refactor: change 'geotiff' to 'GTiff' and 'cog' for #320 (#321)

* refactor: change `'geotiff'` to `'GTiff'` and `'cog'` for #320

* Create pyproject.toml

doc/source/api_reference/compute_LPET_elevations.rst

@@ -4,7 +4,7 @@ compute_LPET_elevation.py
 
 - Calculates long-period equilibrium tides for an input file
 - Uses the summation of fifteen tidal spectral lines from [Cartwright1971]_ [Cartwright1973]_
-- Can read and write ascii, netCDF4, HDF5, parquet and geotiff formats
+- Can read and write ascii, netCDF4, HDF5, (cloud optimized) geotiff and (geo)parquet formats
 
 `Source code`__
 
@@ -20,6 +20,14 @@ Calling Sequence
     :nodescription:
     :nodefault:
 
+    --format -F : @after
+        * ``'csv'``: ascii with comma-separated values
+        * ``'netCDF4'``: Network Common Data Format version 4
+        * ``'HDF5'``: Hierarchical Data Format version 5
+        * ``'GTiff'``: GeoTiff georeferenced raster imagery
+        * ``'cog'``: Cloud Optimized GeoTIFF
+        * ``'parquet'``: Apache (geo)parquet
+
     --variables : @after
         * for csv files: the order of the columns within the file
         * for HDF5, netCDF4 and parquet files: time, y, x and data variable names

doc/source/api_reference/compute_LPT_displacements.rst

@@ -5,7 +5,7 @@ compute_LPT_displacements.py
 - Calculates radial pole load tide displacements for an input file following IERS Convention (2010) guidelines
 
   * `https://iers-conventions.obspm.fr/chapter7.php <https://iers-conventions.obspm.fr/chapter7.php>`_
-- Can read and write ascii, netCDF4, HDF5, parquet and geotiff formats
+- Can read and write ascii, netCDF4, HDF5, (cloud optimized) geotiff and (geo)parquet formats
 
 `Source code`__
 
@@ -21,6 +21,14 @@ Calling Sequence
     :nodescription:
     :nodefault:
 
+    --format -F : @after
+        * ``'csv'``: ascii with comma-separated values
+        * ``'netCDF4'``: Network Common Data Format version 4
+        * ``'HDF5'``: Hierarchical Data Format version 5
+        * ``'GTiff'``: GeoTiff georeferenced raster imagery
+        * ``'cog'``: Cloud Optimized GeoTIFF
+        * ``'parquet'``: Apache (geo)parquet
+
     --variables : @after
         * for csv files: the order of the columns within the file
         * for HDF5, netCDF4 and parquet files: time, y, x and data variable names

doc/source/api_reference/compute_OPT_displacements.rst

@@ -6,7 +6,7 @@ compute_OPT_displacements.py
 
   * `https://iers-conventions.obspm.fr/chapter7.php <https://iers-conventions.obspm.fr/chapter7.php>`_
   * `ftp://tai.bipm.org/iers/conv2010/chapter7/opoleloadcoefcmcor.txt.gz <ftp://tai.bipm.org/iers/conv2010/chapter7/opoleloadcoefcmcor.txt.gz>`_
-- Can read and write ascii, netCDF4, HDF5, parquet and geotiff formats
+- Can read and write ascii, netCDF4, HDF5, (cloud optimized) geotiff and (geo)parquet formats
 
 `Source code`__
 
@@ -22,6 +22,14 @@ Calling Sequence
     :nodescription:
     :nodefault:
 
+    --format -F : @after
+        * ``'csv'``: ascii with comma-separated values
+        * ``'netCDF4'``: Network Common Data Format version 4
+        * ``'HDF5'``: Hierarchical Data Format version 5
+        * ``'GTiff'``: GeoTiff georeferenced raster imagery
+        * ``'cog'``: Cloud Optimized GeoTIFF
+        * ``'parquet'``: Apache (geo)parquet
+
     --variables : @after
         * for csv files: the order of the columns within the file
         * for HDF5, netCDF4 and parquet files: time, y, x and data variable names

doc/source/api_reference/compute_SET_displacements.rst

@@ -5,7 +5,7 @@ compute_SET_displacements.py
 - Calculates radial solid Earth tide displacements for an input file following IERS Convention (2010) guidelines
 
