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import os
import json
import cmor
import unittest
import numpy
from netCDF4 import Dataset
import pyfive
CMIP7_TABLES_PATH = "cmip7-cmor-tables/tables"
CV_PATH = "TestTables/CMIP7_CV.json"
USER_INPUT = {
"_AXIS_ENTRY_FILE": "CMIP7_coordinate.json",
"_FORMULA_VAR_FILE": "CMIP7_formula_terms.json",
"_cmip7_option": 1,
"_controlled_vocabulary_file": CV_PATH,
"activity_id": "CMIP",
"branch_method": "standard",
"branch_time_in_child": 30.0,
"branch_time_in_parent": 10800.0,
"calendar": "360_day",
"cv_version": "6.2.19.0",
"experiment": "Simulation of the pre-industrial climate",
"experiment_id": "piControl",
"forcing_index": "f30",
"grid": "N96",
"grid_label": "gn",
"initialization_index": "i000001d",
"institution_id": "PCMDI",
"license_id": "CC BY 4.0",
"nominal_resolution": "250 km",
"outpath": ".",
"parent_mip_era": "CMIP7",
"parent_time_units": "days since 1850-01-01",
"parent_activity_id": "CMIP",
"parent_source_id": "PCMDI-test-1-0",
"parent_experiment_id": "piControl",
"parent_variant_label": "r1i1p1f3",
"physics_index": "p1",
"realization_index": "r009",
"source_id": "PCMDI-test-1-0",
"source_type": "AOGCM CHEM BGC",
"tracking_prefix": "hdl:21.14100",
"host_collection": "CMIP7",
"frequency": "day",
"region": "glb",
"archive_id": "WCRP",
"output_path_template": "<activity_id><source_id><experiment_id><member_id><variable_id><branding_suffix><grid_label>",
"output_file_template": "<variable_id><branding_suffix><frequency><region><grid_label><source_id><experiment_id><variant_label>",
}
class TestChunking(unittest.TestCase):
def assertCMIP7RepackChunking(self, filename, msg=None):
BYTES_4MiB = 4 * 2**20
""" Chunking checks from cmip7_repack """
f = pyfive.File(filename)
if "time" in f:
# Check for the time coordinates variable having one chunk
t = f["time"]
chunks = t.chunks
if chunks is not None and t.id.get_num_chunks() > 1:
# At least two chunks
message = self._formatMessage(msg,
f"FAIL: File {filename!r} time coordinates variable "
f"'time' has {t.id.get_num_chunks()} chunks "
"(expected 1 chunk or contiguous)"
)
raise self.failureException(message)
# Check for the time bounds variable having one chunk
if "bounds" in t.attrs:
bounds = str(numpy.array(t.attrs["bounds"]).astype("U"))
if bounds in f:
b = f[bounds]
chunks = b.chunks
if chunks is not None and b.id.get_num_chunks() > 1:
# At least two chunks
message = self._formatMessage(msg,
f"FAIL: File {filename!r} time bounds variable "
f"{bounds!r} has {b.id.get_num_chunks()} chunks "
"(expected 1 chunk or contiguous)"
)
raise self.failureException(message)
# Check for the data variable having one chunks of at least ~4MiB
if "variable_id" in f.attrs:
variable_id = str(numpy.array(f.attrs["variable_id"]).astype("U"))
if variable_id in f:
d = f[variable_id]
if chunks is not None and d.id.get_num_chunks() > 1:
# At least two chunks
chunks = d.chunks
wordsize = d.dtype.itemsize
chunksize = numpy.prod(chunks) * wordsize
lee_way = 0
if len(chunks) > 1:
lee_way = numpy.prod(chunks[1:]) * wordsize
if chunksize + lee_way < BYTES_4MiB:
message = self._formatMessage(msg,
f"FAIL: File {filename!r} data variable "
f"{variable_id!r} has uncompressed chunk size "
f"{chunksize} B (expected at least "
f"{BYTES_4MiB - lee_way} B or 1 chunk "
"or contiguous)"
)
raise self.failureException(message)
def setUp(self):
"""
Write out a simple file using CMOR
"""
# Set up CMOR
cmor.setup(inpath=CMIP7_TABLES_PATH, netcdf_file_action=cmor.CMOR_REPLACE)
# Define dataset using USER_INPUT
with open("Test/input_cmip7.json", "w") as input_file_handle:
json.dump(USER_INPUT, input_file_handle, sort_keys=True, indent=4)
# read dataset info
error_flag = cmor.dataset_json("Test/input_cmip7.json")
if error_flag:
raise RuntimeError("CMOR dataset_json call failed")
self.cmor_filepath = ""
def tearDown(self):
if os.path.isfile(self.cmor_filepath):
os.remove(self.cmor_filepath)
def generate_file(self, num_times, num_lat, num_lon):
data = [27] * (num_times * num_lat * num_lon)
pr = numpy.array(data)
pr.shape = (num_times, num_lat, num_lon)
lat_bnds = numpy.linspace(-90., 90., num_lat + 1)
lat = (lat_bnds[:-1] + lat_bnds[1:]) / 2
