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updating docs
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@kujaku11
kujaku11 committed Oct 14, 2024
1 parent d8c11bb commit 293b659
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6 changes: 5 additions & 1 deletion docs/source/examples.rst
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Original file line number Diff line number Diff line change
@@ -1,6 +1,10 @@
Clients
Examples of External Clients
---------------------------------------

These are examples of downloading data from data services like
FDSN and the Geomagnetic Observatory data supplied by the
U.S. Geological Survey.

.. toctree::
:maxdepth: 1

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204 changes: 103 additions & 101 deletions docs/source/file_readers.rst
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Expand Up @@ -270,66 +270,66 @@ If you add a reader, you should also add a `Client`. This should inherit :class
.. code-block:: python
class NewFileTypeClient(ClientBase):
def __init__(
self,
data_path,
save_path=None,
mth5_filename="from_new_file_type.h5",
**kwargs
):
super().__init__(
data_path,
save_path=save_path,
sample_rates=[1],
mth5_filename=mth5_filename,
**kwargs
)
self.collection = NewFileCollection(self.data_path)
def make_mth5_from_new_file_type(self, **kwargs):
"""
Create an MTH5 from the new file type using the newly create Collections
object for the new file type.
:param **kwargs: DESCRIPTION
:type **kwargs: TYPE
:return: DESCRIPTION
:rtype: TYPE
"""
for key, value in kwargs.items():
if value is not None:
setattr(self, key, value)
runs = self.get_run_dict()
with MTH5(**self.h5_kwargs) as m:
m.open_mth5(self.save_path, "w")
# here is where you put the code specific to your
# new file type and how to get the data into an
# mth5. It should be organized as runs with
# logical names and use as much metadata as possible
# from the data.
survey_group = m.add_survey(self.collection.survey_id)
for station_id in runs.keys():
station_group = survey_group.stations_group.add_station(
station_id
)
for run_id, run_df in runs[station_id].items():
run_group = station_group.add_run(run_id)
run_ts = read_file(run_df.fn.to_list())
run_ts.run_metadata.id = run_id
run_group.from_runts(run_ts)
station_group.metadata.update(run_ts.station_metadata)
station_group.write_metadata()
# update survey metadata from input station
survey_group.update_metadata()
return self.save_path
def __init__(
self,
data_path,
save_path=None,
mth5_filename="from_new_file_type.h5",
**kwargs
):
super().__init__(
data_path,
save_path=save_path,
sample_rates=[1],
mth5_filename=mth5_filename,
**kwargs
)
self.collection = NewFileCollection(self.data_path)
def make_mth5_from_new_file_type(self, **kwargs):
"""
Create an MTH5 from the new file type using the newly create Collections
object for the new file type.
:param **kwargs: DESCRIPTION
:type **kwargs: TYPE
:return: DESCRIPTION
:rtype: TYPE
"""
for key, value in kwargs.items():
if value is not None:
setattr(self, key, value)
runs = self.get_run_dict()
with MTH5(**self.h5_kwargs) as m:
m.open_mth5(self.save_path, "w")
# here is where you put the code specific to your
# new file type and how to get the data into an
# mth5. It should be organized as runs with
# logical names and use as much metadata as possible
# from the data.
survey_group = m.add_survey(self.collection.survey_id)
for station_id in runs.keys():
station_group = survey_group.stations_group.add_station(
station_id
)
for run_id, run_df in runs[station_id].items():
run_group = station_group.add_run(run_id)
run_ts = read_file(run_df.fn.to_list())
run_ts.run_metadata.id = run_id
run_group.from_runts(run_ts)
station_group.metadata.update(run_ts.station_metadata)
station_group.write_metadata()
# update survey metadata from input station
survey_group.update_metadata()
return self.save_path
Adding to MakeMTH5
Expand All @@ -339,47 +339,49 @@ If you add a reader, you should also add the client to `MakeMTH5` for convenienc

.. code-block:: python
@classmethod
def from_new_filetype(
cls,
data_path,
mth5_filename=None,
save_path=None,
**kwargs,
):
"""
Doc string
Any H5 file parameters like compression, shuffle, etc need to have a
prefix of 'h5'. For example h5_compression='gzip'.
>>> MakeMTH5.from_lemi424(
data_path, 'test', 'mt01', **{'h5_compression_opts': 1}
)
:param data_path: Directory where data files are, could be a single
station or a full directory of stations.
:type data_path: str or Path
:param mth5_filename: filename for the H5, defaults to 'from_lemi424.h5'
:type mth5_filename: str, optional
:param save_path: path to save H5 file to, defaults to None which will
place the file in `data_path`
:type save_path: str or Path, optional
:return: Path to MTH5 file
:rtype: Path
"""
maker = cls(**kwargs)
kw_dict = maker.get_h5_kwargs()
lemi_client = NewFileClient(
data_path,
save_path=save_path,
mth5_filename=mth5_filename,
**kw_dict,
)
return lemi_client.make_mth5_from_new_file_type(**kwargs**)
class MakeMTH5:
...
@classmethod
def from_new_filetype(
cls,
data_path,
mth5_filename=None,
save_path=None,
**kwargs,
):
"""
Doc string
Any H5 file parameters like compression, shuffle, etc need to have a
prefix of 'h5'. For example h5_compression='gzip'.
>>> MakeMTH5.from_lemi424(
data_path, 'test', 'mt01', **{'h5_compression_opts': 1}
)
:param data_path: Directory where data files are, could be a single
station or a full directory of stations.
:type data_path: str or Path
:param mth5_filename: filename for the H5, defaults to 'from_lemi424.h5'
:type mth5_filename: str, optional
:param save_path: path to save H5 file to, defaults to None which will
place the file in `data_path`
:type save_path: str or Path, optional
:return: Path to MTH5 file
:rtype: Path
"""
maker = cls(**kwargs)
kw_dict = maker.get_h5_kwargs()
new_file_client = NewFileClient(
data_path,
save_path=save_path,
mth5_filename=mth5_filename,
**kw_dict,
)
return new_file_client.make_mth5_from_new_file_type(**kwargs**)
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