def __get_two_pane_one_pane_spec(self):
'''
:return: layout spec with two panes with 2 axes in the first pane and 1 in the other.
'''
major_ratio = [self.majorSplitRatio.value(), 1]
minor_ratio = [self.minorSplitRatio.value(), 1]
if self.chartSplit.currentText() == 'Horizontal':
gs = GridSpec(2,
2,
width_ratios=major_ratio,
height_ratios=minor_ratio,
wspace=self.widthSpacing.value(),
hspace=self.heightSpacing.value())
spec_1 = gs.new_subplotspec((0, 0), 1, 1)
spec_2 = gs.new_subplotspec((1, 0), 1, 1)
spec_3 = gs.new_subplotspec((0, 1), 2, 1)
else:
gs = GridSpec(2,
2,
width_ratios=minor_ratio,
height_ratios=major_ratio,
wspace=self.widthSpacing.value(),
hspace=self.heightSpacing.value())
spec_1 = gs.new_subplotspec((0, 0), 1, 1)
spec_2 = gs.new_subplotspec((0, 1), 1, 1)
spec_3 = gs.new_subplotspec((1, 0), 2, 1)
return spec_1, spec_2, spec_3
def create_canvas(self): # pragma: no cover
self.fig = Figure()
canvas = FigureCanvas(self.fig)
self.ui.mainLayout.addWidget(canvas)
canvas.setFocusPolicy(QtCore.Qt.StrongFocus)
# Add subplots
gridspec = GridSpec(2, 4)
self.map_ax = self.fig.add_subplot(
gridspec.new_subplotspec((0, 0), rowspan=2, colspan=2)
)
self.spectrum_ax = self.fig.add_subplot(
gridspec.new_subplotspec((0, 2), rowspan=1, colspan=2)
)
self.hist_ax = self.fig.add_subplot(
gridspec.new_subplotspec((1, 2), rowspan=1, colspan=1)
)
self.edge_ax = self.fig.add_subplot(
gridspec.new_subplotspec((1, 3), rowspan=1, colspan=1)
)
# Create the colorbar on the histogram axes
self.cbar = plots.draw_histogram_colorbar(ax=self.hist_ax,
cmap="viridis",
norm=Normalize(0, 1))
self.cbar.ax.set_xlabel("Map Value")
# Adjust the margins
self.fig.tight_layout(pad=0)
self.fig.canvas.draw_idle()
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 get_stereo_two_rose(self):
"""
Resets the figure and returns a stereonet two rose diagrams axis.
When the view in the main window is changed to this setting, this
function is called and sets up a plot with a stereonet and two
rose diagram axis. One axis is for azimuth, the other one for
dip.
"""
self.fig.clf()
self.fig.patch.set_facecolor(self.props["canvas_color"])
self.fig.set_dpi(self.props["pixel_density"])
gridspec = GridSpec(2, 4)
sp_stereo = gridspec.new_subplotspec((0, 0), rowspan=2, colspan=2)
sp_cbar = gridspec.new_subplotspec((1, 2), rowspan=1, colspan=1)
sp_rose = gridspec.new_subplotspec((0, 3), rowspan=1, colspan=1)
sp_drose = gridspec.new_subplotspec((1, 3), rowspan=1, colspan=1)
ax_stereo = self.fig.add_subplot(sp_stereo,
projection=self.get_projection())
ax_rose = self.fig.add_subplot(sp_rose, projection="northpolar")
ax_drose = self.fig.add_subplot(sp_drose, projection="dippolar")
ax_cbar = self.fig.add_subplot(sp_cbar)
ax_cbar.axis("off")
ax_cbar.set_aspect(8)
return ax_stereo, ax_rose, ax_drose, ax_cbar
def create_canvas(self):
# Add the canvas to the UI
self.fig = Figure()
canvas = FigureCanvas(self.fig)
self.ui.mainLayout.addWidget(canvas)
# Add subplots
gridspec = GridSpec(2, 4)
self.img_ax = self.fig.add_subplot(
gridspec.new_subplotspec((0, 0), rowspan=2, colspan=2)
)
self.spectrum_ax = self.fig.add_subplot(
gridspec.new_subplotspec((0, 2), rowspan=1, colspan=2)
)
self.hist_ax = self.fig.add_subplot(
gridspec.new_subplotspec((1, 2), rowspan=1, colspan=1)
)
self.edge_ax = self.fig.add_subplot(
gridspec.new_subplotspec((1, 3), rowspan=1, colspan=1)
)
# Create the colorbar on the histogram axes
self.cbar = plots.draw_histogram_colorbar(ax=self.hist_ax,
cmap="viridis",
norm=Normalize(0, 1))
self.cbar.ax.set_xlabel("Intensity")
# Adjust the margins
self.fig.tight_layout(pad=0)
self.fig.canvas.draw_idle()
def get_stereo_rose(self):
"""
Resets the figure and returns a stereonet and rose diagram axis.
When the view in the main window is changed to stereonet and rose
diagram, the figure is reset. The current settings are applied and
two subplots for the stereonet and rose diagram are created. The
axis of the stereonet and rose diagram are returned. This method is
called by the MainWindow "redraw_plot"-method.
"""
self.fig.clf()
self.fig.patch.set_facecolor(self.props["canvas_color"])
self.fig.set_dpi(self.props["pixel_density"])
gridspec = GridSpec(2, 5)
sp_stereo = gridspec.new_subplotspec((0, 0), rowspan=2, colspan=2)
sp_cbar = gridspec.new_subplotspec((1, 2), rowspan=1, colspan=1)
sp_rose = gridspec.new_subplotspec((0, 3), rowspan=2, colspan=2)
ax_stereo = self.fig.add_subplot(sp_stereo,
projection=self.get_projection())
ax_rose = self.fig.add_subplot(sp_rose, projection="northpolar")
ax_cbar = self.fig.add_subplot(sp_cbar)
ax_cbar.axis("off")
ax_cbar.set_aspect(8)
return ax_stereo, ax_rose, ax_cbar
def get_stereo_rose(self):
"""
Resets the figure and returns a stereonet and rose diagram axis.
When the view in the main window is changed to stereonet and rose
diagram, the figure is reset. The current settings are applied and
two subplots for the stereonet and rose diagram are created. The
axis of the stereonet and rose diagram are returned. This method is
called by the MainWindow "redraw_plot"-method.
"""
self.fig.clf()
self.fig.patch.set_facecolor(self.props["canvas_color"])
self.fig.set_dpi(self.props["pixel_density"])
gridspec = GridSpec(2, 5)
sp_stereo = gridspec.new_subplotspec((0, 0),
rowspan=2, colspan=2)
sp_cbar = gridspec.new_subplotspec((1, 2), rowspan=1, colspan=1)
sp_rose = gridspec.new_subplotspec((0, 3),
rowspan=2, colspan=2)
ax_stereo = self.fig.add_subplot(sp_stereo,
projection=self.get_projection())
ax_rose = self.fig.add_subplot(sp_rose, projection="northpolar")
ax_cbar = self.fig.add_subplot(sp_cbar)
ax_cbar.axis("off")
ax_cbar.set_aspect(8)
return ax_stereo, ax_rose, ax_cbar
def get_stereo_two_rose(self):
"""
Resets the figure and returns a stereonet two rose diagrams axis.
When the view in the main window is changed to this setting, this
function is called and sets up a plot with a stereonet and two
rose diagram axis. One axis is for azimuth, the other one for
dip.
"""
self.fig.clf()
self.fig.patch.set_facecolor(self.props["canvas_color"])
self.fig.set_dpi(self.props["pixel_density"])
gridspec = GridSpec(2, 4)
sp_stereo = gridspec.new_subplotspec((0, 0),
rowspan=2, colspan=2)
sp_cbar = gridspec.new_subplotspec((1, 2), rowspan=1, colspan=1)
sp_rose = gridspec.new_subplotspec((0, 3),
rowspan=1, colspan=1)
sp_drose = gridspec.new_subplotspec((1, 3),
rowspan=1, colspan=1)
ax_stereo = self.fig.add_subplot(sp_stereo,
projection=self.get_projection())
ax_rose = self.fig.add_subplot(sp_rose, projection="northpolar")
ax_drose = self.fig.add_subplot(sp_drose, projection="dippolar")
ax_cbar = self.fig.add_subplot(sp_cbar)
ax_cbar.axis("off")
ax_cbar.set_aspect(8)
return ax_stereo, ax_rose, ax_drose, ax_cbar
def __init__(self, main_window, settings, data, add_layer_dataset, add_feature, redraw_main):
"""
Initializes the RotationDialog class.
Requires the main_window object, the settings object (PlotSettings
class) and the data rows to initialize. All the necessary widgets are
loaded from the Glade file. A matplotlib figure is set up and added
to the scrolledwindow. Two axes are set up that show the original and
rotated data.
"""
self.builder = Gtk.Builder()
self.builder.set_translation_domain(i18n().get_ts_domain())
script_dir = os.path.dirname(__file__)
rel_path = "gui_layout.glade"
abs_path = os.path.join(script_dir, rel_path)
self.builder.add_objects_from_file(abs_path,
("dialog_rotation", "adjustment_rotation_dipdir",
"adjustment_rotation_dip", "adjustment_rotation_angle"))
self.dialog = self.builder.get_object("dialog_rotation")
self.dialog.set_transient_for(main_window)
self.settings = settings
self.data = data
self.trans = self.settings.get_transform()
self.add_layer_dataset = add_layer_dataset
self.add_feature = add_feature
self.redraw_main = redraw_main
self.adjustment_rotation_dipdir = self.builder.get_object("adjustment_rotation_dipdir")
self.adjustment_rotation_dip = self.builder.get_object("adjustment_rotation_dip")
self.adjustment_rotation_angle = self.builder.get_object("adjustment_rotation_angle")
self.spinbutton_rotation_dipdir = self.builder.get_object("spinbutton_rotation_dipdir")
self.spinbutton_rotation_dip = self.builder.get_object("spinbutton_rotation_dip")
self.spinbutton_rotation_angle = self.builder.get_object("spinbutton_rotation_angle")
self.scrolledwindow_rotate = self.builder.get_object("scrolledwindow_rotate")
self.fig = Figure(dpi=self.settings.get_pixel_density())
self.canvas = FigureCanvas(self.fig)
self.scrolledwindow_rotate.add_with_viewport(self.canvas)
gridspec = GridSpec(1, 2)
original_sp = gridspec.new_subplotspec((0, 0),
rowspan=1, colspan=1)
rotated_sp = gridspec.new_subplotspec((0, 1),
rowspan=1, colspan=1)
self.original_ax = self.fig.add_subplot(original_sp,
projection=self.settings.get_projection())
self.rotated_ax = self.fig.add_subplot(rotated_sp,
projection=self.settings.get_projection())
self.canvas.draw()
self.redraw_plot()
self.dialog.show_all()
self.builder.connect_signals(self)
if sys.platform == "win32":
translate_gui(self.builder)
def __init__(self, scale, imshape, interval=1):
self.fig = plt.figure(dpi=100)
self.axes = {}
self.artists = []
gridspec = GridSpec(2, 2)
self.axes['raw'] = gridspec.new_subplotspec((0, 0), rowspan=2)
self.axes['draw'] = gridspec.new_subplotspec((0, 1))
self.axes['match'] = gridspec.new_subplotspec((1, 1))
for k, sp in self.axes.items():
self.axes[k] = self.fig.add_subplot(sp)
self.axes['raw'].set_title('raw')
self.axes['raw'].set_xticklabels([])
self.axes['raw'].set_yticklabels([])
self.axes['match'].grid(which='both')
self.lines = {}
self.lines['template'] = self.axes['match'].plot((), (),
marker='x',
color='g')[0]
self.lines['query'] = self.axes['match'].plot((), (),
marker='o',
color='b')[0]
self.lines['draw'] = self.axes['draw'].plot((), (),
color='b',
linewidth=5)[0]
self.axes['match'].set_ylim(-scale // 2 - 10, scale // 2 + 10)
self.axes['match'].set_xlim(-scale // 2 - 10, scale // 2 + 10)
self.axes['draw'].set_ylim(imshape[0], 0)
self.axes['draw'].set_xlim(imshape[1], 0)
self.axes['draw'].xaxis.tick_top()
self.axes['draw'].yaxis.tick_right()
self.imdisp = self.axes['raw'].imshow(np.zeros(imshape,
dtype=np.uint8))
self.fig.tight_layout()
self.bg_cache = {
ax: self.fig.canvas.copy_from_bbox(ax.bbox)
for ax in self.fig.axes
}
self.draw_state = 0
self.drawcount = 0
self.fig.canvas.mpl_connect('button_press_event', self.onclick)
self.fig.canvas.mpl_connect('key_press_event', self.onkey)
self.timer = self.fig.canvas.new_timer(interval=interval)
self.timer.add_callback(self._update)
self.queuelen = 0
def __get_two_pane_spec(self):
'''
:return: layout spec with two panes containing an axes in each.
