def plot_map_w_scalebar2(ax, train_imgs, im_num, mask=True, colorbar=True):
im_lims = train_imgs['longlat_bounds']['img_{:02d}'.format(im_num)][...]
plt.imshow(train_imgs['input_images'][im_num][...],
extent=im_lims,
origin='upper',
cmap='YlGn',
aspect='equal') #, vmin=50, vmax=150
if colorbar:
plt.colorbar()
if mask:
plt.imshow(1 - train_imgs['target_masks'][im_num][...],
alpha=0.2,
extent=im_lims,
origin='upper',
cmap='Greys_r',
aspect='equal')
# np.cos(np.deg2rad(im_lims[2:].mean()))
plt.title('Image #{} with target masks'.format(im_num))
l, r = plt.xlim()
barlength = 0.3 * (r - l)
bartext = '{:2.1f} km'.format(barlength * kmperdeg)
bar = AnchoredSizeBar(ax.transData, barlength, bartext, 4)
ax.add_artist(bar)
ax.grid()
return im_lims
def get_scalebar(trace, list_ax):
trace.x_tick_length = int(trace.x_range / 2)
trace.y_stim_tick_length = trace.y_stim_range / 5
#trace.y_rec_tick_length = trace.y_rec_range / 0.005
x_label = str(trace.x_tick_length) + ' ' + trace.x_tick_units
# needs to be individualized for each ax ------------------------------------------------------------------------------------------------
y_label1 = ' ' + str(y_tick_length1) + ' ' + y_tick_units1
#y_label2 = ' ' + str(y_tick_length2) + ' ' + y_tick_units2
x_scalebar = AnchoredSizeBar(list_ax[0].transData,
trace.x_tick_length,
'',
'center right',
pad=0,
color='black',
frameon=False,
size_vertical=.2)
#y_scalebar1 = AnchoredSizeBar(ax1.transData, 1.4, '', 'lower right', pad=0, color='black', frameon=False, size_vertical= y_tick_length1)
list_ax[0].add_artist(x_scalebar)
#list_ax[0].add_artist(y_scalebar1)(self, parameter_list)
# Add scale and units to error bars
list_ax[0].text(trace.x_max + 75,
trace.y_stim_max - trace.y_stim_range / 2 - 1,
x_label,
size=6)
def plot_scalebar(self, length=1, title=None, loc='upper right'):
"""
Plot a scalebar on the cross section.
Parameters:
-----------
length : number, default=1
The length of the scale bar in world units (e.g. meters)
title: string, default="{length} world units"
The title/label for the scale bar
loc: int or string
The position of the scale bar. Valid parameters are:
'upper right' : 1,
'upper left' : 2,
'lower left' : 3,
'lower right' : 4,
'right' : 5,
'center left' : 6,
'center right' : 7,
'lower center' : 8,
'upper center' : 9,
'center' : 10,
Returns:
--------
A matplotlib AnchoredSizeBar artist.
"""
if title is None:
title = '{} world units'.format(length)
self.sizebar = AnchoredSizeBar(self.ax.transData, length,
title, loc=loc, pad=0.5,
borderpad=0.5, sep=5, frameon=True)
self.ax.add_artist(self.sizebar)
return self.sizebar
def add_scalebar(pseudoimg,
pixelresolution,
barwidth,
barlocation='lower center',
fontprops=None,
scalebar=None):
if fontprops is None:
fontprops = fm.FontProperties(size=16, weight='bold')
ax = pseudoimg.gca()
if scalebar is None:
scalebar = AnchoredSizeBar(ax.transData,
barwidth / pixelresolution,
'2 cm',
barlocation,
pad=0.5,
sep=5,
color='white',
frameon=False,
size_vertical=barwidth / pixelresolution /
30,
fontproperties=fontprops)
ax.add_artist(scalebar)
return ax.get_figure()
def add_scalebar(
ax: mpl.axes.Axes,
scalebar_size: float,
pixel_size: float,
unit: str = "µm",
edgecolor: str = None,
**kwargs,
) -> None:
"""Add a scalebar to the axis."""
