extract Sub-command

Contents

• extract Process Configuration File

• extract Process Configuration File for Resampling

• Dask Cluster Configuration File

• Model Profile Files

extract Process Configuration File

Example:

# Example configuration file for `reshapr extract` sub-command

dataset:
  model profile: SalishSeaCast-201812.yaml
  time base: hour
  variables group: biology

dask cluster: salish_cluster.yaml

start date: 2015-01-01
end date: 2015-01-10

extract variables:
  - diatoms
  - nitrate

# Optional section to specify temporal and spatial selection of a subset of the
# entire variable field
selection:
  # Time interval defaults to 1
  time interval: 3  # multiple of dataset: time base
  depth:
    # depth index min defaults to 0
    depth min: 0
    # depth index max defaults to end of the depth grid
    depth max: 25
    # depth index interval defaults to 1
    depth interval: 1
  grid y:
    # y min defaults to 0
    y min: 600
    # y max defaults to end of the y grid
    y max: 700
    # y interval defaults to 1
    y interval: 10  # multiple of grid y index; e.g. 10 means every 10th grid point
  grid x:
    # x min defaults to 0
    x min: 100
    # x max defaults to the end of the x grid
    x max: 300
    # x interval defaults to 1
    x interval: 5  # multiple of grid x index; e.g. 5 means every 5th grid point

include lons lats: True

extracted dataset:
  name: SalishSeaCast_hour_avg_biology_3h
  description: Hour-averaged diatoms biomass and nitrate every 3rd hour extracted from SalishSeaCast v201812 hindcast
  deflate: True
  format: NETCDF4
  dest dir: /ocean/dlatorne/hour-avg-biology/

Details: Coming soon…

extract Process Configuration File for Resampling

Example:

# Example configuration file for `reshapr extract` sub-command
# to resample day-averaged fields to month-averaged

dataset:
  model profile: SalishSeaCast-201905.yaml
  time base: day
  variables group: biology

dask cluster: salish_cluster.yaml

start date: 2009-02-01
end date: 2009-02-28

extract variables:
  - diatoms
  - nitrate

resample:
  # A pandas time series frequency offset alias with an optional multiplier digit prefix
  # For monthly resampling use MS so that time values are mid-month.
  time interval: 1MS
  # A xarray dataset reduction method to use for aggregation.
  # See the "resampling and grouped operations" subsection in the Time Series Data
  # section of the xarray User Guide.
  # default: mean
  aggregation: mean

extracted dataset:
  name: SalishSeaCast_1m_ptrc_T
  description: Month-averaged diatoms biomass and nitrate extracted from SalishSeaCast v201905 hindcast
  deflate: True
  format: NETCDF4
  dest dir: /ocean/dlatorne/

Details: Coming soon…

Dask Cluster Configuration File

Example:

# Configuration for a dask cluster on salish

name: salish dask cluster
processes: True
number of workers: 4
threads per worker: 4
memory limit: auto

Details: Coming soon…