Format with ruff and enable formating in pre-commit (#116)

* Format with ruff and enable formating in pre-commit

.pre-commit-config.yaml

@@ -5,6 +5,8 @@ repos:
     hooks:
       - id: ruff
         args: ["--fix"]
+      # Run the formatter.
+      - id: ruff-format
   - repo: https://github.com/PyCQA/isort
     rev: 5.13.2
     hooks:

changelog/116.trivial.rst

@@ -0,0 +1 @@
+Format code with ruff and turn on ruff format in pre-commit.

docs/conf.py

@@ -13,8 +13,10 @@
 author = "STIX Team"
 
 from pathlib import Path
+
 # The full version, including alpha/beta/rc tags
 from stixpy import __version__
+
 release = __version__
 is_development = ".dev" in release
 
@@ -89,9 +91,7 @@
 html_theme = "pydata_sphinx_theme"
 
 html_theme_options = {
-    "logo": {
-        "text": "stixpy"
-    },
+    "logo": {"text": "stixpy"},
 }
 
 # Add any paths that contain custom static files (such as style sheets) here,

examples/imaging_demo.py

@@ -58,7 +58,10 @@
 # Set time and energy ranges which will be considered for the science and the background file
 
 time_range_sci = ["2021-09-23T15:21:00", "2021-09-23T15:24:00"]
-time_range_bkg = ["2021-09-23T09:00:00", "2021-09-23T12:00:00"]  # Set this range larger than the actual observation time
+time_range_bkg = [
+    "2021-09-23T09:00:00",
+    "2021-09-23T12:00:00",
+]  # Set this range larger than the actual observation time
 energy_range = [28, 40]
 
 ###############################################################################
@@ -75,9 +78,12 @@
 ###############################################################################
 # Perform background subtraction
 
-meta_pixels_bkg_subtracted = {"abcd_rate_kev_cm": meta_pixels_sci["abcd_rate_kev_cm"] - meta_pixels_bkg["abcd_rate_kev_cm"],
-                              "abcd_rate_error_kev_cm": np.sqrt( meta_pixels_sci["abcd_rate_error_kev_cm"]**2 +
-                                                                 meta_pixels_bkg["abcd_rate_error_kev_cm"]**2)}
+meta_pixels_bkg_subtracted = {
+    "abcd_rate_kev_cm": meta_pixels_sci["abcd_rate_kev_cm"] - meta_pixels_bkg["abcd_rate_kev_cm"],
+    "abcd_rate_error_kev_cm": np.sqrt(
+        meta_pixels_sci["abcd_rate_error_kev_cm"] ** 2 + meta_pixels_bkg["abcd_rate_error_kev_cm"] ** 2
+    ),
+}
 
 ###############################################################################
 # Create visibilites from the meta pixels
@@ -89,8 +95,8 @@
 
 # Extra phase calibration not needed with these
 uv_data = get_uv_points_data()
-vis.u = uv_data['u']
-vis.v = uv_data['v']
+vis.u = uv_data["u"]
+vis.v = uv_data["v"]
 
 cal_vis = calibrate_visibility(vis)
 
@@ -121,16 +127,18 @@
 
 bp_image = vis_to_image(stix_vis, imsize, pixel_size=pixel)
 
-date_avg = Time('2021-09-23T15:22:30')
+date_avg = Time("2021-09-23T15:22:30")
 roll, solo_xyz, pointing = get_hpc_info(date_avg)
 
-solo = HeliographicStonyhurst(*solo_xyz, obstime=date_avg, representation_type='cartesian')
-coord = STIXImaging(0*u.arcsec, 0*u.arcsec, obstime='2021-09-23T15:22:30', observer=solo)
-header = make_fitswcs_header(bp_image, coord, telescope='STIX', observatory='Solar Orbiter', scale=[10,10]*u.arcsec/u.pix)
+solo = HeliographicStonyhurst(*solo_xyz, obstime=date_avg, representation_type="cartesian")
+coord = STIXImaging(0 * u.arcsec, 0 * u.arcsec, obstime="2021-09-23T15:22:30", observer=solo)
+header = make_fitswcs_header(
+    bp_image, coord, telescope="STIX", observatory="Solar Orbiter", scale=[10, 10] * u.arcsec / u.pix
+)
 fd_bp_map = Map((bp_image, header))
 
 hpc_ref = coord.transform_to(Helioprojective(observer=solo, obstime=fd_bp_map.date))  # Center of STIX pointing in HPC
-header_hp = make_fitswcs_header(bp_image, hpc_ref, scale=[10, 10]*u.arcsec/u.pix, rotation_angle=90*u.deg+roll)
+header_hp = make_fitswcs_header(bp_image, hpc_ref, scale=[10, 10] * u.arcsec / u.pix, rotation_angle=90 * u.deg + roll)
 hp_map = Map((bp_image, header_hp))
 hp_map_rotated = hp_map.rotate()
 