'''
if self.chartSplit.currentText() == 'Horizontal':
gs = GridSpec(1, 2, width_ratios=[self.majorSplitRatio.value(), 1],
wspace=self.widthSpacing.value(), hspace=self.heightSpacing.value())
spec_1 = gs.new_subplotspec((0, 0), 1, 1)
spec_2 = gs.new_subplotspec((0, 1), 1, 1)
else:
gs = GridSpec(2, 1, height_ratios=[self.majorSplitRatio.value(), 1],
wspace=self.widthSpacing.value(), hspace=self.heightSpacing.value())
spec_1 = gs.new_subplotspec((0, 0), 1, 1)
spec_2 = gs.new_subplotspec((1, 0), 1, 1)
return spec_1, spec_2
def plot_step_detection():
""" PLOTTING SETUP """
fig = plt.figure()
gridspec = GridSpec(2, 1, height_ratios=[1, 1])
ax1 = fig.add_subplot(gridspec.new_subplotspec((0, 0)))
ax2 = fig.add_subplot(gridspec.new_subplotspec((1, 0)))
# Set up the 2D floor
ax1.set_ylim(0, 2)
""" 2D FLOOR VIEW """
# ax1.set_axis_off()
# ax1.set_xticklabels([])
# ax1.set_yticklabels([])
ax1.scatter(cop.x, cop.y, c=cop.magnitude, cmap='Greys', s=5)
ax1.scatter(rights.x, rights.y, c='red', marker='o')
ax1.scatter(lefts.x, lefts.y, c='blue', marker='o')
ax1.plot(*zip(start.to_array(), end.to_array()), c='r', linestyle=':')
""" COP PARAMS SERIES """
# ax2.set_axis_off()
ax2.set_yticklabels([])
ax2.set_xlim(cop_speed.time[0].values, cop_speed.time[-1].values)
cop_speed.plot(ax=ax2)
(cop_speed_roc / 10).plot(ax=ax2)
for support in steps.dir:
ax2.axvline(support.time.values, c=('r' if support.item() == 'right' else 'b'), linestyle='--')
for strike in floor.heelstrikes.dir:
ax2.axvline(strike.time.values, c='gray', linestyle=':')
plt.setp(ax2.xaxis.get_majorticklabels(), rotation='horizontal', ha='center', size=6)
def gridplot (grid, loc, rowspan=1, colspan=1):
'''
Returns a matplotlib.gridspec.SubplotSpec for a subplot.
The resulting object can then be added to a matplotlib.figure
using the add_subplot() method.
'''
gridspec = GridSpec (grid[0], grid[1])
subplotspec = gridspec.new_subplotspec(loc, rowspan, colspan)
return subplotspec
def __init__(self, chart, measurement_model, display_model, preferences):
self.__chart = chart
self.__measurement_model = measurement_model
self.name = f"multi"
self.__data = MarkerData()
gs = GridSpec(2, 3, width_ratios=[1, 1, 0.75])
self.__magnitude = AnimatedSingleLineMagnitudeModel(self.__chart, self.__measurement_model, display_model,
self.__data, subplot_spec=gs.new_subplotspec((0, 0), 1, 2))
self.__sonagram = ContourModel(self.__chart, self.__measurement_model, display_model, preferences,
subplot_spec=gs.new_subplotspec((1, 0), 1, 2),
redraw_on_display=False, show_crosshairs=True)
self.__polar = PolarModel(self.__chart, self.__measurement_model, display_model, self.__data,
subplotSpec=gs.new_subplotspec((1, 2), 1, 1))
self.__table_axes = self.__chart.canvas.figure.add_subplot(gs.new_subplotspec((0, 2), 1, 1))
self.__table = None
self.__ani = None
self.__stopping = False
self.__mouse_reactor = MouseReactor(0.10, self.propagateCoords)
def create_plot_collage(iteration_step):
# define file paths for 2d and 1d data, then load them in
path_to_2D_data = f'../fargo2d1d/{SIMULATION_DIR}/{SIMULATION_ID}/out/gasdens{iteration_step}.dat'
path_to_1D_data = f'../fargo2d1d/{SIMULATION_DIR}/{SIMULATION_ID}/out/gasdens.ascii_rad.{iteration_step}.dat'
if not os.path.exists(path_to_1D_data):
return
#raise FileNotFoundError(f'could not find file {path_to_1D_data}')
if not os.path.exists(path_to_2D_data):
return
#raise FileNotFoundError(f'could not find file {path_to_2D_data}')
print(f'plotting data for file {iteration_step}')
fig = plt.figure(figsize=(15, 10))
gs = GridSpec(2, 3, figure=fig)
# plot 2d data in rectangular grid
ax = fig.add_subplot(gs.new_subplotspec((0, 0), colspan=3))
create_cartesian_2D_plot(ax, path_to_2D_data, iteration_step)
# plot 1d data
ax = plt.subplot(gs.new_subplotspec((1, 0), colspan=1))
create_1D_plot(ax, path_to_1D_data)
# get info
ax = plt.subplot(gs.new_subplotspec((1, 1), colspan=1))
create_info_box(ax, iteration_step)
# plot 2d data in polar coords
ax = plt.subplot(gs.new_subplotspec((1, 2), colspan=1), projection='polar')
create_polar_2D_plot(ax, path_to_2D_data)
# make sure sorting is done right
if iteration_step < 10:
iteration_step = f'0{iteration_step}'
# save and reset figure
plt.savefig(f'{FIGURES_DIR}all_collages/collage_{iteration_step}.png')
if iteration_step == get_total_nr_of_steps(SIMULATION_DIR,
SIMULATION_ID) - 1:
plt.savefig(f'{FIGURES_DIR}collage_for_outfile_{iteration_step}.png')
plt.clf()
plt.close()
def __init__(self, canvas, num):
backend_gtkagg.FigureManagerGTKAgg.__init__(self, canvas, num)
self.window.maximize()
self.vbox.remove(self.canvas)
self.menu = Menu(self)
self.vbox.pack_start(self.menu, False, True)
self.vbox1 = gtk.VBox()
self.vbox1.pack_start(self.canvas, True, True)
self.vbox1.show()
self.vpane = gtk.HBox()
self.vbox.pack_start(self.vpane, True, True)
self.vpane.pack_start(self.vbox1, True, True)
self.vpane.show()
self.sidebar = Sidebar(self)
self.sidebar.widget.show()
self.vpane.pack_end(self.sidebar.widget, False, True)
grid = GridSpec(4, 1)
spec = grid.new_subplotspec((0, 0), rowspan=3)
self.ax = self.canvas.figure.add_subplot(spec)
spec = grid.new_subplotspec((3, 0), rowspan=1)
self.ax2 = self.canvas.figure.add_subplot(spec, sharex=self.ax)
self.ax2.grid(True)
self.text = self.ax.text(
0.90,
0.90,
r'',
horizontalalignment='center',
verticalalignment='center',
transform=self.ax.transAxes,
fontsize=20,
)
self.reset_margins()
def __init__(self,scale,imshape,interval=1):
self.fig = plt.figure(dpi=100)
self.axes = {}
self.artists = []
gridspec = GridSpec(2,2)
self.axes['raw'] = gridspec.new_subplotspec((0, 0),rowspan=2)
self.axes['draw'] = gridspec.new_subplotspec((0, 1))
self.axes['match'] = gridspec.new_subplotspec((1, 1))
for k,sp in self.axes.items(): self.axes[k] = self.fig.add_subplot(sp)
self.axes['raw'].set_title('raw')
self.axes['raw'].set_xticklabels([])
self.axes['raw'].set_yticklabels([])
self.axes['match'].grid(which='both')
self.lines = {}
self.lines['template'] = self.axes['match'].plot((),(),marker='x',color='g')[0]
self.lines['query'] = self.axes['match'].plot((),(),marker='o',color='b')[0]
self.lines['draw'] = self.axes['draw'].plot((),(),color='b',linewidth=5)[0]
self.axes['match'].set_ylim(-scale//2-10,scale//2+10)
self.axes['match'].set_xlim(-scale//2-10,scale//2+10)
self.axes['draw'].set_ylim(imshape[0],0)
self.axes['draw'].set_xlim(imshape[1],0)
self.axes['draw'].xaxis.tick_top()
self.axes['draw'].yaxis.tick_right()
self.imdisp = self.axes['raw'].imshow(np.zeros(imshape,dtype=np.uint8))
self.fig.tight_layout()
self.bg_cache = {ax:self.fig.canvas.copy_from_bbox(ax.bbox) for ax in self.fig.axes}
self.draw_state = 0
self.drawcount = 0
self.fig.canvas.mpl_connect('button_press_event', self.onclick)
self.fig.canvas.mpl_connect('key_press_event', self.onkey)
self.timer = self.fig.canvas.new_timer(interval=interval)
self.timer.add_callback(self._update)
self.queuelen = 0
def get_stereonet(self):
"""
Resets the figure and returns the stereonet axis.
When the view in the main window is changed to only stereoent. The
figure is reset. Then the current settings are applied and one subplot
for the stereonet is created. This method is called when the
MainWindow "__init__"-method and the "redraw_plot"-method.
"""
self.fig.clf()
self.fig.patch.set_facecolor(self.props["canvas_color"])
self.fig.set_dpi(self.props["pixel_density"])
gridspec = GridSpec(2, 3)
sp_stereo = gridspec.new_subplotspec((0, 0), rowspan=2, colspan=2)
sp_cbar = gridspec.new_subplotspec((1, 2), rowspan=1, colspan=1)
ax_stereo = self.fig.add_subplot(sp_stereo,
projection=self.get_projection())
ax_cbar = self.fig.add_subplot(sp_cbar)
ax_cbar.axis("off")
ax_cbar.set_aspect(8)
return ax_stereo, ax_cbar
def get_pt_view(self):
"""
Resets the canvas and returns the 3 axis of the paleostress view.
When the view in the main window is changed to paleostress the figure
is reset. The current settings are applied and 3 subplots are created.
