xradio 0.0.42__tar.gz → 0.0.43__tar.gz

{xradio-0.0.42/src/xradio.egg-info → xradio-0.0.43}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: xradio
-Version: 0.0.42
+Version: 0.0.43
 Summary:  Xarray Radio Astronomy Data IO
 Author-email: Jan-Willem Steeb <jsteeb@nrao.edu>
 License: BSD 3-Clause License

{xradio-0.0.42 → xradio-0.0.43}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "xradio"
-version = "0.0.42"
+version = "0.0.43"
 description = " Xarray Radio Astronomy Data IO"
 authors = [
     {name = "Jan-Willem Steeb", email="jsteeb@nrao.edu"},

{xradio-0.0.42 → xradio-0.0.43}/src/xradio/measurement_set/_utils/_msv2/conversion.py

@@ -687,6 +687,7 @@ def create_taql_query(partition_info):
         "FIELD_ID",
         "SCAN_NUMBER",
         "STATE_ID",
+        "ANTENNA1",
     ]
 
     taql_where = "WHERE "
@@ -696,6 +697,11 @@ def create_taql_query(partition_info):
                 taql_where
                 + f"({col_name} IN [{','.join(map(str, partition_info[col_name]))}]) AND"
             )
+            if col_name == "ANTENNA1":
+                taql_where = (
+                    taql_where
+                    + f"(ANTENNA2 IN [{','.join(map(str, partition_info[col_name]))}]) AND"
+                )
     taql_where = taql_where[:-3]
 
     return taql_where
@@ -950,7 +956,10 @@ def convert_and_write_partition(
             logger.debug("Time phase_calibration xds  " + str(time.time() - start))
 
             # Change antenna_ids to antenna_names
-            xds = antenna_ids_to_names(xds, ant_xds, is_single_dish)
+            with_antenna_partitioning = "ANTENNA1" in partition_info
+            xds = antenna_ids_to_names(
+                xds, ant_xds, is_single_dish, with_antenna_partitioning
+            )
             # but before, keep the name-id arrays, we need them for the pointing and weather xds
             ant_xds_name_ids = ant_xds["antenna_name"].set_xindex("antenna_id")
             ant_xds_station_name_ids = ant_xds["station"].set_xindex("antenna_id")
@@ -978,7 +987,6 @@ def convert_and_write_partition(
 
             # Create pointing_xds
             pointing_xds = xr.Dataset()
-            print("with_pointing", with_pointing)
             if with_pointing:
                 start = time.time()
                 if pointing_interpolate:
@@ -1125,8 +1133,31 @@ def convert_and_write_partition(
 
 
 def antenna_ids_to_names(
-    xds: xr.Dataset, ant_xds: xr.Dataset, is_single_dish: bool
+    xds: xr.Dataset,
+    ant_xds: xr.Dataset,
+    is_single_dish: bool,
+    with_antenna_partitioning,
 ) -> xr.Dataset:
+    """
+    Turns the antenna_ids that we get from MSv2 into MSv4 antenna_name
+
+    Parameters
+    ----------
+    xds: xr.Dataset
+        A main xds (MSv4)
+    ant_xds: xr.Dataset
+        The antenna_xds for this MSv4
+    is_single_dish: bool
+        Whether a single-dish ("spectrum" data) dataset
+    with_antenna_partitioning: bool
+        Whether the MSv4 partitions include the antenna axis => only
+        one antenna (and implicitly one 'baseline' - auto-correlation)
+
+    Returns
+    ----------
+    xr.Dataset
+        The main xds with antenna_id replaced with antenna_name
+    """
     ant_xds = ant_xds.set_xindex(
         "antenna_id"
     )  # Allows for non-dimension coordinate selection.
@@ -1145,11 +1176,15 @@ def antenna_ids_to_names(
             }
         )
     else:
-        # baseline_antenna1_id will be removed soon below, but it is useful here to know the actual antenna_ids,
-        # as opposed to the baseline_ids which can mismatch when data is missing for some antennas
-        xds["baseline_id"] = ant_xds["antenna_name"].sel(
-            antenna_id=xds["baseline_antenna1_id"]
-        )
+        if not with_antenna_partitioning:
+            # baseline_antenna1_id will be removed soon below, but it is useful here to know the actual antenna_ids,
+            # as opposed to the baseline_ids which can mismatch when data is missing for some antennas
+            xds["baseline_id"] = ant_xds["antenna_name"].sel(
+                antenna_id=xds["baseline_antenna1_id"]
+            )
+        else:
+            xds["baseline_id"] = ant_xds["antenna_name"]
+
         unwanted_coords_from_ant_xds = [
             "antenna_id",
             "antenna_name",

