def create_patches(self):
"""
This function ...
:return:
"""
colors = iter(pretty_colors)
# Loop over the geometries
for label in self.geometries:
geometry = self.geometries[label]
x_center = 0.0
y_center = 0.0
major = None # 2 * major axis radius
minor = None # 2 * minor axis radius
angle = None # in degrees
if isinstance(geometry, SersicModel3D):
major = 2.0 * geometry.effective_radius.to("pc").value
minor = geometry.z_flattening * major
angle = geometry.tilt.to("deg").value
elif isinstance(geometry, ExponentialDiskModel3D):
major = 2.0 * geometry.radial_scale.to("pc").value
minor = 2.0 * geometry.axial_scale.to("pc").value
angle = geometry.tilt.to("deg").value
elif isinstance(geometry, DeprojectionModel3D):
minor = 2.0 * geometry.scale_height.to("pc").value
major = 0.3 * (geometry.pixelscale *
geometry.x_size).to("pc").value
angle = 0.0
if self._min_x is None or 0.5 * major > abs(self._min_x):
self._min_x = -0.5 * major
if self._max_x is None or 0.5 * major > self._max_x:
self._max_x = 0.5 * major
if self._min_y is None or 0.5 * minor > abs(self._min_y):
self._min_y = -0.5 * minor
if self._max_y is None or 0.5 * minor > self._max_y:
self._max_y = 0.5 * minor
# Create the patch
color = next(colors)
ell = plt_Ellipse((x_center, y_center),
major,
minor,
angle,
edgecolor='none',
facecolor=color,
lw=3,
alpha=0.7)
# Add the patch
self.patches[label] = ell
def to_mpl_patch(self):
"""
This function ...
:return:
"""
from matplotlib.patches import Ellipse as plt_Ellipse
return plt_Ellipse((self.center.x, self.center.y), 2.0 * self.radius.x, 2.0 * self.radius.y, self.angle.to("deg").value, edgecolor="red", facecolor="none", lw=5)
def create_patches(self):
"""
This function ...
:return:
"""
colors = iter(pretty_colors)
# Loop over the geometries
for label in self.geometries:
geometry = self.geometries[label]
x_center = 0.0
y_center = 0.0
major = None # 2 * major axis radius
minor = None # 2 * minor axis radius
angle = None # in degrees
if isinstance(geometry, SersicModel3D):
major = 2.0 * geometry.effective_radius.to("pc").value
minor = geometry.z_flattening * major
angle = geometry.tilt.to("deg").value
elif isinstance(geometry, ExponentialDiskModel3D):
major = 2.0 * geometry.radial_scale.to("pc").value
minor = 2.0 * geometry.axial_scale.to("pc").value
angle = geometry.tilt.to("deg").value
elif isinstance(geometry, DeprojectionModel3D):
minor = 2.0 * geometry.scale_height.to("pc").value
major = 0.3 * (geometry.pixelscale * geometry.x_size).to("pc").value
angle = 0.0
if self._min_x is None or 0.5*major > abs(self._min_x): self._min_x = - 0.5*major
if self._max_x is None or 0.5*major > self._max_x: self._max_x = 0.5*major
if self._min_y is None or 0.5*minor > abs(self._min_y): self._min_y = - 0.5*minor
if self._max_y is None or 0.5*minor > self._max_y: self._max_y = 0.5*minor
# Create the patch
color = next(colors)
ell = plt_Ellipse((x_center, y_center), major, minor, angle, edgecolor='none', facecolor=color, lw=3, alpha=0.7)
# Add the patch
self.patches[label] = ell
def add_source(self, source):
"""
This function ...