The 3 axis of the subplots are returned. This method is called by the
MainWindow "redraw_plot"-method when the view has been changed.
"""
self.fig.clf()
self.fig.patch.set_facecolor(self.props["canvas_color"])
self.fig.set_dpi(self.props["pixel_density"])
gridspec = GridSpec(2, 5)
sp_stereo = gridspec.new_subplotspec((0, 0), colspan=3, rowspan=2)
sp_fluc = gridspec.new_subplotspec((0, 3), colspan=2)
sp_mohr = gridspec.new_subplotspec((1, 3), colspan=2)
ax_stereo = self.fig.add_subplot(sp_stereo,
projection=self.get_projection())
ax_fluc = self.fig.add_subplot(sp_fluc, aspect="equal")
ax_mohr = self.fig.add_subplot(sp_mohr, aspect="equal")
return ax_stereo, ax_fluc, ax_mohr
def get_pt_view(self):
"""
Resets the canvas and returns the 3 axis of the paleostress view.
When the view in the main window is changed to paleostress the figure
is reset. The current settings are applied and 3 subplots are created.
The 3 axis of the subplots are returned. This method is called by the
MainWindow "redraw_plot"-method when the view has been changed.
"""
self.fig.clf()
self.fig.patch.set_facecolor(self.props["canvas_color"])
self.fig.set_dpi(self.props["pixel_density"])
gridspec = GridSpec(2, 5)
sp_stereo = gridspec.new_subplotspec((0, 0), colspan=3, rowspan=2)
sp_fluc = gridspec.new_subplotspec((0, 3), colspan=2)
sp_mohr = gridspec.new_subplotspec((1, 3), colspan=2)
ax_stereo = self.fig.add_subplot(sp_stereo,
projection=self.get_projection())
ax_fluc = self.fig.add_subplot(sp_fluc, aspect="equal")
ax_mohr = self.fig.add_subplot(sp_mohr, aspect="equal")
return ax_stereo, ax_fluc, ax_mohr
def get_stereonet(self):
"""
Resets the figure and returns the stereonet axis.
When the view in the main window is changed to only stereoent. The
figure is reset. Then the current settings are applied and one subplot
for the stereonet is created. This method is called when the
MainWindow "__init__"-method and the "redraw_plot"-method.
"""
self.fig.clf()
self.fig.patch.set_facecolor(self.props["canvas_color"])
self.fig.set_dpi(self.props["pixel_density"])
gridspec = GridSpec(2, 3)
sp_stereo = gridspec.new_subplotspec((0, 0), rowspan=2, colspan=2)
sp_cbar = gridspec.new_subplotspec((1, 2), rowspan=1, colspan=1)
ax_stereo = self.fig.add_subplot(sp_stereo,
projection=self.get_projection())
ax_cbar = self.fig.add_subplot(sp_cbar)
ax_cbar.axis("off")
ax_cbar.set_aspect(8)
return ax_stereo, ax_cbar
def consumme_window(window, loader):
""" Consumme a Window object to create a matplotlib figure adjusted by the GridSpec """
fig = figure(window.name, figsize=(15, 10))
grid = GridSpec(window.rows, window.cols, figure=fig)
for i, _ in enumerate(window.content):
span = 0
for j, col in enumerate(window.content[i]):
sub = fig.add_subplot(
grid.new_subplotspec((i, j + span),
colspan=int(window.span[i][j])))
span += int(window.span[i][j]) - 1
load_sub_plots(sub, loader, col, window.cfg)
def get_rose_diagram(self):
"""
Resets the figure and returns the rose diagram axis.
When the view in the main window is changed to rose-diagram-only the
figure is reset. The current settings are applied and one subplot
for the rose diagram is created. The axis of the rose-diagram is
returned. This method is called by the MainWindow "redraw_plot"-method.
"""
self.fig.clf()
self.fig.patch.set_facecolor(self.props["canvas_color"])
self.fig.set_dpi(self.props["pixel_density"])
gridspec = GridSpec(1, 1)
sp_rose = gridspec.new_subplotspec((0, 0))
ax_rose = self.fig.add_subplot(sp_rose, projection="northpolar")
return ax_rose
def get_rose_diagram(self):
"""
Resets the figure and returns the rose diagram axis.
When the view in the main window is changed to rose-diagram-only the
figure is reset. The current settings are applied and one subplot
for the rose diagram is created. The axis of the rose-diagram is
returned. This method is called by the MainWindow "redraw_plot"-method.
"""
self.fig.clf()
self.fig.patch.set_facecolor(self.props["canvas_color"])
self.fig.set_dpi(self.props["pixel_density"])
gridspec = GridSpec(1, 1)
sp_rose = gridspec.new_subplotspec((0, 0))
ax_rose = self.fig.add_subplot(sp_rose, projection="northpolar")
return ax_rose
def get_stereonet(self):
"""
Resets the figure and returns the stereonet axis.
When the view in the main window is changed to only stereoent. The
figure is reset. Then the current settings are applied and one subplot
for the stereonet is created. This method is called when the
MainWindow "__init__"-method and the "redraw_plot"-method.
"""
self.fig.clf()
self.fig.patch.set_facecolor(self.canvas_color)
self.fig.set_dpi(self.pixel_density)
gridspec = GridSpec(1, 1)
sp_stereo = gridspec.new_subplotspec((0, 0))
ax_stereo = self.fig.add_subplot(sp_stereo,
projection=self.get_projection())
return ax_stereo
def plot_motion_similarity():
fig = plt.figure()
cycle = cycles[1]
cycle_cop = cop.sel(time=slice(*cycle.date_window))
cycle_cop_vel = floor.cop_vel.sel(time=slice(*cycle.date_window))
gridspec = GridSpec(1, 2, width_ratios=[2, 1])
ax1 = fig.add_subplot(gridspec.new_subplotspec((0, 0)))
ax2 = fig.add_subplot(gridspec.new_subplotspec((0, 1)))
""" LEFT PLOT """
ax1.plot(*zip(start.to_array(), end.to_array()), c='r', linestyle=':')
ax1.set_xlim(cycle_cop.x.min().item(), cycle_cop.x.max().item())
ax1.quiver(cycle_cop.x, cycle_cop.y, cycle_cop_vel.x, cycle_cop_vel.y,
angles='xy', units='dots', width=5, pivot='mid', cmap='cool')
""" RIGHT PLOT """
ax2.axvline(0, c='r', linestyle=':')
ax2.quiver(cycle.cop_mlap.med, cycle.cop_mlap.ant, cycle.cop_vel_mlap.med, cycle.cop_vel_mlap.ant, range(40),
angles='xy', units='dots', width=5, pivot='mid', cmap='cool')
ax2.set_xlim(-0.5, 0.5)
def initialize_subplots(self):
gs = GridSpec(3, 4)
# X componet
self.subplots['xts'] = gs.new_subplotspec((0, 0), 1, 2)
self.subplots['xke'] = gs.new_subplotspec((0, 2), 1, 1)
self.subplots['xfas'] = gs.new_subplotspec((0, 3), 1, 1)
# Y component
self.subplots['yts'] = gs.new_subplotspec((1, 0), 1, 2)
self.subplots['yke'] = gs.new_subplotspec((1, 2), 1, 1)
self.subplots['yfas'] = gs.new_subplotspec((1, 3), 1, 1)
# Z component
self.subplots['zts'] = gs.new_subplotspec((1, 0), 1, 2)
self.subplots['zke'] = gs.new_subplotspec((1, 2), 1, 1)
self.subplots['zfas'] = gs.new_subplotspec((1, 3), 1, 1)
for k, v in self.subplots.iteritems():
self.subplots[key] = self.add_subplot(val)
return
def plot_lightcurve(
lc1,
time_bin=20, # Minutes
base_model_flux=None,
transit_datetimes=None,
title=None,
colors='rgb',
offset_delta=0.):
# Setup figure
fig = Figure()
FigureCanvas(fig)
fig.set_size_inches(14, 7)
fig.set_facecolor('white')
grid_size = (9, 9)
# Axis for light curve
gs = GridSpec(*grid_size, hspace=0.1)
offset = 0 # offset
# Better time axis ticks
half_hour = mdates.MinuteLocator(interval=30)
h_fmt = mdates.DateFormatter('%H:%M:%S')
for i, color in enumerate(colors):
# Light curve plot
spec1 = gs.new_subplotspec((i * 3, 0), colspan=7, rowspan=2)
lc_ax = fig.add_subplot(spec1)
lc_ax.set_xticks([])
lc_ax.set_ylim([0.93, 1.07])
# Residual
spec2 = gs.new_subplotspec((i * 3 + 2, 0), colspan=7, rowspan=1)
res_scatter_ax = fig.add_subplot(spec2)
res_scatter_ax.set_ylim([-0.05, 0.05])
res_scatter_ax.set_yticks([-0.025, 0.025])
if i != 2:
res_scatter_ax.set_xticks([])
else:
res_scatter_ax.xaxis.set_major_locator(half_hour)
res_scatter_ax.xaxis.set_major_formatter(h_fmt)
# Residual histos
spec = GridSpec(*grid_size).new_subplotspec((i * 3, 7),
colspan=2,
rowspan=3)
res_ax = fig.add_subplot(spec)
res_ax.set_xticks([])
res_ax.set_ylim([-.05, .05])
res_ax.set_yticks([-.025, 0, .025])
res_ax.yaxis.tick_right()
res_ax.yaxis.set_major_formatter(PercentFormatter(xmax=1, decimals=1))
# Get the normalized flux for each channel
flux_df = lc1.loc[lc1.color == color].copy()
# Model flux
if base_model_flux is None:
flux_df['model'] = np.ones_like(flux_df.flux)
else:
