def plot_overview(cube='../nro_maps/12CO_20161002_FOREST-BEARS_spheroidal_xyb_grid7.5_0.099kms.fits',
region_file='../nro_maps/SouthShells.reg', mode='peak', plotname='12co_peak_shells.png',
interactive=False, show_shells=False):
"""
Show full image with all shells.
Parameters
----------
cube : str, optional
Description
region_file : str, optional
Description
mode : str, optional
Description
plotname : str, optional
Description
interactive : bool, optional
Description
show_shells : bool, optional
Description
"""
try:
cube = SpectralCube.read(cube)
except ValueError:
pass
if mode == "peak":
image = cube.max(axis=0)
fig = plt.figure()
wcs = WCS(image.header)
ax = WCSAxes(fig, [0.1,0.1,0.8,0.8], wcs=wcs)
fig.add_axes(ax)
imgplot = plt.imshow(image.data, cmap=cm.gray, origin='lower', interpolation='none',
vmin=0., vmax=100)
cb = plt.colorbar()
cb.set_label(r'K [T$_{MB}$]')
plt.title(r"$^{12}$CO Peak")
if show_shells:
r = pyregion.open(region_file).as_imagecoord(image.header)
patch_list, artist_list = r.get_mpl_patches_texts()
for p in patch_list:
ax.add_patch(p)
for t in artist_list:
ax.add_artist(t)
pass
if interactive:
plt.show()
else:
plt.savefig(plotname)
def test_curvilinear_grid_patches_image(self, generate):
fig = plt.figure(figsize=(8, 8))
ax = WCSAxes(fig, [0.1, 0.1, 0.8, 0.8], wcs=WCS(self.rosat_header), aspect='equal')
fig.add_axes(ax)
ax.set_xlim(-0.5, 479.5)
ax.set_ylim(-0.5, 239.5)
ax.grid(color='black', alpha=1.0, lw=1, linestyle='dashed')
p = Circle((300, 100), radius=40, ec='yellow', fc='none')
ax.add_patch(p)
p = Circle((30., 20.), radius=20., ec='orange', fc='none', transform=ax.get_transform('world'))
ax.add_patch(p)
p = Circle((60., 50.), radius=20., ec='red', fc='none', transform=ax.get_transform('fk5'))
ax.add_patch(p)
p = Circle((40., 60.), radius=20., ec='green', fc='none', transform=ax.get_transform('galactic'))
ax.add_patch(p)
self.generate_or_test(generate, fig, 'curvlinear_grid_patches_image.png')
def test_curvilinear_grid_patches_image(self, generate):
fig = plt.figure(figsize=(8, 8))
ax = WCSAxes(fig, [0.1, 0.1, 0.8, 0.8], wcs=WCS(self.rosat_header), aspect='equal')
fig.add_axes(ax)
ax.set_xlim(-0.5, 479.5)
ax.set_ylim(-0.5, 239.5)
ax.grid(color='black', alpha=1.0, lw=1, linestyle='dashed')
p = Circle((300, 100), radius=40, ec='yellow', fc='none')
ax.add_patch(p)
p = Circle((30., 20.), radius=20., ec='orange', fc='none', transform=ax.get_transform('world'))
ax.add_patch(p)
p = Circle((60., 50.), radius=20., ec='red', fc='none', transform=ax.get_transform('fk5'))
ax.add_patch(p)
p = Circle((40., 60.), radius=20., ec='green', fc='none', transform=ax.get_transform('galactic'))
ax.add_patch(p)
self.generate_or_test(generate, fig, 'curvlinear_grid_patches_image.png')
import pyregion
from astropy.io import fits
# read in the image
xray_name = "pspc_skyview.fits"
f_xray = fits.open(xray_name)
try:
from astropy.wcs import WCS
from wcsaxes import WCSAxes
wcs = WCS(f_xray[0].header)
fig = plt.figure()
ax = WCSAxes(fig, [0.1, 0.1, 0.8, 0.8], wcs=wcs)
fig.add_axes(ax)
except ImportError:
ax = plt.subplot(111)
