apply black formatting

Author: m-stclair

marslab/__init__.py

@@ -1 +1 @@
-__version__ = '0.9.14'
+__version__ = "0.9.14"

marslab/bandset/bandset.py

@@ -17,8 +17,12 @@
 import pandas as pd
 
 from marslab.imgops.debayer import make_bayer, debayer_upsample
-from marslab.imgops.imgutils import absolutely_destroy, mapfilter, \
-    get_all_bands, get_all_bands_from_all
+from marslab.imgops.imgutils import (
+    absolutely_destroy,
+    mapfilter,
+    get_all_bands,
+    get_all_bands_from_all,
+)
 from marslab.imgops.look import Look, save_plainly
 from marslab.poolutils import wait_for_it
 
@@ -40,7 +44,7 @@ def __init__(
         name: str = None,
         threads: Mapping = None,
         raw: MutableMapping = None,
-        special_constants: Collection[Any] = None
+        special_constants: Collection[Any] = None,
     ):
         """
         :param metadata: dataframe containing at least "PATH", "BAND", "IX,
@@ -142,7 +146,8 @@ def load(
             results = []
             for path, band_df in chunked_by_file:
                 results.append(
-                    self.load_method(path, band_df, bands, self.precached))
+                    self.load_method(path, band_df, bands, self.precached)
+                )
                 log.info("loaded " + path)
         else:
             results = {}
@@ -295,7 +300,7 @@ def make_look_set(
         self,
         instructions: Collection[Mapping],
         autoload: bool = True,
-        timeout: Optional[float] = None
+        timeout: Optional[float] = None,
     ):
         # load images and filter instruction set for unavailable bands
         available_instructions = self.prep_look_set(instructions, autoload)
@@ -320,7 +325,7 @@ def make_look_set(
                 op_images = {
                     channel: [
                         self.get_band(band).copy()
-                        for band in instruction['params'][channel]["bands"]
+                        for band in instruction["params"][channel]["bands"]
                     ]
                     for channel in ("red", "green", "blue")
                 }
@@ -331,10 +336,10 @@ def make_look_set(
             pipeline = Look.compile_from_instruction(
                 instruction,
                 metadata=self.metadata,
-                special_constants=self.special_constants
+                special_constants=self.special_constants,
             )
             if "underlay" in instruction.keys():
-                underlay = instruction['underlay']['band']
+                underlay = instruction["underlay"]["band"]
                 if isinstance(underlay, int):
                     pipeline.add_underlay(op_images[underlay])
                 else:
@@ -355,7 +360,7 @@ def make_look_set(
                 log,
                 message="generated ",
                 as_dict=True,
-                timeout=timeout
+                timeout=timeout,
             )
             pool.terminate()
         self.looks |= look_cache
@@ -438,5 +443,3 @@ def __init__(self, path, load_method=None, **bandset_kwargs):
         metadata["BAND"] = self.raw.keys()
         metadata["IX"] = self.raw.keys()
         metadata["PATH"] = path
-
-

marslab/bandset/m3.py

@@ -29,7 +29,7 @@ def setup_m3_bandset_metadata(file_path):
     metadata["IX"] = np.array(range(len(metadata["WAVELENGTH"])))
     # 'channel' or 'channel #' in mission nomenclature
     metadata["BAND"] = metadata["IX"] + 1
-    metadata['PATH'] = file_path
+    metadata["PATH"] = file_path
     return metadata
 
 

marslab/bandset/mastcam.py

@@ -20,7 +20,7 @@ def parse_mcam_fn(mcam_fn):
         "EYE": filename[5],
         "SEQ_ID": f"mcam{int(filename[6:12])}",
         "CAL": filename[26:30],
-        "FILETYPE": filename[22:25]
+        "FILETYPE": filename[22:25],
     }
 
 
@@ -50,7 +50,7 @@ def parse_mcam_files(file_paths):
 def setup_mcam_bandset_metadata(metadata):
     if "FILTER" in metadata.columns:
         metadata = metadata.drop(
-            metadata.loc[metadata.FILTER.isin(('L7', 'R7'))].index
+            metadata.loc[metadata.FILTER.isin(("L7", "R7"))].index
         )
         metadata["BAND"] = metadata["FILTER"]
         metadata.drop("FILTER", axis=1)
@@ -80,7 +80,7 @@ def setup_mcam_bandset_metadata(metadata):
     metadata["BAYER_PIXEL"] = pd.Series(BAND_TO_BAYER["MCAM"])[
         metadata["BAND"]
     ]
-    metadata.loc[metadata['FILETYPE'] != 'C00', 'BAYER_PIXEL'] = None
+    metadata.loc[metadata["FILETYPE"] != "C00", "BAYER_PIXEL"] = None
     return metadata.reset_index(drop=True)
 
