def plot(LSM, fileName=None, labelBy=None):
"""
Shows a simple plot of the sky model.
The circles in the plot are scaled with flux. If the sky model is grouped
into patches, sources are colored by patch and the patch positions are
indicated with stars.
Parameters
----------
LSM : SkyModel object
Input sky model
fileName : str, optional
If given, the plot is saved to a file instead of displayed
labelBy : str, optional
One of 'source' or 'patch': label points using source names ('source') or
patch names ('patch')
Examples:
---------
Plot and display to the screen::
>>> LSM = lsmtool.load('sky.model')
>>> plot(LSM)
Plot and save to a PDF file::
>>> plot(LSM, 'sky_plot.pdf')
"""
try:
import os
if 'DISPLAY' not in os.environ:
import matplotlib
if matplotlib.get_backend() is not 'Agg':
matplotlib.use("Agg")
import matplotlib.pyplot as plt
from matplotlib.ticker import FuncFormatter
except Exception as e:
raise ImportError('PyPlot could not be imported. Plotting is not '
'available: {0}'.format(e.message))
try:
try:
from astropy.visualization.wcsaxes import WCSAxes
hasWCSaxes = True
except:
from wcsaxes import WCSAxes
hasWCSaxes = True
except:
hasWCSaxes = False
import numpy as np
from ..operations_lib import radec2xy, makeWCS
global midRA, midDec, ymin, xmin
if len(LSM) == 0:
log.error('Sky model is empty.')
return
fig = plt.figure(1, figsize=(7.66, 7))
plt.clf()
x, y, midRA, midDec = LSM._getXY()
if hasWCSaxes:
wcs = makeWCS(midRA, midDec)
ax = WCSAxes(fig, [0.16, 0.1, 0.8, 0.8], wcs=wcs)
fig.add_axes(ax)
else:
ax = plt.gca()
if LSM.hasPatches:
nsrc = len(LSM.getPatchNames())
else:
nsrc = len(LSM)
sm = plt.cm.ScalarMappable(cmap=plt.cm.Set3,
norm=plt.Normalize(vmin=0, vmax=nsrc))
sm._A = []
# Set symbol sizes by flux, making sure no symbol is smaller than 50 or
# larger than 1000
s = []
fluxes = LSM.getColValues('I')
if len(fluxes[fluxes > 0.0]) == 0:
minflux = 0.0
else:
minflux = np.min(fluxes[fluxes > 0.0])
for flux in LSM.getColValues('I'):
if flux > 0.0:
s.append(min(1000.0,
(1.0 + 2.0 * np.log10(flux / minflux)) * 50.0))
else:
s.append(50.0)
# Color sources by patch if grouped
c = [0] * len(LSM)
cp = []
if LSM.hasPatches:
for p, patchName in enumerate(LSM.getPatchNames()):
indices = LSM.getRowIndex(patchName)
cp.append(sm.to_rgba(p))
for ind in indices:
c[ind] = sm.to_rgba(p)
else:
c = [sm.to_rgba(0)] * nsrc
# Plot sources
if hasWCSaxes:
RA = LSM.getColValues('Ra')
Dec = LSM.getColValues('Dec')
ax.set_xlim(np.min(x) - 20, np.max(x) + 20)
ax.set_ylim(np.min(y) - 20, np.max(y) + 20)
plt.scatter(x, y, s=s, c=c)
if LSM.hasPatches:
RAp, Decp = LSM.getPatchPositions(asArray=True)
goodInd = np.where((RAp != 0.0) & (Decp != 0.0))
if len(goodInd[0]) < len(RAp):
log.info('Some patch positions are unset. Run setPatchPositions() '
'before plotting to see patch positions and patch names.')
xp, yp = radec2xy(RAp[goodInd], Decp[goodInd], midRA, midDec)
plt.scatter(xp, yp, s=100, c=cp, marker='*')
# Set axis labels, etc.
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)")
if labelBy is not None:
if labelBy.lower() == 'source':
labels = LSM.getColValues('name')
xls = x
yls = y
elif labelBy.lower() == 'patch':
if LSM.hasPatches:
labels = LSM.getPatchNames()
xls = xp
yls = yp
else:
labels = LSM.getColValues('name')
xls = x
yls = y
else:
raise ValueError(
"The lableBy parameter must be one of 'source' or "
"'patch'.")