# NOTE: this is to be moved to dphtools when the package is ready
scalebar_length = scalebar_size / pixel_size
default_scale_bar_kwargs = dict(
loc="lower right",
pad=0.5,
color="white",
frameon=False,
size_vertical=scalebar_length / 10,
fontproperties=fm.FontProperties(weight="bold"),
)
default_scale_bar_kwargs.update(kwargs)
if unit is not None:
label = f"{scalebar_size} {unit}"
else:
label = ""
if "lower" in default_scale_bar_kwargs["loc"]:
default_scale_bar_kwargs["label_top"] = True
scalebar = AnchoredSizeBar(ax.transData, scalebar_length, label, **default_scale_bar_kwargs)
if edgecolor:
scalebar.size_bar.get_children()[0].set_edgecolor(edgecolor)
scalebar.txt_label.get_children()[0].set_path_effects(
[path_effects.Stroke(linewidth=2, foreground=edgecolor), path_effects.Normal()]
)
# add the scalebar
ax.add_artist(scalebar)
def share_maps_cb(df,
year_var,
year,
variable,
color,
title,
source,
vmin,
vmax,
share=True):
'''
Create a map for Peru with regional yearly data. Must give min max for
scale bar, year, variable, color, title and source
df must be geodataframe merged with the regional shape
'''
df = df.to_crs({'init': 'epsg:3857'})
fig_, ax = plt.subplots(1, figsize=(10, 10))
if share: df[variable] = df[variable] * 100
fig = df[df[year_var].astype(int) == year].plot(column=variable,
cmap=color,
ax=ax,
figsize=(10, 10),
linewidth=0.8,
edgecolor='0.8',
vmin=vmin,
vmax=vmax,
legend=True,
norm=plt.Normalize(
vmin=vmin, vmax=vmax))
ax.axis('off')
#title and source
ax.set_title(title, fontdict={'fontsize': '15', 'fontweight': '3'})
plt.figtext(0.28, 0.13, source)
#arrow
x_arr, y_arr, arrow_length = 0.90, 0.99, 0.065
fig.annotate('N',
xy=(x_arr, y_arr),
xytext=(x_arr, y_arr - arrow_length),
arrowprops=dict(facecolor='black', width=2, headwidth=9),
ha='center',
va='center',
fontsize=20,
xycoords=fig.transAxes)
#scale bar
scalebar = AnchoredSizeBar(fig.transData,
500000,
'500 km',
'lower right',
pad=0.1,
color='black',
frameon=False,
size_vertical=1,
fontproperties=fm.FontProperties(size=10))
ax.add_artist(scalebar)
return fig_
def add_sizebar(ax, size):
asb = AnchoredSizeBar(ax.transData,
size,
str(size),
loc=8,
pad=0.1, borderpad=0.5, sep=5,
frameon=False)
ax.add_artist(asb)
def plot_geospace_results_grid():
global geo_data
global geo_headers
global som_data
for i in range(0, len(som_data[0])-3):
x=geo_data[:,0]
y=geo_data[:,1]
z=geo_data[:,(len(som_data[0])+1+i)]
df = pd.DataFrame.from_dict(np.array([x,y,z]).T)
df.columns = ['X_value','Y_value','Z_value']
df['Z_value'] = pd.to_numeric(df['Z_value'])
pivotted= df.pivot('Y_value','X_value','Z_value')
#pivotted=pivotted.fillna(value='nan')
sns.set_style("ticks", {"xtick.major.size": 8, "ytick.major.size": 8})
ax=sns.heatmap(pivotted,cmap='jet', square=True, linewidths=0, xticklabels="auto", yticklabels="auto")
scalebar = AnchoredSizeBar(ax.transData, 3.4, str(geo_data[4][0] - geo_data[0][0]), 1, pad=0.4,
sep=5, borderpad=0.1,
size_vertical=0.2)
#ax.add_artist(scalebar)
# Set tick labels to integers:
fmt = '{:0.0f}'
xticklabels = []
for item in ax.get_xticklabels():
item.set_text(fmt.format(float(item.get_text())))
xticklabels += [item]
yticklabels = []
for item in ax.get_yticklabels():
item.set_text(fmt.format(float(item.get_text())))
yticklabels += [item]
ax.set_xticklabels(xticklabels)
ax.set_yticklabels(yticklabels)
every_nth = round((len(ax.xaxis.get_ticklabels()))/2)
if(every_nth==0):#temp solution, for data sets with only 1 x coordinate
every_nth=1
every_nth_y = round((len(ax.yaxis.get_ticklabels()))/2)
if(every_nth_y==0):#temp solution, for data sets with only 1 x coordinate
every_nth_y=1
for n, label in enumerate(ax.xaxis.get_ticklabels()):
if n % every_nth != 0:
label.set_visible(False)
for n, label in enumerate(ax.yaxis.get_ticklabels()):
if n % every_nth_y != 0:
label.set_visible(False)
ax.xaxis.get_ticklabels()[-1].set_visible(True)
ax.yaxis.get_ticklabels()[-1].set_visible(True)
plt.yticks(rotation=90)
plt.yticks(ha='right')
plt.yticks(va='bottom')
plt.xticks(rotation=0)
plt.xticks(ha='left')
ax.invert_yaxis()
ax.set_title(geo_headers[len(som_data[0])+i+2])
plt.tight_layout()
ax.figure.savefig(working_dir+'/Geo/geoplot_'+str(i+2)+'.png', dpi=300)
plt.clf()
plt.cla()
plt.close()
def share_maps(df, year, variable, color, k, title, source, leg):
'''
Create a map for Peru with regional yearly data and proportion
variable in format [0-1]. Does Natural Breaks Clustering.
