def nbo_vs_year(self):
"""
Plot percent of structures, with different NBO per 1000 atoms levels,
from "good" pdb structures (all PDB files with a single model, no unknown
atom types and good CRYST1 records) VS. year
Second sub plot: the total of "good" structures deposited VS. year
"""
plt.close('all')
# figure parameters
# plt.ion() # enables interactive mode
max_y = 105
fontsize = 20
fig = plt.figure(figsize=(8,10))
gs = GridSpec(2,1,height_ratios=[2,1])
# first subplot
ax1 = plt.subplot(gs[0,0])
ax2 = plt.subplot(gs[1,0])
lines = []
line_type = ['.:','.-','.--']
n = len(line_type)
for i,pd in enumerate(self.plot_data_list):
lt = line_type[i%n]
l, = ax1.plot(pd.years,pd.percent,lt)
lines.append(l)
ax1.set_ylabel('Percent of PDB structures',fontsize=fontsize)
ax1.text(min(self.years)+0.5,max_y-4,'a.',fontsize=fontsize)
ax1.tick_params(axis='both',labelsize=fontsize - 2)
ax1.axes.get_xaxis().set_visible(False)
ax1.set_yticks([5,10,40,70,100])
ax1.set_ylim([0,max_y])
ax1.set_xlim([self.start_year,self.end_year])
# legend
labels = ['NBO per 1000 atom > {}']*len(self.nbo_per_1000_atoms)
labels = [x.format(y) for x,y in zip(labels,self.nbo_per_1000_atoms)]
if self.sym:
legend_pos = [0.96,0.70]
else:
legend_pos = [0.54,0.30]
ax1.legend(
lines,labels,
bbox_to_anchor=legend_pos,
loc=1,borderaxespad=0.0)
# Second subplot
ax2.plot(self.years,self.n_total,'.:g')
ax2.set_xlim([self.start_year,self.end_year])
ax2.set_xlabel('Year',fontsize=fontsize)
ax2.set_ylabel('Number of structures',fontsize=fontsize)
ax2.text(min(self.years)+0.5,max(self.n_total)-5,'b.',fontsize=fontsize)
ax2.tick_params(axis='both',labelsize=fontsize - 2)
ax2.set_xticks([self.start_year,1990,2000,self.end_year])
ax2.set_yscale('log')
ax2.set_yticks([10,100,1000])
#
gs.tight_layout(fig)
gs.update(hspace=0)
s = 'all'*(not self.sym) + 'sym'*self.sym
fig_name = 'nbo_vs_year_{}.png'.format(s)
plt.savefig(fig_name)
fig.show()
def __render_both(self):
''' renders two plots, one with the filtered and one without. '''
times = {'start': time.time()}
if self.__left_axes is None:
self.__width_ratio = self.__make_width_ratio()
gs = GridSpec(1,
2,
width_ratios=self.__make_width_ratio(adjusted=True),
wspace=0.00)
gs.tight_layout(self.__chart.canvas.figure)
self.__left_axes = self.__chart.canvas.figure.add_subplot(
gs.new_subplotspec((0, 0)))
self.__add_grid(self.__left_axes)
self.__right_axes = self.__chart.canvas.figure.add_subplot(
gs.new_subplotspec((0, 1)))
self.__add_grid(self.__right_axes)
times['l_axes_init'] = time.time()
self.__left_scatter = self.__render_scatter(
self.__left_cache, self.__left_axes, self.__left_scatter,
self.__ui.maxFilteredFreq.value(), self.left, 'l', times)
self.__set_limits(self.__left_axes, self.__ui.minFreq,
self.__ui.maxFilteredFreq, self.__ui.minTime,
self.__ui.maxTime)
times['l_limits'] = time.time()
self.__right_scatter = self.__render_scatter(
self.__right_cache, self.__right_axes, self.__right_scatter,
self.__ui.maxUnfilteredFreq.value(), self.right, 'r', times)
self.__right_axes.set_yticklabels([])
self.__right_axes.get_yaxis().set_tick_params(length=0)
self.__set_limits(self.__right_axes, self.__ui.minFreq,
self.__ui.maxUnfilteredFreq, self.__ui.minTime,
self.__ui.maxTime)
times['r_limits'] = time.time()
return times
def vis(name, obj):
data = obj[:]
name = "result_" + name
raw_image = data.sum(-1)
raw_image.T[:] -= raw_image.min(tuple(range(1, raw_image.ndim)))
raw_image.T[:] /= raw_image.max(tuple(range(1, raw_image.ndim)))
pad_width = ((0, 1), ) + ((0, 0), ) * (raw_image.ndim - 1)
raw_image = pad(raw_image,
pad_width=pad_width,
mode='constant',
constant_values=0)
raw_image = raw_image.transpose(roll(range(raw_image.ndim), -1))
scale = obj.attrs['scale'][:] * unit_conversion
X = (scale * data.shape[1:])[1::-1]
extent = [0, X[0], 0, X[1]]
for measure, data1 in zip(("Nucleus", "Actin"), data):
psmooth0 = psmooth / scale
smoothed_data = gaussian_filter(data1, psmooth0).sum(2)
smoothed_data -= smoothed_data.min()
smoothed_data /= smoothed_data.max()
dp = (scale * psmooth0)[:2].mean()
clf()
fig = figure(figsize(22, 10))
gs = GridSpec(1, 2)
ax = []
for gs0 in gs:
ax0 = fig.add_subplot(gs0)
ax0.set_adjustable("box-forced")
ax0.set_xlabel("mm", fontsize="x-large")
ax0.set_ylabel("mm", fontsize="x-large")
ax.append(ax0)
divider = make_axes_locatable(ax[0])
cax = divider.append_axes("right", size="5%", pad=0.05)
im = ax[0].imshow(smoothed_data,
extent=extent,
interpolation="bicubic",
origin="lower")
cb = colorbar(im, cax=cax)
cb.set_label(label="{} Density".format(measure), fontsize="x-large")
ax[1].imshow(raw_image,
extent=extent,
interpolation="bilinear",
origin="lower")
gs.tight_layout(fig)
savefig(join(outdir, name + "_{}.png".format(measure)))
def plot_flux_decomposition(ss, tm, name=None, source_code=None):
f = plt.figure(figsize=(18, 6))
gs = GridSpec(2, 3, wspace=0.5, hspace=0.5)
ax1 = plt.subplot(gs[0, 0])
ax2 = plt.subplot(gs[0, 1])
ax3 = plt.subplot(gs[0, 2])
ax4 = plt.subplot(gs[1, 0])
ax5 = plt.subplot(gs[1, 1])
ax6 = plt.subplot(gs[1, 2])
first_surface = int(len(ss) / 2)
ax1.scatter(range(first_surface), ss[0:first_surface], s=80, c="r")
ax1.set_title("First part of steady state eigenvector")
ax1.set_ylabel("Population")
ax2.scatter(range(first_surface), [tm[i][i + first_surface] for i in range(first_surface)], s=80, c="r")
ax2.set_title("Transition probabilities (unbound to bound)")
ax2.set_ylabel("Probability")
ax3.scatter(range(first_surface), [ss[i] * tm[i][i + first_surface] for i in range(first_surface)], s=80, c="r")
ax3.set_title("Steady state eigenvector * transition probabilities (unbound to bound)")
ax3.set_ylabel("Population * Probability")
ax4.scatter(range(first_surface, 2 * first_surface), ss[first_surface : 2 * first_surface], s=80, c="b")
ax4.set_title("Second part of steady state eigenvector")
ax4.set_ylabel("Population")
ax5.scatter(range(first_surface), [tm[i + first_surface][i] for i in range(first_surface)], s=80, c="b")
ax5.set_title("Transition probabilities (bound to unbound)")
ax5.set_ylabel("Probability")
ax6.scatter(
range(first_surface, 2 * first_surface),
[ss[i] * tm[i + first_surface][i] for i in range(first_surface)],
s=80,
c="b",
)
ax6.set_title("Steady state eigenvector * transition probabilities (bound to unbound)")
ax6.set_ylabel("Population * Probability")
st = datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S")
sts = datetime.datetime.now().strftime("%Y-%m-%d-%H-%M-%S")
if name:
if source_code is not None:
text = st + " " + name + " in " + source_code
else:
text = st + " " + name
f.text(0.0, 0.0, text, fontsize=12, color="black", ha="left", va="bottom", alpha=0.5)
else:
f.text(0.0, 0.0, st, fontsize=12, color="black", ha="left", va="bottom", alpha=0.5)
gs.tight_layout(f, rect=[0, 0, 1, 1])
plt.savefig("Figures/flux-decomposition-{}-{}".format(sts, name), dpi=150)
# plt.show()
plt.close()
def plot_steady_state(unbound, bound, pdf_unbound, pdf_bound, ss, name=None, source_code=None):
f = plt.figure(figsize=(12, 12))
gs = GridSpec(2, 2, wspace=0.5, hspace=0.5)
ax1 = plt.subplot(gs[0, 0])
ax2 = plt.subplot(gs[0, 1])
ax3 = plt.subplot(gs[1, 0])
ax4 = plt.subplot(gs[1, 1])
ax1.scatter(range(len(unbound)), unbound, s=80, c="r")
ax1.plot(range(len(unbound)), unbound, lw=2, c="r")
ax2.scatter(range(len(bound)), bound, s=80, c="b")
ax2.plot(range(len(bound)), bound, lw=2, c="b")
ax1.set_title("Unbound energy surface")
ax2.set_title("Bound energy surface")
bins = int(len(ss) / 2)
ax3.plot(range(len(unbound)), ss[0:bins], lw=2, c="r")
ax3.scatter(range(len(unbound)), ss[0:bins], s=80, c="r")
ax3.plot(range(len(pdf_unbound)), pdf_unbound, lw=4, ls="--", c="k")
ax3.set_title("Boltzmann and forward s.s.")
ax4.plot(range(len(bound)), ss[bins : 2 * bins], lw=2, c="b")
ax4.scatter(range(len(bound)), ss[bins : 2 * bins], s=80, c="b")
ax4.plot(range(len(pdf_bound)), pdf_bound, lw=4, ls="--", c="k")
ax4.set_title("Boltzmann and forward s.s.")
ax4.set_xlabel("Reaction coordinate ($\phi$)")
ax3.set_xlabel("Reaction coordinate ($\phi$)")
ax1.set_ylabel("Energy (a.u.)")
ax2.set_ylabel("Energy (a.u.)")
ax3.set_ylabel("Population")
ax4.set_ylabel("Population")
ax1.set_ylim([-15, 20])
ax2.set_ylim([-15, 20])
ax3.set_ylim([0, 0.6])
ax4.set_ylim([0, 0.6])
st = datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S")
sts = datetime.datetime.now().strftime("%Y-%m-%d-%H-%M-%S")
if name:
if source_code is not None:
text = st + " " + name + " in " + source_code
else:
text = st + " " + name
f.text(0.0, 0.0, text, fontsize=12, color="black", ha="left", va="bottom", alpha=0.5)
else:
f.text(0.0, 0.0, st, fontsize=12, color="black", ha="left", va="bottom", alpha=0.5)
gs.tight_layout(f, rect=[0, 0, 1, 1])
# plt.show()
plt.savefig("Figures/steady-state-{}-{}".format(sts, name), dpi=150)
plt.close()
def plot_images(images, labels):
gs = GridSpec(6, 7)
gs.update(wspace=0.03, hspace=0.03) # set the spacing between axes.
fig = plt.figure(figsize=(12,12))
image_titles = get_label_map('signnames.csv', labels)
for i in range(len(images)-1):
ax = fig.add_subplot(gs[i])
img = images[i]
ax.imshow(img)
ax.set_aspect('equal')
ax.set_title(image_titles[i],fontsize=7)
plt.axis('off')
gs.tight_layout(fig)
plt.show()
def plot_flux(
flux_unbound, unbound_scale, flux_bound, bound_scale, flux_between, between_scale, name=None, source_code=None
):
f = plt.figure(figsize=(12, 12))
gs = GridSpec(2, 2, wspace=0.5, hspace=0.5)
ax1 = plt.subplot(gs[0, 0])
ax2 = plt.subplot(gs[0, 1])
ax3 = plt.subplot(gs[1, 0])
# ax1.scatter(range(len(flux_unbound)), flux_unbound, s=80, c='r')
ax1.plot(range(len(flux_unbound)), flux_unbound * 10 ** unbound_scale, lw=2, c="r")
# ax2.scatter(range(len(flux_bound)), flux_bound, s=80, c='b')
ax2.plot(range(len(flux_bound)), flux_bound * 10 ** bound_scale, lw=2, c="b")
ax1.set_title("Unbound energy surface")
ax2.set_title("Bound energy surface")
# ax3.scatter(range(len(flux_between)), flux_between, s=80, c='k')
ax3.autoscale(enable=False, axis="y")
ax3.plot(range(len(flux_between)), flux_between * 10 ** between_scale, lw=4, ls="-", c="k")
ax3.set_title("Flux between surfaces")
ax3.set_xlabel("Reaction coordinate ($\phi$)")
ax1.set_ylabel("Flux ($\\times 10^{{{}}}$)".format(unbound_scale), size=20)
ax2.set_ylabel("Flux ($\\times 10^{{{}}}$)".format(bound_scale), size=20)
ax3.set_ylabel("Flux ($\\times 10^{{{}}}$)".format(between_scale), size=20)
st = datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S")
sts = datetime.datetime.now().strftime("%Y-%m-%d-%H-%M-%S")
if name:
if source_code is not None:
text = st + " " + name + " in " + source_code
else:
text = st + " " + name
f.text(0.0, 0.0, text, fontsize=12, color="black", ha="left", va="bottom", alpha=0.5)
else:
f.text(0.0, 0.0, st, fontsize=12, color="black", ha="left", va="bottom", alpha=0.5)
gs.tight_layout(f, rect=[0, 0, 1, 1])
plt.savefig("Figures/flux-{}-{}.png".format(sts, name), dpi=150)
# plt.show()
plt.close()
def fig2():
grid = WaveSimulation(2**8, 2**8, length_x=1, length_y=1, zmin=0, zmax=2)
grid.creat_gaussian_beam(0.05)
A_lens, z = grid.lens_phase(focal_length=20, nargout=2)
E_until_lens = grid.E0 * A_lens
plt.imshow(np.abs(E_until_lens))
plt.imshow(np.angle(E_until_lens))
plt.show()
intersity3d = make_intersity3d(grid, E_until_lens, z)
print(np.argmax)
fig2 = plt.figure(2)
gs = GridSpec(4, 4) # 4 rows, 4 columns
gs.tight_layout(fig2, rect=[None, None, None, None])
ax1 = fig2.add_subplot(gs[0:2, 0:2]) # First row, first column
ax1.imshow(intersity3d[:, :, grid.nz // 2])
ax1.set_title("XY")
plt.axis('off')
ax2 = fig2.add_subplot(gs[0:2, 2:4]) # First row, second column
ax2.imshow((intersity3d[grid.n // 2 - 1, :, :].T)**3)
ax2.set_title("XZ")
plt.axis('off')
ax3 = fig2.add_subplot(gs[2, 0]) # First row, third column
plt.axis('off')
ax4 = fig2.add_subplot(gs[2, 1]) # Second row, span all columns
plt.axis('off')
ax5 = fig2.add_subplot(gs[2, 2]) # First row, third column
plt.axis('off')
ax6 = fig2.add_subplot(gs[2, 3]) # Second row, span all columns
plt.axis('off')
ax7 = fig2.add_subplot(gs[3, 0]) # First row, third column
plt.axis('off')
ax8 = fig2.add_subplot(gs[3, 1]) # Second row, span all columns
plt.axis('off')
ax9 = fig2.add_subplot(gs[3, 2]) # First row, third column
plt.axis('off')
ax10 = fig2.add_subplot(gs[3, 3]) # Second row, span all columns
plt.axis('off')
plt.tight_layout()
plt.show()
def _decorate_plot(fig, ax, artist, plot_data, color_data, legend, cmap):
ax.set_xlabel(plot_data.xlabel)
ax.set_ylabel(plot_data.ylabel)
if plot_data.xticks is not None:
ax.set_xticks(np.arange(len(plot_data.xticks)))
ax.set_xticklabels(plot_data.xticks)
if plot_data.yticks is not None:
ax.set_yticks(np.arange(len(plot_data.yticks)))
ax.set_yticklabels(plot_data.yticks)
if color_data.needs_cbar:
cbar = fig.colorbar(artist)
cbar.set_label(color_data.label)
return
if legend and color_data.names is not None and len(color_data.names) <= 20:
# using trick from http://stackoverflow.com/a/19881647/10601
num_colors = len(color_data.names)
if cmap == '_auto':
colors = islice(cycle(COLOR_CYCLE), num_colors)
else:
colors = artist.cmap(np.linspace(0, 1, num_colors))
proxies = [Patch(color=c, label=k) for c,k in zip(colors, color_data.names)]
# Make a new skinny subplot, then cover it with the legend.
# This allows an out-of-axis legend without it getting cut off.
# Uses the trick from http://stackoverflow.com/a/22885327/10601
gs = GridSpec(1, 2, width_ratios=(3, 1), wspace=0.02)
ax.set_position(gs[0].get_position(fig))
ax.set_subplotspec(gs[0])
lx = fig.add_subplot(gs[1])
lx.legend(handles=proxies, title=color_data.label, loc='upper left',
mode='expand', borderaxespad=0, fontsize='small', frameon=False)
lx.axis('off')
gs.tight_layout(fig, w_pad=0)
def plot_completeness(
physgrid_list,
noise_model_list,
output_plot_filename,
param_list=["Av", "Rv", "logA", "f_A", "M_ini", "Z", "distance"],
compl_filter="F475W",
):
"""
Make visualization of the completeness
Parameters
----------
physgrid_list : string or list of strings
Name of the physics model file. If there are multiple physics model
grids (i.e., if there are subgrids), list them all here.
noise_model_list : string or list of strings
Name of the noise model file. If there are multiple files for
physgrid_list (because of subgrids), list the noise model file
associated with each physics model file.
