class Tracks:
def __init__(self, ax, stormcells, tails=None):
self.tracks = None
self.tails = tails
self.update_trackmap(ax, stormcells)
def update_trackmap(self, ax, stormcells):
if self.tracks is not None:
self.tracks.remove()
self.tracks = None
if self.tracks is None:
self.tracks = LineCollection([])
ax.add_collection(self.tracks)
self.trackmap = []
for trackid in range(np.max(stormcells['track_id']) + 1):
indexes = np.where(stormcells['track_id'] == trackid)[0]
# Makes sure the track segments are in chronological order
indexes = indexes[np.argsort(stormcells['frame_index'][indexes])]
self.trackmap.append(indexes)
def update_frame(self, frame_index, stormcells):
segments = []
for trackid, indexes in enumerate(self.trackmap):
trackdata = stormcells[indexes]
trackdata = trackdata[trackdata['frame_index'] <= frame_index]
if self.tails:
mask = trackdata['frame_index'] > (frame_index - self.tails)
trackdata = trackdata[mask]
segments.append(
zip(trackdata['xcent'], trackdata['ycent'])
or [(np.nan, np.nan)])
self.tracks.set_segments(segments)
class Tracks:
def __init__(self, ax, stormcells):
self.tracks = None
self.update_trackmap(ax, stormcells)
def update_trackmap(self, ax, stormcells):
if self.tracks is not None:
self.tracks.remove()
self.tracks = None
if self.tracks is None:
self.tracks = LineCollection([])
ax.add_collection(self.tracks)
self.trackmap = []
for trackid in range(np.max(stormcells['track_id']) + 1):
indexes = np.where(stormcells['track_id'] == trackid)[0]
# Makes sure the track segments are in chronological order
indexes = indexes[np.argsort(stormcells['frame_index'][indexes])]
self.trackmap.append(indexes)
def update_frame(self, frame_index, stormcells):
segments = []
for trackid, indexes in enumerate(self.trackmap):
trackdata = stormcells[indexes]
trackdata = trackdata[trackdata['frame_index'] <= frame_index]
segments.append(zip(trackdata['xcent'], trackdata['ycent'])
or [(np.nan, np.nan)])
self.tracks.set_segments(segments)
class TrailingLine:
'''
This class plots a line that starts out with zero thickness and linearly
increases to thickness max_width along its path.
'''
def __init__(self, x, y, ax, max_width, **kwargs):
self.ax = ax
self.max_width = max_width
lw = self._compute_linewidths(len(x))
self.lc = LineCollection(self._compute_segments(x, y),
linewidths=lw,
**kwargs)
ax.add_collection(self.lc)
def set_data(self, x, y):
self.lc.set_segments(self._compute_segments(x, y))
lw = self._compute_linewidths(len(x))
self.lc.set_linewidth(lw)
@classmethod
def _compute_segments(cls, x, y):
points = np.array([x, y]).T.reshape(-1, 1, 2)
segments = np.concatenate([points[:-1], points[1:]], axis=1)
return segments
def _compute_linewidths(self, npts):
return np.linspace(0, self.max_width, npts)[:-1]
class BatchLineCollection(object):
def __init__(self, ax):
self._ax = ax
self._lc = None
@property
def artists(self):
return [self._lc]
def draw(self, x, y, **kwargs):
segments = []
for x_i, y_i in zip(x, y):
xy_i = np.stack([x_i, y_i], axis=1)
xy_i = xy_i.reshape(-1, 1, 2)
segments_i = np.hstack([xy_i[:-1], xy_i[1:]])
segments.append(segments_i)
segments = np.concatenate(segments, axis=0)
if self._lc is None:
self._lc = PltLineCollection(segments)
self._ax.add_collection(self._lc)
else:
self._lc.set_segments(segments)
if 'color' in kwargs:
self._lc.set_color(np.reshape(kwargs['color'],
[len(segments), -1]))
if 'linewidth' in kwargs:
self._lc.set_linewidth(kwargs['linewidth'])
self._lc.set_joinstyle('round')
self._lc.set_capstyle('round')
class ArrowedLineCollection(LineCollection):
def __init__(self, *kl, **kw):
'''The same arguments as in matplotlib.collections.LineCollection.
To initiate arrows, additionally use 'add_arrows'.
'''
LineCollection.__init__(self, *kl, **kw)
self.kw = kw # to be reused in add_arrows
self.draw_arrows = True
return
def add_arrows(self, arrow_offsets=10, arrow_length=10, arrow_width=5):
'''Draw arrows at the end of every edge.
Parameters
----------
arrow_offsets: a list of length equal to the number of edges. It stores offstets (in pixels) by which arrows
should be moved back to make space for a node. A single value (the same for all) is also accepted.
arrow_length: the length of the arrow head, in pixels?
arrow_width: the width of the arrow head, in pixels?
'''
self.draw_arrows=True
self.arrows = LineCollection([], **self.kw)
self.arrow_length=arrow_length
self.arrow_width=arrow_width
self.arrow_offsets = []
if type(arrow_offsets)==list:
if len(arrow_offsets) != len(self.get_paths()): raise ValueError('arrow_offsets does not match the number of edges.')
self.arrow_offsets = arrow_offsets
else:
self.arrow_offsets = [arrow_offsets]*len(self.get_paths())
return
def draw(self, renderer):
''' Overrides the matplotlib.collections.LineCollection.draw(). Adds arrows.
'''
LineCollection.draw(self, renderer)
if not self.draw_arrows: return
segments=[]
for i,path in enumerate(self.get_paths()):
L= [self.get_transform().transform(numpy.transpose(j[0])) for j in path.iter_segments()]
V=L[1]-L[0]
scale = min(1.0, vector_length(V)/(4*self.arrow_offsets[i])) #make the arrows smaller if their size is comparable with edge length
node_shift = scale * self.arrow_offsets[i] * norm_vector(V)
head_length_vector = scale * self.arrow_length * norm_vector(V)
head_width_vector = scale * self.arrow_width * perpendicular_vector(norm_vector(V))
segments.append((L[1]-head_length_vector+head_width_vector-node_shift, L[1]-node_shift ,L[1]-head_length_vector-head_width_vector-node_shift))
self.arrows.set_segments(segments)
self.arrows.draw(renderer)
return
def do_3d_projection(self, renderer):
'''
Project the points according to renderer matrix.
'''
xyslist = [
proj3d.proj_trans_points(points, renderer.M) for points in
self._segments3d]
segments_2d = [zip(xs, ys) for (xs, ys, zs) in xyslist]
LineCollection.set_segments(self, segments_2d)
minz = 1e9
for (xs, ys, zs) in xyslist:
minz = min(minz, min(zs))
return minz
def do_3d_projection(self, renderer):
'''
Project the points according to renderer matrix.
'''
xyslist = [
proj3d.proj_trans_points(points, renderer.M) for points in
self._segments3d]
segments_2d = [zip(xs, ys) for (xs, ys, zs) in xyslist]
LineCollection.set_segments(self, segments_2d)
minz = 1e9
for (xs, ys, zs) in xyslist:
minz = min(minz, min(zs))
return minz
def do_3d_projection(self, renderer=None):
"""
Project the points according to renderer matrix.
"""
xyslist = [proj3d.proj_trans_points(points, self.axes.M)
for points in self._segments3d]
segments_2d = [np.column_stack([xs, ys]) for xs, ys, zs in xyslist]
LineCollection.set_segments(self, segments_2d)
# FIXME
minz = 1e9
for xs, ys, zs in xyslist:
minz = min(minz, min(zs))
return minz
def do_3d_projection(self, renderer):
"""
Project the points according to renderer matrix.
"""
xyslist = [
proj3d.proj_trans_points(points, renderer.M) for points in
self._segments3d]
segments_2d = [np.column_stack([xs, ys]) for xs, ys, zs in xyslist]
LineCollection.set_segments(self, segments_2d)
# FIXME
minz = 1e9
for xs, ys, zs in xyslist:
minz = min(minz, min(zs))
return minz
class MyCell(matplotlib.table.CustomCell):
""" Extending matplotlib tables.
Adapted from https://stackoverflow.com/a/53573651/505698
"""
def __init__(self, *args, visible_edges, **kwargs):
super().__init__(*args, visible_edges=visible_edges, **kwargs)
seg = np.array([[0.0, 0.0], [1.0, 0.0], [1.0, 1.0], [0.0, 1.0],
[0.0, 0.0]]).reshape(-1, 1, 2)
segments = np.concatenate([seg[:-1], seg[1:]], axis=1)
self.edgelines = LineCollection(segments,
edgecolor=kwargs.get("edgecolor"))
self._text.set_zorder(2)
self.set_zorder(1)
def set_transform(self, trans):
self.edgelines.set_transform(trans)
super().set_transform(trans)
def draw(self, renderer):
c = self.get_edgecolor()
self.set_edgecolor((1, 1, 1, 0))
super().draw(renderer)
self.update_segments(c)
self.edgelines.draw(renderer)
self.set_edgecolor(c)
def update_segments(self, color):
x, y = self.get_xy()
w, h = self.get_width(), self.get_height()
seg = np.array([[x, y], [x + w, y], [x + w, y + h], [x, y + h],
[x, y]]).reshape(-1, 1, 2)
segments = np.concatenate([seg[:-1], seg[1:]], axis=1)
self.edgelines.set_segments(segments)
self.edgelines.set_linewidth(self.get_linewidth())
colors = [
color if edge in self._visible_edges else (1, 1, 1, 0)
for edge in self._edges
]
self.edgelines.set_edgecolor(colors)
def get_path(self):
codes = [Path.MOVETO] + [Path.LINETO] * 3 + [Path.CLOSEPOLY]
return Path(
[[0.0, 0.0], [1.0, 0.0], [1.0, 1.0], [0.0, 1.0], [0.0, 0.0]],
codes,
readonly=True,
)
class Tracks(object):
def __init__(self, ax, tails=None):
self.tracks = None
self.tails = tails
self.initialize_lines(ax)
@staticmethod
def create_trackmap(stormdata):
trackmap = []
for trackid in range(np.max(stormdata['track_id']) + 1):
indexes = np.where(stormdata['track_id'] == trackid)[0]
# Makes sure the track segments are in chronological order
indexes = indexes[np.argsort(stormdata['frame_index'][indexes])]
trackmap.append(indexes)
return trackmap
def remove_lines(self):
if self.tracks is not None:
self.tracks.remove()
self.tracks = None
def initialize_lines(self, ax):
self.remove_lines()
self.tracks = LineCollection([])
ax.add_collection(self.tracks)
def update_lines(self, frame_index, stormdata):
segments = []
for indexes in self.create_trackmap(stormdata):
trackdata = stormdata[indexes]
trackdata = trackdata[trackdata['frame_index'] <= frame_index]
if self.tails:
mask = trackdata['frame_index'] >= (frame_index - self.tails)
trackdata = trackdata[mask]
# There must always be something in a track, even it it is NaNs.
segments.append(
zip(trackdata['xcent'], trackdata['ycent'])
or [(np.nan, np.nan)])
self.tracks.set_segments(segments)
def lolite_line(self, indx):
self.hilite_line(indx, 1)
def hilite_line(self, indx, lw=4):
if indx is not None:
lws = self.tracks.get_linewidths()
lws[indx] = lw
self.tracks.set_linewidths(lws)
def do_3d_projection(self, renderer=None):
"""
Project the points according to renderer matrix.
