imap-processing 0.16.0__py3-none-any.whl → 0.16.2__py3-none-any.whl

imap_processing/hi/utils.py

@@ -64,9 +64,10 @@ class HiConstants:
     TOF3_TICK_DUR = 0.5  # 0.5 ns
 
     # These values are stored in the TOF telemetry when the TOF timer
-    # does not have valid data.
-    TOF1_BAD_VALUES = (511, 1023)
-    TOF2_BAD_VALUES = (1023,)
+    # does not have valid data. See IMAP-Hi Algorithm Document Section
+    # 2.2.5 Annotated Direct Events
+    TOF1_BAD_VALUES = (511,)
+    TOF2_BAD_VALUES = (511,)
     TOF3_BAD_VALUES = (1023,)
 
 

imap_processing/hit/l0/constants.py

@@ -100,7 +100,9 @@ COUNTS_DATA_STRUCTURE = {
     "penfgrates": HITPacking(16, 528, (33,)),  # range 4 foreground rates
     "penbgrates": HITPacking(16, 240, (15,)),  # range 4 background rates
     "ialirtrates": HITPacking(16, 320, (20,)),  # ialirt rates
-    "sectorates": HITPacking(16, 1920, (15, 8)),  # sectored rates
+    "sectorates": HITPacking(
+        16, 1920, (8, 15)
+    ),  # sectored rates (8 zenith angles, 15 azimuth angles)
     "l4fgrates": HITPacking(16, 768, (48,)),  # all range foreground rates
     "l4bgrates": HITPacking(16, 384, (24,)),  # all range foreground rates
 }

imap_processing/hit/l0/decom_hit.py

@@ -89,11 +89,14 @@ def parse_count_rates(sci_dataset: xr.Dataset) -> None:
         if all(x not in field for x in ["hdr", "spare", "pha"]):
             parsed_data = np.vectorize(decompress_rates_16_to_32)(parsed_data)
 
-        # Get dims for data variables (yaml file not created yet)
+        # Get dims for data variables
         if len(field_meta.shape) > 1:
             if "sectorates" in field:
-                # Reshape data to 15x8 for azimuth and zenith look directions
+                # Reshape data into (num_frames, 8, 15) for zenith and azimuth
+                # look directions
                 parsed_data = np.array(parsed_data).reshape((-1, *field_meta.shape))
+                # Transpose data to (num_frames, 15, 8) for flipped look directions
+                parsed_data = np.transpose(parsed_data, axes=(0, 2, 1))
                 dims = ["epoch", "azimuth", "zenith"]
                 # Add angle values to coordinates
                 sci_dataset.coords["zenith"] = xr.DataArray(
@@ -202,9 +205,12 @@ def update_ccsds_header_dims(sci_dataset: xr.Dataset) -> xr.Dataset:
     it will be updated later in the process to represent
     time per science frame, so another time dimension is
     needed for the ccsds header fields.This function
-    updates the dimension for these fields to use sc_tick
-    instead of epoch. sc_tick is the time the packet was
-    created.
+    updates the dimension for all data vars to use sc_tick
+    instead of epoch. It also temporarily sets sc_tick as the
+    dimension for the epoch coordinate (to be updated later
+    in the assemble_science_frames function).
+
+    Note: sc_tick is the time the packet was created.
 
     Parameters
     ----------
@@ -294,7 +300,7 @@ def assemble_science_frames(sci_dataset: xr.Dataset) -> xr.Dataset:
     # Extract data per science frame and organize by L1A data products
     count_rates = []
     pha = []
-    epoch_per_science_frame = np.array([])
+    epoch_per_science_frame = []
     for idx in starting_indices:
         # Data from 20 packets in a science frame
         science_data_frame = science_data[idx : idx + FRAME_SIZE]
@@ -302,12 +308,15 @@ def assemble_science_frames(sci_dataset: xr.Dataset) -> xr.Dataset:
         count_rates.append("".join(science_data_frame[:6]))
         # Last 14 packets contain pulse height event data in binary
         pha.append("".join(science_data_frame[6:]))
-        # Get first packet's epoch for the science frame
-        epoch_per_science_frame = np.append(epoch_per_science_frame, epoch_data[idx])
+        # Get the mean epoch in the frame to use as the data collection time
+        epoch_per_science_frame.append(
+            calculate_epoch_mean(epoch_data, idx, FRAME_SIZE)
+        )
 