param_list : list of strings
names of the parameters to plot
compl_filter : str
filter to use for completeness (required for toothpick model)
output_plot_filename : string
name of the file in which to save the output plot
"""
n_params = len(param_list)
# If there are subgrids, we can't read them all into memory. Therefore,
# we'll go through each one and just grab the relevant parts.
compl_table_list = []
# make a table for each physics model + noise model
for physgrid, noise_model in zip(np.atleast_1d(physgrid_list),
np.atleast_1d(noise_model_list)):
# get the physics model grid - includes priors
modelsedgrid = SEDGrid(str(physgrid))
# get list of filters
short_filters = [
filter.split(sep="_")[-1].upper()
for filter in modelsedgrid.filters
]
if compl_filter.upper() not in short_filters:
raise ValueError("requested completeness filter not present")
filter_k = short_filters.index(compl_filter.upper())
print("Completeness from {0}".format(modelsedgrid.filters[filter_k]))
# read in the noise model
noisegrid = noisemodel.get_noisemodelcat(str(noise_model))
# get the completeness
model_compl = noisegrid["completeness"]
# close the file to save memory
noisegrid.close()
# put it all into a table
table_dict = {x: modelsedgrid[x] for x in param_list}
table_dict["compl"] = model_compl[:, filter_k]
# append to the list
compl_table_list.append(Table(table_dict))
# stack all the tables into one
compl_table = vstack(compl_table_list)
# import pdb; pdb.set_trace()
# figure
fig = plt.figure(figsize=(4 * n_params, 4 * n_params))
# label font sizes
label_font = 25
tick_font = 22
# load in color map
cmap = matplotlib.cm.get_cmap("magma")
# iterate through the panels
for i, pi in enumerate(param_list):
for j, pj in enumerate(param_list[i:], i):
print("plotting {0} and {1}".format(pi, pj))
# not along diagonal
if i != j:
# set up subplot
plt.subplot(n_params, n_params, i + j * (n_params) + 1)
ax = plt.gca()
# create image and labels
x_col, x_bins, x_label = setup_axis(compl_table, pi)
y_col, y_bins, y_label = setup_axis(compl_table, pj)
compl_image, _, _, _ = binned_statistic_2d(
x_col,
y_col,
compl_table["compl"],
statistic="mean",
bins=(x_bins, y_bins),
)
# plot points
im = plt.imshow(
compl_image.T,
# np.random.random((4,4)),
extent=(
np.min(x_bins),
np.max(x_bins),
np.min(y_bins),
np.max(y_bins),
),
cmap="magma",
vmin=0,
vmax=1,
aspect="auto",
origin="lower",
)
ax.tick_params(
axis="both",
which="both",
direction="in",
labelsize=tick_font,
bottom=True,
top=True,
left=True,
right=True,
)
# axis labels and ticks
if i == 0:
ax.set_ylabel(y_label, fontsize=label_font)
# ax.get_yaxis().set_label_coords(-0.35,0.5)
else:
ax.set_yticklabels([])
if j == n_params - 1:
ax.set_xlabel(x_label, fontsize=label_font)
plt.xticks(rotation=-45)
else:
ax.set_xticklabels([])
# along diagonal
if i == j:
# set up subplot
plt.subplot(n_params, n_params, i + j * (n_params) + 1)
ax = plt.gca()
# create histogram and labels
x_col, x_bins, x_label = setup_axis(compl_table, pi)
compl_hist, _, _ = binned_statistic(
x_col,
compl_table["compl"],
statistic="mean",
bins=x_bins,
)
# make histogram
_, _, patches = plt.hist(x_bins[:-1],
x_bins,
weights=compl_hist)
# color each bar by its completeness
for c, comp in enumerate(compl_hist):
patches[c].set_color(cmap(comp))
patches[c].set_linewidth = 0.1
# make a black outline so it stands out as a histogram
plt.hist(x_bins[:-1],
x_bins,
weights=compl_hist,
histtype="step",
color="k")
# axis ranges
plt.xlim(np.min(x_bins), np.max(x_bins))
plt.ylim(0, 1.05)
ax.tick_params(axis="y",
which="both",
length=0,
labelsize=tick_font)
ax.tick_params(axis="x",
which="both",
direction="in",
labelsize=tick_font)
# axis labels and ticks
ax.set_yticklabels([])
if i < n_params - 1:
ax.set_xticklabels([])
if i == n_params - 1:
ax.set_xlabel(x_label, fontsize=label_font)
plt.xticks(rotation=-45)
# plt.subplots_adjust(wspace=0.05, hspace=0.05)
plt.tight_layout()
# add a colorbar
gs = GridSpec(nrows=20, ncols=n_params)
cax = fig.add_subplot(gs[0, 2:])
cbar = plt.colorbar(im, cax=cax, orientation="horizontal")
cbar.set_label("Completeness", fontsize=label_font)
cbar.ax.tick_params(labelsize=tick_font)
gs.tight_layout(fig)
fig.savefig(output_plot_filename)
plt.close(fig)
ax10.set_xlabel(' ')
ax10.set_ylabel(' ')
ax10.set_xlim(axlims)
ax10.set_ylim(axlims)
# ax10.set_title(' ')
ax10.patch.set_facecolor('black')
for comp_map, ax in zip(comp_maps_multi[1:], [ax11, ax12, ax13, ax14]):
try:
comp_map.plot(ax, title=' ')
except:
ValueError
ax.set_xlabel(' ')
ax.set_ylabel(' ')
ax.set_xlim(axlims)
ax.set_ylim(axlims)
# ax.set_title(' ')
ax.patch.set_facecolor('black')
for ax, title in zip(
[ax00, ax01, ax02, ax03, ax04],
["Briggs -2", "Briggs -1", "Briggs 0", "Briggs 1", "Briggs 2"]):
ax.set_title(title)
ax00.set_ylabel("No Multiscale (Solar-Y)")
ax10.set_ylabel("Multiscale (Solar-Y)")
ax10.set_xlabel("Solar-X (arcsec)")
gs.tight_layout(fig, h_pad=-2, w_pad=-2)
plt.savefig("briggs_comparison.png", dpi=400)
plt.show()
norm=MidpointLogNorm(vmin=vmin,
vmax=vmax,
midpoint=1),
edgecolors='face',
cmap='bwr')
ax[i, j].set_xlim(x[0], x[-1])
ax[i, j].set_ylim(y[0], y[-1])
if i != nrows - 1:
ax[i, j].xaxis.set_ticklabels([])
if j == 1:
ax[i, j].yaxis.set_ticklabels([])
ax[0, 0].xaxis.set_label_position("top")
ax[0, 1].xaxis.set_label_position("top")
ax[0, 1].yaxis.set_label_position("right")
ax[1, 1].yaxis.set_label_position("right")
ax[0, 0].set_xlabel('Windowing')
ax[0, 1].set_xlabel('Binning')
ax[1, 0].set_xlabel('Observed Frequency [MHz]', labelpad=10)
ax[1, 0].xaxis.set_label_coords(1, -0.1)
ax[0, 1].set_ylabel('Skewness ($S_3$)')
ax[1, 1].set_ylabel('Kurtosis ($S_4$)')
ax[1, 0].set_ylabel('Window/Bin Size [MHz]', labelpad=10)
ax[1, 0].yaxis.set_label_coords(-0.1, 1)
cbar = fig.colorbar(im, cax=cax, orientation='vertical', label='SNR')
fig.suptitle(t.upper(), x=0.45)
gs0.tight_layout(fig, rect=[0, 0, 1, 1])
fig.canvas.draw()
fig.savefig(stats_dir + 'snr_color_chart_{:s}.pdf'.format(t), dpi=200)
def poincareplot(self,
steps,
extralabel=lambda step: '',
lims=None,
colorbar=True):
"""
Make a set of Poincare plots for a given step of sequence thereof.
Parameters
----------
steps : sequence of int or a single integer
The step(s) to plot
extralabel : callable, optional
A callable with signature `extralabel(step)` that returns an extra
string label to add to the title for a given step number
lims : dict, optional
A dictionary of limits for the Poincaré plots, with keys `'xy.h',
'xy.v', 's.h', 's.v'`, and values corresponding to the magnitude of
the (symmetric) axis limits on the respective plots. The transverse
plots share limits to ensure that they are always comparable, and
because we expect roughly axisymmetric beams.
colorbar : bool, optional
Boolean indicating whether or not to draw colorbars
Returns
-------
poincarefig : Figure
"""
try:
iter(steps)
except TypeError:
steps = [steps]
dx, xp, dy, yp, ds, dps = self.frenet_6D()
hvar_x = 1e3 * dx[steps, :]
vvar_x = 1e3 * xp[steps, :]
hvar_y = 1e3 * dy[steps, :]
vvar_y = 1e3 * yp[steps, :]
hvar_s = 1e3 * ds[steps, :]
vvar_s = dps[steps, :]
# sxy_h = max(np.nanstd(hvar_x, axis=1).max(), np.nanstd(hvar_y, axis=1).max())
# sxy_v = max(np.nanstd(vvar_x, axis=1).max(), np.nanstd(vvar_y, axis=1).max())
# ss_h = np.nanstd(hvar_s, axis=1).max()
# ss_v = np.nanstd(vvar_s, axis=1).max()
sxy_h = max(
np.nanstd(hvar_x, axis=1).mean(),
np.nanstd(hvar_y, axis=1).mean())
sxy_v = max(
np.nanstd(vvar_x, axis=1).mean(),
np.nanstd(vvar_y, axis=1).mean())
ss_h = np.nanstd(hvar_s, axis=1).mean()
ss_v = np.nanstd(vvar_s, axis=1).mean()
_lims = {
'xy.h': 3 * sxy_h,
'xy.v': 3 * sxy_v,
's.h': 3 * ss_h,
's.v': 3 * ss_v,
}
if lims:
_lims.update(lims)
N = len(steps)
if colorbar:
Ncols = 9
else:
Ncols = 3
w_hb = 5
h_hb = 6
w_cb = 1
cb_pad = 1
w_fig = 3 * w_hb + int(Ncols > 3) * (w_cb + cb_pad)
h_fig = N * h_hb
if colorbar:
widths = [8, 1, 3, 8, 1, 3, 8, 1, 3]
else:
widths = [1, 1, 1]
poincarefig = plt.figure(figsize=(w_fig, h_fig), facecolor='white')
gs = GridSpec(nrows=N,
ncols=Ncols,
hspace=0.2,
width_ratios=widths,
figure=poincarefig)
for row, step in enumerate(steps):
hsl = slice(row * h_hb, (row + 1) * h_hb)
if colorbar:
ax_x = plt.subplot(gs[row, 0])
cax_x = plt.subplot(gs[row, 1])
ax_y = plt.subplot(gs[row, 3])
cax_y = plt.subplot(gs[row, 4])
ax_s = plt.subplot(gs[row, 6])
cax_s = plt.subplot(gs[row, 7])
else:
_w = w_fig // 3
ax_x = plt.subplot(gs[row, 0])
ax_y = plt.subplot(gs[row, 1])
ax_s = plt.subplot(gs[row, 2])
ax_x.set_xlabel(r"$\Delta x$ (mm)")
ax_x.set_ylabel(r"$x'$ (mrad)")
hlim, vlim = _lims['xy.h'], _lims['xy.v']
hb_x = ax_x.hexbin(hvar_x[row],
vvar_x[row],
extent=[-hlim, hlim, -vlim, vlim])
if colorbar:
Colorbar(mappable=hb_x, ax=cax_x)
ax_y.set_xlabel(r"$\Delta y$ (mm)")
ax_y.set_ylabel(r"$y'$ (mrad)")
hb_y = ax_y.hexbin(hvar_y[row],
vvar_y[row],
extent=[-hlim, hlim, -vlim, vlim])
ax_y.set_title(f't={self.tns[step]:.2f} ns {extralabel(step)}')
if colorbar:
Colorbar(mappable=hb_y, ax=cax_y)
ax_s.set_xlabel(r"$\Delta s$ (mm)")
ax_s.set_ylabel(r"$\Delta p_s (\beta\gamma)$")
hlim, vlim = _lims['s.h'], _lims['s.v']
hb_s = ax_s.hexbin(hvar_s[row],
vvar_s[row],
extent=[-hlim, hlim, -vlim, vlim])
if colorbar:
Colorbar(
mappable=hb_s,
ax=cax_s,
)
if not colorbar:
gs.tight_layout(poincarefig)
return poincarefig
def run(self, show=False):
# Load data
filename = self.filename
d = pyfits.getdata(filename)
h = pyfits.getheader(filename)
path, filename = os.path.split(filename)
# Get wavelength calibration
z = np.arange(h['naxis3'])
w = h['CRVAL3'] + h['CDELT3'] * (z - h['CRPIX3'])
# Signal-to-noise clipping
s = d.sum(axis=2)
s = s.sum(axis=1)
gauss_pw, _ = self.fit_gaussian(z, s)
log.debug("Gaussian parameters ---")
log.debug("p[0] = %.2f" % gauss_pw[0])
log.debug("p[1] = %.2f" % gauss_pw[1])
log.debug("p[2] = %.2f" % gauss_pw[2])
log.debug("p[3] = %.2f" % gauss_pw[3])
lor_p = self.fit_lorentzian(z, s)
log.debug("Lorentzian parameters ---")
log.debug("p[0] = %.2f" % lor_p[0])
log.debug("p[1] = %.2f" % lor_p[1])
log.debug("p[2] = %.2f" % lor_p[2])
log.debug("p[3] = %.2f" % lor_p[3])
fwhm = np.abs(gauss_pw[2] * 2 * np.sqrt(2 * np.log(2)))
filter_ = np.where(np.abs(z - gauss_pw[1]) < fwhm, True, False)
if show:
plt.plot(z,
self.gaussian(gauss_pw, z),
'r-',
lw=2,
label='Gaussian Fit')
plt.plot(z,
self.lorentzian(lor_p, z),
'b-',
lw=2,
label='Lorentzian Fit')
plt.plot(z, s, 'ko')
plt.plot(z[filter_], s[filter_], 'ro')
plt.title('Cube collapsed in XY and fits.')
plt.grid()
plt.legend(loc='best')
plt.gcf().canvas.mpl_connect('key_press_event', self.on_key_press)
plt.show()
signal = d[filter_].mean(axis=0)
noise = d[np.logical_not(filter_)].mean(axis=0)
target_snr = 3
snr = signal / noise
snr = ndimage.median_filter(snr, 3)
snr_mask = np.where(signal > target_snr * noise, True, False)
snr_laplacian = ndimage.morphological_laplace(snr * snr_mask, size=3)
snr_mask *= np.where(np.abs(snr_laplacian) < 5.0, True, False)
snr_mask = ndimage.binary_opening(snr_mask, iterations=5)
snr_mask = ndimage.binary_closing(snr_mask, iterations=5)
# SNR MASK Based on circular aperture
# aperture_radius = 1 # arcmin
# aperture_radius = aperture_radius / 60 # arcmin to deg
# aperture_radius = np.abs(aperture_radius / h['CD1_1']) # deg to pix
# print(aperture_radius)
# c = SkyCoord('7:41:55.400', '-18:12:33.00', frame=h['RADECSYS'].lower(), unit=(u.hourangle, u.deg))
# x, y = np.arange(h['NAXIS1']), np.arange(h['NAXIS2'])
# X, Y = np.meshgrid(x, y)
# center_wcs = wcs.WCS(h)
# center = center_wcs.wcs_world2pix(c.ra.deg, c.dec.deg, 6563, 1)
# snr_mask = np.sqrt((X - center[0]) ** 2 + (Y - center[1]) ** 2)
# snr_mask = np.where(snr_mask < aperture_radius, True, False)
# plt.imshow(snr_mask)
# plt.show()
# SNR MASK Based on squared area
aperture_width = 256 * 4.048e-1 # arcsec (from original image)
aperture_width /= 3600 # arcsec to deg
aperture_width /= np.abs(h['CD1_1']) # deg to pix
c = SkyCoord('7:41:55.197',
'-18:12:35.97',
frame=h['RADECSYS'].lower(),
unit=(u.hourangle, u.deg))
x, y = np.arange(h['NAXIS1']), np.arange(h['NAXIS2'])
X, Y = np.meshgrid(x, y)
center_wcs = wcs.WCS(h)
center = center_wcs.wcs_world2pix(c.ra.deg, c.dec.deg, 6563, 1)
print(center, np.abs(X - center[0]), np.abs(Y - center[1]),
aperture_width)
X = np.where(np.abs(X - center[0]) < aperture_width / 2, True, False)
Y = np.where(np.abs(Y - center[1]) < aperture_width / 2, True, False)
snr_mask = X * Y
plt.imshow(snr_mask)
plt.gcf().canvas.mpl_connect('key_press_event', self.on_key_press)
plt.show()
if show:
fig1 = plt.figure(figsize=(20, 5))
plt.title('Signal-to-Noise Ratio')
gs = GridSpec(1, 3)
ax1 = plt.subplot(gs[0])
ax1.set_title('SNR')
im1 = ax1.imshow(snr,
cmap='cubehelix',
interpolation='nearest',
origin='lower',
vmin=3,
vmax=20)
div1 = make_axes_locatable(ax1)
cax1 = div1.append_axes("right", size="5%", pad=0.05)
cbar1 = plt.colorbar(mappable=im1,
cax=cax1,
use_gridspec=True,
orientation='vertical')
ax2 = plt.subplot(gs[1])
ax2.set_title('Mask')
im2 = ax2.imshow(np.where(snr_mask, 1, 0),
cmap='gray',
interpolation='nearest',
origin='lower',
vmin=0,
vmax=1)
div2 = make_axes_locatable(ax2)
cax2 = div2.append_axes("right", size="5%", pad=0.05)
cbar2 = plt.colorbar(mappable=im2,
cax=cax2,
use_gridspec=True,
orientation='vertical')
cmap = plt.get_cmap('cubehelix')
cmap.set_bad('w', 1.0)
ax3 = plt.subplot(gs[2])
ax3.set_title('Masked')
im3 = ax3.imshow(np.ma.masked_where(~snr_mask, snr),
cmap=cmap,
interpolation='nearest',
origin='lower',
vmin=0)
div3 = make_axes_locatable(ax3)
cax3 = div3.append_axes("right", size="5%", pad=0.05)
cbar3 = plt.colorbar(mappable=im3,
cax=cax3,
use_gridspec=True,
orientation='vertical')
plt.gcf().canvas.mpl_connect('key_press_event', self.on_key_press)
gs.tight_layout(fig1)
plt.show()
pyfits.writeto(filename.replace('.', '.SNR.'), snr, h, clobber=True)
pyfits.writeto(filename.replace('.', '.SNR_LAPLACIAN.'),
snr_laplacian,
h,
clobber=True)
# Adjust continuum
continuum = self.fit_continuum(d)
# Subtract continuum
continuum = np.reshape(continuum, (continuum.size, 1, 1))
continuum = np.repeat(continuum, d.shape[1], axis=1)
continuum = np.repeat(continuum, d.shape[2], axis=2)
d -= continuum
del continuum
# Integrate along the planetary nebulae
d = d * snr_mask
d = d.sum(axis=2)
d = d.sum(axis=1)
d = d / np.float(h['EXPTIME'])
gauss_pw, _ = self.fit_gaussian(w, d)
gauss_pc, _ = self.fit_gaussian(z, d)
log.info("Gaussian parameters ---")
log.info("p[0] = %.4f ADU/s" % gauss_pw[0])
log.info("p[1] = %.4f A = %.4f channels" % (gauss_pw[1], gauss_pc[1]))
log.info("p[2] = %.4f A = %.4f channels" % (gauss_pw[2], gauss_pc[2]))
log.info("p[3] = %.4f ADU/s" % gauss_pw[3])
# total_flux = (gauss_pc[0] - gauss_pc[3]) * np.sqrt(2 * np.pi) \
# * gauss_pc[2]
# log.info("Total flux = (a - d) * sqrt(2pi) * c")
# log.info(" %.5E ADU/s" % total_flux)
fwhm = np.abs(gauss_pw[2] * 2 * np.sqrt(2 * np.log(2)))
filter_ = np.where(np.abs(w - gauss_pw[1]) < fwhm, True, False)
# d = d - d[~filter_].mean()
if show:
plt.plot(w,
self.gaussian(gauss_pw, w),
'r-',
lw=2,
label='Gaussian Fit')
# plt.plot(w, self.lorentzian(lor_p, w), 'b-', lw=2, label='Lorentzian Fit')
plt.plot(w[~filter_], d[~filter_], 'ko')
plt.plot(w[filter_], d[filter_], 'ro')
plt.title('Spectral profile of the masked area.')