"""
# see _update_scalarmappable docstring for why this must be here
_update_scalarmappable(self)
xyslist = [proj3d.proj_trans_points(points, self.axes.M)
for points in self._segments3d]
segments_2d = [np.column_stack([xs, ys]) for xs, ys, zs in xyslist]
LineCollection.set_segments(self, segments_2d)
# FIXME
minz = 1e9
for xs, ys, zs in xyslist:
minz = min(minz, min(zs))
return minz
class Tracks(object):
def __init__(self, ax, tails=None):
self.tracks = None
self.tails = tails
self.initialize_lines(ax)
@staticmethod
def create_trackmap(stormdata):
trackmap = []
for trackid in range(np.max(stormdata['track_id']) + 1):
indexes = np.where(stormdata['track_id'] == trackid)[0]
# Makes sure the track segments are in chronological order
indexes = indexes[np.argsort(stormdata['frame_index'][indexes])]
trackmap.append(indexes)
return trackmap
def remove_lines(self):
if self.tracks is not None:
self.tracks.remove()
self.tracks = None
def initialize_lines(self, ax):
self.remove_lines()
self.tracks = LineCollection([])
ax.add_collection(self.tracks)
def update_lines(self, frame_index, stormdata):
segments = []
for indexes in self.create_trackmap(stormdata):
trackdata = stormdata[indexes]
trackdata = trackdata[trackdata['frame_index'] <= frame_index]
if self.tails:
mask = trackdata['frame_index'] >= (frame_index - self.tails)
trackdata = trackdata[mask]
# There must always be something in a track, even it it is NaNs.
segments.append(zip(trackdata['xcent'], trackdata['ycent'])
or [(np.nan, np.nan)])
self.tracks.set_segments(segments)
def lolite_line(self, indx):
self.hilite_line(indx, 1)
def hilite_line(self, indx, lw=4):
if indx is not None:
lws = self.tracks.get_linewidths()
lws[indx] = lw
self.tracks.set_linewidths(lws)
class LineCollection(object):
def __init__(self, ax):
self._ax = ax
self._lc = None
@property
def artists(self):
return [self._lc]
def draw(self, x, y, **kwargs):
xy = np.stack([x, y], axis=1)
xy = xy.reshape(-1, 1, 2)
segments = np.hstack([xy[:-1], xy[1:]])
if self._lc is None:
self._lc = PltLineCollection(segments)
self._ax.add_collection(self._lc)
else:
self._lc.set_segments(segments)
if 'color' in kwargs:
self._lc.set_color(kwargs['color'])
class ScatterPlot(object):
def __init__(self, feeder, marker = 'o'):
self.marker = marker
self.feeder = feeder
self.stream = iter(self.feeder)
def get_frames_len(self):
return len(self.feeder.time_intervals) - 1
def get_frame(self):
return self.feeder.frame
def get_limits(self):
return self.feeder.get_limits()
def setup_plot(self):
x, y, c = next(self.stream)
ax = plt.gca()
self.scat = ax.scatter(x, y, c = c, marker = self.marker, s = 25)
return self.scat
def setup_plot_edges(self):
lines = self.feeder.get_current_edges()
ax = plt.gca()
self.lines = LineCollection(lines, linewidths=0.1)
ax.add_collection(self.lines)
def update_edges(self):
lines = self.feeder.get_current_edges()
self.lines.set_segments(lines)
def prev_state(self):
self.feeder.prev()
self.stream = iter(self.feeder)
def update_plot(self):
x, y, _ = next(self.stream)
new_data = np.array(zip(x, y))
self.scat.set_offsets(new_data)
return self.scat
class SURFDemo(ImageProcessDemo):
TITLE = "SURF Demo"
DEFAULT_IMAGE = "lena.jpg"
SETTINGS = ["m_perspective", "hessian_threshold", "n_octaves"]
m_perspective = Array(np.float, (3, 3))
m_perspective2 = Array(np.float, (3, 3))
hessian_threshold = Int(2000)
n_octaves = Int(2)
poly = Instance(PolygonWidget)
def control_panel(self):
return VGroup(
Item("m_perspective",
label="变换矩阵",
editor=ArrayEditor(format_str="%g")),
Item("m_perspective2",
label="变换矩阵",
editor=ArrayEditor(format_str="%g")),
Item("hessian_threshold", label="hessianThreshold"),
Item("n_octaves", label="nOctaves"))
def __init__(self, **kwargs):
super(SURFDemo, self).__init__(**kwargs)
self.poly = None
self.init_points = None
self.lines = LineCollection([], linewidths=1, alpha=0.6, color="red")
self.axe.add_collection(self.lines)
self.connect_dirty("poly.changed,hessian_threshold,n_octaves")
def init_poly(self):
if self.poly is None:
return
h, w, _ = self.img_color.shape
self.init_points = np.array([(w, 0), (2 * w, 0), (2 * w, h), (w, h)],
np.float32)
self.poly.set_points(self.init_points)
self.poly.update()
def init_draw(self):
style = {"marker": "o"}
self.poly = PolygonWidget(axe=self.axe,
points=np.zeros((3, 2)),
style=style)
self.init_poly()
@on_trait_change("hessian_threshold, n_octaves")
def calc_surf1(self):
self.surf = cv2.SURF(self.hessian_threshold, self.n_octaves)
self.key_points1, self.features1 = self.surf.detectAndCompute(
self.img_gray, None)
self.key_positions1 = np.array([kp.pt for kp in self.key_points1])
def _img_changed(self):
self.img_gray = cv2.cvtColor(self.img, cv2.COLOR_BGR2GRAY)
self.img_color = cv2.cvtColor(self.img_gray, cv2.COLOR_GRAY2RGB)
self.img_show = np.concatenate([self.img_color, self.img_color],
axis=1)
self.size = self.img_color.shape[1], self.img_color.shape[0]
self.calc_surf1()
FLANN_INDEX_KDTREE = 1
index_params = dict(algorithm=FLANN_INDEX_KDTREE, trees=5)
search_params = dict(checks=100)
self.matcher = cv2.FlannBasedMatcher(index_params, search_params)
self.init_poly()
def settings_loaded(self):
src = self.init_points.copy()
w, h = self.size
src[:, 0] -= w
dst = cv2.perspectiveTransform(src[None, :, :], self.m_perspective)
dst = dst.squeeze()
dst[:, 0] += w
self.poly.set_points(dst)
self.poly.update()
def draw(self):
if self.poly is None:
return
w, h = self.size
src = self.init_points.copy()
dst = self.poly.points.copy().astype(np.float32)
src[:, 0] -= w
dst[:, 0] -= w
m = cv2.getPerspectiveTransform(src, dst)
self.m_perspective = m
img2 = cv2.warpPerspective(self.img_gray,
m,
self.size,
borderValue=[255] * 4)
self.img_show[:, w:, :] = img2[:, :, None]
key_points2, features2 = self.surf.detectAndCompute(img2, None)
key_positions2 = np.array([kp.pt for kp in key_points2])
match_list = self.matcher.knnMatch(self.features1, features2, k=1)
index1 = np.array([m[0].queryIdx for m in match_list])
index2 = np.array([m[0].trainIdx for m in match_list])
distances = np.array([m[0].distance for m in match_list])
n = min(50, len(distances))
best_index = np.argsort(distances)[:n]
matched_positions1 = self.key_positions1[index1[best_index]]
matched_positions2 = key_positions2[index2[best_index]]
self.m_perspective2, mask = cv2.findHomography(matched_positions1,
matched_positions2,
cv2.RANSAC)
lines = np.concatenate([matched_positions1, matched_positions2],
axis=1)
lines[:, 2] += w
line_colors = COLORS[mask.ravel()]
self.lines.set_segments(lines.reshape(-1, 2, 2))
self.lines.set_color(line_colors)
self.draw_image(self.img_show)
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()
class SpikeBrowserUI(object):
def __init__(self, window):
self.window = window
self.sp_win = [-0.8, 1]
self.spike_collection = None
self.fig = Figure((5, 4), 75)
self.canvas = window.get_canvas(self.fig)
self._mpl_init()
self.canvas.mpl_connect('key_press_event', self._on_key)
self.window.set_scroll_handler(self.OnScrollEvt)
def _mpl_init(self):
self.fig.clf()
self.axes = self.fig.add_axes([0.05, 0.1, 0.95,0.9])
self.ax_prev = self.fig.add_axes([0.8, 0.0, 0.1,0.05])
self.ax_next = self.fig.add_axes([0.9, 0.0, 0.1,0.05])
self.b_next = Button(self.ax_next, 'Next')
self.b_prev = Button(self.ax_prev, "Prev")
self.b_next.on_clicked(self._next_spike)
self.b_prev.on_clicked(self._prev_spike)
self.i_spike = 0
self.i_start = 0
self.line_collection = None
def _next_spike(self, event):
try:
if self.i_spike<len(self.spt)-1:
self.i_spike+=1
t_spk = self.spt[self.i_spike]
i_start = int(np.ceil(t_spk/1000.*self.FS-self.i_window/2.))
i_start = np.maximum(self.i_min, i_start)
i_start = np.minimum(self.i_max, i_start)
self.i_start = i_start
self.i_end = self.i_start + self.i_window
self.window.set_scroll_pos(self.i_start)
self.draw_plot()
except IndexError:
pass
def _prev_spike(self, event):
try:
if self.i_spike>0:
self.i_spike-=1
t_spk = self.spt[self.i_spike]
i_start = int(np.ceil(t_spk/1000.*self.FS-self.i_window/2.))
i_start = np.maximum(self.i_min, i_start)
i_start = np.minimum(self.i_max, i_start)
self.i_start = i_start
self.i_end = self.i_start + self.i_window
self.window.set_scroll_pos(self.i_start)
self.draw_plot()
except IndexError:
pass
def _on_key(self, event):
if event.key=='+' or event.key=='=':
self.ylims/=2.
elif event.key == '-':
self.ylims*=2.
else:
return
offset = self.ylims[1]-self.ylims[0]
self.offsets = np.arange(self.n_chans)*offset
self.draw_plot()
def set_spiketimes(self, spk_idx, labels=None, all_labels=None):
if spk_idx:
self.spt = spk_idx['data']
if labels is not None:
self.labels = labels
if all_labels is None:
self.color_func = label_color(np.unique(labels))
else:
self.color_func = label_color(all_labels)
else:
self.labels = None
self.ax_next.set_visible(True)
self.ax_prev.set_visible(True)
else:
self.spt = None
self.ax_next.set_visible(False)
self.ax_prev.set_visible(False)
def set_data(self, data):
self.x = data['data']
self.FS = data['FS']
n_chans, n_pts = self.x.shape
#reset spike times data/hide buttons
self.set_spiketimes(None)
self.i_window = int(self.winsz/1000.*self.FS)
# Extents of data sequence:
self.i_min = 0
self.i_max = n_pts - self.i_window
self.n_chans = n_chans
self.window.set_scroll_max(self.i_max, self.i_window)
# Indices of data interval to be plotted:
self.i_end = self.i_start + self.i_window
self.time = np.arange(self.i_start,self.i_end)*1./self.FS
self.segs = np.empty((n_chans, self.i_window, 2))
self.segs[:,:,0] = self.time[np.newaxis,:]
self.segs[:,:,1] = self.x[:,self.i_start:self.i_end]
ylims = (self.segs[:,:,1].min(), self.segs[:,:,1].max())
offset = ylims[1]-ylims[0]
self.offsets = np.arange(n_chans)*offset
self.segs[:,:,1] += self.offsets[:,np.newaxis]
self.ylims = np.array(ylims)
if self.line_collection:
self.line_collection.remove()
self.line_collection = LineCollection(self.segs,
offsets=None,
transform=self.axes.transData,
color='k')
self.axes.add_collection(self.line_collection)
self.axes.set_xlim((self.time[0], self.time[-1]))
self.axes.set_ylim((self.ylims[0]+self.offsets.min(),
self.ylims[1]+self.offsets.max()))
self.canvas.draw()
def draw_plot(self):
self.time = np.arange(self.i_start,self.i_end)*1./self.FS
self.segs[:,:,0] = self.time[np.newaxis,:]
self.segs[:,:,1] = self.x[:,self.i_start:self.i_end]+self.offsets[:,np.newaxis]
self.line_collection.set_segments(self.segs)
# Adjust plot limits:
self.axes.set_xlim((self.time[0], self.time[-1]))
self.axes.set_ylim((self.ylims[0]+self.offsets.min(),
self.ylims[1]+self.offsets.max()))
if self.spt is not None:
self.draw_spikes()
# Redraw:
self.canvas.draw()
def draw_spikes(self):
if self.spike_collection is not None:
self.spike_collection.remove()
self.spike_collection = None
sp_win = self.sp_win
time = self.segs[0,:,0]*1000.
t_min, t_max = time[0]-sp_win[0], time[-1]-sp_win[1]
spt = self.spt[(self.spt>t_min) & (self.spt<t_max)]
if len(spt)>0:
n_pts = int((sp_win[1]-sp_win[0])/1000.*self.FS)
sp_segs = np.empty((len(spt), self.n_chans, n_pts, 2))
for i in range(len(spt)):
start, = np.nonzero(time>=(spt[i]+sp_win[0]))
start = start[0]
stop = start+n_pts
sp_segs[i,:,:,0] = (time[np.newaxis,start:stop]/1000.)
sp_segs[i,:,:,1] = self.segs[:, start:stop, 1]
sp_segs = sp_segs.reshape(-1, n_pts, 2)
if self.labels is not None:
labs = self.labels[(self.spt>t_min) & (self.spt<t_max)]
colors = np.repeat(self.color_func(labs), self.n_chans, 0)
else:
colors = 'r'
self.spike_collection = LineCollection(sp_segs,
offsets=None,
color=colors,
transform=self.axes.transData)
self.axes.add_collection(self.spike_collection)
def OnScrollEvt(self, pos):
# Update the indices of the plot:
self.i_start = self.i_min + pos
self.i_end = self.i_min + self.i_window + pos
t_center = (self.i_start+self.i_window/2.)*1000./self.FS
idx, = np.where(self.spt<t_center)
if len(idx)>0:
self.i_spike = idx[-1]
else:
self.i_spike = 0
self.draw_plot()
def set_segments(self, segments):
"""
Set 3D segments.
