def colorbar_legend(ax, values, cmap, vis=True):
"""
Add a vertical colorbar legend to a plot
"""
x_range = ax.get_xlim()[1]-ax.get_xlim()[0]
y_range = ax.get_ylim()[1]-ax.get_ylim()[0]
x = [ax.get_xlim()[0]+x_range*0.05]
y = [ax.get_ylim()[1]-(y_range * 0.25), ax.get_ylim()[1]-(y_range*0.05)]
segs = []
vals=[]
p = (x[0], y[0]+((y[1]-y[0])/256.0))
for i in range(2, 257):
n = (x[0], y[0]+((y[1]-y[0])/256.0)*i)
segs.append((p, n))
p = segs[-1][-1]
vals.append(min(values)+((max(values)-min(values))/256.0)*(i-1))
lcbar = LineCollection(segs, cmap=cmap, lw=15)
lcbar.set_visible(vis)
lcbar.set_array(np.array(vals))
ax.add_collection(lcbar)
lcbar.set_zorder(1)
minlab = str(min(values))[:6]
maxlab = str(max(values))[:6]
ax.text(x[0]+x_range*.02, y[0], minlab, verticalalignment="bottom", visible=vis)
ax.text(x[0]+x_range*.02, y[1], maxlab, verticalalignment="top", visible=vis)
def colorbar_legend(ax, values, cmap, vis=True):
"""
Add a vertical colorbar legend to a plot
"""
x_range = ax.get_xlim()[1]-ax.get_xlim()[0]
y_range = ax.get_ylim()[1]-ax.get_ylim()[0]
x = [ax.get_xlim()[0]+x_range*0.05]
y = [ax.get_ylim()[1]-(y_range * 0.25), ax.get_ylim()[1]-(y_range*0.05)]
segs = []
vals=[]
p = (x[0], y[0]+((y[1]-y[0])/256.0))
for i in range(2, 257):
n = (x[0], y[0]+((y[1]-y[0])/256.0)*i)
segs.append((p, n))
p = segs[-1][-1]
vals.append(min(values)+((max(values)-min(values))/256.0)*(i-1))
lcbar = LineCollection(segs, cmap=cmap, lw=15)
lcbar.set_visible(vis)
lcbar.set_array(np.array(vals))
ax.add_collection(lcbar)
lcbar.set_zorder(1)
minlab = str(min(values))[:6]
maxlab = str(max(values))[:6]
ax.text(x[0]+x_range*.02, y[0], minlab, verticalalignment="bottom", visible=vis)
ax.text(x[0]+x_range*.02, y[1], maxlab, verticalalignment="top", visible=vis)
def add_hrm_hiddenstate_recon(treeplot, liks, nregime,vis=True, width=2, colors=None):
"""
Color branches based on likelihood of being in hidden states.
Args:
liks (np.array): The output of anc_recon run as a hidden-rates reconstruction.
"""
root = treeplot.root
horz_seg_collections = [None] * (len(root)-1)
horz_seg_colors = [None]*(len(root)-1)
vert_seg_collections = [None] * (len(root)-1)
vert_seg_colors = [None] * (len(root)-1)
nchar = liks.shape[1]-2 # Liks has rows equal to nchar+2 (the last two rows are indices)
nobschar = nchar//nregime
if colors is None:
c = _tango
colors = [next(c) for v in range(nregime)]
for i,n in enumerate(root.descendants()):
n_lik = liks[i+1] # Add 1 to the index because the loop is skipping the root
par_lik = liks[n.parent.ni]
n_r1 = sum(n_lik[:nchar//2])# Likelihood of node being in regime 1
p_r1 = sum(par_lik[:nchar//2])# Likelihood of node being in regime 1
n_col = color_map(n_r1, colors[0], colors[1])
par_col = color_map(p_r1, colors[0], colors[1])
n_coords = treeplot.n2c[n]
par_coords = treeplot.n2c[n.parent]
p1 = (n_coords.x, n_coords.y)
p2 = (par_coords.x, n_coords.y)
hsegs,hcols = gradient_segment_horz(p1,p2,n_col,par_col)
horz_seg_collections[i] = hsegs
horz_seg_colors[i] = hcols
vert_seg_collections[i] = ([(par_coords.x,par_coords.y),
(par_coords.x, n_coords.y)])
vert_seg_colors[i] = (par_col)
horz_seg_collections = [i for s in horz_seg_collections for i in s]
horz_seg_colors = [i for s in horz_seg_colors for i in s]
lc = LineCollection(horz_seg_collections + vert_seg_collections,
colors = horz_seg_colors + vert_seg_colors,
lw = width)
lc.set_visible(vis)
treeplot.add_collection(lc)
# leg_ax = treeplot.figure.add_axes([0.3, 0.8, 0.1, 0.1])
# leg_ax.tick_params(which = "both",
# bottom = "off",
# labelbottom="off",
# top = "off",
# left = "off",
# labelleft = "off",
# right = "off")
treeplot.figure.canvas.draw_idle()
def add_ancrecon_hrm(treeplot, liks, vis=True, width=2):
"""
Color branches on tree based on likelihood of being in a state
based on ancestral state reconstruction of a two-character, two-regime
hrm model.
"""
root = treeplot.root
horz_seg_collections = [None] * (len(root)-1)
horz_seg_colors = [None]*(len(root)-1)
vert_seg_collections = [None] * (len(root)-1)
vert_seg_colors = [None] * (len(root)-1)
nchar = liks.shape[1]-2
for i,n in enumerate(root.descendants()):
n_lik = liks[i+1]
par_lik = liks[n.parent.ni]
n_col = twoS_twoR_colormaker(n_lik[:nchar])
par_col = twoS_twoR_colormaker(par_lik[:nchar])
n_coords = treeplot.n2c[n]
par_coords = treeplot.n2c[n.parent]
p1 = (n_coords.x, n_coords.y)
p2 = (par_coords.x, n_coords.y)
hsegs,hcols = gradient_segment_horz(p1,p2,n_col.rgb,par_col.rgb)
horz_seg_collections[i] = hsegs
horz_seg_colors[i] = hcols
vert_seg_collections[i] = ([(par_coords.x,par_coords.y),
(par_coords.x, n_coords.y)])
vert_seg_colors[i] = (par_col.rgb)
horz_seg_collections = [i for s in horz_seg_collections for i in s]
horz_seg_colors = [i for s in horz_seg_colors for i in s]
lc = LineCollection(horz_seg_collections + vert_seg_collections,
colors = horz_seg_colors + vert_seg_colors,
lw = width)
lc.set_visible(vis)
treeplot.add_collection(lc)
leg_ax = treeplot.figure.add_axes([0.3, 0.8, 0.1, 0.1])
leg_ax.tick_params(which = "both",
bottom = "off",
labelbottom="off",
top = "off",
left = "off",
labelleft = "off",
right = "off")
c1 = twoS_twoR_colormaker([1,0,0,0])
c2 = twoS_twoR_colormaker([0,1,0,0])
c3 = twoS_twoR_colormaker([0,0,1,0])
c4 = twoS_twoR_colormaker([0,0,0,1])
grid = np.array([[c1.rgb,c2.rgb],[c3.rgb,c4.rgb]])
leg_ax.imshow(grid, interpolation="bicubic")
treeplot.figure.canvas.draw_idle()
def add_mkmr_heatmap(treeplot, locations, vis=True, seglen=0.02):
"""
Heatmap that shows which portions of the tree are most likely
to contain a switchpoint
To be used with the output from mk_multi_bayes.
Args:
locations (list): List of lists containing node and distance.
The output from the switchpoint stochastic of mk_multi_bayes.
seglen (float): The size of segments to break the tree into.
MUST BE the same as the seglen used in mk_multi_bayes.
