CLI updates (#341)

* Updating CLI to provide more flexible API for generating files, updating CDF generation to move file name creation into imap-data-access

imap_processing/cdf/global_attrs.py

@@ -204,7 +204,7 @@ class AttrBase:
     scale_type : str, default="linear"
         The scale of the axis, "SCALETYP" attribute
     label_axis : str, default=None
-        Axis label, "LABLAXIS" attribute
+        Axis label, "LABLAXIS" attribute. Required. Should be close to 6 letters.
     format : str, default=None
         The format of the data, in Fortran format
     units : str, default=None
@@ -259,6 +259,7 @@ class ScienceAttrs(AttrBase):
     depend_0 : str = None
         The first degree of dependent coordinate variables.
         Although this is an optional keyword, it is required for every instance.
+        This should be the "Epoch" dimension, and should be type datetime64.
     depend_1 : str = None, optional
         The second degree of dependent coordinate variables. This is used for 2d data.
     depend_2 : str = None, optional

imap_processing/cdf/utils.py

@@ -2,9 +2,7 @@
 
 import logging
 from pathlib import Path
-from typing import Optional
 
-import imap_data_access
 import numpy as np
 import xarray as xr
 from cdflib.xarray import xarray_to_cdf
@@ -26,7 +24,7 @@ def calc_start_time(shcoarse_time: int):
     np.datetime64
         The time of the event
 
-    TODO
+    TODO - move this into imap-data-access? How should it be used?
     -----
     This conversion is temporary for now, and will need SPICE in the future.
     Nick Dutton mentioned that s/c clock start epoch is
@@ -38,15 +36,11 @@ def calc_start_time(shcoarse_time: int):
     return launch_time + np.timedelta64(shcoarse_time, "s")
 
 
-def write_cdf(
-    data: xr.Dataset,
-    descriptor: str,
-    directory: Optional[Path] = None,
-):
+def write_cdf(data: xr.Dataset, filepath: Path):
     """Write the contents of "data" to a CDF file using cdflib.xarray_to_cdf.
 
     This function determines the file name to use from the global attributes,
-    fills in the the final attributes, and converts the whole dataset to a CDF.
+    fills in the final attributes, and converts the whole dataset to a CDF.
     The date in the file name is determined by the time of the first Epoch in the
     xarray Dataset.  The first 3 file name fields (mission, instrument, level) are
     determined by the "Logical_source" attribute.  The version is determiend from
@@ -56,74 +50,28 @@ def write_cdf(
     ----------
         data : xarray.Dataset
             The dataset object to convert to a CDF
-        descriptor : str
-            The descriptor to insert into the file name after the
-            orbit, before the SPICE field.  No underscores allowed.
-        directory : pathlib.Path, optional
-            The directory to write the file to. The default is obtained
-            from the global imap_data_access.config["DATA_DIR"].
+        filepath: Path
+            The output path, including filename, to write the CDF to.
 
     Returns
     -------
         pathlib.Path
             Path to the file created
     """
-    # Determine the start date of the data in the file,
-    # based on the time of the first dust impact
-    file_start_date = None
-    if "idex" in data.attrs["Logical_source"]:
-        file_start_date = data["Epoch"][0].data
-    else:
-        start_time = data["Epoch"].data[0]
-        file_start_date = calc_start_time(start_time)
-    if file_start_date is None:
-        raise ValueError(
-            "Unable to determine file start date. Check Logical_source value"
-        )
-
-    date_string = np.datetime_as_string(file_start_date, unit="D").replace("-", "")
-
-    # Determine the file name based on the attributes in the xarray
-    # Set file name based on this convention:
-    # imap_<instrument>_<datalevel>_<descriptor>_<startdate>_<enddate>_<version>.cdf
-    # data.attrs["Logical_source"] has the mission, instrument, and level
-    # like this:
-    #   imap_idex_l1
-    # TODO: add logics for adding endate
-    filename = (
-        f"{data.attrs['Logical_source']}"
-        f"_{descriptor}"
-        f"_{date_string}"
-        f"_{date_string}"
-        f"_v{data.attrs['Data_version']}.cdf"
-    )
-
-    if directory is None:
-        # Storage directory
-        # mission/instrument/data_level/year/month/filename
-        # /<directory | DATA_DIR>/<instrument>/<data_level>/<year>/<month>
-        _, instrument, data_level = data.attrs["Logical_source"].split("_")
-        directory = imap_data_access.config["DATA_DIR"] / instrument / data_level
-        directory /= date_string[:4]
-        directory /= date_string[4:6]
-    filename_and_path = Path(directory)
-    if not filename_and_path.exists():
-        logging.info(
-            "The directory does not exist, creating directory %s", filename_and_path
-        )
-        filename_and_path.mkdir(parents=True)
-    filename_and_path /= filename
+    if not filepath.parent.exists():
+        logging.info("The directory does not exist, creating directory %s", filepath)
+        filepath.parent.mkdir(parents=True)
 
     # Insert the final attribute:
     # The Logical_file_id is always the name of the file without the extension
-    data.attrs["Logical_file_id"] = filename.split(".")[0]
+    data.attrs["Logical_file_id"] = filepath.stem
 
     # Convert the xarray object to a CDF
     xarray_to_cdf(
         data,
-        filename_and_path,
+        str(filepath),
         datetime64_to_cdftt2000=True,
         terminate_on_warning=True,
     )  # Terminate if not ISTP compliant
 
-    return filename_and_path
+    return filepath