Renaming podaac.py to podaac_datasource.py and adding podaacpy dependency
Project: http://git-wip-us.apache.org/repos/asf/climate/repo Commit: http://git-wip-us.apache.org/repos/asf/climate/commit/02e5c2b1 Tree: http://git-wip-us.apache.org/repos/asf/climate/tree/02e5c2b1 Diff: http://git-wip-us.apache.org/repos/asf/climate/diff/02e5c2b1 Branch: refs/heads/master Commit: 02e5c2b1b55a6b621b1650087603a512ab556851 Parents: a67ea7d Author: Omkar20895 <omkarreddy2...@gmail.com> Authored: Sun Aug 21 02:09:47 2016 +0530 Committer: Omkar20895 <omkarreddy2...@gmail.com> Committed: Sun Aug 21 02:09:47 2016 +0530 ---------------------------------------------------------------------- easy-ocw/ocw-pip-dependencies.txt | 1 + ocw/data_source/podaac.py | 111 ------------------------------ ocw/data_source/podaac_datasource.py | 111 ++++++++++++++++++++++++++++++ 3 files changed, 112 insertions(+), 111 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/climate/blob/02e5c2b1/easy-ocw/ocw-pip-dependencies.txt ---------------------------------------------------------------------- diff --git a/easy-ocw/ocw-pip-dependencies.txt b/easy-ocw/ocw-pip-dependencies.txt index bd609dd..91e24be 100644 --- a/easy-ocw/ocw-pip-dependencies.txt +++ b/easy-ocw/ocw-pip-dependencies.txt @@ -9,3 +9,4 @@ esgf-pyclient>=0.1.6 python-dateutil>=2.5.3 mock>=2.0.0 myproxyclient>=1.4.3 +podaacpy>=1.0.1 http://git-wip-us.apache.org/repos/asf/climate/blob/02e5c2b1/ocw/data_source/podaac.py ---------------------------------------------------------------------- diff --git a/ocw/data_source/podaac.py b/ocw/data_source/podaac.py deleted file mode 100644 index e7d7b68..0000000 --- a/ocw/data_source/podaac.py +++ /dev/null @@ -1,111 +0,0 @@ -# Licensed to the Apache Software Foundation (ASF) under one -# or more contributor license agreements. See the NOTICE file -# distributed with this work for additional information -# regarding copyright ownership. The ASF licenses this file -# to you under the Apache License, Version 2.0 (the -# "License"); you may not use this file except in compliance -# with the License. You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, -# software distributed under the License is distributed on an -# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY -# KIND, either express or implied. See the License for the -# specific language governing permissions and limitations -# under the License. - -from podaac.podaac_data_source import Podaac -import numpy as np -from ocw.dataset import Dataset -from netCDF4 import Dataset as netcdf_dataset -from netcdftime import utime -import os - - -def convert_times_to_datetime(time): - '''Convert the time object's values to datetime objects - - The time values are stored as some unit since an epoch. These need to be - converted into datetime objects for the OCW Dataset object. - - :param time: The time object's values to convert - :type time: pydap.model.BaseType - - :returns: list of converted time values as datetime objects - ''' - units = time.units - # parse the time units string into a useful object. - # NOTE: This assumes a 'standard' calendar. It's possible (likely?) that - # users will want to customize this in the future. - parsed_time = utime(units) - return [parsed_time.num2date(x) for x in time[:]] - - -def load_dataset(variable, datasetId='', datasetShortName='', name=''): - '''Loads a Dataset from PODAAC - - :param variable: The name of the variable to read from the dataset. - :type variable: :mod:`string` - - :param datasetId: dataset persistent ID. datasetId or \ - shortName is required for a granule search. Example: \ - PODAAC-ASOP2-25X01 - :type datasetId: :mod:`string` - - :param shortName: the shorter name for a dataset. \ - Either shortName or datasetId is required for a \ - granule search. Example: ASCATA-L2-25km - :type shortName: :mod:`string` - - :param name: (Optional) A name for the loaded dataset. - :type name: :mod:`string` - - :returns: A :class:`dataset.Dataset` containing the dataset pointed to by - the OpenDAP URL. - - :raises: ServerError - ''' - # Downloading the dataset using podaac toolkit - podaac = Podaac() - path = os.path.dirname(os.path.abspath(__file__)) - granuleName = podaac.extract_l4_granule( - dataset_id=datasetId, short_name=datasetShortName, path=path) - path = path + '/' + granuleName - d = netcdf_dataset(path, mode='r') - dataset = d.variables[variable] - - # By convention, but not by standard, if the dimensions exist, they will be in the order: - # time (t), altitude (z), latitude (y), longitude (x) - # but conventions aren't always followed and all dimensions aren't always present so - # see if we can make some educated deductions before defaulting to just pulling the first three - # columns. - temp_dimensions = map(lambda x: x.lower(), dataset.dimensions) - dataset_dimensions = dataset.dimensions - time = dataset_dimensions[temp_dimensions.index( - 'time') if 'time' in temp_dimensions else 0] - lat = dataset_dimensions[temp_dimensions.index( - 'lat') if 'lat' in temp_dimensions else 1] - lon = dataset_dimensions[temp_dimensions.index( - 'lon') if 'lon' in temp_dimensions else 2] - - # Time is given to us in some units since an epoch. We need to convert - # these values to datetime