"""
treelen = treeplot.root.max_tippath()
seglen_px = seglen*treelen
locations = [tuple([treeplot.root[x[0].ni],round(x[1],7)]) for x in locations]
segmap = ivy.chars.mk_mr.tree_map(treeplot.root, seglen=seglen)
segmap = [tuple([x[0],round(x[1],7)]) for x in segmap] # All possible segments to plot
nrep = len(locations)
rates = defaultdict(lambda: 0) # Setting heatmap densities
for l in Counter(locations).items():
rates[l[0]] = l[1]
cmap = RdYlBu
segments = []
values = []
# TODO: radial plot type
for s in segmap:
node = s[0]
c = xy(treeplot, node)
cp = xy(treeplot, node.parent)
x0 = c[0] - s[1] # Start of segment
x1 = x0 - seglen_px# End of segment
if x1 < cp[0]:
x1 = cp[0]
y0 = y1 = c[1]
segments.append(((x0,y0),(x1,y1)))
values.append(rates[s]/nrep)
if s[1] == 0.0 and not s[0].isleaf: # Draw vertical segments
x0 = x1 = c[0]
y0 = xy(treeplot, node.children[0])[1]
y1 = xy(treeplot, node.children[-1])[1]
segments.append(((x0,y0),(x1,y1)))
values.append(rates[s]/nrep)
lc = LineCollection(segments, cmap=RdYlBu, lw=2)
lc.set_array(np.array(values))
treeplot.add_collection(lc)
lc.set_zorder(1)
lc.set_visible(vis)
treeplot.figure.canvas.draw_idle()
def add_ancrecon(treeplot, liks, vis=True, width=2):
"""
Plot ancestor reconstruction for a binary mk model
"""
root = treeplot.root
horz_seg_collections = [None] * (len(root)-1)
horz_seg_colors = [None]*(len(root)-1)
vert_seg_collections = [None] * (len(root)-1)
vert_seg_colors = [None] * (len(root)-1)
nchar = liks.shape[1]-2
for i,n in enumerate(root.descendants()):
n_lik = liks[i+1]
par_lik = liks[n.parent.ni]
n_col = twoS_colormaker(n_lik[:nchar])
par_col = twoS_colormaker(par_lik[:nchar])
n_coords = treeplot.n2c[n]
par_coords = treeplot.n2c[n.parent]
p1 = (n_coords.x, n_coords.y)
p2 = (par_coords.x, n_coords.y)
hsegs,hcols = gradient_segment_horz(p1,p2,n_col.rgb,par_col.rgb)
horz_seg_collections[i] = hsegs
horz_seg_colors[i] = hcols
vert_seg_collections[i] = ([(par_coords.x,par_coords.y),
(par_coords.x, n_coords.y)])
vert_seg_colors[i] = (par_col.rgb)
horz_seg_collections = [i for s in horz_seg_collections for i in s]
horz_seg_colors = [i for s in horz_seg_colors for i in s]
lc = LineCollection(horz_seg_collections + vert_seg_collections,
colors = horz_seg_colors + vert_seg_colors,
lw = width)
lc.set_visible(vis)
treeplot.add_collection(lc)
treeplot.figure.canvas.draw_idle()
class Anim:
def __init__(
self, eddy, intern=False, sleep_event=0.1, graphic_information=False, **kwargs
):
self.eddy = eddy
x_name, y_name = eddy.intern(intern)
self.t, self.x, self.y = eddy.time, eddy[x_name], eddy[y_name]
self.x_core, self.y_core, self.track = eddy["lon"], eddy["lat"], eddy["track"]
self.graphic_informations = graphic_information
self.pause = False
self.period = self.eddy.period
self.sleep_event = sleep_event
self.mappables = list()
self.field_color = None
self.field_txt = None
self.time_field = False
self.setup(**kwargs)
def setup(
self,
cmap="jet",
lut=None,
field_color="time",
field_txt="track",
range_color=(None, None),
nb_step=25,
figsize=(8, 6),
**kwargs,
):
self.field_color = self.eddy[field_color].astype("f4")
self.field_txt = self.eddy[field_txt]
rg = range_color
if rg[0] is None and rg[1] is None and field_color == "time":
self.time_field = True
else:
rg = (
self.field_color.min() if rg[0] is None else rg[0],
self.field_color.max() if rg[1] is None else rg[1],
)
self.field_color = (self.field_color - rg[0]) / (rg[1] - rg[0])
self.colors = pyplot.get_cmap(cmap, lut=lut)
self.nb_step = nb_step
x_min, x_max = self.x_core.min() - 2, self.x_core.max() + 2
d_x = x_max - x_min
y_min, y_max = self.y_core.min() - 2, self.y_core.max() + 2
d_y = y_max - y_min
# plot
self.fig = pyplot.figure(figsize=figsize, **kwargs)
t0, t1 = self.period
self.fig.suptitle(f"{t0} -> {t1}")
self.ax = self.fig.add_axes((0.05, 0.05, 0.9, 0.9), projection="full_axes")
self.ax.set_xlim(x_min, x_max), self.ax.set_ylim(y_min, y_max)
self.ax.set_aspect("equal")
self.ax.grid()
# init mappable
self.txt = self.ax.text(x_min + 0.05 * d_x, y_min + 0.05 * d_y, "", zorder=10)
self.segs = list()
self.t_segs = list()
self.c_segs = list()
self.contour = LineCollection([], zorder=1)
self.ax.add_collection(self.contour)
self.fig.canvas.draw()
self.fig.canvas.mpl_connect("key_press_event", self.keyboard)
self.fig.canvas.mpl_connect("resize_event", self.reset_bliting)
def reset_bliting(self, event):
self.contour.set_visible(False)
self.txt.set_visible(False)
for m in self.mappables:
m.set_visible(False)
self.fig.canvas.draw()
self.bg_cache = self.fig.canvas.copy_from_bbox(self.ax.bbox)
self.contour.set_visible(True)
self.txt.set_visible(True)
for m in self.mappables:
m.set_visible(True)
def show(self, infinity_loop=False):
pyplot.show(block=False)
# save background for future bliting
self.fig.canvas.draw()
self.bg_cache = self.fig.canvas.copy_from_bbox(self.ax.bbox)
loop = True
t0, t1 = self.period
while loop:
self.now = t0
while True:
dt = self.sleep_event
if not self.pause:
d0 = datetime.now()
self.next()
dt_draw = (datetime.now() - d0).total_seconds()
dt = self.sleep_event - dt_draw
if dt < 0:
# self.sleep_event = dt_draw * 1.01
dt = 1e-10
if dt == 0:
dt = 1e-10
self.fig.canvas.start_event_loop(dt)
if self.now > t1:
break
if infinity_loop:
self.fig.canvas.start_event_loop(0.5)
else:
loop = False
def next(self):
self.now += 1
return self.draw_contour()
def prev(self):
self.now -= 1
return self.draw_contour()
def func_animation(self, frame):
while self.mappables:
self.mappables.pop().remove()
self.now = frame
self.update()
artists = [self.contour, self.txt]
artists.extend(self.mappables)
return artists
def update(self):
m = self.t == self.now
if m.sum():
segs = list()
t = list()
c = list()
for i in where(m)[0]:
segs.append(create_vertice(self.x[i], self.y[i]))
c.append(self.field_color[i])
t.append(self.now)
self.segs.append(segs)
self.c_segs.append(c)
self.t_segs.append(t)
self.contour.set_paths(chain(*self.segs))
if self.time_field:
self.contour.set_color(
self.colors(
[
(self.nb_step - self.now + i) / self.nb_step
for i in chain(*self.c_segs)
]
)
)
else:
self.contour.set_color(self.colors(list(chain(*self.c_segs))))
# linewidth will be link to time delay
self.contour.set_lw(
[
(1 - (self.now - i) / self.nb_step) * 2.5 if i <= self.now else 0
for i in chain(*self.t_segs)
]
)
# Update date txt and info
txt = f"{(timedelta(int(self.now)) + datetime(1950,1,1)).strftime('%Y/%m/%d')}"
if self.graphic_informations:
txt += f"- {1/self.sleep_event:.0f} frame/s"
self.txt.set_text(txt)
# Update id txt
for i in where(m)[0]:
mappable = self.ax.text(
self.x_core[i],
self.y_core[i],
self.field_txt[i],
fontsize=12,
fontweight="demibold",
)
self.mappables.append(mappable)
self.ax.draw_artist(mappable)
self.ax.draw_artist(self.contour)
self.ax.draw_artist(self.txt)
# Remove first segment to keep only T contour
if len(self.segs) > self.nb_step:
self.segs.pop(0)
self.t_segs.pop(0)
self.c_segs.pop(0)
def draw_contour(self):
# select contour for this time step
while self.mappables:
self.mappables.pop().remove()
self.ax.figure.canvas.restore_region(self.bg_cache)
self.update()
# paint updated artist
self.ax.figure.canvas.blit(self.ax.bbox)
def keyboard(self, event):
if event.key == "escape":
exit()
elif event.key == " ":
self.pause = not self.pause
elif event.key == "+":
self.sleep_event *= 0.9
elif event.key == "-":
self.sleep_event *= 1.1
elif event.key == "right" and self.pause:
self.next()
elif event.key == "left" and self.pause:
# we remove 2 step to add 1 so we rewind of only one
self.segs.pop(-1)
self.segs.pop(-1)
self.t_segs.pop(-1)
self.t_segs.pop(-1)
self.c_segs.pop(-1)
self.c_segs.pop(-1)
self.prev()
def add_phylorate(treeplot, rates, nodeidx, vis=True):
"""
Add phylorate plot generated from data analyzed with BAMM
(http://bamm-project.org/introduction.html)
Args:
rates (array): Array of rates along branches
created by r_funcs.phylorate
nodeidx (array): Array of node indices matching rates (also created
by r_funcs.phylorate)
WARNING:
Ladderizing the tree can cause incorrect assignment of Ape node index
numbers. To prevent this, call this function or root.ape_node_idx()
before ladderizing the tree to assign correct Ape node index numbers.