flux_df['model'] = base_model_flux
# Residual
flux_df['residual'] = flux_df.flux - flux_df.model
# Start plotting.
# Plot target flux.
flux_df.flux.plot(
yerr=flux_df.flux_err,
marker='o',
ls='',
alpha=0.15,
color=color,
ax=lc_ax,
rot=0, # Don't rotate date labels
legend=False,
)
if time_bin is not None:
# Time-binned
binned_flux_df = flux_df.resample(f'{time_bin}T').apply({
'flux':
np.mean,
'flux_err':
lambda x: np.sum(x**2)
})
# Plot time-binned target flux.
binned_flux_df.plot(
yerr=binned_flux_df.flux_err,
ax=lc_ax,
rot=0,
marker='o',
ms=8,
color=color,
ls='',
label=f'Time-binned - {time_bin}min',
legend=False,
)
# Plot model flux.
flux_df.model.plot(
ax=lc_ax,
ls='-',
color=color,
alpha=0.5,
lw=3,
rot=0, # Don't rotate date labels
label='Model fit',
legend=True)
# Residual scatter
flux_df.residual.plot(
ax=res_scatter_ax,
color=color,
ls='',
marker='o',
rot=0, # Don't rotate date labels
alpha=0.5)
# Residual histogram
res_ax.hist(flux_df.residual,
orientation='horizontal',
color=color,
alpha=0.5)
res_ax.axhline(0, ls='--', color='k', alpha=0.25)
res_ax.set_title(f'σ={flux_df.residual.std():.2%}', y=.82)
# Add the offset
offset += offset_delta
if transit_datetimes is not None:
midpoint, ingress, egress = transit_datetimes
lc_ax.axvline(midpoint, ls='-.', c='g', alpha=0.5)
lc_ax.axvline(ingress, ls='--', c='k', alpha=0.5)
lc_ax.axvline(egress, ls='--', c='k', alpha=0.5)
if title is not None:
fig.suptitle(title, fontsize=18)
return fig
def plot_spectral_levels(yvar, yname, color):
#yvar either vs30 or GMPE site residual
#cbar is True or False for coloring by vs30
fig = plt.figure(figsize=(18, 6))
fig.subplots_adjust(wspace=0)
gs = GridSpec(1, 3)
cmap = mpl.cm.viridis
norm = mpl.colors.Normalize(vmin=min(sitevs30), vmax=max(sitevs30))
s_m = mpl.cm.ScalarMappable(cmap=cmap, norm=norm)
s_m.set_array([])
#1-6Hz subplot
ax1 = plt.subplot(gs.new_subplotspec((0, 0), colspan=1))
if color == True:
plt.scatter(l,
yvar,
marker='o',
s=60,
c=s_m.to_rgba(sitevs30),
edgecolors=s_m.to_rgba(sitevs30))
else:
plt.scatter(l, yvar, marker='o', s=60, c='blue')
for i in range(len(l)): #default 2,5
plt.annotate(site[i],
xy=(l[i], yvar[i]),
xytext=(2, 2),
textcoords='offset points',
fontsize=20)
plt.ylabel(yname)
rval, pval = pearsonr(l, siteterm)
power = statsmodels.stats.power.tt_solve_power(effect_size=rval,
nobs=len(l),
alpha=0.05)
label1 = 'Pearson R : ' + str(round(rval, 4))
label2 = 'power : ' + str(round(power, 4))
plt.annotate(label1,
xy=(0.2, 0.16),
xycoords='figure fraction',
fontsize=16)
plt.annotate(label2,
xy=(0.2, 0.13),
xycoords='figure fraction',
fontsize=16)
#6-14Hz subplot
ax2 = plt.subplot(gs.new_subplotspec((0, 1), colspan=1), sharey=ax1)
plt.setp(ax2.get_yticklabels(), visible=False)
if color == True:
plt.scatter(m,
yvar,
marker='o',
s=60,
c=s_m.to_rgba(sitevs30),
edgecolors=s_m.to_rgba(sitevs30))
else:
plt.scatter(m, yvar, marker='o', s=60, c='blue')
for i in range(len(m)): #default 2,5
plt.annotate(site[i],
xy=(m[i], yvar[i]),
xytext=(2, 2),
textcoords='offset points',
fontsize=20)
rval, pval = pearsonr(m, siteterm)
power = statsmodels.stats.power.tt_solve_power(effect_size=rval,
nobs=len(m),
alpha=0.05)
label1 = 'Pearson R : ' + str(round(rval, 4))
label2 = 'power : ' + str(round(power, 4))
plt.annotate(label1,
xy=(0.5, 0.16),
xycoords='figure fraction',
fontsize=16)
plt.annotate(label2,
xy=(0.5, 0.13),
xycoords='figure fraction',
fontsize=16)
#14-36Hz subplot
ax3 = plt.subplot(gs.new_subplotspec((0, 2), colspan=1), sharey=ax1)
plt.setp(ax3.get_yticklabels(), visible=False)
if color == True:
plt.scatter(h,
yvar,
marker='o',
s=60,
c=s_m.to_rgba(sitevs30),
edgecolors=s_m.to_rgba(sitevs30))
else:
plt.scatter(h, yvar, marker='o', s=60, c='blue')
for i in range(len(h)): #default 2,5
plt.annotate(site[i],
xy=(h[i], yvar[i]),
xytext=(2, 2),
textcoords='offset points',
fontsize=20)
rval, pval = pearsonr(h, siteterm)
power = statsmodels.stats.power.tt_solve_power(effect_size=rval,
nobs=len(h),
alpha=0.05)
label1 = 'Pearson R : ' + str(round(rval, 4))
label2 = 'power : ' + str(round(power, 4))
plt.annotate(label1,
xy=(0.8, 0.16),
xycoords='figure fraction',
fontsize=16)
plt.annotate(label2,
xy=(0.8, 0.13),
xycoords='figure fraction',
fontsize=16)
if color == True:
##add color bar to right
cbar = plt.colorbar(s_m)
cbar.set_label(ur"Vs30 (m/s)", fontsize=18) #"$azimuth$ (\u00b0)"
cbar.ax.tick_params(labelsize=18)
plt.show()
plt.savefig(top_dir + 'tstar/site/' + 'spectral_amplitude_vs_' + yname +
'.png')
def plot_lightcurve_combined(
lc1,
time_bin=20, # Minutes
base_model_flux=None,
transit_datetimes=None,
title=None,
colors='rgb',
offset_delta=0.):
# Setup figure
fig = Figure()
FigureCanvas(fig)
fig.set_size_inches(14, 7)
fig.set_facecolor('white')
grid_size = (9, 9)
# Axis for light curve
gs = GridSpec(*grid_size, hspace=2)
# Main plot
spec1 = gs.new_subplotspec((0, 0), colspan=7, rowspan=7)
lc_ax = fig.add_subplot(spec1)
# Residual
spec2 = gs.new_subplotspec((7, 0), colspan=7, rowspan=2)
res_scatter_ax = fig.add_subplot(spec2)
res_scatter_ax.set_ylim([-0.05, 0.05])
# Residual histos
res_histo_axes = list()
for i in range(3):
spec = GridSpec(*grid_size).new_subplotspec((i * 3, 7),
colspan=2,
rowspan=3)
res_ax = fig.add_subplot(spec)
res_ax.set_xticks([])
res_ax.set_ylim([-.05, .05])
res_ax.set_yticks([-.025, 0, .025])
res_ax.yaxis.tick_right()
res_ax.yaxis.set_major_formatter(PercentFormatter(xmax=1, decimals=1))
res_histo_axes.append(res_ax)
offset = 0 # offset
for i, color in enumerate(colors):
# Get the normalized flux for each channel
color_data = lc1.loc[lc1.color == color].copy()
# Model flux
if base_model_flux is None:
base_model = np.ones_like(color_data.flux)
else:
# Mask the sigma clipped frames
base_model = base_model_flux.copy()
color_data['model'] = base_model
# Get the differential flux and error
f0 = color_data.flux
f0_err = color_data.flux_err
f0_index = color_data.index
m0 = color_data.model
# Flux + offset
flux = f0 + offset
# Residual
residual = flux - base_model
# Build dataframe for differntial flux
flux_df = pd.DataFrame(
{
'flux': flux,
'flux_err': f0_err,
'model': m0,
'residual': residual
},
index=f0_index,
).dropna()
# Start plotting.
# Plot target flux.
flux_df.flux.plot(
yerr=flux_df.flux_err,
marker='o',
ls='',
alpha=0.15,
color=color,
ax=lc_ax,
rot=0, # Don't rotate date labels
legend=False,
)
if time_bin is not None:
# Time-binned
binned_flux_df = flux_df.resample(f'{time_bin}T').apply({
'flux':
np.median,
'flux_err':
lambda x: np.sum(x**2)
})
# Plot time-binned target flux.
binned_flux_df.flux.plot(
yerr=binned_flux_df.flux_err,
ax=lc_ax,
rot=0,
marker='o',
ms=8,
color=color,
ls='',
label=f'Time-binned - {time_bin}min',
legend=False,
)
# Plot model flux.
flux_df.model.plot(
ax=lc_ax,
ls='-',
color=color,
alpha=0.5,
lw=3,
rot=0, # Don't rotate date labels
label='Model fit',
legend=True)
# Residual scatter
flux_df.residual.plot(ax=res_scatter_ax,
color=color,
ls='',
marker='o',
alpha=0.5)
# Residual histogram axis
res_ax = res_histo_axes[i]
res_ax.hist(flux_df.residual,
orientation='horizontal',
color=color,
alpha=0.5)
res_ax.axhline(0, ls='--', color='k', alpha=0.25)
res_ax.set_title(f'σ={flux_df.residual.std():.2%}', y=.82)
# Add the offset
offset += offset_delta
if transit_datetimes is not None:
midpoint, ingress, egress = transit_datetimes
lc_ax.axvline(midpoint, ls='-.', c='g', alpha=0.5)
lc_ax.axvline(ingress, ls='--', c='k', alpha=0.5)
lc_ax.axvline(egress, ls='--', c='k', alpha=0.5)
if title is not None:
fig.suptitle(title, fontsize=18)
# Better time axis ticks
half_hour = mdates.MinuteLocator(interval=30)
h_fmt = mdates.DateFormatter('%H:%M:%S')
lc_ax.xaxis.set_major_locator(half_hour)
lc_ax.xaxis.set_major_formatter(h_fmt)
res_scatter_ax.set_xticks([])
return fig
def plot_scenario_raw(run):
rowcnt = 0
axes = []
axcnt = 0
maxy = 0
# +1 for topology plot in the top left
x = 9999 # used with LAYOUTS; topology is placed here
all_axes = []
layout = LAYOUTS.get(run.get('scenario_switch_cnt'))
cols = len(layout[0])
rows = len(layout)
fig = plt.figure(constrained_layout=True, figsize=(14, 6))
gs = GridSpec(rows, cols, figure=fig)
# first the topology
coords = None
for y in range(rows):
for x in range(cols):
if layout[y][x] == 9999:
if coords:
break
coords = [y, x]
colspan = sum([1 if v == 9999 else 0 for v in layout[y]])
rowspan = sum([1 if 9999 in v else 0 for v in layout])
break
all_axes.append(
plt.subplot(
gs.new_subplotspec((coords[0], coords[1]),
rowspan=rowspan,
colspan=colspan)))
# and then all the other axes
oldval = 0
for y in range(rows):
for x in range(cols):
val = layout[y][x]
if val == 9999:
continue
if val > oldval:
colspan = sum([1 if v == val else 0 for v in layout[y]])
rowspan = sum([1 if val in v else 0 for v in layout])
all_axes.append(
plt.subplot(
gs.new_subplotspec((y, x),
rowspan=rowspan,
colspan=colspan)))
oldval = val
plotted_topo = False
for switch in range(0, run.get('scenario_switch_cnt')):
#try:
# ax = fig.add_subplot(maingrid[rowcnt,axcnt], sharey=axes[0])
#except IndexError:
# ax = fig.add_subplot(maingrid[rowcnt,axcnt])
ax = all_axes[switch + 1]
axes.append(ax)
ax.set_xlim(0, 400)
ax.set_ylabel('Flow table utilization')
thresh = run.get('scenario_table_capacity')
datax = run.get('dts_%d_table_datax' % switch)
datay = run.get('dts_%d_table_datay_raw' % switch)
if max(datay) > maxy:
maxy = max(datay)
ax.plot(list(range(-1 * XOFFSET, 0)) + datax, [0] * XOFFSET + datay,
color='black',
linestyle='-',
linewidth=0.75)
ax.fill_between(datax, [0] * len(datay),
[min(thresh, x) for x in datay],
interpolate=True,
color='orange',
alpha=0.3,
label='Rules in flow table')
# show bottleneck parameters
w1 = str(run.get('scenario_gen_param_topo_bottleneck_cnt'))
w2 = str(run.get('scenario_gen_param_topo_bottleneck_duration')) + "s"
w3 = str(run.get('scenario_gen_param_topo_bottleneck_intensity'))
if run.get('scenario_gen_param_topo_bottleneck_cnt') == 0:
w2 = '-'
w3 = '-'
circled_number = str(switch)
circled_color = 'black'
scenario_concentrated_switches = run.get(
'scenario_concentrated_switches')
if switch in scenario_concentrated_switches:
circled_color = 'red'
ax.text(0.5,
.95,
circled_number,
fontsize=14,
verticalalignment='center',
horizontalalignment='center',
transform=ax.transAxes,
color='white',
alpha=1,
bbox=dict(boxstyle='circle',
facecolor=circled_color,
edgecolor='black'))
ax.hlines(thresh,
0,
400,
color='blue',
label="Flow table capacity",
linestyle='--',
linewidth=1)
d2 = 'dts_%d_table_datay_raw' % (switch)
d3 = 'dts_%d_table_datay' % (switch)
fill_overutil = [True if x > thresh else False for x in datay]
ax.fill_between(datax, [thresh] * len(datax),
datay,
where=fill_overutil,
interpolate=True,
color='red',
alpha=0.2,
label='Bottleneck')
# plot bottlenecks
ax.hlines(-1 * XOFFSET,
-1 * XOFFSET,
400,
color='gray',
linestyle='-',
alpha=0.3,
linewidth=7)
bottleneck_data = run.get('scenario_bottlenecks')
set_label = 0
for start, end, details in bottleneck_data:
if set_label == 0:
ax.hlines(-1 * XOFFSET,
start,
end,
color='red',
linestyle='-',
alpha=0.3,
linewidth=7)
set_label = 1
else:
ax.hlines(-1 * XOFFSET,
start,
end,
color='red',
linestyle='-',
alpha=0.3,
linewidth=7)
# ----------------- plot topology if not yet done (first ax)
if not plotted_topo:
plotted_topo = True
#ax = fig.add_subplot(maingrid[rowcnt+1,axcnt])
hosts_of_switch = {}
edges = run.get('scenario_edges')
for k, v in run.get('scenario_hosts_of_switch').items():
hosts_of_switch[int(k)] = v
plt_switches = list(range(0, run.get('scenario_switch_cnt')))
utils.plot_topo_small(all_axes[0],
hosts_of_switch,
edges,
plt_switches,
scenario_concentrated_switches,
switch_node_size=250,
font_size=15)
axcnt += 1
rowcnt += 1
for ax in axes:
ax.set_ylim(-120, maxy + 500)
ax.spines['top'].set_visible(False)
ax.spines['right'].set_visible(False)
for ax in axes[-4:]:
ax.set_xlabel('Time (s)')
for ax in []:
ax.set_ylabel('Flow table utilization')
handles, labels = axes[-1].get_legend_handles_labels()
fig.legend(handles, labels, loc='upper left', ncol=1, fontsize=16)
return fig
def make_summary_plot(summary_figure, normalized_spectrum, figure=None):
"""
:param summary_figure:
A dict containing information about how to plot the summary figure
:param normalized_spectrum:
specutils.Spectrum1D
:param figure:
matplotlib figure object to make plot in.