plt.xlabel(u'Wavelenght [$\AA$]')
plt.ylabel(u'Integrated Count Level [ADU/s]')
plt.grid()
plt.legend(loc='best')
plt.gcf().canvas.mpl_connect('key_press_event', self.on_key_press)
plt.show()
integrated_flux = (gauss_pc[0] - gauss_pc[3]) \
* (gauss_pc[2] * np.sqrt(2 * np.pi))
log.info("Total flux: %.4E adu/s" % (integrated_flux))
snr_mask = np.where(snr_mask, 1, 0)
pyfits.writeto(os.path.join(path,
filename.replace('.fits', '.mask.fits')),
snr_mask,
h,
clobber=True)
return
def dustCorrection(self):
U = 0.3543 #um
G = 0.4770 #um
R = 0.6231 #um
Rv = 3.1
Cu = self.a(1. / U) + self.b(1. / U) / Rv
Cg = self.a(1. / G) + self.b(1. / G) / Rv
Cr = self.a(1. / R) + self.b(1. / R) / Rv
logging.info("dust correction")
mainsequence = np.genfromtxt(
"/home/conor/scripts/StarBug/catalogs/mainsequence.cat")
mask = (mainsequence[:, 1] < 0.6) * (mainsequence[:, 1] > -0.5)
mainsequence = mainsequence[mask]
coeffs = np.polyfit(mainsequence[:, 1], mainsequence[:, 2], 4)
deriv_coeffs = list(
reversed([i * c for i, c in enumerate(reversed(coeffs))]))[:-1]
x = np.arange(-0.7, 0.75, 0.001)
y = np.polyval(coeffs, x)
dy = np.polyval(deriv_coeffs, x)
#for s in self.sourcelist: s.mag[:,1] += 0.1
Av = np.linspace(0.0, 2.5, 60)
Chivals = np.zeros(Av.shape)
#fig = plt.figure()
for i, av in enumerate(Av):
for s in self.sourcelist:
s.construct_colours([2, 0], [0, 1])
if (s.colours[0] < 2 and s.colours[1] > 0.3):
s.colours[1] = np.nan
s.colours[0] -= ((Cu - Cg) * av)
s.colours[1] -= ((Cg - Cr) * av)
#schi = ((s.colours[0] - np.polyval(coeffs, s.colours[1]))**2.0)/(s.colourError[0]**2.0 + (np.polyval(deriv_coeffs, s.colours[1])*s.colourError[1])**2.0 )
error = np.sqrt(s.colourError[0]**2.0 +
(np.polyval(deriv_coeffs, s.colours[1]) *
s.colourError[1])**2.0)
schi = chisqd(coeffs, s.colours[1], s.colours[0], error)
if (np.isfinite(schi)):
Chivals[i] += schi
#plt.scatter(s.colours[1], s.colours[0],c='k', s=0.1)
#plt.scatter(s.colours[1], np.polyval(coeffs, s.colours[1]), c='k')
print(av, Chivals[i], av * (Cu - Cg))
minAv = Av[np.argmin(Chivals)]
print(Cu, Cg, Cr)
print("E(U,G): %f" % (minAv * (Cu - Cg)))
print("E(G,R): %f" % (minAv * (Cg - Cr)))
print("E(B-V): %f" % (0.336748 * minAv))
print(minAv)
print("Au: %f" % (minAv * Cu))
print("Ar: %f" % (minAv * Cr))
print("Ag: %f" % (minAv * Cg))
avLow = 0
avHigh = 0
for i in range(len(Chivals) - 1):
if ((Chivals[i] > (min(Chivals) + 1)) and (Chivals[i + 1] <
(min(Chivals) + 1))):
avLow = Av[i]
if ((Chivals[i] < (min(Chivals) + 1)) and (Chivals[i + 1] >
(min(Chivals) + 1))):
avHigh = Av[i]
chix = []
chiy = []
chiyerr = []
fig = plt.figure(figsize=(6, 8))
gs = GridSpec(5, 3, hspace=0.9)
ax = plt.subplot(gs[:3, :])
ax.set_ylim(-1, 3)
plt.gca().invert_yaxis()
ax2 = plt.subplot(gs[3:, :])
#ax.axvline(-0.526)
#ax.axhline(-0.252)
ax.scatter(mainsequence[:, 1], mainsequence[:, 2], c='k', s=10)
for s in self.sourcelist:
s.construct_colours([2, 0], [0, 1])
ax.scatter(s.colours[1], s.colours[0], c='r', marker='*', s=10)
s.mag[:, 0] -= (Cg * minAv)
s.mag[:, 1] -= (Cr * minAv) #+0.07
s.mag[:, 2] -= (Cu * minAv)
s.magerr[:, 0] = np.sqrt(s.magerr[:, 0]**2.0 +
(Cg * 0.5 * (avLow + avHigh))**2.0)
s.magerr[:, 1] = np.sqrt(s.magerr[:, 1]**2.0 +
(Cr * 0.5 * (avLow + avHigh))**2.0)
s.magerr[:, 2] = np.sqrt(s.magerr[:, 2]**2.0 +
(Cu * 0.5 * (avLow + avHigh))**2.0)
s.construct_colours([2, 0], [0, 1])
ax.scatter(s.colours[1], s.colours[0], c='b', marker='*', s=10)
#print(get_CHIerr(chix,chiy,chiyerr, coeffs))
ax.plot(x, y)
ax.tick_params(direction='in',
which='both',
right=True,
top=True,
axis='both')
ax2.tick_params(direction='in',
which='both',
right=True,
top=True,
axis='both')
#plt.axvline(0.3)
#plt.axhline(2)
ax.set_xlabel("(g-r)")
ax.set_ylabel("(u-g)")
startx = 0.7
starty = 0
ax.arrow(startx,
starty,
-((Cg - Cr) * minAv * 0.5),
-((Cu - Cg) * minAv * 0.4),
head_width=0.02)
ax.arrow(startx,
starty,
0,
-((Cu - Cg) * minAv * 0.4),
head_width=0.02)
ax.arrow(startx,
starty - ((Cu - Cg) * minAv * 0.5),
-((Cg - Cr) * minAv * 0.5),
0,
head_width=0.02)
ax.plot(np.nan, np.nan, marker='*', c='r', label="Reddened")
ax.plot(np.nan, np.nan, marker='*', c='b', label="DeReddened")
ax.plot(np.nan, np.nan, marker='*', c='k', label="Pleiades")
ax.legend(loc=3)
ax2.plot(Av,
Chivals,
c='k',
label=r"$Av: %.3f^{+%.3f}_{-%.3f}$" %
(minAv, avHigh - minAv, minAv - avLow))
ax2.set_xlabel('Av')
ax2.set_ylabel(r'$\chi^2$')
ax2.legend()
ax2.axvline(avLow, c='r')
ax2.axvline(minAv, c='b')
ax2.axvline(avHigh, c='g')
gs.tight_layout(fig)
fig.savefig('out/%s_dust.png' % self.name)
# Axes labels
fig.text(0.01, 0.5, ylabels[stat], rotation='vertical',
horizontalalignment='left', verticalalignment='center')
fig.text(0.5, 0.01, 'Frequency [MHz]', horizontalalignment='center',
verticalalignment='bottom')
fig.text(0.5, 0.99, 'Ionized Fraction', horizontalalignment='center',
verticalalignment='top')
# Legend
# Legend parameters
handlers = [
Line2D([], [], linestyle=':', color='black', linewidth=1),
Line2D([], [], linestyle='--', color='black', linewidth=1),
Line2D([], [], linestyle='-', color='black', linewidth=1),
Patch(color='0.85'),
Patch(color='0.7'),
Patch(color='0.55')
]
labels = ['MWA Phase I Core', 'HERA37', 'HERA331',
'MWA Phase I Core Error', 'HERA37 Error', 'HERA331 Error']
plt.figlegend(handles=handlers, labels=labels, loc=(0.6, 0.8),
ncol=1, fontsize='medium')
# Tidy up
gs.tight_layout(fig, rect=[0.02, 0.02, 0.99, 0.98])
gs.update(wspace=0, hspace=0)
fig.canvas.draw()
fig.savefig(stats_dir + stat + '_poster.pdf', dpi=200)
plt.close()
verticalalignment='top',
horizontalalignment='left',
transform=pax.transAxes)
pax.xaxis.set_major_locator(FixedLocator([-10, -1, 0, 1, 10]))
minor_locs = np.hstack(
(range(-15, -10), range(-9, -1), np.arange(-0.9, 0, 0.1),
np.arange(0.1, 1.0, 0.1), range(2, 10), range(11, 16)))
pax.xaxis.set_minor_locator(FixedLocator(minor_locs))
# Label images
bbox = dict(boxstyle="round", fc='0.8', alpha=0.8, edgecolor='black')
for ax, lb in zip(imax, labels):
ax.text(0.03,
0.97,
lb,
transform=ax.transAxes,
horizontalalignment='left',
verticalalignment='top',
color='black',
bbox=bbox,
size='small')
# Tidy up
gs0.tight_layout(fig, rect=[0, -0.01, 1, 0.98])
gs0.update(hspace=0.22)
fig.canvas.draw()
fig.savefig(pdf_dir +
'mwa128_pdf_maps_xi{:.3f}_{:.3f}MHz.pdf'.format(xi, f),
dpi=200)
plt.close()
class ConstantViewer(object):
"""
Class meant to visualize the constants of a log file for the Motion Profiler of Walton Robotics
"""
def __init__(self,
clf,
automatically_find_remove_outliers: bool = False,
manually_find_remove_outliers: bool = True) -> None:
"""
:param clf: the model to use to separate the data
:param automatically_find_remove_outliers: True if black dots should be placed in the 3d plot to represent the outliers False otherwise
"""
super().__init__()
self.manually_find_remove_outliers = manually_find_remove_outliers
self.showing = False
self.show_outliers = automatically_find_remove_outliers
self.clf = clf
self.fig = None
self.gs = None
self.master_plot = None
self.time_power = None
self.time_velocity = None
self.power_velocity = None
self.file_data = None
self.headers = None
self.new_scaled_features = None
self.features = None
self.outliers = None
self.labels = None
self.color_labels = None
self.outlier_detector = None
self.kV = 1
self.kK = 1
self.kAcc = 1
def show(self):
"""
Shows the figure
"""
if not self.showing:
self.fig = plt.figure("Scaled 3d data")
fig_manager = plt.get_current_fig_manager()
fig_manager.window.showMaximized()
self.gs = GridSpec(3, 4, self.fig)
self.master_plot = self.fig.add_subplot(self.gs[:3, :3],
projection='3d')
self.time_velocity = self.fig.add_subplot(self.gs[0, -1])
self.time_power = self.fig.add_subplot(self.gs[1, -1])
self.power_velocity = self.fig.add_subplot(self.gs[2, -1])
self.gs.tight_layout(self.fig)
self.clear_graphs()
plot_subplots(
self.new_scaled_features, self.headers,
(self.time_velocity, self.time_power, self.power_velocity),
self.color_labels)
self.plot_3d_plot(self.new_scaled_features, self.headers,
self.color_labels)
if self.show_outliers:
self.master_plot.scatter(self.outliers[:, 0],
self.outliers[:, 1],
self.outliers[:, 2],
c="black")
plot_hyperplane(self.outlier_detector,
self.master_plot,
interval=.04,
colors="orange")
self.show_constants_graph(self.features,
self.file_data,
self.labels,
c=self.color_labels)
self.fig.show()
plt.show()
self.showing = True
def close_all(self):
"""
Closes the figure
"""
if self.showing:
self.showing = False
plt.close(self.fig)
def plot_3d_plot(self, features, headers, labels):
"""
PLots the features in a 3d plot including the hyperplane that separates the data
:param features: the features to use to plot in the graph
:param headers: the axis titles
:param labels: the color of each data point
"""
self.master_plot.scatter(features[:, 0],
features[:, 1],
features[:, 2],
c=labels)
self.master_plot.set_xlabel(headers[0])
self.master_plot.set_ylabel(headers[1])
self.master_plot.set_zlabel(headers[2])
plot_hyperplane(self.clf, self.master_plot, colors='orange')
def graph(self, file_data):
"""
Graphs the features from the log file. Creates a 3D graph with time, average power to motors and velocity as axises.
It also decomposes the dimensions into individual 2D graphs.
:param file_data: the log file to use to extract the data from
"""
self.file_data = file_data
self.features, self.headers = get_features(file_data)
# FIXME make it so that the outliers can be visualized as well
self.new_scaled_features, self.features = manipulate_features(
self.features, file_data)
# features = scaler.inverse_transform(new_scaled_features)
if self.show_outliers:
self.new_scaled_features, self.outliers, self.outlier_detector = find_and_remove_outliers(
self.new_scaled_features)
if self.manually_find_remove_outliers:
selector = remove_outliers(self.new_scaled_features)
self.new_scaled_features = self.new_scaled_features[
selector.indexes]
self.features = self.features[selector.indexes]
self.labels = self.clf.predict(self.new_scaled_features)
self.color_labels = list(
map(lambda x: 'r' if x == 0 else 'b', self.labels))
def clear_graphs(self):
"""
Clears all the axes
"""
for ax in (self.master_plot, self.time_velocity, self.time_power,
self.power_velocity):
ax.cla()
def show_grid(self):
"""
Shows the grids for the major ticks in the plot.
"""
for ax in (self.time_velocity, self.time_power, self.power_velocity):
ax.grid(True)
def show_constants_graph(self, features, file_data, labels, c=None):
"""
Creates an addition figure that will display the a graph with the constants on it and also the lines of best fit of
the accelerating portion of it, the decelerating portion of it and the average of both of those lines
:param features: the features to use to show the graph and find the constants from
:param file_data: the whole file data
:param labels: the labels to say if a data point is accelerating or not
:param c: the color to plot the points
:return the constants for the motion profiling kV, kK and kAcc
"""
if is_straight_line(file_data):
easygui.msgbox(
"It was determined that the robot was trying to go straight. "
"As an ongoing feature the program will be able detect kLag, etc... "
"however for the instance this features has not been added")
constant_figure = plt.figure("Constants graph")
constants_plot = constant_figure.gca()
constants_plot.set_xlabel("Velocity")
constants_plot.set_ylabel("Average Power")
# fig_manager = plt.get_current_fig_manager()
# fig_manager.window.showMaximized()
constant_figure.canvas.manager.window.showMaximized()
x = features[:, 1]
y = features[:, 0]
constants_plot.scatter(x, y, c=labels if c is None else c)
acceleration_mask = labels == visualize.ACCELERATING
coef_accelerating, intercept_accelerating = find_linear_best_fit_line(
x[acceleration_mask], y[acceleration_mask])
deceleration_mask = labels == visualize.DECELERATING
coef_decelerating, intercept_decelerating = find_linear_best_fit_line(
x[deceleration_mask], y[deceleration_mask])
x_lim = np.array(constants_plot.get_xlim())
y_lim = np.array(constants_plot.get_ylim())
x, y = get_xy_limited(intercept_accelerating, coef_accelerating, x_lim,
y_lim)
constants_plot.plot(x, y)
x, y = get_xy_limited(intercept_decelerating, coef_decelerating, x_lim,
y_lim)
constants_plot.plot(x, y)
# constants_plot.plot(x_lim, coef_accelerating * x_lim + intercept_accelerating)
# constants_plot.plot(x_lim, coef_decelerating * x_lim + intercept_decelerating)
average_coef = (coef_accelerating + coef_decelerating) / 2
average_intercept = (intercept_accelerating +
intercept_decelerating) / 2
# constants_plot.plot(x_lim, average_coef * x_lim + average_intercept)
x, y = get_xy_limited(average_intercept, average_coef, x_lim, y_lim)
constants_plot.plot(x, y)
acceleration_coefficient = (coef_accelerating - average_coef)
acceleration_intercept = (intercept_accelerating - average_intercept)
k_acc = ((x.max() + x.min()) /
2) * acceleration_coefficient + acceleration_intercept
self.kV = average_coef
self.kK = average_intercept
self.kAcc = k_acc
bbox_props = dict(boxstyle="round,pad=0.3", fc="cyan", ec="b", lw=2)
constants_plot.text(x_lim[0],
y_lim[1],
"kV: {}\nkK: {}\nkAcc: {}".format(
average_coef, average_intercept, k_acc),
ha="left",
va="top",
bbox=bbox_props)
self.copy_constants()
constant_figure.canvas.callbacks.connect('button_press_event',
self.handle_mouse_click)
return average_coef, average_intercept, k_acc
def handle_mouse_click(self, event):
if event.dblclick:
self.copy_constants()
def copy_constants(self):
easygui.msgbox(
"The constants have been saved into your clipboard. Press Ctrl+V to paste them."
)
constants = "public static final double kV = {0};\r\n" \
"public static final double kK = {1};\r\n" \
"public static final double kAcc = {2};\r\n" \
.format(self.kV, self.kK, self.kAcc)
pyperclip.copy(constants)
def get_estimator_boundingbox(tiff_file,
channel=0,
outputdir='.',
w0=1,
w1=100,
h0=10,
h1=1000,
acut=0.9,
aratio_min=2.,
aratio_max=100.,
border_pad=5,
emin=1.0e-4,
debug=False,
threshold=None):
"""
INPUT:
* file to a tiff image.
* (w0,w1): minimum and maximum width for bounding box in pixels.
* (l0,l1): minimum and maximum length for bounding box in pixels.
* acut: minimum area/rectangle bounding box ratio.
* threshold is a lower threshold (everything below is set to zero). Value must be a float between 0 and 1. 1 is the maximum, eg. 255 or 65535.
OUTPUT:
* 2D matrix of weights corresponding to the probability that a pixel belongs to a cell.
