astro-otter 0.0.1__py3-none-any.whl

otter/plotter/otter_plotter.py

@@ -0,0 +1,67 @@
+"""
+OtterPlotter Class which handles the backend of the plotting.
+
+Currently supported backends are:
+- matplotlib
+- plotly
+"""
+
+import importlib
+
+
+class OtterPlotter:
+    def __init__(self, backend):
+        """
+        Handles the backend for the "plotter" module
+
+        Args:
+            backend [string]: a string of the module name to import and use
+                              as the backend. Currently supported are "matplotlib",
+                              "matplotlib.pyplot", "plotly", and "plotly.graph_objects"
+        """
+        if backend == "matplotlib.pyplot":
+            self.backend = backend
+        elif backend == "pyplot.graph_objects":
+            self.backend = backend
+        elif "plotly" in backend and "graph_objects" not in backend:
+            self.backend = "plotly.graph_objects"
+        elif "matplotlib" in backend and "pyplot" not in backend:
+            self.backend = "matplotlib.pyplot"
+        else:
+            raise ValueError("Not a valid backend string!")
+
+        self.plotter = importlib.import_module(self.backend)
+
+        if self.backend == "matplotlib.pyplot":
+            self.plot = self._plot_matplotlib
+        elif self.backend == "plotly.graph_objects":
+            self.plot = self._plot_plotly
+        else:
+            raise ValueError("Unknown backend!")
+
+    def _plot_matplotlib(self, x, y, xerr=None, yerr=None, ax=None, **kwargs):
+        """
+        General plots using matplotlib, is called by _matplotlib_light_curve and
+        _matplotlib_sed
+        """
+
+        if ax is None:
+            _, ax = self.plotter.subplots()
+
+        ax.errorbar(x, y, xerr=xerr, yerr=yerr, **kwargs)
+        return ax
+
+    def _plot_plotly(self, x, y, xerr=None, yerr=None, go=None, *args, **kwargs):
+        """
+        General plotting method using plotly, is called by _plotly_light_curve and
+        _plotly_sed
+        """
+
+        if go is None:
+            go = self.plotter.Figure()
+
+        fig = go.add_scatter(
+            x=x, y=y, error_x=dict(array=xerr), error_y=dict(array=yerr)
+        )
+
+        return fig

otter/plotter/plotter.py

@@ -0,0 +1,95 @@
+"""
+Some utilities to create common plots for transients that use the OtterPlotter
+"""
+
+from .otter_plotter import OtterPlotter
+
+
+def plot_light_curve(
+    date: float,
+    flux: float,
+    date_err: float = None,
+    flux_err: float = None,
+    fig=None,
+    ax=None,
+    backend: str = "matplotlib",
+    xlabel: str = "Date",
+    ylabel: str = "Flux",
+    **kwargs,
+):
+    """
+    Plot the light curve for the input data
+
+    Args:
+        date [float]: MJD dates
+        flux [float]: Flux
+        date_err [float]: optional error on the MJD dates
+        flux_err [float]: optional error on the flux
+        fig [float]: matplotlib fig object, optional. Will be created if not provided.
+        ax [float]: matplitlib axis object, optional. Will be created if not provided.
+        backend [str]: backend for plotting. options: "matplotlib" (default) or "plotly"
+        xlabel [str]: x-axis label
+        ylabel [str]: y-axis label
+        **kwargs: keyword arguments to pass to either plotly.graph_objects.add_scatter
+                  or matplotlib.pyplot.errorbar
+
+    Returns:
+       Either a matplotlib axis or plotly figure
+    """
+
+    plt = OtterPlotter(backend)
+    fig = plt.plot(date, flux, date_err, flux_err, ax=ax, **kwargs)
+
+    if backend == "matplotlib":
+        fig.set_ylabel(ylabel)
+        fig.set_xlabel(xlabel)
+
+    elif backend == "plotly":
+        fig.update_layout(xaxis_title=xlabel, yaxis_title=ylabel, **kwargs)
+
+    return fig
+
+
+def plot_sed(
+    wave_or_freq: float,
+    flux: float,
+    wave_or_freq_err: float = None,
+    flux_err: float = None,
+    fig=None,
+    ax=None,
+    backend: str = "matplotlib",
+    xlabel: str = "Frequency or Wavelength",
+    ylabel: str = "Flux",
+    **kwargs,
+):
+    """
+    Plot the SED for the input data
+
+    Args:
+        wave_or_freq [float]: wave or frequency array
+        flux [float]: Flux
+        wave_or_freq_err [float]: optional error on the MJD dates
+        flux_err [float]: optional error on the flux
+        fig [float]: matplotlib fig object, optional. Will be created if not provided.