"""
if not treeplot.root.apeidx:
treeplot.root.ape_node_idx()
segments = []
values = []
if treeplot.plottype == "radial":
radpatches = [] # For use in drawing arcs for radial plots
for n in treeplot.root.descendants():
n.rates = rates[nodeidx==n.apeidx]
c = treeplot.n2c[n]
pc = treeplot._path_to_parent(n)[0][1]
xd = c.x - pc[0]
yd = c.y - pc[1]
xseg = xd/len(n.rates)
yseg = yd/len(n.rates)
for i, rate in enumerate(n.rates):
x0 = pc[0] + i*xseg
y0 = pc[1] + i*yseg
x1 = x0 + xseg
y1 = y0 + yseg
segments.append(((x0, y0), (x1, y1)))
values.append(rate)
curverts = treeplot._path_to_parent(n)[0][2:]
curcodes = treeplot._path_to_parent(n)[1][2:]
curcol = RdYlBu(n.rates[0])
radpatches.append(PathPatch(
Path(curverts, curcodes), lw=2, edgecolor = curcol,
fill=False))
else:
for n in treeplot.root.descendants():
n.rates = rates[nodeidx==n.apeidx]
c = treeplot.n2c[n]
pc = treeplot.n2c[n.parent]
seglen = (c.x-pc.x)/len(n.rates)
for i, rate in enumerate(n.rates):
x0 = pc.x + i*seglen
x1 = x0 + seglen
segments.append(((x0, c.y), (x1, c.y)))
values.append(rate)
segments.append(((pc.x, pc.y), (pc.x, c.y)))
values.append(n.rates[0])
lc = LineCollection(segments, cmap=RdYlBu, lw=2)
lc.set_array(np.array(values))
treeplot.add_collection(lc)
lc.set_zorder(1)
if treeplot.plottype == "radial":
arccol = matplotlib.collections.PatchCollection(radpatches,
match_original=True)
treeplot.add_collection(arccol)
arccol.set_visible(vis)
arccol.set_zorder(1)
lc.set_visible(vis)
colorbar_legend(treeplot, values, RdYlBu, vis=vis)
treeplot.figure.canvas.draw_idle()
class HoughDemo(ImageProcessDemo):
TITLE = u"Hough Demo"
DEFAULT_IMAGE = "stuff.jpg"
SETTINGS = ["th2", "show_canny", "rho", "theta", "hough_th",
"minlen", "maxgap", "dp", "mindist", "param2",
"min_radius", "max_radius", "blur_sigma",
"linewidth", "alpha", "check_line", "check_circle"]
check_line = Bool(True)
check_circle = Bool(True)
#Gaussian blur parameters
blur_sigma = Range(0.1, 5.0, 2.0)
show_blur = Bool(False)
# Canny parameters
th2 = Range(0.0, 255.0, 200.0)
show_canny = Bool(False)
# HoughLine parameters
rho = Range(1.0, 10.0, 1.0)
theta = Range(0.1, 5.0, 1.0)
hough_th = Range(1, 100, 40)
minlen = Range(0, 100, 10)
maxgap = Range(0, 20, 10)
# HoughtCircle parameters
dp = Range(1.0, 5.0, 1.9)
mindist = Range(1.0, 100.0, 50.0)
param2 = Range(5, 100, 50)
min_radius = Range(5, 100, 20)
max_radius = Range(10, 100, 70)
# draw parameters
linewidth = Range(1.0, 3.0, 1.0)
alpha = Range(0.0, 1.0, 0.6)
def control_panel(self):
return VGroup(
Group(
Item("blur_sigma", label=u"标准方差"),
Item("show_blur", label=u"显示结果"),
label=u"高斯模糊参数"
),
Group(
Item("th2", label=u"阈值2"),
Item("show_canny", label=u"显示结果"),
label=u"边缘检测参数"
),
Group(
Item("rho", label=u"偏移分辨率(像素)"),
Item("theta", label=u"角度分辨率(角度)"),
Item("hough_th", label=u"阈值"),
Item("minlen", label=u"最小长度"),
Item("maxgap", label=u"最大空隙"),
label=u"直线检测"
),
Group(
Item("dp", label=u"分辨率(像素)"),
Item("mindist", label=u"圆心最小距离(像素)"),
Item("param2", label=u"圆心检查阈值"),
Item("min_radius", label=u"最小半径"),
Item("max_radius", label=u"最大半径"),
label=u"圆检测"
),
Group(
Item("linewidth", label=u"线宽"),
Item("alpha", label=u"alpha"),
HGroup(
Item("check_line", label=u"直线"),
Item("check_circle", label=u"圆"),
),
label=u"绘图参数"
)
)
def __init__(self, **kwargs):
super(HoughDemo, self).__init__(**kwargs)
self.connect_dirty("th2, show_canny, show_blur, rho, theta, hough_th,"
"min_radius, max_radius, blur_sigma,"
"minlen, maxgap, dp, mindist, param2, "
"linewidth, alpha, check_line, check_circle")
self.lines = LineCollection([], linewidths=2, alpha=0.6)
self.axe.add_collection(self.lines)
self.circles = EllipseCollection(
[], [], [],
units="xy",
facecolors="none",
edgecolors="red",
linewidths=2,
alpha=0.6,
transOffset=self.axe.transData)
self.axe.add_collection(self.circles)
def _img_changed(self):
self.img_gray = cv2.cvtColor(self.img, cv2.COLOR_BGR2GRAY)
def draw(self):
img_smooth = cv2.GaussianBlur(self.img_gray, (0, 0), self.blur_sigma, self.blur_sigma)
img_edge = cv2.Canny(img_smooth, self.th2 * 0.5, self.th2)
if self.show_blur and self.show_canny:
show_img = cv2.cvtColor(np.maximum(img_smooth, img_edge), cv2.COLOR_BAYER_BG2BGR)
elif self.show_blur:
show_img = cv2.cvtColor(img_smooth, cv2.COLOR_BAYER_BG2BGR)
elif self.show_canny:
show_img = cv2.cvtColor(img_edge, cv2.COLOR_GRAY2BGR)
else:
show_img = self.img
if self.check_line:
theta = self.theta / 180.0 * np.pi
lines = cv2.HoughLinesP(img_edge,
self.rho, theta, self.hough_th,
minLineLength=self.minlen,
maxLineGap=self.maxgap)
if lines is not None:
lines = lines[0]
lines.shape = -1, 2, 2
self.lines.set_segments(lines)
self.lines.set_visible(True)
else:
self.lines.set_visible(False)
else:
self.lines.set_visible(False)
if self.check_circle:
circles = cv2.HoughCircles(img_smooth, 3,
self.dp, self.mindist,
param1=self.th2,
param2=self.param2,
minRadius=self.min_radius,
maxRadius=self.max_radius)
if circles is not None:
circles = circles[0]
self.circles._heights = self.circles._widths = circles[:, 2]
self.circles.set_offsets(circles[:, :2])
self.circles._angles = np.zeros(len(circles))
self.circles._transOffset = self.axe.transData
self.circles.set_visible(True)
else:
self.circles.set_visible(False)
else:
self.circles.set_visible(False)
self.lines.set_linewidths(self.linewidth)
self.circles.set_linewidths(self.linewidth)
self.lines.set_alpha(self.alpha)
self.circles.set_alpha(self.alpha)
self.draw_image(show_img)
class Anim:
def __init__(self,
eddy,
intern=False,
sleep_event=0.1,
graphic_information=False,
**kwargs):
self.eddy = eddy
x_name, y_name = eddy.intern(intern)
self.t, self.x, self.y = eddy.time, eddy[x_name], eddy[y_name]
self.x_core, self.y_core, self.track = eddy["lon"], eddy["lat"], eddy[
"track"]
self.graphic_informations = graphic_information
self.pause = False
self.period = self.eddy.period
self.sleep_event = sleep_event
self.mappables = list()
self.setup(**kwargs)
def setup(self, cmap="jet", nb_step=25, figsize=(8, 6), **kwargs):
cmap = pyplot.get_cmap(cmap)
self.colors = cmap(arange(nb_step + 1) / nb_step)
self.nb_step = nb_step
x_min, x_max = self.x_core.min() - 2, self.x_core.max() + 2
d_x = x_max - x_min
y_min, y_max = self.y_core.min() - 2, self.y_core.max() + 2
d_y = y_max - y_min
# plot
self.fig = pyplot.figure(figsize=figsize, **kwargs)
t0, t1 = self.period
self.fig.suptitle(f"{t0} -> {t1}")
self.ax = self.fig.add_axes((0.05, 0.05, 0.9, 0.9))
self.ax.set_xlim(x_min, x_max), self.ax.set_ylim(y_min, y_max)
self.ax.set_aspect("equal")
self.ax.grid()
# init mappable
self.txt = self.ax.text(x_min + 0.05 * d_x,
y_min + 0.05 * d_y,
"",
zorder=10)
self.segs = list()
self.contour = LineCollection([], zorder=1)
self.ax.add_collection(self.contour)
self.fig.canvas.draw()
self.fig.canvas.mpl_connect("key_press_event", self.keyboard)
self.fig.canvas.mpl_connect("resize_event", self.reset_bliting)
def reset_bliting(self, event):
self.contour.set_visible(False)
self.txt.set_visible(False)
for m in self.mappables:
m.set_visible(False)
self.fig.canvas.draw()
self.bg_cache = self.fig.canvas.copy_from_bbox(self.ax.bbox)
self.contour.set_visible(True)
self.txt.set_visible(True)