{xradio-0.0.42 → xradio-0.0.43}/src/xradio/measurement_set/_utils/_msv2/create_field_and_source_xds.py

@@ -618,9 +618,14 @@ def extract_source_info(
 
     # This source table time is not the same as the time in the field_and_source_xds that is derived from the main MSv4 time axis.
     # The source_id maps to the time axis in the field_and_source_xds. That is why "if len(source_id) == 1" is used to check if there should be a time axis.
-    assert len(source_xds.TIME) <= len(
-        unique_source_id
-    ), "Can only process source table with a single time entry for a source_id and spectral_window_id."
+    # assert len(source_xds.TIME) <= len(
+    #     unique_source_id
+    # ), "Can only process source table with a single time entry for a source_id and spectral_window_id."
+    if len(source_xds.TIME) > len(unique_source_id):
+        logger.warning(
+            f"Source table has more than one time entry for a source_id and spectral_window_id. This is not currently supported. Only the first time entry will be used."
+        )
+        source_xds = source_xds.drop_duplicates("SOURCE_ID", keep="first")
 
     source_xds = source_xds.isel(TIME=0, SPECTRAL_WINDOW_ID=0, drop=True)
     source_column_description = source_xds.attrs["other"]["msv2"]["ctds_attrs"][

{xradio-0.0.42 → xradio-0.0.43}/src/xradio/measurement_set/_utils/_msv2/partition_queries.py

@@ -54,6 +54,7 @@ def create_partitions(in_file: str, partition_scheme: list):
     par_df["SCAN_NUMBER"] = main_tb.getcol("SCAN_NUMBER")
     par_df["STATE_ID"] = main_tb.getcol("STATE_ID")
     par_df["OBSERVATION_ID"] = main_tb.getcol("OBSERVATION_ID")
+    par_df["ANTENNA1"] = main_tb.getcol("ANTENNA1")
     par_df = par_df.drop_duplicates()
 
     field_tb = tables.table(
@@ -123,6 +124,9 @@ def create_partitions(in_file: str, partition_scheme: list):
         "OBS_MODE",
         "SUB_SCAN_NUMBER",
     ]
+    if "ANTENNA1" in partition_scheme:
+        partition_axis_names.append("ANTENNA1")
+
     for idx, pair in enumerated_partitions:
         query = ""
         for i, par in enumerate(partition_scheme_updated):

{xradio-0.0.42 → xradio-0.0.43}/src/xradio/measurement_set/convert_msv2_to_processing_set.py

@@ -82,6 +82,11 @@ def convert_msv2_to_processing_set(
             + str(partition_info["FIELD_ID"])
             + ", SCAN "
             + str(partition_info["SCAN_NUMBER"])
+            + (
+                ", ANTENNA " + str(partition_info["ANTENNA1"])
+                if "ANTENNA1" in partition_info
+                else ""
+            )
         )
 
         # prepend '0' to ms_v4_id as needed

{xradio-0.0.42 → xradio-0.0.43}/src/xradio/measurement_set/measurement_set_xds.py

@@ -3,6 +3,8 @@ from xradio._utils.list_and_array import to_list
 import xarray as xr
 import numbers
 import os
+from collections.abc import Mapping, Iterable
+from typing import Any, Union
 
 
 class MeasurementSetXds(xr.Dataset):
@@ -53,16 +55,37 @@ class MeasurementSetXds(xr.Dataset):
             copy_cor_xds, os.path.join(store, "correlated_xds"), **kwargs
         )
 