ax.imshow(f_xray[0].data, cmap=cm.gray, vmin=0., vmax=0.00038, origin="lower")
reg_name = "test.reg"
r = pyregion.open(reg_name).as_imagecoord(f_xray[0].header)
patch_list, text_list = r.get_mpl_patches_texts()
for p in patch_list:
ax.add_patch(p)
for t in text_list:
ax.add_artist(t)
plt.show()
ax.imshow(f_xray[0].data, cmap=cm.gray, vmin=0., vmax=0.00038, origin="lower")
reg_name = "test.reg"
r = pyregion.open(reg_name).as_imagecoord(header=f_xray[0].header)
from pyregion.mpl_helper import properties_func_default
# Use custom function for patch attribute
def fixed_color(shape, saved_attrs):
attr_list, attr_dict = saved_attrs
attr_dict["color"] = "red"
kwargs = properties_func_default(shape, (attr_list, attr_dict))
return kwargs
# select region shape with tag=="Group 1"
r1 = pyregion.ShapeList([rr for rr in r if rr.attr[1].get("tag") == "Group 1"])
patch_list1, artist_list1 = r1.get_mpl_patches_texts(fixed_color)
r2 = pyregion.ShapeList([rr for rr in r if rr.attr[1].get("tag") != "Group 1"])
patch_list2, artist_list2 = r2.get_mpl_patches_texts()
for p in patch_list1 + patch_list2:
ax.add_patch(p)
for t in artist_list1 + artist_list2:
ax.add_artist(t)
plt.show()
def plot_state(directions_list, trim_names=True):
"""
Plots the facets of a run
"""
global midRA, midDec, fig, at, selected_direction
selected_direction = None
# Set up coordinate system and figure
points, midRA, midDec = factor.directions.getxy(directions_list)
fig = plt.figure(1, figsize=(10, 9))
if hasWCSaxes:
wcs = factor.directions.makeWCS(midRA, midDec)
ax = WCSAxes(fig, [0.16, 0.1, 0.8, 0.8], wcs=wcs)
fig.add_axes(ax)
else:
ax = plt.gca()
field_x = min(points[0])
field_y = max(points[1])
adjust_xy = True
while adjust_xy:
adjust_xy = False
for xy in points:
dist = np.sqrt((xy[0] - field_x)**2 + (xy[1] - field_y)**2)
if dist < 10.0:
field_x -= 1
field_y += 1
adjust_xy = True
break
field_ra, field_dec = factor.directions.xy2radec([field_x], [field_y],
refRA=midRA,
refDec=midDec)
field = Direction('field',
field_ra[0],
field_dec[0],
factor_working_dir=directions_list[0].working_dir)
directions_list.append(field)
ax.set_title('Overview of FACTOR run in\n{}'.format(
directions_list[0].working_dir))
# Plot facets
markers = []
for direction in directions_list:
if direction.name != 'field':
vertices = read_vertices(direction.vertices_file)
RAverts = vertices[0]
Decverts = vertices[1]
xverts, yverts = factor.directions.radec2xy(RAverts,
Decverts,
refRA=midRA,
refDec=midDec)
xyverts = [np.array([xp, yp]) for xp, yp in zip(xverts, yverts)]
mpl_poly = Polygon(np.array(xyverts),
edgecolor='#a9a9a9',
facecolor='#F2F2F2',
clip_box=ax.bbox,
picker=3.0,
linewidth=2)
else:
xverts = [field_x]
yverts = [field_y]
mpl_poly = Circle((field_x, field_y),
radius=5.0,
edgecolor='#a9a9a9',
facecolor='#F2F2F2',
clip_box=ax.bbox,
picker=3.0,
linewidth=2)
mpl_poly.facet_name = direction.name
mpl_poly.completed_ops = get_completed_ops(direction)
mpl_poly.started_ops = get_started_ops(direction)
mpl_poly.current_op = get_current_op(direction)
set_patch_color(mpl_poly, direction)
ax.add_patch(mpl_poly)
# Add facet names
if direction.name != 'field':