USEFUL DOCUMENTATION:
* https://docs.opencv.org/3.4.3/dd/d49/tutorial_py_contour_features.html
* https://docs.opencv.org/2.4/modules/imgproc/doc/filtering.html?highlight=blur#blur
* https://docs.opencv.org/3.1.0/da/d22/tutorial_py_canny.html
* https://docs.opencv.org/3.4/d7/d4d/tutorial_py_thresholding.html
* https://docs.opencv.org/3.4/db/d5c/tutorial_py_bg_subtraction.html
"""
bname = os.path.splitext(os.path.basename(tiff_file))[0]
## read the input tiff_file
img = get_tiff2ndarray(tiff_file, channel=channel)
#img0 = np.copy(img)
# rescale dynamic range linearly (important for OTSU)
amin = np.min(img)
amax = np.max(img)
print "amin = {:.1g} amax = {:.1g}".format(amin, amax)
img = (np.float_(img) - amin) / (amax - amin)
## thresholding to binary mask
norm8 = float(2**8 - 1)
norm16 = float(2**16 - 1)
if threshold is None:
print "OTSU thresholding"
# convert to 8-bit image (Open CV requirement for OTSU)
img = np.array(255 * img, np.uint8)
img8 = np.copy(img)
# OTSU threshold
ret, img = cv2.threshold(img, 0, 255,
cv2.THRESH_BINARY + cv2.THRESH_OTSU)
thres1 = float(ret) / norm8 * (amax - amin) + amin
thres8 = np.uint8(thres1 * norm8)
thres16 = np.uint16(thres1 * norm16)
else:
thres1 = threshold
thres8 = np.uint8(thres1 * norm8)
thres16 = np.uint16(thres1 * norm16)
ret = max((thres1 - amin) / (amax - amin), 0) # value in rescaled DNR
ret = np.uint8(255 * ret) # uint8
print "thres1 = {:.1g} threshold_rescaled_DNR_uint8 = {:d}".format(
thres1, ret)
# convert to 8-bit image (Open CV requirement for OTSU)
img = np.array(255 * img, np.uint8)
img8 = np.copy(img)
# input threshold
ret1, img = cv2.threshold(img, ret, 255, cv2.THRESH_BINARY)
print "thres1 = {:.1g} thres8 = {:d} thres16 = {:d}".format(
thres1, thres8, thres16)
img_bin = np.copy(img)
## opening/closing operations
kernel = np.ones((3, 3), np.uint8) # smoothing kernel
img = cv2.morphologyEx(img, cv2.MORPH_OPEN, kernel)
#img_opening = np.copy(img)
img = cv2.erode(img, kernel, iterations=1)
#img_closing = np.copy(img)
img = cv2.dilate(img, kernel, iterations=1)
img_morph = np.copy(img)
## find connected components
ncomp, labels = cv2.connectedComponents(img)
print "Found {:d} objects".format(ncomp)
## compute the bounding box for the identified labels
#for n in range(ncomp):
height, width = img.shape
Y, X = np.mgrid[0:height, 0:width]
boundingboxes = []
boundingboxes_upright = []
pointsperbox = []
for n in np.arange(ncomp):
idx = (labels == n)
# pixels coordinates for the label
points = np.transpose([X[idx], Y[idx]])
pointsperbox.append(len(points))
# upright rectangles
bb = cv2.boundingRect(points)
boundingboxes_upright.append(bb)
# rotated rectangles
bb = cv2.minAreaRect(points)
boundingboxes.append(bb)
# estimator matrix
## compute scores
scores = []
for n in np.arange(ncomp):
bb = boundingboxes[n]
bb_upright = boundingboxes_upright[n]
area = pointsperbox[n]
# get bounding box width and height
xymid, wh, angle = bb
w, h = wh
if w > h:
wtp = w
w = h
h = wtp
area_rect = w * h
aval = area / area_rect
aratio = h / w
# print "w={:.1f} h={:.1f} aval={:.2e} aratio={:.1f}".format(w,h,aval,aratio)
# computing score
score = 1.
score *= min(1, np.exp((w - w0))) # penalize w < w0
score *= min(1, np.exp(w1 - w)) # penalize w > w1
score *= min(1, np.exp((h - h0))) # penalize w < w0
score *= min(1, np.exp(h1 - h)) # penalize w > w1
score *= min(1, np.exp(aval - acut)) # penalize area/rect < acut
score *= min(1, np.exp(aratio -
aratio_min)) # penalize aratio < aratio_min
score *= min(1, np.exp(aratio_max -
aratio)) # penalize aratio > aratio_max
# check that box corners of an upright bounding box are within the image plus some pad
x, y, ww, hh = bb_upright
x0 = x - border_pad
y0 = y - border_pad
x1 = x + ww + border_pad
y1 = y + hh + border_pad
# print "a0 = {:d} b0 = {:d}".format(x,y)
# print "a1 = {:d} b1 = {:d}".format(x+ww,y+hh)
# print "x0 = {:d} y0 = {:d}".format(x0,y0)
# print "x1 = {:d} y1 = {:d}".format(x1,y1)
if not (x0 >= 0 and x1 < width and y0 >= 0 and y1 < height):
score = 0.
# discard small values
if score < emin:
score = 0.
scores.append(score)
# estimator matrix
eimg = np.zeros(img.shape, dtype=np.float_)
for n in np.arange(ncomp):
idx = (labels == n)
eimg[idx] = scores[n]
nz = np.sum(eimg > 0.)
ntot = len(np.ravel(eimg))
print "nz = {:d} / {:d} sparcity index = {:.2e}".format(
nz, ntot,
float(nz) / float(ntot))
efname = bname
#efile = os.path.join(outputdir,efname+'.txt')
#efile = os.path.join(outputdir,efname+'.pkl')
efile = os.path.join(outputdir, efname + '.npz')
with open(efile, 'w') as fout:
#np.savetxt(fout, eimg)
#pkl.dump(eimg,fout)
ssp.save_npz(efile, ssp.coo_matrix(eimg), compressed=False)
print "{:<20s}{:<s}".format('est. file', efile)
if debug:
debugdir = os.path.join(outputdir, 'debug')
if not os.path.isdir(debugdir):
os.makedirs(debugdir)
# plots
import matplotlib.pyplot as plt
import matplotlib.patches
from matplotlib.path import Path
import matplotlib.collections
from matplotlib.gridspec import GridSpec
## rescale dynamic range linearly
img_base = np.array(img8, dtype=np.float_) / 255.
img_base = (img_base - np.min(img_base)) / (np.max(img_base) -
np.min(img_base))
img_base = np.array(img_base * 255, dtype=np.uint8)
ncolors = (20 - 1)
labels_iterated = np.uint8(labels -
np.int_(labels / ncolors) * ncolors) + 1
images = [img_base, img_bin, img_morph, labels_iterated, eimg]
titles = [
'original', 'binary (thres = {:d})'.format(thres8),
'closing/opening', 'bounding box', 'estimator'
]
cmaps = ['gray', 'gray', 'gray', 'tab20c', 'viridis']
nfig = len(images)
nrow = int(np.ceil(np.sqrt(nfig)))
ncol = nfig / nrow
if (ncol * nrow < nfig): ncol += 1
fig = plt.figure(num=None, figsize=(ncol * 4, nrow * 3))
gs = GridSpec(nrow, ncol, figure=fig)
axes = []
for r in range(nrow):
for c in range(ncol):
ind = r * ncol + c
if not (ind < nfig):
break
ax = fig.add_subplot(gs[r, c])
axes.append(ax)
ax.set_title(titles[ind].upper())
cf = ax.imshow(images[ind], cmap=cmaps[ind])
ax.set_xticks([]), ax.set_yticks([])
if titles[ind] == 'bounding box':
# draw bounding boxes
rects = []
rects_upright = []
codes = [
Path.MOVETO, Path.LINETO, Path.LINETO, Path.LINETO,
Path.CLOSEPOLY
]
for n in range(ncomp):
bb_upright = boundingboxes_upright[n]
bb = boundingboxes[n]
# upright rect
xlo, ylo, w, h = bb_upright
rect = matplotlib.patches.Rectangle((xlo, ylo),
width=w,
height=h,
fill=False)
rects_upright.append(rect)
# rect
verts = cv2.boxPoints(bb)
verts = np.concatenate((verts, [verts[0]]))
path = Path(verts, codes)
rect = matplotlib.patches.PathPatch(path)
rects.append(rect)
col = matplotlib.collections.PatchCollection(
rects_upright,
edgecolors='k',
facecolors='none',
linewidths=0.5)
ax.add_collection(col)
col = matplotlib.collections.PatchCollection(
rects,
edgecolors='r',
facecolors='none',
linewidths=0.5)
ax.add_collection(col)
if titles[ind] == 'estimator':
fig.colorbar(cf, ax=ax)
fname = "{}_estimator_debug".format(bname)
fileout = os.path.join(debugdir, fname + '.png')
gs.tight_layout(fig, w_pad=0)
plt.savefig(fileout, dpi=300)
print "{:<20s}{:<s}".format('debug file', fileout)
plt.close('all')
# from agarpad code: end """
""" canny: start
#test canny filtering
print np.min(img), np.max(img)
maxthres=2500
minthres=100
edges = cv2.Canny(img,threshold1=minthres,threshold2=maxthres,apertureSize=5)
print np.unique(edges)
print "START TEST"
import matplotlib.pyplot as plt
fig = plt.figure(num=None,figsize=(8,4))
plt.subplot(121)
plt.imshow(img, cmap='gray')
plt.xticks([]),plt.yticks([])
plt.subplot(122)
plt.imshow(edges, cmap='gray')
plt.xticks([]),plt.yticks([])
fileout = os.path.join(os.getcwd(),'test_get_estimator_contours.png')
fig.tight_layout()
plt.savefig(fileout,dpi=300)
print "writing: ", fileout
plt.close('all')
fig = plt.figure(num=None,figsize=(4,4))
hist,hedges = np.histogram(np.ravel(img), bins='auto')
plt.bar(hedges[:-1], hist, np.diff(hedges), facecolor='blue', lw=0)
fileout = os.path.join(os.getcwd(),'test_get_estimator_contours_histogram.png')
fig.tight_layout()
plt.savefig(fileout,dpi=300)
print "writing: ", fileout
plt.close('all')
sys.exit()
print "END TEST"
#test
# canny: start """
return os.path.realpath(efile)
def fit_continuum(self, data):
"""
Use the data and the mask to estimate and fit the continuum levels.
:param collapsed_data: data-cube in 3D array.
:return: array containing the fitted polynomium.
"""
collapsed_data = np.mean(data, axis=0)
norm = ImageNormalize(vmin=collapsed_data.min(),
vmax=collapsed_data.max(),
stretch=LogStretch())
fig = plt.figure(figsize=(8, 6))
fig.suptitle('Draw a rectangle using the mouse. \nPress <ENTER> to ' +
'accept it and carry on or "Q" to leave.')
gs = GridSpec(3, 3, height_ratios=[1, 12, 3], width_ratios=[1, 10, 1])
ax1 = plt.subplot(gs[4])
im1 = ax1.imshow(collapsed_data,
origin='lower',
interpolation='nearest',
cmap='hot_r',
norm=norm)
ax1.grid()
self.ax2 = plt.subplot(gs[7])
self.ax2.xaxis.set_ticklabels([])
self.ax2.yaxis.set_ticklabels([])
self.RS = MyRectangleSelector(ax1,
self.line_select_callback,
drawtype='box',
useblit=True,
button=[1],
minspanx=5,
minspany=5,
spancoords='pixels',
rectprops=dict(facecolor='green',
edgecolor='green',
alpha=0.5,
fill=True))
self.RS.set_active(True)
self.RS.connect_event('button_press_event', self.on_mouse_click)
self.RS.connect_event('button_release_event',
lambda e: self.on_mouse_release(e, data))
self.RS.connect_event('key_press_event', self.on_key_press)
gs.tight_layout(fig)
plt.show()
x1 = min(self.x1, self.x2)
x2 = max(self.x1, self.x2)
y1 = min(self.y1, self.y2)
y2 = max(self.y1, self.y2)
if x1 == x2:
log.warning('x1 and x2 are the same. Using the whole image width.')
x1 = 0
x2 = -1
if y1 == y2:
log.warning(
'y1 and y2 are the same. Using the whole image height.')
y1 = 0
y2 = -1
data = data[:, y1:y2, x1:x2]
data = data.mean(axis=1)
data = data.mean(axis=1)
median, std = np.median(data), np.std(data)
c = np.where(np.abs(data - median) < std, True, False)
x = np.arange(data.size)
p = np.polyfit(x[c], data[c], 3)
y = np.polyval(p, x)
return y
l1 = dax.plot(x, s, label='Field {:d}'.format(field), zorder=3)
l2 = dax.plot(x, s_mean, 'k:', label='Full sky', zorder=3)
l3 = dax.fill_between(x,
s_mean - s_err,
s_mean + s_err,
label='Single-field sample variance',
color='0.5',
alpha=0.5,
zorder=2)
dax.axhline(0, ls='--', color='k', zorder=0)
dax.set_xlim(x[0], x[-1])
dax.spines['top'].set_visible(False)
dax.set_xlabel('Observed Frequency [MHz]')
dax.set_ylabel('Kurtosis')
gs.tight_layout(fig, rect=[0, 0, 0.95, 0.92])
gs.update(hspace=0.1, wspace=0)
cbar = fig.colorbar(im, cax=cax)
# Draw lines from peaks to spines of images
fx1, fy1 = fig.transFigure.inverted().transform(
dax.transData.transform([158.435, 3.61]))
fx2, fy2 = fig.transFigure.inverted().transform(
dax.transData.transform([170.035, 0.025]))
m1xl, m1yl = fig.transFigure.inverted().transform(
max1.transAxes.transform([0, 0]))
m1xr, m1yr = fig.transFigure.inverted().transform(
max1.transAxes.transform([1, 0]))
m2xl, m2yl = fig.transFigure.inverted().transform(
max2.transAxes.transform([0, 0]))
m2xr, m2yr = fig.transFigure.inverted().transform(
def run(self, show=False):
# Load data
filename = self.filename
d = pyfits.getdata(filename)
h = pyfits.getheader(filename)
path, filename = os.path.split(filename)
# Get wavelength calibration
z = np.arange(h['naxis3'])
w = h['CRVAL3'] + h['CDELT3'] * (z - h['CRPIX3'])
# Convert wavelength from nm to Angstrom
# if w.all() < 1000.:
# w *= 10
# Signal-to-noise clipping
s = d.sum(axis=2)
s = s.sum(axis=1)
gauss_p, _ = self.fit_gaussian(z, s)
log.debug("Gaussian parameters ---")
log.debug("p[0] = %.2f" % gauss_p[0])
log.debug("p[1] = %.2f" % gauss_p[1])
log.debug("p[2] = %.2f" % gauss_p[2])
log.debug("p[3] = %.2f" % gauss_p[3])
lor_p = self.fit_lorentzian(z, s)
log.debug("Lorentzian parameters ---")
log.debug("p[0] = %.2f" % lor_p[0])
log.debug("p[1] = %.2f" % lor_p[1])
log.debug("p[2] = %.2f" % lor_p[2])
log.debug("p[3] = %.2f" % lor_p[3])
fwhm = np.abs(gauss_p[2] * 2 * np.sqrt(2 * np.log(2)))
filter_ = np.where(np.abs(z - gauss_p[1]) < fwhm, True, False)
if show:
plt.plot(z, self.gaussian(gauss_p, z), 'r-', lw=2, label='Gaussian Fit')
plt.plot(z, self.lorentzian(lor_p, z), 'b-', lw=2, label='Lorentzian Fit')
plt.plot(z, s, 'ko')
plt.plot(z[filter_], s[filter_], 'ro')
plt.title('Cube collapsed in XY and fits.')
