better logging

docs/source/tutorials/MUSTANG-2_cluster.ipynb

@@ -33,6 +33,7 @@
     "    units=\"Jy/pixel\",  # Units of the input map\n",
     ")\n",
     "\n",
+    "input_map.data *= 1e1\n",
     "input_map.to(units=\"uK_RJ\").plot()"
    ]
   },
@@ -137,26 +138,6 @@
     "tod = sim.run()"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "tod.metadata"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from maria.spectrum import AtmosphericSpectrum\n",
-    "\n",
-    "AtmosphericSpectrum(region=tod.metadata[\"region\"])"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -220,26 +201,6 @@
     "output_map = mapper.run()"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "sim.atmosphere.weather.pwv"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import pandas as pd\n",
-    "\n",
-    "pd.read_csv(\"/Users/tom/maria/src/maria/site/regions.csv\").dtypes"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},

maria/__init__.py

@@ -5,7 +5,6 @@
 
 import logging
 
-from . import utils  # noqa
 from ._version import __version__, __version_tuple__  # noqa
 from .instrument import Band, Instrument, all_instruments, get_instrument  # noqa
 from .map import ProjectedMap  # noqa

maria/atmosphere/__init__.py

@@ -13,7 +13,8 @@
 
 from ..functions import approximate_normalized_matern
 from ..spectrum import AtmosphericSpectrum
-from ..utils import compute_aligning_transform, human_time
+from ..utils import compute_aligning_transform
+from ..io import humanize_time
 from ..weather import Weather
 from .extrusion import ProcessExtrusion, generate_layers
 
@@ -23,6 +24,8 @@
 
 SUPPORTED_MODELS_LIST = ["2d", "3d"]
 
+DEFAULT_ATMOSPHERE_KWARGS = {}
+
 
 class Atmosphere:
     def __init__(
@@ -194,7 +197,7 @@ def initialize(self, sim, timestep: float = 1e-1, max_height=3e3):
             triangulation = sp.spatial.Delaunay(tp[..., 1:])
 
             logger.debug(
-                f"Computed process bounds in {human_time(ttime.monotonic() - process_init_s)}."
+                f"Computed process bounds in {humanize_time(ttime.monotonic() - process_init_s)}."
             )
             # proc_s = ttime.monotonic()
 

maria/calibration/__init__.py

@@ -0,0 +1 @@
+from .calibration import Calibration  # noqa

maria/units/calibration.py → maria/calibration/calibration.py

@@ -3,7 +3,7 @@
 import numpy as np
 import pandas as pd
 
-from .quantities import parse_units, QUANTITIES
+from ..units import parse_units, QUANTITIES
 from ..spectrum import AtmosphericSpectrum
 from ..constants import k_B, T_CMB
 from ..functions.radiometry import (

maria/coords/coordinates.py

@@ -17,8 +17,8 @@
 from scipy.interpolate import interp1d
 from copy import deepcopy
 
-from ..io import DEFAULT_TIME_FORMAT
-from ..utils import repr_lat_lon, human_time
+from ..io import humanize_time, DEFAULT_TIME_FORMAT
+from ..utils import repr_lat_lon
 from .transforms import (
     dx_dy_to_phi_theta,
     get_center_phi_theta,
@@ -119,7 +119,7 @@ def __init__(
         self.compute_transforms()
         duration_s = ttime.monotonic() - ref_time
         logger.debug(
-            f"Initialized coordinates with shape {self.shape} in {human_time(duration_s)}.",
+            f"Initialized coordinates with shape {self} in {humanize_time(duration_s)}.",
         )  # noqa
 
     def compute_transforms(self):

maria/instrument/band/__init__.py

@@ -12,7 +12,7 @@
 from ...functions import planck_spectrum
 from ...utils import flatten_config, read_yaml
 from ...spectrum import AtmosphericSpectrum
-from ...units import Calibration
+from ...calibration import Calibration
 from ...constants import T_CMB, c, k_B
 
 here, this_filename = os.path.split(__file__)

maria/instrument/configs/test.yml

@@ -4,13 +4,21 @@
   aliases: ["test_1deg"]
   description: A simple test array
   array:
-    field_of_view: 1
+    field_of_view: 0.5
     primary_size: 5
     bands:
+      f090:
+        center: 90
+        width: 30
+        efficiency: 0.6
       f150:
         center: 150
-        width: 30
+        width: 40
         efficiency: 0.5
+      f220:
+        center: 220
+        width: 50
+        efficiency: 0.4
 