'''
#create maps
df = df.to_crs({'init': 'epsg:3857'})
fig_, ax = plt.subplots(1, figsize=(15, 8))
df[variable] = df[variable] * 100
fig = df[df['anio'].astype(int) == year].plot(column=variable,
cmap=color,
linewidth=0.5,
ax=ax,
edgecolor='0.2',
scheme='naturalbreaks',
k=k,
legend=True)
#title and source
ax.set_title(title, fontdict={'fontsize': '15', 'fontweight': '3'})
plt.figtext(0.38, 0.13, source)
#legend
ax.axis('off')
ax.get_legend().set_bbox_to_anchor((0.40, 0.26))
ax.get_legend().set_title(leg)
leg = fig.get_legend()
for lbl in leg.get_texts():
label_text = lbl.get_text()
lower = label_text.split()[0]
upper = label_text.split()[2]
new_text = f'{float(lower):,.1f} - {float(upper):,.1f}'
lbl.set_text(new_text)
#arrow
x_arr, y_arr, arrow_length = 0.90, 0.99, 0.065
ax.annotate('N',
xy=(x_arr, y_arr),
xytext=(x_arr, y_arr - arrow_length),
arrowprops=dict(facecolor='black', width=2, headwidth=9),
ha='center',
va='center',
fontsize=20,
xycoords=ax.transAxes)
#scale bar
scalebar = AnchoredSizeBar(ax.transData,
500000,
'500 km',
'lower right',
pad=0.1,
color='black',
frameon=False,
size_vertical=1,
fontproperties=fm.FontProperties(size=10))
ax.add_artist(scalebar)
return fig_
def render(self, ax):
# Remove the white patch behind each axes
ax.patch.set_facecolor('none')
# Add scale bar -- code is placed here so a scale bar can be drawn on any track instance
if self.options['scale_bar'] is not None:
bar = AnchoredSizeBar(ax.transData,
self.options['scale_bar'],
label="%d nt" % self.options['scale_bar'],
loc=self.options['scale_bar_loc'],
frameon=False)
ax.add_artist(bar)
def add_scalebar(pseudoimg,
pixelresolution,
barwidth,
barlabel,
barlocation='lower center',
fontprops=None,
scalebar=None):
"""Add scalebar to matplotlib false color image
Parameters
----------
pseudoimg : matplotlib figure
false color image
pixelresolution : int
physical size represented by a pixel in mm
barwidth : float
size of the scale bar in mm
barlabel : str
text for the bar label
barlocation : str or tuple
position of scale bar in figure, optional
fontprops : mpl.fm
font properties as specified by matplotlib.font_manager, optional
scalebar : mpl axis object
a preestablished scale bar, optional
Returns
-------
pseudoimg with a scalebar : matplotlib figure
"""
if fontprops is None:
fontprops = fm.FontProperties(size=8, weight='bold')
ax = pseudoimg.gca()
if scalebar is None:
scalebar = AnchoredSizeBar(ax.transData,
barwidth / pixelresolution,
barlabel,
barlocation,
pad=0.15,
sep=3,
color='white',
frameon=False,
size_vertical=barwidth / pixelresolution /
40,
fontproperties=fontprops)
ax.add_artist(scalebar)
return ax.get_figure()
def addScaleBar(axes):
"adds a scale bar to the figure and removes the ticks"
axes.get_xaxis().set_visible(False)
axes.get_yaxis().set_visible(False)
bar = AnchoredSizeBar(axes.transData,
20,
'',
loc=4,
sep=5,
borderpad=0.5,
frameon=False)
axes.add_artist(bar)
def test_inset_axes():
def get_demo_image():
from matplotlib.cbook import get_sample_data
import numpy as np
f = get_sample_data("axes_grid/bivariate_normal.npy", asfileobj=False)
z = np.load(f)
# z is a numpy array of 15x15
return z, (-3, 4, -4, 3)
fig, ax = plt.subplots(figsize=[5, 4])
# prepare the demo image
Z, extent = get_demo_image()
Z2 = np.zeros([150, 150], dtype="d")
ny, nx = Z.shape
Z2[30 : 30 + ny, 30 : 30 + nx] = Z
# extent = [-3, 4, -4, 3]
ax.imshow(Z2, extent=extent, interpolation="nearest", origin="lower")
# creating our inset axes with a bbox_transform parameter
axins = inset_axes(
ax, width=1.0, height=1.0, bbox_to_anchor=(1, 1), bbox_transform=ax.transAxes
)
axins.imshow(Z2, extent=extent, interpolation="nearest", origin="lower")
axins.yaxis.get_major_locator().set_params(nbins=7)
axins.xaxis.get_major_locator().set_params(nbins=7)
# sub region of the original image
x1, x2, y1, y2 = -1.5, -0.9, -2.5, -1.9
axins.set_xlim(x1, x2)
axins.set_ylim(y1, y2)
plt.xticks(visible=False)
plt.yticks(visible=False)
# draw a bbox of the region of the inset axes in the parent axes and
# connecting lines between the bbox and the inset axes area
mark_inset(ax, axins, loc1=2, loc2=4, fc="none", ec="0.5")
asb = AnchoredSizeBar(
ax.transData,
0.5,
"0.5",
loc="lower center",
pad=0.1,
borderpad=0.5,
sep=5,
frameon=False,
)
ax.add_artist(asb)
def draw_sizebar(ax):
from mpl_toolkits.axes_grid1.anchored_artists import AnchoredSizeBar
# draw a horizontal bar with length of 0.1 in Data coordinate
# (ax.transData) with a label underneath.
asb = AnchoredSizeBar(ax.transData,
0.1,
r"1$^{\prime}$",
loc=8,
pad=0.1,
borderpad=0.5,
sep=5,
frameon=False)
ax.add_artist(asb)
def draw_sizebar(ax):
"""
Draw a horizontal bar with length of 0.1 in data coordinates,
with a fixed label underneath.
