From 9d0b93c4b6e6dff777b032f5bfb18e44e5b8af64 Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Fri, 30 Aug 2019 14:23:22 -0700 Subject: [PATCH 1/4] Deprecate manifold in favor of pixel_origin and pixel_deltas --- core/nwb.ophys.yaml | 37 +++++++++++++++++++++++++++++++++---- 1 file changed, 33 insertions(+), 4 deletions(-) diff --git a/core/nwb.ophys.yaml b/core/nwb.ophys.yaml index ef3b7887..f48d14c4 100644 --- a/core/nwb.ophys.yaml +++ b/core/nwb.ophys.yaml @@ -206,8 +206,8 @@ groups: - null - null - 3 - doc: "Physical position of each pixel. 'xyz' represents the position\ - \ of the pixel relative to the defined coordinate space." + doc: "DEPRECATED Physical position of each pixel. 'xyz' represents the position\ + \ of the pixel relative to the defined coordinate space. Deprecated in favor of pixel_origin and pixel_deltas." quantity: '?' attributes: - name: conversion @@ -224,9 +224,38 @@ groups: - name: unit dtype: text default_value: meters - doc: Base unit of measurement for working with the data. The default value - is 'meters'. + doc: Base unit of measurement for working with the data. The default value is 'meters'. required: false + - name: pixel_origin + dtype: float + dims: + - x, y + - x, y, z + shape: + - 2 + - 3 + doc: Location of the origin in x, y or x, y, z, in meters + required: false + attributes: + - name: unit + dtype: text + default_value: meters + doc: Measurement units for pixel_origin. The default value is 'meters'. + - name: pixel_deltas + dtype: float + dims: + - x, y + - x, y, z + shape: + - 2 + - 3 + doc: Space between pixels in x, y or x, y, z directions. Assumes imaging plane is a regular grid. + required: false + attributes: + - name: unit + dtype: text + default_value: meters + doc: Measurement units for pixel_deltas. The default value is 'meters'. - name: reference_frame dtype: text doc: Describes position and reference frame of manifold based on position of From a918207994bcda7426ab1b0add07080a4c0bad51 Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Fri, 30 Aug 2019 14:24:59 -0700 Subject: [PATCH 2/4] Clarify doc --- core/nwb.ophys.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/core/nwb.ophys.yaml b/core/nwb.ophys.yaml index f48d14c4..d6c9ad87 100644 --- a/core/nwb.ophys.yaml +++ b/core/nwb.ophys.yaml @@ -234,7 +234,7 @@ groups: shape: - 2 - 3 - doc: Location of the origin in x, y or x, y, z, in meters + doc: Location of the origin in x, y or x, y, z, in the specified unit. required: false attributes: - name: unit @@ -249,7 +249,8 @@ groups: shape: - 2 - 3 - doc: Space between pixels in x, y or x, y, z directions. Assumes imaging plane is a regular grid. + doc: Space between pixels in x, y or x, y, z directions, in the specified unit. + Assumes imaging plane is a regular grid. required: false attributes: - name: unit From 54a7bd210110d37d073dae6bdcf4b4e5bd1165b0 Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Mon, 7 Oct 2019 15:24:52 -0700 Subject: [PATCH 3/4] Change new dataset names --- core/nwb.ophys.yaml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/core/nwb.ophys.yaml b/core/nwb.ophys.yaml index d6c9ad87..6e91362a 100644 --- a/core/nwb.ophys.yaml +++ b/core/nwb.ophys.yaml @@ -226,7 +226,7 @@ groups: default_value: meters doc: Base unit of measurement for working with the data. The default value is 'meters'. required: false - - name: pixel_origin + - name: origin_coords dtype: float dims: - x, y @@ -234,14 +234,14 @@ groups: shape: - 2 - 3 - doc: Location of the origin in x, y or x, y, z, in the specified unit. + doc: Location of the origin in (x, y) or (x, y, z), in the specified unit. required: false attributes: - name: unit dtype: text default_value: meters - doc: Measurement units for pixel_origin. The default value is 'meters'. - - name: pixel_deltas + doc: Measurement units for origin_coords. The default value is 'meters'. + - name: grid_spacing dtype: float dims: - x, y @@ -249,14 +249,14 @@ groups: shape: - 2 - 3 - doc: Space between pixels in x, y or x, y, z directions, in the specified unit. + 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. required: false attributes: - name: unit dtype: text default_value: meters - doc: Measurement units for pixel_deltas. The default value is 'meters'. + doc: Measurement units for grid_spacing. The default value is 'meters'. - name: reference_frame dtype: text doc: Describes position and reference frame of manifold based on position of From 762686d03798c060adf129c396b2667572ac2505 Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Mon, 7 Oct 2019 15:25:17 -0700 Subject: [PATCH 4/4] More changes to dataset names --- core/nwb.ophys.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/core/nwb.ophys.yaml b/core/nwb.ophys.yaml index 6e91362a..9740ce72 100644 --- a/core/nwb.ophys.yaml +++ b/core/nwb.ophys.yaml @@ -207,7 +207,7 @@ groups: - null - 3 doc: "DEPRECATED Physical position of each pixel. 'xyz' represents the position\ - \ of the pixel relative to the defined coordinate space. Deprecated in favor of pixel_origin and pixel_deltas." + \ of the pixel relative to the defined coordinate space. Deprecated in favor of origin_coords and grid_spacing." quantity: '?' attributes: - name: conversion