poly_tuple = tuple([(xp, yp) for xp, yp in zip(xverts, yverts)])
xmid = SPolygon(poly_tuple).centroid.x
ymid = SPolygon(poly_tuple).centroid.y
else:
xmid = field_x
ymid = field_y
if trim_names:
name = direction.name.split('_')[-1]
else:
name = direction.name
marker = ax.text(xmid,
ymid,
name,
color='k',
clip_on=True,
clip_box=ax.bbox,
ha='center',
va='bottom')
marker.set_zorder(1001)
markers.append(marker)
# Add info box
at = AnchoredText("Selected direction: None",
prop=dict(size=12),
frameon=True,
loc=3)
at.patch.set_boxstyle("round,pad=0.,rounding_size=0.2")
at.set_zorder(1002)
ax.add_artist(at)
ax.relim()
ax.autoscale()
ax.set_aspect('equal')
if hasWCSaxes:
RAAxis = ax.coords['ra']
RAAxis.set_axislabel('RA', minpad=0.75)
RAAxis.set_major_formatter('hh:mm:ss')
DecAxis = ax.coords['dec']
DecAxis.set_axislabel('Dec', minpad=0.75)
DecAxis.set_major_formatter('dd:mm:ss')
ax.coords.grid(color='black', alpha=0.5, linestyle='solid')
else:
plt.xlabel("RA (arb. units)")
plt.ylabel("Dec (arb. units)")
# Define coodinate formater to show RA and Dec under mouse pointer
ax.format_coord = formatCoord
# Show legend
not_processed_patch = plt.Rectangle((0, 0),
1,
1,
edgecolor='#a9a9a9',
facecolor='#F2F2F2',
linewidth=2)
processing_patch = plt.Rectangle((0, 0),
1,
1,
edgecolor='#a9a9a9',
facecolor='#F2F5A9',
linewidth=2)
selfcal_ok_patch = plt.Rectangle((0, 0),
1,
1,
edgecolor='#a9a9a9',
facecolor='#A9F5A9',
linewidth=2)
selfcal_not_ok_patch = plt.Rectangle((0, 0),
1,
1,
edgecolor='#a9a9a9',
facecolor='#F5A9A9',
linewidth=2)
l = ax.legend([
not_processed_patch, processing_patch, selfcal_ok_patch,
selfcal_not_ok_patch
], ['Unprocessed', 'Processing', 'Completed', 'Failed'])
l.set_zorder(1002)
# Add check for mouse clicks and key presses
fig.canvas.mpl_connect('pick_event', on_pick)
fig.canvas.mpl_connect('key_press_event', on_press)
# Add timer to update the plot every 60 seconds
timer = fig.canvas.new_timer(interval=60000)
timer.add_callback(update_plot)
timer.start()
# Show plot
plt.show()
plt.close(fig)
# Clean up any temp pyrap images
if os.path.exists('/tmp/tempimage'):
shutil.rmtree('/tmp/tempimage')
def plot_state(directions_list, trim_names=True):
"""
Plots the facets of a run
"""
global midRA, midDec, fig, at, selected_direction
selected_direction = None
# Set up coordinate system and figure
points, midRA, midDec = factor.directions.getxy(directions_list)
fig = plt.figure(1, figsize=(10,9))
if hasWCSaxes:
wcs = factor.directions.makeWCS(midRA, midDec)
ax = WCSAxes(fig, [0.16, 0.1, 0.8, 0.8], wcs=wcs)
fig.add_axes(ax)
else:
ax = plt.gca()
field_x = min(points[0])
field_y = max(points[1])
adjust_xy = True
while adjust_xy:
adjust_xy = False
for xy in points:
dist = np.sqrt( (xy[0] - field_x)**2 + (xy[1] - field_y)**2 )
if dist < 10.0:
field_x -= 1
field_y += 1
adjust_xy = True
break
field_ra, field_dec = factor.directions.xy2radec([field_x], [field_y],
refRA=midRA, refDec=midDec)
field = Direction('field', field_ra[0], field_dec[0],
factor_working_dir=directions_list[0].working_dir)
directions_list.append(field)
ax.set_title('Overview of FACTOR run in\n{}'.format(directions_list[0].working_dir))