"""
self._segments3d = segments
LineCollection.set_segments(self, [])
class SkeletonBuilder:
def __init__(self, config_path):
self.config_path = config_path
self.cfg = read_config(config_path)
# Find uncropped labeled data
self.df = None
found = False
root = os.path.join(self.cfg["project_path"], "labeled-data")
for dir_ in os.listdir(root):
folder = os.path.join(root, dir_)
if os.path.isdir(folder) and not any(
folder.endswith(s) for s in ("cropped", "labeled")):
self.df = pd.read_hdf(
os.path.join(folder,
f'CollectedData_{self.cfg["scorer"]}.h5'))
row, col = self.pick_labeled_frame()
if "individuals" in self.df.columns.names:
self.df = self.df.xs(col, axis=1, level="individuals")
self.xy = self.df.loc[row].values.reshape((-1, 2))
missing = np.flatnonzero(np.isnan(self.xy).all(axis=1))
if not missing.size:
found = True
break
if self.df is None:
raise IOError("No labeled data were found.")
self.bpts = self.df.columns.get_level_values("bodyparts").unique()
if not found:
warnings.warn(
f"A fully labeled animal could not be found. "
f"{', '.join(self.bpts[missing])} will need to be manually connected in the config.yaml."
)
self.tree = KDTree(self.xy)
# Handle image previously annotated on a different platform
sep = "/" if "/" in row else "\\"
if sep != os.path.sep:
row = row.replace(sep, os.path.sep)
self.image = io.imread(os.path.join(self.cfg["project_path"], row))
self.inds = set()
self.segs = set()
# Draw the skeleton if already existent
if self.cfg["skeleton"]:
for bone in self.cfg["skeleton"]:
pair = np.flatnonzero(self.bpts.isin(bone))
if len(pair) != 2:
continue
pair_sorted = tuple(sorted(pair))
self.inds.add(pair_sorted)
self.segs.add(tuple(map(tuple, self.xy[pair_sorted, :])))
self.lines = LineCollection(self.segs,
colors=mcolors.to_rgba(
self.cfg["skeleton_color"]))
self.lines.set_picker(True)
self.show()
def pick_labeled_frame(self):
# Find the most 'complete' animal
try:
count = self.df.groupby(level="individuals", axis=1).count()
if "single" in count:
count.drop("single", axis=1, inplace=True)
except KeyError:
count = self.df.count(axis=1).to_frame()
mask = count.where(count == count.values.max())
kept = mask.stack().index.to_list()
np.random.shuffle(kept)
row, col = kept.pop()
return row, col
def show(self):
self.fig = plt.figure()
ax = self.fig.add_subplot(111)
ax.axis("off")
lo = np.nanmin(self.xy, axis=0)
hi = np.nanmax(self.xy, axis=0)
center = (hi + lo) / 2
w, h = hi - lo
ampl = 1.3
w *= ampl
h *= ampl
ax.set_xlim(center[0] - w / 2, center[0] + w / 2)
ax.set_ylim(center[1] - h / 2, center[1] + h / 2)
ax.imshow(self.image)
ax.scatter(*self.xy.T, s=self.cfg["dotsize"]**2)
ax.add_collection(self.lines)
ax.invert_yaxis()
self.lasso = LassoSelector(ax, onselect=self.on_select)
ax_clear = self.fig.add_axes([0.85, 0.55, 0.1, 0.1])
ax_export = self.fig.add_axes([0.85, 0.45, 0.1, 0.1])
self.clear_button = Button(ax_clear, "Clear")
self.clear_button.on_clicked(self.clear)
self.export_button = Button(ax_export, "Export")
self.export_button.on_clicked(self.export)
self.fig.canvas.mpl_connect("pick_event", self.on_pick)
plt.show()
def clear(self, *args):
self.inds.clear()
self.segs.clear()
self.lines.set_segments(self.segs)
def export(self, *args):
inds_flat = set(ind for pair in self.inds for ind in pair)
unconnected = [i for i in range(len(self.xy)) if i not in inds_flat]
if len(unconnected):
warnings.warn(
f'Unconnected {", ".join(self.bpts[unconnected])}. '
f"It is desirable that all bodyparts be connected for multi-animal projects."
)
self.cfg["skeleton"] = [
tuple(self.bpts[list(pair)]) for pair in self.inds
]
write_config(self.config_path, self.cfg)
def on_pick(self, event):
if event.mouseevent.button == 3:
removed = event.artist.get_segments().pop(event.ind[0])
self.segs.remove(tuple(map(tuple, removed)))
self.inds.remove(tuple(self.tree.query(removed)[1]))
def on_select(self, verts):
self.path = Path(verts)
self.verts = verts
inds = self.tree.query_ball_point(verts, 5)
inds_unique = []
for lst in inds:
if len(lst) and lst[0] not in inds_unique:
inds_unique.append(lst[0])
for pair in zip(inds_unique, inds_unique[1:]):
pair_sorted = tuple(sorted(pair))
self.inds.add(pair_sorted)
self.segs.add(tuple(map(tuple, self.xy[pair_sorted, :])))
self.lines.set_segments(self.segs)
self.fig.canvas.draw_idle()
def draw_prediction_on_image(image,
keypoints_with_scores,
crop_region=None,
close_figure=False,
output_image_height=None):
"""Draws the keypoint predictions on image.
Args:
image: A numpy array with shape [height, width, channel] representing the
pixel values of the input image.
keypoints_with_scores: A numpy array with shape [1, 1, 17, 3] representing
the keypoint coordinates and scores returned from the MoveNet model.
crop_region: A dictionary that defines the coordinates of the bounding box
of the crop region in normalized coordinates (see the init_crop_region
function below for more detail). If provided, this function will also
draw the bounding box on the image.
output_image_height: An integer indicating the height of the output image.
Note that the image aspect ratio will be the same as the input image.
Returns:
A numpy array with shape [out_height, out_width, channel] representing the
image overlaid with keypoint predictions.
"""
height, width, channel = image.shape
aspect_ratio = float(width) / height
fig, ax = plt.subplots(figsize=(12 * aspect_ratio, 12))
# To remove the huge white borders
fig.tight_layout(pad=0)
ax.margins(0)
ax.set_yticklabels([])
ax.set_xticklabels([])
plt.axis('off')
im = ax.imshow(image)
line_segments = LineCollection([], linewidths=(4), linestyle='solid')
ax.add_collection(line_segments)
# Turn off tick labels
scat = ax.scatter([], [], s=60, color='#FF1493', zorder=3)
(keypoint_locs, keypoint_edges,
edge_colors) = _keypoints_and_edges_for_display(keypoints_with_scores,
height, width)
line_segments.set_segments(keypoint_edges)
line_segments.set_color(edge_colors)
if keypoint_edges.shape[0]:
line_segments.set_segments(keypoint_edges)
line_segments.set_color(edge_colors)
if keypoint_locs.shape[0]:
scat.set_offsets(keypoint_locs)
if crop_region is not None:
xmin = max(crop_region['x_min'] * width, 0.0)
ymin = max(crop_region['y_min'] * height, 0.0)
rec_width = min(crop_region['x_max'], 0.99) * width - xmin
rec_height = min(crop_region['y_max'], 0.99) * height - ymin
rect = patches.Rectangle((xmin, ymin),
rec_width,
rec_height,
linewidth=1,
edgecolor='b',
facecolor='none')
ax.add_patch(rect)
fig.canvas.draw()
image_from_plot = np.frombuffer(fig.canvas.tostring_rgb(), dtype=np.uint8)
image_from_plot = image_from_plot.reshape(
fig.canvas.get_width_height()[::-1] + (3, ))
plt.close(fig)
if output_image_height is not None:
output_image_width = int(output_image_height / height * width)
image_from_plot = cv2.resize(image_from_plot,
dsize=(output_image_width,
output_image_height),
interpolation=cv2.INTER_CUBIC)
return image_from_plot
def make_labeled_images_from_dataframe(
df,
cfg,
destfolder="",
scale=1.0,
dpi=100,
keypoint="+",
draw_skeleton=True,
color_by="bodypart",
):
"""
Write labeled frames to disk from a DataFrame.
Parameters
----------
df : pd.DataFrame
DataFrame containing the labeled data. Typically, the DataFrame is obtained
through pandas.read_csv() or pandas.read_hdf().
cfg : dict
Project configuration.
destfolder : string, optional
Destination folder into which images will be stored. By default, same location as the labeled data.
Note that the folder will be created if it does not exist.
scale : float, optional
Up/downscale the output dimensions.
By default, outputs are of the same dimensions as the original images.
dpi : int, optional
Output resolution. 100 dpi by default.
keypoint : str, optional
Keypoint appearance. By default, keypoints are marked by a + sign.
Refer to https://matplotlib.org/3.2.1/api/markers_api.html for a list of all possible options.
draw_skeleton : bool, optional
Whether to draw the animal skeleton as defined in *cfg*. True by default.
color_by : str, optional
Color scheme of the keypoints. Must be either 'bodypart' or 'individual'.
By default, keypoints are colored relative to the bodypart they represent.
"""
bodyparts = df.columns.get_level_values("bodyparts")
bodypart_names = bodyparts.unique()
nbodyparts = len(bodypart_names)
bodyparts = bodyparts[::2]
draw_skeleton = (draw_skeleton
and cfg["skeleton"]) # Only draw if a skeleton is defined
if color_by == "bodypart":
map_ = bodyparts.map(dict(zip(bodypart_names, range(nbodyparts))))
cmap = get_cmap(nbodyparts, cfg["colormap"])
colors = cmap(map_)
elif color_by == "individual":
try:
individuals = df.columns.get_level_values("individuals")
individual_names = individuals.unique().to_list()
nindividuals = len(individual_names)
individuals = individuals[::2]
map_ = individuals.map(
dict(zip(individual_names, range(nindividuals))))
cmap = get_cmap(nindividuals, cfg["colormap"])
colors = cmap(map_)
except KeyError as e:
raise Exception(
"Coloring by individuals is only valid for multi-animal data"
) from e
else:
raise ValueError(
"`color_by` must be either `bodypart` or `individual`.")
bones = []
if draw_skeleton:
for bp1, bp2 in cfg["skeleton"]:
match1, match2 = [], []
for j, bp in enumerate(bodyparts):
if bp == bp1:
match1.append(j)
elif bp == bp2:
match2.append(j)
bones.extend(zip(match1, match2))
ind_bones = tuple(zip(*bones))
images_list = [
os.path.join(cfg["project_path"], *tuple_)
for tuple_ in df.index.tolist()
]
if not destfolder:
destfolder = os.path.dirname(images_list[0])
tmpfolder = destfolder + "_labeled"
attempttomakefolder(tmpfolder)
ic = io.imread_collection(images_list)
h, w = ic[0].shape[:2]
all_same_shape = True
for array in ic[1:]:
if array.shape[:2] != (h, w):
all_same_shape = False
break
xy = df.values.reshape((df.shape[0], -1, 2))
segs = xy[:, ind_bones].swapaxes(1, 2)
s = cfg["dotsize"]
alpha = cfg["alphavalue"]
if all_same_shape: # Very efficient, avoid re-drawing the whole plot
fig, ax = prepare_figure_axes(w, h, scale, dpi)
im = ax.imshow(np.zeros((h, w)), "gray")
pts = [
ax.plot([], [], keypoint, ms=s, alpha=alpha, color=c)[0]
for c in colors
]
coll = LineCollection([], colors=cfg["skeleton_color"], alpha=alpha)
ax.add_collection(coll)
for i in trange(len(ic)):
filename = ic.files[i]
ind = images_list.index(filename)
coords = xy[ind]
img = ic[i]
if img.ndim == 2 or img.shape[-1] == 1:
img = color.gray2rgb(ic[i])
im.set_data(img)
for pt, coord in zip(pts, coords):
pt.set_data(*coord)
if ind_bones:
coll.set_segments(segs[ind])
imagename = os.path.basename(filename)
fig.subplots_adjust(left=0,
bottom=0,
right=1,
top=1,
wspace=0,
hspace=0)
fig.savefig(
os.path.join(tmpfolder,
imagename.replace(".png", f"_{color_by}.png")),
dpi=dpi,
)
plt.close(fig)
else: # Good old inelegant way
for i in trange(len(ic)):
filename = ic.files[i]
ind = images_list.index(filename)
coords = xy[ind]
image = ic[i]
h, w = image.shape[:2]
fig, ax = prepare_figure_axes(w, h, scale, dpi)
ax.imshow(image)
for coord, c in zip(coords, colors):
ax.plot(*coord, keypoint, ms=s, alpha=alpha, color=c)
if ind_bones:
coll = LineCollection(segs[ind],
colors=cfg["skeleton_color"],
alpha=alpha)
ax.add_collection(coll)
imagename = os.path.basename(filename)
fig.subplots_adjust(left=0,
bottom=0,
right=1,
top=1,
wspace=0,
hspace=0)
fig.savefig(
os.path.join(tmpfolder,
imagename.replace(".png", f"_{color_by}.png")),
dpi=dpi,
)
plt.close(fig)
def set_segments(self, segments):
"""
Set 3D segments.