-    def sel(self, data_group_name=None, **kwargs):
+    def sel(
+        self,
+        indexers: Union[Mapping[Any, Any], None] = None,
+        method: Union[str, None] = None,
+        tolerance: Union[int, float, Iterable[Union[int, float]], None] = None,
+        drop: bool = False,
+        **indexers_kwargs: Any,
+    ):
         """
-        Select data along dimension(s) by label.
-
-        Args:
-            **kwargs: Keyword arguments to be passed to `xarray.Dataset.sel`. See https://xarray.pydata.org/en/stable/generated/xarray.Dataset.sel.html for more information.
+        Select data along dimension(s) by label. Overrides `xarray.Dataset.sel <https://xarray.pydata.org/en/stable/generated/xarray.Dataset.sel.html>`__ so that a data group can be selected by name by using the `data_group_name` parameter.
+        For more information on data groups see `Data Groups <https://xradio.readthedocs.io/en/latest/measurement_set_overview.html#Data-Groups>`__ section. See `xarray.Dataset.sel <https://xarray.pydata.org/en/stable/generated/xarray.Dataset.sel.html>`__ for parameter descriptions.
 
         Returns:
             MeasurementSetXds
+
+        Examples
+        --------
+        >>> # Select data group 'corrected' and polarization 'XX'.
+        >>> selected_ms_xds = ms_xds.sel(data_group_name='corrected', polarization='XX')
+
+        >>> # Select data group 'corrected' and polarization 'XX' using a dict.
+        >>> selected_ms_xds = ms_xds.sel({'data_group_name':'corrected', 'polarization':'XX')
         """
+        if "data_group_name" in indexers_kwargs:
+            data_group_name = indexers_kwargs["data_group_name"]
+            del indexers_kwargs["data_group_name"]
+        if (indexers is not None) and ("data_group_name" in indexers):
+            data_group_name = indexers["data_group_name"]
+            del indexers["data_group_name"]
+        else:
+            data_group_name = None
 
         if data_group_name is not None:
             sel_data_group_set = set(
@@ -77,7 +100,11 @@ class MeasurementSetXds(xr.Dataset):
             data_variables_to_drop = list(set(data_variables_to_drop))
 
             return MeasurementSetXds(
-                super().sel(**kwargs).drop_vars(data_variables_to_drop)
+                super()
+                .sel(indexers, method, tolerance, drop, **indexers_kwargs)
+                .drop_vars(data_variables_to_drop)
             )
         else:
-            return MeasurementSetXds(super().sel(**kwargs))
+            return MeasurementSetXds(
+                super().sel(indexers, method, tolerance, drop, **indexers_kwargs)
+            )

{xradio-0.0.42 → xradio-0.0.43}/src/xradio/measurement_set/processing_set.py

@@ -312,7 +312,7 @@ class ProcessingSet(dict):
         ----------
         **kwargs : dict
             Keyword arguments representing dimension names and the labels to select along those dimensions.
-            These are passed directly to the `xarray.Dataset.sel` method.
+            These are passed directly to the `xarray.Dataset.sel <https://docs.xarray.dev/en/latest/generated/xarray.Dataset.sel.html>`__ method.
 
         Returns
         -------
@@ -334,7 +334,7 @@ class ProcessingSet(dict):
         ----------
         **kwargs : dict
             Keyword arguments representing dimension names and the integer indices to select along those dimensions.
-            These are passed directly to the `isel` method.
+            These are passed directly to the `xarray.Dataset.isel <https://docs.xarray.dev/en/latest/generated/xarray.Dataset.isel.html>`__ method.
 
         Returns
         -------
@@ -359,7 +359,7 @@ class ProcessingSet(dict):
             The filesystem path to the Zarr store directory where the data will be saved.
         **kwargs : dict, optional
             Additional keyword arguments to be passed to the `xarray.Dataset.to_zarr` method.
-            Refer to the [xarray documentation](https://docs.xarray.dev/en/latest/generated/xarray.Dataset.to_zarr.html)
+            Refer to the `xarray.Dataset.to_zarr <https://docs.xarray.dev/en/latest/generated/xarray.Dataset.to_zarr.html>`__
             for available options.
 