 10deg:
   aliases: ["test_10deg"]

maria/io/__init__.py

@@ -1,3 +1,4 @@
 from .caching import *  # noqa
+from .logging import *  # noqa
 
 DEFAULT_TIME_FORMAT = "YYYY-MM-DD HH:mm:ss.SSS ZZ"

maria/io/logging.py

@@ -0,0 +1,27 @@
+import time as ttime
+import logging
+from ..units import prefixes
+
+
+def humanize_time(seconds):
+
+    for _, prefix in prefixes.iterrows():
+        if prefix.time:
+            value = seconds / prefix.factor
+            if value < 1e3:
+                break
+
+    if value > 100:
+        value = round(value)
+    elif value > 10:
+        value = round(value, 1)
+    else:
+        value = round(value, 2)
+
+    return f"{value} {prefix.name}s"
+
+
+def log_duration(ref_time, message, level="debug"):
+    logger = logging.getLogger("maria")
+    string = f"{message} in {humanize_time(ttime.monotonic() - ref_time)}."
+    getattr(logger, level)(string)

maria/map/base.py

@@ -12,7 +12,8 @@
 
 from ..instrument import Band
 from ..constants import k_B
-from ..units import Angle, Calibration, parse_units  # noqa
+from ..calibration import Calibration
+from ..units import parse_units
 
 # from ..plotting import plot_map
 

maria/map/projected.py

@@ -13,7 +13,8 @@
 
 
 from .base import Map
-from ..units import prefixes, QUANTITIES, parse_units
+from ..units import QUANTITIES, parse_units
+from ..units import prefixes
 
 
 here, this_filename = os.path.split(__file__)

maria/mappers/base.py

@@ -12,7 +12,7 @@
 from ..map import ProjectedMap
 from ..tod import TOD
 
-from ..utils import human_time
+from ..io import humanize_time
 
 # np.seterr(invalid="ignore")
 
@@ -93,7 +93,7 @@ def run(self):
             band_start_s = ttime.monotonic()
             self.map_data[band] = self._run(band)
             logger.info(
-                f"Ran mapper for band {band.name} in {human_time(ttime.monotonic() - band_start_s)}."
+                f"Ran mapper for band {band.name} in {humanize_time(ttime.monotonic() - band_start_s)}."
             )
 
         map_data = np.zeros((len(self.map_data), 1, self.n_y, self.n_x))
@@ -121,8 +121,12 @@ def run(self):
             map_data[i, :] = band_map_numer / band_map_denom
             map_weight[i, :] = band_map_denom
 
+        map_offsets = np.nansum(map_data * map_weight, axis=(-1, -2)) / map_weight.sum(
+            axis=(-1, -2)
+        )
+
         return ProjectedMap(
-            data=map_data,
+            data=map_data - map_offsets[..., None, None],
             weight=map_weight,
             nu=map_freqs,
             resolution=self.resolution,

maria/plotting/tod.py

@@ -10,12 +10,13 @@
 from matplotlib.collections import EllipseCollection
 from matplotlib.patches import Patch
 
-from maria.instrument.beam import compute_angular_fwhm
-from maria.units import Angle, parse_units
-from maria.utils.signal import detrend as detrend_signal
-from maria.utils.signal import remove_slope
+from ..instrument.beam import compute_angular_fwhm
+from ..units import Angle, parse_units
+from ..utils.signal import detrend as detrend_signal
+from ..utils.signal import remove_slope
 
-from ..units import QUANTITIES, prefixes
+from ..units import QUANTITIES
+from ..units import prefixes
 
 
 def tod_plot(

maria/sim/simulation.py

@@ -15,6 +15,7 @@
 from ..cmb import CMB, generate_cmb, get_cmb, DEFAULT_CMB_KWARGS
 from ..errors import PointingError
 from ..instrument import Instrument
+from ..io import humanize_time
 from ..map import Map
 from ..plan import Plan
 from ..site import Site
@@ -23,7 +24,6 @@
 from .map import MapMixin
 from .noise import NoiseMixin
 
-from ..utils import human_time
 
 here, this_filename = os.path.split(__file__)
 logger = logging.getLogger("maria")
@@ -70,7 +70,7 @@ def __init__(
         )
 
         logger.debug(
-            f"Initialized generic simulation in {human_time(ttime.monotonic() - sim_init_start_s)}."
+            f"Initialized generic simulation in {humanize_time(ttime.monotonic() - sim_init_start_s)}."
         )
         base_init_s = ttime.monotonic()
 
