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Commit c9acd43b authored by matthmey's avatar matthmey
Browse files

added first version of freeze node

parent d80db24e
...@@ -20,39 +20,36 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, ...@@ -20,39 +20,36 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.""" SOFTWARE."""
from ..global_config import get_setting, setting_exists, set_setting
from ..core.graph import StuettNode, configuration
from ..convenience import read_csv_with_store, to_csv_with_store, DirectoryStore
from ..convenience import indexers_to_request as i2r
import os
import dask
import logging
import obspy
from obspy.clients.fdsn import Client
from obspy import UTCDateTime
from obsplus import obspy_to_array
from copy import deepcopy
import io
from tqdm import tqdm
import zarr
import xarray as xr
from PIL import Image
import base64 import base64
import datetime as dt
import io
import logging
import os
import re import re
from pathlib import Path
import warnings import warnings
from copy import deepcopy
from pathlib import Path
import dask
# TODO: revisit the following packages # TODO: revisit the following packages
import numpy as np import numpy as np
import obspy
import pandas as pd import pandas as pd
import datetime as dt import torch
from pathlib import Path import xarray as xr
import zarr
from obsplus import obspy_to_array
from obspy import UTCDateTime
from obspy.clients.fdsn import Client
from PIL import Image
from torch.utils.data import Dataset
from tqdm import tqdm
from ..convenience import DirectoryStore
from ..convenience import indexers_to_request as i2r
from ..convenience import read_csv_with_store, to_csv_with_store
from ..core.graph import StuettNode, configuration
from ..global_config import get_setting, set_setting, setting_exists
class DataSource(StuettNode): class DataSource(StuettNode):
...@@ -1073,8 +1070,63 @@ class MHDSLRImages(MHDSLRFilenames): ...@@ -1073,8 +1070,63 @@ class MHDSLRImages(MHDSLRFilenames):
class Freezer(StuettNode): class Freezer(StuettNode):
def __init__(self, store): def __init__(self, store, groupname, dim, offset, sort_after_load=False):
self.store = store # synchronizer = zarr.ThreadSynchronizer()
# synchronizer = zarr.ProcessSynchronizer(filename+'.sync')
if dim != 'time':
raise NotImplementedError('Currently Freezer only supports `time` dimension')
try:
meta = read_csv_with_store(store,groupname+'.csv')
except Exception as e:
print(e)
# create meta
# TODO: use zarr store (with xarray dataset) since we need to make use of the synchronizers
meta = pd.DataFrame(columns=[dim])
to_csv_with_store(store,groupname+'.csv',meta,{'index':False})
super().__init__(store=store, groupname=groupname, dim=dim, offset=offset, sort_after_load=sort_after_load)
# Init storage if non-existent
def __call__(self, data=None, request=None, delayed=False):
# DataSource only require a request
# Therefore merge permanent-config and request
config = self.config.copy() # TODO: do we need a deep copy?
if request is not None:
config.update(request)
# TODO: change when rewriting for general indices
if "start_time" in config and config["start_time"] is not None:
config["start_time"] = pd.to_datetime(
config["start_time"], utc=True
).tz_localize(
None
) # TODO: change when xarray #3291 is fixed
if "end_time" in config and config["end_time"] is not None:
config["end_time"] = pd.to_datetime(
config["end_time"], utc=True
).tz_localize(
None
) # TODO: change when xarray #3291 is fixed
if delayed:
return dask.delayed(self.forward)(data, config)
else:
return self.forward(data, config)
def to_chunk_indexers(self,index, offset):
offset = self.config['offset']
# TODO: make this index type dependant
reference_value = pd.to_datetime('2000-01-01')
index = pd.to_datetime(index)
chunk_index = np.floor((index - reference_value)/offset)*offset+reference_value
return chunk_index
def configure(self, requests): def configure(self, requests):
""" """
...@@ -1087,36 +1139,106 @@ class Freezer(StuettNode): ...@@ -1087,36 +1139,106 @@ class Freezer(StuettNode):
""" """
requests = super().configure(requests) requests = super().configure(requests)