for label, xl, yl in zip(labels, xls, yls):
plt.annotate(label,
xy=(xl, yl),
xytext=(-2, 2),
textcoords='offset points',
ha='right',
va='bottom')
# Define coodinate formater to show RA and Dec under mouse pointer
RAformatter = FuncFormatter(RAtickformatter)
ax.format_coord = formatCoord
if fileName is not None:
plt.savefig(fileName)
else:
plt.show()
plt.close(fig)
def plot_state(directions_list, trim_names=True):
"""
Plots the facets of a run
"""
global midRA, midDec, fig, at, selected_direction, choose_from_list
selected_direction = None
choose_from_list = False
# 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='#A4A4A4', linewidth=2)
processing_error = plt.Rectangle((0, 0), 1, 1, edgecolor='#a9a9a9',
facecolor='#F5A9A9', linewidth=2)
patch_list=[not_processed_patch, processing_patch, processing_error, selfcal_not_ok_patch, selfcal_ok_patch]
label_list=['Unprocessed', 'Processing', 'Pipeline Error', 'Selfcal Failed', 'Selfcal OK']
for i in range(options['reimages']):
label_list.append('Image '+str(i+1))
color=(0.66/(i+2)**0.5, 0.96/(i+2)**0.5, 0.66/(i+2)**0.5, 1.0)
reimage_patch=plt.Rectangle((0, 0), 1, 1, edgecolor='#a9a9a9',
facecolor=color, linewidth=2)
patch_list.append(reimage_patch)
l = ax.legend(patch_list, label_list, loc="upper right")
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 casacore images
if not hasaplpy:
if os.path.exists('/tmp/tempimage'):
try:
shutil.rmtree('/tmp/tempimage')
except OSError:
pass
def plot_state(directions_list, trim_names=True):
"""
Plots the facets of a run
"""
global midRA, midDec, fig, at, selected_direction, choose_from_list
selected_direction = None
choose_from_list = False
# 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='#A4A4A4',
linewidth=2)
processing_error = plt.Rectangle((0, 0),
1,
1,
edgecolor='#a9a9a9',
facecolor='#F5A9A9',
linewidth=2)
patch_list = [
not_processed_patch, processing_patch, processing_error,
selfcal_not_ok_patch, selfcal_ok_patch
]
label_list = [
'Unprocessed', 'Processing', 'Pipeline Error', 'Selfcal Failed',
'Selfcal OK'
]
for i in range(options['reimages']):
label_list.append('Image ' + str(i + 1))
color = (0.66 / (i + 2)**0.5, 0.96 / (i + 2)**0.5, 0.66 / (i + 2)**0.5,
1.0)
reimage_patch = plt.Rectangle((0, 0),
1,
1,
edgecolor='#a9a9a9',
facecolor=color,
linewidth=2)
patch_list.append(reimage_patch)
l = ax.legend(patch_list, label_list, loc="upper right")
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 casacore images
if not hasaplpy:
if os.path.exists('/tmp/tempimage'):
try:
shutil.rmtree('/tmp/tempimage')
except OSError:
pass
def plot(LSM, fileName=None, labelBy=None):
"""
Shows a simple plot of the sky model.
The circles in the plot are scaled with flux. If the sky model is grouped
into patches, sources are colored by patch and the patch positions are
indicated with stars.