"""
from mpl_toolkits.axes_grid1.anchored_artists import AnchoredSizeBar
asb = AnchoredSizeBar(ax.transData,
0.1,
r"1$^{\prime}$",
loc='lower center',
pad=0.1, borderpad=0.5, sep=5,
frameon=False)
ax.add_artist(asb)
def add_scalebar(ax, bar_len, resolution, units = 'um', n_dec = 0, pad = 0.35, \
fontsize = 16, frameon = True, color = 'black', loc = 'lower center'):
# bar_len : float, length of bar, e.g. 100 micron
# resolution : float, pixel size, in units/pixel, e.g. 1.1 microns / pixel
# units : str, what units?
# n_dec : number of decimals in number displayed below scalebar
fontprops = fm.FontProperties(size=fontsize)
n_pix = bar_len / resolution
scalebar = AnchoredSizeBar(ax.transData, n_pix, ("%."+ "%if"%n_dec)%bar_len + " " + units, loc, \
pad=pad, color=color, frameon=frameon, size_vertical=1, fontproperties=fontprops)
ax.add_artist(scalebar)
return ax
def plot_scalebar(self, **kwargs):
length = kwargs.pop('length', 1)
title = kwargs.pop('title', '{} world units'.format(length))
dat_bar_length = length / self.vol.dxW
kwargs['loc'] = kwargs.get('loc', 1)
kwargs['pad'] = kwargs.get('pad', 0.5)
kwargs['borderpad'] = kwargs.get('borderpad', 0.5)
kwargs['sep'] = kwargs.get('sep', 5)
kwargs['frameon'] = kwargs.get('frameon', True)
self.sizebar = AnchoredSizeBar(self.ax.transData, dat_bar_length,
title, **kwargs)
self.ax.add_artist(self.sizebar)
return self.sizebar
def vis_clean(set, key, cmap, thick=False, cbar=True):
title = key
print("Plotting ", set.file_dat)
data = np.load(set.file_dat + '.npz')
fig, ax = plt.subplots(frameon=False)
image = data[key]
if thick:
selem = morph.disk(5)
image = morph.dilation(image, selem)
image = np.ma.masked_where(image == 0, image)
im = ax.imshow(image, cmap=cmap)
scaling = set.pixel_scaling
# correction of scalebar_size to get 1,10,50... um
# used in pretty mode
allowed_scalebars = np.append([10**i for i in range(10)],
[5* 10**i for i in range(10)] )
scalebar_size = closest_number(allowed_scalebars,
400 * scaling)
pixels_scalebar = scalebar_size/scaling
scalebar = AnchoredSizeBar(ax.transData,
pixels_scalebar, str(scalebar_size) + r' $\mu$m',
'lower right',
pad=0.3,
color='black',
frameon=False,
size_vertical=1)
ax.add_artist(scalebar)
ax.axis('off')
ax.set_yticks([])
ax.set_xticks([])
# ax.set_title(title)
cbar = fig.colorbar(im)
fig.tight_layout()
cbar.ax.get_yaxis().labelpad = 15
cbar.ax.set_ylabel('intensity (a.u.)', rotation=270)
plt.savefig(set.file_plot + title + '.pdf', dpi=600, bbox_inches='tight')
plt.close()
def plot_image(self, **kwargs):
from mpl_toolkits.axes_grid1.anchored_artists import AnchoredSizeBar
scale_bar = kwargs.pop('scale_bar', False)
if len(self.dset.shape) > 2:
self.axis.set_title(self.dset.title +
'_image {}'.format(self.image_number))
else:
self.axis.set_title(self.dset.title)
self.img = self.axis.imshow(
np.squeeze(self.dset[tuple(self.selection)]).T,
extent=self.dset.get_extent(self.image_dims),
**kwargs)
self.axis.set_xlabel("{} [{}]".format(
self.dset.axes[self.image_dims[0]].quantity,
self.dset.axes[self.image_dims[0]].units))
self.axis.set_ylabel("{} [{}]".format(
self.dset.axes[self.image_dims[1]].quantity,
self.dset.axes[self.image_dims[1]].units))
if scale_bar:
plt.axis('off')
extent = self.dset.get_extent(self.image_dims)
size_of_bar = int((extent[1] - extent[0]) / 10 + .5)
if size_of_bar < 1:
size_of_bar = 1
scalebar = AnchoredSizeBar(
plt.gca().transData,
size_of_bar,
'{} {}'.format(size_of_bar,
self.dset.axes[self.image_dims[0]].units),
'lower left',
pad=1,
color='white',
frameon=False,
size_vertical=.2)
plt.gca().add_artist(scalebar)
else:
cbar = self.fig.colorbar(self.img)
cbar.set_label("{} [{}]".format(self.dset.quantity,
self.dset.units))
self.axis.ticklabel_format(style='sci', scilimits=(-2, 3))
self.fig.tight_layout()
self.img.axes.figure.canvas.draw_idle()
def plot_size_bar(ax,
value,
value_str,
loc=4,
pad=0.1,
borderpad=0.5,
sep=5,
frameon=False):
asb = AnchoredSizeBar(ax.transData,
value,
value_str,
loc=loc,
pad=pad,
borderpad=borderpad,
sep=sep,
frameon=frameon)
ax.add_artist(asb)
def draw_sizebar(obj,ax, scale, regrid=False):
"""
Draw a horizontal bar with length of 0.1 in data coordinates,
with a fixed label underneath.