 

marslab/bandset/mastcamz.py

@@ -15,7 +15,8 @@
 
 from marslab.bandset import BandSet
 from marslab.compat.xcam import (
-    DERIVED_CAM_DICT, BAND_TO_BAYER,
+    DERIVED_CAM_DICT,
+    BAND_TO_BAYER,
 )
 from marslab.imgops.debayer import RGGB_PATTERN
 from marslab.imgops.loaders import pdr_load
@@ -122,8 +123,10 @@ def check_onboard_debayer(self, *, fix_metadata=False):
         references to additional bands of R0 / L0 image files (that don't
         exist in raw bayer images).
         """
-        if tuple(self.precached.values())[0].metaget(
-                'BAYER_METHOD') == 'RAW_BAYER':
+        if (
+            tuple(self.precached.values())[0].metaget("BAYER_METHOD")
+            == "RAW_BAYER"
+        ):
             return False
         if fix_metadata:
             self.metadata["BAYER_PIXEL"] = None

marslab/compat/sel_to_roi.py

@@ -10,8 +10,11 @@
 import scipy.io
 from astropy.io import fits
 
-from marslab.compat.mertools import MERSPECT_MSL_COLOR_MAPPINGS, \
-    MERSPECT_M20_COLOR_MAPPINGS, MERSPECT_COLOR_MAPPINGS
+from marslab.compat.mertools import (
+    MERSPECT_MSL_COLOR_MAPPINGS,
+    MERSPECT_M20_COLOR_MAPPINGS,
+    MERSPECT_COLOR_MAPPINGS,
+)
 from marslab.imgops.regions import select_roi_by_ix, make_roi_hdu
 
 
@@ -35,7 +38,7 @@ def is_sel_file(roi_path: Union[str, Path]) -> bool:
                     "right_pos",
                     "sel_file_format_major_version",
                     "sel_file_format_minor_version",
-                    "sel_file_format_date"
+                    "sel_file_format_date",
                 }
             )
             return True

marslab/geom.py

@@ -47,18 +47,15 @@
 
 # TODO: this may be cruft.
 def get_geometry_value(
-    entity_name: str,
-    frame_name: str,
-    axis_name: str,
-    data: pdr.Data
+    entity_name: str, frame_name: str, axis_name: str, data: pdr.Data
 ) -> Union[float, int, str]:
     """
     Fetch the value named `entity_name` for the axis named `axis_name` of the
     coordinate frame named `frame_name`, as defined in the metadata of `data`.
     """
     return get_from(
         data.metaget(f"{frame_name}_DERIVED_GEOMETRY_PARMS"),
-        (f"{entity_name}_{axis_name}", "value")
+        (f"{entity_name}_{axis_name}", "value"),
     )
 
 
@@ -72,7 +69,8 @@ def get_coordinate_system_properties(
     If there is no coordinate system named `frame_name`, returns None.
     """
     syskeys = [
-        k for k in data.metadata.fieldcounts
+        k
+        for k in data.metadata.fieldcounts
         if re.match(f"{frame_name}_COORD(INATE)?_SYSTEM(_PARMS)?$", k)
     ]
     if len(syskeys) == 0:
@@ -83,12 +81,12 @@ def get_coordinate_system_properties(
         "reference_frame": system.get("REFERENCE_COORD_SYSTEM_NAME"),
         "quaternion": np.array(system.get("ORIGIN_ROTATION_QUATERNION")),
         "offset": np.array(system.get("ORIGIN_OFFSET_VECTOR")),
-        "orientation": system.get("POSITIVE_AZIMUTH_DIRECTION")
+        "orientation": system.get("POSITIVE_AZIMUTH_DIRECTION"),
     }
 
 
 def get_coordinate_systems(
-    data: pdr.Data
+    data: pdr.Data,
 ) -> dict[str, dict[str, Union[np.ndarray, str, float]]]:
     """
     Fetch and format information about all VICAR-style coordinate systems
@@ -120,10 +118,7 @@ def _check_unit_of_angle(unit: str) -> None:
 
