Glows L2 initial setup (#1156)

* Setting up

* first pass at making histl2 dataclass

* L2 processing updates

* Renaming variance variables to std_dev

* fixing flag dimensions

* WIP L2

* Removing unneeded files

* Updating docs

* Updating docs

* mypy ignore

* Fixing docs

imap_processing/cdf/config/imap_glows_l1b_variable_attrs.yaml

@@ -251,13 +251,13 @@ filter_temperature_average:
   LABLAXIS: Avgd Temperature
   VALIDMAX: 255
 
-filter_temperature_variance:
+filter_temperature_std_dev:
   <<: *support_data_defaults
-  CATDESC: spin-block-averaged variance of filter temperature
-  FIELDNAM: Variance of filter temperature
+  CATDESC: spin-block-averaged std_dev of filter temperature
+  FIELDNAM: std_dev of filter temperature
   FILLVAL: *max_uint32
   FORMAT: I6
-  LABLAXIS: Variance
+  LABLAXIS: std_dev
   VALIDMAX: *max_uint16
 
 hv_voltage_average:
@@ -269,12 +269,12 @@ hv_voltage_average:
   LABLAXIS: Avg voltage
   VALIDMAX: *max_uint16
 
-hv_voltage_variance:
+hv_voltage_std_dev:
   <<: *support_data_defaults
-  CATDESC: variance of  HV voltage on the CEM, uint encoded
-  FIELDNAM: HV voltage variance
+  CATDESC: std_dev of  HV voltage on the CEM, uint encoded
+  FIELDNAM: HV voltage std_dev
   FILLVAL: *int_fillval
-  LABLAXIS: Variance
+  LABLAXIS: std_dev
   VALIDMAX: *max_uint32
 
 spin_period_average:
@@ -291,13 +291,13 @@ spin_period_average:
   VALIDMIN: 45000 # TBC 14.63 s where 20.9712 s = 65535, rounded down
   VAR_TYPE: support_data
 
-spin_period_variance:
+spin_period_std_dev:
   <<: *support_data_defaults
-  CATDESC: spin-block-averaged variance of spin period
-  FIELDNAM: variance of spin period
+  CATDESC: spin-block-averaged std_dev of spin period
+  FIELDNAM: std_dev of spin period
   FILLVAL: *int_fillval
   FORMAT: I10
-  LABLAXIS: Variance
+  LABLAXIS: std_dev
   VALIDMAX: *max_uint32
 
 # TODO review these
@@ -315,13 +315,13 @@ spin_period_ground_average:
   VALIDMIN: 45000 # TBC 14.63 s where 20.9712 s = 65535, rounded down
   VAR_TYPE: support_data
 
-spin_period_ground_variance:
+spin_period_ground_std_dev:
   <<: *support_data_defaults
-  CATDESC: spin-block-averaged variance of spin period on ground
-  FIELDNAM: ground variance of spin period
+  CATDESC: spin-block-averaged std_dev of spin period on ground
+  FIELDNAM: ground std_dev of spin period
   FILLVAL: *int_fillval
   FORMAT: I10
-  LABLAXIS: Variance
+  LABLAXIS: std_dev
   VALIDMAX: *max_uint32
 
 pulse_length_average:
@@ -333,13 +333,13 @@ pulse_length_average:
   LABLAXIS: Avg pulse len
   VALIDMAX: 255
 
-pulse_length_variance:
+pulse_length_std_dev:
   <<: *support_data_defaults
-  CATDESC: spin-block-averaged variance of pulse length
-  FIELDNAM: Variance of pulse length
+  CATDESC: spin-block-averaged std_dev of pulse length
+  FIELDNAM: std_dev of pulse length
   FILLVAL: *max_uint32
   FORMAT: I10
-  LABLAXIS: Variance
+  LABLAXIS: std_dev
   VALIDMAX: *max_uint16
 
 position_angle_offset_average:
@@ -350,21 +350,21 @@ position_angle_offset_average:
   FORMAT: I4
   LABLAXIS: Avg pos angle
 
-position_angle_offset_variance:
+position_angle_offset_std_dev:
   <<: *support_data_defaults
-  CATDESC: spin-block averaged variance of position angle offset
-  FIELDNAM: Variance of position angle offset
+  CATDESC: spin-block averaged std_dev of position angle offset
+  FIELDNAM: std_dev of position angle offset
   FILLVAL: *max_uint16
   FORMAT: I4
-  LABLAXIS: Variance
+  LABLAXIS: std_dev
 
