"""
Module with reading functionalities of color and magnitude
data from photometric and libraries.
"""
import os
from configparser import ConfigParser
from typing import Optional, Tuple
import h5py
import numpy as np
from typeguard import typechecked
from species.core.box import ColorColorBox, ColorMagBox, create_box
from species.read.read_spectrum import ReadSpectrum
from species.util.convert_util import apparent_to_absolute, parallax_to_distance
from species.util.core_util import print_section
[docs]
class ReadColorMagnitude:
"""
Class for reading color-magnitude data from the database.
"""
@typechecked
def __init__(
self, library: str, filters_color: Tuple[str, str], filter_mag: str
) -> None:
"""
Parameters
----------
library : str
Photometric ('vlm-plx' or 'leggett') or spectral ('irtf' or
'spex') library.
filters_color : tuple(str, str)
Filter names for the color. For a photometric library,
these have to be present in the database (typically in the
MKO, 2MASS, or WISE system). For a spectral library, any
filter names can be provided as long as they overlap with
the wavelength range of the spectra.
filter_mag : str
Filter name for the absolute magnitudes (see also
description of ``filters_color``).
Returns
-------
NoneType
None
"""
print_section("Read color-magnitude")
self.library = library
self.filters_color = filters_color
self.filter_mag = filter_mag
config_file = os.path.join(os.getcwd(), "species_config.ini")
config = ConfigParser()
config.read(config_file)
self.database = config["species"]["database"]
with h5py.File(self.database, "r") as hdf_file:
if "photometry" in hdf_file and self.library in hdf_file["photometry"]:
self.lib_type = "phot_lib"
elif "spectra" in hdf_file and self.library in hdf_file["spectra"]:
self.lib_type = "spec_lib"
else:
raise ValueError(
f"The '{self.library}' library is not present in the database."
)
print(f"Database tag: {self.library}")
print(f"Library type: {self.lib_type}")
print(f"Filters color: {self.filters_color}")
print(f"Filter magnitude: {self.filter_mag}")
[docs]
@typechecked
def get_color_magnitude(self, object_type: Optional[str] = None) -> ColorMagBox:
"""
Function for extracting color-magnitude data from the selected
library.
Parameters
----------
object_type : str, None
Object type for which the colors and magnitudes are
extracted. Either field dwarfs ('field') or
young/low-gravity objects ('young'). All objects are
selected if set to ``None``.
Returns
-------
species.core.box.ColorMagBox
Box with the colors and magnitudes.
"""
print_section("Get color-magnitude")
print(f"Object type: {object_type}")
if self.lib_type == "phot_lib":
with h5py.File(self.database, "r") as h5_file:
sptype = np.asarray(h5_file[f"photometry/{self.library}/sptype"])
parallax = np.asarray(h5_file[f"photometry/{self.library}/parallax"])
parallax_error = np.asarray(
h5_file[f"photometry/{self.library}/parallax_error"]
)
flag = np.asarray(h5_file[f"photometry/{self.library}/flag"])
obj_names = np.asarray(h5_file[f"photometry/{self.library}/name"])
for i in range(sptype.shape[0]):
if isinstance(sptype[i], bytes):
sptype[i] = sptype[i].decode("utf-8")
if isinstance(flag[i], bytes):
flag[i] = flag[i].decode("utf-8")
if isinstance(obj_names[i], bytes):
obj_names[i] = obj_names[i].decode("utf-8")
if object_type is None:
indices = np.arange(0, np.size(sptype), 1)
elif object_type == "field":
indices = np.where(flag == "null")[0]
elif object_type == "young":
indices = []
for j, object_flag in enumerate(flag):
if "young" in object_flag:
indices.append(j)
elif "lowg" in object_flag:
indices.append(j)
indices = np.array(indices)
if indices.size > 0:
with h5py.File(self.database, "r") as h5_file:
filter_list = []
for item in list(h5_file[f"photometry/{self.library}/MKO"]):
filter_list.append(f"MKO/{item}")
for item in list(h5_file[f"photometry/{self.library}/2MASS"]):
filter_list.append(f"2MASS/{item}")
for item in list(h5_file[f"photometry/{self.library}/Keck"]):
filter_list.append(f"Keck/{item}")
if f"photometry/{self.library}/{self.filters_color[0]}" in h5_file:
mag1 = np.asarray(
h5_file[
f"photometry/{self.library}/{self.filters_color[0]}"
]
)
else:
raise ValueError(
f"The '{self.filters_color[0]}' "
"filter is not available in the "
f"'{self.library}' library. Please "
"select any of the following "
f"filters: {filter_list}"
)
if f"photometry/{self.library}/{self.filters_color[1]}" in h5_file:
mag2 = np.asarray(
h5_file[
f"photometry/{self.library}/{self.filters_color[1]}"
]
)
else:
raise ValueError(
f"The '{self.filters_color[1]}' "
"filter is not available in the "
f"'{self.library}' library. Please "
"select any of the following "
f"filters: {filter_list}"
)
else:
raise ValueError(
f"There is not data available from '{self.library}' for "
f"'{object_type}' type objects with the chosen filters."
