Merge pull request #181 from davidhassell/subsampled-docs

Subsampled docs tidy
NCAS-CMS · Mar 21, 2022 · 1e1c74a · 1e1c74a
2 parents dc3e37f + 0c6f2d7
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diff --git a/Changelog.rst b/Changelog.rst
@@ -1,3 +1,13 @@
+Version 1.9.1.0
+---------------
+
+**2022-??-??**
+
+* Implement (bar writing to netCDF files) lossy compression by
+  coordinate subsampling (https://github.com/NCAS-CMS/cfdm/issues/167)
+
+  ----
+
 Version 1.9.0.3
 ---------------
 

diff --git a/README.md b/README.md
@@ -84,8 +84,9 @@ The ``cfdm`` package can:
 * create subspaces of field and domain constructs,
 * incorporate, and create, metadata stored in external files, and
 * read, write, and create data that have been compressed by convention
-  (i.e. ragged or gathered arrays), whilst presenting a view of the
-  data in its uncompressed form.
+  (i.e. ragged or gathered arrays, or coordinate arrays compressed by
+  subsampling), whilst presenting a view of the data in its
+  uncompressed form.
 
 Command line utility
 ====================

diff --git a/cfdm/data/abstract/compressedarray.py b/cfdm/data/abstract/compressedarray.py
@@ -388,7 +388,7 @@ def compressed_dimensions(self):
         return self._get_component("compressed_dimensions").copy()
 
     def conformed_data(self):
-        """The data as required by the decompression algorthm.
+        """The data as required by the decompression algorithm.
 
         .. versionadded:: (cfdm) 1.9.TODO.0
 
@@ -473,7 +473,7 @@ def subarrays(self, shapes=-1):
 
         :Returns:
 
-            sequence of iterables
+            sequence of iterable
                 Each iterable iterates over a particular descriptor
                 from each subarray.
 

diff --git a/docs/source/class/cfdm.AuxiliaryCoordinate.rst b/docs/source/class/cfdm.AuxiliaryCoordinate.rst
@@ -176,6 +176,7 @@ Miscellaneous
    ~cfdm.AuxiliaryCoordinate.equals
    ~cfdm.AuxiliaryCoordinate.uncompress
    ~cfdm.AuxiliaryCoordinate.get_filenames
+   ~cfdm.AuxiliaryCoordinate.to_memory
 
 NetCDF
 ------

diff --git a/docs/source/class/cfdm.Bounds.rst b/docs/source/class/cfdm.Bounds.rst
@@ -91,6 +91,7 @@ Miscellaneous
    ~cfdm.Bounds.has_bounds
    ~cfdm.Bounds.uncompress
    ~cfdm.Bounds.get_filenames
+   ~cfdm.Bounds.to_memory
 
 NetCDF
 ------

diff --git a/docs/source/class/cfdm.CellMeasure.rst b/docs/source/class/cfdm.CellMeasure.rst
@@ -106,6 +106,7 @@ Miscellaneous
    ~cfdm.CellMeasure.has_bounds
    ~cfdm.CellMeasure.uncompress
    ~cfdm.CellMeasure.get_filenames
+   ~cfdm.CellMeasure.to_memory
 
 NetCDF
 ------

diff --git a/docs/source/class/cfdm.CompressedArray.rst b/docs/source/class/cfdm.CompressedArray.rst
@@ -37,9 +37,14 @@ Compression
    :toctree: ../method/
    :template: method.rst
 
+   ~cfdm.CompressedArray.compressed_dimensions
    ~cfdm.CompressedArray.get_compressed_axes
    ~cfdm.CompressedArray.get_compressed_dimension
    ~cfdm.CompressedArray.get_compression_type
+   ~cfdm.CompressedArray.subarray_shapes
+   ~cfdm.CompressedArray.subarrays
+   ~cfdm.CompressedArray.get_Subarray
+   ~cfdm.CompressedArray.conformed_data
 
 Miscellaneous
 -------------

diff --git a/docs/source/class/cfdm.Count.rst b/docs/source/class/cfdm.Count.rst
@@ -90,6 +90,7 @@ Miscellaneous
    ~cfdm.Count.get_filenames
    ~cfdm.Count.has_bounds
    ~cfdm.Count.uncompress
+   ~cfdm.Count.to_memory
 
 NetCDF
 ------

diff --git a/docs/source/class/cfdm.Data.rst b/docs/source/class/cfdm.Data.rst
@@ -282,6 +282,15 @@ Miscellaneous
    ~cfdm.Data.get_filenames
    ~cfdm.Data.source
 
+.. rubric:: Attributes
+
+.. autosummary::
+   :nosignatures:
+   :toctree: ../attribute/
+   :template: attribute.rst
+
+    ~cfdm.Data.data
+
 Performance
 -----------
 

diff --git a/docs/source/class/cfdm.DimensionCoordinate.rst b/docs/source/class/cfdm.DimensionCoordinate.rst
@@ -176,6 +176,7 @@ Miscellaneous
    ~cfdm.DimensionCoordinate.equals
    ~cfdm.DimensionCoordinate.uncompress
    ~cfdm.DimensionCoordinate.get_filenames
+   ~cfdm.DimensionCoordinate.to_memory
 
