import warnings
import numpy as np
from astropy import table
from matplotlib.colors import cnames
from specutils import Spectrum1D
from jdaviz.core.events import SpectralMarksChangedMessage, LineIdentifyMessage
from jdaviz.core.registries import viewer_registry
from jdaviz.core.marks import SpectralLine
from jdaviz.core.linelists import load_preset_linelist, get_available_linelists
from jdaviz.core.freezable_state import FreezableProfileViewerState
from jdaviz.configs.default.plugins.viewers import JdavizProfileView
__all__ = ['SpecvizProfileView']
[docs]
@viewer_registry("specviz-profile-viewer", label="Profile 1D (Specviz)")
class SpecvizProfileView(JdavizProfileView):
# categories: zoom resets, zoom, pan, subset, select tools, shortcuts
tools_nested = [
['jdaviz:homezoom', 'jdaviz:prevzoom'],
['jdaviz:boxzoom', 'jdaviz:xrangezoom', 'jdaviz:yrangezoom'],
['jdaviz:panzoom', 'jdaviz:panzoom_x', 'jdaviz:panzoom_y'],
['bqplot:xrange'],
['jdaviz:selectline'],
['jdaviz:sidebar_plot', 'jdaviz:sidebar_export']
]
default_class = Spectrum1D
spectral_lines = None
_state_cls = FreezableProfileViewerState
_default_profile_subset_type = 'spectral'
@property
def redshift(self):
return self.jdaviz_helper._redshift
[docs]
def load_line_list(self, line_table, replace=False, return_table=False, show=True):
# If string, load the named preset list and don't show by default
# since there might be too many lines
if isinstance(line_table, str):
self.load_line_list(load_preset_linelist(line_table),
replace=replace, return_table=return_table,
show=False)
return
elif not isinstance(line_table, table.QTable):
raise TypeError("Line list must be an astropy QTable with\
(minimally) 'linename' and 'rest' columns")
if "linename" not in line_table.columns:
raise ValueError("Line table must have a 'linename' column'")
if "rest" not in line_table.columns:
raise ValueError("Line table must have a 'rest' column'")
if np.any(line_table['rest'] <= 0):
raise ValueError("all rest values must be positive")
# Use the redshift of the displayed spectrum if no redshifts are specified
if "redshift" in line_table.colnames:
warnings.warn("per line/list redshifts not supported, use viz.set_redshift")
# Set whether to show all of the lines on the plot by default on load
# We convert bool to int to work around ipywidgets json serialization
line_table["show"] = int(show)
# If there is already a loaded table, convert units to match. This
# attempts to do some sane rounding after the unit conversion.
# TODO: Fix this so that things don't get rounded to 0 in some cases
"""
if self.spectral_lines is not None:
sig_figs = []
for row in line_table:
rest_str = str(row["rest"].value).replace(".", "").split("e")[0]
sig_figs.append(len(rest_str))
line_table["rest"] = line_table["rest"].to(self.spectral_lines["rest"].unit)
line_table["sig_figs"] = sig_figs
for row in line_table:
row["rest"] = row["rest"].round(row["sig_figs"])
del line_table["sig_figs"]
"""
# Combine name and rest value for indexing
if "name_rest" not in line_table.colnames:
line_table["name_rest"] = None
for row in line_table:
row["name_rest"] = "{} {}".format(row["linename"], row["rest"].value)
# If no name was given to this list, consider it part of the "Custom" list
if "listname" not in line_table.colnames:
line_table["listname"] = "Custom"
else:
for row in line_table:
if row["listname"] is None:
row["listname"] = "Custom"
# Convert colors to hexa values, or set to default (red)
if "colors" not in line_table.colnames:
line_table["colors"] = "#FF0000FF"
else:
for row in line_table:
if row["colors"][0] == "#":
if len(row["colors"]) == 6:
row["colors"] += "FF"
else:
row["colors"] = cnames[row["colors"]] + "FF"
# Create or update the main spectral_lines astropy table
if self.spectral_lines is None or replace:
self.spectral_lines = line_table
else:
self.spectral_lines = table.vstack([self.spectral_lines, line_table])
self.spectral_lines = table.unique(self.spectral_lines, keys='name_rest')