for m in self.mappables:
m.set_visible(True)
def show(self, infinity_loop=False):
pyplot.show(block=False)
# save background for future bliting
self.fig.canvas.draw()
self.bg_cache = self.fig.canvas.copy_from_bbox(self.ax.bbox)
loop = True
t0, t1 = self.period
while loop:
self.now = t0
while True:
dt = self.sleep_event
if not self.pause:
d0 = datetime.now()
self.next()
dt_draw = (datetime.now() - d0).total_seconds()
dt = self.sleep_event - dt_draw
if dt < 0:
# self.sleep_event = dt_draw * 1.01
dt = 1e-10
self.fig.canvas.start_event_loop(dt)
if self.now > t1:
break
if infinity_loop:
self.fig.canvas.start_event_loop(0.5)
else:
loop = False
def next(self):
self.now += 1
return self.draw_contour()
def prev(self):
self.now -= 1
return self.draw_contour()
def func_animation(self, frame):
while self.mappables:
self.mappables.pop().remove()
self.now = frame
self.update()
artists = [self.contour, self.txt]
artists.extend(self.mappables)
return artists
def update(self):
m = self.t == self.now
if m.sum():
self.segs.append(
create_vertice(flatten_line_matrix(self.x[m]),
flatten_line_matrix(self.y[m])))
else:
self.segs.append(empty((0, 2)))
self.contour.set_paths(self.segs)
self.contour.set_color(self.colors[-len(self.segs):])
self.contour.set_lw(arange(len(self.segs)) / len(self.segs) * 2.5)
txt = f"{self.now}"
if self.graphic_informations:
txt += f"- {1/self.sleep_event:.0f} frame/s"
self.txt.set_text(txt)
for i in where(m)[0]:
mappable = self.ax.text(self.x_core[i],
self.y_core[i],
self.track[i],
fontsize=8)
self.mappables.append(mappable)
self.ax.draw_artist(mappable)
self.ax.draw_artist(self.contour)
self.ax.draw_artist(self.txt)
# Remove first segment to keep only T contour
if len(self.segs) > self.nb_step:
self.segs.pop(0)
def draw_contour(self):
# select contour for this time step
while self.mappables:
self.mappables.pop().remove()
self.ax.figure.canvas.restore_region(self.bg_cache)
self.update()
# paint updated artist
self.ax.figure.canvas.blit(self.ax.bbox)
def keyboard(self, event):
if event.key == "escape":
exit()
elif event.key == " ":
self.pause = not self.pause
elif event.key == "+":
self.sleep_event *= 0.9
elif event.key == "-":
self.sleep_event *= 1.1
elif event.key == "right" and self.pause:
self.next()
elif event.key == "left" and self.pause:
self.segs.pop(-1)
self.segs.pop(-1)
self.prev()
class HoughDemo(ImageProcessDemo):
TITLE = u"Hough Demo"
DEFAULT_IMAGE = "stuff.jpg"
SETTINGS = ["th2", "show_canny", "rho", "theta", "hough_th",
"minlen", "maxgap", "dp", "mindist", "param2",
"min_radius", "max_radius", "blur_sigma",
"linewidth", "alpha", "check_line", "check_circle"]
check_line = Bool(True)
check_circle = Bool(True)
#Gaussian blur parameters
blur_sigma = Range(0.1, 5.0, 2.0)
show_blur = Bool(False)
# Canny parameters
th2 = Range(0.0, 255.0, 200.0)
show_canny = Bool(False)
# HoughLine parameters
rho = Range(1.0, 10.0, 1.0)
theta = Range(0.1, 5.0, 1.0)
hough_th = Range(1, 100, 40)
minlen = Range(0, 100, 10)
maxgap = Range(0, 20, 10)
# HoughtCircle parameters
dp = Range(1.0, 5.0, 1.9)
mindist = Range(1.0, 100.0, 50.0)
param2 = Range(5, 100, 50)
min_radius = Range(5, 100, 20)
max_radius = Range(10, 100, 70)
# draw parameters
linewidth = Range(1.0, 3.0, 1.0)
alpha = Range(0.0, 1.0, 0.6)
def control_panel(self):
return VGroup(
Group(
Item("blur_sigma", label=u"标准方差"),
Item("show_blur", label=u"显示结果"),
label=u"高斯模糊参数"
),
Group(
Item("th2", label=u"阈值2"),
Item("show_canny", label=u"显示结果"),
label=u"边缘检测参数"
),
Group(
Item("rho", label=u"偏移分辨率(像素)"),
Item("theta", label=u"角度分辨率(角度)"),
Item("hough_th", label=u"阈值"),
Item("minlen", label=u"最小长度"),
Item("maxgap", label=u"最大空隙"),
label=u"直线检测"
),
Group(
Item("dp", label=u"分辨率(像素)"),
Item("mindist", label=u"圆心最小距离(像素)"),
Item("param2", label=u"圆心检查阈值"),
Item("min_radius", label=u"最小半径"),
Item("max_radius", label=u"最大半径"),
label=u"圆检测"
),
Group(
Item("linewidth", label=u"线宽"),
Item("alpha", label=u"alpha"),
HGroup(
Item("check_line", label=u"直线"),
Item("check_circle", label=u"圆"),
),
label=u"绘图参数"
)
)
def __init__(self, **kwargs):
super(HoughDemo, self).__init__(**kwargs)
self.connect_dirty("th2, show_canny, show_blur, rho, theta, hough_th,"
"min_radius, max_radius, blur_sigma,"
"minlen, maxgap, dp, mindist, param2, "
"linewidth, alpha, check_line, check_circle")
self.lines = LineCollection([], linewidths=2, alpha=0.6)
self.axe.add_collection(self.lines)
self.circles = EllipseCollection(
[], [], [],
units="xy",
facecolors="none",
edgecolors="red",
linewidths=2,
alpha=0.6,
transOffset=self.axe.transData)
self.axe.add_collection(self.circles)
def _img_changed(self):
self.img_gray = cv2.cvtColor(self.img, cv2.COLOR_BGR2GRAY)
def draw(self):
img_smooth = cv2.GaussianBlur(self.img_gray, (0, 0), self.blur_sigma, self.blur_sigma)
img_edge = cv2.Canny(img_smooth, self.th2 * 0.5, self.th2)
if self.show_blur and self.show_canny:
show_img = cv2.cvtColor(np.maximum(img_smooth, img_edge), cv2.COLOR_BAYER_BG2BGR)
elif self.show_blur:
show_img = cv2.cvtColor(img_smooth, cv2.COLOR_BAYER_BG2BGR)
elif self.show_canny:
show_img = cv2.cvtColor(img_edge, cv2.COLOR_GRAY2BGR)
else:
show_img = self.img
if self.check_line:
theta = self.theta / 180.0 * np.pi
lines = cv2.HoughLinesP(img_edge,
self.rho, theta, self.hough_th,
minLineLength=self.minlen,
maxLineGap=self.maxgap)
if lines is not None:
lines = lines[0]
lines.shape = -1, 2, 2
self.lines.set_segments(lines)
self.lines.set_visible(True)
else:
self.lines.set_visible(False)
else:
self.lines.set_visible(False)
if self.check_circle:
circles = cv2.HoughCircles(img_smooth, 3,
self.dp, self.mindist,
param1=self.th2,
param2=self.param2,
minRadius=self.min_radius,
maxRadius=self.max_radius)
if circles is not None:
circles = circles[0]
self.circles._heights = self.circles._widths = circles[:, 2]
self.circles.set_offsets(circles[:, :2])
self.circles._angles = np.zeros(len(circles))
self.circles._transOffset = self.axe.transData
self.circles.set_visible(True)
else:
self.circles.set_visible(False)
else:
self.circles.set_visible(False)
self.lines.set_linewidths(self.linewidth)
self.circles.set_linewidths(self.linewidth)
self.lines.set_alpha(self.alpha)
self.circles.set_alpha(self.alpha)
self.draw_image(show_img)
class Visualisation(FigureCanvasWxAgg):
def __init__(self, gui):
self.fig = pl.figure() #(9,8), 90)
FigureCanvasWxAgg.__init__(self, gui, -1, self.fig)
self.xlim, self.ylim, self.dataon = (), (), False
# c'est la GUI e tle modele
self.gui, self.core = gui, gui.core
# polygone d'interaction sur une zone (pour pouvoir la modifier)
self.polyInteract = None
# liste de variables, sert pour la GUI et le combobox sur les variables
self.listeNomVar = []
for mod in self.core.modelList:
for k in gui.linesDic[mod].keys():
self.listeNomVar.extend(gui.linesDic[mod][k])
self.curVar, self.curContour = None, 'Charge' # variable courante selectionne
self.curMedia, self.curOri, self.curPlan, self.curGroupe = 0, 'Z', 0, None
# variable pour savoir si on est en cours de tracage d'une zone
self.typeZone = -1
# coordonnees et zone de la zone que l'on est en train de creer
self.curZone = None # objet graphique (ligne, point, rect..)