         Returns

{xradio-0.0.42 → xradio-0.0.43}/src/xradio/measurement_set/schema.py

@@ -1573,6 +1573,36 @@ class WeatherXds:
 class PointingXds:
     """
     Pointing dataset: antenna pointing information.
+
+    In the past the relationship and definition of the pointing infromation has not been clear. Here we attempt to clarify it by explaining the relationship between the ASDM, MSv2 and MSv4 pointing information.
+
+    The following abreviations are used:
+
+    - M2: Measurement Set version 2
+    - M4: Measurement Set version 4
+    - A : ASDM
+
+    The following definitions come from the ASDM's `SDM Tables Short Description <https://drive.google.com/file/d/16a3g0GQxgcO7N_ZabfdtexQ8r2jRbYIS/view>`_ page 97-99:
+
+    - A_encoder: The values measured from the antenna. They may be however affected by metrology, if applied. Note that for ALMA this column will contain positions obtained using the AZ POSN RSP and EL POSN RSP monitor points of the ACU and not the GET AZ ENC and GET EL ENC monitor points (as these do not include the metrology corrections). It is agreed that the the vendor pointing model will never be applied. AZELNOWAntenna.position
+    - A_pointingDirection: This is the commanded direction of the antenna. It is obtained by adding the target and offset columns, and then applying the pointing model referenced by PointingModelId. The pointing model can be the composition of the absolute pointing model and of a local pointing model. In that case their coefficients will both be in the PointingModel table.
+    - A_target: This is the field center direction (as given in the Field Table), possibly affected by the optional antenna-based sourceOffset. This column is in horizontal coordinates. AZELNOWAntenna.position
+    - A_offset: Additional offsets in horizontal coordinates (usually meant for measuring the pointing corrections, mapping the antenna beam, ...). AZELNOWAntenna.positiontarget
+    - A_sourceOffset : Optionally, the antenna-based mapping offsets in the field. These are in the equatorial system, and used, for instance, in on-the-fly mapping when the antennas are driven independently across the field.
+
+    M2_DIRECTION = rotate(A_target,A_offset)   #A_target is rotated to by A_offset
+
+    if withPointingCorrection : M2_DIRECTION = rotate(A_target,A_offset) + (A_encoder - A_pointingDirection)
+
+    M2_TARGET = A_target
+    M2_POINTING_OFFSET = A_offset
+    M2_ENCODER = A_encoder
+
+    It should be noted that definition of M2_direction is not consistent, it depends if withPointingCorrection is set to True or False (see the `importasdm documenation <https://casadocs.readthedocs.io/en/v6.2.0/api/tt/casatasks.data.importasdm.html#with-pointing-correction>`_  and `code <https://open-bitbucket.nrao.edu/projects/CASA/repos/casa6/browse/casatools/src/tools/sdm/sdm_cmpt.cc#2257>`_ for details).
+
+    M4_DIRECTION = M2_DIRECTION (withPointingCorrection=True)
+    M4_ENCODER = M2_ENCODER
+
     """
 
     antenna_name: Coordof[AntennaNameArray]
@@ -1595,7 +1625,7 @@ class PointingXds:
         LocalSkyCoordArray,
     ]
     """
-    Antenna pointing direction, optionally expressed as polynomial coefficients. DIRECTION in MSv3.
+    The direction of the peak response of the beam and is equavalent to the MSv2 DIRECTION (M2_direction) with_pointing_correction=True, optionally expressed as polynomial coefficients.
     """
 
     time: Optional[Coordof[TimeInterpolatedCoordArray]] = None
@@ -1619,11 +1649,14 @@ class PointingXds:
     ] = None
     """
     The current encoder values on the primary axes of the mount type for
-    the antenna. ENCODER in MSv3.
+    the antenna. ENCODER in MSv2 (M2_encoder).
     """
     POINTING_OVER_THE_TOP: Optional[
         Data[Union[tuple[Time, AntennaName], tuple[TimePointing, AntennaName]], bool]
     ] = None
+    """
+    True if the antenna was driven to this position ”over the top” (az-el mount).
+    """
 
     # Attributes
     type: Attr[Literal["pointing"]] = "pointing"

{xradio-0.0.42 → xradio-0.0.43/src/xradio.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: xradio
-Version: 0.0.42
+Version: 0.0.43
 Summary:  Xarray Radio Astronomy Data IO
 Author-email: Jan-Willem Steeb <jsteeb@nrao.edu>
 License: BSD 3-Clause License