The function will adjust the figure object
If not specified (None), creates a new figure and returns it.
"""
all_axes_names = [
"top_left", "top_right", "middle", "bottom_left", "bottom_right"
]
# Validate file names
spectra_filenames = []
Tlit = []
Teff = []
for spectrum_list in summary_figure["spectra_filenames"]:
spectra_filenames.append(spectrum_list[0])
Tlit.append(int(spectrum_list[1]))
Teff.append(int(spectrum_list[2]))
for key in all_axes_names:
for spectrum_to_plot in summary_figure[key]["spectra_to_plot"]:
assert spectrum_to_plot in spectra_filenames, spectrum_to_plot
# Color palette generated from seaborn.color_palette("hls",6)
hls_colors = [(0.86, 0.37119999999999997, 0.33999999999999997),
(0.82879999999999987, 0.86, 0.33999999999999997),
(0.33999999999999997, 0.86, 0.37119999999999997),
(0.33999999999999997, 0.82879999999999987, 0.86),
(0.37119999999999997, 0.33999999999999997, 0.86),
(0.86, 0.33999999999999997, 0.82879999999999987)]
# Load spectra
spectra_objects = {}
spectra_colors = {}
# HACK data path
data_dir = os.path.dirname(os.path.abspath(__file__)) + "/data/spectra"
for i, spectrum_filename in enumerate(spectra_filenames):
fname = "{}/{}.fits".format(data_dir, spectrum_filename)
if os.path.exists(fname):
spectra_objects[spectrum_filename] = specutils.Spectrum1D.read(
fname)
spectra_colors[spectrum_filename] = hls_colors[i % len(hls_colors)]
else:
logger.warn("Could not find spectrum data file {}".format(fname))
# Make figure object and axes
if figure == None:
figure = plt.figure(figsize=(10, 8))
figure.subplots_adjust(left=0.10, right=0.95)
figure.patch.set_facecolor("w")
gs = GridSpec(4, 2)
gs.update(top=0.77)
ax_top_left = figure.add_subplot(gs.new_subplotspec((0, 0), rowspan=2))
ax_top_right = figure.add_subplot(gs.new_subplotspec((0, 1), rowspan=2))
ax_middle = figure.add_subplot(gs.new_subplotspec((2, 0), colspan=2))
ax_bot_left = figure.add_subplot(gs.new_subplotspec((3, 0)))
ax_bot_right = figure.add_subplot(gs.new_subplotspec((3, 1)))
all_axes = [
ax_top_left, ax_top_right, ax_middle, ax_bot_left, ax_bot_right
]
# HACK
def _label_Teff(ax, spectra_filenames, Tlit, Teff):
ii = np.argsort(Tlit)
spectra_filenames = list(np.array(spectra_filenames)[ii])
Tlit = list(np.array(Tlit)[ii])
Teff = list(np.array(Teff)[ii])
temp_lit = [[r"$T_{\rm lit}$", 'k']]
temp_eff = [[r"$T_{\rm eff}$", 'k']]
for spec_name, _Tlit, _Teff in zip(spectra_filenames, Tlit, Teff):
temp_lit.append([str(_Tlit), spectra_colors[spec_name]])
temp_eff.append([str(_Teff), spectra_colors[spec_name]])
print(temp_lit)
print(temp_eff)
coord = 100
for i, (entrylit, entryeff) in enumerate(zip(temp_lit, temp_eff)):
ax.annotate(entrylit[0],
xy=(4858.33, 0),
xytext=(40, coord),
textcoords='offset points',
size=10,
color=entrylit[1])
ax.annotate(entryeff[0],
xy=(4858.33, 0),
xytext=(270, coord),
textcoords='offset points',
size=10,
color=entryeff[1])
coord -= 15
# Plot
for key, ax in zip(all_axes_names, all_axes):
ax_dict = summary_figure[key]
this_star, = ax.plot(normalized_spectrum.dispersion,
normalized_spectrum.flux, 'k')
for spec_name in ax_dict["spectra_to_plot"]:
spec = spectra_objects[spec_name]
ax.plot(spec.dispersion,
spec.flux,
color=spectra_colors[spec_name])
ax.set_ylabel(ax_dict["label"])
ax.set_xlim(ax_dict["wavelength_range"])
ax.set_ylim(ax_dict["ylim"])
formatter = plt.matplotlib.ticker.ScalarFormatter(useOffset=False)
ax.xaxis.set_major_formatter(formatter)
if ax_dict["label"] == "H-beta":
_label_Teff(ax, spectra_filenames, Tlit, Teff)
handles = [this_star]
labels = ["This star"]
for i, spec_name in enumerate(spectra_filenames):
color = spectra_colors[spec_name]
artist = plt.Line2D((0, 1), (0, 0), color=color)
handles.append(artist)
labels.append(spec_name)
figure.legend(handles, labels, (.6, .8), prop={'size': 12}, ncol=2)
return figure
def plot_log(log: LogFile):
np_data = log.data.to_numpy()
func_data = {}
for row in np_data:
func_name, ts, te = row[:3]
exec_time = te - ts
if func_name in func_data:
func_data[func_name]['num_calls'] += 1
func_data[func_name]['total_exec_time'] += exec_time
last_min = func_data[func_name]['min']
func_data[func_name]['min'] = min(exec_time, last_min)
last_max = func_data[func_name]['max']
func_data[func_name]['max'] = max(exec_time, last_max)
else:
func_data[func_name] = {
'num_calls': 1,
'total_exec_time': exec_time,
'min': exec_time,
'max': exec_time,
}
for func_name in func_data:
# calculate and average
total_exec_time = func_data[func_name]['total_exec_time']
num_calls = func_data[func_name]['num_calls']
func_data[func_name]['avg'] = total_exec_time / num_calls
fig = plt.figure(figsize=(12, 12))
# use GridSpec for more organized layout
# https://matplotlib.org/3.2.1/gallery/subplots_axes_and_figures/gridspec_multicolumn.html
gs = GridSpec(2, 2, figure=fig)
# Plot 1: total amount of time for each methods
# https://matplotlib.org/tutorials/introductory/pyplot.html#plotting-with-categorical-variables
ax = plt.subplot(gs.new_subplotspec((0, 0)))
ax.set_title('total amount of execution time')
names = []
values = []
for func_name in func_data:
names.append(func_name)
values.append(func_data[func_name]['total_exec_time'])
bars = ax.bar(names, values)
plot_values_on_top_of_bars(
ax=ax,
bars=bars,
values=[f'{x:.2f}' for x in values],
max_bar_height=max(values),
)
# Plot 2: number of calls for each methods
ax = plt.subplot(gs.new_subplotspec((0, 1)))
ax.set_title('number of calls')
names = []
values = []
for func_name in func_data:
names.append(func_name)
values.append(func_data[func_name]['num_calls'])
bars = ax.bar(names, values)
plot_values_on_top_of_bars(
ax=ax,
bars=bars,
values=[repr(x) for x in values],
max_bar_height=max(values),
)
# Plot 3: plot max, min, and average for each methods
# We use grouped barplot here.
# https://python-graph-gallery.com/11-grouped-barplot/
ax = plt.subplot(gs.new_subplotspec((1, 0), colspan=2))
ax.set_title('max, min, and avg execution time')
min_bars = []
max_bars = []
avg_bars = []
group_labels = []
for func_name in func_data:
min_bars.append(func_data[func_name]['min'])
max_bars.append(func_data[func_name]['max'])
avg_bars.append(func_data[func_name]['avg'])
group_labels.append(func_name)
bar_width = .25
# bar width * (number of group + 1) for x-axis spacing
# 1 unit for spacing
min_bars_xs = np.arange(len(min_bars)) * (bar_width * (3 + 1))
avg_bars_xs = [bar_width + x for x in min_bars_xs]
max_bars_xs = [bar_width + x for x in avg_bars_xs]
bars = ax.bar(
x=min_bars_xs,
height=min_bars,
color='#ff0000',
width=bar_width,
label='min',
)
plot_values_on_top_of_bars(
ax=ax,
bars=bars,
values=[f'{x:.4f}' for x in min_bars],
max_bar_height=max(max_bars),
)
bars = ax.bar(
x=avg_bars_xs,
height=avg_bars,
color='#00ff00',
width=bar_width,
label='avg',
)
plot_values_on_top_of_bars(
ax=ax,
bars=bars,
values=[f'{x:.4f}' for x in avg_bars],
max_bar_height=max(max_bars),
)
bars = ax.bar(
x=max_bars_xs,
height=max_bars,
color='#0000ff',
width=bar_width,
label='max',
)
plot_values_on_top_of_bars(
ax=ax,
bars=bars,
values=[f'{x:.5f}' for x in max_bars],
max_bar_height=max(max_bars),
)
# group label x position to middle bar
ax.set_xticks(avg_bars_xs)
ax.set_xticklabels(group_labels)
ax.legend()
plt.show()
Brune = (2. * np.pi * (f_bins) * omega0) / (1. + ((1. / fc) * f_bins)**2.)