-    # Add new data variables to the dataset
-    sci_dataset = sci_dataset.drop_vars("epoch")
-    sci_dataset.coords["epoch"] = epoch_per_science_frame
+    # Add new data variables to the dataset and update epoch coordinate
+    sci_dataset.coords["epoch"] = xr.DataArray(
+        np.array(epoch_per_science_frame, dtype=np.int64), dims=["epoch"]
+    )
     sci_dataset["count_rates_raw"] = xr.DataArray(
         count_rates, dims=["epoch"], name="count_rates_raw"
     )
@@ -373,6 +382,31 @@ def decompress_rates_16_to_32(packed: int) -> int:
     return decompressed_int
 
 
+def calculate_epoch_mean(
+    epoch_data: np.ndarray, idx: int, frame_size: int
+) -> np.floating:
+    """
+    Calculate the mean epoch for a science frame.
+
+    This function is used to get the center collection time for science data.
+
+    Parameters
+    ----------
+    epoch_data : np.ndarray
+        Array of epoch values for every science packet.
+    idx : int
+        Starting index of the science frame.
+    frame_size : int
+        Number of packets in the science frame.
+
+    Returns
+    -------
+    float
+        Mean epoch value for the science frame.
+    """
+    return np.mean([epoch_data[idx], epoch_data[idx + frame_size - 1]])
+
+
 def decom_hit(sci_dataset: xr.Dataset) -> xr.Dataset:
     """
     Group and decode HIT science data packets.

imap_processing/hit/l1a/hit_l1a.py

@@ -13,7 +13,11 @@ from imap_processing.hit.hit_utils import (
     get_datasets_by_apid,
     process_housekeeping_data,
 )
-from imap_processing.hit.l0.constants import MOD_10_MAPPING
+from imap_processing.hit.l0.constants import (
+    AZIMUTH_ANGLES,
+    MOD_10_MAPPING,
+    ZENITH_ANGLES,
+)
 from imap_processing.hit.l0.decom_hit import decom_hit
 
 logger = logging.getLogger(__name__)
@@ -104,12 +108,16 @@ def subcom_sectorates(sci_dataset: xr.Dataset) -> xr.Dataset:
     hdr_min_count_mod_10 = updated_dataset.hdr_minute_cnt.values % 10
 
     # Reference mod 10 mapping to initialize data structure for species and
-    # energy ranges and add 15x8 arrays with fill values for each science frame.
+    # energy ranges and add arrays with fill values for each science frame.
     num_frames = len(hdr_min_count_mod_10)
     data_by_species_and_energy_range = {
         key: {
             **value,
-            "counts": np.full((num_frames, 15, 8), fill_value=fillval, dtype=np.int64),
+            "counts": np.full(
+                (num_frames, len(AZIMUTH_ANGLES), len(ZENITH_ANGLES)),
+                fill_value=fillval,
+                dtype=np.int64,
+            ),
         }
         for key, value in MOD_10_MAPPING.items()
     }
@@ -279,39 +287,38 @@ def process_science(
     # Calculate uncertainties for count rates
     count_rates_dataset = calculate_uncertainties(count_rates_dataset)
 
-    # Logical sources for the two products.
-    logical_sources = ["imap_hit_l1a_counts", "imap_hit_l1a_direct-events"]
+    l1a_datasets: dict = {
+        "imap_hit_l1a_counts": count_rates_dataset,
+        "imap_hit_l1a_direct-events": pha_raw_dataset,
+    }
 