   * `https://iers-conventions.obspm.fr/chapter7.php <https://iers-conventions.obspm.fr/chapter7.php>`_
-- Can read and write ascii, netCDF4, HDF5, parquet and geotiff formats
+- Can read and write ascii, netCDF4, HDF5, (cloud optimized) geotiff and (geo)parquet formats
 
 `Source code`__
 
@@ -21,6 +21,14 @@ Calling Sequence
     :nodescription:
     :nodefault:
 
+    --format -F : @after
+        * ``'csv'``: ascii with comma-separated values
+        * ``'netCDF4'``: Network Common Data Format version 4
+        * ``'HDF5'``: Hierarchical Data Format version 5
+        * ``'GTiff'``: GeoTiff georeferenced raster imagery
+        * ``'cog'``: Cloud Optimized GeoTIFF
+        * ``'parquet'``: Apache (geo)parquet
+
     --variables : @after
         * for csv files: the order of the columns within the file
         * for HDF5, netCDF4 and parquet files: time, y, x and data variable names

doc/source/api_reference/compute_tidal_currents.rst

@@ -5,7 +5,7 @@ compute_tidal_currents.py
 - Calculates tidal currents for an input file following [Egbert2002]_
 - Can use OTIS format tidal solutions provided by Oregon State University and ESR
 - Can use Finite Element Solution (FES) models provided by AVISO
-- Can read and write ascii, netCDF4, HDF5, parquet and geotiff formats
+- Can read and write ascii, netCDF4, HDF5, (cloud optimized) geotiff and (geo)parquet formats
 
 `Source code`__
 
@@ -21,6 +21,14 @@ Calling Sequence
     :nodescription:
     :nodefault:
 
+    --format -F : @after
+        * ``'csv'``: ascii with comma-separated values
+        * ``'netCDF4'``: Network Common Data Format version 4
+        * ``'HDF5'``: Hierarchical Data Format version 5
+        * ``'GTiff'``: GeoTiff georeferenced raster imagery
+        * ``'cog'``: Cloud Optimized GeoTIFF
+        * ``'parquet'``: Apache (geo)parquet
+
     --variables : @after
         * for csv files: the order of the columns within the file
         * for HDF5, netCDF4 and parquet files: time, y, x and data variable names

doc/source/api_reference/compute_tidal_elevations.rst

@@ -6,7 +6,7 @@ compute_tidal_elevations.py
 - Can use OTIS format tidal solutions provided by Oregon State University and ESR
 - Can use Global Tide Model (GOT) solutions provided by Richard Ray at GSFC
 - Can use Finite Element Solution (FES) models provided by AVISO
-- Can read and write ascii, netCDF4, HDF5, parquet and geotiff formats
+- Can read and write ascii, netCDF4, HDF5, (cloud optimized) geotiff and (geo)parquet formats
 
 `Source code`__
 
@@ -22,6 +22,14 @@ Calling Sequence
     :nodescription:
     :nodefault:
 
+    --format -F : @after
+        * ``'csv'``: ascii with comma-separated values
+        * ``'netCDF4'``: Network Common Data Format version 4
+        * ``'HDF5'``: Hierarchical Data Format version 5
+        * ``'GTiff'``: GeoTiff georeferenced raster imagery
+        * ``'cog'``: Cloud Optimized GeoTIFF
+        * ``'parquet'``: Apache (geo)parquet
+
     --variables : @after
         * for csv files: the order of the columns within the file
         * for HDF5, netCDF4 and parquet files: time, y, x and data variable names

doc/source/api_reference/spatial.rst

@@ -4,6 +4,8 @@ spatial
 
 Utilities for reading, writing and operating on spatial data
 
+ - Can read netCDF4, HDF5, (cloud optimized) geotiff or (geo)parquet files
+
 Calling Sequence
 ----------------
 

pyTMD/spatial.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 u"""
 spatial.py
-Written by Tyler Sutterley (07/2024)
+Written by Tyler Sutterley (08/2024)
 