shift = np.mean(np.log10(event_spec[27:70]) - np.log10(Brune[27:70]))
# Brune = 10.**(np.log10(Brune)+shift)
# plot the station spectra
fig = plt.figure(figsize=(22, 14))
plt.suptitle('event ' + eventid + ', magnitude ' + str(ml) +
', recorded on station ' + station + ', distance ' +
str(round(dist_km, 2)) + ' km ')
plt.tight_layout(pad=0.01, w_pad=0.01, h_pad=0.01)
plt.subplots_adjust(left=0.06, right=0.99, top=0.92, bottom=0.05)
gs = GridSpec(3, 2)
plt.subplot(gs.new_subplotspec((0, 0), colspan=1))
# plt.title('event ' + eventid + ', magnitude ' + str(ml) + ', recorded on station ' + station + ', distance ' + str(round(dist_km,2)) + ' km ')
x = np.arange(0, len(dataE), 1) / 100.
plt.plot(x, dataE, color='black', label='EW')
# plt.plot(x, dataN, color = 'red', label = 'NS')
plt.xlim(-2, 65)
plt.legend(loc=1, borderaxespad=0.)
plt.gca().yaxis.get_major_formatter().set_powerlimits((0, 1))
plt.ylabel('Velocity (m/s)')
plt.ylim(min(dataN), max(dataN))
plt.annotate('seconds',
va='center',
xy=(0.48, -0.12),
xycoords='axes fraction')
plt.annotate('(a)',
def lpf_event_display(xhit, nhit, fit_result, hit_is_used, xiter, **kwargs):
"""
Event display
:param xhit:
:param nhit:
:param fit_result:
:param hit-is_used:
:param xiter:
:param kwargs:
:return:
"""
xhit = np.array(xhit)
nhit = np.array(nhit)
plot_range = kwargs.pop('range', None)
zoom = kwargs.pop('zoom', -1)
nbins = kwargs.pop('nbins', 15)
if plot_range == 'None':
plot_range = ((0, 100), (0, 100))
if zoom > 0:
plot_range = ((fit_result[0] - zoom / 2, fit_result[0] + zoom / 2),
(fit_result[1] - zoom / 2, fit_result[1] + zoom / 2))
print("Reconstruction::lpf_event_display() ")
fig = plt.figure(figsize=(16, 6))
gs = GridSpec(2, 2, figure=fig)
ax0 = plt.subplot(gs.new_subplotspec((0, 0), rowspan=2))
ax1 = plt.subplot(gs.new_subplotspec((0, 1), rowspan=1))
ax2 = plt.subplot(gs.new_subplotspec((1, 1), rowspan=1))
# ax1 = plt.subplot(222)
# ax2 = plt.subplot(224)
# fig, ax0 = plt.subplots(nrows=1)
# make a list of the intermediate steps
xp = []
yp = []
nn = []
iiter = []
for i in range(len(xiter)):
if xiter[i][3] != 0:
xp.append(xiter[i][0])
yp.append(xiter[i][1])
nn.append(xiter[i][2])
iiter.append(i)
xp = np.array(xp)
yp = np.array(yp)
nn = np.array(nn)
iiter = np.array(iiter)
niter = len(xp)
ax1.plot(iiter, xp - fit_result[0])
ax1.plot(iiter, yp - fit_result[1])
ax1.set_xlabel('iteration')
ax2.plot(iiter, nn)
ax2.set_xlabel('iteration')
# make these smaller to increase the resolution
dx, dy = (plot_range[0][1] - plot_range[0][0]) / 400, (
plot_range[1][1] - plot_range[1][0]) / 400
# generate 2 2d grids for the x & y bounds
x = np.arange(plot_range[0][0], plot_range[0][1], dx)
y = np.arange(plot_range[1][0], plot_range[1][1], dy)
z = np.zeros((len(y), len(x)))
#print(x,y)
for i in range(len(x)):
for j in range(len(y)):
xx = x[i]
yy = y[j]
xff = np.array([xx, yy, 0])
#print('xfit =',xff,' r0 =',xiter[niter-1][2])
z[j][i] = lpf_lnlike_plot(xhit, nhit, hit_is_used, xff,
xiter[niter - 1][2])
# z = z[:-1, :-1]
levels = MaxNLocator(nbins=nbins).tick_values(z.min(), z.max())
# cmap = plt.get_cmap('afmhot')
cmap = plt.get_cmap('PiYG')
# norm = BoundaryNorm(levels, ncolors=cmap.N, clip=True)
# ax0 = fig.gca()
cf = ax0.contourf(x + dx / 2., y + dy / 2., z, levels=levels, cmap=cmap)
fig.colorbar(cf, ax=ax0)
title_string = 'x = {:8.2f} y = {:8.2f} r0= {:8.2f}'.format(
fit_result[0], fit_result[1], fit_result[2])
ax0.set_title(title_string)
# add the light detectors
mx_eff = -1
for ih in range(len(nhit)):
if nhit[ih] > mx_eff:
mx_eff = nhit[ih]
for ih in range(len(nhit)):
# draw location of SiPM
xs = xhit[ih]
# plot sensor only if in range
if (xs[0] > plot_range[0][0]) & (xs[0] < plot_range[0][1]) & \
(xs[1] > plot_range[1][0]) & (xs[1] < plot_range[1][1]):
#dx = nhit[ih] / mx_eff *10
rr = (nhit[ih] + 0.25) / mx_eff * 10
#sq = plt.Rectangle(xy=(xs[0] - dx / 2, xs[1] - dx / 2),
# height=dx,
# width=dx,
# fill=False, color='red')
if nhit[ih] > 0:
if hit_is_used[ih]:
color = 'red'
else:
color = 'black'
sq = plt.Circle(xy=(xs[0], xs[1]),
radius=rr,
fill=False,
color=color)
else:
sq = plt.Circle(xy=(xs[0], xs[1]),
radius=rr,
fill=False,
color='black')
ax0.add_artist(sq)
# write number of detected photons
### txs = str(nhit[ih])
### ax0.text(xs[0] + dx / 2 + 2.5, xs[1], txs, color='red')
# initial position
ax0.plot(xiter[0][0], xiter[0][1], 'o', markersize=10, color='cyan')
ax0.plot(xp, yp, 'w-o', markersize=5)
# true position
# plt.plot(self.sim.get_x0()[0], self.sim.get_x0()[1], 'x', markersize=14, color='cyan')
# reconstructed position
# if abs(self.fdata['xr']) < 100:
ax0.plot(fit_result[0], fit_result[1], 'wo', markersize=10)
ax0.set_xlabel('x (mm)', fontsize=18)
ax0.set_ylabel('y (mm)', fontsize=18)
ax0.set_xlim([plot_range[0][0], plot_range[0][1]])
ax0.set_ylim([plot_range[1][0], plot_range[1][1]])
plt.show()
istat = int(input("Type: 0 to continue, 1 to make pdf, 2 to quit...."))
if istat == 1:
fname = 'event.pdf'
fig.savefig(fname)
fname = 'event.png'
fig.savefig(fname)
clear_output()
return istat
def plot_cplap_ternary(output='plot-2d.pdf',
grid_file='grid.dat', txt_file='2Dplot.txt',
xmin=None, ymin=None,
style=['ggplot'], cmap='viridis',
width=6, height=4, ratio=[4],
gridlines=None):
# Set Truetype PDF/PS fonts unless overruled by style file
matplotlib.rcParams['pdf.fonttype'] = 42
matplotlib.rcParams['ps.fonttype'] = 42
if len(style) > 0:
matplotlib.style.use(style)
fig = plt.figure(figsize=(width, height))
if len(ratio) == 1:
ratio += [1]
elif len(ratio) > 2:
raise ValueError('Ratio can be given as one or two integers. '
'{} is too many!'.format(len(ratio)))
gs = GridSpec(1, ratio[0] + ratio[1])
ax = fig.add_subplot(gs.new_subplotspec((0, ratio[1]), colspan=ratio[0]))
cax = fig.add_subplot(gs.new_subplotspec((0, 0), colspan=ratio[1]))
with open('grid.dat', 'rt') as f:
# Scroll to formula and read
for _ in range(3):
line = f.readline()
el_matches = re.findall(r'\d+ (\w+)', line)
# Scroll to number of points and read
for _ in range(4):
line = f.readline()
npts = 5
npts_matches = re.findall(r'first\s+(\d+) points', line)
if len(npts_matches) == 1:
npts = int(npts_matches[0])
else:
raise Exception("Couldn't read number of polyhedron corners")
# Scroll to data lines and read coordinates from npts lines
for _ in range(5):
f.readline()
region = np.zeros((npts, 2))
for i in range(npts):
line = f.readline().split()
x, y = float(line[0]), float(line[1])
region[i, :] = x, y
# # Use convex hull solver to draw polyhedron edges in correct order
# hull = np.array([region[i] for i in ConvexHull(region).vertices])
# region_patch = Polygon(hull, facecolor=(0.6, 0.6, 0.6))
# ax.add_patch(region_patch)
# Read in rest of mesh, skipping header, region and '|' column
mesh = np.genfromtxt('grid.dat', skip_header=(12 + npts),
usecols=(0, 1, 3))
mesh_x = sorted(set(mesh[:, 0]))
mesh_y = sorted(set(mesh[:, 1]))
mesh_z = np.zeros((len(mesh_y), len(mesh_x))) * np.NaN
for x, y, z in mesh:
ix = mesh_x.index(x)
iy = mesh_y.index(y)
mesh_z[iy, ix] = z
mesh_z = np.ma.masked_invalid(mesh_z)
dep_mu = ax.pcolormesh(mesh_x, mesh_y, mesh_z, rasterized=True, cmap=cmap)
cbar = fig.colorbar(dep_mu, cax=cax)
cbar.set_label(r'$\mu$ ({}) / eV'.format(el_matches[2]))
with open('2Dplot.txt', 'rt') as f:
lines = f.readlines()
data = OrderedDict()
for i in range(len(lines) // 4 + 1):
species = lines[i * 4][1:-1]
x1, y1 = map(float, lines[i * 4 + 1].split())
x2, y2 = map(float, lines[i * 4 + 2].split())
data[species] = [[x1, x2], [y1, y2]]
if xmin is None:
xmin = ceil(min(min(coords[0]) for coords in data.values()))
if ymin is None:
ymin = ceil(min(min(coords[1]) for coords in data.values()))
for species, (x, y) in data.items():
ax.plot(x, y, '-', label=format_chem(species))
ax.legend()
ax.set_xlim(xmin, 0)
ax.set_ylim(ymin, 0)
ax.set_xlabel(r'$\mu$ ({}) / eV'.format(el_matches[0]))
ax.xaxis.set_label_position('top')
ax.xaxis.set_ticks_position('top')
ax.set_ylabel(r'$\mu$ ({}) / eV'.format(el_matches[1]))
ax.yaxis.set_label_position('right')
ax.yaxis.set_ticks_position('right')
# Gridlines option can overrule style defaults
if gridlines is not None:
ax.grid(gridlines)
fig.tight_layout()
if output is None:
plt.show()
else:
fig.savefig(output)
def zernikePyramid(xs,
ys,
zs,
figsize=(13, 8),
vmin=-1,
vmax=1,
vdim=True,
s=5,
title=None,
filename=None,
fig=None,
**kwargs):
"""Make a multi-zernike plot in a pyramid shape.