self.x1, self.y1 = [], []
self.tempZoneVal = [] # liste de values pour polyV
self.calcE = 0
self.calcT = 0
self.calcR = 0
# dit si calcule effectue ou non
# dictionnaire qui est compose des variables de l'Aquifere
# a chaque variable est associe une liste de zones
self.listeZone, self.listeZoneText, self.listeZmedia = {}, {}, {}
for i in range(len(self.listeNomVar)):
#print self.listeNomVar[i]
self.listeZone[self.listeNomVar[i]] = []
self.listeZoneText[self.listeNomVar[i]] = []
self.listeZmedia[self.listeNomVar[i]] = []
# toolbar de la visu, de type NavigationToolbar2Wx
self.toolbar = NavigationToolbar2Wx(self)
self.toolbar.Realize()
# ajout du subplot a la figure
self.cnv = self.fig.add_axes([.05, .05, .9,
.88]) #left,bottom, wide,height
self.toolbar.update()
self.pos = self.mpl_connect('motion_notify_event', self.onPosition)
# create teh major objects:
self.Contour, self.ContourF, self.ContourLabel, self.Vector = None, None, None, None
self.Grid, self.Particles, self.Image, self.Map = None, None, None, None
#####################################################################
# Divers accesseur/mutateurs
#####################################################################
def GetToolBar(self):
return self.toolbar
def getcurVisu(self):
return [self.curGroupe, self.curNom, self.curObj]
def onPosition(self, evt):
self.gui.onPosition(' x: ' + str(evt.xdata)[:6] + ' y: ' +
str(evt.ydata)[:6])
def delAllObjects(self):
for v in self.listeZone:
self.listeZone[v] = []
self.listeZoneText[v] = []
self.cnv.lines = []
self.cnv.collections = []
self.cnv.artists = []
self.cnv.images = []
self.cnv.cla()
self.draw()
def setVisu(self, core):
"""creer les objets graphiques a partir des caracteristiques d'un modele
importe.
creer les zones avec setAllzones, puis le contour et les vectors ecoult,
les lignes etle contour pour tracer, contour pour reaction
depend de l'etat du systeme de la liste graphique
comme ca tout ca pourra etre visualise sans faire de nouveau calcul
"""
self.delAllObjects()
for mod in self.core.modelList:
self.setAllZones(core.diczone[mod].dic)
self.initDomain()
self.draw()
def setDataOn(self, bool):
"""definit l'affichage ou non des donnees qaund contour"""
self.dataon = bool
def redraw(self):
#self.cnv.set_xlim(self.xlim)
#self.cnv.set_ylim(self.ylim)
self.draw()
# def changeTitre(self,titre):
# s='';ori=self.curOri
# if ori in ['X','Y','Z']:
# plan=self.curPlan;
# x1,y1 = self.model.Aquifere.getXYticks()
# zl = self.model.Aquifere.getParm('zList')
# if ori=='Z': s=' Z = '+ str(zl[plan])
# if ori=='X': s=' X = '+ str(x1[plan])
# if ori=='Y': s=' Y = '+ str(y1[plan])
# pl.title(self.traduit(str(titre))+s[:9],fontsize=20)
def createAndShowObject(self, dataM, dataV, opt, value=None, color=None):
"""create the Contour, Vector, opt is contour or vector
"""
if dataM == None: self.drawContour(False)
else: self.createContour(dataM, value, color)
if dataV == None: self.drawVector(False)
else: self.createVector(dataV)
def drawObject(self, typObj, bool):
if typObj == 'Map' and self.Map == None and bool == False: return
exec('self.draw' + typObj + '(' + str(bool) + ')')
def changeObject(self, groupe, name, value, color):
if name == 'Grid': self.changeGrid(color)
elif name == 'Particles':
self.changeParticles(value=value, color=color)
elif name == 'Veloc-vect':
self.changeVector(value, color)
#elif name=='Visible': self.changeData(value,color)
else:
self.changeContour(value, color)
#####################################################################
# Gestion de l'affichage de la grid/map
#####################################################################
# methode qui change la taille du domaine d'etude (les values de l'axe
# de la figure matplotlib en fait) et la taille des cellules d'etude
def initDomain(self):
# change value of the axes
grd = self.core.addin.getFullGrid()
self.xlim = (grd['x0'], grd['x1'])
self.ylim = (grd['y0'], grd['y1'])
p, = pl.plot([0, 1], 'b')
p.set_visible(False)
self.transform = p.get_transform()
self.cnv.set_xlim(self.xlim)
self.cnv.set_ylim(self.ylim)
self.createGrid()
# add basic vector as a linecollection
dep = rand(2, 2) * 0.
arr = dep * 1.
self.Vector = LineCollection(zip(dep, arr))
self.Vector.set_transform(self.transform)
self.Vector.set_visible(False)
#pl.setp(lc,linewidth=.5);
self.cnv.collections.append(self.Vector)
self.Vector.data = [0, 0, None, None]
# def changeDomain(self):
# self.changeAxesOri('Z',0)
#
def changeAxesOri(self, ori):
# change orientation de la visu
zb = self.core.Zblock
zlim = (amin(zb), amax(zb))
if ori == 'Z':
self.cnv.set_xlim(self.xlim)
self.cnv.set_ylim(self.ylim)
elif ori == 'X':
self.cnv.set_xlim(self.ylim)
self.cnv.set_ylim(zlim)
elif ori == 'Y':
self.cnv.set_xlim(self.xlim)
self.cnv.set_ylim(zlim)
self.draw()
def createGrid(self, col=None):
if self.Grid == None:
col = (.6, .6, .6)
self.Grid = [0, 0, col]
#self.cnv.collections=[0,0];
else:
for i in range(2):
self.Grid[i].set_visible(False)
if col == None: col = self.Grid[2]
else: self.Grid[2] = col
#print 'create grid',self.Grid,col
nx, ny, xt, yt = getXYvects(self.core)
#print 'visu,grid',nx,ny,xt,yt
if len(self.cnv.collections) < 2: self.cnv.collections = [0, 0]
l = len(ravel(xt))
dep = concatenate([xt.reshape((l, 1)), ones((l, 1)) * min(yt)], axis=1)
arr = concatenate([xt.reshape((l, 1)), ones((l, 1)) * max(yt)], axis=1)
self.Grid[0] = LineCollection(zip(dep, arr))
self.cnv.collections[0] = self.Grid[0]
l = len(ravel(yt))
dep = concatenate([ones((l, 1)) * min(xt), yt.reshape((l, 1))], axis=1)
arr = concatenate([ones((l, 1)) * max(xt), yt.reshape((l, 1))], axis=1)
self.Grid[1] = LineCollection(zip(dep, arr))
self.cnv.collections[1] = self.Grid[1]
for i in [0, 1]:
self.Grid[i].set_transform(self.transform)
self.Grid[i].set_color(col)
self.redraw()
def drawGrid(self, bool): # works only to remove not to recreate
col = self.Grid[2]
for i in [0, 1]:
self.Grid[i].set_visible(bool)
self.Grid[i].set_color(col)
self.redraw()
def changeGrid(self, color):
a = color.Get()
col = (a[0] / 255, a[1] / 255, a[2] / 255)
for i in [0, 1]:
self.Grid[i].set_color(col)
self.Grid[2] = col
self.redraw()
#####################################################################
# Affichage d'une variable sous forme d'image
#####################################################################
# l'image se met en position 1 dans la liste des images
def createMap(self):
file = self.gui.map
mat = Im.imread(file)
org = 'upper'
ext = (self.xlim[0], self.xlim[1], self.ylim[0], self.ylim[1])
self.Map = pl.imshow(mat,
origin=org,
extent=ext,
aspect='auto',
interpolation='nearest')
self.cnv.images = [self.Map] #
self.cnv.images[0].set_visible(True)
self.redraw()
def drawMap(self, bool):
if self.Map == None: self.createMap()
# self.Map.set_visible(bool)
self.cnv.images = [self.Map] #
self.cnv.images[0].set_visible(bool)
self.redraw()
def createImage(self, data):
#print 'vis img',len(xt),len(yt),shape(mat)
X, Y, Z = data
image = pl.pcolormesh(X, Y, Z) #,norm='Normalize')
self.cnv.images = [image]
self.redraw()
def drawImage(self, bool):
if len(self.cnv.images) > 0:
self.cnv.images[0].set_visible(bool)
self.redraw()
#####################################################################
# Gestion de l'affichage des contours
#####################################################################
def createContour(self, data, value=None, col=None):
""" calcul des contour sa partir de value : value[0] : min
[1] : max, [2] nb contours, [3] decimales, [4] : 'lin' log' ou 'fix',
si [4]:fix, alors [5] est la serie des values de contours"""
X, Y, Z = data
#print 'visu controu',value,col
self.cnv.collections = self.cnv.collections[:3]
self.cnv.artists = []
V = 11
Zmin = amin(amin(Z))
Zmax = amax(amax(Z * (Z < 1e5)))
if Zmax == Zmin: # test min=max -> pas de contour
self.gui.onMessage(' values all equal to ' + str(Zmin))
return
if value == None:
value = [Zmin, Zmax, (Zmax - Zmin) / 10., 2, 'auto', []]
# adapter le namebre et la value des contours
val2 = [float(a) for a in value[:3]]
if value[4] == 'log': # cas echelle log
n = int((log10(val2[1]) - log10(max(val2[0], 1e-4))) / val2[2]) + 1
V = logspace(log10(max(val2[0], 1e-4)), log10(val2[1]), n)
elif (value[4]
== 'fix') and (value[5] != None): # fixes par l'utilisateur
V = value[5] * 1
V.append(V[-1] * 2.)