 NetCDF
 ------

diff --git a/docs/source/class/cfdm.Domain.rst b/docs/source/class/cfdm.Domain.rst
@@ -117,6 +117,7 @@ Miscellaneous
    ~cfdm.Domain.has_geometry
    ~cfdm.Domain.apply_masking   
    ~cfdm.Domain.get_filenames
+   ~cfdm.Domain.uncompress
 
 NetCDF
 ------

diff --git a/docs/source/class/cfdm.DomainAncillary.rst b/docs/source/class/cfdm.DomainAncillary.rst
@@ -161,6 +161,7 @@ Miscellaneous
    ~cfdm.DomainAncillary.equals
    ~cfdm.DomainAncillary.uncompress
    ~cfdm.DomainAncillary.get_filenames
+   ~cfdm.DomainAncillary.to_memory
 
 NetCDF
 ------

diff --git a/docs/source/class/cfdm.Field.rst b/docs/source/class/cfdm.Field.rst
@@ -184,6 +184,7 @@ Miscellaneous
    ~cfdm.Field.has_geometry
    ~cfdm.Field.uncompress
    ~cfdm.Field.get_filenames
+   ~cfdm.Field.to_memory
 
 .. _Field-NetCDF:
 

diff --git a/docs/source/class/cfdm.FieldAncillary.rst b/docs/source/class/cfdm.FieldAncillary.rst
@@ -101,6 +101,7 @@ Miscellaneous
    ~cfdm.FieldAncillary.has_bounds
    ~cfdm.FieldAncillary.uncompress
    ~cfdm.FieldAncillary.get_filenames
+   ~cfdm.FieldAncillary.to_memory
 
 NetCDF
 ------

diff --git a/docs/source/class/cfdm.GatheredArray.rst b/docs/source/class/cfdm.GatheredArray.rst
@@ -20,6 +20,7 @@ Inspection
    :toctree: ../method/
    :template: method.rst
 
+   ~cfdm.GatheredArray.compressed_dimensions
    ~cfdm.GatheredArray.get_compressed_axes
    ~cfdm.GatheredArray.get_compressed_dimension
    ~cfdm.GatheredArray.get_compression_type
@@ -53,6 +54,10 @@ Miscellaneous
    ~cfdm.GatheredArray.get_subspace
    ~cfdm.GatheredArray.source
    ~cfdm.GatheredArray.to_memory
+   ~cfdm.GatheredArray.subarray_shapes
+   ~cfdm.GatheredArray.subarrays
+   ~cfdm.GatheredArray.get_Subarray
+   ~cfdm.GatheredArray.conformed_data
 
 Special
 -------

diff --git a/docs/source/class/cfdm.Index.rst b/docs/source/class/cfdm.Index.rst
@@ -90,6 +90,7 @@ Miscellaneous
    ~cfdm.Index.get_filenames
    ~cfdm.Index.has_bounds
    ~cfdm.Index.uncompress
+   ~cfdm.Index.to_memory
 
 NetCDF
 ------

diff --git a/docs/source/class/cfdm.InteriorRing.rst b/docs/source/class/cfdm.InteriorRing.rst
@@ -90,6 +90,7 @@ Miscellaneous
    ~cfdm.InteriorRing.has_bounds
    ~cfdm.InteriorRing.uncompress
    ~cfdm.InteriorRing.get_filenames
+   ~cfdm.InteriorRing.to_memory
 
 NetCDF
 ------

diff --git a/docs/source/class/cfdm.List.rst b/docs/source/class/cfdm.List.rst
@@ -90,6 +90,7 @@ Miscellaneous
    ~cfdm.List.get_filenames
    ~cfdm.List.has_bounds
    ~cfdm.List.uncompress
+   ~cfdm.List.to_memory
 
 NetCDF
 ------

diff --git a/docs/source/class/cfdm.NetCDFArray.rst b/docs/source/class/cfdm.NetCDFArray.rst
@@ -54,6 +54,7 @@ File
    ~cfdm.NetCDFArray.get_filename
    ~cfdm.NetCDFArray.get_group
    ~cfdm.NetCDFArray.get_mask
+   ~cfdm.NetCDFArray.file_address
 
 Miscellaneous
 -------------

diff --git a/docs/source/class/cfdm.RaggedContiguousArray.rst b/docs/source/class/cfdm.RaggedContiguousArray.rst
@@ -20,7 +20,8 @@ Inspection
    :toctree: ../method/
    :template: method.rst
 
-    ~cfdm.RaggedContiguousArray.get_compressed_axes
+   ~cfdm.RaggedContiguousArray.compressed_dimensions
+   ~cfdm.RaggedContiguousArray.get_compressed_axes
    ~cfdm.RaggedContiguousArray.get_compressed_dimension
    ~cfdm.RaggedContiguousArray.get_compression_type
    ~cfdm.RaggedContiguousArray.get_count
@@ -53,6 +54,11 @@ Miscellaneous
    ~cfdm.RaggedContiguousArray.get_subspace
    ~cfdm.RaggedContiguousArray.source
    ~cfdm.RaggedContiguousArray.to_memory
+   ~cfdm.RaggedContiguousArray.subarray_shapes
+   ~cfdm.RaggedContiguousArray.subarrays
+   ~cfdm.RaggedContiguousArray.get_Subarray
+   ~cfdm.RaggedContiguousArray.conformed_data
+   ~cfdm.RaggedContiguousArray.get_index
 
