From c3c06518170a624b2d73645d5fa598cbd4a5951a Mon Sep 17 00:00:00 2001
From: amsnyder <asnyder@usgs.gov>
Date: Thu, 11 Jan 2024 14:18:49 -0600
Subject: [PATCH] updates to fix variable pull and auto-fill x,y,t dims in dims
dict
---
catalog/conus404-daily/collection.json | 2 +-
.../conus404-daily/conus404-daily.json | 2 +-
...e_collection_from_zarr_conus404-daily.ipynb | 18 +++++++++++-------
.../create_item_from_zarr_conus404-daily.ipynb | 18 +++++++++++-------
4 files changed, 24 insertions(+), 16 deletions(-)
diff --git a/catalog/conus404-daily/collection.json b/catalog/conus404-daily/collection.json
index 7e99fdd5..c1243093 100644
--- a/catalog/conus404-daily/collection.json
+++ b/catalog/conus404-daily/collection.json
@@ -32,8 +32,8 @@
},
"x": {
"type": "spatial",
- "description": "x coordinate of projection",
"axis": "x",
+ "description": "x coordinate of projection",
"extent": [
-2732097.901153542,
2731902.098846458
diff --git a/catalog_items/conus404-daily/conus404-daily.json b/catalog_items/conus404-daily/conus404-daily.json
index fcbb6847..417a2ab3 100644
--- a/catalog_items/conus404-daily/conus404-daily.json
+++ b/catalog_items/conus404-daily/conus404-daily.json
@@ -16,8 +16,8 @@
},
"x": {
"type": "spatial",
- "description": "x coordinate of projection",
"axis": "x",
+ "description": "x coordinate of projection",
"extent": [
-2732097.901153542,
2731902.098846458
diff --git a/workflows/examples/create_collection_from_zarr_conus404-daily.ipynb b/workflows/examples/create_collection_from_zarr_conus404-daily.ipynb
index 2fcdba41..602f929c 100644
--- a/workflows/examples/create_collection_from_zarr_conus404-daily.ipynb
+++ b/workflows/examples/create_collection_from_zarr_conus404-daily.ipynb
@@ -567,12 +567,16 @@
"outputs": [],
"source": [
"# create a dictionary of datacube dimensions you would like to assign to this dataset\n",
- "# dimension name should come from the coordinates printed above\n",
+ "# dimension name should come from the dims printed in above cell\n",
+ "\n",
+ "# x, y, t dimension info is pulled out automatically using the dim dict we created above\n",
+ "# all other dims listed in above cell need to be manually written in\n",
+ "\n",
"# we do not recommend including redundant dimensions (do not include x,y if you have lon,lat)\n",
"# note that the extent of each dimension should be pulled from the dataset\n",
- "dims_dict = {'time': pystac.extensions.datacube.Dimension({'type': 'temporal', 'description': get_long_name(ds, 'time'), 'extent': [temporal_extent_lower.strftime('%Y-%m-%dT%XZ'), temporal_extent_upper.strftime('%Y-%m-%dT%XZ')], 'step': pd.Timedelta(get_step(ds, 'time')).isoformat()}),\n",
- " 'x': pystac.extensions.datacube.Dimension({'type': 'spatial', 'description': get_long_name(ds, 'x'), 'axis': 'x', 'extent': [xy_bounds[0], xy_bounds[2]], 'step': get_step(ds, 'x'), 'reference_system': projjson}),\n",
- " 'y': pystac.extensions.datacube.Dimension({'type': 'spatial', 'axis': 'y', 'description': get_long_name(ds, 'y'), 'extent': [xy_bounds[1], xy_bounds[3]], 'step': get_step(ds, 'y'), 'reference_system': projjson}),\n",
+ "dims_dict = {dim_names_dict['T']: pystac.extensions.datacube.Dimension({'type': 'temporal', 'description': get_long_name(ds, dim_names_dict['T']), 'extent': [temporal_extent_lower.strftime('%Y-%m-%dT%XZ'), temporal_extent_upper.strftime('%Y-%m-%dT%XZ')], 'step': pd.Timedelta(get_step(ds, dim_names_dict['T'])).isoformat()}),\n",
+ " dim_names_dict['X']: pystac.extensions.datacube.Dimension({'type': 'spatial', 'axis': 'x', 'description': get_long_name(ds, dim_names_dict['X']), 'extent': [xy_bounds[0], xy_bounds[2]], 'step': get_step(ds, dim_names_dict['X']), 'reference_system': projjson}),\n",
+ " dim_names_dict['Y']: pystac.extensions.datacube.Dimension({'type': 'spatial', 'axis': 'y', 'description': get_long_name(ds, dim_names_dict['Y']), 'extent': [xy_bounds[1], xy_bounds[3]], 'step': get_step(ds, dim_names_dict['Y']), 'reference_system': projjson}),\n",
" 'bottom_top_stag': pystac.extensions.datacube.Dimension({'type': 'spatial', 'axis': 'z', 'description': get_long_name(ds, 'bottom_top_stag')}),\n",
" 'bottom_top': pystac.extensions.datacube.Dimension({'type': 'spatial', 'axis': 'z', 'description': get_long_name(ds, 'bottom_top')}),\n",
