def detect(self, channel, i_time, header, bins, bin_range):
"""
For a given timestep, map the intensity along the loop to the 3D field and
return the Hi-C data product.
Parameters
----------
channel : `dict`
i_time : `int`
header : `~sunpy.util.metadata.MetaDict`
bins : `~synthesizAR.util.SpatialPair`
bin_range : `~synthesizAR.util.SpatialPair`
Returns
-------
AIA data product : `~sunpy.map.Map`
"""
with h5py.File(self.counts_file, 'r') as hf:
weights = np.array(hf[channel['name']][i_time, :])
units = u.Unit(get_keys(hf[channel['name']].attrs, ('unit','units')))
hpc_coordinates = self.total_coordinates
dz = np.diff(bin_range.z)[0].cgs / bins.z * (1. * u.pixel)
visible = is_visible(hpc_coordinates, self.observer_coordinate)
hist, _, _ = np.histogram2d(hpc_coordinates.Tx.value, hpc_coordinates.Ty.value,
bins=(bins.x.value, bins.y.value),
range=(bin_range.x.value, bin_range.y.value),
weights=visible * weights * dz.value)
header['bunit'] = (units * dz.unit).to_string()
counts = gaussian_filter(hist.T, (channel['gaussian_width']['y'].value,
channel['gaussian_width']['x'].value))
return Map(counts.astype(np.float32), header)
def make_los_velocity_map(time: u.s, field, instr, **kwargs):
"""
Return map of LOS velocity at a given time for a given instrument resolution.
"""
plot_settings = {
'cmap': cm.get_cmap('bwr'),
'norm': colors.SymLogNorm(10, vmin=-1e8, vmax=1e8)
}
plot_settings.update(kwargs.get('plot_settings', {}))
bins, bin_range = instr.make_detector_array(field)
visible = is_visible(instr.total_coordinates, instr.observer_coordinate)
hist_coordinates, _, _ = np.histogram2d(instr.total_coordinates.Tx.value,
instr.total_coordinates.Ty.value,
bins=(bins.x.value, bins.y.value),
range=(bin_range.x.value,
bin_range.y.value),
weights=visible)
with h5py.File(instr.counts_file, 'r') as hf:
try:
i_time = np.where(
np.array(hf['time']) *
u.Unit(hf['time'].attrs['units']) == time)[0][0]
except IndexError:
raise IndexError(
f'{time} is not a valid time in observing time for {instr.name}'
)
v_x = u.Quantity(hf['velocity_x'][i_time, :],
hf['velocity_x'].attrs['units'])
v_y = u.Quantity(hf['velocity_y'][i_time, :],
hf['velocity_y'].attrs['units'])
v_z = u.Quantity(hf['velocity_z'][i_time, :],
hf['velocity_z'].attrs['units'])
v_los = instr.los_velocity(v_x, v_y, v_z)
hist, _, _ = np.histogram2d(instr.total_coordinates.Tx.value,
instr.total_coordinates.Ty.value,
bins=(bins.x.value, bins.y.value),
range=(bin_range.x.value, bin_range.y.value),
weights=v_los.value * visible)
hist /= np.where(hist_coordinates == 0, 1, hist_coordinates)
meta = instr.make_fits_header(field, instr.channels[0])
del meta['wavelnth']
del meta['waveunit']
meta['bunit'] = v_los.unit.to_string()
meta['detector'] = 'LOS Velocity'
meta['comment'] = 'LOS velocity calculated by synthesizAR'
return GenericMap(hist.T, meta, plot_settings=plot_settings)
def peek_fieldlines(magnetogram, fieldlines, **kwargs):
"""
Quick plot of streamlines overplotted on magnetogram
Parameters
----------
magnetogram : `~sunpy.map.Map`
fieldlines : `list`
"""
fig = plt.figure(figsize=kwargs.get('figsize', (8, 8)))
ax = fig.gca(projection=magnetogram)
# Plot map
norm = kwargs.get('norm', Normalize(vmin=-1.5e3, vmax=1.5e3))
magnetogram.plot(axes=ax,
title=False,
cmap=kwargs.get('cmap', 'hmimag'),
norm=norm)
# Grid
ax.grid(alpha=0.)