n = len(V)
elif value[4] == 'lin': # cas echelle lineaire
n = int((val2[1] - val2[0]) / val2[2]) + 1
V = linspace(val2[0], val2[1], n)
else: # cas automatique
n = 11
V = linspace(Zmin, Zmax, n)
# ONE DIMENSIONAL
r, c = shape(X)
if r == 1:
X = concatenate([X, X])
Y = concatenate([Y - Y * .45, Y + Y * .45])
Z = concatenate([Z, Z])
Z2 = ma.masked_where(Z.copy() > 1e5, Z.copy())
#print value,n,V
# definir les couleurs des contours
if col == None: # or (col==[(0,0,0),(0,0,0),(0,0,0),10]):
cf = pl.contourf(pl.array(X), pl.array(Y), Z2, V)
c = pl.contour(pl.array(X), pl.array(Y), Z2, V)
col = [(0, 0, 255), (0, 255, 0), (255, 0, 0), 10]
else:
r, g, b = [], [], []
lim=((0.,1.,0.,0.),(.1,1.,0.,0.),(.25,.8,0.,0.),(.35,0.,.8,0.),(.45,0.,1.,0.),\
(.55,0.,1.,0.),(.65,0.,.8,0.),(.75,0.,0.,.8),(.9,0.,0.,1.),(1.,0.,0.,1.))
for i in range(len(lim)):
c1 = lim[i][1] * col[0][0] / 255. + lim[i][2] * col[1][
0] / 255. + lim[i][3] * col[2][0] / 255.
r.append((lim[i][0], c1, c1))
c2 = lim[i][1] * col[0][1] / 255. + lim[i][2] * col[1][
1] / 255. + lim[i][3] * col[2][1] / 255.
g.append((lim[i][0], c2, c2))
c3 = lim[i][1] * col[0][2] / 255. + lim[i][2] * col[1][
2] / 255. + lim[i][3] * col[2][2] / 255.
b.append((lim[i][0], c3, c3))
cdict = {'red': r, 'green': g, 'blue': b}
my_cmap = mpl.colors.LinearSegmentedColormap(
'my_colormap', cdict, 256)
cf = pl.contourf(pl.array(X), pl.array(Y), Z2, V, cmap=my_cmap)
c = pl.contour(pl.array(X), pl.array(Y), Z2, V, cmap=my_cmap)
#print col[3]
for c0 in cf.collections:
c0.set_alpha(int(col[3]) / 100.)
#print cl
if value == None: fmt = '%1.3f'
else: fmt = '%1.' + str(value[3]) + 'f'
cl = pl.clabel(c, color='black', fontsize=9, fmt=fmt)
self.Contour = c
self.ContourF = cf
self.ContourLabel = cl
self.Contour.data = data
self.redraw()
def changeContour(self, value, col):
""" modifie les values d'un contour existant"""
self.drawContour(False)
self.createContour(self.Contour.data, value, col)
def drawContour(self, bool):
self.cnv.collections = self.cnv.collections[:3]
self.cnv.artists = []
self.draw()
#~ for c in self.Contour.collections :c.set_visible(False)
#~ for c in self.ContourF.collections :c.set_visible(False)
#~ for a in self.ContourLabel: a.set_visible(False)
#~ #self.cnv.collections = self.cnv.collections[:3]
#~ self.redraw()
#####################################################################
# Gestion de l'affichage de vectors
#####################################################################
"""vector has been created as the first item of lincollection list
during domain intialization"""
def createVector(self, data):
X, Y, U, V = data
""" modifie les values de vectors existants"""
if self.Vector.data[3] == None: #first vector no color
ech = 1.
col = (0, 0, 1)
else:
a, b, ech, col = self.Vector.data
self.drawVector(False)
l = len(ravel(X))
dep = concatenate([X.reshape((l, 1)), Y.reshape((l, 1))], axis=1)
b = X + U * ech
c = Y + V * ech
arr = concatenate([b.reshape((l, 1)), c.reshape((l, 1))], axis=1)
self.Vector = LineCollection(zip(dep, arr))
self.Vector.set_transform(self.transform)
self.Vector.set_color(col)
if len(self.cnv.collections) > 2: self.cnv.collections[2] = self.Vector
else: self.cnv.collections.append(self.Vector)
self.Vector.set_visible(True)
self.Vector.data = [dep, arr, ech, col]
#print self.Vector.data
self.redraw()
def drawVector(self, bool):
""" dessine les vectors vitesse a partir de x,y,u,v et du
booleen qui dit s'il faut dessiner ou non """
self.Vector.set_visible(bool)
self.redraw()
def changeVector(self, ech, col=wx.Color(0, 0, 255)):
""" modifie les values de vectors existants"""
#self.drawVector(False)
ech = float(ech)
#change coordinates
dep, arr_old, ech_old, col_old = self.Vector.data
#print shape(dep),shape(arr_old),ech,ech_old
arr = dep + (arr_old - dep) * ech / ech_old
# new object
#self.Vector = LineCollection(zip(dep,arr))
self.Vector.set_segments(zip(dep, arr))
#self.Vector.set_transform(self.transform)
a = col.Get()
col = (a[0] / 255, a[1] / 255, a[2] / 255)
self.Vector.set_color(col)
self.Vector.set_visible(True)
#self.cnv.collections[2]=self.Vector
self.Vector.data = [dep, arr, ech, col]
self.redraw()
#####################################################################
# Gestion de l'affichage de particules
#####################################################################
def startParticles(self):
if self.Particles != None:
self.partVisible(False)
self.Particles = {
'line': [],
'txt': [],
'data': [],
'color': wx.Color(255, 0, 0)
}
self.mpl_disconnect(self.toolbar._idPress)
self.mpl_disconnect(self.toolbar._idRelease)
self.mpl_disconnect(self.toolbar._idDrag)
# on capte le clic gauche de la souris
self.m3 = self.mpl_connect('button_press_event', self.mouseParticles)
self.stop = False
#self.createParticles()
#wx.EVT_LEAVE_WINDOW(self,self.finParticules) # arrete particules qd on sort de visu
def mouseParticles(self, evt):
#test pour savoir si le curseur est bien dans les axes de la figure
if self.stop: return
if evt.inaxes is None: return
if evt.button == 1:
[xp, yp, tp] = self.core.addin.calcParticle(evt.xdata, evt.ydata)
#print xp,yp,tp
self.updateParticles(xp, yp, tp)
elif evt.button == 3:
self.mpl_disconnect(self.m3)
self.stop = True
self.gui.actions('zoneEnd')
def updateParticles(self, X, Y, T, freq=10):
""" rajouter une ligne dans le groupe de particules"""
ligne, = pl.plot(pl.array(X), pl.array(Y), 'r')
if freq > 0:
tx, ty, tt = X[0::freq], Y[0::freq], T[0::freq]
txt = []
for i in range(len(tx)):
a = str(tt[i])
b = a.split('.')
ln = max(4, len(b[0]))
txt.append(pl.text(tx[i], ty[i], a[:ln], fontsize='8'))
self.Particles['line'].append(ligne)
self.Particles['txt'].append(txt)
self.Particles['data'].append((X, Y, T))
self.gui_repaint() # bug matplotlib v2.6 for direct draw!!!