"""
self._segments3d = np.asanyarray(segments)
LineCollection.set_segments(self, [])
def set_segments(self, segments):
"""
Set 3D segments.
"""
self._segments3d = np.asanyarray(segments)
LineCollection.set_segments(self, [])
def set_segments(self, segments):
'''
Set 3D segments
'''
self._segments3d = segments
LineCollection.set_segments(self, [])
class ScatterLayerArtist(MatplotlibLayerArtist):
_layer_state_cls = ScatterLayerState
def __init__(self, axes, viewer_state, layer_state=None, layer=None):
super(ScatterLayerArtist, self).__init__(axes, viewer_state,
layer_state=layer_state, layer=layer)
# Watch for changes in the viewer state which would require the
# layers to be redrawn
self._viewer_state.add_global_callback(self._update_scatter)
self.state.add_global_callback(self._update_scatter)
# Scatter
self.scatter_artist = self.axes.scatter([], [])
self.plot_artist = self.axes.plot([], [], 'o', mec='none')[0]
self.errorbar_artist = self.axes.errorbar([], [], fmt='none')
self.vector_artist = None
self.line_collection = LineCollection(np.zeros((0, 2, 2)))
self.axes.add_collection(self.line_collection)
# Scatter density
self.density_auto_limits = DensityMapLimits()
self.density_artist = ScatterDensityArtist(self.axes, [], [], color='white',
vmin=self.density_auto_limits.min,
vmax=self.density_auto_limits.max)
self.axes.add_artist(self.density_artist)
self.mpl_artists = [self.scatter_artist, self.plot_artist,
self.errorbar_artist, self.vector_artist,
self.line_collection, self.density_artist]
self.errorbar_index = 2
self.vector_index = 3
self.reset_cache()
def reset_cache(self):
self._last_viewer_state = {}
self._last_layer_state = {}
@defer_draw
def _update_data(self, changed):
# Layer artist has been cleared already
if len(self.mpl_artists) == 0:
return
try:
x = self.layer[self._viewer_state.x_att].ravel()
except (IncompatibleAttribute, IndexError):
# The following includes a call to self.clear()
self.disable_invalid_attributes(self._viewer_state.x_att)
return
else:
self.enable()
try:
y = self.layer[self._viewer_state.y_att].ravel()
except (IncompatibleAttribute, IndexError):
# The following includes a call to self.clear()
self.disable_invalid_attributes(self._viewer_state.y_att)
return
else:
self.enable()
if self.state.markers_visible:
if self.state.density_map:
self.density_artist.set_xy(x, y)
self.plot_artist.set_data([], [])
self.scatter_artist.set_offsets(np.zeros((0, 2)))
else:
if self.state.cmap_mode == 'Fixed' and self.state.size_mode == 'Fixed':
# In this case we use Matplotlib's plot function because it has much
# better performance than scatter.
self.plot_artist.set_data(x, y)
self.scatter_artist.set_offsets(np.zeros((0, 2)))
self.density_artist.set_xy([], [])
else:
self.plot_artist.set_data([], [])
offsets = np.vstack((x, y)).transpose()
self.scatter_artist.set_offsets(offsets)
self.density_artist.set_xy([], [])
else:
self.plot_artist.set_data([], [])
self.scatter_artist.set_offsets(np.zeros((0, 2)))
self.density_artist.set_xy([], [])
if self.state.line_visible:
if self.state.cmap_mode == 'Fixed':
points = np.array([x, y]).transpose()
self.line_collection.set_segments([points])
else:
# In the case where we want to color the line, we need to over
# sample the line by a factor of two so that we can assign the
# correct colors to segments - if we didn't do this, then
# segments on one side of a point would be a different color
# from the other side. With oversampling, we can have half a
# segment on either side of a point be the same color as a
# point
x_fine = np.zeros(len(x) * 2 - 1, dtype=float)
y_fine = np.zeros(len(y) * 2 - 1, dtype=float)
x_fine[::2] = x
x_fine[1::2] = 0.5 * (x[1:] + x[:-1])
y_fine[::2] = y
y_fine[1::2] = 0.5 * (y[1:] + y[:-1])
points = np.array([x_fine, y_fine]).transpose().reshape(-1, 1, 2)
segments = np.concatenate([points[:-1], points[1:]], axis=1)
self.line_collection.set_segments(segments)
else:
self.line_collection.set_segments(np.zeros((0, 2, 2)))
for eartist in list(self.errorbar_artist[2]):
if eartist is not None:
try:
eartist.remove()
except ValueError:
pass
except AttributeError: # Matplotlib < 1.5
pass
if self.vector_artist is not None:
self.vector_artist.remove()
self.vector_artist = None
if self.state.vector_visible:
if self.state.vx_att is not None and self.state.vy_att is not None:
vx = self.layer[self.state.vx_att].ravel()
vy = self.layer[self.state.vy_att].ravel()
if self.state.vector_mode == 'Polar':
ang = vx
length = vy
# assume ang is anti clockwise from the x axis
vx = length * np.cos(np.radians(ang))
vy = length * np.sin(np.radians(ang))
else:
vx = None
vy = None
if self.state.vector_arrowhead:
hw = 3
hl = 5
else:
hw = 1
hl = 0
v = np.hypot(vx, vy)
vmax = np.nanmax(v)
vx = vx / vmax
vy = vy / vmax
self.vector_artist = self.axes.quiver(x, y, vx, vy, units='width',
pivot=self.state.vector_origin,
headwidth=hw, headlength=hl,
scale_units='width',
scale=10 / self.state.vector_scaling)
self.mpl_artists[self.vector_index] = self.vector_artist
if self.state.xerr_visible or self.state.yerr_visible:
if self.state.xerr_visible and self.state.xerr_att is not None:
xerr = self.layer[self.state.xerr_att].ravel()
else:
xerr = None
if self.state.yerr_visible and self.state.yerr_att is not None:
yerr = self.layer[self.state.yerr_att].ravel()
else:
yerr = None
self.errorbar_artist = self.axes.errorbar(x, y, fmt='none',
xerr=xerr, yerr=yerr)
self.mpl_artists[self.errorbar_index] = self.errorbar_artist
@defer_draw
def _update_visual_attributes(self, changed, force=False):
if not self.enabled:
return
if self.state.markers_visible:
if self.state.density_map:
if self.state.cmap_mode == 'Fixed':
if force or 'color' in changed or 'cmap_mode' in changed:
self.density_artist.set_color(self.state.color)
self.density_artist.set_c(None)
self.density_artist.set_clim(self.density_auto_limits.min,
self.density_auto_limits.max)
elif force or any(prop in changed for prop in CMAP_PROPERTIES):
c = self.layer[self.state.cmap_att].ravel()
set_mpl_artist_cmap(self.density_artist, c, self.state)
if force or 'stretch' in changed:
self.density_artist.set_norm(ImageNormalize(stretch=STRETCHES[self.state.stretch]()))
if force or 'dpi' in changed:
self.density_artist.set_dpi(self._viewer_state.dpi)
if force or 'density_contrast' in changed:
self.density_auto_limits.contrast = self.state.density_contrast
self.density_artist.stale = True
else:
if self.state.cmap_mode == 'Fixed' and self.state.size_mode == 'Fixed':
if force or 'color' in changed:
self.plot_artist.set_color(self.state.color)
if force or 'size' in changed or 'size_scaling' in changed:
self.plot_artist.set_markersize(self.state.size *
self.state.size_scaling)
else:
# TEMPORARY: Matplotlib has a bug that causes set_alpha to
# change the colors back: https://github.com/matplotlib/matplotlib/issues/8953
if 'alpha' in changed:
force = True
if self.state.cmap_mode == 'Fixed':
if force or 'color' in changed or 'cmap_mode' in changed:
self.scatter_artist.set_facecolors(self.state.color)
self.scatter_artist.set_edgecolor('none')
elif force or any(prop in changed for prop in CMAP_PROPERTIES):
c = self.layer[self.state.cmap_att].ravel()
set_mpl_artist_cmap(self.scatter_artist, c, self.state)
self.scatter_artist.set_edgecolor('none')
if force or any(prop in changed for prop in MARKER_PROPERTIES):
if self.state.size_mode == 'Fixed':
s = self.state.size * self.state.size_scaling
s = broadcast_to(s, self.scatter_artist.get_sizes().shape)
else:
s = self.layer[self.state.size_att].ravel()
s = ((s - self.state.size_vmin) /
(self.state.size_vmax - self.state.size_vmin)) * 30
s *= self.state.size_scaling
# Note, we need to square here because for scatter, s is actually
# proportional to the marker area, not radius.
self.scatter_artist.set_sizes(s ** 2)
if self.state.line_visible:
if self.state.cmap_mode == 'Fixed':
if force or 'color' in changed or 'cmap_mode' in changed:
self.line_collection.set_array(None)
self.line_collection.set_color(self.state.color)
elif force or any(prop in changed for prop in CMAP_PROPERTIES):
# Higher up we oversampled the points in the line so that
# half a segment on either side of each point has the right
# color, so we need to also oversample the color here.
c = self.layer[self.state.cmap_att].ravel()
cnew = np.zeros((len(c) - 1) * 2)
cnew[::2] = c[:-1]
cnew[1::2] = c[1:]
set_mpl_artist_cmap(self.line_collection, cnew, self.state)
if force or 'linewidth' in changed:
self.line_collection.set_linewidth(self.state.linewidth)
if force or 'linestyle' in changed:
self.line_collection.set_linestyle(self.state.linestyle)
if self.state.vector_visible and self.vector_artist is not None:
if self.state.cmap_mode == 'Fixed':
if force or 'color' in changed or 'cmap_mode' in changed:
self.vector_artist.set_array(None)
self.vector_artist.set_color(self.state.color)
elif force or any(prop in changed for prop in CMAP_PROPERTIES):
c = self.layer[self.state.cmap_att].ravel()
set_mpl_artist_cmap(self.vector_artist, c, self.state)
if self.state.xerr_visible or self.state.yerr_visible:
for eartist in list(self.errorbar_artist[2]):
if eartist is None:
continue
if self.state.cmap_mode == 'Fixed':
if force or 'color' in changed or 'cmap_mode' in changed:
eartist.set_color(self.state.color)
elif force or any(prop in changed for prop in CMAP_PROPERTIES):
c = self.layer[self.state.cmap_att].ravel()
set_mpl_artist_cmap(eartist, c, self.state)
if force or 'alpha' in changed:
eartist.set_alpha(self.state.alpha)
if force or 'visible' in changed:
eartist.set_visible(self.state.visible)
if force or 'zorder' in changed:
eartist.set_zorder(self.state.zorder)
for artist in [self.scatter_artist, self.plot_artist,
self.vector_artist, self.line_collection,
self.density_artist]:
if artist is None:
continue
if force or 'alpha' in changed:
artist.set_alpha(self.state.alpha)
if force or 'zorder' in changed:
artist.set_zorder(self.state.zorder)
if force or 'visible' in changed:
artist.set_visible(self.state.visible)
self.redraw()
@defer_draw
def _update_scatter(self, force=False, **kwargs):
if (self._viewer_state.x_att is None or
self._viewer_state.y_att is None or
self.state.layer is None):
return
# Figure out which attributes are different from before. Ideally we shouldn't
# need this but currently this method is called multiple times if an
# attribute is changed due to x_att changing then hist_x_min, hist_x_max, etc.
# If we can solve this so that _update_histogram is really only called once
# then we could consider simplifying this. Until then, we manually keep track
# of which properties have changed.
changed = set()
if not force:
for key, value in self._viewer_state.as_dict().items():
if value != self._last_viewer_state.get(key, None):
changed.add(key)
for key, value in self.state.as_dict().items():
if value != self._last_layer_state.get(key, None):
changed.add(key)
self._last_viewer_state.update(self._viewer_state.as_dict())
self._last_layer_state.update(self.state.as_dict())
if force or len(changed & DATA_PROPERTIES) > 0:
self._update_data(changed)
force = True
if force or len(changed & VISUAL_PROPERTIES) > 0:
self._update_visual_attributes(changed, force=force)
def get_layer_color(self):
if self.state.cmap_mode == 'Fixed':
return self.state.color
else:
return self.state.cmap
@defer_draw
def update(self):
self._update_scatter(force=True)
self.redraw()
def make_labeled_images_from_dataframe(
df,
cfg,
destfolder="",
scale=1.0,
dpi=100,
keypoint="+",
draw_skeleton=True,
color_by="bodypart",
):
"""
Write labeled frames to disk from a DataFrame.