# It seems that we need to recreate this index after v-stacking.
self.spectral_lines.add_index("name_rest")
self.spectral_lines.add_index("linename")
self.spectral_lines.add_index("listname")
self._broadcast_plotted_lines()
if return_table:
return line_table
def _broadcast_plotted_lines(self, marks=None):
if marks is None:
marks = [x for x in self.figure.marks if isinstance(x, SpectralLine)]
msg = SpectralMarksChangedMessage(marks, sender=self)
self.session.hub.broadcast(msg)
if not np.any([mark.identify for mark in marks]):
# then clear the identified entry
msg = LineIdentifyMessage(name_rest='', sender=self)
self.session.hub.broadcast(msg)
[docs]
def erase_spectral_lines(self, name=None, name_rest=None, show_none=True):
"""
Erase either all spectral lines, all spectral lines sharing the same
name (e.g. 'He II') or a specific name-rest value combination (e.g.
'HE II 1640.5', stored in SpectralLine as 'table_index').
"""
fig = self.figure
if name is None and name_rest is None:
fig.marks = [x for x in fig.marks if not isinstance(x, SpectralLine)]
if show_none:
self.spectral_lines["show"] = False
self._broadcast_plotted_lines([])
else:
temp_marks = []
# Toggle "show" value in main astropy table. The astropy table
# machinery only allows updating a single row at a time.
if name_rest is not None:
if isinstance(name_rest, str):
self.spectral_lines.loc[name_rest]["show"] = False
elif isinstance(name_rest, list):
for nr in name_rest:
self.spectral_lines.loc[nr]["show"] = False
# Get rid of the marks we no longer want
for x in fig.marks:
if isinstance(x, SpectralLine):
if name is not None:
self.spectral_lines.loc[name]["show"] = False
if x.name == name:
continue
else:
if isinstance(name_rest, str):
if x.table_index == name_rest:
continue
elif isinstance(name_rest, list):
if x.table_index in name_rest:
continue
temp_marks.append(x)
fig.marks = temp_marks
self._broadcast_plotted_lines()
[docs]
def plot_spectral_line(self, line, global_redshift=None, plot_units=None, **kwargs):
if isinstance(line, str):
# Try the full index first (for backend calls), otherwise name only
try:
line = self.spectral_lines.loc[line]
except KeyError:
line = self.spectral_lines.loc["linename", line]
if plot_units is None:
plot_units = self.data()[0].spectral_axis.unit
if global_redshift is None:
redshift = self.redshift
else:
redshift = global_redshift
line_mark = SpectralLine(self,
line['rest'].to_value(plot_units),
redshift,
name=line["linename"],
table_index=line["name_rest"],
colors=[line["colors"]], **kwargs)
# Erase this line if it already existed, to avoid duplication
self.erase_spectral_lines(name_rest=line["name_rest"])
self.figure.marks = self.figure.marks + [line_mark]
line["show"] = True
self._broadcast_plotted_lines()
[docs]
def plot_spectral_lines(self, colors=["blue"], global_redshift=None, **kwargs):
"""
Plots a user-provided astropy table of spectral lines in the viewer.
"""
fig = self.figure
self.erase_spectral_lines(show_none=False)
# Check to see if colors were defined for each line
if "colors" in self.spectral_lines.columns:
colors = self.spectral_lines["colors"]
elif len(colors) != len(self.spectral_lines):
colors = colors*len(self.spectral_lines)
lines = self.spectral_lines
plot_units = self.data()[0].spectral_axis.unit
if global_redshift is None:
redshift = self.redshift
else:
redshift = global_redshift
marks = []
for line, color in zip(lines, colors):
if not line["show"]:
continue
line = SpectralLine(self,
line['rest'].to_value(plot_units),
redshift,
name=line["linename"],
table_index=line["name_rest"],
colors=[color], **kwargs)
marks.append(line)
fig.marks = fig.marks + marks
self._broadcast_plotted_lines()
[docs]
def available_linelists(self):
return get_available_linelists()