plt.grid()
plt.legend(loc='best')
plt.gcf().canvas.mpl_connect('key_press_event', self.on_key_press)
plt.show()
signal = d[filter_].mean(axis=0)
noise = d[np.logical_not(filter_)].mean(axis=0)
snr = signal / noise
snr = ndimage.median_filter(snr, 3)
snr_mask = np.where(snr > 2, True, False)
snr_laplacian = ndimage.morphological_laplace(snr * snr_mask, size=3)
snr_mask *= np.where(np.abs(snr_laplacian) < 5.0, True, False)
snr_mask = ndimage.binary_opening(snr_mask, iterations=5)
snr_mask = ndimage.binary_closing(snr_mask, iterations=5)
if show:
fig1 = plt.figure(figsize=(20, 5))
plt.title('Signal-to-Noise Ratio')
gs = GridSpec(1, 3)
ax1 = plt.subplot(gs[0])
ax1.set_title('SNR')
im1 = ax1.imshow(snr, cmap='cubehelix', interpolation='nearest',
origin='lower', vmin=0)
div1 = make_axes_locatable(ax1)
cax1 = div1.append_axes("right", size="5%", pad=0.05)
cbar1 = plt.colorbar(mappable=im1, cax=cax1, use_gridspec=True,
orientation='vertical')
ax2 = plt.subplot(gs[1])
ax2.set_title('Mask')
im2 = ax2.imshow(np.where(snr_mask, 1, 0), cmap='gray',
interpolation='nearest', origin='lower',
vmin=0, vmax=1)
div2 = make_axes_locatable(ax2)
cax2 = div2.append_axes("right", size="5%", pad=0.05)
cbar2 = plt.colorbar(mappable=im2, cax=cax2, use_gridspec=True,
orientation='vertical')
cmap = plt.get_cmap('cubehelix')
cmap.set_bad('w', 1.0)
ax3 = plt.subplot(gs[2])
ax3.set_title('Masked')
im3 = ax3.imshow(np.ma.masked_where(~snr_mask, snr), cmap=cmap, interpolation='nearest',
origin='lower', vmin=0)
div3 = make_axes_locatable(ax3)
cax3 = div3.append_axes("right", size="5%", pad=0.05)
cbar3 = plt.colorbar(mappable=im3, cax=cax3, use_gridspec=True, orientation='vertical')
plt.gcf().canvas.mpl_connect('key_press_event', self.on_key_press)
gs.tight_layout(fig1)
plt.show()
pyfits.writeto(filename.replace('.','.SNR.'), snr, h, clobber=True)
pyfits.writeto(filename.replace('.','.SNR_LAPLACIAN.'), snr_laplacian, h, clobber=True)
# Adjust continuum
continuum = self.fit_continuum(d)
# Subtract continuum
continuum = np.reshape(continuum, (continuum.size, 1, 1))
continuum = np.repeat(continuum, d.shape[1], axis=1)
continuum = np.repeat(continuum, d.shape[2], axis=2)
d -= continuum
del continuum
# Save the data-cube with the continuum subtracted
pyfits.writeto(os.path.join(path,
filename.replace('.fits', '.no_cont.fits')),
d, h, clobber=True)
# Adjust each pixel to a gaussian
flux = np.zeros_like(snr) - np.inf
velocity = np.zeros_like(snr) - np.inf
width = np.zeros_like(snr) - np.inf
continuum = np.zeros_like(snr) - np.inf
niter = np.zeros_like(snr) - np.inf
fit_gauss_cube = np.zeros_like(d)
for (j, i) in itertools.product(range(d.shape[1]), range(d.shape[2])):
if snr_mask[j, i]:
p, s = self.fit_gaussian(w, d[:,j,i])
else:
p, s = [-np.inf, -np.inf, -np.inf, -np.inf], -1
flux[j, i] = p[0]
velocity[j, i] = p[1]
width[j, i] = p[2]
continuum[j, i] = p[3]
niter[j,i] = s
fit_gauss_cube[:, j, i] = self.gaussian(p, w)
log.debug("%04d %04d" % (j, i))
mask = np.ma.masked_equal(snr_mask, False)
pyfits.writeto(os.path.join(path,
filename.replace('.fits', '.GAUSS.fits')),
fit_gauss_cube, h, clobber=True)
if show:
fig1 = plt.figure(figsize=(16,6))
plt.title('Final Results')
gs = GridSpec(2, 3)
magma = plt.get_cmap('magma')
magma.set_bad('w', 1.0)
ax1 = plt.subplot(gs[0])
ax1.set_title('Collapsed cube')
im1 = ax1.imshow(np.ma.masked_where(~snr_mask, d.sum(axis=0)),
cmap=magma, interpolation='nearest',
origin='lower')
divider1 = make_axes_locatable(ax1)
cax1 = divider1.append_axes("right", size="5%", pad=0.05)
cbar1 = plt.colorbar(mappable=im1, cax=cax1, use_gridspec=True,
orientation='vertical')
viridis = plt.get_cmap('viridis')
viridis.set_bad('w', 1.0)
ax2 = plt.subplot(gs[1])
ax2.set_title('Fit n-iteractions')
im2 = ax2.imshow(np.ma.masked_where(~snr_mask, niter),
cmap=viridis, interpolation='nearest',
origin='lower')
divider2 = make_axes_locatable(ax2)
cax2 = divider2.append_axes("right", size="5%", pad=0.05)
cbar2 = plt.colorbar(mappable=im2, cax=cax2, use_gridspec=True,
orientation='vertical')
ax3 = plt.subplot(gs[3])
ax3.set_title('Flux')
divider3 = make_axes_locatable(ax3)
cax3 = divider3.append_axes("right", size="5%", pad=0.05)
im3 = ax3.imshow(flux * mask, cmap=viridis,
interpolation='nearest', origin='lower')
cbar3 = plt.colorbar(mappable=im3, cax=cax3, use_gridspec=True,
orientation='vertical')
RdYlBu = plt.get_cmap('RdYlBu')
RdYlBu.set_bad('w', 1.0)
ax4 = plt.subplot(gs[4])
ax4.set_title('Center')
vmin = np.median(velocity * mask) - 2 * np.std(velocity * mask)
vmax = np.median(velocity * mask) + 2 * np.std(velocity * mask)
im4 = ax4.imshow(velocity * mask, cmap=RdYlBu,
interpolation='nearest', origin='lower',
vmin=vmin, vmax=vmax)
divider4 = make_axes_locatable(ax4)
cax4 = divider4.append_axes("right", size="5%", pad=0.05)
cbar4 = plt.colorbar(mappable=im4, cax=cax4, use_gridspec=True,
orientation='vertical')
ax5 = plt.subplot(gs[5])
ax5.set_title('Width')
vmin = np.median(width * mask) - 2 * np.std(width * mask)
vmax = np.median(width * mask) + 2 * np.std(width * mask)
im5 = ax5.imshow(width * mask, cmap=viridis,
interpolation='nearest', origin='lower')
divider5 = make_axes_locatable(ax5)
cax5 = divider5.append_axes("right", size="5%", pad=0.05)
cbar5 = plt.colorbar(mappable=im5, cax=cax5, use_gridspec=True,
orientation='vertical')
plt.gcf().canvas.mpl_connect('key_press_event', self.on_key_press)
plt.tight_layout()
plt.show()
del h['CRVAL3']
del h['CDELT3']
del h['CRPIX3']
del h['CTYPE3']
del h['CUNIT3']
del h['C3_3']
del h['CD3_3']
pyfits.writeto(
os.path.join(path, filename.replace('.fits', '.flux.fits')),
flux, h, clobber=True)
pyfits.writeto(
os.path.join(path, filename.replace('.fits', '.velo.fits')),
velocity, h, clobber=True)
pyfits.writeto(
os.path.join(path, filename.replace('.fits', '.width.fits')),
width, h, clobber=True)
pyfits.writeto(
os.path.join(path, filename.replace('.fits', '.cont.fits')),
continuum, h, clobber=True)
return
def setup_settings(self):
setting_fig = plt.figure("Settings")
grid = GridSpec(12, 3, setting_fig)
textbox_ax = plt.subplot(grid[0, 1:])
self.create_text_box(textbox_ax, "Min Ingot Width",
lambda: self.width[0], self.set_min_width)
textbox_ax = plt.subplot(grid[1, 1:])
self.create_text_box(textbox_ax, "Max Ingot Width",
lambda: self.width[1], self.set_max_width)
textbox_ax = plt.subplot(grid[2, 1:])
self.create_text_box(textbox_ax, "Min Ingot Height",
lambda: self.height[0], self.set_min_height)
textbox_ax = plt.subplot(grid[3, 1:])
self.create_text_box(textbox_ax, "Max Ingot Height",
lambda: self.height[1], self.set_max_height)
textbox_ax = plt.subplot(grid[4, 1:])
self.create_text_box(textbox_ax,
"Number of shelves",
lambda: self.number_of_shelves,
self.set_number_of_shelves,
data_type=int)
textbox_ax = plt.subplot(grid[5, 1:])
self.create_text_box(textbox_ax, "Shelve width",
lambda: self.shelve_spec[0],
self.set_shelve_width)
textbox_ax = plt.subplot(grid[6, 1:])
self.create_text_box(textbox_ax, "Shelve height",
lambda: self.shelve_spec[1],
self.set_shelve_height)
textbox_ax = plt.subplot(grid[7, 1:])
self.create_text_box(textbox_ax,
"Number of ingots",
lambda: self.number_of_ingot,
self.set_number_of_ingots,
data_type=int)
textbox_ax = plt.subplot(grid[8, 1:])
self.create_text_box(textbox_ax, "Air Gap Width",
lambda: self.air_gap_width,
self.set_air_gap_width)
valid_algorithms = list(Viewer.valid_stacking_algorithms.keys())
stacking_algorithm_ax = plt.subplot(grid[9, :])
radio_buttons = MyRadioButtons(stacking_algorithm_ax,
valid_algorithms,
orientation="horizontal")
index = valid_algorithms.index(self.stacking_algorithm)
radio_buttons.set_active(index)
radio_buttons.on_clicked(self.set_stacking_algorithm)
self.setting_widgets.append(radio_buttons)
# TODO fix checkbox scaling
show_animation_ax = plt.subplot(grid[10, 1])
check = CheckButtons(show_animation_ax, ['Show Animation'],
[self.show_animation])
check.on_clicked(self.set_show_animation)
self.setting_widgets.append(check)
random_ax = plt.subplot(grid[-1, 0])
random_button = Button(random_ax, "Randomize")
random_button.on_clicked(self.randomize)
self.setting_widgets.append(random_button)
apply_ax = plt.subplot(grid[-1, 1])
apply_button = Button(apply_ax, "Apply/Reset")
apply_button.on_clicked(self.apply)
self.setting_widgets.append(apply_button)
run_ax = plt.subplot(grid[-1, 2])
run_button = Button(run_ax, "Run")
run_button.on_clicked(self.run)
self.setting_widgets.append(run_button)
grid.tight_layout(setting_fig, h_pad=.1)
def plot_indiv_pdfs(pdf1d_file, pdf2d_file, starnum):
"""
Make a triangle/corner plot with the 1D and 2D PDFs of a star
Parameters
----------
pdf1d_file : str
path+file for the BEAST 1D PDFs
pdf2d_file : list of strings
path+file for the BEAST 2D PDFs
starnum : int
the index of the star to plot
"""
with fits.open(pdf2d_file) as hdu_2d, fits.open(pdf1d_file) as hdu_1d:
# start with the 2D PDF file to figure out which parameters to plot
# list of extension names
# - skip the extension named "PRIMARY"
# - skip any extension with a dimension of 1 (means that param wasn't fit)
ext_list = [
hdu_2d[i].name for i in range(len(hdu_2d))
if ("PRIMARY" not in hdu_2d[i].name) and (
1 not in hdu_2d[i].data.shape)
]
# grab the parameter names
param_list_temp = [i for x in ext_list for i in x.split("+")]
# put them in the order we want
_plot_order = ["M_ini", "logA", "distance", "Z", "Av", "Rv", "f_A"]
param_list = [p for p in _plot_order if p in param_list_temp]
# if there are parameters not in the predetermined plot order, append them
for p in param_list_temp:
if p not in param_list:
param_list.append(p)
# total number of parameters
n_params = len(param_list)
# figure
fig = plt.figure(figsize=(4 * n_params, 4 * n_params))
# label font sizes
label_font = 25
tick_font = 22
# iterate through the panels
for i, pi in enumerate(param_list):
for j, pj in enumerate(param_list[i:], i):
# print('plotting {0} and {1}'.format(pi, pj))
# not along diagonal
if i != j:
# set up subplot
plt.subplot(n_params, n_params, i + j * (n_params) + 1)
ax = plt.gca()
# find the 2D PDF and make sure it's properly rotated
try:
image = hdu_2d[pi + "+" + pj].data[starnum, :, :].T
except KeyError:
image = hdu_2d[pj + "+" + pi].data[starnum, :, :]
except Exception:
raise
# create axis/labels
x_bins, x_label = setup_axis(pi, hdu_1d)
y_bins, y_label = setup_axis(pj, hdu_1d)
# plot 2D PDF image
im = plt.imshow(
np.log(image / np.max(image)),
extent=(
np.min(x_bins),
np.max(x_bins),
np.min(y_bins),
np.max(y_bins),
),
cmap="magma",
vmin=-10,
vmax=0,
aspect="auto",
origin="lower",
)
# attempt to plot 1/2/3 sigma contours
# (doesn't work if the probability is super concentrated,
# which is generally due to the grid being really coarse)
try:
im_sort = np.sort(image, axis=None)[::-1]
cumsum = np.cumsum(im_sort)
cumsum /= np.max(cumsum)
clevels = [
np.log(im_sort[np.where(cumsum <= p)[0][-1]])
for p in [0.68, 0.95, 0.997]
]
plt.contour(
x_bins,
y_bins,
image,
levels=clevels,
colors="k",
linestyles="-",
)
except IndexError:
# print(" can't make contours for this")
pass
except ValueError:
pass
except Exception:
raise
ax.tick_params(
axis="both",
which="both",
direction="in",
labelsize=tick_font,
bottom=True,
top=True,
left=True,
right=True,
)
# axis labels and ticks
if i == 0:
ax.set_ylabel(y_label, fontsize=label_font)
# ax.get_yaxis().set_label_coords(-0.35,0.5)
else:
ax.set_yticklabels([])
if j == n_params - 1:
ax.set_xlabel(x_label, fontsize=label_font)
plt.xticks(rotation=-45)
else:
ax.set_xticklabels([])
# along diagonal
if i == j:
# set up subplot
plt.subplot(n_params, n_params, i + j * (n_params) + 1)
ax = plt.gca()
# create axis/labels
x_bins, x_label = setup_axis(pi, hdu_1d)
# make histogram
_pdf = hdu_1d[pi].data[starnum, :]
plt.plot(
x_bins,
_pdf / np.max(_pdf),
marker="o",
mew=0,
color="black",
markersize=2,
linestyle="-",
)
# axis ranges
plt.xlim(np.min(x_bins), np.max(x_bins))
plt.ylim(0, 1.05)
ax.tick_params(axis="y",
which="both",
length=0,
labelsize=tick_font)
ax.tick_params(axis="x",
which="both",
direction="in",
labelsize=tick_font)
# axis labels and ticks
ax.set_yticklabels([])
if i < n_params - 1:
ax.set_xticklabels([])
if i == n_params - 1:
ax.set_xlabel(x_label, fontsize=label_font)
plt.xticks(rotation=-45)
# plt.subplots_adjust(wspace=0.05, hspace=0.05)
plt.tight_layout()
# add a colorbar
gs = GridSpec(nrows=20, ncols=n_params)
cax = fig.add_subplot(gs[0, 2:])
cbar = plt.colorbar(im, cax=cax, orientation="horizontal")
cbar.set_label("Log Likelihood", fontsize=label_font)
cbar.ax.tick_params(labelsize=tick_font)
gs.tight_layout(fig)
fig.savefig(
pdf1d_file.replace("pdf1d.fits",
"pdfs_starnum_{0}.pdf".format(starnum)))
plt.close(fig)
def calculateDistance(self):
"""
TMP gets distance to ngc from pleiedes
"""
pleiades = np.genfromtxt(
"/home/conor/scripts/StarBug/catalogs/pleiades_sloane")
pleiades = pleiades[np.where(pleiades[:, 0] < 15)]
pleiades = pleiades[np.where(pleiades[:, 1] < 0.3)]
#pleiades = pleiades[np.where( pleiades[:,1] >-0.7)]
pli_distance = 134
#pli_distance = 2327#NOT PLI
ig = 0
igr = 1
iug = 2
fig = plt.figure()
gs = GridSpec(5, 2)
ax0 = plt.subplot(gs[0:3, :])
ax0.scatter(pleiades[:, 1], pleiades[:, ig], c='k', marker='*')
for s in self.sourcelist:
s.construct_colours([2, 0], [0, 1])
if (s.colours[1] > 0.25 or s.colours[1] < -0.6):
s.colours[1] = np.nan
ax0.scatter(s.colours[1], s.MAG[0], c='b', marker='*')
plt.gca().invert_yaxis()
ax2 = plt.subplot(gs[3:, :], sharex=ax0)
colourmin = np.nanmin(pleiades[:, 1])
colourmax = np.nanmax(pleiades[:, 1])
sourceG_R = []
sourceG = []
sourcedG = []
for s in self.sourcelist:
c = s.colours[1]
if (np.isfinite(c)):
sourceG_R.append(c)
sourceG.append(s.MAG[0])
sourcedG.append(s.MAGERR[0])
if c < colourmin: colourmin = c
if c > colourmax: colourmax = c
Range = np.linspace(colourmin, colourmax, 50)
sourceG = np.array(sourceG)
sourcedG = np.array(sourcedG)
dm = []
ddm = []
colour = []
for i in range(len(Range[:-1])):
c0 = Range[i]
c1 = Range[i + 1]
pliMask = (pleiades[:, 1] >= c0) * (pleiades[:, 1] < c1)
pliMean = np.mean(pleiades[:, ig][pliMask])
catMask = (sourceG_R >= c0) * (sourceG_R < c1)
catMean = np.nanmean(sourceG[catMask])
if (np.isfinite(catMean) and np.isfinite(pliMean)):
pliErr = np.std(pleiades[:, ig][pliMask])
catErr = np.sqrt(
sum([(em / len(sourcedG[catMask]))**2.
for em in sourcedG[catMask]]))
if (pliErr < 1 and catErr < 1 and Range[i] < 0.17):
dm.append(pliMean - catMean)
colour.append(Range[i])
ddm.append(np.sqrt(pliErr**2. + catErr**2.))
ax0.scatter(c0, catMean, c='r', marker='x')
#ax0.scatter(c0, pliMean, c='r', marker='x')
deltaM = np.nanmean(dm)
deltaMerr = np.sqrt(np.nansum([(x / len(dm))**2. for x in ddm]))
Dn = pli_distance * 10.0**(-deltaM / 5.)
dDn = np.sqrt(
(((-pli_distance * np.log(10) / 5.) * 10.0**(-deltaM / 5.)) *
deltaMerr)**2.0)
print(Dn, dDn)
print("Distance Modulus: %f" % (-5.0 * np.log10(Dn / 10.0)))
ax2.scatter(colour, dm, s=5, c='k')
ax2.errorbar(colour, dm, yerr=ddm, linewidth=0, elinewidth=1, c='k')
ax0.tick_params(direction='in', labelbottom=False)
ax2.tick_params(direction='in')
#ax2.axhline(deltaM, c='xkcd:magenta')
ax2.axhline(deltaM + deltaMerr, c='xkcd:magenta')
ax2.axhline(deltaM - deltaMerr, c='xkcd:magenta')
ax2.set_xlabel(r'$(g-r)_0$')
ax2.set_ylabel(r'$\Delta$M')
ax0.set_ylabel(r'$g_0$')
gs.tight_layout(fig)
for s in self.sourcelist:
s.set_distance(Dn, dDn)
s._voidCalcAbsoluteMagnitudes()
#plt.show()
fig.savefig('out/%s_distance.png' % self.name)
for j in range(ncols):
k = i * ncols + j
if i == 0 and j == 0:
maps_ax[i, j] = fig.add_subplot(gs2[1 + i, j],
projection=wcs[k])
else:
maps_ax[i, j] = fig.add_subplot(gs2[1 + i, j],
sharex=maps_ax[0, 0],
sharey=maps_ax[0, 0],
projection=wcs[k])
plot_stat(stat_ax)
plot_maps(maps_ax)
xlocs = [145.115, 148.155, 163.355, 178.555, 187.675, 193.755]
ylocs = np.ones_like(xlocs) * 2.0
label_plots(xlocs, ylocs)
# fig.text(0.01, (1-1./(nrows+1))*1.2, ylabels[stat],
# rotation='vertical', verticalalignment='center')
# fig.text(0.5, 0.01, 'Right Ascension [$^{\circ}$]',
# horizontalalignment='center')
fig.text(0.01,
1. / (nrows + 1),
'Declination [$^{\circ}$]',
rotation='vertical',
verticalalignment='center')
stat_ax.set_ylabel(ylabels[stat])
maps_ax[1, 1].set_xlabel('Right Ascension [$^{\circ}$]')
# maps_ax[0, 0].set_ylabel('Declination [$^{\circ}$]')
gs0.tight_layout(fig, rect=[-0.02, 0.05, 1, 1])
# plt.tight_layout()
# plt.show()
plt.savefig('kurt_maps_hera331_bw3MHz.pdf', dpi=200)
def fit_continuum(self, data):
"""
Use the data and the mask to estimate and fit the continuum levels.
:param collapsed_data: data-cube in 3D array.
:return: array containing the fitted polynomium.