+        ax [float]: matplitlib axis object, optional. Will be created if not provided.
+        backend [str]: backend for plotting. Options: "matplotlib" (default) or "plotly"
+        xlabel [str]: x-axis label
+        ylabel [str]: y-axis label
+        **kwargs: keyword arguments to pass to either plotly.graph_objects.add_scatter
+                  or matplotlib.pyplot.errorbar
+
+    Returns:
+       Either a matplotlib axis or plotly figure
+    """
+
+    plt = OtterPlotter(backend)
+    fig = plt.plot(wave_or_freq, flux, wave_or_freq_err, flux_err, ax=ax, **kwargs)
+
+    if backend == "matplotlib":
+        fig.set_ylabel(ylabel)
+        fig.set_xlabel(xlabel)
+
+    elif backend == "plotly":
+        fig.update_layout(xaxis_title=xlabel, yaxis_title=ylabel, **kwargs)
+
+    return fig

otter/util.py

@@ -0,0 +1,510 @@
+"""
+Some constants, mappings, and functions to be used across the software
+"""
+
+import os
+import ads
+import astropy.units as u
+
+"""
+Helper functions first that just don't belong anywhere else
+"""
+
+
+def filter_to_obstype(band_name):
+    """
+    Converts a band name to either 'radio', 'uvoir', 'xray'
+    """
+
+    try:
+        wave_eff = FILTER_MAP_WAVE[band_name] * u.nm
+    except KeyError as exc:
+        raise Exception(
+            f"No Effective Wavelength Known for {band_name}, please add it to constants"
+        ) from exc
+
+    if wave_eff > 1 * u.mm:
+        return "radio"
+    elif wave_eff <= 1 * u.mm and wave_eff >= 10 * u.nm:
+        return "uvoir"
+    else:
+        return "xray"
+
+
+def clean_schema(schema):
+    """
+    Clean out Nones and empty lists from the given subschema
+    """
+    for key, val in list(schema.items()):
+        if val is None or (isinstance(val, (list, dict)) and len(val) == 0):
+            del schema[key]
+    return schema
+
+
+def bibcode_to_hrn(bibcode):
+    """
+    Converts a bibcode to a human_readable_name (hrn) using ADSQuery
+    """
+
+    try:
+        adsquery = list(ads.SearchQuery(bibcode=bibcode))[0]
+    except IndexError:
+        raise ValueError(f"Could not find {bibcode} on ADS!")
+
+    authors = adsquery.author
+    year = adsquery.year
+
+    if len(authors) == 0:
+        raise ValueError("This ADS bibcode does not exist!")
+    elif len(authors) == 1:
+        author = authors[0]
+    elif len(authors) == 2:
+        author = authors[0] + " & " + authors[1]
+    else:  # longer than 2
+        author = authors[0] + " et al."
+
+    # generate the human readable name
+    hrn = author + " (" + year + ")"
+    return hrn
+
+
+"""
+Then the constants and dictionary mappings used throughout
+"""
+
+# gives the effective wavelength for each filter given
+# these are all in nanometers!
+FILTER_MAP_WAVE = {
+    "FUV": 153.8620701901866,
+    "NUV": 231.56631043707714,
+    "UVW2": 207.98754332676123,
+    "uvw2": 207.98754332676123,
+    "W2": 207.98754332676123,
+    "2": 207.98754332676123,
+    "uw2": 207.98754332676123,
+    "UVM2": 225.47802478793594,
+    "uvm2": 225.47802478793594,
+    "M2": 225.47802478793594,
+    "M": 225.47802478793594,
+    "um2": 225.47802478793594,
+    "UVW1": 261.3713060531025,
+    "uvw1": 261.3713060531025,
+    "W1": 261.3713060531025,
+    "1": 261.3713060531025,
+    "uw1": 261.3713060531025,
+    "u": 356.17887353001856,
+    "u'": 356.17887353001856,
+    "up": 356.17887353001856,
+    "uprime": 356.17887353001856,
+    "U_S": 347.06360491031495,
+    "s": 347.06360491031495,
+    "us": 347.06360491031495,
+    "U": 353.10502283105023,
+    "B": 443.0539845758355,
+    "B_S": 435.912081730874,
+    "b": 435.912081730874,
+    "bs": 435.912081730874,
+    "g": 471.8872246248687,
+    "g'": 471.8872246248687,