 Utilities for reading, writing and operating on spatial data
 
@@ -30,6 +30,7 @@
     crs.py: Coordinate Reference System (CRS) routines
 
 UPDATE HISTORY:
+    Updated 08/2024: changed from 'geotiff' to 'GTiff' and 'cog' formats
     Updated 07/2024: added functions to convert to and from DMS
     Updated 06/2024: added function to write parquet files with metadata
     Updated 05/2024: added function to read from parquet files
@@ -195,7 +196,7 @@ def from_file(filename: str, format: str, **kwargs):
         dinput = from_netCDF4(filename, **kwargs)
     elif (format == 'HDF5'):
         dinput = from_HDF5(filename, **kwargs)
-    elif (format == 'geotiff'):
+    elif format in ('GTiff','cog'):
         dinput = from_geotiff(filename, **kwargs)
     elif (format == 'parquet'):
         dinput = from_parquet(filename, **kwargs)
@@ -750,7 +751,7 @@ def to_file(
         to_netCDF4(output, attributes, filename, **kwargs)
     elif (format == 'HDF5'):
         to_HDF5(output, attributes, filename, **kwargs)
-    elif (format == 'geotiff'):
+    elif format in ('GTiff','cog'):
         to_geotiff(output, attributes, filename, **kwargs)
     elif (format == 'parquet'):
         to_parquet(output, attributes, filename, **kwargs)
@@ -1083,7 +1084,7 @@ def to_geotiff(
         **kwargs
     ):
     """
-    Write data to a geotiff file
+    Write data to a (cloud optimized) geotiff file
 
     Parameters
     ----------

pyproject.toml

@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools", "setuptools_scm"]
+build-backend = "setuptools.build_meta"

scripts/compute_LPET_elevations.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 u"""
 compute_LPET_elevations.py
-Written by Tyler Sutterley (07/2024)
+Written by Tyler Sutterley (08/2024)
 Calculates long-period equilibrium tidal elevations for an input file
 
 INPUTS:
@@ -17,7 +17,8 @@
         netCDF4
         HDF5
         parquet
-        geotiff
+        GTiff
+        cog
     -v X, --variables X: variable names of data in csv, HDF5 or netCDF4 file
         for csv files: the order of the columns within the file
         for HDF5, netCDF4 and parquet files: time, y, x and data variable names
@@ -69,6 +70,7 @@
     predict.py: calculates long-period equilibrium ocean tides
 
 UPDATE HISTORY:
+    Updated 08/2024: changed from 'geotiff' to 'GTiff' and 'cog' formats
     Updated 07/2024: assert that data type is a known value
     Updated 06/2024: include attributes in output parquet files
     Updated 05/2024: use function to reading parquet files to allow
@@ -171,7 +173,7 @@ def compute_LPET_elevations(input_file, output_file,
         dinput = pyTMD.spatial.from_HDF5(input_file,
             field_mapping=field_mapping)
         attributes = dinput['attributes']
-    elif (FORMAT == 'geotiff'):
+    elif FORMAT in ('GTiff', 'cog'):
         dinput = pyTMD.spatial.from_geotiff(input_file)
         attributes = dinput['attributes']
     elif (FORMAT == 'parquet'):
@@ -277,19 +279,20 @@ def compute_LPET_elevations(input_file, output_file,
     elif (FORMAT == 'HDF5'):
         # write to HDF5
         pyTMD.spatial.to_HDF5(output, attrib, output_file)
-    elif (FORMAT == 'geotiff'):
+    elif FORMAT in ('GTiff', 'cog'):
         # write raster data to geotiff
         # copy global geotiff attributes for projection and grid parameters
         for att_name in ['projection','wkt','spacing','extent']:
             attrib[att_name] = attributes[att_name]
         pyTMD.spatial.to_geotiff(output, attrib, output_file,
-            varname='tide_lpe')
+            varname='tide_lpe', driver=FORMAT)
     elif (FORMAT == 'parquet'):
         # write to (geo)parquet
         geoparquet = attributes.get('geoparquet', False)
         geometry_encoding = attributes.get('geometry_encoding', None)
         pyTMD.spatial.to_parquet(output, attrib, output_file,
-            geoparquet=geoparquet, geometry_encoding=geometry_encoding, crs=4326)
+            geoparquet=geoparquet, geometry_encoding=geometry_encoding,
+            crs=4326)
     # change the permissions level to MODE
     output_file.chmod(mode=MODE)
 