:param source:
:return:
"""
# Create buffer and figure
buf = io.BytesIO()
fig = plt.figure(figsize=(15, 15))
# Add first subplot
ax = fig.add_subplot(2, 3, 1)
# Plot the frame (before removal)
norm = ImageNormalize(stretch=LogStretch())
norm_residual = ImageNormalize(stretch=LogStretch())
min_value = np.nanmin(self.frame)
max_value = 0.5 * (np.nanmax(self.frame) + min_value)
ax.imshow(self.frame,
origin="lower",
interpolation="nearest",
vmin=min_value,
vmax=max_value,
norm=norm)
r = plt_Rectangle((source.x_min, source.y_min),
source.xsize,
source.ysize,
edgecolor="yellow",
facecolor="none",
lw=5)
ax.add_patch(r)
if isinstance(self.principal_shape, PixelEllipseRegion):
ell = plt_Ellipse(
(self.principal_shape.center.x, self.principal_shape.center.y),
2.0 * self.principal_shape.radius.x,
2.0 * self.principal_shape.radius.y,
self.principal_shape.angle.to("deg").value,
edgecolor="red",
facecolor="none",
lw=5)
ax.add_patch(ell)
ax.get_xaxis().set_visible(False)
ax.get_yaxis().set_visible(False)
# Add the second subplot
ax = fig.add_subplot(2, 3, 2)
frame_xsize = self.frame.xsize
frame_ysize = self.frame.ysize
new_xmin = int(source.center.x - 0.1 * frame_xsize)
new_xmax = int(source.center.x + 0.1 * frame_xsize)
new_ymin = int(source.center.y - 0.1 * frame_ysize)
new_ymax = int(source.center.y + 0.1 * frame_ysize)
if new_xmin < 0: new_xmin = 0
if new_ymin < 0: new_ymin = 0
if new_xmax > frame_xsize: new_xmax = frame_xsize
if new_ymax > frame_ysize: new_ymax = frame_ysize
ax.imshow(self.frame[new_ymin:new_ymax, new_xmin:new_xmax],
origin="lower",
interpolation="nearest",
vmin=min_value,
vmax=max_value,
norm=norm)
r = plt_Rectangle((source.x_min - new_xmin, source.y_min - new_ymin),
source.xsize,
source.ysize,
edgecolor="yellow",
facecolor="none",
lw=5)
ax.add_patch(r)
ax.get_xaxis().set_visible(False)
ax.get_yaxis().set_visible(False)
# Add the third subplot
ax = fig.add_subplot(2, 3, 3)
# Adapt the mask
self.mask[source.y_slice, source.x_slice] += source.mask
# Plot the mask
# ax.imshow(self.mask[new_ymin:new_ymax, new_xmin:new_xmax], origin="lower", cmap='Greys')
ax.imshow(self.mask, origin="lower", cmap="Greys")
ax.get_xaxis().set_visible(False)
ax.get_yaxis().set_visible(False)
# Add the fourth subplot
ax = fig.add_subplot(2, 3, 4)
# Plot the source cutout
# ax.imshow(source.cutout, origin="lower", interpolation="nearest", vmin=min_value, vmax=max_value, norm=norm)
ax.imshow(np.ma.MaskedArray(source.cutout,
mask=source.background_mask),
origin="lower",
interpolation="nearest",
vmin=min_value,
vmax=max_value,
norm=norm)
ax.get_xaxis().set_visible(False)
ax.get_yaxis().set_visible(False)
# ell = plt_Ellipse((source.center.x-source.x_min, source.center.y-source.y_min), 2.0*source.radius.x, 2.0*source.radius.y, edgecolor="yellow", facecolor="none", lw=5)
# ax.add_patch(ell)
ax.get_xaxis().set_visible(False)
ax.get_yaxis().set_visible(False)
# Add the fourth subplot
ax = fig.add_subplot(2, 3, 5)
# Plot the source background
# ax.imshow(np.ma.MaskedArray(source.cutout, mask=source.mask), origin="lower", interpolation="nearest", vmin=min_value, vmax=max_value, norm=norm)
new_cutout = source.cutout.copy()
new_cutout[source.mask] = source.background[source.mask]
ax.imshow(new_cutout,
origin="lower",
interpolation="nearest",
vmin=min_value,
vmax=max_value,
norm=norm)
# ell = plt_Ellipse((source.center.x-source.x_min, source.center.y-source.y_min), 2.0 * source.radius.x, 2.0 * source.radius.y, edgecolor="yellow", facecolor="none", lw=5)
# ax.add_patch(ell)
ax.get_xaxis().set_visible(False)
ax.get_yaxis().set_visible(False)
# Add the sixth subplot
ax = fig.add_subplot(2, 3, 6)
# Plot the residual cutout (background removed)
ax.imshow(source.subtracted,
origin="lower",
interpolation="nearest",
vmin=0.0,
vmax=max_value,
norm=norm_residual)
ax.get_xaxis().set_visible(False)
ax.get_yaxis().set_visible(False)
plt.tight_layout()
plt.savefig(buf, format="png")
plt.close()
buf.seek(0)
im = imageio.imread(buf)
buf.close()
self.add_frame(im)
def add_source(self, source):
"""
This function ...