 Special
 -------

diff --git a/docs/source/class/cfdm.RaggedIndexedArray.rst b/docs/source/class/cfdm.RaggedIndexedArray.rst
@@ -20,6 +20,7 @@ Inspection
    :toctree: ../method/
    :template: method.rst
 
+   ~cfdm.RaggedIndexedArray.compressed_dimensions
    ~cfdm.RaggedIndexedArray.get_compressed_axes
    ~cfdm.RaggedIndexedArray.get_compressed_dimension
    ~cfdm.RaggedIndexedArray.get_compression_type
@@ -53,6 +54,11 @@ Miscellaneous
    ~cfdm.RaggedIndexedArray.get_subspace
    ~cfdm.RaggedIndexedArray.source
    ~cfdm.RaggedIndexedArray.to_memory
+   ~cfdm.RaggedIndexedArray.subarray_shapes
+   ~cfdm.RaggedIndexedArray.subarrays
+   ~cfdm.RaggedIndexedArray.get_Subarray
+   ~cfdm.RaggedIndexedArray.conformed_data
+   ~cfdm.RaggedIndexedArray.get_count
 
 Special
 -------

diff --git a/docs/source/class/cfdm.RaggedIndexedContiguousArray.rst b/docs/source/class/cfdm.RaggedIndexedContiguousArray.rst
@@ -20,6 +20,7 @@ Inspection
    :toctree: ../method/
    :template: method.rst
 
+   ~cfdm.RaggedIndexedContiguousArray.compressed_dimensions
    ~cfdm.RaggedIndexedContiguousArray.get_compressed_axes
    ~cfdm.RaggedIndexedContiguousArray.get_compressed_dimension
    ~cfdm.RaggedIndexedContiguousArray.get_compression_type
@@ -54,6 +55,10 @@ Miscellaneous
    ~cfdm.RaggedIndexedContiguousArray.get_subspace
    ~cfdm.RaggedIndexedContiguousArray.source
    ~cfdm.RaggedIndexedContiguousArray.to_memory
+   ~cfdm.RaggedIndexedContiguousArray.subarray_shapes
+   ~cfdm.RaggedIndexedContiguousArray.subarrays
+   ~cfdm.RaggedIndexedContiguousArray.get_Subarray
+   ~cfdm.RaggedIndexedContiguousArray.conformed_data
 
 Special
 -------

diff --git a/docs/source/introduction.rst b/docs/source/introduction.rst
@@ -100,8 +100,9 @@ The cfdm package can
 * incorporate, and create, metadata stored in external files, and
 
 * read, write, and create data that have been compressed by convention
-  (i.e. ragged or gathered arrays), whilst presenting a view of the
-  data in its uncompressed form.
+  (i.e. ragged or gathered arrays, or coordinate arrays compressed by
+  subsampling), whilst presenting a view of the data in its
+  uncompressed form.
 
 Note that the cfdm package enables the representation and creation of
 CF field constructs, but it is largely :ref:`up to the user to use

diff --git a/docs/source/sample_files/subsampled.nc b/docs/source/sample_files/subsampled.nc
diff --git a/docs/source/spelling_false_positives.txt b/docs/source/spelling_false_positives.txt
@@ -108,6 +108,8 @@ Signell
 situ
 spatiotemporal
 str
+subarray
+subarrays
 subceed
 subclassed
 subclassing

diff --git a/docs/source/tutorial.py b/docs/source/tutorial.py
@@ -726,7 +726,7 @@
 # uncompressed shape
 array = cfdm.RaggedContiguousArray(
 compressed_array=ragged_array,
-shape=(2, 4), size=8, ndim=2,
+shape=(2, 4),
 count_variable=count_variable)
 
 # Create the field construct with the domain axes and the ragged
@@ -775,8 +775,8 @@
 # shape
 array = cfdm.GatheredArray(
 compressed_array=gathered_array,
-compressed_dimension=1,
-shape=(2, 3, 2), size=12, ndim=3,
+compressed_dimensions={1: (1, 2)},
+shape=(2, 3, 2),
 list_variable=list_variable)
 
 # Create the field construct with the domain axes and the gathered
@@ -801,3 +801,19 @@
 list_variable
 print(list_variable.data.array)
 cfdm.write(P, 'P_gathered.nc')
+f = cfdm.read('subsampled.nc')[0]
+print(f)
+lon = f.construct('longitude')
+lon
+lon.data.source()
+print(lon.data.array)
+lon.data.source().source()
+print(lon.data.source().source().array)
+print(lon.data.array)
+g = f[0, 6, :]
+print(g)
+print(g.construct('longitude').data.array)
+lon = f.construct('longitude')
+d = lon.data.source()
+d.get_tie_point_indices()
+d.get_computational_precision()