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Fix dims and shape of ImagingPlane and TwoPhotonSeries datasets (#445)
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rly authored May 29, 2020
1 parent 25f1312 commit aa7702e
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Showing 5 changed files with 27 additions and 21 deletions.
2 changes: 1 addition & 1 deletion core/nwb.file.yaml
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Expand Up @@ -7,7 +7,7 @@ groups:
attributes:
- name: nwb_version
dtype: text
value: 2.2.4
value: 2.2.5
doc: File version string. Use semantic versioning, e.g. 1.2.1. This will be the
name of the format with trailing major, minor and patch numbers.
datasets:
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2 changes: 1 addition & 1 deletion core/nwb.namespace.yaml
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Expand Up @@ -57,4 +57,4 @@ namespaces:
- doc: This source module contains neurodata_type for retinotopy data.
source: nwb.retinotopy.yaml
title: Retinotopy
version: 2.2.4
version: 2.2.5
20 changes: 10 additions & 10 deletions core/nwb.ophys.yaml
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Expand Up @@ -17,8 +17,8 @@ groups:
- name: field_of_view
dtype: float32
dims:
- width|height
- width|height|depth
- - width|height
- - width|height|depth
shape:
- - 2
- - 3
Expand Down Expand Up @@ -232,11 +232,11 @@ groups:
- name: origin_coords
dtype: float32
dims:
- x, y
- x, y, z
- - x, y
- - x, y, z
shape:
- 2
- 3
- - 2
- - 3
doc: Physical location of the first element of the imaging plane (0, 0) for 2-D data or (0, 0, 0) for 3-D data.
See also reference_frame for what the physical location is relative to (e.g., bregma).
quantity: '?'
Expand All @@ -248,11 +248,11 @@ groups:
- name: grid_spacing
dtype: float32
dims:
- x, y
- x, y, z
- - x, y
- - x, y, z
shape:
- 2
- 3
- - 2
- - 3
doc: Space between pixels in (x, y) or voxels in (x, y, z) directions, in the specified unit.
Assumes imaging plane is a regular grid. See also reference_frame to interpret the grid.
quantity: '?'
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4 changes: 2 additions & 2 deletions docs/format/source/conf.py
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Expand Up @@ -36,7 +36,7 @@ def run_doc_autogen(_):

def setup(app):
app.connect('builder-inited', run_doc_autogen)
app.add_stylesheet("theme_overrides.css") # overrides for wide tables in RTD theme
app.add_css_file("theme_overrides.css") # overrides for wide tables in RTD theme


# -- ext settings -----------------------------------------------------
Expand Down Expand Up @@ -83,7 +83,7 @@ def setup(app):
# built documents.
#
# The short X.Y version.
version = 'v2.2.4'
version = 'v2.2.5'
# The full version, including alpha/beta/rc tags.
release = version

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20 changes: 13 additions & 7 deletions docs/format/source/format_release_notes.rst
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@@ -1,30 +1,36 @@
Release Notes
=============

2.2.5 (May 29, 2020)
----------------------

- Add schema validation CI.
- Fix incorrect dims and shape for ``ImagingPlane.origin_coords`` and ``ImagingPlane.grid_spacing``, and fix incorrect dims for ``TwoPhotonSeries.field_of_view``.

2.2.4 (April 14, 2020)
----------------------

- Fix typo in nwb.ophys.yaml that prevents proper parsing of the schema.
- Fix typo in ``nwb.ophys.yaml`` that prevents proper parsing of the schema.

2.2.3 (April 13, 2020)
----------------------

- Move nested type definitions to root of YAML files. This does not functionally change the schema but simplifies parsing of the schema and extensions by APIs.
- Make `ImagingPlane.imaging_rate` optional to handle cases where an imaging plane is associated with multiple time series with different rates.
- Make ``ImagingPlane.imaging_rate`` optional to handle cases where an imaging plane is associated with multiple time series with different rates.
- Add release process documentation.

2.2.2 (March 2, 2020)
---------------------

- Fix shape and dims of `OpticalSeries.data` for color images
- Allow more than one `OpticalChannel` object in `ImagingPlane`
- Update hdmf-common-schema to 1.1.3. This fixes missing 'shape' and 'dims' key for types `VectorData`, `VectorIndex`, and `DynamicTableRegion`.
- Revert changes to retinotopy.yaml in 2.1.0 which break backward compatibility and were not supported by the APIs in any case. Changes will be revisited in a future version.
- Fix shape and dims of ``OpticalSeries.data`` for color images
- Allow more than one ``OpticalChannel`` object in ``ImagingPlane``
- Update hdmf-common-schema to 1.1.3. This fixes missing 'shape' and 'dims' key for types ``VectorData``, ``VectorIndex``, and ``DynamicTableRegion``.
- Revert changes to ``nwb.retinotopy.yaml`` in 2.1.0 which break backward compatibility and were not supported by the APIs in any case. Changes will be revisited in a future version.

2.2.1 (January 14, 2020)
------------------------

- Fixed incorrect version numbers in nwb.file.yaml and hdmf-common namespace.yaml.
- Fixed incorrect version numbers in ``nwb.file.yaml`` and ``hdmf-common-schema/common/namespace.yaml``.

2.2.0 (January 6, 2020)
-----------------------
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