"""
if regrid:
length = 0.1/obj.factor.to(u.Mpc/u.deg)/(scale[1]*obj.pix_size)
else:
length = 0.1/obj.factor.to(u.Mpc/u.deg)
from mpl_toolkits.axes_grid1.anchored_artists import AnchoredSizeBar
asb = AnchoredSizeBar(ax.transData,length.value*2.5,
r"250 kpc",
loc='lower center',
pad=0.1, borderpad=0.5, sep=5,
frameon=False, color='white')#, fontsize=labelsize)
ax.add_artist(asb)
def _add_scalebar_artist(self, axis, size_scaled=5):
"""
Cheap scalebar, from matplotlib cook-book.
"""
scalebar_size_pix = size_scaled / self._ps
scalebar = AnchoredSizeBar(
transform=axis.transData,
size=scalebar_size_pix,
label='{0:d} {1}'.format(int(round(size_scaled)), self._pu),
loc='lower left',
pad=1,
color='white',
frameon=False,
label_top=True,
size_vertical=8,
)
axis.add_artist(scalebar)
def addSBar(self, ax, pos=3, scaleb=1000, hideax=False):
bar = AnchoredSizeBar(ax.transData,
scaleb,
'',
loc=pos,
pad=1,
sep=1,
borderpad=0.01,
frameon=False) #,prop=None)
rect = bar.size_bar._children[0]
rect.set_ec("white")
rect.set_height(200)
rect.set_fc('white')
ax.add_artist(bar)
if hideax:
ax.xaxis.set_visible(False)
ax.yaxis.set_visible(False)
def plot_heat_map_ticks_latex(data, filename, v_min, v_max, scale=(500/90.8), log=False):
"""
Function plots heat maps of data numpy 2d array and save result to filename.png.
"""
#heat map plotting
x_phys_length = data.shape[1]*scale #physical length of x-axis
y_phys_length = data.shape[0]*scale #physical length of y-axis
fig, ax = plt.subplots(figsize=(20.0*data.shape[1]/1920.0, 10*data.shape[0]/1200.0), dpi=300)
plt.rcParams['text.latex.preamble'] = [r'\boldmath']
mpl.rcParams.update({'font.size': 22}) #fontsize
#ax.set_xlabel(r'$x$, $\mu$\textbf{m}')
#ax.set_ylabel(r'$y$, $\mu$\textbf{m}')
#plt.minorticks_on()
#plt.tick_params(axis='x', pad=7)
#plt.tick_params(axis='y', pad=5)
ax.get_xaxis().set_ticks([]) #unset labels
ax.get_yaxis().set_ticks([])
plt.grid(False)
extent = (0, x_phys_length, 0, y_phys_length)
####################################################################################
### barbarbar!!! ###
from mpl_toolkits.axes_grid1.anchored_artists import AnchoredSizeBar
import matplotlib.font_manager as fm
bar_label = r'$' + str(bar_length) + r'\,\mu$' + r'\textbf{m}'
scalebar = AnchoredSizeBar(ax.transData, bar_length, bar_label, 'lower right', pad=0.5, sep=7.0, color='white', frameon=False, size_vertical=0, label_top=True)
ax.add_artist(scalebar)
####################################################################################
if log==True:
im = ax.imshow(data, cmap='jet', vmin=v_min, vmax=v_max, norm=mplc.LogNorm(), extent=extent)
#plt.plot((100,297), (100, 100), 'k', color='w')
else:
im = ax.imshow(data, cmap='jet', vmin=v_min, vmax=v_max, extent=extent)
fig.colorbar(im)
plt.savefig(filename, bbox_inches='tight')
plt.close()
return True
def test_inset_axes():
fig, ax = plt.subplots(figsize=[5, 4])
# prepare the demo image
# Z is a 15x15 array
Z = cbook.get_sample_data("axes_grid/bivariate_normal.npy", np_load=True)
extent = (-3, 4, -4, 3)
Z2 = np.zeros((150, 150))
ny, nx = Z.shape
Z2[30:30 + ny, 30:30 + nx] = Z
# extent = [-3, 4, -4, 3]
ax.imshow(Z2, extent=extent, interpolation="nearest", origin="lower")
# creating our inset axes with a bbox_transform parameter
axins = inset_axes(ax,
width=1.,
height=1.,
bbox_to_anchor=(1, 1),
bbox_transform=ax.transAxes)
axins.imshow(Z2, extent=extent, interpolation="nearest", origin="lower")
axins.yaxis.get_major_locator().set_params(nbins=7)
axins.xaxis.get_major_locator().set_params(nbins=7)
# sub region of the original image
x1, x2, y1, y2 = -1.5, -0.9, -2.5, -1.9
axins.set_xlim(x1, x2)
axins.set_ylim(y1, y2)
plt.xticks(visible=False)
plt.yticks(visible=False)
# draw a bbox of the region of the inset axes in the parent axes and
# connecting lines between the bbox and the inset axes area
mark_inset(ax, axins, loc1=2, loc2=4, fc="none", ec="0.5")
asb = AnchoredSizeBar(ax.transData,
0.5,
'0.5',
loc='lower center',
pad=0.1,
borderpad=0.5,
sep=5,
frameon=False)
ax.add_artist(asb)
def add_anchored_size_bar(
ax,
transform,
loc='center',
color='k',