-    datasets = []
     # Update attributes and dimensions
-    for ds, logical_source in zip(
-        [count_rates_dataset, pha_raw_dataset], logical_sources
-    ):
+    for logical_source, ds in l1a_datasets.items():
         ds.attrs = attr_mgr.get_global_attributes(logical_source)
 
-        # TODO: Add CDF attributes to yaml once they're defined for L1A science data
         # Assign attributes and dimensions to each data array in the Dataset
         for field in ds.data_vars.keys():
             try:
-                # Create a dict of dimensions using the DEPEND_I keys in the
-                # attributes
-                dims = {
-                    key: value
-                    for key, value in attr_mgr.get_variable_attributes(field).items()
-                    if "DEPEND" in key
-                }
                 ds[field].attrs = attr_mgr.get_variable_attributes(field)
-                ds[field].assign_coords(dims)
             except KeyError:
                 print(f"Field {field} not found in attribute manager.")
                 logger.warning(f"Field {field} not found in attribute manager.")
 
-        # Skip schema check for epoch to prevent attr_mgr from adding the
-        # DEPEND_0 attribute which isn't required for epoch
-        ds.epoch.attrs = attr_mgr.get_variable_attributes("epoch", check_schema=False)
-
-        datasets.append(ds)
+        # check_schema=False to avoid attr_mgr adding stuff dimensions don't need
+        for dim in ds.dims:
+            ds[dim].attrs = attr_mgr.get_variable_attributes(dim, check_schema=False)
+            # TODO: should labels be added as coordinates? Check with SPDF
+            if dim != "epoch":
+                label_array = xr.DataArray(
+                    ds[dim].values.astype(str),
+                    name=f"{dim}_label",
+                    dims=[dim],
+                    attrs=attr_mgr.get_variable_attributes(
+                        f"{dim}_label", check_schema=False
+                    ),
+                )
+                ds.coords[f"{dim}_label"] = label_array
 
         logger.info(f"HIT L1A dataset created for {logical_source}")
 
-    return datasets
+    return list(l1a_datasets.values())

imap_processing/hit/l2/hit_l2.py

@@ -134,18 +134,15 @@ def add_cdf_attributes(
         dataset[dim].attrs = attr_mgr.get_variable_attributes(dim, check_schema=False)
         # TODO: should labels be added as coordinates? Check with SPDF
         if dim != "epoch":
-            dataset = dataset.assign_coords(
-                {
-                    f"{dim}_label": xr.DataArray(
-                        dataset[dim].values.astype(str),
-                        name=f"{dim}_label",
-                        dims=[dim],
-                        attrs=attr_mgr.get_variable_attributes(
-                            f"{dim}_label", check_schema=False
-                        ),
-                    )
-                }
+            label_array = xr.DataArray(
+                dataset[dim].values.astype(str),
+                name=f"{dim}_label",
+                dims=[dim],
+                attrs=attr_mgr.get_variable_attributes(
+                    f"{dim}_label", check_schema=False
+                ),
             )
+            dataset.coords[f"{dim}_label"] = label_array
 
     return dataset
 

imap_processing/ialirt/l0/process_codice.py

@@ -6,10 +6,6 @@ from typing import Any
 
 import xarray as xr
 
-from imap_processing.codice import constants
-from imap_processing.ialirt.utils.time import calculate_time
-from imap_processing.spice.time import met_to_ttj2000ns, met_to_utc
-
 logger = logging.getLogger(__name__)
 
 FILLVAL_FLOAT32 = Decimal(str(-1.0e31))
@@ -28,7 +24,7 @@ def process_codice(
 
     Returns
     -------
-    codice_data : list[dict]
+    codice_data : tuple[list[dict[str, Any]], list[dict[str, Any]]]:
         Dictionary of final data product.
 
