refactor: change 'geotiff' to 'GTiff' and 'cog'

tsutterley · Aug 22, 2024 · e3122fe · e3122fe
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diff --git a/DEM/MPI_interpolate_DEM.py b/DEM/MPI_interpolate_DEM.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 u"""
 MPI_interpolate_DEM.py
-Written by Tyler Sutterley (05/2024)
+Written by Tyler Sutterley (08/2024)
 Determines which digital elevation model tiles for an input file
 Reads 3x3 array of tiles for points within bounding box of central mosaic tile
 Interpolates digital elevation model to coordinates
@@ -33,7 +33,8 @@
         csv (default)
         netCDF4
         HDF5
-        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 and netCDF4 files: time, y, x and data variable names
@@ -84,6 +85,7 @@
     https://nsidc.org/data/nsidc-0645/versions/1
 
 UPDATE HISTORY:
+    Updated 08/2024: changed from 'geotiff' to 'GTiff' and 'cog' formats
     Updated 05/2024: use wrapper to importlib for optional dependencies
     Updated 07/2023: using pathlib to define and operate on paths
         use geoms attribute for shapely 2.0 compliance
@@ -168,7 +170,8 @@ def arguments():
         help='Digital Elevation Model to run')
     # input and output data format
     parser.add_argument('--format','-F',
-        type=str, default='csv', choices=('csv','netCDF4','HDF5','geotiff'),
+        type=str, default='csv',
+        choices=('csv','netCDF4','HDF5','GTiff','cog'),
         help='Input and output data format')
     # variable names (for csv names of columns)
     parser.add_argument('--variables','-v',
@@ -475,7 +478,7 @@ def main():
         attrib[args.variables[2]] = dinput['attributes']['x']
         attrib[args.variables[1]] = dinput['attributes']['y']
         attrib[args.variables[0]] = dinput['attributes']['time']
-    elif (args.format == 'geotiff') and (comm.rank == 0):
+    elif (args.format in ('GTiff','cog')) and (comm.rank == 0):
         dinput = pyTMD.spatial.from_geotiff(args.infile,
             verbose=args.verbose)
         # copy global geotiff attributes for projection and grid parameters
@@ -710,9 +713,10 @@ def main():
         elif (args.format == 'HDF5'):
             pyTMD.spatial.to_HDF5(output, attrib, args.outfile,
                 verbose=args.verbose)
-        elif (args.format == 'geotiff'):
+        elif args.format in ('GTiff','cog'):
             pyTMD.spatial.to_geotiff(output, attrib, args.outfile,
-                varname='dem_h', verbose=args.verbose)
+                varname='dem_h', driver=args.format,
+                verbose=args.verbose)
         # change the permissions level to MODE
         args.outfile.chmod(mode=args.mode)
 

diff --git a/GZ/calculate_grounding_zone.py b/GZ/calculate_grounding_zone.py
@@ -460,7 +460,7 @@ def arguments():
         help='Digital Elevation Model to run')
     # input and output data format
     parser.add_argument('--format','-F',
-        type=str, default='csv', choices=('csv','netCDF4','HDF5','geotiff'),
+        type=str, default='csv', choices=('csv','netCDF4','HDF5'),
         help='Input and output data format')
     # variable names (for csv names of columns)
     parser.add_argument('--variables','-v',

diff --git a/doc/source/api_reference/DEM/MPI_interpolate_DEM.rst b/doc/source/api_reference/DEM/MPI_interpolate_DEM.rst
@@ -2,7 +2,7 @@
 MPI_interpolate_DEM.py
 ======================
 
-- Determines which digital elevation model tiles for an input file (ascii, netCDF4, HDF5, geotiff)
+- Determines which digital elevation model tiles for an input file (ascii, netCDF4, HDF5, GTiff, cog)
 - Reads 3\ |times|\ 3 array of tiles for points within bounding box of central mosaic tile
 - Interpolates digital elevation model to coordinates
 

diff --git a/subset/reduce_ICESat2_ATL06_raster.py b/subset/reduce_ICESat2_ATL06_raster.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 u"""
 reduce_ICESat2_ATL06_raster.py
-Written by Tyler Sutterley (05/2024)
+Written by Tyler Sutterley (08/2024)
 