Parameters
----------
LSM : SkyModel object
Input sky model
fileName : str, optional
If given, the plot is saved to a file instead of displayed
labelBy : str, optional
One of 'source' or 'patch': label points using source names ('source') or
patch names ('patch')
Examples:
---------
Plot and display to the screen::
>>> LSM = lsmtool.load('sky.model')
>>> plot(LSM)
Plot and save to a PDF file::
>>> plot(LSM, 'sky_plot.pdf')
"""
try:
import os
if 'DISPLAY' not in os.environ:
import matplotlib
if matplotlib.get_backend() is not 'Agg':
matplotlib.use("Agg")
import matplotlib.pyplot as plt
from matplotlib.ticker import FuncFormatter
except Exception as e:
raise ImportError('PyPlot could not be imported. Plotting is not '
'available: {0}'.format(e.message))
try:
try:
from astropy.visualization.wcsaxes import WCSAxes
hasWCSaxes = True
except:
from wcsaxes import WCSAxes
hasWCSaxes = True
except:
hasWCSaxes = False
import numpy as np
from ..operations_lib import radec2xy, makeWCS
global midRA, midDec, ymin, xmin
if len(LSM) == 0:
log.error('Sky model is empty.')
return
fig = plt.figure(1,figsize=(7.66,7))
plt.clf()
x, y, midRA, midDec = LSM._getXY()
if hasWCSaxes:
wcs = makeWCS(midRA, midDec)
ax = WCSAxes(fig, [0.16, 0.1, 0.8, 0.8], wcs=wcs)
fig.add_axes(ax)
else:
ax = plt.gca()
if LSM.hasPatches:
nsrc = len(LSM.getPatchNames())
else:
nsrc = len(LSM)
sm = plt.cm.ScalarMappable(cmap=plt.cm.Set3, norm=plt.Normalize(vmin=0,
vmax=nsrc))
sm._A = []
# Set symbol sizes by flux, making sure no symbol is smaller than 50 or
# larger than 1000
s = []
fluxes = LSM.getColValues('I')
if len(fluxes[fluxes > 0.0]) == 0:
minflux = 0.0
else:
minflux = np.min(fluxes[fluxes > 0.0])
for flux in LSM.getColValues('I'):
if flux > 0.0:
s.append(min(1000.0, (1.0+2.0*np.log10(flux/minflux))*50.0))
else:
s.append(50.0)
# Color sources by patch if grouped
c = [0]*len(LSM)
cp = []
if LSM.hasPatches:
for p, patchName in enumerate(LSM.getPatchNames()):
indices = LSM.getRowIndex(patchName)
cp.append(sm.to_rgba(p))
for ind in indices:
c[ind] = sm.to_rgba(p)
else:
c = [sm.to_rgba(0)] * nsrc
# Plot sources
if hasWCSaxes:
RA = LSM.getColValues('Ra')
Dec = LSM.getColValues('Dec')
ax.set_xlim(np.min(x)-20, np.max(x)+20)
ax.set_ylim(np.min(y)-20, np.max(y)+20)
plt.scatter(x, y, s=s, c=c)
if LSM.hasPatches:
RAp, Decp = LSM.getPatchPositions(asArray=True)
goodInd = np.where( (RAp != 0.0) & (Decp != 0.0) )
if len(goodInd[0]) < len(RAp):
log.info('Some patch positions are unset. Run setPatchPositions() '
'before plotting to see patch positions and patch names.')
xp, yp = radec2xy(RAp[goodInd], Decp[goodInd], midRA, midDec)
plt.scatter(xp, yp, s=100, c=cp, marker='*')
# Set axis labels, etc.
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)")
if labelBy is not None:
if labelBy.lower() == 'source':
labels = LSM.getColValues('name')
xls = x
yls = y
elif labelBy.lower() == 'patch':
if LSM.hasPatches:
labels = LSM.getPatchNames()
xls = xp
yls = yp
else:
labels = LSM.getColValues('name')
xls = x
yls = y
else:
raise ValueError("The lableBy parameter must be one of 'source' or "
"'patch'.")
for label, xl, yl in zip(labels, xls, yls):
plt.annotate(label, xy = (xl, yl), xytext = (-2, 2), textcoords=
'offset points', ha='right', va='bottom')
# Define coodinate formater to show RA and Dec under mouse pointer
RAformatter = FuncFormatter(RAtickformatter)
ax.format_coord = formatCoord
if fileName is not None:
plt.savefig(fileName)
else:
plt.show()
plt.close(fig)