lon_bnds = numpy.linspace(0., 180., num_lon + 1)
lon = (lon_bnds[:-1] + lon_bnds[1:]) / 2
time = numpy.arange(num_times) + 0.5
time_bnds = numpy.arange(num_times + 1)
cmor.load_table("CMIP7_atmos.json")
cmorlat = cmor.axis("latitude",
coord_vals=lat,
cell_bounds=lat_bnds,
units="degrees_north")
cmorlon = cmor.axis("longitude",
coord_vals=lon,
cell_bounds=lon_bnds,
units="degrees_east")
cmortime = cmor.axis("time",
coord_vals=time,
cell_bounds=time_bnds,
units="days since 2018")
axes = [cmortime, cmorlat, cmorlon]
cmorpr = cmor.variable("pr_tavg-u-hxy-u", "kg m-2 s-1", axes)
self.assertEqual(cmor.write(cmorpr, pr), 0)
self.cmor_filepath = cmor.close(cmorpr, file_name=True)
self.assertEqual(cmor.close(), 0)
def test_few_small_timesteps(self):
num_times = 4
num_lat = 100
num_lon = 100
self.generate_file(num_times, num_lat, num_lon)
self.assertCMIP7RepackChunking(self.cmor_filepath)
def test_many_small_timesteps(self):
num_times = 200
num_lat = 100
num_lon = 100
self.generate_file(num_times, num_lat, num_lon)
self.assertCMIP7RepackChunking(self.cmor_filepath)
def test_large_timesteps(self):
num_times = 10
num_lat = 1000
num_lon = 1000
self.generate_file(num_times, num_lat, num_lon)
self.assertCMIP7RepackChunking(self.cmor_filepath)
def test_writing_one_timestep_at_a_time(self):
num_times = 4
num_lat = 100
num_lon = 100
data = [27] * (num_times * num_lat * num_lon)
pr = numpy.array(data)
pr.shape = (num_times, num_lat, num_lon)
lat_bnds = numpy.linspace(-90., 90., num_lat + 1)
lat = (lat_bnds[:-1] + lat_bnds[1:]) / 2
lon_bnds = numpy.linspace(0., 180., num_lon + 1)
lon = (lon_bnds[:-1] + lon_bnds[1:]) / 2
time = numpy.arange(num_times) + 0.5
time_bnds = numpy.arange(num_times + 1)
cmor.load_table("CMIP7_atmos.json")
cmorlat = cmor.axis("latitude",
coord_vals=lat,
cell_bounds=lat_bnds,
units="degrees_north")
cmorlon = cmor.axis("longitude",
coord_vals=lon,
cell_bounds=lon_bnds,
units="degrees_east")
cmortime = cmor.axis("time",
units="days since 2018")
axes = [cmortime, cmorlat, cmorlon]
cmorpr = cmor.variable("pr_tavg-u-hxy-u", "kg m-2 s-1", axes)
for i in range(num_times):
self.assertEqual(cmor.write(cmorpr, pr[i,:,:], time_vals=time[i], time_bnds=time_bnds[i:i+2]), 0)
self.cmor_filepath = cmor.close(cmorpr, file_name=True)
self.assertEqual(cmor.close(), 0)
with Dataset(self.cmor_filepath, 'r') as dataset:
pr_chunks = dataset.variables['pr'].chunking()
self.assertEqual(pr_chunks, [1, num_lat, num_lon])
time_chunks = dataset.variables['time'].chunking()
self.assertEqual(time_chunks, [512])
time_bnds_chunks = dataset.variables['time_bnds'].chunking()
self.assertEqual(time_bnds_chunks, [512, 2])
def test_user_defined_variable_chunking(self):
num_times = 40
num_lat = 100
num_lon = 100
chunking_dims = [8, 20, 20]
data = [27] * (num_times * num_lat * num_lon)
pr = numpy.array(data)
pr.shape = (num_times, num_lat, num_lon)
lat_bnds = numpy.linspace(-90., 90., num_lat + 1)
lat = (lat_bnds[:-1] + lat_bnds[1:]) / 2
lon_bnds = numpy.linspace(0., 180., num_lon + 1)
lon = (lon_bnds[:-1] + lon_bnds[1:]) / 2
time = numpy.arange(num_times) + 0.5
time_bnds = numpy.arange(num_times + 1)
cmor.load_table("CMIP7_atmos.json")
cmorlat = cmor.axis("latitude",
coord_vals=lat,
cell_bounds=lat_bnds,
units="degrees_north")
cmorlon = cmor.axis("longitude",
coord_vals=lon,
cell_bounds=lon_bnds,
units="degrees_east")
cmortime = cmor.axis("time",
units="days since 2018")
axes = [cmortime, cmorlat, cmorlon]
cmorpr = cmor.variable("pr_tavg-u-hxy-u", "kg m-2 s-1", axes)
cmor.set_chunking(cmorpr, chunking_dims)
for i in range(num_times):
self.assertEqual(cmor.write(cmorpr, pr[i,:,:], time_vals=time[i], time_bnds=time_bnds[i:i+2]), 0)
self.cmor_filepath = cmor.close(cmorpr, file_name=True)
self.assertEqual(cmor.close(), 0)
with Dataset(self.cmor_filepath, 'r') as dataset:
pr_chunks = dataset.variables['pr'].chunking()
self.assertEqual(pr_chunks, chunking_dims)
time_chunks = dataset.variables['time'].chunking()
self.assertEqual(time_chunks, [512])
time_bnds_chunks = dataset.variables['time_bnds'].chunking()
self.assertEqual(time_bnds_chunks, [512, 2])
if __name__ == '__main__':
unittest.main()
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