format
+      dtype: text
+      doc: Format of image. Right now only 'raw' is supported.
+  - name: sign_map
     dtype: float32
     dims:
-    - row_col
-    shape:
-    - 2
-    doc: Size of viewing area, in meters.
-
-- neurodata_type_def: AxisMap
-  neurodata_type_inc: RetinotopyMap
-  dtype: float32
-  dims:
-  - num_rows
-  - num_cols
-  shape:
-  - null
-  - null
-  doc: Abstract two-dimensional map of responses to stimuli along a single response axis (e.g. eccentricity)
-  attributes:
-  - name: unit
-    dtype: text
-    doc: Unit that axis data is stored in (e.g., degrees).
-- neurodata_type_def: RetinotopyImage
-  neurodata_type_inc: GrayscaleImage
-  dtype: uint16
-  doc: 'Gray-scale image related to retinotopic mapping. Array structure: [num_rows][num_columns]'
-  attributes:
-  - name: bits_per_pixel
-    dtype: int32
-    doc: Number of bits used to represent each value. This is necessary to determine
-      maximum (white) pixel value.
-  - name: dimension
-    dtype: int32
-    dims:
-    - row_col
+    - num_rows
+    - num_cols
     shape:
-    - 2
-    doc: 'Number of rows and columns in the image. NOTE: row, column representation
-      is equivalent to height, width.'
-  - name: field_of_view
-    dtype: float32
+    - null
+    - null
+    doc: Sine of the angle between the direction of the gradient in axis_1 and axis_2.
+    quantity: '?'
+    attributes:
+    - name: dimension
+      dtype: int32
+      dims:
+      - num_rows, num_cols
+      shape:
+      - 2
+      doc: 'Number of rows and columns in the image. NOTE: row, column representation
+        is equivalent to height, width.'
+    - name: field_of_view
+      dtype: float32
+      dims:
+      - height, width
+      shape:
+      - 2
+      doc: Size of viewing area, in meters.
+  - name: vasculature_image
+    dtype: uint16
     dims:
-    - row_col
+    - num_rows
+    - num_cols
     shape:
-    - 2
-    doc: Size of viewing area, in meters.
-  - name: format
-    dtype: text
-    doc: Format of image. Right now only 'raw' is supported.
+    - null
+    - null
+    doc: 'Gray-scale anatomical image of cortical surface. Array structure: [rows][columns]'
+    attributes:
+    - name: bits_per_pixel
+      dtype: int32
+      doc: Number of bits used to represent each value. This is necessary to determine
+        maximum (white) pixel value
+    - name: dimension
+      dtype: int32
+      dims:
+      - num_rows, num_cols
+      shape:
+      - 2
+      doc: 'Number of rows and columns in the image. NOTE: row, column representation
+        is equivalent to height, width.'
+    - name: field_of_view
+      dtype: float32
+      dims:
+      - height, width
+      shape:
+      - 2
+      doc: Size of viewing area, in meters.
+    - name: format
+      dtype: text
+      doc: Format of image. Right now only 'raw' is supported.