)
color = mag1 - mag2
distance = parallax_to_distance((parallax, parallax_error))
if self.filter_mag == self.filters_color[0]:
mag, _ = apparent_to_absolute((mag1, None), (distance[0], distance[1]))
elif self.filter_mag == self.filters_color[1]:
mag, _ = apparent_to_absolute((mag2, None), (distance[0], distance[1]))
else:
raise ValueError(
"The argument of filter_mag is set "
f"to {self.filter_mag} but should be "
"the same as one of the two values of "
"filters_color."
)
color = color[indices]
mag = mag[indices]
sptype = sptype[indices]
obj_names = obj_names[indices]
indices = []
for i in range(color.size):
if not np.isnan(color[i]) and not np.isnan(mag[i]):
indices.append(i)
colormag_box = create_box(
boxtype="colormag",
library=self.library,
object_type=object_type,
filters_color=self.filters_color,
filter_mag=self.filter_mag,
color=color[indices],
magnitude=mag[indices],
sptype=sptype[indices],
names=obj_names[indices],
)
elif self.lib_type == "spec_lib":
read_spec_0 = ReadSpectrum(
spec_library=self.library, filter_name=self.filters_color[0]
)
read_spec_1 = ReadSpectrum(
spec_library=self.library, filter_name=self.filters_color[1]
)
read_spec_2 = ReadSpectrum(
spec_library=self.library, filter_name=self.filter_mag
)
phot_box_0 = read_spec_0.get_magnitude(sptypes=None)
phot_box_1 = read_spec_1.get_magnitude(sptypes=None)
phot_box_2 = read_spec_2.get_magnitude(sptypes=None)
colormag_box = create_box(
boxtype="colormag",
library=self.library,
object_type=object_type,
filters_color=self.filters_color,
filter_mag=self.filter_mag,
color=phot_box_0.app_mag[:, 0] - phot_box_1.app_mag[:, 0],
magnitude=phot_box_2.abs_mag[:, 0],
sptype=phot_box_0.sptype,
names=None,
)
n_objects = len(colormag_box.sptype)
print(f"Returning ColorMagBox with {n_objects} objects")
return colormag_box
[docs]
class ReadColorColor:
"""
Class for reading color-color data from the database.
"""
@typechecked
def __init__(
self, library: str, filters_colors: Tuple[Tuple[str, str], Tuple[str, str]]
) -> None:
"""
Parameters
----------
library : str
Photometric ('vlm-plx' or 'leggett') or spectral ('irtf' or
'spex') library.
filters_colors : tuple(tuple(str, str), tuple(str, str))
Filter names for the colors. For a photometric library,
these have to be present in the database (typically in the
MKO, 2MASS, or WISE system). For a spectral library, any
filter names can be provided as long as they overlap with
the wavelength range of the spectra.