magnetogram.draw_grid(axes=ax,
grid_spacing=10 * u.deg,
alpha=0.75,
color='k')
# Lines
line_frequency = kwargs.get('line_frequency', 5)
for line in fieldlines[::line_frequency]:
try:
coord = line.transform_to(magnetogram.coordinate_frame)
except AttributeError:
# This try-catch is due to a bug where to convert out of an HEEQ frame
# one must first transform to a polar HGS frame
# FIXME: once this is fixed upstream in SunPy, this can be removed
coord = line.transform_to(HeliographicStonyhurst).transform_to(
magnetogram.coordinate_frame)
# Mask lines behind the solar disk
i_visible = np.where(is_visible(coord,
magnetogram.observer_coordinate))
coord_visible = SkyCoord(Tx=coord.Tx[i_visible],
Ty=coord.Ty[i_visible],
distance=coord.distance[i_visible],
frame=magnetogram.coordinate_frame)
ax.plot_coord(coord_visible,
'-',
color=kwargs.get('color', 'k'),
lw=kwargs.get('lw', 1),
alpha=kwargs.get('alpha', 0.5))
plt.show()
def make_temperature_map(time: u.s, field, instr, **kwargs):
"""
Return map of column-averaged electron temperature at a given time for a given instrument
resolution.
"""
plot_settings = {'cmap': cm.get_cmap('inferno')}
plot_settings.update(kwargs.get('plot_settings', {}))
bins, bin_range = instr.make_detector_array(field)
visible = is_visible(instr.total_coordinates, instr.observer_coordinate)
hist_coordinates, _, _ = np.histogram2d(instr.total_coordinates.Tx.value,
instr.total_coordinates.Ty.value,
bins=(bins.x.value, bins.y.value),
range=(bin_range.x.value,
bin_range.y.value),
weights=visible)
with h5py.File(instr.counts_file, 'r') as hf:
try:
i_time = np.where(
u.Quantity(hf['time'], get_keys(hf['time'].attrs), (
'unit', 'units')) == time)[0][0]
except IndexError:
raise IndexError(
f'{time} is not a valid time in observing time for {instr.name}'
)
weights = np.array(hf['electron_temperature'][i_time, :])
units = u.Unit(
get_keys(hf['electron_temperature'].attrs, ('unit', 'units')))
hist, _, _ = np.histogram2d(instr.total_coordinates.Tx.value,
instr.total_coordinates.Ty.value,
bins=(bins.x.value, bins.y.value),
range=(bin_range.x.value, bin_range.y.value),
weights=weights * visible)
hist /= np.where(hist_coordinates == 0, 1, hist_coordinates)
meta = instr.make_fits_header(field, instr.channels[0])
del meta['wavelnth']
del meta['waveunit']
meta['bunit'] = units.to_string()
meta['detector'] = 'Electron Temperature'
meta[
'comment'] = 'Column-averaged electron temperature calculated by synthesizAR'
return GenericMap(hist.T, meta, plot_settings=plot_settings)
def integrate_los(self, time, channel, skeleton, coordinates,
coordinates_centers):
client = distributed.get_client()
# Get Coordinates
coords = coordinates_centers.transform_to(self.projected_frame)
# Compute weights
i_time = np.where(time == self.observing_time)[0][0]
widths = np.concatenate(
[l.field_aligned_coordinate_width for l in skeleton.loops])
loop_area = np.concatenate(
[l.cross_sectional_area for l in skeleton.loops])
root = skeleton.loops[0].zarr_root
# NOTE: do this outside of the client.map call to make Dask happy
path = f'{{}}/{self.name}/{channel.name}'
kernels = np.concatenate(
client.gather(
client.map(
lambda l: root[path.format(l.name)][i_time, :],
skeleton.loops,
)))
unit_kernel = u.Unit(
root[f'{skeleton.loops[0].name}/{self.name}/{channel.name}'].
attrs['unit'])
area_ratio = (loop_area / self.pixel_area).decompose()
weights = area_ratio * widths * (kernels * unit_kernel)
visible = is_visible(coords, self.observer)
# Bin
bins, (blc, trc) = self.get_detector_array(coordinates)
hist, _, _ = np.histogram2d(
coords.Tx.value,
coords.Ty.value,
bins=bins,
range=((blc.Tx.value, trc.Tx.value), (blc.Ty.value, trc.Ty.value)),
weights=weights.value * visible,
)
header = self.get_header(channel, coordinates)
header['bunit'] = weights.unit.decompose().to_string()
header['date-obs'] = (self.observer.obstime + time).isot
return Map(hist.T, header)
def _detect(self, channel, i_time, header, bins, bin_range):
"""
For a given channel and timestep, map the intensity along the loop to the 3D field and
return the XRT data product.