horizontal_size=3,
label=None,
label_top=True,
pad=0.3,
fontproperties=None,
borderpad=0.1,
sep=0.2,
bar_height=0.015,
frameon=True,
fill_bar=True,
bbox_to_anchor=(0.5, 0.02, 1, 0.08), # (x0, y0, x1, y1),
bbox_transform='figure'):
if bbox_transform == 'figure':
bbox_transform = ax.figure.transFigure
bar = AnchoredSizeBar(transform=transform,
loc=loc,
color=color,
size=horizontal_size,
size_vertical=bar_height,
label=label,
label_top=label_top,
pad=pad,
fontproperties=fontproperties,
borderpad=borderpad,
sep=sep,
frameon=frameon,
fill_bar=fill_bar,
bbox_to_anchor=Bbox.from_extents(bbox_to_anchor),
bbox_transform=bbox_transform)
ax.add_artist(bar)
#window_extent = bar.get_window_extent(ax.figure.canvas.get_renderer())
#figure_window_extent = ax.figure.transFigure.inverted().transform(window_extent)
#x0, y0, x1, x1 = figure_window_extent.ravel()
return bar
def vis_mask(set):
title = 'mask'
print("Plotting ", set.file_dat)
data = np.load(set.file_dat + '.npz')
fig, ax = plt.subplots(frameon=False)
selem = morph.disk(5)
thick_skeleton = morph.dilation(data['skeleton'], selem)
image = data['mask'] + thick_skeleton
image = np.ma.masked_where(image == 0, image)
levels = [0, 1, 2,3]
colors = ['white', '#8d8dbc' , '#51517c']
cmap, norm = mpl.colors.from_levels_and_colors(levels, colors)
ax.imshow(image, cmap=cmap, norm=norm, interpolation='none')
scaling = set.pixel_scaling
# correction of scalebar_size to get 1,10,50... um
# used in pretty mode
allowed_scalebars = np.append([10**i for i in range(10)],
[5* 10**i for i in range(10)] )
scalebar_size = closest_number(allowed_scalebars,
400 * scaling)
pixels_scalebar = scalebar_size/scaling
scalebar = AnchoredSizeBar(ax.transData,
pixels_scalebar, str(scalebar_size) + r' $\mu$m',
'lower right',
pad=0.3,
color='black',
frameon=False,
size_vertical=1)
ax.add_artist(scalebar)
ax.axis('off')
ax.set_yticks([])
ax.set_xticks([])
# ax.set_title(title)
fig.tight_layout()
plt.savefig(set.file_plot + title + '.pdf', dpi=600, bbox_inches='tight')
plt.close()
def draw_scalebar(self, ax, img_shape, scale_bar_pos):
# find closest standard size to bar length ~= 1/6 fig_width
target_phy_bar_length = self.scale * img_shape[1] / 6
diff = np.abs(self.phy_bar_lengths - target_phy_bar_length)
phy_bar_length = self.phy_bar_lengths[np.argmin(diff)]
px_bar_length = phy_bar_length / self.scale
# scalebar https://stackoverflow.com/questions/39786714/how-to-insert-scale-bar-in-a-map-in-matplotlib
scalebar = AnchoredSizeBar(ax.transData,
px_bar_length,
'{} μm'.format(phy_bar_length),
scale_bar_pos,
pad=0.5,
color='white',
frameon=False,
size_vertical=min(10, px_bar_length / 10),
fontproperties=fm.FontProperties(size=18))
ax.add_artist(scalebar)
def create_scalebar(data, ax, scalebar_color):
"""
Description:
Compute and create an horizontal scalebar in kilometer or meter to be added to the map.
-----
Input:
data: xarray to be mapped
ax: matplotlib.axes to work on
scalebar_color (OPTIONAL): scalebar color (e.g.'orangered')
https://matplotlib.org/examples/color/named_colors.html)
Output:
Scalebar to be added
"""
# Convert lenght at average latitude from decimal degree into kilometer
ave_lat = ((min(data.latitude) + max(data.latitude)) / 2).values
lon_km = dd2km(ave_lat,
min(data.longitude).values, ave_lat,
max(data.longitude).values)
# Calculate the scalebar caracteristics (rounded value of 1/4 of lengths)
lon_px = len(data.longitude)
bar_len = lon_km * 0.25 # 25% of the map width
if bar_len >= 1:
units = 'kilometer'
bar_len = round(bar_len)
bar_px = round(lon_px * bar_len / lon_km)
else:
units = 'meter'
bar_len = round(bar_len * 10) * 100
bar_px = round(lon_px * bar_len / 1000 / lon_km)
# add the scalebar
fontprops = fm.FontProperties(size=18)
scalebar = AnchoredSizeBar(ax.transData,
bar_px,
'%i %s' % (bar_len, units),
'lower right',
pad=0.1,
color=scalebar_color,
frameon=False,
size_vertical=1,
label_top=True,
fontproperties=fontprops)
return (scalebar)
def show_image(self, image=None, cropped=True, title=None, colorbar=False, scalebar=False, scalebar_length=None):
"""
Displays the most recently acquired image.