self.draw()
def drawParticles(self, bool, value=None):
if self.Particles == None: return
self.partVisible(bool)
self.gui_repaint()
self.draw()
def changeParticles(self, value=None, color=wx.Color(255, 0, 0)):
self.partVisible(False)
self.Particles['color'], self.Particles['txt'] = color, []
for i, data in enumerate(self.Particles['data']):
X, Y, T = data
tx, ty, tt = self.ptsPartic(X, Y, T, float(value))
txt = []
for i in range(len(tx)):
a = str(tt[i])
b = a.split('.')
ln = max(4, len(b[0]))
txt.append(pl.text(tx[i], ty[i], a[:ln], fontsize='8'))
self.Particles['txt'].append(txt)
self.partVisible(True)
self.gui_repaint()
self.draw()
def partVisible(self, bool):
a = self.Particles['color'].Get()
color = (a[0] / 255, a[1] / 255, a[2] / 255)
for line in self.Particles['line']:
line.set_visible(bool)
line.set_color(color)
for points in self.Particles['txt']:
for txt in points:
txt.set_visible(bool)
def ptsPartic(self, X, Y, T, dt):
#tx,ty,tt,i1=iphtC1.ptsLigne(X,Y,T,dt);
tmin = amin(T)
tmax = amax(T)
t1 = linspace(tmin, tmax, int((tmax - tmin) / dt))
f = interp1d(T, X)
xn = f(t1)
f = interp1d(T, Y)
yn = f(t1)
return xn, yn, t1
#####################################################################
# Gestion des zones de la visu
#####################################################################
# affichage de toutes les zones d'une variable
def showVar(self, var, media):
self.setUnvisibleZones()
self.curVar, self.curMedia = var, media
for i in range(len(self.listeZone[var])):
#print 'vis showvar',self.listeZmedia[var][i]
if (media in self.listeZmedia[var][i]) or (media == -1):
self.listeZone[var][i].set_visible(True)
self.visibleText(self.listeZoneText[var][i], True)
#self.changeTitre(var)
self.redraw()
def showData(self, liForage, liData):
self.setUnvisibleZones()
self.curVar = 'data'
self.listeZoneText['data'] = []
for zone in self.listeZone['Forages']:
zone.set_visible(True)
lZone = self.model.Aquifere.getZoneList('Forages')
txt = []
for z in lZone:
x, y = zip(*z.getXy())
name = z.getNom()
if name in liForage:
ind = liForage.index(name)
txt.append(
pl.text(mean(x), mean(y), name + '\n' + str(liData[ind])))
obj = GraphicObject('zoneText', txt, True, None)
self.addGraphicObject(obj)
self.redraw()
def changeData(self, taille, col):
obj = self.listeZoneText['data'][0].getObject()
for txt in obj:
txt.set_size(taille)
txt.set_color(col)
def getcurZone(self):
return self.curZone
def setcurZone(self, zone):
self.curZone = zone
# methode qui efface toutes les zones de toutes les variables
def setUnvisibleZones(self):
for v in self.listeZone:
for zone in self.listeZone[v]:
zone.set_visible(False)
for txt in self.listeZoneText[v]:
if type(txt) == type([5, 6]):
for t in txt:
t.set_visible(False)
else:
txt.set_visible(False)
# methode appelee par la GUI lorsqu'on veut creer une nouvelle zone
def setZoneReady(self, typeZone, curVar):
self.typeZone = typeZone
self.curVar = curVar
self.tempZoneVal = []
# on deconnecte la toolbar pour activer la formaiton de zones
self.mpl_disconnect(self.toolbar._idPress)
self.mpl_disconnect(self.toolbar._idRelease)
self.mpl_disconnect(self.toolbar._idDrag)
# on capte le clic gauche de la souris
self.m1 = self.mpl_connect('button_press_event', self.mouse_clic)
def setZoneEnd(self, evt):
# on informe la GUI qui informera le model
xv, yv = self.getcurZone().get_xdata(), self.getcurZone().get_ydata()
if len(self.tempZoneVal) > 1: xy = zip(xv, yv, self.tempZoneVal)
else: xy = zip(xv, yv)
# effacer zone pour si cancel, remettre de l'ordre
self.curZone.set_visible(False)
self.curZone = None
self.x1, self.y1 = [], []
self.gui.addBox.onZoneCreate(self.typeZone, xy)
def addZone(self, media, name, val, coords, visible=True):
""" ajout de la zone et du texte (name+value) sur visu
"""
#print 'visu',coords
a = zip(*coords)
txt = []
#print name,a
if len(a) == 0: return
if len(a) == 2: x, y = a
elif len(a) == 3: x, y, z = a
if len(x) == 1:
zone = Line2D(x, y, marker='+', markersize=10, markeredgecolor='r')
else:
zone = Line2D(x, y)
zone.verts = coords
zone.set_visible(visible)
if type(media) != type([2]): media = [int(media)]
self.curMedia = media
self.cnv.add_line(zone)
if self.typeZone == "POLYV" or len(coords[0]) == 3:
txt = [
pl.text(
mean(x) * .1 + x[0] * .9,
mean(y) * .1 + y[0] * .9, name + '\n' + str(val)[:16])
]
for i in range(len(x)):
t = pl.text(x[i], y[i], str(z[i]))
t.set_visible(visible)
txt.append(t)
else:
txt = pl.text(
mean(x) * .1 + x[0] * .9,
mean(y) * .1 + y[0] * .9, name + '\n' + str(val)[:16])
self.listeZone[self.curVar].append(zone)
self.listeZmedia[self.curVar].append(media)
self.listeZoneText[self.curVar].append(txt)
if visible: self.redraw()
def delZone(self, Variable, ind):
"""methode de suppression de la zone d'indice ind de Variable
"""
if self.listeZone.has_key(Variable) == False: return
if len(self.listeZone[Variable]) > ind:
self.listeZone[Variable][ind].set_visible(False)
self.visibleText(self.listeZoneText[Variable][ind], False)
self.listeZone[Variable][ind:ind + 1] = []
self.listeZoneText[Variable][ind:ind + 1] = []
self.listeZmedia[Variable].pop(ind)
self.redraw()
def visibleText(self, text, bool):
if type(text) == type([5, 6]):
for t in text:
t.set_visible(bool)
else:
text.set_visible(bool)
def delAllZones(self, Variable):
lz = self.listeZone[Variable]
for i in range(len(lz)):
lz[i].setVisible(False)
self.listeZoneText[Variable][i].set_visible(False)
self.listeZone[Variable] = []
self.listeZmedia[Variable] = []
self.listeZoneText[Variable] = []
self.redraw()
def modifValZone(self, nameVar, ind, val, xy):
"""modify the value (or list of value) for the zone nameVar
the text contains name et value"""
def modifZoneAttr(self, nameVar, ind, val, media, xy):
# modify xy
zone = self.listeZone[nameVar][ind]
if len(xy[0]) == 3: x, y, z = zip(*xy)
else: x, y = zip(*xy)
zone.set_data(x, y)
# modify media
if type(media) != type([2]): media = [int(media)]
self.listeZmedia[nameVar][ind] = media
# modify text
textObj = self.listeZoneText[nameVar][ind]
if type(textObj) == type([2, 3]):
name = pl.getp(textObj[0], 'text').split('\n')[0]
pl.setp(textObj[0], text=name + '\n' + str(val)[:16])
for i in range(len(z)):
pl.setp(textObj[i + 1], text=str(z[i]))
else:
name = pl.getp(textObj, 'text').split('\n')[0]
pl.setp(textObj, text=name + '\n' + str(val)[:16])
self.redraw()
def modifZone(self, nameVar, ind):
""" modification interactive des points de la zone d'indice ind de name nameVar
"""
zone = self.listeZone[nameVar][ind]
self.polyInteract = PolygonInteractor(self, zone, nameVar, ind)
zone.set_visible(False)
self.cnv.add_line(self.polyInteract.line)
self.draw()
def finModifZone(self):
"""fonction qui met fin a la modification de la zone courante"""
if self.polyInteract != None:
self.polyInteract.set_visible(False)
self.polyInteract.disable()
# on informe la GUI des nouvelles coordonnees
var, ind = self.polyInteract.typeVariable, self.polyInteract.ind
x, y = self.polyInteract.lx, self.polyInteract.ly
#print x,y
xy = zip(x, y)
self.gui.modifBox.onModifZoneCoord(var, ind, xy)
zone = self.listeZone[var][ind]
zone.set_data(x, y)
zone.set_visible(True)
# on modifie la position du texte
txt = self.listeZoneText[var][ind]
if type(txt) == type([5, 6]):
txt[0].set_position((x[0], y[0]))
for i in range(1, len(txt)):