 
 def cart2sph(
-    x0: ArrayLike,
-    y0: ArrayLike,
-    z0: ArrayLike,
-    unit: UnitOfAngle = "degrees"
+    x0: ArrayLike, y0: ArrayLike, z0: ArrayLike, unit: UnitOfAngle = "degrees"
 ) -> Union[pd.DataFrame, tuple[Real, Real, Real]]:
     """
     Classic Cartesian-to-spherical coordinate representation converter.
@@ -163,7 +158,7 @@ def sph2cart(
     lat: ArrayLike,
     lon: ArrayLike,
     radius: ArrayLike = 1,
-    unit: UnitOfAngle = "degrees"
+    unit: UnitOfAngle = "degrees",
 ) -> Union[pd.DataFrame, tuple[Real, Real, Real]]:
     """
     Classic spherical-to-Cartesian coordinate representation converter. By
@@ -217,10 +212,7 @@ def invert_quaternion(quat: Quaternion) -> Quaternion:
 
 
 def rotate_unit_vector(
-    alt: float,
-    az: float,
-    quat: Quaternion,
-    clockwise: bool = True
+    alt: float, az: float, quat: Quaternion, clockwise: bool = True
 ) -> np.ndarray:
     """
     Apply a rotation expressed as a unit quaternion to a unit vector expressed
@@ -234,22 +226,20 @@ def rotate_unit_vector(
         source_cartesian *= np.array([-1, -1, 1])
     zero_quaternion = np.array([0, *source_cartesian])
     inverse_rotation = invert_quaternion(quat)
-    q_times_0_v = quaternion_multiplication(
-        quat, zero_quaternion
-    )
+    q_times_0_v = quaternion_multiplication(quat, zero_quaternion)
     v_prime = quaternion_multiplication(q_times_0_v, inverse_rotation)
     assert np.isclose(v_prime[0], 0)
     target_cartesian = v_prime[1:]
     if clockwise is True:
         target_cartesian *= np.array([-1, -1, 1])
     # TODO: it's pointless to return the third (radius) element, because
-    #  the result will always be a unit vector. Will probably need to modify 
+    #  the result will always be a unit vector. Will probably need to modify
     #  downstream to make this change.
     return np.array(cart2sph(*target_cartesian))
 
 
 def get_coordinates(
-    data: pdr.Data
+    data: pdr.Data,
 ) -> dict[str, dict[str, dict[Literal["AZIMUTH", "ELEVATION"], float]]]:
     """
     Fetch and organize all VICAR-style azimuth/elevation values mentioned in
@@ -273,11 +263,13 @@ def get_coordinates(
     axes = ("AZIMUTH", "ELEVATION")
     entities = set()
     for axis in axes:
-        entities.update({
-            k.replace(f"_{axis}", "")
-            for k in data.metadata.fieldcounts
-            if k.endswith(f"_{axis}")
-        })
+        entities.update(
+            {
+                k.replace(f"_{axis}", "")
+                for k in data.metadata.fieldcounts
+                if k.endswith(f"_{axis}")
+            }
+        )
     coordinates = NestingDict()
     syskeys = filter(
         lambda k: k.endswith("_GEOMETRY_PARMS"), data.metadata.fieldcounts
@@ -288,7 +280,7 @@ def get_coordinates(
             continue
         record = block.get(f"{entity}_{axis}")
         if record is not None:
-            coordinates[key.split("_")[0]][entity][axis] = record['value']
+            coordinates[key.split("_")[0]][entity][axis] = record["value"]
     return coordinates.todict()
 
 
@@ -323,9 +315,9 @@ def transform_angle(
         quaternion = source_info["quaternion"]
     coord = coordinates[source_frame][entity]
     if target_info is not None:
-        clockwise = "clockwise" in target_info['orientation'].lower()
+        clockwise = "clockwise" in target_info["orientation"].lower()
     else:
-        clockwise = "clockwise" in source_info['orientation'].lower()
+        clockwise = "clockwise" in source_info["orientation"].lower()
     return rotate_unit_vector(
-        coord['ELEVATION'], coord['AZIMUTH'], quaternion, clockwise
+        coord["ELEVATION"], coord["AZIMUTH"], quaternion, clockwise
     )

marslab/imgops/debayer.py

@@ -109,7 +109,7 @@ def mask_bayer_pixels(
     pixel: Union[str, Sequence[str]],
     pattern: Mapping[str, tuple] = None,
     masks: Mapping[str, tuple] = None,
-    default = 0,
+    default=0,
     **_kwargs  # TODO: hacky!
 ) -> np.ndarray:
     """