"""
if image is None:
if cropped:
image = self.image_cropped
else:
image = self.image
fig, ax = plt.subplots(figsize=(15,10))
plt.imshow(image.T, origin='lower')
if title:
plt.title(title)
if scalebar:
scalebar = AnchoredSizeBar(ax.transData,
scalebar_length/self.scale[0],
f'{1e6*scalebar_length} um',
'upper right',
pad=1,
color='white',
frameon=False,
size_vertical=0.5,
sep = 10,
fontproperties=fontprops)
ax.add_artist(scalebar)
plt.xlabel('x (px)')
plt.ylabel('y (px)')
fig.patch.set_facecolor('white')
if colorbar:
divider = make_axes_locatable(ax)
cax = divider.append_axes("right", size="5%", pad=0.05)
plt.colorbar(cax=cax, label='counts')
plt.show()
class Scalebar(object):
def __init__(self, parent):
# Retrieve info from parent figure
self._ax = parent.ax
self._wcs = parent._wcs
self._figure = parent._figure
self._dimensions = [parent.x, parent.y]
# Initialize settings
self._base_settings = {}
self._scalebar_settings = {}
self._label_settings = {}
self._label_settings['fontproperties'] = FontProperties()
# LAYOUT
@auto_refresh
def show(self, length, label=None, corner='bottom right', frame=False,
borderpad=0.4, pad=0.5, **kwargs):
"""
Overlay a scale bar on the image.
Parameters
----------
length : float, or quantity
The length of the scalebar in degrees, an angular quantity, or angular unit
label : str, optional
Label to place below the scalebar
corner : int, optional
Where to place the scalebar. Acceptable values are:, 'left',
'right', 'top', 'bottom', 'top left', 'top right', 'bottom
left' (default), 'bottom right'
frame : str, optional
Whether to display a frame behind the scalebar (default is False)
kwargs
Additional arguments are passed to the matplotlib Rectangle and
Text classes. See the matplotlib documentation for more details.
In cases where the same argument exists for the two objects, the
argument is passed to both the Text and Rectangle instance.
"""
self._length = length
self._base_settings['corner'] = corner
self._base_settings['frame'] = frame
self._base_settings['borderpad'] = borderpad
self._base_settings['pad'] = pad
if isinstance(length, u.Quantity):
length = length.to(u.degree).value
elif isinstance(length, u.Unit):
length = length.to(u.degree)
if self._wcs.is_celestial:
pix_scale = proj_plane_pixel_scales(self._wcs)
sx = pix_scale[self._dimensions[0]]
sy = pix_scale[self._dimensions[1]]
degrees_per_pixel = np.sqrt(sx * sy)
else:
raise ValueError("Cannot show scalebar when WCS is not celestial")
length = length / degrees_per_pixel
try:
self._scalebar.remove()
except Exception:
pass
if isinstance(corner, str):
corner = corners[corner]
self._scalebar = AnchoredSizeBar(self._ax.transData, length, label,
corner, pad=pad, borderpad=borderpad,
sep=5, frameon=frame)
self._ax.add_artist(self._scalebar)
self.set(**kwargs)
@auto_refresh
def _remove(self):
self._scalebar.remove()
@auto_refresh
def hide(self):
"""
Hide the scalebar.
"""
try:
self._scalebar.remove()
except Exception:
pass
@auto_refresh
def set_length(self, length):
"""
Set the length of the scale bar.
"""
self.show(length, **self._base_settings)
self._set_scalebar_properties(**self._scalebar_settings)
self._set_label_properties(**self._scalebar_settings)
@auto_refresh
def set_label(self, label):
"""
Set the label of the scale bar.
"""
self._set_label_properties(text=label)
@auto_refresh
def set_corner(self, corner):
"""
Set where to place the scalebar.
Acceptable values are 'left', 'right', 'top', 'bottom', 'top left',
'top right', 'bottom left' (default), and 'bottom right'.
"""
self._base_settings['corner'] = corner
self.show(self._length, **self._base_settings)
self._set_scalebar_properties(**self._scalebar_settings)
self._set_label_properties(**self._scalebar_settings)
@auto_refresh
def set_frame(self, frame):
"""
Set whether to display a frame around the scalebar.
"""
self._base_settings['frame'] = frame
self.show(self._length, **self._base_settings)
self._set_scalebar_properties(**self._scalebar_settings)
self._set_label_properties(**self._scalebar_settings)
# APPEARANCE
@auto_refresh
def set_linewidth(self, linewidth):
"""
Set the linewidth of the scalebar, in points.
"""
self._set_scalebar_properties(linewidth=linewidth)
@auto_refresh
def set_linestyle(self, linestyle):
"""
Set the linestyle of the scalebar.
Should be one of 'solid', 'dashed', 'dashdot', or 'dotted'.
"""
self._set_scalebar_properties(linestyle=linestyle)
@auto_refresh
def set_alpha(self, alpha):
"""
Set the alpha value (transparency).
This should be a floating point value between 0 and 1.
"""
self._set_scalebar_properties(alpha=alpha)
self._set_label_properties(alpha=alpha)
@auto_refresh
def set_color(self, color):
"""
Set the label and scalebar color.