 Create masks for reducing ICESat-2 ATL06 data using raster imagery
 
@@ -10,7 +10,8 @@
     -F X, --format X: Input raster file format
         netCDF4
         HDF5
-        geotiff
+        GTiff
+        cog
     -v X, --variables X: variable names of data in HDF5 or netCDF4 file
         x, y and data variable names
     -P X, --projection X: spatial projection as EPSG code or PROJ4 string
@@ -43,6 +44,7 @@
     utilities.py: download and management utilities for syncing files
 
 UPDATE HISTORY:
+    Updated 08/2024: changed from 'geotiff' to 'GTiff' and 'cog' formats
     Updated 05/2024: use wrapper to importlib for optional dependencies
         moved from icesat2_toolkit to Grounding-Zones package
     Updated 04/2024: use timescale for temporal operations
@@ -578,7 +580,8 @@ def arguments():
         type=pathlib.Path,
         help='Input raster file')
     parser.add_argument('--format','-F',
-        type=str, default='geotiff', choices=('netCDF4','HDF5','geotiff'),
+        type=str, default='GTiff',
+        choices=('netCDF4','HDF5','GTiff','cog'),
         help='Input raster file format')
     # variable names of data in HDF5 or netCDF4 file
     parser.add_argument('--variables','-v',

diff --git a/subset/reduce_ICESat2_ATL07_raster.py b/subset/reduce_ICESat2_ATL07_raster.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 u"""
 reduce_ICESat2_ATL07_raster.py
-Written by Tyler Sutterley (05/2024)
+Written by Tyler Sutterley (08/2024)
 
 Create masks for reducing ICESat-2 ATL07 data using raster imagery
 
@@ -10,7 +10,8 @@
     -F X, --format X: Input raster file format
         netCDF4
         HDF5
-        geotiff
+        GTiff
+        cog
     -v X, --variables X: variable names of data in HDF5 or netCDF4 file
         x, y and data variable names
     -P X, --projection X: spatial projection as EPSG code or PROJ4 string
@@ -43,6 +44,7 @@
     utilities.py: download and management utilities for syncing files
 
 UPDATE HISTORY:
+    Updated 08/2024: changed from 'geotiff' to 'GTiff' and 'cog' formats
     Updated 05/2024: use wrapper to importlib for optional dependencies
         moved from icesat2_toolkit to Grounding-Zones package
     Updated 04/2024: use timescale for temporal operations
@@ -614,7 +616,8 @@ def arguments():
         type=pathlib.Path,
         help='Input raster file')
     parser.add_argument('--format','-F',
-        type=str, default='geotiff', choices=('netCDF4','HDF5','geotiff'),
+        type=str, default='GTiff',
+        choices=('netCDF4','HDF5','GTiff','cog'),
         help='Input raster file format')
     # variable names of data in HDF5 or netCDF4 file
     parser.add_argument('--variables','-v',

diff --git a/subset/reduce_ICESat2_ATL10_raster.py b/subset/reduce_ICESat2_ATL10_raster.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 u"""
 reduce_ICESat2_ATL10_raster.py
-Written by Tyler Sutterley (05/2024)
+Written by Tyler Sutterley (08/2024)
 
 Create masks for reducing ICESat-2 ATL10 data using raster imagery
 
@@ -10,7 +10,8 @@
     -F X, --format X: Input raster file format
         netCDF4
         HDF5
-        geotiff
+        GTiff
+        cog
     -v X, --variables X: variable names of data in HDF5 or netCDF4 file
         x, y and data variable names
     -P X, --projection X: spatial projection as EPSG code or PROJ4 string
@@ -43,6 +44,7 @@
     utilities.py: download and management utilities for syncing files
 