"""
collapsed_data = np.mean(data, axis=0)
norm = ImageNormalize(vmin=collapsed_data.min(), vmax=collapsed_data.max(), stretch=LogStretch())
fig = plt.figure(figsize=(8, 6))
fig.suptitle('Draw a rectangle using the mouse. \nPress <ENTER> to ' +
'accept it and carry on or "Q" to leave.')
gs = GridSpec(3, 3, height_ratios=[1, 12, 3], width_ratios=[1, 10, 1])
ax1 = plt.subplot(gs[4])
im1 = ax1.imshow(collapsed_data, origin='lower', interpolation='nearest',
cmap='hot_r', norm=norm)
ax1.grid()
self.ax2 = plt.subplot(gs[7])
self.ax2.xaxis.set_ticklabels([])
self.ax2.yaxis.set_ticklabels([])
self.RS = MyRectangleSelector(ax1, self.line_select_callback, drawtype='box',
useblit=True, button=[1], minspanx=5,
minspany=5, spancoords='pixels',
rectprops = dict(facecolor='green',
edgecolor = 'green',
alpha=0.5, fill=True))
self.RS.set_active(True)
self.RS.connect_event('button_press_event', self.on_mouse_click)
self.RS.connect_event('button_release_event', lambda e: self.on_mouse_release(e, data))
self.RS.connect_event('key_press_event', self.on_key_press)
gs.tight_layout(fig)
plt.show()
x1 = min(self.x1, self.x2)
x2 = max(self.x1, self.x2)
y1 = min(self.y1, self.y2)
y2 = max(self.y1, self.y2)
if x1 == x2:
log.warning('x1 and x2 are the same. Using the whole image width.')
x1 = 0
x2 = -1
if y1 == y2:
log.warning('y1 and y2 are the same. Using the whole image height.')
y1 = 0
y2 = -1
data = data[:, y1:y2, x1:x2]
data = data.mean(axis=1)
data = data.mean(axis=1)
median, std = np.median(data), np.std(data)
c = np.where(np.abs(data - median) < std, True, False)
x = np.arange(data.size)
p = np.polyfit(x[c], data[c], 3)
y = np.polyval(p, x)
return y
def __init__(self,
nodes=50,
coupling_network=nx.complete_graph,
distribution=np.random.standard_normal,
timesteps=200,
t_end=None,
symmetric=False,
interval=25,
**osc_params):
"""
:param nodes: The number of oscillators to simulate (default 50)
:param coupling_network: Networkx graph construction function
representing the coupling topology (default is nx.complete_graph). The
function should take a single argument, the number of nodes, and return
a graph.
:param distribution: Function to generate the frequency distribution.
It should take an single argument, the number of nodes, and return a
numpy array containing the frequency
:param timesteps:
:param t_end:
:param symmetric:
:param interval:
:param osc_params:
"""
self.t_end = t_end
self.n = nodes
if symmetric:
freq = list(distribution(int(nodes / 2)))
freq += [-f for f in freq]
if nodes % 2 == 1:
freq.append(0)
self.omega = np.array(sorted(freq))
else:
self.omega = np.array(sorted(distribution(int(nodes))))
self.graph = coupling_network(nodes)
if t_end:
self.t = np.linspace(0, t_end, timesteps).T
self.z = np.zeros((nodes, timesteps), dtype=np.complex)
else:
self.z = np.zeros((nodes, 1), dtype=np.complex)
self.z[:, 0] = np.random.uniform(low=-1, high=1, size=self.z[:,
0].shape) + 1j * np.random.uniform(
low=-1, high=1, size=self.z[:, 0].shape)
if t_end:
self._solve_ode(**osc_params)
max_z = max(min(abs(self.z).max(), 5), 1)
#max_z = 2
fig = plt.figure()
gs = GridSpec(2, 5)
self.ax_phase = plt.subplot(gs[0, :3])
self.ax_complex = plt.subplot(gs[0, 3:])
self.ax_r = plt.subplot(gs[1, :])
self._init_phase_axis()
self._init_complex_plane(extent=max_z)
if not t_end:
self.t_max = 50
else:
self.t_max = t_end
self.t_max_step = 25
self._init_r_axis(t_max=self.t_max, r_max=max_z)
gs.tight_layout(fig)
self.o_line = Line2D([], [], color='none', marker='.',
markerfacecolor='r')
self.ax_phase.add_line(self.o_line)
self.c_line = Line2D([], [], color='none', marker='.',
markerfacecolor='r')
self.cz_line = Line2D([], [], color='none', marker='o',
markeredgecolor='b')
self.ax_complex.add_line(self.c_line)
self.ax_complex.add_line(self.cz_line)
self.r_line = Line2D([], [], color='red')
self.ax_r.add_line(self.r_line)
self._sn = 1./np.sqrt(nodes)
if t_end:
self.rn_line = Line2D([0, t_end],[self._sn, self._sn], linestyle=':')
else:
self.rn_line = Line2D([0, self.t_max], [self._sn, self._sn],
linestyle=':')
self._running = False
self.ax_r.add_line(self.rn_line)
self._gen_args = osc_params
self._timestep = 2 * interval / 1000.0
animation.TimedAnimation.__init__(self, fig, interval=interval, blit=True)
def make_evaluation_plots_from_data(
data: Sequence[ExperimentResult],
exp_name: str,
param_labels: Sequence[str],
bar_plot_xlabel: str,
fig_save_path: Path = Path('../results/plots'),
sim_non_cli_opts: Optional[PandemicSimNonCLIOpts] = None,
max_hospital_capacities: Optional[List[int]] = None,
show_summary_plots: bool = True,
show_cumulative_reward: bool = False,
show_time_to_peak: bool = True,
show_pandemic_duration: bool = True,
show_stage_trials: bool = False,
annotate_stages: Union[bool, Sequence[bool]] = False,
figsize: Optional[Tuple[int, int]] = None):
n_params = len(param_labels)
os.makedirs(str(fig_save_path.absolute()), exist_ok=True)
annotate_stages = [annotate_stages] * n_params if isinstance(
annotate_stages, bool) else annotate_stages
sim_non_cli_opts = sim_non_cli_opts or PandemicSimNonCLIOpts(
small_town_population_params)
hp = sim_non_cli_opts.population_params.location_type_to_params[Hospital]
max_hospital_capacities = ([hp.num * hp.visitor_capacity] *
len(data) if max_hospital_capacities is None
else max_hospital_capacities)
gis_legend = [summ.value for summ in sorted_infection_summary]
sup_title = f"{' '.join([s.capitalize() for s in exp_name.split(sep='_')])}"
plot_ref_labels = string.ascii_lowercase + string.ascii_uppercase
plot_ref_label_i = 0
gs1: Optional[GridSpec] = None
if show_summary_plots:
figsize = figsize if figsize is not None else ((
16, 6) if n_params <= 5 else (20, 12))
fig = plt.figure(num=sup_title, figsize=figsize)
gs1 = GridSpec(n_params, 3)
axs = np.array([fig.add_subplot(sp)
for sp in gs1]).reshape(n_params, 3)
for i, (exp_result, param_label, max_hospital_capacity,
ann_stages) in enumerate(
zip(data, param_labels, max_hospital_capacities,
annotate_stages)):
plot_global_infection_summary(exp_result,
ax=axs[i, 0],
annotate_stages=ann_stages)
if show_stage_trials:
seed_indices = np.random.permutation(
len(exp_result.obs_trajectories.stage.shape[1]))[:3]
for seed_i in seed_indices:
axs[i, 2].plot(exp_result.obs_trajectories.stage[:, seed_i,
0])
axs[i, 2].set_title(
f'Stages over Time\n(shown for {len(seed_indices)} trials)'
)
axs[i, 2].set_yticks(
[0, np.max(exp_result.obs_trajectories.stage)])
axs[i, 2].set_yticklabels([
'Open\n(Stage-0)',
f'Lockdown\n(Stage-{int(np.max(exp_result.obs_trajectories.stage))})'
])
axs[i, 2].set_xlabel('time (days)')
else:
plot_global_infection_summary(exp_result,
testing_summary=True,
annotate_stages=ann_stages,
ax=axs[i, 1])
plot_critical_summary(exp_result,
max_hospitals_capacity=max_hospital_capacity,
annotate_stages=ann_stages,
ax=axs[i,
1] if show_stage_trials else axs[i,
2])
for j, ax in enumerate(axs[i]):
ref_label_offset = 20
ax.yaxis.tick_right()
ax.yaxis.set_label_position("right")
ax.set_ylabel(ax.get_ylabel(), rotation=-90, labelpad=10)
if i < (axs.shape[0] - 1):
ax.set_xlabel('')
ref_label_offset = 0
if j < (axs.shape[1] - 1):
ax.set_ylabel('')
if i > 0:
ax.set_title('')
axs[i, j].annotate(f'({plot_ref_labels[plot_ref_label_i]})',
(0.5, 0.),
xytext=(0, -25 - ref_label_offset),
textcoords='offset points',
xycoords='axes fraction',
ha='center',
va='center',
size=14)
plot_ref_label_i += 1
axs[i, 0].annotate(f'{param_label}', (0, 0.5),
xytext=(-15, 0),
textcoords='offset points',
xycoords='axes fraction',
ha='center',
va='center',
size=14,
rotation=90)
handles = (axs[0, 0].get_legend_handles_labels()[0] +
axs[0, 2].get_legend_handles_labels()[0][-1:])
axs[0, 0].legend(handles,
gis_legend +
['Max hospital capacity', 'cumulative_reward'],
fancybox=True,
loc='best',
fontsize=4 if n_params > 3 else 6)
with warnings.catch_warnings():
warnings.simplefilter("ignore", UserWarning)
# This raises warnings since tight layout cannot
# handle gridspec automatically. We are going to
# do that manually so we can filter the warning.
gs1.tight_layout(fig, rect=[0.01, None, 0.6, None])
else:
figsize = figsize if figsize is not None else (10, 3)
fig = plt.figure(num=sup_title, figsize=figsize)
bar_plots_2d = (3 + int(show_time_to_peak) + int(show_pandemic_duration) +
int(show_cumulative_reward))
bar_plots_3d = 0
total_bar_plots = bar_plots_2d + bar_plots_3d
n_cols = int(np.round(np.sqrt(total_bar_plots)))
n_rows = int(n_cols) if n_cols**2 >= total_bar_plots else n_cols + 1
gs2 = gridspec.GridSpec(n_rows, n_cols)
axs = []
plot_i = 0
for sp in gs2:
if plot_i < bar_plots_2d:
axs.append(fig.add_subplot(sp))
elif plot_i < (bar_plots_2d + bar_plots_3d):
axs.append(fig.add_subplot(sp, projection='3d'))
plot_i += 1
plot_multi_params_summary(
data,
param_labels=param_labels,
xlabel=bar_plot_xlabel,
max_hospitals_capacities=max_hospital_capacities,
show_cumulative_reward_plot=show_cumulative_reward,
show_time_to_peak=show_time_to_peak,
show_pandemic_duration=show_pandemic_duration,
axs=axs)
for ax in axs:
if ax.axison or isinstance(ax, Axes3D):
offset = 20 if max([len(label)
for label in param_labels]) < 5 else 30
ax.annotate(f'({plot_ref_labels[plot_ref_label_i]})', (0.5, 0.),
xytext=(0, -25 - offset),
textcoords='offset points',
xycoords='axes fraction',
ha='center',
va='center',
size=14)
plot_ref_label_i += 1
if gs1:
with warnings.catch_warnings():
# This raises warnings since tight layout cannot
# handle gridspec automatically. We are going to
# do that manually so we can filter the warning.
warnings.simplefilter("ignore", UserWarning)
gs2.tight_layout(fig, rect=[0.6, None, None, None])
top = min(gs1.top, gs2.top)
bottom = max(gs1.bottom, gs2.bottom)
gs1.update(top=top, bottom=bottom)
gs2.update(top=top, bottom=bottom)
plt.annotate(bar_plot_xlabel, (0.01, 0.5),
xytext=(0, 0),
textcoords='offset points',
xycoords='figure fraction',
ha='center',
va='center',
size=16,
rotation=90)
else:
plt.tight_layout()
plt.savefig(fig_save_path / (exp_name + '.pdf'))
def mountains_series():
def format_axes(fig):
for i, ax in enumerate(fig.axes):
ax.tick_params(labelbottom=False,
labelleft=False,
bottom=False,
left=False)
fig = plt.figure(constrained_layout=False, frameon=False)
ax = fig.add_axes([0, 0, 1, 1])
ax.set_facecolor((0.88, 0.87, 0.9))
gs = GridSpec(3, 3, figure=fig, wspace=0, hspace=0.05)
axes = []
axes.append(fig.add_subplot(gs[0, :]))
axes.append(fig.add_subplot(gs[1, :-1]))
axes.append(fig.add_subplot(gs[1:, -1]))
axes.append(fig.add_subplot(gs[-1, 0]))
axes.append(fig.add_subplot(gs[-1, -2]))
# sizes_y = [15, 10, 5, 5, 5]
# sizes_x = [5, 5, 10, 5, 5]
sizes_y = [20, 12, 5, 5, 5]
sizes_x = [5, 5, 10, 5, 5]
for i in range(5):
debug = False
rand_color = randomcolor.RandomColor()
size_x = sizes_x[i]
size_y = sizes_y[i]
upscale_factor = 10
n_labels = 5
sigma = 1
buffer = 0.005
hsv_index = 1
segment_spacing = [10, 10]
image_rgb = np.random.uniform(0, 1, (size_x, size_y, 3))
labels = np.random.randint(n_labels + 1, size=(
size_x, size_y)) * np.random.randint(0, 2, size=(size_x, size_y))
# segment random image
segments = random_walker(
image_rgb,
labels,
multichannel=True,
beta=250,
copy=False,
spacing=segment_spacing,
)
all_colors = np.array(
rand_color.generate(
hue="purple",
# luminosity='bright',
count=n_labels,
format_='Array_rgb')) / 256.