objects. Note that we use the main object's - # time object and not the dataset specific reference to it. We need to - # grab the 'units' from it and it fails on the dataset specific object. - times = np.array(convert_times_to_datetime(d[time])) - lats = np.array(d.variables[lat][:]) - lons = np.array(d.variables[lon][:]) - values = np.array(dataset[:]) - origin = { - 'source': 'PO.DAAC', - 'url': 'podaac.jpl.nasa.gov/ws' - } - - # Removing the downloaded temporary granule before creating the OCW - # dataset. - d.close() - path = os.path.join(os.path.dirname(__file__), granuleName) - os.remove(path) - - return Dataset(lats, lons, times, values, variable, name=name, origin=origin) http://git-wip-us.apache.org/repos/asf/climate/blob/02e5c2b1/ocw/data_source/podaac_datasource.py ---------------------------------------------------------------------- diff --git a/ocw/data_source/podaac_datasource.py b/ocw/data_source/podaac_datasource.py new file mode 100644 index 0000000..d06c73f --- /dev/null +++ b/ocw/data_source/podaac_datasource.py @@ -0,0 +1,111 @@ +# Licensed to the Apache Software Foundation (ASF) under one +# or more contributor license agreements. See the NOTICE file +# distributed with this work for additional information +# regarding copyright ownership. The ASF licenses this file +# to you under the Apache License, Version 2.0 (the +# "License"); you may not use this file except in compliance +# with the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, +# software distributed under the License is distributed on an +# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +# KIND, either express or implied. See the License for the +# specific language governing permissions and limitations +# under the License. + +from podaac.podaac import Podaac +import numpy as np +from ocw.dataset import Dataset +from netCDF4 import Dataset as netcdf_dataset +from netcdftime import utime +import os + + +def convert_times_to_datetime(time): + '''Convert the time object's values to datetime objects + + The time values are stored as some unit since an epoch. These need to be + converted into datetime objects for the OCW Dataset object. + + :param time: The time object's values to convert + :type time: pydap.model.BaseType + + :returns: list of converted time values as datetime objects + ''' + units = time.units + # parse the time units string into a useful object. + # NOTE: This assumes a 'standard' calendar. It's possible (likely?) that + # users will want to customize this in the future. + parsed_time = utime(units) + return [parsed_time.num2date(x) for x in time[:]] + + +def load_dataset(variable, datasetId='', datasetShortName='', name=''): + '''Loads a Dataset from PODAAC + + :param variable: The name of the variable to read from the dataset. + :type variable: :mod:`string` + + :param datasetId: dataset persistent ID. datasetId or \ + shortName is required for a granule search. Example: \ + PODAAC-ASOP2-25X01 + :type datasetId: :mod:`string` + + :param shortName: the shorter name for a dataset. \ + Either shortName or datasetId is required for a \ + granule search. Example: ASCATA-L2-25km + :type shortName: :mod:`string` + + :param name: (Optional) A name for the loaded dataset. + :type name: :mod:`string` + + :returns: A :class:`dataset.Dataset` containing the dataset pointed to by + the OpenDAP URL. + + :raises: ServerError + ''' + # Downloading the dataset using podaac toolkit + podaac = Podaac() + path = os.path.dirname(os.path.abspath(__file__)) + granuleName = podaac.extract_l4_granule( + dataset_id=datasetId, short_name=datasetShortName, path=path) + path = path + '/' + granuleName + d = netcdf_dataset(path, mode='r') + dataset = d.variables[variable] + + # By convention, but not by standard, if the dimensions exist, they will be in the order: + # time (t), altitude (z), latitude (y), longitude (x) + # but conventions aren't always followed and all dimensions aren't always present so + # see if we can make some educated deductions before defaulting to just pulling the first three + # columns. + temp_dimensions = map(lambda x: x.lower(), dataset.dimensions) + dataset_dimensions = dataset.dimensions + time = dataset_dimensions[temp_dimensions.index( + 'time') if 'time' in temp_dimensions else 0] + lat = dataset_dimensions[temp_dimensions.index( + 'lat') if 'lat' in temp_dimensions else 1] + lon = dataset_dimensions[temp_dimensions.index( + 'lon') if 'lon' in temp_dimensions else 2] + + # Time is given to us in some units since an epoch. We need to convert + # these values to datetime objects. Note that we use the main object's + # time object and not the dataset specific reference to it. We need to + # grab the 'units' from it and it fails on the dataset specific object. + times = np.array(convert_times_to_datetime(d[time])) + lats = np.array(d.variables[lat][:]) + lons = np.array(d.variables[lon][:]) + values = np.array(dataset[:]) + origin = { + 'source': 'PO.DAAC', + 'url': 'podaac.jpl.nasa.gov/ws' + } + + # Removing the downloaded temporary granule before creating the OCW + # dataset. + d.close() + path = os.path.join(os.path.dirname(__file__), granuleName) + os.remove(path) + + return Dataset(lats, lons, times, values, variable, name=name, origin=origin)