-spin_axis_orientation_variance:
+spin_axis_orientation_std_dev:
   <<: *support_data_defaults
-  CATDESC: spin-block averaged variance of spin axis orientation
-  FIELDNAM: Variance of spin axis orientation
+  CATDESC: spin-block averaged std_dev of spin axis orientation
+  FIELDNAM: std_dev of spin axis orientation
   FILLVAL: *max_uint16
   FORMAT: I4
-  LABLAXIS: Variance
+  LABLAXIS: std_dev
 
 spin_axis_orientation_average:
   <<: *support_data_defaults
@@ -383,14 +383,14 @@ spacecraft_location_average:
   FORMAT: I4
   LABLAXIS: Avg spacecraft location
 
-spacecraft_location_variance:
+spacecraft_location_std_dev:
   <<: *support_data_defaults
   DEPEND_1: ecliptic
-  CATDESC: spin-block averaged variance of spacecraft location
-  FIELDNAM: Variance of spacecraft location
+  CATDESC: spin-block averaged std_dev of spacecraft location
+  FIELDNAM: std_dev of spacecraft location
   FILLVAL: *max_uint16
   FORMAT: I4
-  LABLAXIS: Variance
+  LABLAXIS: std_dev
 
 spacecraft_velocity_average:
   <<: *support_data_defaults
@@ -401,14 +401,14 @@ spacecraft_velocity_average:
   FORMAT: I4
   LABLAXIS: Avg spacecraft velocity
 
-spacecraft_velocity_variance:
+spacecraft_velocity_std_dev:
   <<: *support_data_defaults
   DEPEND_1: ecliptic
-  CATDESC: spin-block averaged variance of spacecraft velocity
-  FIELDNAM: Variance of spacecraft velocity
+  CATDESC: spin-block averaged std_dev of spacecraft velocity
+  FIELDNAM: std_dev of spacecraft velocity
   FILLVAL: *max_uint16
   FORMAT: I4
-  LABLAXIS: Variance
+  LABLAXIS: std_dev
 
 # End of not-in--dicts in generate_de_dataset
 

imap_processing/glows/l1b/glows_l1b.py

@@ -255,10 +255,10 @@ def process_histogram(l1a: xr.Dataset) -> xr.Dataset:
         "imap_spin_angle_bin_cntr": ["bins"],
         "histogram_flag_array": ["bad_angle_flags", "bins"],
         "spacecraft_location_average": ["ecliptic"],
-        "spacecraft_location_variance": ["ecliptic"],
+        "spacecraft_location_std_dev": ["ecliptic"],
         "spacecraft_velocity_average": ["ecliptic"],
-        "spacecraft_velocity_variance": ["ecliptic"],
-        "flags": ["flag_dim", "bins"],
+        "spacecraft_velocity_std_dev": ["ecliptic"],
+        "flags": ["flag_dim"],
     }
 
     # For each attribute, retrieve the dims from output_dimension_mapping or use an

imap_processing/glows/l1b/glows_l1b_data.py

@@ -417,19 +417,19 @@ class HistogramL1B:
         IMAP spin angle ψ for bin centers
     filter_temperature_average
         block-averaged value, decoded to Celsius degrees using Eq. (47)
-    filter_temperature_variance
+    filter_temperature_std_dev
         standard deviation (1 sigma), decoded to Celsius degrees using Eq. (51)
     hv_voltage_average
         block-averaged value, decoded to volts using Eq. (47)
-    hv_voltage_variance
+    hv_voltage_std_dev
         standard deviation (1 sigma), decoded to volts using Eq. (51)
     spin_period_average
         block-averaged onboard value, decoded to seconds using Eq. (47)
-    spin_period_variance
+    spin_period_std_dev
         standard deviation (1 sigma), decoded to seconds using Eq. (51)
     pulse_length_average
         block-averaged value, decoded to μs using Eq. (47)
-    pulse_length_variance
+    pulse_length_std_dev
     standard deviation (1 sigma), decoded to μs using Eq. (51)
     glows_start_time
         GLOWS clock, subseconds as decimal part of float
@@ -444,24 +444,24 @@ class HistogramL1B:
         is_inside_excluded_region, is_excluded_by_instr_team, is_suspected_transient]
     spin_period_ground_average
         block-averaged value computed on ground
-    spin_period_ground_variance
+    spin_period_ground_std_dev
         standard deviation (1 sigma)
     position_angle_offset_average
         block-averaged value in degrees
-    position_angle_offset_variance
+    position_angle_offset_std_dev
         standard deviation (1 sigma)
-    spin_axis_orientation_variance
+    spin_axis_orientation_std_dev
         standard deviation( 1 sigma): ∆λ, ∆φ for ⟨λ⟩, ⟨φ⟩
     spin_axis_orientation_average
         block-averaged spin-axis ecliptic longitude ⟨λ⟩ and latitude ⟨φ⟩ in degrees
     spacecraft_location_average
         block-averaged Cartesian ecliptic coordinates ⟨X⟩, ⟨Y ⟩, ⟨Z⟩ [km] of IMAP
-    spacecraft_location_variance
+    spacecraft_location_std_dev
         standard deviations (1 sigma) ∆X, ∆Y , ∆Z for ⟨X⟩, ⟨Y ⟩, ⟨Z⟩
     spacecraft_velocity_average
         block-averaged values ⟨VX⟩, ⟨VY⟩, ⟨VZ⟩ [km/s] of IMAP velocity components
         (Cartesian ecliptic frame)
-    spacecraft_velocity_variance
+    spacecraft_velocity_std_dev
         standard deviations (1 sigma) ∆VX , ∆VY , ∆VZ for ⟨VX ⟩, ⟨VY ⟩, ⟨VZ ⟩
     flags
         flags for extra information, per histogram. This should be a human-readable
@@ -470,9 +470,7 @@ class HistogramL1B:
 