for color_index in np.unique(segments):
color_hsv = color.rgb2hsv(all_colors[color_index - 1])
# color_hsv[2] = 0.6 + (color_index - 1) * 0.4 / n_labels
color_rgb = color.hsv2rgb(color_hsv)
image_rgb[segments == color_index] = color_rgb
# transform segmented image so it is large, preserving blobs, and blurry
image_rgb = rescale(image_rgb,
upscale_factor,
anti_aliasing=False,
multichannel=True)
image_rgb = gaussian(image_rgb, sigma=sigma, multichannel=True)
image_hsv = color.rgb2hsv(image_rgb)
if debug:
plt.figure()
plt.imshow(image_rgb)
plt.show()
for pix_frac in [0.9]:
total_pixels_switched = int(image_rgb.shape[0] *
image_rgb.shape[0] * pix_frac)
print(total_pixels_switched)
for _ in range(total_pixels_switched):
rand_x, rand_y = np.random.choice(
image_hsv.shape[0]), np.random.choice(image_hsv.shape[1])
orig_rgb = image_rgb[rand_x, rand_y]
rand_value = image_hsv[rand_x, rand_y, hsv_index]
x, y = np.where(
(rand_value *
(1 + 0.5 * buffer) >= image_hsv[:, :, hsv_index])
& (rand_value *
(1 - 2 * buffer) < image_hsv[:, :, hsv_index]))
if len(x) == 0:
continue
idx = np.random.choice(len(x))
update_rgb = image_rgb[x[idx], y[idx]]
image_rgb[x[idx], y[idx]] = orig_rgb
image_rgb[rand_x, rand_y] = update_rgb
if debug:
plt.figure()
plt.title(pix_frac)
plt.imshow(image_rgb)
plt.show()
if debug:
plt.figure()
plt.imshow(image_rgb)
plt.show()
# filtered_img = prewitt_v(color.rgb2hsv(image_rgb)[:, :, 0])
# filtered_img = meijering(color.rgb2hsv(image_rgb)[:, :, 0])
# filtered_img = sato(color.rgb2hsv(image_rgb)[:, :, 0])
# filtered_details = frangi(color.rgb2hsv(image_rgb)[:, :, 0],
# sigmas=range(3, 8, 10),
# black_ridges=True,
# beta=0.1,
# )
filtered_img = frangi(
color.rgb2hsv(image_rgb)[:, :, 0],
sigmas=range(3, 8, 10),
black_ridges=True,
# beta=0.1,
)
from skimage.filters.rank import median
from skimage.morphology import disk, ball
filtered_img = median(filtered_img / np.max(filtered_img), disk(10))
filtered_img = filtered_img
filtered_img = 1.5 * (filtered_img + np.abs(
np.min(filtered_img))) / np.max(filtered_img +
np.abs(np.min(filtered_img)))
filtered_img += 0.6
if debug:
plt.figure()
plt.imshow(filtered_img, cmap='gray')
plt.colorbar()
plt.show()
num_erosions = 5
eroded_image = hessian(color.rgb2hsv(image_rgb)[:, :, 0])
eroded_aug = np.zeros_like(eroded_image)
for n in range(num_erosions):
eroded_aug += 1 * eroded_image
eroded_image = erosion(eroded_image)
if debug:
plt.figure()
plt.imshow(image_rgb)
plt.show()
image_hsv = color.rgb2hsv(image_rgb)
image_hsv[:, :, 2] *= filtered_img
image_hsv[:, :, 2] *= 1 - (0.8 * eroded_aug / np.max(eroded_aug))
image_rgb_shadow_aug = color.hsv2rgb(image_hsv)
# plt.figure()
# plt.imshow(image_rgb_shadow_aug)
# plt.show()
axes[i].imshow(image_rgb_shadow_aug)
format_axes(fig)
gs.tight_layout(fig, pad=1.2, h_pad=0.5)
plt.show()
fig = plt.figure(figsize=(8,2.5))
gs1 = GridSpec(1, 4)
p1 = fig.add_subplot(gs1[0])
p2 = fig.add_subplot(gs1[1])
p3 = fig.add_subplot(gs1[2])
p4 = fig.add_subplot(gs1[3])
p1.pie([ss, sd, sh], autopct='%1.1f%%', pctdistance=1.4, colors=["lightgrey", "grey", "darkgrey"])
p1.set_title("Structural")
p1.axis("equal")
p2.pie([bs, bd, bh], autopct='%1.1f%%', pctdistance=1.4, colors=["lightgrey", "grey", "darkgrey"])
p2.set_title("Behavioural")
p2.axis("equal")
p3.pie([cs, cd, ch], autopct='%1.1f%%', pctdistance=1.4, colors=["lightgrey", "grey", "darkgrey"])
p3.set_title("Creationnal")
p3.axis("equal")
gs1.tight_layout(fig)
p, _ , _=p4.pie([cs, cd, ch], autopct='%1.1f%%', colors=["lightgrey", "grey", "darkgrey"])
p4.axis("equal")
p4.set_visible(False)
lgd = fig.legend(p, ["Static", "Dynamic", "Hybrid"], loc="right")
fig.savefig("../img/analysis_v_pattern.png")
#plt.savefig("../img/creationnal.png", bbox_extra_artists=(lgd,), bbox_inches='tight')
def plot_results_year_round_team_color(results, constructors_df, drivers_df,
win_type='race',
result_type='Race Wins'):
fig = plt.figure(figsize=(8.1, 9))
gs = GridSpec(1, 3, width_ratios=[1.3, 0.4, 0.4], wspace=0.1)
team_results = results['team']
driver_results = results['driver']
color_names_sq = np.array(
['white'] * (constructors_df.index.max() + 1), dtype='U16'
)
color_names_sq[constructors_df.index] = constructors_df['parent'].apply(
lambda t: TEAM_COLORS.get(t, TEAM_COLORS['others'])[0]
)
# print(color_names_sq[131])
cmap_sq = ListedColormap(color_names_sq)
# Plot
ax_results = plt.subplot(gs[0])
# ax_results_right = ax_results.twinx()
ax_team_legend = plt.subplot(gs[1])
ax_driver_legend = plt.subplot(gs[2])
xlims = (0.5, team_results.shape[1] + 0.5)
ylims = (F1_LATEST_YEAR + 0.5, F1_FIRST_YEAR - 0.5)
# Races
handles_team = []
labels_team = []
handles_driver = []
labels_driver = []
total_races = np.sum(team_results != 0)
remaining_races = total_races
ax_results.imshow(
team_results, cmap=cmap_sq, vmin=0, vmax=constructors_df.index.max(),
extent=(*xlims, *ylims)
)
team_ref_view = constructors_df.set_index('constructorRef')
driver_ref_view = drivers_df.set_index('driverRef')
team_n_races = []
for n, team_id in enumerate(TEAM_COLORS):
if team_id == 'others':
name = 'Others'
team_ids = constructors_df[
~constructors_df['parent'].isin(TEAM_COLORS)
].index
else:
name = team_ref_view.loc[team_id]['name']
team_ids = constructors_df[constructors_df['parent'] == team_id].index
race_wins = np.isin(team_results, team_ids)
wins = np.sum(race_wins[:, :MAX_RACES_YEAR])
y, x = np.nonzero(race_wins)
x += 1 # shift round #
y += 1950 # shift year
if wins == 0:
continue
colors = TEAM_COLORS[team_id]
if wins == 1:
wins_label = f'{wins} {win_type}'
else:
wins_label = f'{wins} {win_type}s'
label = f'{name} ({wins_label})'
team_n_races.append((n, team_id, wins))
h1, = ax_results.plot(np.nan, 's', ms=7, color=colors[0])
h2, = ax_results.plot(x, y, 'o', ms=2, color=colors[1])
handles_team.append((h1, h2))
labels_team.append(label)
driver_n_races = []
for n, driver_ref in enumerate(DRIVER_COLORS):
name = driver_ref_view.loc[driver_ref]['name']
driver_ids = drivers_df[drivers_df['driverRef'] == driver_ref].index
race_wins = np.isin(driver_results, driver_ids)
wins = np.sum(race_wins[:, :MAX_RACES_YEAR])
y, x = np.nonzero(race_wins)
x += 1 # shift round #
y += 1950 # shift year
if wins == 0:
continue
color = DRIVER_COLORS[driver_ref]
if wins == 1:
wins_label = f'{wins} {win_type}'
else:
wins_label = f'{wins} {win_type}s'
first_year = min(y)
last_year = max(y)
label = f'{name}\n{first_year}-{last_year}\n({wins_label})'
driver_n_races.append((n, driver_ref, wins))
h, = ax_results.plot(x, y, 's', ms=6, color=color,
markeredgewidth=1,
markerfacecolor='none')
handles_driver.append(h)
labels_driver.append(label)
team_n_races = np.array(team_n_races, dtype=('u4,U16,u4'))
driver_n_races = np.array(driver_n_races, dtype=('u4,U16,u4'))
order_team = np.hstack((
np.argsort(team_n_races[
~np.isin(team_n_races['f1'], ['indy500', 'others'])
]['f2'])[::-1],
np.nonzero(team_n_races['f1'] == 'indy500')[0],
np.nonzero(team_n_races['f1'] == 'others')[0],
))
order_driver = np.argsort(driver_n_races['f2'])[::-1]
# ax_results.axis('off')
ax_results.invert_yaxis()
# ax_results.invert_yaxis()
ax_results.set_xticks([1] + [i for i in range(5, 21, 5)])
ax_results.set_yticks(
[ i for i in range(F1_FIRST_YEAR, F1_LATEST_YEAR, 5)] + [F1_LATEST_YEAR]
)
# ax_results_right.set_yticks(
# [ i for i in range(F1_FIRST_YEAR, F1_LATEST_YEAR, 5)] + [F1_LATEST_YEAR]
# )
ax_results.set_xlim(*xlims)
ax_results.set_ylim(*ylims)
# ax_results_right.set_ylim(*ylims)
ax_results.set_xlabel('Race #')
ax_results.set_ylabel('Year')
# ax_results_right.set_ylabel('Year')
# ax_results.axis('equal')
# ax_results_right.axis('equal')
# Champions
ax_results.axvline(MAX_RACES_YEAR + 1.5, ls='--', color='k')
last_col = team_results.shape[1]
def add_line_label(x, y, label, ha='center', va='top', color='black'):
signal = 1 if va == 'top' else -1
line = mlines.Line2D(
[x, x],
[y + 1 * signal, y + 2 * signal],
ls='-', color=color
)
line.set_clip_on(False)
ax_results.add_line(line)
ax_results.text(x, y + 2 * signal, label,
ha=ha, va=va, color=color)
add_line_label(last_col - 4, F1_LATEST_YEAR, 'WCC ',
ha='center', va='top', color='cyan')
add_line_label(last_col - 3, F1_FIRST_YEAR, 'Constructor\nwith most wins',
ha='right', va='bottom', color='blue')
add_line_label(last_col - 1, F1_LATEST_YEAR, ' WDC',
ha='center', va='top', color='brown')
add_line_label(last_col - 0, F1_FIRST_YEAR, 'Driver with\nmost wins',
ha='left', va='bottom', color='orange')
# Team legend
handles_team = [handles_team[n] for n in order_team]
labels_team = [labels_team[n] for n in order_team]
ax_team_legend.legend(handles_team, labels_team, loc='center',
facecolor=(.85, .85, .85))
ax_team_legend.axis('off')
# Driver legend
# handles_driver = [handles_driver[n] for n in order_driver]
# labels_driver = [labels_driver[n] for n in order_driver]
ax_driver_legend.legend(handles_driver, labels_driver, loc='center',
facecolor=(.75, .75, .75))
ax_driver_legend.axis('off')
plt.suptitle(f'F1 {result_type} by Constructor and Driver')
gs.tight_layout(fig, rect=(0,0,1,0.95))
class ConstantViewer(object):
"""
Class meant to visualize the constants of a log file for the Motion Profiler of Walton Robotics
"""
def __init__(self, clf, show_outliers: bool = False) -> None:
"""
:param clf: the model to use to separate the data
:param show_outliers: True if black dots should be placed in the 3d plot to represent the outliers False otherwise
"""
super().__init__()
self.showing = False
self.show_outliers = show_outliers
self.clf = clf
self.fig = plt.figure("Scaled 3d data")
fig_manager = plt.get_current_fig_manager()
fig_manager.window.showMaximized()
self.gs = GridSpec(3, 4, self.fig)
self.master_plot = self.fig.add_subplot(self.gs[:3, :3], projection='3d')
self.time_velocity = self.fig.add_subplot(self.gs[0, -1])
self.time_power = self.fig.add_subplot(self.gs[1, -1])
self.power_velocity = self.fig.add_subplot(self.gs[2, -1])
def show(self):
"""
Shows the figure
"""
if not self.showing:
self.gs.tight_layout(self.fig)
self.fig.show()
self.showing = True
def close_all(self):
"""
Closes the figure
"""
if self.showing:
self.showing = False
plt.close(self.fig)
def plot_3d_plot(self, features, headers, labels):
"""
PLots the features in a 3d plot including the hyperplane that separates the data
:param features: the features to use to plot in the graph
:param headers: the axis titles
:param labels: the color of each data point
"""
self.master_plot.scatter(features[:, 0], features[:, 1], features[:, 2], c=labels)
self.master_plot.set_xlabel(headers[0])
self.master_plot.set_ylabel(headers[1])
self.master_plot.set_zlabel(headers[2])
plot_hyperplane(self.clf, self.master_plot, colors='orange')
def manipulate_features(self, features: np.ndarray, file_data: np.ndarray) -> (np.ndarray, np.ndarray):
"""
Return the features manipulated in a way as to make the algorithm for separating the data more accurate.
:param features: the features to use
:param file_data: the log file's data
:return: the manipulated features array, the outliers of the data set and the data scaler
"""
if contains_key(file_data, "motionState"):
moving_mask = file_data["motionState"] == "MOVING"
features = features[moving_mask]
file_data = file_data[moving_mask]
new_features = None
scalers = {}
if contains_key(file_data, "pathNumber"):
for i in range(file_data["pathNumber"].min(), file_data["pathNumber"].max() + 1):
min_max_scaler = MinMaxScaler()
path_number = file_data["pathNumber"] == i
scalers[min_max_scaler] = path_number
features_at_path = features[path_number]
half = features_at_path.shape[0] // 2
coefficient, _ = find_linear_best_fit_line(features_at_path[:half, 2], features_at_path[:half, 0])
if coefficient < 0:
features_at_path[:, 0] *= - 1
features_at_path = min_max_scaler.fit_transform(features_at_path)
outliers_free_features = features_at_path
if new_features is None:
new_features = outliers_free_features
else:
new_features = np.concatenate((new_features, outliers_free_features), 0)
else:
min_max_scaler = MinMaxScaler()
scalers[min_max_scaler] = np.full(features.shape[0], True)
new_features = min_max_scaler.fit_transform(features)
outlier_detector = OneClassSVM(gamma=10) # Seems to work best
outlier_detector.fit(new_features)
outlier_prediction = outlier_detector.predict(new_features)
outliers = new_features[outlier_prediction == -1]
new_features = new_features[outlier_prediction == 1]
features = self.reverse_scalling(new_features, scalers, outlier_prediction)
if self.show_outliers:
plot_hyperplane(outlier_detector, self.master_plot, interval=.04, colors="orange")
return new_features, outliers, features
def reverse_scalling(self, features, scalers, outlier_prediction):
features = np.copy(features)
for scaler, index in zip(scalers.keys(), scalers.values()):
index = index[outlier_prediction == 1]
features[index] = scaler.inverse_transform(features[index])
return features
def graph(self, file_data):
"""
Graphs the features from the log file. Creates a 3D graph with time, average power to motors and velocity as axises.
It also decomposes the dimensions into individual 2D graphs.
:param file_data: the log file to use to extract the data from
"""
self.clear_graphs()
features, headers = get_features(file_data)
new_scaled_features, outliers, features = self.manipulate_features(features, file_data)
# features = scaler.inverse_transform(new_scaled_features)
labels = self.clf.predict(new_scaled_features)
color_labels = list(map(lambda x: 'r' if x == 0 else 'b', labels))
self.plot_3d_plot(new_scaled_features, headers, color_labels)
if self.show_outliers:
self.master_plot.scatter(outliers[:, 0], outliers[:, 1], outliers[:, 2], c="black")
self.show_constants_graph(features, file_data, labels, c=color_labels)
plot_subplots(new_scaled_features, headers, (self.time_velocity, self.time_power, self.power_velocity),
color_labels)
plt.draw()
def clear_graphs(self):
"""
Clears all the axes
"""
for ax in (self.master_plot, self.time_velocity, self.time_power, self.power_velocity):
ax.cla()
def show_grid(self):
"""
Shows the grids for the major ticks in the plot.
"""
for ax in (self.time_velocity, self.time_power, self.power_velocity):
ax.grid(True)
def show_constants_graph(self, features, file_data, labels, c=None):
"""
Creates an addition figure that will display the a graph with the constants on it and also the lines of best fit of
the accelerating portion of it, the decelerating portion of it and the average of both of those lines
:param features: the features to use to show the graph and find the constants from
:param file_data: the whole file data
:param labels: the labels to say if a data point is accelerating or not
:param c: the color to plot the points
:return the constants for the motion profiling kV, kK and kAcc
"""
if is_straight_line(file_data):
easygui.msgbox("It was determined that the robot was trying to go straight. "
"As an ongoing feature the program will be able detect kLag, etc... "
"however for the instance this features has not been added")
figure = plt.figure("Constants graph")
constants_plot = figure.gca()
constants_plot.set_xlabel("Velocity")
constants_plot.set_ylabel("Average Power")
fig_manager = plt.get_current_fig_manager()
fig_manager.window.showMaximized()
x = features[:, 1]
y = features[:, 0]
constants_plot.scatter(x, y, c=labels if c is None else c)
acceleration_mask = labels == visualize.ACCELERATING
coef_accelerating, intercept_accelerating = find_linear_best_fit_line(x[acceleration_mask],
y[acceleration_mask])
deceleration_mask = labels == visualize.DECELERATING
coef_decelerating, intercept_decelerating = find_linear_best_fit_line(x[deceleration_mask],
y[deceleration_mask])
x_lim = np.array(constants_plot.get_xlim())
y_lim = np.array(constants_plot.get_ylim())
x, y = get_xy_limited(intercept_accelerating, coef_accelerating, x_lim, y_lim)
constants_plot.plot(x, y)
x, y = get_xy_limited(intercept_decelerating, coef_decelerating, x_lim, y_lim)
constants_plot.plot(x, y)
# constants_plot.plot(x_lim, coef_accelerating * x_lim + intercept_accelerating)
# constants_plot.plot(x_lim, coef_decelerating * x_lim + intercept_decelerating)
average_coef = (coef_accelerating + coef_decelerating) / 2
average_intercept = (intercept_accelerating + intercept_decelerating) / 2
# constants_plot.plot(x_lim, average_coef * x_lim + average_intercept)
x, y = get_xy_limited(average_intercept, average_coef, x_lim, y_lim)
constants_plot.plot(x, y)
acceleration_coefficient = (coef_accelerating - average_coef)
acceleration_intercept = (intercept_accelerating - average_intercept)
k_acc = ((x.max() + x.min()) / 2) * acceleration_coefficient + acceleration_intercept
bbox_props = dict(boxstyle="round,pad=0.3", fc="cyan", ec="b", lw=2)
constants_plot.text(x_lim[0], y_lim[1],
"kV: {}\nkK: {}\nkAcc: {}".format(average_coef, average_intercept, k_acc), ha="left",
va="top", bbox=bbox_props)
return average_coef, average_intercept, k_acc
def run(self, show=False):
# Load data
filename = self.filename
d = pyfits.getdata(filename)
h = pyfits.getheader(filename)
path, filename = os.path.split(filename)
# Get wavelength calibration
z = np.arange(h['naxis3'])
w = h['CRVAL3'] + h['CDELT3'] * (z - h['CRPIX3'])
# Signal-to-noise clipping
s = d.sum(axis=2)
s = s.sum(axis=1)
gauss_pw, _ = self.fit_gaussian(z, s)
log.debug("Gaussian parameters ---")
log.debug("p[0] = %.2f" % gauss_pw[0])
log.debug("p[1] = %.2f" % gauss_pw[1])
log.debug("p[2] = %.2f" % gauss_pw[2])
log.debug("p[3] = %.2f" % gauss_pw[3])
lor_p = self.fit_lorentzian(z, s)
log.debug("Lorentzian parameters ---")
log.debug("p[0] = %.2f" % lor_p[0])
log.debug("p[1] = %.2f" % lor_p[1])
log.debug("p[2] = %.2f" % lor_p[2])
log.debug("p[3] = %.2f" % lor_p[3])
fwhm = np.abs(gauss_pw[2] * 2 * np.sqrt(2 * np.log(2)))
filter_ = np.where(np.abs(z - gauss_pw[1]) < fwhm, True, False)
if show:
plt.plot(z, self.gaussian(gauss_pw, z), 'r-', lw=2, label='Gaussian Fit')
plt.plot(z, self.lorentzian(lor_p, z), 'b-', lw=2, label='Lorentzian Fit')
plt.plot(z, s, 'ko')
plt.plot(z[filter_], s[filter_], 'ro')
plt.title('Cube collapsed in XY and fits.')