@@ -160,17 +168,24 @@
 # Use estimated flare location to create more accurate visibilities
 
 meta_pixels_sci = create_meta_pixels(
-    cpd_sci, time_range=time_range_sci, energy_range=energy_range, phase_center=[max_hpc.Tx, max_hpc.Ty], no_shadowing=True
+    cpd_sci,
+    time_range=time_range_sci,
+    energy_range=energy_range,
+    phase_center=[max_hpc.Tx, max_hpc.Ty],
+    no_shadowing=True,
 )
 
-meta_pixels_bkg_subtracted = {"abcd_rate_kev_cm": meta_pixels_sci["abcd_rate_kev_cm"] - meta_pixels_bkg["abcd_rate_kev_cm"],
-                              "abcd_rate_error_kev_cm": np.sqrt( meta_pixels_sci["abcd_rate_error_kev_cm"]**2 +
-                                                                 meta_pixels_bkg["abcd_rate_error_kev_cm"]**2)}
+meta_pixels_bkg_subtracted = {
+    "abcd_rate_kev_cm": meta_pixels_sci["abcd_rate_kev_cm"] - meta_pixels_bkg["abcd_rate_kev_cm"],
+    "abcd_rate_error_kev_cm": np.sqrt(
+        meta_pixels_sci["abcd_rate_error_kev_cm"] ** 2 + meta_pixels_bkg["abcd_rate_error_kev_cm"] ** 2
+    ),
+}
 
 vis = create_visibility(meta_pixels_bkg_subtracted)
 uv_data = get_uv_points_data()
-vis.u = uv_data['u']
-vis.v = uv_data['v']
+vis.u = uv_data["u"]
+vis.v = uv_data["v"]
 cal_vis = calibrate_visibility(vis, [max_hpc.Tx, max_hpc.Ty])
 
 ###############################################################################

setup.py

@@ -5,6 +5,7 @@
 from itertools import chain
 
 from setuptools import setup  # isort:skip
+
 try:
     # Recommended for setuptools 61.0.0+
     # (though may disappear in the future)

stixpy/calibration/detector.py

@@ -8,7 +8,7 @@
 from stixpy.calibration.transmission import Transmission
 from stixpy.io.readers import read_energy_channel_index, read_sci_energy_channels
 
-__all__ = ['get_srm','get_pixel_srm','get_sci_channels']
+__all__ = ["get_srm", "get_pixel_srm", "get_sci_channels"]
 
 SCI_INDEX = None
 SCI_CHANNELS = {}

stixpy/calibration/energy.py

@@ -7,7 +7,7 @@
 from stixpy.product import Product
 from stixpy.utils.rebining import rebin_proportional
 
-__all__ = ['get_elut','correct_counts']
+__all__ = ["get_elut", "correct_counts"]
 
 
 def get_elut(date):

stixpy/calibration/grid.py

@@ -8,7 +8,8 @@
 import numpy as np
 from astropy.table import Table
 
-__all__ = ["get_grid_transmission","_calculate_grid_transmission"]
+__all__ = ["get_grid_transmission", "_calculate_grid_transmission"]
+
 
 def get_grid_transmission(xy_flare):
     r"""

stixpy/calibration/livetime.py

@@ -82,13 +82,13 @@ def pileup_correction_factor():
     """
 
     subc_str = read_subc_params()
-    large_pixel_area = (subc_str['L Pixel Xsize'] * subc_str['L Pixel Ysize'])[0]
-    small_pixel_area = (subc_str['S Pixel Xsize'] * subc_str['S Pixel Ysize'])[0]
+    large_pixel_area = (subc_str["L Pixel Xsize"] * subc_str["L Pixel Ysize"])[0]
+    small_pixel_area = (subc_str["S Pixel Xsize"] * subc_str["S Pixel Ysize"])[0]
     # half a small pixel overlaps each big pixel
     large_pixel_area_corrected = large_pixel_area - 0.5 * small_pixel_area
-    detector_area = (subc_str['Detect Xsize'] * subc_str['Detect Ysize'])[0]
-    big_pixel_fraction = large_pixel_area_corrected/detector_area
-    prob_diff_pix = (2/big_pixel_fraction - 1)/(2/big_pixel_fraction)
+    detector_area = (subc_str["Detect Xsize"] * subc_str["Detect Ysize"])[0]
+    big_pixel_fraction = large_pixel_area_corrected / detector_area
+    prob_diff_pix = (2 / big_pixel_fraction - 1) / (2 / big_pixel_fraction)
 