Subplots show individual Zernikes over a range of x and y (presumably a
field of view).
Parameters
----------
xs, ys: array of float
Field angles (or other spatial coordinate over which to plot Zernikes)
zs: array of float, shape (jmax, xymax)
Zernike values. First index labels the particular Zernike coefficient,
second index labels spatial coordinate. First index implicitly starts
at j=4 defocus.
"""
import warnings
import galsim
jmax = zs.shape[0] + 3
nmax, _ = galsim.zernike.noll_to_zern(jmax)
nrow = nmax - 1
ncol = nrow + 2
gridspec = GridSpec(nrow, ncol)
def shift(pos, amt):
return [pos.x0 + amt, pos.y0, pos.width, pos.height]
def shiftAxes(axes, amt):
for ax in axes:
ax.set_position(shift(ax.get_position(), amt))
if fig is None:
fig = Figure(figsize=figsize, **kwargs)
axes = {}
shiftLeft = []
shiftRight = []
for j in range(4, jmax + 1):
n, m = galsim.zernike.noll_to_zern(j)
if n % 2 == 0:
row, col = n - 2, m // 2 + ncol // 2
else:
row, col = n - 2, (m - 1) // 2 + ncol // 2
subplotspec = gridspec.new_subplotspec((row, col))
axes[j] = fig.add_subplot(subplotspec)
axes[j].set_aspect('equal')
if nrow % 2 == 0 and n % 2 == 0:
shiftLeft.append(axes[j])
if nrow % 2 == 1 and n % 2 == 1:
shiftRight.append(axes[j])
cbar = {}
for j, ax in axes.items():
n, _ = galsim.zernike.noll_to_zern(j)
ax.set_title("Z{}".format(j))
if vdim:
_vmin = vmin / n
_vmax = vmax / n
else:
_vmin = vmin
_vmax = vmax
scat = ax.scatter(xs,
ys,
c=zs[j - 4],
s=s,
linewidths=0.5,
cmap='Spectral_r',
rasterized=True,
vmin=_vmin,
vmax=_vmax)
cbar[j] = fig.colorbar(scat, ax=ax)
ax.set_xticks([])
ax.set_yticks([])
if title:
fig.suptitle(title, x=0.1)
# Mistakenly raises MatplotlibDeprecationWarning.
# See https://github.com/matplotlib/matplotlib/issues/19486
with warnings.catch_warnings():
warnings.simplefilter("ignore")
fig.tight_layout()
amt = 0.5 * (axes[4].get_position().x0 - axes[5].get_position().x0)
shiftAxes(shiftLeft, -amt)
shiftAxes(shiftRight, amt)
shiftAxes([cbar[j].ax for j in cbar.keys() if axes[j] in shiftLeft], -amt)
shiftAxes([cbar[j].ax for j in cbar.keys() if axes[j] in shiftRight], amt)
if filename:
fig.savefig(filename)
return fig
def add_subplot(location, rowspan=1, colspan=1): gridspec = GridSpec(2, 3) subplotspec = gridspec.new_subplotspec(location, rowspan, colspan) return fig.add_subplot(subplotspec)
def zernikePyramid(xs,
ys,
zs,
figsize=(13, 8),
vmin=-1,
vmax=1,
vdim=True,
s=5,
title=None,
filename=None,
fig=None,
**kwargs):
import galsim
jmax = zs.shape[0] + 3
nmax, _ = galsim.zernike.noll_to_zern(jmax)
nrow = nmax - 1
ncol = nrow + 2
gridspec = GridSpec(nrow, ncol)
def shift(pos, amt):
return [pos.x0 + amt, pos.y0, pos.width, pos.height]
def shiftAxes(axes, amt):
for ax in axes:
ax.set_position(shift(ax.get_position(), amt))
if fig is None:
fig = Figure(figsize=figsize, **kwargs)
axes = {}
shiftLeft = []
shiftRight = []
for j in range(4, jmax + 1):
n, m = galsim.zernike.noll_to_zern(j)
if n % 2 == 0:
row, col = n - 2, m // 2 + ncol // 2
else:
row, col = n - 2, (m - 1) // 2 + ncol // 2
subplotspec = gridspec.new_subplotspec((row, col))
axes[j] = fig.add_subplot(subplotspec)
axes[j].set_aspect('equal')
if nrow % 2 == 0 and n % 2 == 0:
shiftLeft.append(axes[j])
if nrow % 2 == 1 and n % 2 == 1:
shiftRight.append(axes[j])
cbar = {}
for j, ax in axes.items():
n, _ = galsim.zernike.noll_to_zern(j)
ax.set_title("Z{}".format(j))
if vdim:
_vmin = vmin / n
_vmax = vmax / n
else:
_vmin = vmin
_vmax = vmax
scat = ax.scatter(xs,
ys,
c=zs[j - 4],
s=s,
linewidths=0.5,
cmap='Spectral_r',
rasterized=True,
vmin=_vmin,
vmax=_vmax)
cbar[j] = fig.colorbar(scat, ax=ax)
ax.set_xticks([])
ax.set_yticks([])
if title:
fig.suptitle(title, x=0.1)
fig.tight_layout()
amt = 0.5 * (axes[4].get_position().x0 - axes[5].get_position().x0)
shiftAxes(shiftLeft, -amt)
shiftAxes(shiftRight, amt)
shiftAxes([cbar[j].ax for j in cbar.keys() if axes[j] in shiftLeft], -amt)
shiftAxes([cbar[j].ax for j in cbar.keys() if axes[j] in shiftRight], amt)
if filename:
fig.savefig(filename)
return fig
def add_subplot(location, rowspan=1, colspan=1):
gridspec = GridSpec(2, 3)
subplotspec = gridspec.new_subplotspec(location, rowspan, colspan)
return fig.add_subplot(subplotspec)
return dec_to_clk(time_dec)
fig = plt.figure(figsize=(10, 6), num='Sunrise / Sunset')
plt.subplots_adjust(top=.925, left=0.100, right=.950, wspace=0.1)
gs = GridSpec(28, 28, figure=fig)
# date list for x axis of all plots
base = datetime.strptime(str(year) + '0101', '%Y%m%d')
date_list = [base + timedelta(days=x) for x in range(0, num_days)]
# main plot
y_rise = [i.sunrise_dec for i in data_dst]
y_set = [i.sunset_dec for i in data_dst]
y_solar_noon = [i.solar_noon_dec for i in data_dst]
ax_0_0 = plt.subplot(gs.new_subplotspec((0, 2), colspan=25, rowspan=10))
ax_0_0.set_title(plot_title)
ax_0_0.grid(which='major', linestyle='-', linewidth=0.5, color='grey')
ax_0_0.set_xlabel('Day of Year')
ax_0_0.xaxis.set_major_locator(mdates.MonthLocator())
ax_0_0.xaxis.set_major_formatter(mdates.DateFormatter('%b'))
ax_0_0.xaxis.set_minor_locator(mdates.DayLocator())
ax_0_0.set_ylabel('Time (24-hour)')
ax_0_0.yaxis.set_major_formatter(tick.FuncFormatter(dec_to_clk_ff))
ax_0_0.set_ylim(0, 24)
ax_0_0.plot(date_list, y_rise, 'b')
ax_0_0.plot(date_list, y_set, 'r')
ax_0_0.plot(date_list, y_solar_noon, 'k-.', label='Solar Noon')
ax_0_0.legend(loc='best', fontsize='small')
# Day Length
def plot_field_map(model, feature, radius, **kwargs):
"""
This function plots the synthetic values generated by a given spherical harmonic model within the domain of
geomagnetism. It computes the design matrix G, based on the length of the input model, m, and uses it in the
forward problem:
d = G.m
The user has several options for plotting different field features in different plotting views. This function
serves well as a first investigation of a given model, but it is not flexible for more advanced visualisation
goals. The user is encouraged to visit https://scitools.org.uk/cartopy for learning how to use cartopy for
plotting, which is relatively simply. The complexity of the below function is due to the different options
given, but a cartopy map projection can actually be carried out in a few lines of code.
Args:
model (ndarray): model coefficients used for computing d = G.m, where m is the model
feature (str): geomagnetic field feature to be plotted, options: 'B_r', 'B_t', 'B_p', 'F', 'D', 'I' or 'H'
radius (float): the radius at which the synthetic field values should be generated
**kwargs (optional):
value_limits (float list): upper and lower value limits e.g. [-1e3, 1e3]
mesh_size (float): mesh size for the synthetic grid, below .5 computations are heavy
lat_limits (float list): limits on latitude, order does not matter e.g. [90, -90]
lon_limits (float list): limits on longitude, order does not matter e.g. [-180, 180]
main_projection (object): Cartopy projection object e.g. ccrs.Mollweide()
for full list of projections see: https://scitools.org.uk/cartopy
plot_poles (boolean): Whether to plot poles or not, default is True
polar_limit (float): Bounding latitude for the polar plots default is 60N and 60S
contour_labels (float list): list of contour line labels plotted if feature=='D'
e.g. [-30, -15, -5, 0, 5, 15, 30]
microtesla (boolean): Set to false for plotting in nanoTesla
savefig (boolean): save figure True/False
colormap (str): Choose from matplotlibs color map options e.g. 'PuOr_r' or 'RdBu'
title_string (str): set a customized title string
colorbar_string (str): set a customized colorbar string
figure_size (float tuple): figure size, (width, height) in inches.
title_pos (float): position of the title text, e.g. 1.1
label_pos (int): spacing in points between the colobar label and the x-axis.
Returns:
None
Notes:
- Contour lines are only plotted on declination plots
- Contour lines are omitted in polar plots. Calling the function with plot_poles=False and
projection_type=ccrs.LambertAzimuthalEqualArea(), will produce a polar plot with contours.
Examples:
# Example1
model = np.loadtxt('coefficients_L2.txt')
plot_feature = 'B_r'
radius_core = 3480.
plot_field_map(model, plot_feature, radius_core)
# Example2:
plot_feature = 'D'
radius_surface = 6371.2
plot_field_map(model, plot_feature, radius_surface, value_limits=[-40, 40], no_poles=True, colormap='RdBu')
@author: Eigil Y. H. Lippert, Student DTU Space, <*****@*****.**>
"""
# set default values
value_limits = [-1e3, 1e3]
mesh_size = 1
lat_limits = [90, -90]
lon_limits = [-180, 180]
main_projection = ccrs.Mollweide()
plot_poles = True
polar_limit = 60
contour_labels = [-30, -15, -5, 0, 5, 15, 30]
microtesla = True
savefig = False
colormap = 'PuOr_r'
title_string = None
colorbar_string = None
figure_size = (12, 12)
title_pos = 1.
label_pos = 5.