     Notes
@@ -58,34 +54,8 @@ def process_codice(
     # Create mock dataset for I-ALiRT SIT
     # TODO: Once I-ALiRT test data is acquired that actually has data in it,
     #       we should be able to properly populate the I-ALiRT data, but for
-    #       now, just create lists of dicts with FILLVALs
-    cod_lo_data = []
-    cod_hi_data = []
-
-    for epoch in range(len(dataset.epoch.data)):
-        sc_sclk_sec = dataset.sc_sclk_sec.data[epoch]
-        sc_sclk_sub_sec = dataset.sc_sclk_sub_sec.data[epoch]
-        met = calculate_time(sc_sclk_sec, sc_sclk_sub_sec, 256)
-        utc = met_to_utc(met).split(".")[0]
-        ttj2000ns = int(met_to_ttj2000ns(met))
-
-        epoch_data = {
-            "apid": int(dataset.pkt_apid[epoch].data),
-            "met": met,
-            "met_to_utc": utc,
-            "ttj2000ns": ttj2000ns,
-        }
-
-        # Add in CoDICE-Lo specific data
-        cod_lo_epoch_data = epoch_data.copy()
-        for field in constants.CODICE_LO_IAL_DATA_FIELDS:
-            cod_lo_epoch_data[f"codicelo_{field}"] = FILLVAL_FLOAT32
-        cod_lo_data.append(cod_lo_epoch_data)
-
-        # Add in CoDICE-Hi specific data
-        cod_hi_epoch_data = epoch_data.copy()
-        for field in constants.CODICE_HI_IAL_DATA_FIELDS:
-            cod_hi_epoch_data[f"codicehi_{field}"] = FILLVAL_FLOAT32
-        cod_hi_data.append(cod_hi_epoch_data)
+    #       now, just create lists of dicts.
+    cod_lo_data: list[dict[str, Any]] = []
+    cod_hi_data: list[dict[str, Any]] = []
 
     return cod_lo_data, cod_hi_data

imap_processing/ialirt/l0/process_swapi.py

@@ -170,7 +170,7 @@ def process_swapi_ialirt(unpacked_data: xr.Dataset) -> list[dict]:
         logger.warning(
             "There was an issue with the SWAPI grouping process, returning empty data."
         )
-        return [{}]
+        return []
 
     for group in np.unique(grouped_dataset["group"]):
         # Sequence values for the group should be 0-11 with no duplicates.
@@ -202,7 +202,7 @@ def process_swapi_ialirt(unpacked_data: xr.Dataset) -> list[dict]:
         swapi_data.append(
             {
                 "apid": 478,
-                "met": met_values[entry],
+                "met": int(met_values[entry]),
                 "met_in_utc": met_to_utc(met_values[entry]).split(".")[0],
                 "ttj2000ns": int(met_to_ttj2000ns(met_values[entry])),
                 "swapi_pseudo_proton_speed": Decimal(solution["pseudo_speed"][entry]),

{imap_processing-0.16.0.dist-info → imap_processing-0.16.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: imap-processing
-Version: 0.16.0
+Version: 0.16.2
 Summary: IMAP Science Operations Center Processing
 License: MIT
 Keywords: IMAP,SDC,SOC,Science Operations