Parameters
----------
df : pd.DataFrame
DataFrame containing the labeled data. Typically, the DataFrame is obtained
through pandas.read_csv() or pandas.read_hdf().
cfg : dict
Project configuration.
destfolder : string, optional
Destination folder into which images will be stored. By default, same location as the labeled data.
Note that the folder will be created if it does not exist.
scale : float, optional
Up/downscale the output dimensions.
By default, outputs are of the same dimensions as the original images.
dpi : int, optional
Output resolution. 100 dpi by default.
keypoint : str, optional
Keypoint appearance. By default, keypoints are marked by a + sign.
Refer to https://matplotlib.org/3.2.1/api/markers_api.html for a list of all possible options.
draw_skeleton : bool, optional
Whether to draw the animal skeleton as defined in *cfg*. True by default.
color_by : str, optional
Color scheme of the keypoints. Must be either 'bodypart' or 'individual'.
By default, keypoints are colored relative to the bodypart they represent.
"""
bodyparts = df.columns.get_level_values("bodyparts")
bodypart_names = bodyparts.unique()
nbodyparts = len(bodypart_names)
bodyparts = bodyparts[::2]
if color_by == "bodypart":
map_ = bodyparts.map(dict(zip(bodypart_names, range(nbodyparts))))
cmap = get_cmap(nbodyparts, cfg["colormap"])
colors = cmap(map_)
elif color_by == "individual":
try:
individuals = df.columns.get_level_values("individuals")
individual_names = individuals.unique().to_list()
nindividuals = len(individual_names)
individuals = individuals[::2]
map_ = individuals.map(
dict(zip(individual_names, range(nindividuals))))
cmap = get_cmap(nindividuals, cfg["colormap"])
colors = cmap(map_)
except KeyError as e:
raise Exception(
"Coloring by individuals is only valid for multi-animal data"
) from e
else:
raise ValueError(
"`color_by` must be either `bodypart` or `individual`.")
bones = []
if draw_skeleton:
for bp1, bp2 in cfg["skeleton"]:
match1, match2 = [], []
for j, bp in enumerate(bodyparts):
if bp == bp1:
match1.append(j)
elif bp == bp2:
match2.append(j)
bones.extend(zip(match1, match2))
ind_bones = tuple(zip(*bones))
sep = "/" if "/" in df.index[0] else "\\"
images = cfg["project_path"] + sep + df.index
if sep != os.path.sep:
images = images.str.replace(sep, os.path.sep)
if not destfolder:
destfolder = os.path.dirname(images[0])
tmpfolder = destfolder + "_labeled"
attempttomakefolder(tmpfolder)
ic = io.imread_collection(images.to_list())
h, w = ic[0].shape[:2]
fig, ax = prepare_figure_axes(w, h, scale, dpi)
im = ax.imshow(np.zeros((h, w)), "gray")
scat = ax.scatter([], [],
s=cfg["dotsize"],
alpha=cfg["alphavalue"],
marker=keypoint)
scat.set_color(colors)
xy = df.values.reshape((df.shape[0], -1, 2))
segs = xy[:, ind_bones].swapaxes(1, 2)
coll = LineCollection([], colors=cfg["skeleton_color"])
ax.add_collection(coll)
for i in trange(len(ic)):
coords = xy[i]
im.set_array(ic[i])
scat.set_offsets(coords)
if ind_bones:
coll.set_segments(segs[i])
imagename = os.path.basename(ic.files[i])
fig.savefig(
os.path.join(tmpfolder,
imagename.replace(".png", f"_{color_by}.png")))
plt.close(fig)
def set_segments(self, segments):
'''
Set 3D segments
'''
self._segments3d = np.asanyarray(segments)
LineCollection.set_segments(self, [])
class SURFDemo(ImageProcessDemo):
TITLE = "SURF Demo"
DEFAULT_IMAGE = "lena.jpg"
SETTINGS = ["m_perspective", "hessian_threshold", "n_octaves"]
m_perspective = Array(np.float, (3, 3))
m_perspective2 = Array(np.float, (3, 3))
hessian_threshold = Int(2000)
n_octaves = Int(2)
poly = Instance(PolygonWidget)
def control_panel(self):
return VGroup(
Item("m_perspective", label=u"变换矩阵", editor=ArrayEditor(format_str="%g")),
Item("m_perspective2", label=u"变换矩阵", editor=ArrayEditor(format_str="%g")),
Item("hessian_threshold", label=u"hessianThreshold"),
Item("n_octaves", label=u"nOctaves")
)
def __init__(self, **kwargs):
super(SURFDemo, self).__init__(**kwargs)
self.poly = None
self.init_points = None
self.lines = LineCollection([], linewidths=1, alpha=0.6, color="red")
self.axe.add_collection(self.lines)
self.connect_dirty("poly.changed,hessian_threshold,n_octaves")
def init_poly(self):
if self.poly is None:
return
h, w, _ = self.img_color.shape
self.init_points = np.array([(w, 0), (2*w, 0), (2*w, h), (w, h)], np.float32)
self.poly.set_points(self.init_points)
self.poly.update()
def init_draw(self):
style = {"marker": "o"}
self.poly = PolygonWidget(axe=self.axe, points=np.zeros((3, 2)), style=style)
self.init_poly()
@on_trait_change("hessian_threshold, n_octaves")
def calc_surf1(self):
self.surf = cv2.SURF(self.hessian_threshold, self.n_octaves)
self.key_points1, self.features1 = self.surf.detectAndCompute(self.img_gray, None)
self.key_positions1 = np.array([kp.pt for kp in self.key_points1])
def _img_changed(self):
self.img_gray = cv2.cvtColor(self.img, cv2.COLOR_BGR2GRAY)
self.img_color = cv2.cvtColor(self.img_gray, cv2.COLOR_GRAY2RGB)
self.img_show = np.concatenate([self.img_color, self.img_color], axis=1)
self.size = self.img_color.shape[1], self.img_color.shape[0]
self.calc_surf1()
FLANN_INDEX_KDTREE = 1
index_params = dict(algorithm=FLANN_INDEX_KDTREE, trees=5)
search_params = dict(checks=100)
self.matcher = cv2.FlannBasedMatcher(index_params, search_params)
self.init_poly()
def settings_loaded(self):
src = self.init_points.copy()
w, h = self.size
src[:, 0] -= w
dst = cv2.perspectiveTransform(src[None, :, :], self.m_perspective)
dst = dst.squeeze()
dst[:, 0] += w
self.poly.set_points(dst)
self.poly.update()
def draw(self):
if self.poly is None:
return
w, h = self.size
src = self.init_points.copy()
dst = self.poly.points.copy().astype(np.float32)
src[:, 0] -= w
dst[:, 0] -= w
m = cv2.getPerspectiveTransform(src, dst)
self.m_perspective = m
img2 = cv2.warpPerspective(self.img_gray, m, self.size, borderValue=[255]*4)
self.img_show[:, w:, :] = img2[:, :, None]
key_points2, features2 = self.surf.detectAndCompute(img2, None)
key_positions2 = np.array([kp.pt for kp in key_points2])
match_list = self.matcher.knnMatch(self.features1, features2, k=1)
index1 = np.array([m[0].queryIdx for m in match_list])
index2 = np.array([m[0].trainIdx for m in match_list])
distances = np.array([m[0].distance for m in match_list])
n = min(50, len(distances))
best_index = np.argsort(distances)[:n]
matched_positions1 = self.key_positions1[index1[best_index]]
matched_positions2 = key_positions2[index2[best_index]]
self.m_perspective2, mask = cv2.findHomography(matched_positions1, matched_positions2, cv2.RANSAC)
lines = np.concatenate([matched_positions1, matched_positions2], axis=1)
lines[:, 2] += w
line_colors = COLORS[mask.ravel()]
self.lines.set_segments(lines.reshape(-1, 2, 2))
self.lines.set_color(line_colors)
self.draw_image(self.img_show)
class AnimationPlot:
def __init__(self, x_min, y_min, x_max, y_max):
# Create the figure
self.figure = plt.figure(figsize=((x_max - x_min)/(y_max - y_min), 4), facecolor='black')
def create_texture(self, texture, texture_length):
# Create texture x values
self.texture_x = np.linspace(0, texture_length, 100*texture_length)
# Plot the texture
self.texture_line, = self.animation_axis.plot([], [], color='white', lw=1)
def create_whiskers(self, n_whiskers):
# Initialize the list of whisker lines & colors
# Note: colors are initialized to span the range (0, 1) in order to set the correct max & min for the subsequent animation
self.whisker_lines = [[(0, 0), (0, 0)]]*n_whiskers
self.whisker_colors = np.linspace(0, 1, n_whiskers)
# Create a line collection from the whisker lines & colors
self.whisker_line_collection = LineCollection(self.whisker_lines, array=self.whisker_colors, cmap=cm.rainbow, lw=0.5)
self.animation_axis.add_collection(self.whisker_line_collection)
def create_animation_plot(self, x_min, y_min, x_max, y_max):
self.animation_axis = plt.Axes(self.figure, [0, 0.66, 1, 0.33])
self.figure.add_axes(self.animation_axis)
self.animation_axis.set_axis_off()
self.animation_axis.set_xlim(x_min, x_max)
self.animation_axis.set_ylim(x_min - 1, y_max + 1)
def create_whisker_deflection_plot(self, n_whiskers):
self.whisker_deflection_axis = plt.Axes(self.figure, [0, 0.33, 1, 0.33])
self.figure.add_axes(self.whisker_deflection_axis)
self.whisker_deflection_axis.set_axis_off()
self.whisker_deflection_axis.set_xlim(-0.5, n_whiskers - 0.5)
self.whisker_deflection_axis.set_ylim(0, 1)
self.whisker_deflection_lines = []
# Update whisker deflection lines
for n in range(n_whiskers):
# Set starting x & y coordinates of the whisker deflection line
x_start = n_whiskers - n
y_start = 0.1
# Set ending x & y coordinates of the whisker deflection line
x_end = n_whiskers - n
y_end = 0.9
self.whisker_deflection_lines.append([(x_start, y_start), (x_end, y_end)])
# Initialize the list of sensory whisker deflection colors
self.whisker_deflection_colors = np.linspace(0, 1, n_whiskers)
# Create a line collection from the whisker deflection lines & colors
self.whisker_deflection_line_collection = LineCollection(self.whisker_deflection_lines, array=self.whisker_deflection_colors, cmap=cm.rainbow, lw=5)
self.whisker_deflection_axis.add_collection(self.whisker_deflection_line_collection)
def create_sensory_cell_activity_plot(self, n_sensory_cells):
self.sensory_cell_activity_axis = plt.Axes(self.figure, [0, 0, 1, 0.33])
self.figure.add_axes(self.sensory_cell_activity_axis)
self.sensory_cell_activity_axis.set_axis_off()
self.sensory_cell_activity_axis.set_xlim(-0.5, n_sensory_cells - 0.5)
self.sensory_cell_activity_axis.set_ylim(0, 1)
self.sensory_cell_activity_lines = []
# Update sensory cell activity lines
for n in range(n_sensory_cells):
# Set starting x & y coordinates of the cell activity line
x_start = n_sensory_cells - n
y_start = 0.1
# Set ending x & y coordinates of the cell activity line
x_end = n_sensory_cells - n
y_end = 0.9
self.sensory_cell_activity_lines.append([(x_start, y_start), (x_end, y_end)])
# Initialize the list of sensory cell activity colors
self.sensory_cell_activity_colors = np.linspace(0, 1, n_sensory_cells)
# Create a line collection from the sensory cell activity lines & colors
self.sensory_cell_activity_line_collection = LineCollection(self.sensory_cell_activity_lines, array=self.sensory_cell_activity_colors, cmap=cm.rainbow, lw=5)
self.sensory_cell_activity_axis.add_collection(self.sensory_cell_activity_line_collection)
def update_plot(self, i):
# Call the update function to update the agent and/or texture
texture, agent = self.update_func(i)
# Update texture y values
texture_y = texture.value(self.texture_x)
# Update whisker lines
for n in range(agent.n_whiskers):
# Get the whisker angle & deflection amount
whisker_angle = agent.whiskers.whisker_angles[n]
deflection = agent.whiskers.deflections[n]
# Set starting x & y coordinates of the whisker
y_start = 0.5*agent.whiskers.whisker_lengths[0]*np.sin(whisker_angle)
x_start = agent.x + 0.5*agent.whiskers.whisker_lengths[0]*np.cos(whisker_angle)
# Set ending x & y coordinates of the whisker
x_end = agent.x + (agent.whiskers.whisker_lengths[n] - deflection)*np.cos(whisker_angle)
y_end = (agent.whiskers.whisker_lengths[n] - deflection)*np.sin(whisker_angle)
# Update the whisker color
self.whisker_colors[n] = deflection/np.amax(agent.whiskers.whisker_lengths)
# Update the whisker line
self.whisker_lines[n] = [(x_start, y_start), (x_end, y_end)]
# Update sensory cell activity lines
for n in range(agent.n_sensory_cells):
# Get cell activities
cell_activity = agent.sensory_cells.activity[n]
max_activity = np.amax(agent.sensory_cells.activity)
if max_activity > 0:
# Update the cell activity line color
self.sensory_cell_activity_colors[n] = cell_activity/np.amax(agent.sensory_cells.activity)
else:
self.sensory_cell_activity_colors[n] = 0
# Update whisker deflection lines
for n in range(agent.n_whiskers):
# Get whisker deflection
deflection = agent.whiskers.deflections[n]
# Update the whisker deflection line color
self.whisker_deflection_colors[n] = deflection/agent.whiskers.whisker_lengths[n]
# Update the whisker line collection
self.whisker_line_collection.set_array(self.whisker_colors)
self.whisker_line_collection.set_segments(self.whisker_lines)
# Update the whisker deflection line collection
self.whisker_deflection_line_collection.set_array(self.whisker_deflection_colors)
# Update the cell activation line collection
self.sensory_cell_activity_line_collection.set_array(self.sensory_cell_activity_colors)
# Update the texture line data
self.texture_line.set_data(self.texture_x, texture_y)
return self.texture_line, self.whisker_line_collection, self.whisker_deflection_line_collection, self.sensory_cell_activity_line_collection
def animate(self, update_func):
self.update_func = update_func
# Create the animation
anim = animation.FuncAnimation(self.figure, self.update_plot, init_func=lambda:[self.texture_line, self.whisker_line_collection, self.whisker_deflection_line_collection, self.sensory_cell_activity_line_collection], interval=1, blit=True)
# Show the plot
plt.show()
ax.set_aspect('equal')
ax.grid()
ax.set_xlim(0, 10)
ax.set_ylim(0, 10)
#=======================================================
segmentsCollection = LineCollection([], linestyle='solid', color='r')
ax.add_collection(segmentsCollection)
peaksCollection = LineCollection([], linestyle='solid', color='b')
ax.add_collection(peaksCollection)
segs2 = [[[2, 5], [6, 8]], [[1, 2], [6, 4]], [[2, 2], [8, 2]]]
segmentsCollection.set_segments(segs2)