Returns
-------
NoneType
None
"""
print_section("Read color-magnitude")
self.library = library
self.filters_colors = filters_colors
config_file = os.path.join(os.getcwd(), "species_config.ini")
config = ConfigParser()
config.read(config_file)
self.database = config["species"]["database"]
with h5py.File(self.database, "r") as hdf_file:
if "photometry" in hdf_file and self.library in hdf_file["photometry"]:
self.lib_type = "phot_lib"
elif "spectra" in hdf_file and self.library in hdf_file["spectra"]:
self.lib_type = "spec_lib"
else:
raise ValueError(
f"The '{self.library}' library is not present in the database."
)
print(f"Database tag: {self.library}")
print(f"Library type: {self.lib_type}")
print(f"Filters colors: {self.filters_colors}")
[docs]
@typechecked
def get_color_color(self, object_type: Optional[str] = None) -> ColorColorBox:
"""
Function for extracting color-color data from the selected
library.
Parameters
----------
object_type : str, None
Object type for which the colors and magnitudes are
extracted. Either field dwarfs ('field') or
young/low-gravity objects ('young'). All objects are
selected if set to ``None``.
Returns
-------
species.core.box.ColorColorBox
Box with the colors.
"""
print_section("Get color-magnitude")
print(f"Object type: {object_type}")
if self.lib_type == "phot_lib":
h5_file = h5py.File(self.database, "r")
sptype = np.asarray(h5_file[f"photometry/{self.library}/sptype"])
flag = np.asarray(h5_file[f"photometry/{self.library}/flag"])
obj_names = np.asarray(h5_file[f"photometry/{self.library}/name"])
if object_type is None:
indices = np.arange(0, np.size(sptype), 1)
elif object_type == "field":
indices = np.where(flag == "null")[0]
elif object_type == "young":
indices = []
for j, object_flag in enumerate(flag):
if "young" in object_flag:
indices.append(j)
elif "lowg" in object_flag:
indices.append(j)
indices = np.array(indices)
mag1 = np.asarray(
h5_file[f"photometry/{self.library}/{self.filters_colors[0][0]}"]
)
mag2 = np.asarray(
h5_file[f"photometry/{self.library}/{self.filters_colors[0][1]}"]
)
mag3 = np.asarray(
h5_file[f"photometry/{self.library}/{self.filters_colors[1][0]}"]
)
mag4 = np.asarray(
h5_file[f"photometry/{self.library}/{self.filters_colors[1][1]}"]
)
color1 = mag1 - mag2
color2 = mag3 - mag4
color1 = color1[indices]
color2 = color2[indices]
sptype = sptype[indices]
obj_names = obj_names[indices]
indices = []
for i in range(color1.size):
if not np.isnan(color1[i]) and not np.isnan(color2[i]):
indices.append(i)
colorbox = create_box(
boxtype="colorcolor",
library=self.library,
object_type=object_type,
filters=self.filters_colors,
color1=color1[indices],
color2=color2[indices],
sptype=sptype[indices],
names=obj_names[indices],
)
h5_file.close()
elif self.lib_type == "spec_lib":
read_spec_0 = ReadSpectrum(
spec_library=self.library, filter_name=self.filters_colors[0][0]
)
read_spec_1 = ReadSpectrum(
spec_library=self.library, filter_name=self.filters_colors[0][1]
)
read_spec_2 = ReadSpectrum(
spec_library=self.library, filter_name=self.filters_colors[1][0]
)
read_spec_3 = ReadSpectrum(
spec_library=self.library, filter_name=self.filters_colors[1][1]
)
phot_box_0 = read_spec_0.get_magnitude(sptypes=None)
phot_box_1 = read_spec_1.get_magnitude(sptypes=None)
phot_box_2 = read_spec_2.get_magnitude(sptypes=None)
phot_box_3 = read_spec_3.get_magnitude(sptypes=None)
colorbox = create_box(
boxtype="colorcolor",
library=self.library,
object_type=object_type,
filters=self.filters_colors,
color1=phot_box_0.app_mag[:, 0] - phot_box_1.app_mag[:, 0],
color2=phot_box_2.app_mag[:, 0] - phot_box_3.app_mag[:, 0],
sptype=phot_box_0.sptype,
names=None,
)
n_objects = len(colorbox.sptype)
print(f"Returning ColorColorBox with {n_objects} objects")
return colorbox