:param source:
:return:
"""
# Create buffer and figure
buf = io.BytesIO()
fig = plt.figure(figsize=(15, 15))
# Add first subplot
ax = fig.add_subplot(2, 3, 1)
# Plot the frame (before removal)
norm = ImageNormalize(stretch=LogStretch())
norm_residual = ImageNormalize(stretch=LogStretch())
min_value = np.nanmin(self.frame)
max_value = 0.5 * (np.nanmax(self.frame) + min_value)
ax.imshow(self.frame, origin="lower", interpolation="nearest", vmin=min_value, vmax=max_value, norm=norm)
r = plt_Rectangle((source.x_min, source.y_min), source.xsize, source.ysize, edgecolor="yellow",
facecolor="none", lw=5)
ax.add_patch(r)
if isinstance(self.principal_shape, Ellipse):
ell = plt_Ellipse((self.principal_shape.center.x, self.principal_shape.center.y),
2.0 * self.principal_shape.radius.x, 2.0 * self.principal_shape.radius.y,
self.principal_shape.angle.to("deg").value, edgecolor="red", facecolor="none", lw=5)
ax.add_patch(ell)
ax.get_xaxis().set_visible(False)
ax.get_yaxis().set_visible(False)
# Add the second subplot
ax = fig.add_subplot(2, 3, 2)
frame_xsize = self.frame.xsize
frame_ysize = self.frame.ysize
new_xmin = int(source.center.x - 0.1 * frame_xsize)
new_xmax = int(source.center.x + 0.1 * frame_xsize)
new_ymin = int(source.center.y - 0.1 * frame_ysize)
new_ymax = int(source.center.y + 0.1 * frame_ysize)
if new_xmin < 0: new_xmin = 0
if new_ymin < 0: new_ymin = 0
if new_xmax > frame_xsize: new_xmax = frame_xsize
if new_ymax > frame_ysize: new_ymax = frame_ysize
ax.imshow(self.frame[new_ymin:new_ymax, new_xmin:new_xmax], origin="lower", interpolation="nearest",
vmin=min_value, vmax=max_value, norm=norm)
r = plt_Rectangle((source.x_min - new_xmin, source.y_min - new_ymin), source.xsize, source.ysize,
edgecolor="yellow", facecolor="none", lw=5)
ax.add_patch(r)
ax.get_xaxis().set_visible(False)
ax.get_yaxis().set_visible(False)
# Add the third subplot
ax = fig.add_subplot(2, 3, 3)
# Adapt the mask
self.mask[source.y_slice, source.x_slice] += source.mask
# Plot the mask
# ax.imshow(self.mask[new_ymin:new_ymax, new_xmin:new_xmax], origin="lower", cmap='Greys')
ax.imshow(self.mask, origin="lower", cmap="Greys")
ax.get_xaxis().set_visible(False)
ax.get_yaxis().set_visible(False)
# Add the fourth subplot
ax = fig.add_subplot(2, 3, 4)
# Plot the source cutout
# ax.imshow(source.cutout, origin="lower", interpolation="nearest", vmin=min_value, vmax=max_value, norm=norm)
ax.imshow(np.ma.MaskedArray(source.cutout, mask=source.background_mask), origin="lower",
interpolation="nearest", vmin=min_value, vmax=max_value, norm=norm)
ax.get_xaxis().set_visible(False)
ax.get_yaxis().set_visible(False)
# ell = plt_Ellipse((source.center.x-source.x_min, source.center.y-source.y_min), 2.0*source.radius.x, 2.0*source.radius.y, edgecolor="yellow", facecolor="none", lw=5)
# ax.add_patch(ell)
ax.get_xaxis().set_visible(False)
ax.get_yaxis().set_visible(False)
# Add the fourth subplot
ax = fig.add_subplot(2, 3, 5)
# Plot the source background
# ax.imshow(np.ma.MaskedArray(source.cutout, mask=source.mask), origin="lower", interpolation="nearest", vmin=min_value, vmax=max_value, norm=norm)
new_cutout = source.cutout.copy()
new_cutout[source.mask] = source.background[source.mask]
ax.imshow(new_cutout, origin="lower", interpolation="nearest", vmin=min_value, vmax=max_value, norm=norm)
# ell = plt_Ellipse((source.center.x-source.x_min, source.center.y-source.y_min), 2.0 * source.radius.x, 2.0 * source.radius.y, edgecolor="yellow", facecolor="none", lw=5)
# ax.add_patch(ell)
ax.get_xaxis().set_visible(False)
ax.get_yaxis().set_visible(False)
# Add the sixth subplot
ax = fig.add_subplot(2, 3, 6)
# Plot the residual cutout (background removed)
ax.imshow(source.subtracted, origin="lower", interpolation="nearest", vmin=0.0, vmax=max_value,
norm=norm_residual)
ax.get_xaxis().set_visible(False)
ax.get_yaxis().set_visible(False)
plt.tight_layout()
plt.savefig(buf, format="png")
plt.close()
buf.seek(0)
im = imageio.imread(buf)
buf.close()
self.add_frame(im)
