# !usr/bin/env python
# -*- coding: utf-8 -*-
#
# Licensed under a 3-clause BSD license.
#
# @Author: Brian Cherinka
# @Date: 2018-10-11 17:51:43
# @Last modified by: Brian Cherinka
# @Last Modified time: 2018-11-29 17:23:15
from __future__ import print_function, division, absolute_import
import numpy as np
import astropy
import astropy.units as u
import marvin.tools
from marvin.tools.quantities.spectrum import Spectrum
from marvin.utils.general.general import get_drpall_table
from marvin.utils.plot.scatter import plot as scatplot
from .base import VACMixIn, VACTarget
[docs]class HIVAC(VACMixIn):
"""Provides access to the MaNGA-HI VAC.
VAC name: HI
URL: link
Description: Returns HI summary data and spectra
Authors: David Stark and Karen Masters
"""
# Required parameters
name = 'HI'
description = 'Returns HI summary data and spectra'
version = {'MPL-7': 'v1_0_1', 'DR15': 'v1_0_1', 'DR16': 'v1_0_2'}
# optional Marvin Tools to attach your vac to
include = (marvin.tools.cube.Cube, marvin.tools.maps.Maps, marvin.tools.modelcube.ModelCube)
# optional methods to attach to your main VAC tool in ~marvin.tools.vacs.VACs
add_methods = ['plot_mass_fraction']
# Required method
[docs] def set_summary_file(self, release):
''' Sets the path to the HI summary file '''
# define the variables to build a unique path to your VAC file
self.path_params = {'ver': self.version[release], 'type': 'all', 'program': 'GBT16A_095'}
# get_path returns False if the files do not exist locally
self.summary_file = self.get_path("mangahisum", path_params=self.path_params)
# Required method
[docs] def get_target(self, parent_object):
''' Accesses VAC data for a specific target from a Marvin Tool object '''
# get any parameters you need from the parent object
plateifu = parent_object.plateifu
# download the vac from the SAS if it does not already exist locally
if not self.file_exists(self.summary_file):
self.summary_file = self.download_vac('mangahisum', path_params=self.path_params)
# get path to ancillary VAC file for target HI spectra
self.update_path_params({'plateifu': plateifu})
specfile = self.get_path('mangahispectra', path_params=self.path_params)
# create container for more complex return data
hidata = HITarget(plateifu, vacfile=self.summary_file, specfile=specfile)
# get the spectral data for that row if it exists
if hidata._indata and not self.file_exists(specfile):
hidata._specfile = self.download_vac('mangahispectra', path_params=self.path_params)
return hidata
[docs]class HITarget(VACTarget):
''' A customized target class to also display HI spectra
This class handles data from both the HI summary file and the
individual spectral files. Row data from the summary file for the given target
is returned via the `data` property. Spectral data can be displayed via
the the `plot_spectrum` method.
Parameters:
targetid (str):
The plateifu or mangaid designation
vacfile (str):
The path of the VAC summary file
specfile (str):
The path to the HI spectra
Attributes:
data:
The target row data from the main VAC file
targetid (str):
The target identifier
'''
def __init__(self, targetid, vacfile, specfile=None):
super(HITarget, self).__init__(targetid, vacfile)
self._specfile = specfile
self._specdata = None
[docs] def plot_spectrum(self):
''' Plot the HI spectrum '''
if self._specfile:
if not self._specdata:
self._specdata = self._get_data(self._specfile)
vel = self._specdata['VHI'][0]
flux = self._specdata['FHI'][0]
spec = Spectrum(flux, unit=u.Jy, wavelength=vel,
wavelength_unit=u.km / u.s)
ax = spec.plot(
ylabel='HI\ Flux', xlabel='Velocity', title=self.targetid, ytrim='minmax'
)
return ax
return None
#
# Functions to become available on your VAC in marvin.tools.vacs.VACs
[docs]def plot_mass_fraction(vacdata_object):
''' Plot the HI mass fraction
Computes and plots the HI mass fraction using
the NSA elliptical Petrosian stellar mass from the
MaNGA DRPall file. Only plots data for subset of
targets in both the HI VAC and the DRPall file.
Parameters:
vacdata_object (object):
The `~.VACDataClass` instance of the HI VAC
Example:
>>> from marvin.tools.vacs import VACs
>>> v = VACs()
>>> hi = v.HI
>>> hi.plot_mass_fraction()
'''
drpall = get_drpall_table()
drpall.add_index('plateifu')
data = vacdata_object.data[1].data
subset = drpall.loc[data['plateifu']]
log_stmass = np.log10(subset['nsa_elpetro_mass'])
diff = data['logMHI'] - log_stmass
fig, axes = scatplot(
log_stmass,
diff,
with_hist=False,
ylim=[-5, 5],
xlabel=r'log $M_*$',
ylabel=r'log $M_{HI}/M_*$',
)
return axes[0]