+    "gp": 471.8872246248687,
+    "gprime": 471.8872246248687,
+    "F475W": 471.8872246248687,
+    "g-DECam": 482.6787274749997,
+    "c": 540.8724658332794,
+    "cyan": 540.8724658332794,
+    "V": 553.7155963302753,
+    "V_S": 543.0131091205997,
+    "v": 543.0131091205997,
+    "vs": 543.0131091205997,
+    "Itagaki": 651.0535687558726,
+    "white": 752.0,
+    "unfilt.": 616.690135,
+    "0": 616.690135,
+    "C": 616.690135,
+    "clear": 616.690135,
+    "pseudobolometric": 616.690135,
+    "griz": 616.690135,
+    "RGB": 616.690135,
+    "LGRB": 616.690135,
+    "G": 673.5412573108297,
+    "Kepler": 641.6835660569259,
+    "TESS": 797.2360657697333,
+    "DLT40": 615.8130149792426,
+    "Open": 615.8130149792426,
+    "Clear": 615.8130149792426,
+    "w": 638.9300625093831,
+    "o": 686.6260690394873,
+    "orange": 686.6260690394873,
+    "r": 618.5194476741524,
+    "r'": 618.5194476741524,
+    "rp": 618.5194476741524,
+    "rprime": 618.5194476741524,
+    "F625W": 618.5194476741524,
+    "r-DECam": 643.2062638192127,
+    "R": 646.9439215118385,
+    "Rc": 646.9439215118385,
+    "R_s": 646.9439215118385,
+    "i": 749.9704174464691,
+    "i'": 749.9704174464691,
+    "ip": 749.9704174464691,
+    "iprime": 749.9704174464691,
+    "F775W": 749.9704174464691,
+    "i-DECam": 782.6680306208917,
+    "I": 788.558706467662,
+    "Ic": 788.558706467662,
+    "z_s": 867.9495480864285,
+    "zs": 867.9495480864285,
+    "z": 896.1488333992431,
+    "z'": 896.1488333992431,
+    "zp": 896.1488333992431,
+    "zprime": 896.1488333992431,
+    "z-DECam": 917.8949537472383,
+    "y": 963.3308299506817,
+    "y-DECam": 989.965087304703,
+    "J": 1255.0918319447906,
+    "H": 1630.5155019191195,
+    "K": 2157.3600605745955,
+    "Ks": 2157.3600605745955,
+    "F070W": 705.5727879998312,
+    "F090W": 904.2281265089156,
+    "F115W": 1157.001589027877,
+    "F150W": 1503.9880463410511,
+    "F200W": 1993.3922957570885,
+    "F225W": 2372.81,
+    "F277W": 2769.332372846113,
+    "F300M": 2990.7606605760484,
+    "F335M": 3363.887076210947,
+    "F356W": 3576.787256375927,
+    "F360M": 3626.0578695682693,
+    "F444W": 4415.974447587756,
+    "F560W": 5645.279496731566,
+    "F770W": 7663.455798629626,
+    "F1000W": 9968.161727011531,
+    "F1130W": 11310.984595876938,
+    "F1280W": 12831.396996921212,
+    "F1500W": 15091.367399905488,
+    "F1800W": 18006.083119653664,
+    "F2100W": 20842.526633138932,
+    "F2550W": 25408.228367890282,
+}
+
+# gives the effective frequency for all filters
+# These are all in THz
+FILTER_MAP_FREQ = {
+    "FUV": 1975.086895569116,
+    "NUV": 1346.3548820463916,
+    "UVW2": 1531.4976984760474,
+    "uvw2": 1531.4976984760474,
+    "W2": 1531.4976984760474,
+    "2": 1531.4976984760474,
+    "uw2": 1531.4976984760474,
+    "UVM2": 1360.083095675749,
+    "uvm2": 1360.083095675749,
+    "M2": 1360.083095675749,
+    "M": 1360.083095675749,
+    "um2": 1360.083095675749,
+    "UVW1": 1236.8527545450256,
+    "uvw1": 1236.8527545450256,
+    "W1": 1236.8527545450256,
+    "1": 1236.8527545450256,
+    "uw1": 1236.8527545450256,
+    "u": 849.2871562331687,
+    "u'": 849.2871562331687,
+    "up": 849.2871562331687,
+    "uprime": 849.2871562331687,
+    "U_S": 875.611103788721,
+    "s": 875.611103788721,
+    "us": 875.611103788721,
+    "U": 858.321721875779,
+    "B": 688.8500955332158,
+    "B_S": 696.7876979144597,
+    "b": 696.7876979144597,
+    "bs": 696.7876979144597,
+    "g": 648.9823425403824,
+    "g'": 648.9823425403824,
+    "gp": 648.9823425403824,
+    "gprime": 648.9823425403824,
+    "F475W": 648.9823425403824,
+    "g-DECam": 635.8015668464043,
+    "c": 580.1132515050684,
+    "cyan": 580.1132515050684,