     return prob_diff_pix
 

stixpy/calibration/tests/test_visibility.py

@@ -9,33 +9,46 @@
 @pytest.fixture
 @pytest.mark.remote_data
 def flare_cpd():
-    return Product('https://pub099.cs.technik.fhnw.ch/fits/L1/2022/08/28/SCI/solo_L1_stix-sci-xray-cpd_20220828T154401-20220828T161600_V02_2208284257-61808.fits')
+    return Product(
+        "https://pub099.cs.technik.fhnw.ch/fits/L1/2022/08/28/SCI/"
+        "solo_L1_stix-sci-xray-cpd_20220828T154401-20220828T161600_V02_2208284257-61808.fits"
+    )
 
 
 @pytest.fixture
 @pytest.mark.remote_data
 def background_cpd():
-    return Product('https://pub099.cs.technik.fhnw.ch/fits/L1/2022/08/24/SCI/solo_L1_stix-sci-xray-cpd_20220824T140037-20220824T145017_V02_2208242079-61784.fits')
+    return Product(
+        "https://pub099.cs.technik.fhnw.ch/fits/L1/2022/08/24/SCI/"
+        "solo_L1_stix-sci-xray-cpd_20220824T140037-20220824T145017_V02_2208242079-61784.fits"
+    )
 
 
 def test_get_uv_points_data():
     uv_data = get_uv_points_data()
-    assert uv_data['u'][0] == -0.03333102271709666 / u.arcsec
-    assert uv_data['v'][0] == 0.005908224739704219 / u.arcsec
-    assert uv_data['isc'][0] == 1
-    assert uv_data['label'][0] == '3c'
+    assert uv_data["u"][0] == -0.03333102271709666 / u.arcsec
+    assert uv_data["v"][0] == 0.005908224739704219 / u.arcsec
+    assert uv_data["isc"][0] == 1
+    assert uv_data["label"][0] == "3c"
 
 
 def test_create_meta_pixels(background_cpd):
-    time_range = ['2022-08-24T14:00:37.271', '2022-08-24T14:50:17.271']
+    time_range = ["2022-08-24T14:00:37.271", "2022-08-24T14:50:17.271"]
     energy_range = [20, 76]
-    meta_pixels = create_meta_pixels(background_cpd, time_range=time_range, energy_range=energy_range,
-                                     phase_center=[0,0]*u.arcsec, no_shadowing=True)
-
-    assert_quantity_allclose([0.17628464, 0.17251869,
-                              0.16275495, 0.19153585] * u.ct / (u.keV * u.cm ** 2 * u.s),
-                             meta_pixels['abcd_rate_kev_cm'][0, :])
-
-    assert_quantity_allclose([0.18701911, 0.18205339,
-                              0.18328145, 0.17945563] * u.ct / (u.keV * u.cm ** 2 * u.s),
-                             meta_pixels['abcd_rate_kev_cm'][-1, :])
+    meta_pixels = create_meta_pixels(
+        background_cpd,
+        time_range=time_range,
+        energy_range=energy_range,
+        phase_center=[0, 0] * u.arcsec,
+        no_shadowing=True,
+    )
+
+    assert_quantity_allclose(
+        [0.17628464, 0.17251869, 0.16275495, 0.19153585] * u.ct / (u.keV * u.cm**2 * u.s),
+        meta_pixels["abcd_rate_kev_cm"][0, :],
+    )
+
+    assert_quantity_allclose(
+        [0.18701911, 0.18205339, 0.18328145, 0.17945563] * u.ct / (u.keV * u.cm**2 * u.s),
+        meta_pixels["abcd_rate_kev_cm"][-1, :],
+    )

stixpy/calibration/visibility.py

@@ -11,12 +11,15 @@
 from stixpy.calibration.livetime import get_livetime_fraction
 from stixpy.io.readers import read_subc_params
 