# Plot facets
markers = []
for direction in directions_list:
if direction.name != 'field':
vertices = read_vertices(direction.vertices_file)
RAverts = vertices[0]
Decverts = vertices[1]
xverts, yverts = factor.directions.radec2xy(RAverts, Decverts,
refRA=midRA, refDec=midDec)
xyverts = [np.array([xp, yp]) for xp, yp in zip(xverts, yverts)]
mpl_poly = Polygon(np.array(xyverts), edgecolor='#a9a9a9', facecolor='#F2F2F2',
clip_box=ax.bbox, picker=3.0, linewidth=2)
else:
xverts = [field_x]
yverts = [field_y]
mpl_poly = Circle((field_x, field_y), radius=5.0, edgecolor='#a9a9a9', facecolor='#F2F2F2',
clip_box=ax.bbox, picker=3.0, linewidth=2)
mpl_poly.facet_name = direction.name
mpl_poly.completed_ops = get_completed_ops(direction)
mpl_poly.started_ops = get_started_ops(direction)
mpl_poly.current_op = get_current_op(direction)
set_patch_color(mpl_poly, direction)
ax.add_patch(mpl_poly)
# Add facet names
if direction.name != 'field':
poly_tuple = tuple([(xp, yp) for xp, yp in zip(xverts, yverts)])
xmid = SPolygon(poly_tuple).centroid.x
ymid = SPolygon(poly_tuple).centroid.y
else:
xmid = field_x
ymid = field_y
if trim_names:
name = direction.name.split('_')[-1]
else:
name = direction.name
marker = ax.text(xmid, ymid, name, color='k', clip_on=True,
clip_box=ax.bbox, ha='center', va='bottom')
marker.set_zorder(1001)
markers.append(marker)
# Add info box
at = AnchoredText("Selected direction: None", prop=dict(size=12), frameon=True,
loc=3)
at.patch.set_boxstyle("round,pad=0.,rounding_size=0.2")
at.set_zorder(1002)
ax.add_artist(at)
ax.relim()
ax.autoscale()
ax.set_aspect('equal')
if hasWCSaxes:
RAAxis = ax.coords['ra']
RAAxis.set_axislabel('RA', minpad=0.75)
RAAxis.set_major_formatter('hh:mm:ss')
DecAxis = ax.coords['dec']
DecAxis.set_axislabel('Dec', minpad=0.75)
DecAxis.set_major_formatter('dd:mm:ss')
ax.coords.grid(color='black', alpha=0.5, linestyle='solid')
else:
plt.xlabel("RA (arb. units)")
plt.ylabel("Dec (arb. units)")
# Define coodinate formater to show RA and Dec under mouse pointer
ax.format_coord = formatCoord
# Show legend
not_processed_patch = plt.Rectangle((0, 0), 1, 1, edgecolor='#a9a9a9',
facecolor='#F2F2F2', linewidth=2)
processing_patch = plt.Rectangle((0, 0), 1, 1, edgecolor='#a9a9a9',
facecolor='#F2F5A9', linewidth=2)
selfcal_ok_patch = plt.Rectangle((0, 0), 1, 1, edgecolor='#a9a9a9',
facecolor='#A9F5A9', linewidth=2)
selfcal_not_ok_patch =plt.Rectangle((0, 0), 1, 1, edgecolor='#a9a9a9',
facecolor='#F5A9A9', linewidth=2)
l = ax.legend([not_processed_patch, processing_patch, selfcal_ok_patch, selfcal_not_ok_patch],
['Unprocessed', 'Processing', 'Completed', 'Failed'])
l.set_zorder(1002)
# Add check for mouse clicks and key presses
fig.canvas.mpl_connect('pick_event', on_pick)
fig.canvas.mpl_connect('key_press_event', on_press)
# Add timer to update the plot every 60 seconds
timer = fig.canvas.new_timer(interval=60000)
timer.add_callback(update_plot)
timer.start()
# Show plot
plt.show()
plt.close(fig)
# Clean up any temp pyrap images
if not hasaplpy:
if os.path.exists('/tmp/tempimage'):
try:
shutil.rmtree('/tmp/tempimage')
except OSError:
pass