@@ -119,7 +119,7 @@ def __init__(
             self.atmosphere.initialize(self)
 
         logger.debug(
-            f"Initialized atmosphere simulation in {human_time(ttime.monotonic() - base_init_s)}."
+            f"Initialized atmosphere simulation in {humanize_time(ttime.monotonic() - base_init_s)}."
         )
         atmosphere_init_s = ttime.monotonic()
 
@@ -137,7 +137,7 @@ def __init__(
                 raise ValueError(f"Invalid value for cmb: '{cmb}'.")
 
         logger.debug(
-            f"Initialized CMB simulation in {human_time(ttime.monotonic() - atmosphere_init_s)}."
+            f"Initialized CMB simulation in {humanize_time(ttime.monotonic() - atmosphere_init_s)}."
         )
         cmb_init_s = ttime.monotonic()
 
@@ -159,20 +159,20 @@ def __init__(
             self.map = map.to(units="K_RJ")
 
         logger.debug(
-            f"Initialized map simulation in {human_time(ttime.monotonic() - cmb_init_s)}."
+            f"Initialized map simulation in {humanize_time(ttime.monotonic() - cmb_init_s)}."
         )
         map_init_s = ttime.monotonic()
 
         if noise:
             pass
 
         logger.debug(
-            f"Initialized noise simulation in {human_time(ttime.monotonic() - map_init_s)}."
+            f"Initialized noise simulation in {humanize_time(ttime.monotonic() - map_init_s)}."
         )
         # noise_init_s = ttime.monotonic()
 
         logger.debug(
-            f"Initialized simulation in {human_time(ttime.monotonic() - sim_init_start_s)}."
+            f"Initialized simulation in {humanize_time(ttime.monotonic() - sim_init_start_s)}."
         )
 
     def _run(self):

maria/tests/test_calibration.py

@@ -3,7 +3,7 @@
 import numpy as np
 
 from maria import Simulation
-from maria.units import Calibration
+from maria.calibration import Calibration
 
 
 def test_brightness_temperature_to_spectral_flux_density_per_pixel():
@@ -13,7 +13,7 @@ def test_brightness_temperature_to_spectral_flux_density_per_pixel():
     )
 
 
-def test_decalibration():
+def test_involution():
 
     sim = Simulation(
         instrument="MUSTANG-2",

maria/tests/test_cmb.py

@@ -15,8 +15,8 @@ def test_cmb_calibration():
 
     plan = maria.Plan(
         scan_pattern="daisy",
-        scan_options={"radius": 5, "speed": 1},  # in degrees
-        duration=60,  # in seconds
+        scan_options={"radius": 10, "speed": 1},  # in degrees
+        duration=120,  # in seconds
         sample_rate=50,  # in Hz
         scan_center=(150, 10),
         jitter=0,
@@ -33,6 +33,10 @@ def test_cmb_calibration():
 
     tod = sim.run().to("uK_CMB")
 
+    tod.to("uK_CMB").signal.std(axis=1).compute()
+
+    # should be around 110 uK
     cmb_rms_uK = tod.signal.std(axis=-1).compute()
 
-    assert 90 < cmb_rms_uK.mean() < 130  # should be around 110 uK
+    assert all(cmb_rms_uK > 80)
+    assert all(cmb_rms_uK < 150)

maria/tests/test_maps.py

@@ -30,6 +30,23 @@ def test_fetch_fits_map(map_name):
     m.plot()
 
 
+@pytest.mark.parametrize(
+    "map_name",
+    ["maps/cluster.fits", "maps/big_cluster.fits", "maps/galaxy.fits"],
+)  # noqa
+def test_map_units_conversion(map_name):
+    map_filename = fetch(map_name)
+    m = maria.map.load(
+        filename=map_filename,
+        nu=90,
+        resolution=1 / 1024,
+        center=(150, 10),
+        units="Jy/pixel",
+    )
+
+    assert np.allclose(m.to("K_RJ").to("Jy/pixel").data, m.data).compute()
+
+
 @pytest.mark.parametrize("map_name", ["maps/sun.h5"])  # noqa
 def test_fetch_hdf_map(map_name):
     map_filename = fetch(map_name)