Parameters
----------
channel : `dict`
i_time : `int`
header : `~sunpy.util.metadata.MetaDict`
bins : `SpatialPair`
bin_range : `SpatialPair`
Returns
-------
XRT data product : `~sunpy.Map`
"""
with h5py.File(self.counts_file, 'r') as hf:
weights = np.array(hf[channel['name']][i_time, :])
units = u.Unit(
get_keys(hf[channel['name']].attrs, ('unit', 'units')))
hpc_coordinates = self.total_coordinates
dz = np.diff(bin_range.z).cgs[0] / bins.z * (1. * u.pixel)
visible = is_visible(hpc_coordinates, self.observer_coordinate)
hist, _, _ = np.histogram2d(hpc_coordinates.Tx.value,
hpc_coordinates.Ty.value,
bins=(bins.x.value, bins.y.value),
range=(bin_range.x.value,
bin_range.y.value),
weights=visible * weights * dz.value)
header['bunit'] = (units * dz.unit).to_string()
if self.apply_psf:
counts = self.psf_smooth(hist.T, header)
return Map(counts, header)
def make_emission_measure_map(time: u.s,
field,
instr,
temperature_bin_edges=None,
**kwargs):
"""
Compute true emission meausure in each pixel as a function of electron temperature.
Parameters
----------
time : `~astropy.units.Quantity`
field : `~synthesizAR.Field`
instr : `~synthesizAR.instruments.InstrumentBase`
temperature_bin_edges : `~astropy.units.Quantity`
Other Parameters
----------------
plot_settings : `dict`
Returns
-------
`~synthesizAR.maps.EMCube`
"""
plot_settings = {
'cmap': cm.get_cmap('magma'),
'norm': colors.SymLogNorm(1, vmin=1e25, vmax=1e29)
}
plot_settings.update(kwargs.get('plot_settings', {}))
# read unbinned temperature and density
with h5py.File(instr.counts_file, 'r') as hf:
try:
i_time = np.where(
np.array(hf['time']) *
u.Unit(hf['time'].attrs['units']) == time)[0][0]
except IndexError:
raise IndexError(
f'{time} is not a valid time in observing time for {instr.name}'
)
unbinned_temperature = np.array(hf['electron_temperature'][i_time, :])
temperature_unit = u.Unit(hf['electron_temperature'].attrs['units'])
unbinned_density = np.array(hf['density'][i_time, :])
density_unit = u.Unit(hf['density'].attrs['units'])
# setup bin edges and weights
if temperature_bin_edges is None:
temperature_bin_edges = 10.**(np.arange(5.5, 7.5, 0.1)) * u.K
bins, bin_range = instr.make_detector_array(field)
x_bin_edges = (
np.diff(bin_range.x) / bins.x.value * np.arange(bins.x.value + 1) +
bin_range.x[0])
y_bin_edges = (
np.diff(bin_range.y) / bins.y.value * np.arange(bins.y.value + 1) +
bin_range.y[0])
dh = np.diff(bin_range.z).cgs[0] / bins.z * (1. * u.pixel)
visible = is_visible(instr.total_coordinates, instr.observer_coordinate)
emission_measure_weights = (unbinned_density**2) * dh * visible
# bin in x,y,T space with emission measure weights
xyT_coordinates = np.append(np.stack(
[instr.total_coordinates.Tx, instr.total_coordinates.Ty], axis=1),
unbinned_temperature[:, np.newaxis],
axis=1)
hist, _ = np.histogramdd(
xyT_coordinates,
bins=[x_bin_edges, y_bin_edges, temperature_bin_edges.value],
weights=emission_measure_weights)
meta_base = instr.make_fits_header(field, instr.channels[0])
del meta_base['wavelnth']
del meta_base['waveunit']
meta_base['detector'] = r'Emission measure'
meta_base['comment'] = 'LOS Emission Measure distribution'
em_unit = density_unit * density_unit * dh.unit
data = np.transpose(hist, (1, 0, 2)) * em_unit
return EMCube(data,
meta_base,
temperature_bin_edges,
plot_settings=plot_settings)