{imap_processing-0.16.0.dist-info → imap_processing-0.16.2.dist-info}/RECORD

@@ -1,5 +1,5 @@
 imap_processing/__init__.py,sha256=b9xHlf8_0OtN_OyhPlrC6ayahYR0QTt_e713NjxZObw,1305
-imap_processing/_version.py,sha256=eLPvHzTLNE19Gzow2bKK6dlgu7T2y85RkAQPjNmibUA,127
+imap_processing/_version.py,sha256=Ni8iNB9b0Tb7TQE3aSvQE4pU0inSecIcucdCW22PAOs,127
 imap_processing/ancillary/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 imap_processing/ancillary/ancillary_dataset_combiner.py,sha256=Pxg1wQLjPKzEkgE3a4Tart5TfeuH9rqyCKTd5GbgiL0,9602
 imap_processing/ccsds/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -22,7 +22,7 @@ imap_processing/cdf/config/imap_glows_l2_variable_attrs.yaml,sha256=eHGzS5_ctJ3g
 imap_processing/cdf/config/imap_hi_global_cdf_attrs.yaml,sha256=28VVPcB_dRsk24Rba-nVsyivixnCOBEEHqL6oUu61Vc,2509
 imap_processing/cdf/config/imap_hi_variable_attrs.yaml,sha256=VsIpaOP7SrwsWqiFo-Dhcz1iBVnZE7PmzzVaGwKZ_YI,14678
 imap_processing/cdf/config/imap_hit_global_cdf_attrs.yaml,sha256=zjHAXLlXrrQPgzKh3aTuoY1qb41J0i8zQ81xLTf7Y7g,3121
-imap_processing/cdf/config/imap_hit_l1a_variable_attrs.yaml,sha256=5X8V6Hzg7UGP6HeqHGKy-ogJP3K-V4sLi5271N8fBNw,11281
+imap_processing/cdf/config/imap_hit_l1a_variable_attrs.yaml,sha256=nVphxZP1hc8EHgR9K0Qh7HZd-G8iM0C0gSXeEyRdx0M,48050
 imap_processing/cdf/config/imap_hit_l1b_variable_attrs.yaml,sha256=gxeC7-SUKkWiy1OE6MgfKxeV-0bdXuauodOIfFtQ3JQ,11287
 imap_processing/cdf/config/imap_hit_l2_variable_attrs.yaml,sha256=f8ZLlF9EIes8BcFrpKTO8Mb_VVnP2d9HoLtQVOgz23Q,61402
 imap_processing/cdf/config/imap_ialirt_global_cdf_attrs.yaml,sha256=AGQ9J0zEdWRZ_AR6_AYYHkRb57mYIe2jVflhYv8SEsQ,961
@@ -102,18 +102,18 @@ imap_processing/hi/hi_l1c.py,sha256=lT_XFSRME1ol7Bo2y38RCHghEEXeW21oQ2Rcj2fmjDo,
 imap_processing/hi/hi_l2.py,sha256=veO2FdinuiRcONQ5JucnRj8lvs6wwLVrA_oveqsFzFE,9360
 imap_processing/hi/packet_definitions/TLM_HI_COMBINED_SCI.xml,sha256=Cwu_sE-b6lpXtuikQKuU5uQ_pMFTG9HoZeH9c-QDQgU,251743
 imap_processing/hi/packet_definitions/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-imap_processing/hi/utils.py,sha256=mZZtOK4S2Mu0uBfPY72x74gtt70anu4sA62PKUjwERk,8097
+imap_processing/hi/utils.py,sha256=5_JowCx2jQsI58M0vCHOgtib_a6Jll9U2vOylpB26A4,8166
 imap_processing/hit/__init__.py,sha256=Ga6Ioj68HnQ4moi7SxJdOyYmGHcRvKOh4uZUEPJZHl4,20
 imap_processing/hit/hit_utils.py,sha256=-O8xt90w6sMPQ2t4CYmqrwkBw3rF1h1dMn58Q3Ioz3g,13371
 imap_processing/hit/l0/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-imap_processing/hit/l0/constants.py,sha256=MlLaYv73tTxVi4MNZL8oP-Ddnj92Xq_f1Ep0Jo2hkHU,5605
-imap_processing/hit/l0/decom_hit.py,sha256=ur0M3AVhuptWRvUVUvugxfAMf6yKI0Xee_7RNqJyF4E,15391
+imap_processing/hit/l0/constants.py,sha256=hJnOMvRVt3gm9mZY8iTVc1mBYq_MNuTz9twkuF4G1F0,5656