+    "V": 548.3068934496129,
+    "V_S": 554.9815375506427,
+    "v": 554.9815375506427,
+    "vs": 554.9815375506427,
+    "Itagaki": 577.0861573682259,
+    "white": 30079.243284322874,
+    "unfilt.": 601.5655810567023,
+    "0": 601.5655810567023,
+    "C": 601.5655810567023,
+    "clear": 601.5655810567023,
+    "pseudobolometric": 601.5655810567023,
+    "griz": 601.5655810567023,
+    "RGB": 601.5655810567023,
+    "LGRB": 601.5655810567023,
+    "G": 518.6766845466752,
+    "Kepler": 519.5058608954615,
+    "TESS": 403.1881955125893,
+    "DLT40": 629.637672549936,
+    "Open": 629.637672549936,
+    "Clear": 629.637672549936,
+    "w": 520.8387777057242,
+    "o": 451.71177203298663,
+    "orange": 451.71177203298663,
+    "r": 489.2629992899134,
+    "r'": 489.2629992899134,
+    "rp": 489.2629992899134,
+    "rprime": 489.2629992899134,
+    "F625W": 489.2629992899134,
+    "r-DECam": 472.4459671948087,
+    "R": 471.26223689126897,
+    "Rc": 471.26223689126897,
+    "R_s": 471.26223689126897,
+    "i": 402.8409598867557,
+    "i'": 402.8409598867557,
+    "ip": 402.8409598867557,
+    "iprime": 402.8409598867557,
+    "F775W": 402.8409598867557,
+    "i-DECam": 386.62233825433924,
+    "I": 382.7915178046724,
+    "Ic": 382.7915178046724,
+    "z_s": 346.66628641927826,
+    "zs": 346.66628641927826,
+    "z": 337.7343708777923,
+    "z'": 337.7343708777923,
+    "zp": 337.7343708777923,
+    "zprime": 337.7343708777923,
+    "z-DECam": 328.753462451287,
+    "y": 312.24818210606065,
+    "y-DECam": 303.4727730182509,
+    "J": 239.862442505934,
+    "H": 185.33613196897403,
+    "K": 139.79431978859097,
+    "Ks": 139.79431978859097,
+    "F070W": 431.04176743403116,
+    "F090W": 336.17431986268366,
+    "F115W": 262.87628654288676,
+    "F150W": 201.94374815011136,
+    "F200W": 152.56522352568953,
+    "F277W": 110.05136786468209,
+    "F300M": 100.56915203596012,
+    "F335M": 89.41072625742719,
+    "F356W": 85.01984846997881,
+    "F360M": 82.9357933095218,
+    "F444W": 68.96667222373961,
+    "F560W": 53.67852315133938,
+    "F770W": 39.87175477126777,
+    "F1000W": 30.349460503852665,
+    "F1130W": 26.53952983680919,
+    "F1280W": 23.59741975845449,
+    "F1500W": 20.08679352819493,
+    "F1800W": 16.773842151606242,
+    "F2100W": 14.581938602646188,
+    "F2550W": 11.919267708332558,
+}
+
+# x-ray telescope areas for converting
+# NOTE: these are estimates from the links provided
+# Since this is inherently instrument dependent they are not entirely reliable
+# All are for 1-2 keV
+XRAY_AREAS = {
+    # https://swift.gsfc.nasa.gov/about_swift/Sci_Fact_Sheet.pdf
+    "swift": 135 * u.cm**2,
+    # https://heasarc.gsfc.nasa.gov/docs/rosat/ruh/handbook/node39.html#SECTION00634000000000000000
+    "rosat": 400 * u.cm**2,
+    # https://www.cosmos.esa.int/web/xmm-newton/technical-details-mirrors
+    "xmm": 1500 * u.cm**2,
+    "xmm slew": 1500 * u.cm**2,
+    "xmm pointed": 1500 * u.cm**2,
+    # https://cxc.harvard.edu/cdo/about_chandra
+    "chandra": 600 * u.cm**2,
+}
+
+# define a working base directory constant
+BASEDIR = os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
+DATADIR = os.path.join(BASEDIR, "data", "base")
+
+# Overarching schema that stops once we get down to a string or list
+schema = {
+    "schema_version": {"value": "0", "comment": "Copied from tde.space"},
+    "name": {"default_name": None, "alias": []},
+    "coordinate": [],
+    "distance": [],
+    "classification": [],
+    "reference_alias": [],
+    "date_reference": [],
+    "photometry": [],
+    "spectra": [],
+    "filter_alias": [],
+}
+
+
+# sub schemas that get filled into lists
+name_alias_schema = {"value": None, "reference": None}