"""
self._set_scalebar_properties(color=color)
self._set_label_properties(color=color)
@auto_refresh
def set_font(self, family=None, style=None, variant=None, stretch=None,
weight=None, size=None, fontproperties=None):
"""
Set the font of the tick labels
Parameters
----------
common: family, style, variant, stretch, weight, size, fontproperties
Notes
-----
Default values are set by matplotlib or previously set values if
set_font has already been called. Global default values can be set by
editing the matplotlibrc file.
"""
if family:
self._label_settings['fontproperties'].set_family(family)
if style:
self._label_settings['fontproperties'].set_style(style)
if variant:
self._label_settings['fontproperties'].set_variant(variant)
if stretch:
self._label_settings['fontproperties'].set_stretch(stretch)
if weight:
self._label_settings['fontproperties'].set_weight(weight)
if size:
self._label_settings['fontproperties'].set_size(size)
if fontproperties:
self._label_settings['fontproperties'] = fontproperties
self._set_label_properties(fontproperties=self._label_settings['fontproperties'])
@auto_refresh
def _set_label_properties(self, **kwargs):
"""
Modify the scalebar label properties.
All arguments are passed to the matplotlib Text class. See the
matplotlib documentation for more details.
"""
for kwarg, val in kwargs.items():
try:
# Only set attributes that exist
kvpair = {kwarg: val}
self._scalebar.txt_label.get_children()[0].set(**kvpair)
self._label_settings[kwarg] = val
except AttributeError:
warnings.warn("Text labels do not have attribute {0}. Skipping.".format(kwarg))
@auto_refresh
def _set_scalebar_properties(self, **kwargs):
"""
Modify the scalebar properties.
All arguments are passed to the matplotlib Rectangle class. See the
matplotlib documentation for more details.
"""
for kwarg, val in kwargs.items():
try:
kvpair = {kwarg: val}
self._scalebar.size_bar.get_children()[0].set(**kvpair)
self._scalebar_settings[kwarg] = val
except AttributeError:
warnings.warn("Scalebar does not have attribute {0}. Skipping.".format(kwarg))
@auto_refresh
def set(self, **kwargs):
"""
Modify the scalebar and scalebar properties.
All arguments are passed to the matplotlib Rectangle and Text classes.
See the matplotlib documentation for more details. In cases where the
same argument exists for the two objects, the argument is passed to
both the Text and Rectangle instance.
"""
for kwarg in kwargs:
kwargs_single = {kwarg: kwargs[kwarg]}
try:
self._set_label_properties(**kwargs_single)
except (AttributeError, TypeError):
pass
try:
self._set_scalebar_properties(**kwargs_single)
except (AttributeError, TypeError):
pass
# DEPRECATED
@auto_refresh
def set_font_family(self, family):
warnings.warn("scalebar.set_font_family is deprecated - use scalebar.set_font instead", DeprecationWarning)
self.set_font(family=family)
@auto_refresh
def set_font_weight(self, weight):
warnings.warn("scalebar.set_font_weight is deprecated - use scalebar.set_font instead", DeprecationWarning)
self.set_font(weight=weight)
@auto_refresh
def set_font_size(self, size):
warnings.warn("scalebar.set_font_size is deprecated - use scalebar.set_font instead", DeprecationWarning)
self.set_font(size=size)
@auto_refresh
def set_font_style(self, style):
warnings.warn("scalebar.set_font_style is deprecated - use scalebar.set_font instead", DeprecationWarning)
self.set_font(style=style)
def show(self, length, label=None, corner='bottom right', frame=False,
borderpad=0.4, pad=0.5, **kwargs):
"""
Overlay a scale bar on the image.
Parameters
----------
length : float, or quantity
The length of the scalebar in degrees, an angular quantity, or angular unit
label : str, optional
Label to place below the scalebar
corner : int, optional
Where to place the scalebar. Acceptable values are:, 'left',
'right', 'top', 'bottom', 'top left', 'top right', 'bottom
left' (default), 'bottom right'
frame : str, optional
Whether to display a frame behind the scalebar (default is False)
kwargs
Additional arguments are passed to the matplotlib Rectangle and
Text classes. See the matplotlib documentation for more details.
In cases where the same argument exists for the two objects, the
argument is passed to both the Text and Rectangle instance.
"""
self._length = length
self._base_settings['corner'] = corner
self._base_settings['frame'] = frame
self._base_settings['borderpad'] = borderpad
self._base_settings['pad'] = pad
if isinstance(length, u.Quantity):
length = length.to(u.degree).value
elif isinstance(length, u.Unit):
length = length.to(u.degree)
if self._wcs.is_celestial:
pix_scale = proj_plane_pixel_scales(self._wcs)
sx = pix_scale[self._dimensions[0]]
sy = pix_scale[self._dimensions[1]]
degrees_per_pixel = np.sqrt(sx * sy)
else:
raise ValueError("Cannot show scalebar when WCS is not celestial")
length = length / degrees_per_pixel
try:
self._scalebar.remove()
except Exception:
pass
if isinstance(corner, str):
corner = corners[corner]
self._scalebar = AnchoredSizeBar(self._ax.transData, length, label,
corner, pad=pad, borderpad=borderpad,
sep=5, frameon=frame)
self._ax.add_artist(self._scalebar)
self.set(**kwargs)