# I would like to save segment number data in the LineCollection instance (peaksCollection)
# Don't know how to store this extra information in the segment of the LineCollection object.
peaksInSegment = []
#=======================================================
def draw_tick(segment, x, y, length=0.25):
line = LineString(segment)
left = line.parallel_offset(length, 'left')
right0 = line.parallel_offset(length, 'right')
right = LineString([right0.boundary.geoms[1], right0.boundary.geoms[0]
]) # flip because 'right' orientation
point = Point(x, y)
a = left.interpolate(line.project(point))
class ScatterLayerArtist(MatplotlibLayerArtist):
_layer_state_cls = ScatterLayerState
def __init__(self, axes, viewer_state, layer_state=None, layer=None):
super(ScatterLayerArtist, self).__init__(axes,
viewer_state,
layer_state=layer_state,
layer=layer)
# Watch for changes in the viewer state which would require the
# layers to be redrawn
self._viewer_state.add_global_callback(self._update_scatter)
self.state.add_global_callback(self._update_scatter)
# Scatter
self.scatter_artist = self.axes.scatter([], [])
self.plot_artist = self.axes.plot([], [], 'o', mec='none')[0]
self.errorbar_artist = self.axes.errorbar([], [], fmt='none')
self.vector_artist = None
self.line_collection = LineCollection(np.zeros((0, 2, 2)))
self.axes.add_collection(self.line_collection)
# Scatter density
self.density_auto_limits = DensityMapLimits()
self.density_artist = ScatterDensityArtist(
self.axes, [], [],
color='white',
vmin=self.density_auto_limits.min,
vmax=self.density_auto_limits.max)
self.axes.add_artist(self.density_artist)
self.mpl_artists = [
self.scatter_artist, self.plot_artist, self.errorbar_artist,
self.vector_artist, self.line_collection, self.density_artist
]
self.errorbar_index = 2
self.vector_index = 3
self.reset_cache()
def reset_cache(self):
self._last_viewer_state = {}
self._last_layer_state = {}
@defer_draw
def _update_data(self, changed):
# Layer artist has been cleared already
if len(self.mpl_artists) == 0:
return
try:
x = self.layer[self._viewer_state.x_att].ravel()
except (IncompatibleAttribute, IndexError):
# The following includes a call to self.clear()
self.disable_invalid_attributes(self._viewer_state.x_att)
return
else:
self.enable()
try:
y = self.layer[self._viewer_state.y_att].ravel()
except (IncompatibleAttribute, IndexError):
# The following includes a call to self.clear()
self.disable_invalid_attributes(self._viewer_state.y_att)
return
else:
self.enable()
if self.state.markers_visible:
if self.state.density_map:
self.density_artist.set_xy(x, y)
self.plot_artist.set_data([], [])
self.scatter_artist.set_offsets(np.zeros((0, 2)))
else:
if self.state.cmap_mode == 'Fixed' and self.state.size_mode == 'Fixed':
# In this case we use Matplotlib's plot function because it has much
# better performance than scatter.
self.plot_artist.set_data(x, y)
self.scatter_artist.set_offsets(np.zeros((0, 2)))
self.density_artist.set_xy([], [])
else:
self.plot_artist.set_data([], [])
offsets = np.vstack((x, y)).transpose()
self.scatter_artist.set_offsets(offsets)
self.density_artist.set_xy([], [])
else:
self.plot_artist.set_data([], [])
self.scatter_artist.set_offsets(np.zeros((0, 2)))
self.density_artist.set_xy([], [])
if self.state.line_visible:
if self.state.cmap_mode == 'Fixed':
points = np.array([x, y]).transpose()
self.line_collection.set_segments([points])
else:
# In the case where we want to color the line, we need to over
# sample the line by a factor of two so that we can assign the
# correct colors to segments - if we didn't do this, then
# segments on one side of a point would be a different color
# from the other side. With oversampling, we can have half a
# segment on either side of a point be the same color as a
# point
x_fine = np.zeros(len(x) * 2 - 1, dtype=float)
y_fine = np.zeros(len(y) * 2 - 1, dtype=float)
x_fine[::2] = x
x_fine[1::2] = 0.5 * (x[1:] + x[:-1])
y_fine[::2] = y
y_fine[1::2] = 0.5 * (y[1:] + y[:-1])
points = np.array([x_fine,
y_fine]).transpose().reshape(-1, 1, 2)
segments = np.concatenate([points[:-1], points[1:]], axis=1)
self.line_collection.set_segments(segments)
else:
self.line_collection.set_segments(np.zeros((0, 2, 2)))
for eartist in list(self.errorbar_artist[2]):
if eartist is not None:
try:
eartist.remove()
except ValueError:
pass
except AttributeError: # Matplotlib < 1.5
pass
if self.vector_artist is not None:
self.vector_artist.remove()
self.vector_artist = None
if self.state.vector_visible:
if self.state.vx_att is not None and self.state.vy_att is not None:
vx = self.layer[self.state.vx_att].ravel()
vy = self.layer[self.state.vy_att].ravel()
if self.state.vector_mode == 'Polar':
ang = vx
length = vy
# assume ang is anti clockwise from the x axis
vx = length * np.cos(np.radians(ang))
vy = length * np.sin(np.radians(ang))
else:
vx = None
vy = None
if self.state.vector_arrowhead:
hw = 3
hl = 5
else:
hw = 1
hl = 0
v = np.hypot(vx, vy)
vmax = np.nanmax(v)
vx = vx / vmax
vy = vy / vmax
self.vector_artist = self.axes.quiver(
x,
y,
vx,
vy,
units='width',
pivot=self.state.vector_origin,
headwidth=hw,
headlength=hl,
scale_units='width',
scale=10 / self.state.vector_scaling)
self.mpl_artists[self.vector_index] = self.vector_artist
if self.state.xerr_visible or self.state.yerr_visible:
if self.state.xerr_visible and self.state.xerr_att is not None:
xerr = self.layer[self.state.xerr_att].ravel()
else:
xerr = None
if self.state.yerr_visible and self.state.yerr_att is not None:
yerr = self.layer[self.state.yerr_att].ravel()
else:
yerr = None
self.errorbar_artist = self.axes.errorbar(x,
y,
fmt='none',
xerr=xerr,
yerr=yerr)
self.mpl_artists[self.errorbar_index] = self.errorbar_artist
@defer_draw
def _update_visual_attributes(self, changed, force=False):
if not self.enabled:
return
if self.state.markers_visible:
if self.state.density_map:
if self.state.cmap_mode == 'Fixed':
if force or 'color' in changed or 'cmap_mode' in changed:
self.density_artist.set_color(self.state.color)
self.density_artist.set_c(None)
self.density_artist.set_clim(
self.density_auto_limits.min,
self.density_auto_limits.max)
elif force or any(prop in changed for prop in CMAP_PROPERTIES):
c = self.layer[self.state.cmap_att].ravel()
set_mpl_artist_cmap(self.density_artist, c, self.state)
if force or 'stretch' in changed:
self.density_artist.set_norm(
ImageNormalize(
stretch=STRETCHES[self.state.stretch]()))
if force or 'dpi' in changed:
self.density_artist.set_dpi(self._viewer_state.dpi)
if force or 'density_contrast' in changed:
self.density_auto_limits.contrast = self.state.density_contrast
self.density_artist.stale = True
else:
if self.state.cmap_mode == 'Fixed' and self.state.size_mode == 'Fixed':
if force or 'color' in changed:
self.plot_artist.set_color(self.state.color)
if force or 'size' in changed or 'size_scaling' in changed:
self.plot_artist.set_markersize(
self.state.size * self.state.size_scaling)
else:
# TEMPORARY: Matplotlib has a bug that causes set_alpha to
# change the colors back: https://github.com/matplotlib/matplotlib/issues/8953
if 'alpha' in changed:
force = True
if self.state.cmap_mode == 'Fixed':
if force or 'color' in changed or 'cmap_mode' in changed:
self.scatter_artist.set_facecolors(
self.state.color)
self.scatter_artist.set_edgecolor('none')
elif force or any(prop in changed
for prop in CMAP_PROPERTIES):
c = self.layer[self.state.cmap_att].ravel()
set_mpl_artist_cmap(self.scatter_artist, c, self.state)
self.scatter_artist.set_edgecolor('none')
if force or any(prop in changed
for prop in MARKER_PROPERTIES):
if self.state.size_mode == 'Fixed':
s = self.state.size * self.state.size_scaling
s = broadcast_to(
s,
self.scatter_artist.get_sizes().shape)
else:
s = self.layer[self.state.size_att].ravel()
s = ((s - self.state.size_vmin) /
(self.state.size_vmax -
self.state.size_vmin)) * 30
s *= self.state.size_scaling
# Note, we need to square here because for scatter, s is actually
# proportional to the marker area, not radius.
self.scatter_artist.set_sizes(s**2)
if self.state.line_visible:
if self.state.cmap_mode == 'Fixed':
if force or 'color' in changed or 'cmap_mode' in changed:
self.line_collection.set_array(None)
self.line_collection.set_color(self.state.color)
elif force or any(prop in changed for prop in CMAP_PROPERTIES):