 UPDATE HISTORY:
+    Updated 08/2024: changed from 'geotiff' to 'GTiff' and 'cog' formats
     Updated 05/2024: use wrapper to importlib for optional dependencies
         moved from icesat2_toolkit to Grounding-Zones package
     Updated 04/2024: use timescale for temporal operations
@@ -573,7 +575,8 @@ def arguments():
         type=pathlib.Path,
         help='Input raster file')
     parser.add_argument('--format','-F',
-        type=str, default='geotiff', choices=('netCDF4','HDF5','geotiff'),
+        type=str, default='GTiff',
+        choices=('netCDF4','HDF5','GTiff','cog'),
         help='Input raster file format')
     # variable names of data in HDF5 or netCDF4 file
     parser.add_argument('--variables','-v',

diff --git a/subset/reduce_ICESat2_ATL11_raster.py b/subset/reduce_ICESat2_ATL11_raster.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 u"""
 reduce_ICESat2_ATL11_raster.py
-Written by Tyler Sutterley (05/2024)
+Written by Tyler Sutterley (08/2024)
 
 Create masks for reducing ICESat-2 ATL11 data using raster imagery
 
@@ -10,7 +10,8 @@
     -F X, --format X: Input raster file format
         netCDF4
         HDF5
-        geotiff
+        GTiff
+        cog
     -v X, --variables X: variable names of data in HDF5 or netCDF4 file
         x, y and data variable names
     -P X, --projection X: spatial projection as EPSG code or PROJ4 string
@@ -43,6 +44,7 @@
     utilities.py: download and management utilities for syncing files
 
 UPDATE HISTORY:
+    Updated 08/2024: changed from 'geotiff' to 'GTiff' and 'cog' formats
     Updated 05/2024: use wrapper to importlib for optional dependencies
         moved from icesat2_toolkit to Grounding-Zones package
     Updated 04/2024: use timescale for temporal operations
@@ -583,7 +585,8 @@ def arguments():
         type=pathlib.Path,
         help='Input raster file')
     parser.add_argument('--format','-F',
-        type=str, default='geotiff', choices=('netCDF4','HDF5','geotiff'),
+        type=str, default='GTiff',
+        choices=('netCDF4','HDF5','GTiff','cog'),
         help='Input raster file format')
     # variable names of data in HDF5 or netCDF4 file
     parser.add_argument('--variables','-v',

diff --git a/subset/reduce_ICESat_GLA12_raster.py b/subset/reduce_ICESat_GLA12_raster.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 u"""
 reduce_ICESat_GLA12_raster.py
-Written by Tyler Sutterley (05/2024)
+Written by Tyler Sutterley (08/2024)
 
 Create masks for reducing ICESat/GLAS L2 GLA12 Antarctic and Greenland
     Ice Sheet elevation data data using raster imagery
@@ -11,7 +11,8 @@
     -F X, --format X: Input raster file format
         netCDF4
         HDF5
-        geotiff
+        GTiff
+        cog
     -v X, --variables X: variable names of data in HDF5 or netCDF4 file
         x, y and data variable names
     -P X, --projection X: spatial projection as EPSG code or PROJ4 string
@@ -44,6 +45,7 @@
     utilities.py: download and management utilities for syncing files
 
 UPDATE HISTORY:
+    Updated 08/2024: changed from 'geotiff' to 'GTiff' and 'cog' formats
     Updated 05/2024: use wrapper to importlib for optional dependencies
     Updated 04/2024: use timescale for temporal operations
     Updated 03/2024: use pathlib to define and operate on paths
@@ -520,7 +522,8 @@ def arguments():
         type=pathlib.Path,
         help='Input raster file')
     parser.add_argument('--format','-F',
-        type=str, default='geotiff', choices=('netCDF4','HDF5','geotiff'),
+        type=str, default='GTiff',
+        choices=('netCDF4','HDF5','GTiff','cog'),
         help='Input raster file format')
     # variable names of data in HDF5 or netCDF4 file
     parser.add_argument('--variables','-v',

diff --git a/tides/mosaic_tide_adjustment.py b/tides/mosaic_tide_adjustment.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 """
 mosaic_tide_adjustment.py
-Written by Tyler Sutterley (05/2024)
+Written by Tyler Sutterley (08/2024)
 