txt[i].set_position((x[i - 1], y[i - 1]))
else:
txt.set_position(
(mean(x) * .1 + x[0] * .9, mean(y) * .1 + y[0] * .9))
self.draw()
def setAllZones(self, dicZone):
"""updates all zones when a file is imported
"""
for var in dicZone.keys():
self.listeZone[var] = []
self.curVar = var
lz = dicZone[var]
nbz = len(lz['name'])
for i in range(nbz):
if lz['name'][i] == '': continue
coords = lz['coords'][i]
self.addZone(lz['media'][i], lz['name'][i], lz['value'][i],
coords)
self.setUnvisibleZones()
#self.redraw()
#####################################################################
# Gestion de l'interaction de la souris
# pour la creation des zones
#####################################################################
#methode executee lors d'un clic de souris dans le canvas
def mouse_clic(self, evt):
if evt.inaxes is None:
return
if self.curZone == None: # au depart
self.x1 = [float(str(evt.xdata)[:6])
] # pour aovir chiffre pas trop long
self.y1 = [float(str(evt.ydata)[:6])]
self.setcurZone(Line2D(self.x1, self.y1))
self.cnv.add_line(self.curZone)
self.m2 = self.mpl_connect('motion_notify_event',
self.mouse_motion)
if self.typeZone == "POLYV":
self.polyVdialog()
if self.typeZone == "POINT":
self.deconnecte()
self.setZoneEnd(evt)
else: # points suivants
if self.typeZone == "POLYV": # and evt.button ==1:
if evt.button == 3: self.deconnecte()
rep = self.polyVdialog() # dialog for the current value of z
if rep == False: return
self.x1.append(float(str(evt.xdata)[:6]))
self.y1.append(float(str(evt.ydata)[:6]))
if self.typeZone == "LINE" or self.typeZone == "RECT":
self.deconnecte() #fin des le 2eme point
self.setZoneEnd(evt)
if self.typeZone in ["POLY", "POLYV"
] and evt.button == 3: # fin du polygone
self.deconnecte()
self.setZoneEnd(evt)
#methode executee lors du deplacement de la souris dans le canvas suite a un mouse_clic
def mouse_motion(self, evt):
time.sleep(0.1)
if evt.inaxes is None: return
lx, ly = self.x1 * 1, self.y1 * 1
if self.typeZone == "RECT":
xr, yr = self.creeRectangle(self.x1[0], self.y1[0], evt.xdata,
evt.ydata)
self.curZone.set_data(xr, yr)
else: # autres cas
lx.append(evt.xdata)
ly.append(evt.ydata)
self.curZone.set_data(lx, ly)
self.draw()
def polyVdialog(self):
lst0 = [('Value', 'Text', 0)]
dialg = config.dialogs.genericDialog(self.gui, 'value', lst0)
values = dialg.getValues()
if values != None:
val = float(values[0])
#print val*2
self.tempZoneVal.append(val)
return True
else:
return False
def creeRectangle(self, x1, y1, x2, y2):
xr = [x1, x2, x2, x1, x1]
yr = [y1, y1, y2, y2, y1]
return [xr, yr]
def deconnecte(self):
# deconnecter la souris
self.mpl_disconnect(self.m1)
self.mpl_disconnect(self.m2)
###################################################################
# deplacer une zone ##############################
def startMoveZone(self, nameVar, ind):
""" methode qui demarre les interactions avec la souris"""
# reperer la zone et rajouter un point de couleur
self.nameVar, self.ind = nameVar, ind
zone = self.listeZone[nameVar][ind]
self.curZone = zone
self.lx, self.ly = zone.get_xdata(), zone.get_ydata()
self.xstart = self.lx[0] * 1.
self.ystart = self.ly[0] * 1.
self.ptstart = Line2D([self.xstart], [self.ystart],
marker='o',
markersize=7,
markerfacecolor='r')
self.cnv.add_line(self.ptstart)
self.m1 = self.mpl_connect('button_press_event', self.zoneM_clic)
self.draw()
def zoneM_clic(self, evt):
""" action au premier clic"""
if evt.inaxes is None: return
#if evt.button==3: self.finMoveZone(evt) # removed OA 6/2/13
d = sqrt((evt.xdata - self.xstart)**2 + (evt.ydata - self.ystart)**2)
xmn, xmx = self.xlim
ymn, ymx = self.ylim
dmax = sqrt((xmx - xmn)**2 + (ymx - ymn)**2) / 100
if d > dmax: return
self.m2 = self.mpl_connect('motion_notify_event', self.zone_motion)
self.m3 = self.mpl_connect('button_release_event', self.finMoveZone)
self.mpl_disconnect(self.m1)
def zone_motion(self, evt):
""" methode pour deplacer la zone quand on deplace la souris"""
# reperer le curseur proche du point de couleur
time.sleep(0.1)
if evt.inaxes is None: return
# changer els coord du polygone lorsque l'on deplace la souris
lx = [a + evt.xdata - self.xstart for a in self.lx]
ly = [a + evt.ydata - self.ystart for a in self.ly]
self.ptstart.set_data(lx[0], ly[0])
self.curZone.set_data(lx, ly)
self.draw()
def finMoveZone(self, evt):
""" methode pour arret de deplacement de la zone"""
# lorsque l'on relache la souris arreter les mpl connect
self.mpl_disconnect(self.m2)
self.mpl_disconnect(self.m3)
# renvoyer les nouvelels coordonnes au modele
lx, ly = self.curZone.get_xdata(), self.curZone.get_ydata()
self.listeZone[self.nameVar][self.ind].set_data(lx, ly)
xy = zip(lx, ly)
self.gui.modifBox.onModifZoneCoord(self.nameVar, self.ind, xy)
# on modifie la position du texte
txt = self.listeZoneText[self.nameVar][self.ind]
if type(txt) == type([5, 6]):
txt[0].set_position((lx[0], ly[0]))
for i in range(1, len(txt)):
txt[i].set_position(
(lx[i - 1],
ly[i - 1])) #-1 because 1st position zone names
else:
txt.set_position(
(mean(lx) * .1 + lx[0] * .9, mean(ly) * .1 + ly[0] * .9))
self.ptstart.set_visible(False)
self.ptstart = None
self.curZone = None
self.draw()
def add_phylorate(treeplot, rates, nodeidx, vis=True):
"""
Add phylorate plot generated from data analyzed with BAMM
(http://bamm-project.org/introduction.html)
Args:
rates (array): Array of rates along branches
created by r_funcs.phylorate
nodeidx (array): Array of node indices matching rates (also created
by r_funcs.phylorate)
WARNING:
Ladderizing the tree can cause incorrect assignment of Ape node index
numbers. To prevent this, call this function or root.ape_node_idx()
before ladderizing the tree to assign correct Ape node index numbers.
"""
if not treeplot.root.apeidx:
treeplot.root.ape_node_idx()
segments = []
values = []
if treeplot.plottype == "radial":
radpatches = [] # For use in drawing arcs for radial plots
for n in treeplot.root.descendants():
n.rates = rates[nodeidx==n.apeidx]
c = treeplot.n2c[n]
pc = treeplot._path_to_parent(n)[0][1]
xd = c.x - pc[0]
yd = c.y - pc[1]
xseg = xd/len(n.rates)
yseg = yd/len(n.rates)
for i, rate in enumerate(n.rates):
x0 = pc[0] + i*xseg
y0 = pc[1] + i*yseg
x1 = x0 + xseg
y1 = y0 + yseg
segments.append(((x0, y0), (x1, y1)))
values.append(rate)
curverts = treeplot._path_to_parent(n)[0][2:]
curcodes = treeplot._path_to_parent(n)[1][2:]
curcol = RdYlBu(n.rates[0])
radpatches.append(PathPatch(
Path(curverts, curcodes), lw=2, edgecolor = curcol,
fill=False))
else:
for n in treeplot.root.descendants():
n.rates = rates[nodeidx==n.apeidx]
c = treeplot.n2c[n]
pc = treeplot.n2c[n.parent]
seglen = (c.x-pc.x)/len(n.rates)
for i, rate in enumerate(n.rates):
x0 = pc.x + i*seglen
x1 = x0 + seglen
segments.append(((x0, c.y), (x1, c.y)))
values.append(rate)
segments.append(((pc.x, pc.y), (pc.x, c.y)))
values.append(n.rates[0])
lc = LineCollection(segments, cmap=RdYlBu, lw=2)
lc.set_array(np.array(values))
treeplot.add_collection(lc)
lc.set_zorder(1)
if treeplot.plottype == "radial":
arccol = matplotlib.collections.PatchCollection(radpatches,
match_original=True)
treeplot.add_collection(arccol)
arccol.set_visible(vis)
arccol.set_zorder(1)
lc.set_visible(vis)
colorbar_legend(treeplot, values, RdYlBu, vis=vis)
treeplot.figure.canvas.draw_idle()