     histogram: np.ndarray
     flight_software_version: str
-    # pkts_file_name: str TODO: add this in L0
     seq_count_in_pkts_file: int
-    # l1a_file_name: str TODO: add this
     # ancillary_data_files: np.ndarray TODO Add this
     first_spin_id: int
     last_spin_id: int
@@ -482,13 +480,17 @@ class HistogramL1B:
     number_of_bins_per_histogram: int
     number_of_events: int
     filter_temperature_average: np.double
-    filter_temperature_variance: np.double
+    filter_temperature_variance: InitVar[np.double]
+    filter_temperature_std_dev: np.double = field(init=False)
     hv_voltage_average: np.double
-    hv_voltage_variance: np.double
+    hv_voltage_variance: InitVar[np.double]
+    hv_voltage_std_dev: np.double = field(init=False)
     spin_period_average: np.double
-    spin_period_variance: np.double
+    spin_period_variance: InitVar[np.double]
+    spin_period_std_dev: np.double = field(init=False)
     pulse_length_average: np.double
-    pulse_length_variance: np.double
+    pulse_length_variance: InitVar[np.double]
+    pulse_length_std_dev: np.double = field(init=False)
     imap_start_time: np.double  # No conversion needed from l1a->l1b
     imap_time_offset: np.double  # No conversion needed from l1a->l1b
     glows_start_time: np.double  # No conversion needed from l1a->l1b
@@ -499,40 +501,60 @@ class HistogramL1B:
     imap_spin_angle_bin_cntr: np.ndarray = field(init=False)  # Same size as bins
     histogram_flag_array: np.ndarray = field(init=False)
     spin_period_ground_average: np.double = field(init=False)  # retrieved from SPICE?
-    spin_period_ground_variance: np.double = field(init=False)  # retrieved from SPICE?
+    spin_period_ground_std_dev: np.double = field(init=False)  # retrieved from SPICE?
     position_angle_offset_average: np.double = field(init=False)  # retrieved from SPICE
-    position_angle_offset_variance: np.double = field(init=False)  # from SPICE
-    spin_axis_orientation_variance: np.double = field(init=False)  # from SPICE
+    position_angle_offset_std_dev: np.double = field(init=False)  # from SPICE
+    spin_axis_orientation_std_dev: np.double = field(init=False)  # from SPICE
     spin_axis_orientation_average: np.double = field(init=False)  # retrieved from SPICE
     spacecraft_location_average: np.ndarray = field(init=False)  # retrieved from SPIC
-    spacecraft_location_variance: np.ndarray = field(init=False)  # retrieved from SPIC
+    spacecraft_location_std_dev: np.ndarray = field(init=False)  # retrieved from SPIC
     spacecraft_velocity_average: np.ndarray = field(init=False)  # retrieved from SPIC
-    spacecraft_velocity_variance: np.ndarray = field(init=False)  # retrieved from SPIC
+    spacecraft_velocity_std_dev: np.ndarray = field(init=False)  # retrieved from SPIC
     flags: np.ndarray = field(init=False)
     # TODO:
     # - Determine a good way to output flags as "human readable"
     # - Add spice pieces
-    # - add in the filenames for the input files - should they be global attributes?
     # - also unique identifiers
     # - Bad angle algorithm using SPICE locations
     # - Move ancillary file to AWS
 