@@ -313,7 +316,7 @@ def arguments():
     # input and output data format
     parser.add_argument('--format','-F',
         type=str, default='csv',
-        choices=('csv','netCDF4','HDF5','geotiff','parquet'),
+        choices=('csv','netCDF4','HDF5','GTiff','cog','parquet'),
         help='Input and output data format')
     # variable names (for csv names of columns)
     parser.add_argument('--variables','-v',

scripts/compute_LPT_displacements.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 u"""
 compute_LPT_displacements.py
-Written by Tyler Sutterley (07/2024)
+Written by Tyler Sutterley (08/2024)
 Calculates radial load pole tide displacements for an input file
     following IERS Convention (2010) guidelines
     https://iers-conventions.obspm.fr/chapter7.php
@@ -19,7 +19,8 @@
         netCDF4
         HDF5
         parquet
-        geotiff
+        GTiff
+        cog
     -v X, --variables X: variable names of data in csv, HDF5 or netCDF4 file
         for csv files: the order of the columns within the file
         for HDF5, netCDF4 and parquet files: time, y, x and data variable names
@@ -78,6 +79,7 @@
     utilities.py: download and management utilities for syncing files
 
 UPDATE HISTORY:
+    Updated 08/2024: changed from 'geotiff' to 'GTiff' and 'cog' formats
     Updated 07/2024: assert that data type is a known value
     Updated 06/2024: include attributes in output parquet files
     Updated 05/2024: use function to reading parquet files to allow
@@ -192,7 +194,7 @@ def compute_LPT_displacements(input_file, output_file,
         dinput = pyTMD.spatial.from_HDF5(input_file,
             field_mapping=field_mapping)
         attributes = dinput['attributes']
-    elif (FORMAT == 'geotiff'):
+    elif FORMAT in ('GTiff', 'cog'):
         dinput = pyTMD.spatial.from_geotiff(input_file)
         attributes = dinput['attributes']
     elif (FORMAT == 'parquet'):
@@ -350,19 +352,20 @@ def compute_LPT_displacements(input_file, output_file,
     elif (FORMAT == 'HDF5'):
         # write to HDF5
         pyTMD.spatial.to_HDF5(output, attrib, output_file)
-    elif (FORMAT == 'geotiff'):
+    elif FORMAT in ('GTiff', 'cog'):
         # write raster data to geotiff
         # copy global geotiff attributes for projection and grid parameters
         for att_name in ['projection','wkt','spacing','extent']:
             attrib[att_name] = attributes[att_name]
         pyTMD.spatial.to_geotiff(output, attrib, output_file,
-            varname='tide_pole')
+            varname='tide_pole', driver=FORMAT)
     elif (FORMAT == 'parquet'):
         # write to (geo)parquet
         geoparquet = attributes.get('geoparquet', False)
         geometry_encoding = attributes.get('geometry_encoding', None)
         pyTMD.spatial.to_parquet(output, attrib, output_file,
-            geoparquet=geoparquet, geometry_encoding=geometry_encoding, crs=4326)
+            geoparquet=geoparquet, geometry_encoding=geometry_encoding,
+            crs=4326)
     # change the permissions level to MODE
     output_file.chmod(mode=MODE)
 
@@ -386,7 +389,7 @@ def arguments():
     # input and output data format
     parser.add_argument('--format','-F',
         type=str, default='csv',
-        choices=('csv','netCDF4','HDF5','geotiff','parquet'),
+        choices=('csv','netCDF4','HDF5','GTiff','cog','parquet'),
         help='Input and output data format')
     # variable names (for csv names of columns)
     parser.add_argument('--variables','-v',