+imap_processing/hit/l0/decom_hit.py,sha256=o8rPVfGm67v1M4GUIjtSF7FpaQnYZbVRHJR79olDZOs,16436
 imap_processing/hit/l1a/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-imap_processing/hit/l1a/hit_l1a.py,sha256=BWxm73t6CeNXBt23NArnkXufeRH_OkhVOReLXEpiD3M,11241
+imap_processing/hit/l1a/hit_l1a.py,sha256=gy1wGEJZOxb-sZnlQACv7FVD966fek1EBvE8jzpZdWg,11345
 imap_processing/hit/l1b/constants.py,sha256=ZL5h2GgC5j_s11YgMxtY4EHpmkfo6IXnniCv-iXdG84,9692
 imap_processing/hit/l1b/hit_l1b.py,sha256=nXy8SUXJujFcWOrOBufmdrxq9xzdmB9dyZQOYz3-xiM,18489
 imap_processing/hit/l2/constants.py,sha256=jvs7Uic3Bl1wyRC01s1-F5LAsTzTwi089TpN19fvlFg,18813
-imap_processing/hit/l2/hit_l2.py,sha256=E_3hyn_XzmnUbAFqTSHeM_QQtCYqMnOzLm6Km_crmOk,27102
+imap_processing/hit/l2/hit_l2.py,sha256=qVGTHGO6tXNmz0nqKg3MEEqjlVGHhVsff5uS4jNajsk,26998
 imap_processing/hit/packet_definitions/hit_packet_definitions.xml,sha256=CyYmMnuObmk2y1nlrd7xOZnwZ_qZ3X__AhhKmRyNOvg,136147
 imap_processing/ialirt/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 imap_processing/ialirt/constants.py,sha256=mwVPgSVNuPpTO4zx3LeUW7L5a6aJG2ZrezObPvR9s1c,1241
@@ -121,9 +121,9 @@ imap_processing/ialirt/l0/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJW
 imap_processing/ialirt/l0/ialirt_spice.py,sha256=WNuMlxA5UDGiBd8ap2k_dHxFmi2UCFgnQ4_wEZUhVU0,5649
 imap_processing/ialirt/l0/mag_l0_ialirt_data.py,sha256=vgIerXkk4ZoOxxVaNEgvM1ESWVkGusSZ-3k73-Cl_tI,5276
 imap_processing/ialirt/l0/parse_mag.py,sha256=v5Efczml4s-TFdREhjg3A6PzEFTYAx4dbJyeACmkbPc,12787
-imap_processing/ialirt/l0/process_codice.py,sha256=_LvZJ-dt7Qbw41glYS4BdIJZhhChBIk8DvueyNphW4g,3062
+imap_processing/ialirt/l0/process_codice.py,sha256=-gjxJltAGqqnIflvs5-wrZ2sS-1BjHYk0cMGxxhRdi0,1935
 imap_processing/ialirt/l0/process_hit.py,sha256=HJ_h8nd5Xs0NC-mWNS7Ce3D86H1408lT6ZCdXlNQv48,5408
-imap_processing/ialirt/l0/process_swapi.py,sha256=EBr-wQB4IDrdYON80g8f9neNkUXTAAUMv3wlB1MXfr4,7490
+imap_processing/ialirt/l0/process_swapi.py,sha256=spcxacRDdHBpga1ZoAHN5EMUz-pDHdfazuYOrvzdywE,7493
 imap_processing/ialirt/l0/process_swe.py,sha256=QXp6rmlxw8K5M0bapKwAArCd_99qHFS8sxOnhHLVkhU,17953
 imap_processing/ialirt/packet_definitions/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 imap_processing/ialirt/packet_definitions/ialirt.xml,sha256=-hlT16Mr2Q6uCUfJ3jdpw0mPdeGCcZiWiorbkiEanwA,40784
@@ -258,8 +258,8 @@ imap_processing/ultra/packet_definitions/__init__.py,sha256=47DEQpj8HBSa-_TImW-5
 imap_processing/ultra/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 imap_processing/ultra/utils/ultra_l1_utils.py,sha256=W1wABph96AJVkFNGrmq_0Vf6i__fIFxIVTvjCPbysY0,5321
 imap_processing/utils.py,sha256=zdcBXBQKL2NnElJcEbd-2QPeEDz0H3Yy0hVjRy9xcCE,14062
-imap_processing-0.16.0.dist-info/LICENSE,sha256=F2rxhvc6auEI0Dk9IGjglQSQQk60EvTe8M1dORMZPOg,1098
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