-    def __post_init__(self) -> None:
-        """Will process data."""
+    def __post_init__(
+        self,
+        filter_temperature_variance: np.double,
+        hv_voltage_variance: np.double,
+        spin_period_variance: np.double,
+        pulse_length_variance: np.double,
+    ) -> None:
+        """
+        Will process data.
+
+        The input variance values are used to calculate the output standard deviation.
+
+        Parameters
+        ----------
+        filter_temperature_variance : numpy.double
+            Encoded filter temperature variance.
+        hv_voltage_variance : numpy.double
+            Encoded HV voltage variance.
+        spin_period_variance : numpy.double
+            Encoded spin period variance.
+        pulse_length_variance : numpy.double
+            Encoded pulse length variance.
+        """
         # self.histogram_flag_array = np.zeros((2,))
 
         # TODO: These pieces will need to be filled in from SPICE kernels. For now,
         #  they are placeholders. GLOWS example code has better placeholders if needed.
         self.spin_period_ground_average = np.double(-999.9)
-        self.spin_period_ground_variance = np.double(-999.9)
+        self.spin_period_ground_std_dev = np.double(-999.9)
         self.position_angle_offset_average = np.double(-999.9)
-        self.position_angle_offset_variance = np.double(-999.9)
-        self.spin_axis_orientation_variance = np.double(-999.9)
+        self.position_angle_offset_std_dev = np.double(-999.9)
+        self.spin_axis_orientation_std_dev = np.double(-999.9)
         self.spin_axis_orientation_average = np.double(-999.9)
         self.spacecraft_location_average = np.array([-999.9, -999.9, -999.9])
-        self.spacecraft_location_variance = np.array([-999.9, -999.9, -999.9])
+        self.spacecraft_location_std_dev = np.array([-999.9, -999.9, -999.9])
         self.spacecraft_velocity_average = np.array([-999.9, -999.9, -999.9])
-        self.spacecraft_velocity_variance = np.array([-999.9, -999.9, -999.9])
+        self.spacecraft_velocity_std_dev = np.array([-999.9, -999.9, -999.9])
         # Will require some additional inputs
         self.imap_spin_angle_bin_cntr = np.zeros((3600,))
 
@@ -546,34 +568,34 @@ def __post_init__(self) -> None:
         self.filter_temperature_average = self.ancillary_parameters.decode(
             "filter_temperature", self.filter_temperature_average
         )
-        self.filter_temperature_variance = self.ancillary_parameters.decode_std_dev(
-            "filter_temperature", self.filter_temperature_variance
+        self.filter_temperature_std_dev = self.ancillary_parameters.decode_std_dev(
+            "filter_temperature", filter_temperature_variance
         )
 
         self.hv_voltage_average = self.ancillary_parameters.decode(
             "hv_voltage", self.hv_voltage_average
         )
-        self.hv_voltage_variance = self.ancillary_parameters.decode_std_dev(
-            "hv_voltage", self.hv_voltage_variance
+        self.hv_voltage_std_dev = self.ancillary_parameters.decode_std_dev(
+            "hv_voltage", hv_voltage_variance
         )
         self.spin_period_average = self.ancillary_parameters.decode(
             "spin_period", self.spin_period_average
         )
-        self.spin_period_variance = self.ancillary_parameters.decode_std_dev(
-            "spin_period", self.spin_period_variance
+        self.spin_period_std_dev = self.ancillary_parameters.decode_std_dev(
+            "spin_period", spin_period_variance
         )
         self.pulse_length_average = self.ancillary_parameters.decode(
             "pulse_length", self.pulse_length_average
         )
-        self.pulse_length_variance = self.ancillary_parameters.decode_std_dev(
-            "pulse_length", self.pulse_length_variance
+        self.pulse_length_std_dev = self.ancillary_parameters.decode_std_dev(
+            "pulse_length", pulse_length_variance
         )
 
         self.histogram_flag_array = np.zeros((4, 3600), dtype=np.uint8)
         # self.unique_block_identifier = np.datetime_as_string(
         #     np.datetime64(int(self.imap_start_time), "ns"), "s"
         # )
-        self.flags = np.zeros((17, 3600), dtype=np.uint8)
+        self.flags = np.ones((17,), dtype=np.uint8)
 
     def output_data(self) -> tuple:
         """