# Higher up we oversampled the points in the line so that
# half a segment on either side of each point has the right
# color, so we need to also oversample the color here.
c = self.layer[self.state.cmap_att].ravel()
cnew = np.zeros((len(c) - 1) * 2)
cnew[::2] = c[:-1]
cnew[1::2] = c[1:]
set_mpl_artist_cmap(self.line_collection, cnew, self.state)
if force or 'linewidth' in changed:
self.line_collection.set_linewidth(self.state.linewidth)
if force or 'linestyle' in changed:
self.line_collection.set_linestyle(self.state.linestyle)
if self.state.vector_visible and self.vector_artist is not None:
if self.state.cmap_mode == 'Fixed':
if force or 'color' in changed or 'cmap_mode' in changed:
self.vector_artist.set_array(None)
self.vector_artist.set_color(self.state.color)
elif force or any(prop in changed for prop in CMAP_PROPERTIES):
c = self.layer[self.state.cmap_att].ravel()
set_mpl_artist_cmap(self.vector_artist, c, self.state)
if self.state.xerr_visible or self.state.yerr_visible:
for eartist in list(self.errorbar_artist[2]):
if eartist is None:
continue
if self.state.cmap_mode == 'Fixed':
if force or 'color' in changed or 'cmap_mode' in changed:
eartist.set_color(self.state.color)
elif force or any(prop in changed for prop in CMAP_PROPERTIES):
c = self.layer[self.state.cmap_att].ravel()
set_mpl_artist_cmap(eartist, c, self.state)
if force or 'alpha' in changed:
eartist.set_alpha(self.state.alpha)
if force or 'visible' in changed:
eartist.set_visible(self.state.visible)
if force or 'zorder' in changed:
eartist.set_zorder(self.state.zorder)
for artist in [
self.scatter_artist, self.plot_artist, self.vector_artist,
self.line_collection, self.density_artist
]:
if artist is None:
continue
if force or 'alpha' in changed:
artist.set_alpha(self.state.alpha)
if force or 'zorder' in changed:
artist.set_zorder(self.state.zorder)
if force or 'visible' in changed:
artist.set_visible(self.state.visible)
self.redraw()
@defer_draw
def _update_scatter(self, force=False, **kwargs):
if (self._viewer_state.x_att is None
or self._viewer_state.y_att is None
or self.state.layer is None):
return
# Figure out which attributes are different from before. Ideally we shouldn't
# need this but currently this method is called multiple times if an
# attribute is changed due to x_att changing then hist_x_min, hist_x_max, etc.
# If we can solve this so that _update_histogram is really only called once
# then we could consider simplifying this. Until then, we manually keep track
# of which properties have changed.
changed = set()
if not force:
for key, value in self._viewer_state.as_dict().items():
if value != self._last_viewer_state.get(key, None):
changed.add(key)
for key, value in self.state.as_dict().items():
if value != self._last_layer_state.get(key, None):
changed.add(key)
self._last_viewer_state.update(self._viewer_state.as_dict())
self._last_layer_state.update(self.state.as_dict())
if force or len(changed & DATA_PROPERTIES) > 0:
self._update_data(changed)
force = True
if force or len(changed & VISUAL_PROPERTIES) > 0:
self._update_visual_attributes(changed, force=force)
def get_layer_color(self):
if self.state.cmap_mode == 'Fixed':
return self.state.color
else:
return self.state.cmap
@defer_draw
def update(self):
self._update_scatter(force=True)
self.redraw()
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 SpikeBrowserUI(object):
def __init__(self, window):
self.window = window
self.sp_win = [-0.8, 1]
self.spike_collection = None
self.fig = Figure((5, 4), 75)
self.canvas = window.get_canvas(self.fig)
self._mpl_init()
self.canvas.mpl_connect('key_press_event', self._on_key)
self.window.set_scroll_handler(self.OnScrollEvt)
def _mpl_init(self):
self.fig.clf()
self.axes = self.fig.add_axes([0.05, 0.1, 0.95, 0.9])
self.ax_prev = self.fig.add_axes([0.8, 0.0, 0.1, 0.05])
self.ax_next = self.fig.add_axes([0.9, 0.0, 0.1, 0.05])
self.b_next = Button(self.ax_next, 'Next')
self.b_prev = Button(self.ax_prev, "Prev")
self.b_next.on_clicked(self._next_spike)
self.b_prev.on_clicked(self._prev_spike)
self.i_spike = 0
self.i_start = 0
self.line_collection = None
def _next_spike(self, event):
try:
if self.i_spike < len(self.spt) - 1:
self.i_spike += 1
t_spk = self.spt[self.i_spike]
i_start = int(np.ceil(t_spk / 1000. * self.FS -
self.i_window / 2.))
i_start = np.maximum(self.i_min, i_start)
i_start = np.minimum(self.i_max, i_start)
self.i_start = i_start
self.i_end = self.i_start + self.i_window
self.window.set_scroll_pos(self.i_start)
self.draw_plot()
except IndexError:
pass
def _prev_spike(self, event):
try:
if self.i_spike > 0:
self.i_spike -= 1
t_spk = self.spt[self.i_spike]
i_start = int(np.ceil(t_spk / 1000. * self.FS -
self.i_window / 2.))
i_start = np.maximum(self.i_min, i_start)
i_start = np.minimum(self.i_max, i_start)
self.i_start = i_start
self.i_end = self.i_start + self.i_window
self.window.set_scroll_pos(self.i_start)
self.draw_plot()
except IndexError:
pass
def _on_key(self, event):
if event.key == '+' or event.key == '=':
self.ylims /= 2.
elif event.key == '-':
self.ylims *= 2.
else:
return
offset = self.ylims[1] - self.ylims[0]
self.offsets = np.arange(self.n_chans) * offset
self.draw_plot()
def set_spiketimes(self, spk_idx, labels=None, all_labels=None):
if spk_idx:
self.spt = spk_idx['data']
if labels is not None:
self.labels = labels
if all_labels is None:
self.color_func = label_color(np.unique(labels))
else:
self.color_func = label_color(all_labels)
else:
self.labels = None
self.ax_next.set_visible(True)
self.ax_prev.set_visible(True)
else:
self.spt = None
self.ax_next.set_visible(False)
self.ax_prev.set_visible(False)
def set_data(self, data):
self.x = data['data']
self.FS = data['FS']
n_chans, n_pts = self.x.shape
#reset spike times data/hide buttons
self.set_spiketimes(None)
self.i_window = int(self.winsz / 1000. * self.FS)
# Extents of data sequence:
self.i_min = 0
self.i_max = n_pts - self.i_window
self.n_chans = n_chans
self.window.set_scroll_max(self.i_max, self.i_window)
# Indices of data interval to be plotted:
self.i_end = self.i_start + self.i_window
self.time = np.arange(self.i_start, self.i_end) * 1. / self.FS
self.segs = np.empty((n_chans, self.i_window, 2))
self.segs[:, :, 0] = self.time[np.newaxis, :]
self.segs[:, :, 1] = self.x[:, self.i_start:self.i_end]
ylims = (self.segs[:, :, 1].min(), self.segs[:, :, 1].max())
offset = ylims[1] - ylims[0]
self.offsets = np.arange(n_chans) * offset
self.segs[:, :, 1] += self.offsets[:, np.newaxis]
self.ylims = np.array(ylims)
if self.line_collection:
self.line_collection.remove()
self.line_collection = LineCollection(self.segs,
offsets=None,
transform=self.axes.transData,
color='k')
self.axes.add_collection(self.line_collection)
self.axes.set_xlim((self.time[0], self.time[-1]))
self.axes.set_ylim((self.ylims[0] + self.offsets.min(),
self.ylims[1] + self.offsets.max()))
self.canvas.draw()
def draw_plot(self):
self.time = np.arange(self.i_start, self.i_end) * 1. / self.FS
self.segs[:, :, 0] = self.time[np.newaxis, :]
self.segs[:, :, 1] = self.x[:, self.i_start:self.
i_end] + self.offsets[:, np.newaxis]
self.line_collection.set_segments(self.segs)
# Adjust plot limits:
self.axes.set_xlim((self.time[0], self.time[-1]))
self.axes.set_ylim((self.ylims[0] + self.offsets.min(),
self.ylims[1] + self.offsets.max()))
if self.spt is not None:
self.draw_spikes()
# Redraw:
self.canvas.draw()
def draw_spikes(self):
if self.spike_collection is not None:
self.spike_collection.remove()
self.spike_collection = None
sp_win = self.sp_win
time = self.segs[0, :, 0] * 1000.
t_min, t_max = time[0] - sp_win[0], time[-1] - sp_win[1]
spt = self.spt[(self.spt > t_min) & (self.spt < t_max)]
if len(spt) > 0:
n_pts = int((sp_win[1] - sp_win[0]) / 1000. * self.FS)
sp_segs = np.empty((len(spt), self.n_chans, n_pts, 2))
for i in range(len(spt)):
start, = np.nonzero(time >= (spt[i] + sp_win[0]))
start = start[0]
stop = start + n_pts
sp_segs[i, :, :, 0] = (time[np.newaxis, start:stop] / 1000.)
sp_segs[i, :, :, 1] = self.segs[:, start:stop, 1]
sp_segs = sp_segs.reshape(-1, n_pts, 2)
if self.labels is not None:
labs = self.labels[(self.spt > t_min) & (self.spt < t_max)]
colors = np.repeat(self.color_func(labs), self.n_chans, 0)
else:
colors = 'r'
self.spike_collection = LineCollection(
sp_segs,
offsets=None,
color=colors,
transform=self.axes.transData)
self.axes.add_collection(self.spike_collection)
def OnScrollEvt(self, pos):
# Update the indices of the plot:
self.i_start = self.i_min + pos
self.i_end = self.i_min + self.i_window + pos
t_center = (self.i_start + self.i_window / 2.) * 1000. / self.FS
idx, = np.where(self.spt < t_center)
if len(idx) > 0:
self.i_spike = idx[-1]
else:
self.i_spike = 0
self.draw_plot()
class MemmapViewer(object):
def __init__(self, df, label=None):
self.df = df
self.label = label
if self.label is None:
self.label = 'id = {index} size = {Size} timestamp = {timestamp}'
self.fig = plt.gcf()
self.fig.set_size_inches([25, 15], forward=True)
gs = gridspec.GridSpec(2, 1, height_ratios=[20, 1])
self._ax = self.fig.add_subplot(gs[0, 0])
self._ax.set_ylim([-0.2, 0.2])
# create artists
self._lc = draw_memmap('0x0, 17179869184, 0;', ax=self._ax)
self._text = self._ax.text(0.5,
0.8,
"",
ha='center',
va='baseline',
fontsize=25,
transform=self._ax.transAxes)
# lc and texts for allocators
self._lcalloc = LineCollection([[(0, 0.1), (17179869184, 0.1)]],
linewidths=10)
self._ax.add_collection(self._lcalloc)
self._textalloc = []
pu.cleanup_axis_bytes(self._ax.xaxis)
init_frame = 0
self._step(init_frame)
# add a slider
axstep = self.fig.add_subplot(gs[1, 0],
facecolor='lightgoldenrodyellow')
self._stepSlider = Slider(axstep,
'ID',
0,
len(df),
closedmax=False,
valinit=init_frame,
valfmt='%d',
valstep=1,
dragging=True)
def update(val):
self._step(int(val))
self.fig.canvas.draw_idle()
self._stepSlider.on_changed(update)
# listen key press
self.fig.canvas.mpl_connect('key_press_event',
lambda evt: self._keydown(evt))
def _step(self, i):
"""draw step"""
row = self.df.iloc[i]
mapdf, _ = draw_on_lc(row.MemMap, self._lc)
self._text.set_text(self.label.format(index=i, **dict(row.items())))
# draw some lines showing each allocator
nAlloc = len(mapdf.Name.unique())
while len(self._textalloc) < nAlloc:
self._textalloc.append(
self._ax.text(0, 0, "", ha='center', va='baseline'))
allocSeg = []
for (name, grp), t in zip(mapdf.groupby('Name'), self._textalloc):
rgmin, rgmax = grp.NOrigin.min(), grp.NEnd.max()
yval = -.1
allocSeg.append([[rgmin, yval], [rgmax, yval]])
t.set_text(name)
t.set_position([(rgmin + rgmax) / 2, yval * 1.2])
self._lcalloc.set_segments(allocSeg)
self._ax.set_xlim([mapdf.NOrigin.min(), mapdf.NEnd.max()])
def _keydown(self, evt):
if evt.key == 'left':
newval = max(self._stepSlider.val - 1, self._stepSlider.valmin)
self._stepSlider.set_val(newval)
elif evt.key == 'right':
newval = min(self._stepSlider.val + 1, self._stepSlider.valmax - 1)
self._stepSlider.set_val(newval)
self.fig.canvas.draw_idle()
class MemmapViewer(object):
def __init__(self,
df,
colormap,
ptr2sess,
label=None,
doPreprocess=False,
hdf=None):
self.label = label
if self.label is None:
self.label = 'id = {index} timestamp = {timestamp}'
self.colormap = colormap
self.ptr2sess = ptr2sess
self._do_preprocess = doPreprocess
self._hdf = hdf
if doPreprocess:
self.data = preprocess_memmap2(df, self.colormap, self.ptr2sess)
else:
self.data = df
self.fig = plt.gcf()
self.fig.set_size_inches([25, 15], forward=True)
gs = gridspec.GridSpec(2, 1, height_ratios=[20, 1])
self._ax = self.fig.add_subplot(gs[0, 0])
self._ax.set_ylim([-0.2, 0.2])
# create artists
self._lc = draw_memmap('0x0, 17179869184, 0, 0;', ax=self._ax)
self._text = self._ax.text(0.5,
0.8,
"",
ha='center',
va='baseline',
fontsize=25,
transform=self._ax.transAxes)
# lc and texts for bins
self._lcalloc = LineCollection([[(0, 0.1), (17179869184, 0.1)]],
linewidths=10)
self._ax.add_collection(self._lcalloc)
self._textalloc = []
pu.cleanup_axis_bytes(self._ax.xaxis)
init_frame = 0
self._step(init_frame)
# session legend
self._ax.legend(handles=[
mpatches.Patch(color=c, label=sess)
for sess, c in self.colormap.items()
])
# add a slider
axstep = self.fig.add_subplot(gs[1, 0],
facecolor='lightgoldenrodyellow')
self._stepSlider = Slider(axstep,
'ID',
0,
len(self.data) - 1,
valinit=init_frame,
valfmt='%d',
valstep=1,
dragging=True)
def update(val):
self._step(int(val))
self.fig.canvas.draw_idle()
self._stepSlider.on_changed(update)
# timer
self._timer = None
# listen key press
self.fig.canvas.mpl_connect('key_press_event',
lambda evt: self._keydown(evt))
def _data(self, i):
if self._do_preprocess:
return self.data[i]
else:
if self._hdf is None:
try:
row = self.data.iloc[i]
except AttributeError:
row = self.data[i]
return _preprocess_memmap_row((i, row), self.ptr2sess,
self.colormap)
else:
ts = self.data[i]
mapdf = pd.from_hdf(self._hdf, str(ts))
return ts, mapdf
def _step(self, i):
"""draw step"""
ts, mapdf = self._data(i)
try:
mapdf, _ = draw_on_lc(mapdf, self._lc)
except ValueError:
print('Error when parsing memmap for index at {}'.format(i))
return
self._text.set_text(self.label.format(index=i, timestamp=ts))