+coordinate_schema = {
+    "ra": None,
+    "dec": None,
+    "l": None,
+    "b": None,
+    "lon": None,
+    "lat": None,
+    "ra_units": None,
+    "dec_units": None,
+    "l_units": None,
+    "b_units": None,
+    "lon_units": None,
+    "lat_units": None,
+    "ra_error": None,
+    "dec_error": None,
+    "l_error": None,
+    "b_error": None,
+    "lon_error": None,
+    "lat_error": None,
+    "epoch": None,
+    "frame": None,
+    "coord_type": None,
+    "computed": None,
+    "reference": None,
+    "default": None,
+}
+
+distance_schema = {
+    "value": None,
+    "unit": None,
+    "error": None,
+    "cosmology": None,
+    "reference": None,
+    "computed": None,
+    "uuid": None,
+    "default": None,
+    "distance_type": None,
+}
+
+classification_schema = {
+    "object_class": None,
+    "confidence": None,
+    "class_type": None,
+    "reference": None,
+    "default": None,
+}
+
+reference_alias_schema = {"name": None, "human_readable_name": None}
+
+date_reference_schema = {
+    "value": None,
+    "date_format": None,
+    "date_type": None,
+    "reference": None,
+    "computed": None,
+}
+
+photometry_schema = {
+    "raw": None,
+    "raw_err": None,
+    "raw_units": None,
+    "value": None,
+    "value_err": None,
+    "value_units": None,
+    "epoch_zeropoint": None,
+    "epoch_redshift": None,
+    "filter": None,
+    "filter_key": None,
+    "obs_type": None,
+    "telescope_area": None,
+    "date": None,
+    "date_format": None,
+    "date_err": None,
+    "ignore": None,
+    "upperlimit": None,
+    "sigma": None,
+    "sky": None,
+    "telescope": None,
+    "instrument": None,
+    "phot_type": None,
+    "exptime": None,
+    "aperature": None,
+    "observer": None,
+    "reducer": None,
+    "pipeline": None,
+    "corr_k": None,
+    "corr_av": None,
+    "corr_host": None,
+    "corr_hostav": None,
+    "val_k": None,
+    "val_s": None,
+    "val_av": None,
+    "val_host": None,
+    "val_hostav": None,
+}
+
+spectra_schema = {
+    "wavelength": None,
+    "wavelength_units": None,
+    "flux": None,
+    "fluxerr": None,
+    "raw": None,
+    "raw_err": None,
+    "sky": None,
+    "lamp": None,
+    "flux_units": None,
+    "telescope": None,
+    "instrument": None,
+    "date": None,
+    "date_format": None,
+    "date_err": None,
+    "exptime": None,
+    "slit": None,
+    "airmass": None,
+    "disperser": None,
+    "resolution": None,
+    "resolution_units": None,
+    "min_wave": None,
+    "max_wave": None,
+    "filter": None,
+    "filter_key": None,
+    "standard_name": None,
+    "ignore": None,
+    "spec_type": None,
+    "aperture": None,
+    "observer": None,
+    "reducer": None,
+    "pipeline": None,
+    "corr_k": None,
+    "corr_av": None,
+    "corr_host": None,
+    "corr_hostav": None,
+    "corr_flux": None,
+    "corr_phot": None,
+    "val_k": None,
+    "val_av": None,
+    "val_host": None,
+    "val_hostav": None,
+}
+
+filter_alias_schema = {
+    "filter_key": None,
+    "wave_eff": None,
+    "wave_min": None,
+    "wave_max": None,
+    "freq_eff": None,
+    "freq_min": None,
+    "freq_max": None,
+    "zp": None,
+    "wave_units": None,
+    "freq_units": None,
+    "zp_units": None,
+    "zp_system": None,
+}
+
+# package the subschemas by the key used for that location in the Transient object
+subschema = {
+    "name/alias": name_alias_schema,
+    "coordinate": coordinate_schema,
+    "distance": distance_schema,
+    "classification": classification_schema,
+    "reference_alias": reference_alias_schema,
+    "date_reference": date_reference_schema,
+    "photometry": photometry_schema,
+    "spectra": spectra_schema,
+    "filter_alias": filter_alias_schema,
+}