 Creates a mosaic of interpolated tidal adjustment scale factors
 
@@ -18,6 +18,7 @@
     -M X, --mode X: Local permissions mode of the output mosaic
 
 UPDATE HISTORY:
+    Updated 08/2024: changed from 'geotiff' to 'GTiff' and 'cog' formats
     Updated 05/2024: use wrapper to importlib for optional dependencies
     Updated 12/2023: don't have a default tide model in arguments
     Updated 11/2023: mask individual tiles before building mosaic
@@ -101,7 +102,7 @@ def mosaic_tide_adjustment(base_dir, output_file,
         # read mask from geotiff file
         # flip to be monotonically increasing in y dimension
         MASK = pathlib.Path(MASK).expanduser().absolute()
-        raster = gz.io.raster().from_file(MASK, format='geotiff').flip()
+        raster = gz.io.raster().from_file(MASK, format='GTiff').flip()
 
     # pyproj transformer for converting to polar stereographic
     EPSG = dict(N=3413, S=3031)[HEM]

diff --git a/tides/tidal_histogram_ICESat2_ATL11.py b/tides/tidal_histogram_ICESat2_ATL11.py
@@ -241,13 +241,13 @@ def tidal_histogram(tile_file,
         SUB,PRD,TRK,GRAN,SCYC,ECYC,RL,VERS,AUX = R2.findall(ATL11).pop()
         # read tide model corrections
         if TIDE_MODEL:
-            # ATL11 tide correction HDF5 file
+            # read ATL11 tide correction HDF5 file
             a3 = (PRD,TIDE_MODEL,'_TIDES',TRK,GRAN,SCYC,ECYC,RL,VERS,AUX)
             FILE3 = d1.joinpath(file_format.format(*a3))
             f3 = gz.io.multiprocess_h5py(FILE3, mode='r')
         # read inverse barometer correction
         if REANALYSIS:
-            # read inverse barometer HDF5 file
+            # read ATL11 inverse barometer HDF5 file
             a4 = (PRD,REANALYSIS,'IB',TRK,GRAN,SCYC,ECYC,RL,VERS,AUX)
             FILE4 = d1.joinpath(file_format.format(*a4))
             f4 = gz.io.multiprocess_h5py(FILE4, mode='r')
@@ -273,15 +273,15 @@ def tidal_histogram(tile_file,
                 )
             # read tide model corrections
             if TIDE_MODEL:
-                # read data and reduce to indices
+                # read tide data and reduce to indices
                 temp = f3[ptx]['cycle_stats']['tide_ocean'][:].copy()
                 tide_ocean = temp[indices,:]
             else:
                 tide_ocean = np.zeros((file_length,ncycles))
             # read inverse barometer correction
             if REANALYSIS:
-                # read data and reduce to indices
-                temp = f3[ptx]['cycle_stats']['ib'][:].copy()
+                # read IB data and reduce to indices
+                temp = f4[ptx]['cycle_stats']['ib'][:].copy()
                 IB = temp[indices,:]
             else:
                 # reduce DAC to indices
@@ -303,7 +303,7 @@ def tidal_histogram(tile_file,
                 # reference heights to geoid
                 h1 -= mds[ptx]['ref_surf']['geoid_h'][indices]
                 h2 -= mds[ptx]['ref_surf']['geoid_h'][indices]
-                # correct heights for DAC
+                # correct heights for DAC/IB
                 h1 -= IB[:,k]
                 h2 -= IB[:,k+1]
                 # correct heights for ocean tides