" 'soil_layers_stag': pystac.extensions.datacube.Dimension({'type': 'spatial', 'axis': 'z', 'description': get_long_name(ds, 'soil_layers_stag')}),\n",
@@ -635,13 +639,13 @@
"metadata": {},
"outputs": [],
"source": [
- "# pull list of vars from dataset\n",
- "vars = list(ds.variables)\n",
- "\n",
"# drop metpy_crs coordinate we have added\n",
"if 'metpy_crs' in ds.coords:\n",
" ds = ds.drop_vars('metpy_crs')\n",
"\n",
+ "# pull list of vars from dataset\n",
+ "vars = list(ds.variables)\n",
+ "\n",
"# spec says that the keys of cube:dimensions and cube:variables should be unique together; a key like lat should not be both a dimension and a variable.\n",
"# we will drop all values in dims from vars\n",
"vars = [v for v in vars if v not in dims]\n",
diff --git a/workflows/examples/create_item_from_zarr_conus404-daily.ipynb b/workflows/examples/create_item_from_zarr_conus404-daily.ipynb
index 473e8b1d..eeee7798 100644
--- a/workflows/examples/create_item_from_zarr_conus404-daily.ipynb
+++ b/workflows/examples/create_item_from_zarr_conus404-daily.ipynb
@@ -577,12 +577,16 @@
"outputs": [],
"source": [
"# create a dictionary of datacube dimensions you would like to assign to this dataset\n",
- "# dimension name should come from the coordinates printed above\n",
+ "# dimension name should come from the dims printed in above cell\n",
+ "\n",
+ "# x, y, t dimension info is pulled out automatically using the dim dict we created above\n",
+ "# all other dims listed in above cell need to be manually written in\n",
+ "\n",
"# we do not recommend including redundant dimensions (do not include x,y if you have lon,lat)\n",
"# note that the extent of each dimension should be pulled from the dataset\n",
- "dims_dict = {'time': pystac.extensions.datacube.Dimension({'type': 'temporal', 'description': get_long_name(ds, 'time'), 'extent': [temporal_extent_lower.strftime('%Y-%m-%dT%XZ'), temporal_extent_upper.strftime('%Y-%m-%dT%XZ')], 'step': pd.Timedelta(get_step(ds, 'time')).isoformat()}),\n",
- " 'x': pystac.extensions.datacube.Dimension({'type': 'spatial', 'description': get_long_name(ds, 'x'), 'axis': 'x', 'extent': [xy_bounds[0], xy_bounds[2]], 'step': get_step(ds, 'x'), 'reference_system': projjson}),\n",
- " 'y': pystac.extensions.datacube.Dimension({'type': 'spatial', 'axis': 'y', 'description': get_long_name(ds, 'y'), 'extent': [xy_bounds[1], xy_bounds[3]], 'step': get_step(ds, 'y'), 'reference_system': projjson}),\n",
+ "dims_dict = {dim_names_dict['T']: pystac.extensions.datacube.Dimension({'type': 'temporal', 'description': get_long_name(ds, dim_names_dict['T']), 'extent': [temporal_extent_lower.strftime('%Y-%m-%dT%XZ'), temporal_extent_upper.strftime('%Y-%m-%dT%XZ')], 'step': pd.Timedelta(get_step(ds, dim_names_dict['T'])).isoformat()}),\n",
+ " dim_names_dict['X']: pystac.extensions.datacube.Dimension({'type': 'spatial', 'axis': 'x', 'description': get_long_name(ds, dim_names_dict['X']), 'extent': [xy_bounds[0], xy_bounds[2]], 'step': get_step(ds, dim_names_dict['X']), 'reference_system': projjson}),\n",
+ " dim_names_dict['Y']: pystac.extensions.datacube.Dimension({'type': 'spatial', 'axis': 'y', 'description': get_long_name(ds, dim_names_dict['Y']), 'extent': [xy_bounds[1], xy_bounds[3]], 'step': get_step(ds, dim_names_dict['Y']), 'reference_system': projjson}),\n",
" 'bottom_top_stag': pystac.extensions.datacube.Dimension({'type': 'spatial', 'axis': 'z', 'description': get_long_name(ds, 'bottom_top_stag')}),\n",
" 'bottom_top': pystac.extensions.datacube.Dimension({'type': 'spatial', 'axis': 'z', 'description': get_long_name(ds, 'bottom_top')}),\n",
" 'soil_layers_stag': pystac.extensions.datacube.Dimension({'type': 'spatial', 'axis': 'z', 'description': get_long_name(ds, 'soil_layers_stag')}),\n",
@@ -645,12 +649,12 @@
"metadata": {},
"outputs": [],
"source": [
- "# pull list of vars from dataset\n",
- "vars = list(ds.variables)\n",
- "\n",
"# drop metpy_crs coordinate we have added\n",
"if 'metpy_crs' in ds.coords:\n",
" ds = ds.drop_vars('metpy_crs')\n",
+ " \n",
+ "# pull list of vars from dataset\n",
+ "vars = list(ds.variables)\n",
"\n",
"# spec says that the keys of cube:dimensions and cube:variables should be unique together; a key like lat should not be both a dimension and a variable.\n",
"# we will drop all values in dims from vars\n",
--
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