# TODO: check if data is available for requested time period dim = self.config['dim']
# TODO: change to indexers
# if dim not in request['indexers']:
# # return ...
# start_index = request['indexers'][dim].start
# end_index = request['indexers'][dim].stop
offset = self.config['offset']
start_chunk = self.to_chunk_indexers(requests['start_time'],offset)
end_chunk = self.to_chunk_indexers(requests['end_time'],offset)
# Note: the chunks used in this freeze module is different from the chunks used to store the data
# One freeze_chunk can include many down to zero data points. Thus the availability of a freeze_chunk
# Does not necessarily mean that there is data available. It means that we have tried to load the data
# from the underlying source once before and stored the result (no matter how much data the source provided)
meta = read_csv_with_store(self.config['store'],self.config['groupname']+'.csv')
if start_chunk > end_chunk:
raise RuntimeError('start_index is greater than end_index. Freezer cannot handle it')
reload = False
current_chunk = start_chunk
while current_chunk <= end_chunk:
if current_chunk not in meta[dim]:
reload = True
current_chunk = current_chunk + offset
if not reload:
# if we return None the previous node will be cut out of the graph
# and this freeze node gets the request to provide the data
return None
# else we will give the previous node the request to load/compute the values for the required chunks
# additionally we will update the request for this node to contain the original indexers
# requests['frozen_indexers'] = requests['indexers'] # TODO: change to indexers
requests[f"{self.config['groupname']}_indexers"] = {'time':slice(requests['start_time'],requests['end_time'])}
requests['start_time'] = start_chunk
requests['end_time'] = end_chunk + offset
requests["requires_request"] = True
# TODO: check how we need to update the boundaries such that we get data that fits and that is available # TODO: check how we need to update the boundaries such that we get data that fits and that is available
# TODO: with only one start/end_time it might be inefficient for the case where [unavailable,available,unavailable] since we need to load everything # TODO: with only one start/end_time it might be inefficient for the case where [unavailable,available,unavailable] since we need to load everything
# one option could be to duplicate the graph by returning multiple requests... # one option could be to duplicate the graph by returning multiple requests...
# TODO: make a distinction between requested start_time and freeze_output_start_time
# TODO: add node specific hash to freeze_output_start_time (there might be multiple in the graph) <- probably not necessary because we receive a copy of the request which is unique to this node # TODO: add node specific hash to freeze_output_start_time (there might be multiple in the graph) <- probably not necessary because we receive a copy of the request which is unique to this node
# TODO: maybe the configuration method must add (and delete) the node name in the request? # TODO: maybe the configuration method must add (and delete) the node name in the request?
# we always require a request to crop out the right time period
requests["requires_request"] = True
return requests return requests
def to_zarr(self, x): def to_zarr(self, data, request):
x = x.to_dataset(name="frozen") x = data.to_dataset(name="frozen")
# x = x.chunk({name: x[name].shape for name in list(x.dims)}) # x = x.chunk({name: x[name].shape for name in list(x.dims)})
# zarr_dataset = zarr.open(self.store, mode='r') # zarr_dataset = zarr.open(self.store, mode='r')
x.to_zarr(self.store, append_dim="time") x.to_zarr(request['store'], append_dim="time")
def open_zarr(self, requests): def open_zarr(self, request):
ds_zarr = xr.open_zarr(self.store) ds_zarr = xr.open_zarr(request['store'])
print("read", ds_zarr) if f"{self.config['groupname']}_indexers" in request:
ds_zarr = ds_zarr.sortby('time')
indexers = request[f"{self.config['groupname']}_indexers"]
ds_zarr = ds_zarr.sel(indexers)
return ds_zarr
def forward(self, data=None, request=None): def forward(self, data=None, request=None):
if request is not None and 'bypass' in request and request['bypass']:
return data
dim = self.config['dim']
if data is not None:
indexers = request[f"{self.config['groupname']}_indexers"]
start_chunk = self.to_chunk_indexers(indexers['time'].start,self.config['offset'])
end_chunk = self.to_chunk_indexers(indexers['time'].stop,self.config['offset'])
meta = read_csv_with_store(self.config['store'],self.config['groupname']+'.csv')
current_chunk = start_chunk
offset = self.config['offset']
meta_list = []
while current_chunk <= end_chunk:
print(current_chunk, end_chunk)
if current_chunk not in meta[dim]:
meta_list.append(current_chunk)
if current_chunk+offset != end_chunk:
# avoid having data points twice
off = offset - pd.to_timedelta('1 ns')
else:
off = offset
current_indexers = {'time':slice(current_chunk,current_chunk+off)}
self.to_zarr(data.sel(current_indexers),request)
current_chunk = current_chunk + offset
meta_update = pd.DataFrame(meta_list,columns=[dim])
meta = pd.concat([meta,meta_update])
to_csv_with_store(self.config['store'],self.config['groupname']+'.csv',meta,{'index':False})
self.to_zarr(data) data = data.sel(indexers)
self.open_zarr(request) else:
data = self.open_zarr(request)
return data return data
# TODO: check request start_time and load the data which is available, store the data which is not available # TODO: check request start_time and load the data which is available, store the data which is not available
...@@ -1324,8 +1446,6 @@ def get_dataset_slices(dims, dataset_slice, stride={}): ...@@ -1324,8 +1446,6 @@ def get_dataset_slices(dims, dataset_slice, stride={}):
return np.array(all_slices) return np.array(all_slices)
from torch.utils.data import Dataset
import torch
# from numba import jit # from numba import jit
......