plt.grid()
plt.legend(loc='best')
plt.gcf().canvas.mpl_connect('key_press_event', self.on_key_press)
plt.show()
signal = d[filter_].mean(axis=0)
noise = d[np.logical_not(filter_)].mean(axis=0)
target_snr = 3
snr = signal / noise
snr = ndimage.median_filter(snr, 3)
snr_mask = np.where(signal > target_snr * noise, True, False)
snr_laplacian = ndimage.morphological_laplace(snr * snr_mask, size=3)
snr_mask *= np.where(np.abs(snr_laplacian) < 5.0, True, False)
snr_mask = ndimage.binary_opening(snr_mask, iterations=5)
snr_mask = ndimage.binary_closing(snr_mask, iterations=5)
# SNR MASK Based on circular aperture
# aperture_radius = 1 # arcmin
# aperture_radius = aperture_radius / 60 # arcmin to deg
# aperture_radius = np.abs(aperture_radius / h['CD1_1']) # deg to pix
# print(aperture_radius)
# c = SkyCoord('7:41:55.400', '-18:12:33.00', frame=h['RADECSYS'].lower(), unit=(u.hourangle, u.deg))
# x, y = np.arange(h['NAXIS1']), np.arange(h['NAXIS2'])
# X, Y = np.meshgrid(x, y)
# center_wcs = wcs.WCS(h)
# center = center_wcs.wcs_world2pix(c.ra.deg, c.dec.deg, 6563, 1)
# snr_mask = np.sqrt((X - center[0]) ** 2 + (Y - center[1]) ** 2)
# snr_mask = np.where(snr_mask < aperture_radius, True, False)
# plt.imshow(snr_mask)
# plt.show()
# SNR MASK Based on squared area
aperture_width = 256 * 4.048e-1 # arcsec (from original image)
aperture_width /= 3600 # arcsec to deg
aperture_width /= np.abs(h['CD1_1']) # deg to pix
c = SkyCoord('7:41:55.197', '-18:12:35.97', frame=h['RADECSYS'].lower(), unit=(u.hourangle, u.deg))
x, y = np.arange(h['NAXIS1']), np.arange(h['NAXIS2'])
X, Y = np.meshgrid(x, y)
center_wcs = wcs.WCS(h)
center = center_wcs.wcs_world2pix(c.ra.deg, c.dec.deg, 6563, 1)
print(center, np.abs(X - center[0]), np.abs(Y - center[1]), aperture_width)
X = np.where(np.abs(X - center[0]) < aperture_width / 2, True, False)
Y = np.where(np.abs(Y - center[1]) < aperture_width / 2, True, False)
snr_mask = X * Y
plt.imshow(snr_mask)
plt.gcf().canvas.mpl_connect('key_press_event', self.on_key_press)
plt.show()
if show:
fig1 = plt.figure(figsize=(20, 5))
plt.title('Signal-to-Noise Ratio')
gs = GridSpec(1, 3)
ax1 = plt.subplot(gs[0])
ax1.set_title('SNR')
im1 = ax1.imshow(snr, cmap='cubehelix', interpolation='nearest',
origin='lower', vmin=3, vmax=20)
div1 = make_axes_locatable(ax1)
cax1 = div1.append_axes("right", size="5%", pad=0.05)
cbar1 = plt.colorbar(mappable=im1, cax=cax1, use_gridspec=True,
orientation='vertical')
ax2 = plt.subplot(gs[1])
ax2.set_title('Mask')
im2 = ax2.imshow(np.where(snr_mask, 1, 0), cmap='gray',
interpolation='nearest', origin='lower',
vmin=0, vmax=1)
div2 = make_axes_locatable(ax2)
cax2 = div2.append_axes("right", size="5%", pad=0.05)
cbar2 = plt.colorbar(mappable=im2, cax=cax2, use_gridspec=True,
orientation='vertical')
cmap = plt.get_cmap('cubehelix')
cmap.set_bad('w', 1.0)
ax3 = plt.subplot(gs[2])
ax3.set_title('Masked')
im3 = ax3.imshow(np.ma.masked_where(~snr_mask, snr), cmap=cmap, interpolation='nearest',
origin='lower', vmin=0)
div3 = make_axes_locatable(ax3)
cax3 = div3.append_axes("right", size="5%", pad=0.05)
cbar3 = plt.colorbar(mappable=im3, cax=cax3, use_gridspec=True, orientation='vertical')
plt.gcf().canvas.mpl_connect('key_press_event', self.on_key_press)
gs.tight_layout(fig1)
plt.show()
pyfits.writeto(filename.replace('.','.SNR.'), snr, h, clobber=True)
pyfits.writeto(filename.replace('.','.SNR_LAPLACIAN.'), snr_laplacian, h, clobber=True)
# Adjust continuum
continuum = self.fit_continuum(d)
# Subtract continuum
continuum = np.reshape(continuum, (continuum.size, 1, 1))
continuum = np.repeat(continuum, d.shape[1], axis=1)
continuum = np.repeat(continuum, d.shape[2], axis=2)
d -= continuum
del continuum
# Integrate along the planetary nebulae
d = d * snr_mask
d = d.sum(axis=2)
d = d.sum(axis=1)
d = d / np.float(h['EXPTIME'])
gauss_pw, _ = self.fit_gaussian(w, d)
gauss_pc, _ = self.fit_gaussian(z, d)
log.info("Gaussian parameters ---")
log.info("p[0] = %.4f ADU/s" % gauss_pw[0])
log.info("p[1] = %.4f A = %.4f channels" % (gauss_pw[1], gauss_pc[1]))
log.info("p[2] = %.4f A = %.4f channels" % (gauss_pw[2], gauss_pc[2]))
log.info("p[3] = %.4f ADU/s" % gauss_pw[3])
# total_flux = (gauss_pc[0] - gauss_pc[3]) * np.sqrt(2 * np.pi) \
# * gauss_pc[2]
# log.info("Total flux = (a - d) * sqrt(2pi) * c")
# log.info(" %.5E ADU/s" % total_flux)
fwhm = np.abs(gauss_pw[2] * 2 * np.sqrt(2 * np.log(2)))
filter_ = np.where(np.abs(w - gauss_pw[1]) < fwhm, True, False)
# d = d - d[~filter_].mean()
if show:
plt.plot(w, self.gaussian(gauss_pw, w), 'r-', lw=2, label='Gaussian Fit')
# plt.plot(w, self.lorentzian(lor_p, w), 'b-', lw=2, label='Lorentzian Fit')
plt.plot(w[~filter_], d[~filter_], 'ko')
plt.plot(w[filter_], d[filter_], 'ro')
plt.title('Spectral profile of the masked area.')
plt.xlabel(u'Wavelenght [$\AA$]')
plt.ylabel(u'Integrated Count Level [ADU/s]')
plt.grid()
plt.legend(loc='best')
plt.gcf().canvas.mpl_connect('key_press_event', self.on_key_press)
plt.show()
integrated_flux = (gauss_pc[0] - gauss_pc[3]) \
* (gauss_pc[2] * np.sqrt(2 * np.pi))
log.info("Total flux: %.4E adu/s" % (integrated_flux))
snr_mask = np.where(snr_mask, 1, 0)
pyfits.writeto(
os.path.join(path, filename.replace('.fits', '.mask.fits')),
snr_mask, h, clobber=True)
return
bounds = np.unique(np.array(bounds))
axes[i].plot(heights, density_sine(heights), '-', color=colors[b_factor])
axes[i].plot(bounds, density_sine(bounds), 'o', color="C1", markersize=4)
# Configure axes
axes[i].set_ylim(-0.2, 1.2)
axes[i].set_yticks([])
axes[i].set_xticks([bottom, top])
axes[i].set_xticklabels([r"$r_1$", r"$r_2$"])
axes[i].set_xlabel("Depth")
if i == 0:
axes[i].set_title("(b)")
# Plot number of tesseroids (sine)
# --------------------------------
ax = plt.subplot(outer_grid[2])
ax.plot(b_factors, n_tess, 'o')
ax.grid()
ax.set_ylim(2, 21)
ax.yaxis.tick_right()
ax.yaxis.set_label_position("right")
ax.set_yticks(np.arange(3, 21, 2))
ax.set_xticks(np.arange(1, 11, 2))
ax.set_xlabel(r"$b$")
ax.set_ylabel("Number of tesseroids")
ax.set_title("(c)")
outer_grid.tight_layout(fig)
plt.savefig(figure_fname, dpi=300)
plt.show()
def plot_flux_annotated(
unbound, bound, flux_unbound, flux_bound, flux_between, k_cat_bin, scaling=None, name=None, source_code=None
):
fig = plt.figure(figsize=(6, 6))
gs = GridSpec(1, 1, wspace=0.5, hspace=0.5)
ax1 = plt.subplot(gs[0, 0])
bins = len(unbound)
ax1.scatter(range(len(bound)), bound, s=80, c="b")
ax1.scatter(range(len(unbound)), unbound, s=80, c="r")
if not scaling:
scaling = 10 ** 3
rng = range(bins)
for i in range(bins - 1):
if flux_bound[i, 1] < 0:
af.right_to_left_bound_arrow(plt, flux_bound[i, 1], i, rng, unbound, bound, scaling)
else:
af.left_to_right_bound_arrow(plt, flux_bound[i, 1], i, rng, unbound, bound, scaling)
for i in range(bins - 1):
if flux_unbound[i, 1] < 0:
af.right_to_left_unbound_arrow(plt, flux_unbound[i, 1], i, rng, unbound, bound, scaling)
else:
af.left_to_right_unbound_arrow(plt, flux_unbound[i, 1], i, rng, unbound, bound, scaling)
for i in range(bins):
# DRS: This is correct. Verified for group meeting 2015-10-05.
if flux_between[i, 1] < 0:
af.bound_to_unbound_arrow(plt, flux_between[i, 1], i, rng, unbound, bound, scaling)
else:
af.unbound_to_bound_arrow(plt, flux_between[i, 1], i, rng, unbound, bound, scaling)
max_flux = max(abs(flux_between[:, 1]))
max_index = np.where(abs(flux_between[:, 1]) == max_flux)[0]
ax1.set_title("Flux visualized")
ax1.set_xlabel("Reaction coordinate ($\phi$)")
ax1.set_ylabel("Energy (a.u.)")
bbox_props = dict(fc="white", alpha=0.65)
ax1.annotate(
af.format_decimal(decimal.Decimal(max_flux)),
xy=(max_index, unbound[max_index]),
xycoords="data",
xytext=(+100, +120),
textcoords="offset points",
fontsize=22,
bbox=bbox_props,
arrowprops=dict(arrowstyle="->", facecolor="black", color="black", connectionstyle="arc3,rad=0.4", linewidth=2),
)
ax1.annotate(
af.format_decimal(decimal.Decimal(flux_between[k_cat_bin, 1])),
xy=(k_cat_bin, bound[k_cat_bin]),
xycoords="data",
xytext=(+100, -40),
textcoords="offset points",
fontsize=22,
bbox=bbox_props,
arrowprops=dict(
arrowstyle="->", facecolor="black", color="black", connectionstyle="arc3,rad=-0.4", linewidth=2
),
)
st = datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S")
sts = datetime.datetime.now().strftime("%Y-%m-%d-%H-%M-%S")
if name:
if source_code is not None:
text = st + " " + name + " in " + source_code
else:
text = st + " " + name
fig.text(0.0, 0.0, text, fontsize=12, color="black", ha="left", va="bottom", alpha=0.5)
else:
f.text(0.0, 0.0, st, fontsize=12, color="black", ha="left", va="bottom", alpha=0.5)
gs.tight_layout(fig, rect=[0, 0, 1, 1])
# plt.savefig('Figures/flux-annotated-{}-{}.png'.format(sts, name), dpi=150)
plt.show()
plt.close()
ax2 = fig.add_subplot(gs[1, 0], facecolor="cornflowerblue")
ax2.scatter(x2, y2, s=20, c="grey", marker="s", linewidths=2, edgecolors="k")
ax2.set_ylabel("YLabel10", bbox=box)
ax2.set_xlabel("XLabel10", bbox=box)
for ticklabel in ax2.get_xticklabels():
ticklabel.set_rotation(45)
ax2.yaxis.set_label_coords(-0.25, 0.5)
ax2.xaxis.set_label_coords(0.5, -0.25)
# subplot(2,2,4)
x3 = np.linspace(0, 10, 100)
y3 = np.exp(-x3)
ax3 = fig.add_subplot(gs[1, 1])
ax3.errorbar(x3,
y3,
fmt="b-",
yerr=0.6 * y3,
ecolor="lightsteelblue",
elinewidth=2,
capsize=0,
errorevery=5)
ax3.set_ylabel("YLabel11", bbox=box)
ax3.set_xlabel("XLabel11", bbox=box)
ax3.xaxis.set_label_coords(0.5, -0.25)
ax3.set_ylim(-0.1, 1.1)
ax3.set_yticks(np.arange(0, 1.1, 0.1))
gs.tight_layout(fig)
plt.show()
def plot_flux_single_annotated(surface, flux, scaling=None, name=None, source_code=None):
fig = plt.figure(figsize=(12, 12))
gs = GridSpec(1, 1, wspace=0.5, hspace=0.5)
ax1 = plt.subplot(gs[0, 0])
bins = len(surface)
ax1.scatter(range(len(surface)), surface, s=80, c="k")
if not scaling:
scaling = 10 ** 3
rng = range(bins)
for i in range(bins - 1):
if flux[i, 1] < 0:
plt.annotate(
"",
xy=(flux[i, 0], surface[i]),
xycoords="data",
xytext=(flux[i + 1, 0], surface[i + 1]),
textcoords="data",
arrowprops=dict(
arrowstyle="->, head_width=0.5",
color="b",
shrinkA=10,
shrinkB=10,
linewidth=abs(flux[i, 1]) * scaling,
),
)
else:
plt.annotate(
"",
xy=(flux[i + 1, 0], surface[i + 1]),
xycoords="data",
xytext=(flux[i, 0], surface[i]),
textcoords="data",
arrowprops=dict(
arrowstyle="->, head_width=0.5",
color="b",
shrinkA=10,
shrinkB=10,
linewidth=abs(flux[i, 1]) * scaling,
),
)
ax1.set_title("Flux visualized")
ax1.set_xlabel("Reaction coordinate ($\phi$)")
ax1.set_ylabel("Energy (a.u.)")
st = datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S")
sts = datetime.datetime.now().strftime("%Y-%m-%d-%H-%M-%S")
if name:
if source_code is not None:
text = st + " " + name + " in " + source_code
else:
text = st + " " + name
fig.text(0.0, 0.0, text, fontsize=12, color="black", ha="left", va="bottom", alpha=0.5)
else:
f.text(0.0, 0.0, st, fontsize=12, color="black", ha="left", va="bottom", alpha=0.5)
gs.tight_layout(fig, rect=[0, 0, 1, 1])
# plt.savefig(name+'-flux-cat-bin-{}.png'.format(k_cat_bin), dpi=150)
plt.show()
plt.close()
def _spectrogram(tr,
starttime,
endtime,
is_infrasound,
win_dur=5,
db_lim=None,
freq_lim=None):
"""
Make a combination waveform and spectrogram plot for an infrasound or
seismic signal.
Args:
tr (:class:`~obspy.core.trace.Trace`): Input data, usually starts
before `starttime` and ends after `endtime` (this function expects
the response to be removed!)
starttime (:class:`~obspy.core.utcdatetime.UTCDateTime`): Start time
endtime (:class:`~obspy.core.utcdatetime.UTCDateTime`): End time
is_infrasound (bool): `True` if infrasound, `False` if seismic
win_dur (int or float): Duration of window [s] (this usually must be
adjusted depending upon the total duration of the signal)
db_lim (tuple): Tuple specifying colorbar / colormap limits [dB]
freq_lim (tuple): Tuple defining frequency limits for spectrogram plot
Returns:
Tuple of (`fig`, `spec_line`, `wf_line`, `time_box`)
"""
if is_infrasound:
ref_val = REFERENCE_PRESSURE
ylab = 'Pressure (Pa)'
clab = 'Power (dB$_{%g\ \mathrm{μPa}}$/Hz)' % (REFERENCE_PRESSURE *
1e6)
rescale = 1
else:
ref_val = REFERENCE_VELOCITY
ylab = 'Velocity (μm/s)'
clab = 'Power (dB$_{%g\ \mathrm{m/s}}$/Hz)' % REFERENCE_VELOCITY
rescale = 1e6 # Converting to μm/s
fs = tr.stats.sampling_rate
nperseg = int(win_dur * fs) # Samples
nfft = np.power(2,
int(np.ceil(np.log2(nperseg))) + 1) # Pad fft with zeroes
f, t, sxx = signal.spectrogram(tr.data,
fs,
window='hann',
nperseg=nperseg,
nfft=nfft)
sxx_db = 20 * np.log10(np.sqrt(sxx) / ref_val) # [dB / Hz]
t_mpl = tr.stats.starttime.matplotlib_date + (t / mdates.SEC_PER_DAY)
fig = plt.figure(figsize=np.array(RESOLUTION) / DPI)
# width_ratios effectively controls the colorbar width
gs = GridSpec(2, 2, figure=fig, height_ratios=[2, 1], width_ratios=[40, 1])
spec_ax = fig.add_subplot(gs[0, 0])
wf_ax = fig.add_subplot(gs[1, 0], sharex=spec_ax) # Share x-axis with spec
cax = fig.add_subplot(gs[0, 1])
wf_ax.plot(tr.times('matplotlib'), tr.data * rescale, 'k', linewidth=0.5)
wf_ax.set_ylabel(ylab)
wf_ax.grid(linestyle=':')
max_value = np.abs(tr.copy().trim(starttime, endtime).data).max() * rescale
wf_ax.set_ylim(-max_value, max_value)
im = spec_ax.pcolormesh(t_mpl,
f,
sxx_db,
cmap=cc.m_rainbow,
rasterized=True)
spec_ax.set_ylabel('Frequency (Hz)')
spec_ax.grid(linestyle=':')
spec_ax.set_ylim(freq_lim)
# Tick locating and formatting
locator = mdates.AutoDateLocator()
wf_ax.xaxis.set_major_locator(locator)
wf_ax.xaxis.set_major_formatter(_UTCDateFormatter(locator))
fig.autofmt_xdate()
# "Crop" x-axis!
wf_ax.set_xlim(starttime.matplotlib_date, endtime.matplotlib_date)
# Initialize animated stuff
line_kwargs = dict(x=starttime.matplotlib_date, color='red', linewidth=1)
spec_line = spec_ax.axvline(**line_kwargs)
wf_line = wf_ax.axvline(**line_kwargs)
time_box = AnchoredText(
s=starttime.strftime('%H:%M:%S'),
pad=0.2,
loc='lower right',
borderpad=0,
prop=dict(color='red'),
)
spec_ax.add_artist(time_box)
# Clip image to db_lim if provided (doesn't clip if db_lim=None)
db_min, db_max = im.get_clim()
im.set_clim(db_lim)
# Automatically determine whether to show triangle extensions on colorbar
# (kind of adopted from xarray)
if db_lim:
min_extend = db_min < db_lim[0]
max_extend = db_max > db_lim[1]
else:
min_extend = False
max_extend = False
if min_extend and max_extend:
extend = 'both'
elif min_extend:
extend = 'min'
elif max_extend:
extend = 'max'
else:
extend = 'neither'
fig.colorbar(im, cax, extend=extend, extendfrac=EXTENDFRAC, label=clab)
spec_ax.set_title('.'.join([
tr.stats.network, tr.stats.station, tr.stats.location, tr.stats.channel
]))
# Repeat tight_layout and update, janky but works...
for _ in range(2):
gs.tight_layout(fig)
gs.update(hspace=0, wspace=0.05)
# Finnicky formatting to get extension triangles (if they exist) to extend
# above and below the vertical extent of the spectrogram axes
pos = cax.get_position()
triangle_height = EXTENDFRAC * pos.height
ymin = pos.ymin
height = pos.height
if min_extend and max_extend:
ymin -= triangle_height
height += 2 * triangle_height
elif min_extend and not max_extend:
ymin -= triangle_height
height += triangle_height
elif max_extend and not min_extend:
height += triangle_height
else:
pass
cax.set_position([pos.xmin, ymin, pos.width, height])
return fig, spec_line, wf_line, time_box
for ticklabel in ax2.get_xticklabels():
ticklabel.set_rotation(45)
ax2.yaxis.set_label_coords(-0.04, 0.5)
ax2.xaxis.set_label_coords(0.5, -0.12)
# 第三个子图位置
colors = ['#e41a1c', '#377eb8', '#4daf4a', '#984ea3', '#ff7f00', '#00FFFF']
ax3 = fig.add_subplot(gs[1, 1]) #绘制在第2行和第2列
ax3.bar(GDP.index.values,
GDP.GDP,
width=0.6,
align='center',
color=colors,
tick_label=GDP.Province)
ax3.set_xlabel('省份', fontsize=20, labelpad=15)
ax3.set_ylabel('GDP产值(万亿)', fontsize=20, labelpad=15)
# 添加表格
col_labels = ['GDP(万亿)']
row_labels = GDP.Province
table_vals = np.array(GDP.GDP.values).reshape(-1, 1)
col_colors = ['#e41a1c', '#377eb8', '#4daf4a', '#984ea3', '#ff7f00', '#00FFFF']
my_table = plt.table(cellText=table_vals,
cellLoc='center',
colWidths=[0.1] * 6,
rowLabels=row_labels,
colLabels=col_labels,
rowColours=col_colors,
bbox=[0.8, 0.7, 0.1, 0.25])
# 显示
gs.tight_layout(fig) #控制子图参数的
plt.show()