-__all__ = ["get_subcollimator_info",
-           "create_meta_pixels",
-           "create_visibility",
-           "get_uv_points_data",
-           "calibrate_visibility",
-           "sas_map_center"]
+__all__ = [
+    "get_subcollimator_info",
+    "create_meta_pixels",
+    "create_visibility",
+    "get_uv_points_data",
+    "calibrate_visibility",
+    "sas_map_center",
+]
+
 
 def get_subcollimator_info():
     r"""
@@ -160,7 +163,7 @@ def create_meta_pixels(pixel_data, time_range, energy_range, phase_center, no_sh
     e_cor_high, e_cor_low = get_elut_correction(e_ind, pixel_data)
 
     counts = pixel_data.data["counts"].astype(float)
-    count_errors = np.sqrt(pixel_data.data["counts_comp_err"].astype(float).value**2 + counts.value) * u.ct
+    count_errors = np.sqrt(pixel_data.data["counts_comp_err"].astype(float).value ** 2 + counts.value) * u.ct
     ct = counts[t_ind][..., e_ind]
     ct[..., 0:8, 0] = ct[..., 0:8, 0] * e_cor_low[..., 0:8]
     ct[..., 0:8, -1] = ct[..., 0:8, -1] * e_cor_high[..., 0:8]
@@ -170,7 +173,7 @@ def create_meta_pixels(pixel_data, time_range, energy_range, phase_center, no_sh
 
     lt = (livefrac * pixel_data.data["timedel"].reshape(-1, 1).to("s"))[t_ind].sum(axis=0)
 
-    ct_summed = ct.sum(axis=(0, 3))#.astype(float)
+    ct_summed = ct.sum(axis=(0, 3))  # .astype(float)
     ct_error_summed = np.sqrt(np.sum(ct_error**2, axis=(0, 3)))
 
     if not no_shadowing:
@@ -179,7 +182,9 @@ def create_meta_pixels(pixel_data, time_range, energy_range, phase_center, no_sh
         ct_error_summed = ct_error_summed / grid_shadowing.reshape(-1, 1) / 4
 
     abcd_counts = ct_summed.reshape(ct_summed.shape[0], -1, 4)[:, [0, 1], :].sum(axis=1)
-    abcd_count_errors = np.sqrt((ct_error_summed.reshape(ct_error_summed.shape[0], -1, 4)[:, [0, 1], :] ** 2).sum(axis=1))
+    abcd_count_errors = np.sqrt(
+        (ct_error_summed.reshape(ct_error_summed.shape[0], -1, 4)[:, [0, 1], :] ** 2).sum(axis=1)
+    )
 
     abcd_rate = abcd_counts / lt.reshape(-1, 1)
     abcd_rate_error = abcd_count_errors / lt.reshape(-1, 1)
@@ -297,7 +302,7 @@ def create_visibility(meta_pixels):
 
 
 @u.quantity_input
-def get_uv_points_data(d_det: u.Quantity[u.mm] = 47.78 * u.mm, d_sep:u.Quantity[u.mm] = 545.30 * u.mm):
+def get_uv_points_data(d_det: u.Quantity[u.mm] = 47.78 * u.mm, d_sep: u.Quantity[u.mm] = 545.30 * u.mm):
     r"""
     Return the STIX (u,v) points coordinates defined in [1], ordered with respect to the detector index.
 
@@ -339,17 +344,21 @@ def get_uv_points_data(d_det: u.Quantity[u.mm] = 47.78 * u.mm, d_sep:u.Quantity[
     front_unit_vector_comp = (((d_det + d_sep) / subc_imaging["Front Pitch"]) / u.rad).to(1 / u.arcsec)
     rear_unit_vector_comp = ((d_det / subc_imaging["Rear Pitch"]) / u.rad).to(1 / u.arcsec)
 
-    uu = np.cos(subc_imaging["Front Orient"].to("deg")) * front_unit_vector_comp - np.cos(
-        subc_imaging["Rear Orient"].to("deg")) * rear_unit_vector_comp
-    vv = np.sin(subc_imaging["Front Orient"].to("deg")) * front_unit_vector_comp - np.sin(
-        subc_imaging["Rear Orient"].to("deg")) * rear_unit_vector_comp
+    uu = (
+        np.cos(subc_imaging["Front Orient"].to("deg")) * front_unit_vector_comp
+        - np.cos(subc_imaging["Rear Orient"].to("deg")) * rear_unit_vector_comp
+    )
+    vv = (
+        np.sin(subc_imaging["Front Orient"].to("deg")) * front_unit_vector_comp
+        - np.sin(subc_imaging["Rear Orient"].to("deg")) * rear_unit_vector_comp
+    )
 
     uu = -uu * phase_sense
     vv = -vv * phase_sense
 
     uv_data = {
-        "isc": isc,     # sub-collimator indices
-        "label": label, # sub-collimator labels
+        "isc": isc,  # sub-collimator indices
+        "label": label,  # sub-collimator labels
         "u": uu,
         "v": vv,
     }