...@@ -197,6 +197,7 @@ class LTTBDownsampling(StuettNode): ...@@ -197,6 +197,7 @@ class LTTBDownsampling(StuettNode):
array = xr.concat(argmaxes,'time') array = xr.concat(argmaxes,'time')
# print(array) # print(array)
# TODO: integrate nicely
use_pkg = False use_pkg = False
if use_pkg: if use_pkg:
# This is quite hacky and works only if the the selected dimension is a datetime # This is quite hacky and works only if the the selected dimension is a datetime
......
...@@ -123,22 +123,52 @@ def test_freeze(): ...@@ -123,22 +123,52 @@ def test_freeze():
# account_key = stuett.global_config.get_setting('azure')['account_key'] if stuett.global_config.setting_exists('azure') else None # account_key = stuett.global_config.get_setting('azure')['account_key'] if stuett.global_config.setting_exists('azure') else None
# store = zarr.ABSStore(container='hackathon-on-permafrost', prefix='dataset/test.zarr', account_name=account_name, account_key=account_key, blob_service_kwargs={}) # store = zarr.ABSStore(container='hackathon-on-permafrost', prefix='dataset/test.zarr', account_name=account_name, account_key=account_key, blob_service_kwargs={})
freezer = stuett.data.Freezer(store) freezer = stuett.data.Freezer(store,'testgroup','time',pd.to_timedelta('5 hours'))
request = {"start_time": "2017-07-01", "end_time": "2017-08-01"} request = {"start_time": "2017-07-01", "end_time": "2017-07-04"}
x = node(request=request) x = node(delayed=True)
x = freezer(x) x = freezer(x,delayed=True)
x = stuett.core.configuration(x, request)
print('x1',x.compute())
# trying to load the same request but from disk
x = freezer(delayed=True)
x = stuett.core.configuration(x, request)
print("from disk", x.compute())
exit()
# Note there is a gap
request = {"start_time": "2017-09-01", "end_time": "2017-10-01"} request = {"start_time": "2017-09-01", "end_time": "2017-10-01"}
x = freezer(node(request=request)) x = node(delayed=True)
x = freezer(x,delayed=True)
x = stuett.core.configuration(x, request)
print('x2',x.compute())
exit()
# x = freezer() # x = freezer()
print("final", x) # Load everything that was saved (but not the gap)
request = {"start_time": "2017-07-01 16:00:00", "end_time": "2017-10-01"}
x = freezer(request=request)
print("x1 and x2", x)
# Now add somethinge before the time frame and with a gap
request = {"start_time": "2017-05-01", "end_time": "2017-05-31"}
x = node(request=request)
x = freezer(x)
print('before',x)
# Load everything that was saved (but not the gap)
request = {"start_time": "2017-05-01", "end_time": "2017-10-01"}
x = freezer(request=request)
print("x1 and x2", x)
print(x['frozen'].values.shape)
shutil.rmtree(store_name, ignore_errors=True) shutil.rmtree(store_name, ignore_errors=True)
# test_freeze() test_freeze()
def test_image_filenames(): def test_image_filenames():
...@@ -284,4 +314,4 @@ def test_datasets(): ...@@ -284,4 +314,4 @@ def test_datasets():
# x = dataset[0] # x = dataset[0]
test_datasets() # test_datasets()
...@@ -120,6 +120,7 @@ def test_lttbdownsampling(): ...@@ -120,6 +120,7 @@ def test_lttbdownsampling():
# compare channel-wise if values are correct # compare channel-wise if values are correct
for i,c in enumerate(da['channel']): for i,c in enumerate(da['channel']):
continue
# we can only compare values not timestamps # we can only compare values not timestamps
print(x.values[:,i]) print(x.values[:,i])
print(result_list[i][:,1]) print(result_list[i][:,1])
...@@ -129,7 +130,7 @@ def test_lttbdownsampling(): ...@@ -129,7 +130,7 @@ def test_lttbdownsampling():
#TODO: assert if timestamps are correct #TODO: assert if timestamps are correct
# print(x) print(x)
test_lttbdownsampling() test_lttbdownsampling()
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