# update defaults based on used input
for key, value in kwargs.items():
if key == 'value_limits':
value_limits = value
elif key == 'mesh_size':
mesh_size = value
elif key == 'lat_limits':
lat_limits = value
elif key == 'lon_limits':
lon_limits = value
elif key == 'main_projection':
main_projection = value
elif key == 'plot_poles':
plot_poles = value
elif key == 'polar_limit':
polar_limit = value
elif key == 'contour_labels':
contour_labels = value
elif key == 'microtesla':
microtesla = value
elif key == 'savefig':
savefig = value
elif key == 'colormap':
colormap = value
elif key == 'title_string':
title_string = value
elif key == 'colorbar_string':
colorbar_string = value
elif key == 'figure_size':
figure_size = value
elif key == 'title_pos':
title_pos = value
elif key == 'label_pos':
label_pos = value
# set constants
degree = int(-1 + np.sqrt(1 + len(model)))
r_surface = 6371.2
rad = np.pi / 180
lat_bound = [np.max(lat_limits), np.min(lat_limits)]
lon_bound = [np.min(lon_limits), np.max(lon_limits)]
# make range of lat/lon
lat = 90 - np.arange(lat_bound[0], lat_bound[1] - mesh_size, -mesh_size) # lat/theta array between 90 and 90
lon = np.arange(lon_bound[0], lon_bound[1] + mesh_size, mesh_size)
# remove pole points
lat = np.delete(lat, np.where(lat == 0))
lat = np.delete(lat, np.where(lat == 180.))
# compute(lat, lon) - grid
lon_grid, lat_grid = np.meshgrid(lon, lat)
rows, cols = np.shape(lon_grid)
# reshape for design_SHA to work
lon_grid = lon_grid.reshape(-1, )
lat_grid = lat_grid.reshape(-1, )
[Gr, Gt, Gp] = design_SHA(radius / r_surface, lat_grid * rad, lon_grid * rad, degree)
G = np.vstack((Gr, Gt, Gp))
# compute synthetic field
B_synth = G.dot(model)
# seperate into components
step = int(len(B_synth) / 3)
Br_synth = B_synth[0:step]
Bt_synth = B_synth[step:step * 2]
Bp_synth = B_synth[step * 2::]
# reshape back for pcolormesh to work
lon_grid = lon_grid.reshape(rows, cols)
lat_grid = (90 - lat_grid).reshape(rows, cols)
# reshape field components into size of grid as well
Br_synth = Br_synth.reshape(rows, cols)
Bt_synth = Bt_synth.reshape(rows, cols)
Bp_synth = Bp_synth.reshape(rows, cols)
# chosen feature:
for feature_name in [feature]:
if feature_name == 'B_r':
feature_name = feature_name + '-component'
# compute Br component
feat = Br_synth
unit = 'B_r, [nT]'
if microtesla:
feat = feat * 1e-3
unit = 'B_r, [\mu T]'
elif feature_name == 'B_t':
feature_name = feature_name + '-component'
# compute Bt component
feat = Bt_synth
unit = 'B_t, [nT]'
if microtesla:
feat = feat * 1e-3
unit = 'B_t, [\mu T]'
elif feature_name == 'B_p':
feature_name = feature_name + '-component'
# compute Bp component
feat = Bp_synth
unit = 'B_p, [nT]'
if microtesla:
feat = feat * 1e-3
unit = 'B_p, [\mu T]'
elif feature_name == 'F':
feature_name = feature_name + ', field intensity'
# compute F, intensity
feat = np.sqrt(Br_synth ** 2 + Bt_synth ** 2 + Bp_synth ** 2)
unit = 'F, [nT]'
if microtesla:
feat = feat * 1e-3
unit = 'F, [\mu T]'
elif feature_name == 'D':
feature_name = feature_name + ', declination'
X_synth = -Bt_synth
Y_synth = Bp_synth
# compute D, declination
feat = np.arctan2(Y_synth, X_synth) * 180 / np.pi
unit = 'D, [degree]'
elif feature_name == 'I':
feature_name = feature_name + ', inclination'
X_synth = -Bt_synth
Y_synth = Bp_synth
Z_synth = -Br_synth
H_synth = np.sqrt(X_synth ** 2 + Y_synth ** 2)
# compute I, inclination
feat = np.arctan2(Z_synth, H_synth) * 180 / np.pi
unit = 'I, [degree]'
elif feature_name == 'H':
feature_name = feature_name + ', horisontal component'
X_synth = -Bt_synth
Y_synth = Bp_synth
# compute H, horisontal component
feat = np.sqrt(X_synth ** 2 + Y_synth ** 2)
unit = 'H, [nT]'
if microtesla:
feat = feat * 1e-3
unit = 'H, [\mu T]'
else:
print('Feature not known please choose B_r, B_t, B_p, F, D, I or H')
# creates a list of projections for a combined main projection polar projection figure
projections = [main_projection,
ccrs.LambertAzimuthalEqualArea(central_longitude=0., central_latitude=90.),
ccrs.LambertAzimuthalEqualArea(central_longitude=0., central_latitude=-90.)]
# if no poles, only use one figure position
if not plot_poles:
subplot_position = [(0, 0)]
else:
subplot_position = [(0, 0), (2, 0), (2, 2)]
colspan = 4
f = plt.figure(figsize=figure_size)
gs = GridSpec(4, 4, figure=f)
for i, pos in enumerate(subplot_position):
# change colspan for polar plots
if i > 0:
colspan = 2
if not plot_poles:
ax = plt.subplot(projection=projections[0])
else:
ax = plt.subplot(gs.new_subplotspec(pos, colspan=colspan, rowspan=2), projection=projections[i])
# select polar values of interest for pcolormesh.
if (i == 1) or (i == 2):
lat_bound = [(90, 60), (-90, -60)]
if i == 1:
lat_bound = [90, polar_limit]
polar_mask = lat_grid >= lat_bound[1]
elif i == 2:
lat_bound = [-90, -polar_limit]
polar_mask = lat_grid <= lat_bound[1]
# the masked array is 1-d so reshape with same number of columns as before:
lat_grid_polar = np.reshape(lat_grid[polar_mask], (-1, lat_grid.shape[1]))
b_r_polar = np.reshape(feat[polar_mask], (-1, lon_grid.shape[1]))
lon_grid_polar = lon_grid[0:lat_grid_polar.shape[0], :]
h1 = ax.pcolormesh(lon_grid_polar, lat_grid_polar, b_r_polar, cmap=colormap,
transform=ccrs.PlateCarree(),
vmin=value_limits[0], vmax=value_limits[1])
ax.set_extent([-180, 180, lat_bound[0], lat_bound[1]], ccrs.PlateCarree())
# make circular boundary on projection
theta = np.linspace(0, 2 * np.pi, 100)
center, radius = [0.5, 0.5], 0.5
verts = np.vstack([np.sin(theta), np.cos(theta)]).T
circle = mpath.Path(verts * radius + center)
ax.set_boundary(circle, transform=ax.transAxes)
else:
# If declination draw contour lines
if unit == 'D, [degree]':
feat_flatten = feat.flatten()
lon_grid_flatten = lon_grid.flatten()
lat_grid_flatten = lat_grid.flatten()
h1 = ax.scatter(x=lon_grid_flatten, y=lat_grid_flatten, s=20, c=feat_flatten, edgecolors='none',
transform=ccrs.PlateCarree(), cmap=colormap, vmin=value_limits[0],
vmax=value_limits[1])
c1 = ax.contour(lon, 90 - lat, feat, contour_labels, colors='black',
linewidths=2.5, linestyles='solid', alpha=0.6, transform=ccrs.PlateCarree())
cl = plt.clabel(c1, fontsize=10, colors='k', inline=1, inline_spacing=8,
fmt='%i', rightside_up=True, use_clabeltext=True)
else:
h1 = ax.pcolormesh(lon_grid, lat_grid, feat, cmap=colormap, transform=ccrs.PlateCarree(),
vmin=value_limits[0], vmax=value_limits[1])
ax.coastlines(linewidth=1.1)
ax.gridlines()
# we need to set axes_class=plt.Axes, else it attempts to create a GeoAxes as colorbar
if i == 0:
divider = make_axes_locatable(ax)
ax_cb = divider.new_vertical(size="5%", pad=0.1, axes_class=plt.Axes, pack_start=True)
f.add_axes(ax_cb)
# colorbar and properties
cbar = plt.colorbar(h1, cax=ax_cb, orientation="horizontal")
if colorbar_string is None:
colorbar_string = r'${}$'.format(unit)
cbar.set_label(colorbar_string, rotation=0, labelpad=label_pos, fontsize='xx-large')
cbar.ax.tick_params(labelsize=15)
if title_string is None:
title_string = 'Field map of {}'.format(feature_name)
ax.set_title(title_string,
weight='bold', fontsize='xx-large', y=title_pos)
if savefig:
plt.savefig('Field_map_of_the_{}_component'.format(feature_name) + '.png')
plt.show()
return
def __calculate_layout(self):
'''
Creates the subplot specs for the chart layout, options are
3 panes, horizontal, split right
-------------------
| | |
| |--------|
| | |
-------------------
3 panes, horizontal, split left
-------------------
| | |
|--------| |
| | |
-------------------
3 panes, vertical, split bottom
-------------------
| |
|-----------------|
| | |
-------------------
3 panes, vertical, split top
-------------------
| | |
|-----------------|
| |
-------------------
2 panes, vertical
-------------------
| |
|-----------------|
| |
-------------------
2 panes, horizontal
-------------------
| | |
| | |
| | |
-------------------
1 pane
-------------------
| |
| |
| |
-------------------
:return: image_spec, chart_spec, filter_spec
'''
layout = self.chartLayout.currentText()
filter_spec = None
image_spec = None
chart_spec = None
if layout == "Image | Chart, Filters":
image_spec, chart_spec, filter_spec = self.__get_one_pane_two_pane_spec(
)
elif layout == "Image | Filters, Chart":
image_spec, filter_spec, chart_spec = self.__get_one_pane_two_pane_spec(
)
elif layout == "Chart | Image, Filter":
chart_spec, image_spec, filter_spec = self.__get_one_pane_two_pane_spec(
)
elif layout == "Chart | Filters, Image":
chart_spec, filter_spec, image_spec = self.__get_one_pane_two_pane_spec(
)
elif layout == "Filters | Image, Chart":
filter_spec, image_spec, chart_spec = self.__get_one_pane_two_pane_spec(
)
elif layout == "Filters | Chart, Image":
filter_spec, chart_spec, image_spec = self.__get_one_pane_two_pane_spec(
)
elif layout == 'Image, Filters | Chart':
image_spec, filter_spec, chart_spec = self.__get_two_pane_one_pane_spec(
)
elif layout == 'Filters, Image | Chart':
filter_spec, image_spec, chart_spec = self.__get_two_pane_one_pane_spec(
)
elif layout == 'Chart, Image | Filters':
chart_spec, image_spec, filter_spec = self.__get_two_pane_one_pane_spec(
)
elif layout == 'Image, Chart | Filters':
image_spec, chart_spec, filter_spec = self.__get_two_pane_one_pane_spec(
)
elif layout == 'Filters, Chart | Image':
filter_spec, chart_spec, image_spec = self.__get_two_pane_one_pane_spec(
)
elif layout == 'Chart, Filters | Image':
chart_spec, filter_spec, image_spec = self.__get_two_pane_one_pane_spec(
)
elif layout == "Chart | Filters":
chart_spec, filter_spec = self.__get_two_pane_spec()
elif layout == "Filters | Chart":
filter_spec, chart_spec = self.__get_two_pane_spec()
elif layout == "Chart | Image":
chart_spec, image_spec = self.__get_two_pane_spec()
elif layout == "Image | Chart":
image_spec, chart_spec = self.__get_two_pane_spec()
elif layout == "Pixel Perfect Image | Chart":
gs = GridSpec(1,
1,
wspace=self.widthSpacing.value(),
hspace=self.heightSpacing.value())
chart_spec = gs.new_subplotspec((0, 0), 1, 1)
self.__prepare_for_pixel_perfect()
return image_spec, chart_spec, filter_spec