# draw some lines showing each allocator...
nAlloc = len(mapdf.Bin.unique())
while len(self._textalloc) < nAlloc:
self._textalloc.append(
self._ax.text(0,
0,
"",
rotation='vertical',
ha='center',
va='baseline'))
# ... and clear any extra ones
for t in self._textalloc[nAlloc:]:
t.set_text('')
allocSeg = []
for (bsize, grp), t in zip(mapdf.groupby('Bin'), self._textalloc):
rgmin, rgmax = grp.NOrigin.min(), grp.NEnd.max()
yval = -.1
allocSeg.append([[rgmin, yval], [rgmax, yval]])
t.set_text('Bin({})'.format(pu.bytes2human(bsize)))
t.set_position([(rgmin + rgmax) / 2, yval * 1.2])
self._lcalloc.set_segments(allocSeg)
self._ax.set_xlim([mapdf.NOrigin.min(), mapdf.NEnd.max()])
def _keydown(self, evt):
if evt.key == 'left':
self.prev()
elif evt.key == 'right':
self.next()
elif evt.key == ' ':
if self._timer is None:
self._timer = self.fig.canvas.new_timer(interval=100)
def autonext():
self.next()
if self._stepSlider.val == self._stepSlider.valmax:
# stop timer
self._timer.stop()
self._timer = None
self._timer.add_callback(autonext)
self._timer.start()
else:
self._timer.stop()
self._timer = None
else:
print(evt.key)
def next(self):
newval = min(self._stepSlider.val + 1, self._stepSlider.valmax)
self._stepSlider.set_val(newval)
self.fig.canvas.draw_idle()
def prev(self):
newval = max(self._stepSlider.val - 1, self._stepSlider.valmin)
self._stepSlider.set_val(newval)
self.fig.canvas.draw_idle()
def goto(self, val):
self._stepSlider.set_val(val)
self.fig.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)
def set_segments(self, segments):
'''
Set 3D segments
'''
self._segments3d = segments
LineCollection.set_segments(self, [])
class Visualization(object):
# Visualization tools
def __init__(self):
self.fig = plt.figure()
self.ax = self.fig.add_subplot(111)
self.ax.set_aspect('equal')
plt.ion()
plt.axis('off')
plt.tight_layout()
self.particle_handle = None
self.true_pose_handle = None
self.mean_pose_handle = None
self.lidar_handle = None
# Function to draw the gridmap
# gridmap: An instance of the Gridmap class that specifies
# an occupancy grid representation of the map
# where 1: occupied and 0: free
def drawGridmap(self, gridmap):
(m, n) = gridmap.getShape()
# Set the axis size
self.ax.set_xlim(0, (n) * gridmap.xres, True, False)
self.ax.set_ylim(0, (m) * gridmap.yres, True, False)
for j in range(n):
for i in range(m):
# x0 = (j-1)*gridmap.xres
# y0 = (i-1)*gridmap.yres
x0 = (j) * gridmap.xres
y0 = (i) * gridmap.yres
#y0 = ((m-1) - i)*gridmap.yres
if gridmap.inCollision(j, i, True):
self.ax.add_patch(
patches.Rectangle((x0, y0), gridmap.xres,
gridmap.yres))
self.fig.canvas.draw()
# Function to draw particles
# particles: An N x 3 array where each column is a particle
# weights: An N x 1 array of particle weights
def drawParticles(self, particles, weights=None):
if self.particle_handle == None:
self.particle_handle, = self.ax.plot(particles[0, :],
particles[1, :], 'k.')
else:
self.particle_handle.set_xdata(particles[0, :])
self.particle_handle.set_ydata(particles[1, :])
self.fig.canvas.draw()
# Function to draw ground-truth pose
# x, y, theta: Position and orientation
def drawGroundTruthPose(self, x, y, theta):
if self.true_pose_handle == None:
self.true_pose_handle, = self.ax.plot(x, y, 'r.')
else:
self.true_pose_handle.set_xdata(x)
self.true_pose_handle.set_ydata(y)
self.fig.canvas.draw()
# Function to draw mean pose
# x, y, theta: Position and orientation
def drawMeanPose(self, x, y, theta):
if self.mean_pose_handle == None:
self.mean_pose_handle, = self.ax.plot(x, y, 'go')
else:
self.mean_pose_handle.set_xdata(x)
self.mean_pose_handle.set_ydata(y)
self.fig.canvas.draw()
# Function to draw a LIDAR scan
# range: Array of ranges
# bearing: Array of bearings
# (x,y,theta) Pose from which scan was acquired
def drawLidar(self, range, bearing, x, y, theta):
# Get the XY points corresponding to range and bearing in the LIDAR frame
CosSin = np.vstack((np.cos(bearing[:]), np.sin(bearing[:])))
XY_lidar = np.tile(range.transpose(), (2, 1)) * CosSin
# Define the rotation matrix
R = np.array([[np.cos(theta), -np.sin(theta)],
[np.sin(theta), np.cos(theta)]])
XY_robot = np.tile(np.array([[x], [y]]), (1, bearing.shape[0]))
XY_world = R.dot(
XY_lidar
) + XY_robot #np.tile(np.array([[x],[y]]),(1,bearing.shape[0]))
# Restructure the data to make it suitable for LineCollection
# (a bit ugly, but it works)
XY_worldT = XY_world.transpose()
temp3 = XY_worldT.reshape(-1, 1, 2)
XY_robotT = XY_robot.transpose()
temp4 = XY_robotT.reshape(-1, 1, 2)
lines = np.hstack((temp3, temp4))
if self.lidar_handle == None:
# for i in range(XY_world.shape[1]):
# self.line_handle,
self.lidar_handle = LineCollection(lines,
cmap=plt.cm.gist_ncar,
linewidths=0.5,
color='red')
self.ax.add_collection(self.lidar_handle)
else:
self.lidar_handle.set_segments(lines)
self.fig.canvas.draw()
def create_video_with_keypoints_only(
df,
output_name,
ind_links=None,
pcutoff=0.6,
dotsize=8,
alpha=0.7,
background_color="k",
skeleton_color="navy",
color_by="bodypart",
colormap="viridis",
fps=25,
dpi=200,
codec="h264",
):
bodyparts = df.columns.get_level_values("bodyparts")[::3]
bodypart_names = bodyparts.unique()
n_bodyparts = len(bodypart_names)
nx = int(np.nanmax(df.xs("x", axis=1, level="coords")))
ny = int(np.nanmax(df.xs("y", axis=1, level="coords")))
n_frames = df.shape[0]
xyp = df.values.reshape((n_frames, -1, 3))
if color_by == "bodypart":
map_ = bodyparts.map(dict(zip(bodypart_names, range(n_bodyparts))))
cmap = plt.get_cmap(colormap, n_bodyparts)
elif color_by == "individual":
try:
individuals = df.columns.get_level_values("individuals")[::3]
individual_names = individuals.unique().to_list()
n_individuals = len(individual_names)
map_ = individuals.map(
dict(zip(individual_names, range(n_individuals))))
cmap = plt.get_cmap(colormap, n_individuals)
except KeyError as e:
raise Exception(
"Coloring by individuals is only valid for multi-animal data"
) from e
else:
raise ValueError(f"Invalid color_by={color_by}")
prev_backend = plt.get_backend()
plt.switch_backend("agg")
fig = plt.figure(frameon=False, figsize=(nx / dpi, ny / dpi))
ax = fig.add_subplot(111)
scat = ax.scatter([], [], s=dotsize**2, alpha=alpha)
coords = xyp[0, :, :2]
coords[xyp[0, :, 2] < pcutoff] = np.nan
scat.set_offsets(coords)
colors = cmap(map_)
scat.set_color(colors)
segs = coords[tuple(zip(
*tuple([ind_links])))].swapaxes(0, 1) if ind_links else []
coll = LineCollection(segs, colors=skeleton_color, alpha=alpha)
ax.add_collection(coll)
ax.set_xlim(0, nx)
ax.set_ylim(0, ny)
ax.axis("off")
ax.add_patch(
plt.Rectangle((0, 0),
1,
1,
facecolor=background_color,
transform=ax.transAxes,
zorder=-1))
ax.invert_yaxis()
plt.subplots_adjust(left=0, bottom=0, right=1, top=1, wspace=0, hspace=0)
writer = FFMpegWriter(fps=fps, codec=codec)
with writer.saving(fig, output_name, dpi=dpi):
writer.grab_frame()
for index, _ in enumerate(trange(n_frames - 1), start=1):
coords = xyp[index, :, :2]
coords[xyp[index, :, 2] < pcutoff] = np.nan
scat.set_offsets(coords)
if ind_links:
segs = coords[tuple(zip(*tuple([ind_links])))].swapaxes(0, 1)
coll.set_segments(segs)
writer.grab_frame()
plt.close(fig)
plt.switch_backend(prev_backend)
class TutorialLayerArtist(MatplotlibLayerArtist):
_layer_state_cls = TutorialLayerState
def __init__(self, axes, *args, **kwargs):
super(TutorialLayerArtist, self).__init__(axes, *args, **kwargs)
#self.artist = self.axes.plot([], [], 'o', mec='none')[0]
self.lc = LineCollection([], color='k', linestyle='solid')
self.artist = self.axes.add_collection(self.lc)
self.mpl_artists.append(self.artist)
self.state.add_callback('visible', self._on_visual_change)
self.state.add_callback('zorder', self._on_visual_change)
self.state.add_callback('color', self._on_visual_change)
self.state.add_callback('alpha', self._on_visual_change)
self.state.add_callback('linewidth', self._on_visual_change)
self._viewer_state.add_callback('x_att', self._on_attribute_change)
self._viewer_state.add_callback('y_att', self._on_attribute_change)
self._viewer_state.add_callback('orientation',
self._on_attribute_change)
def _on_visual_change(self, value=None):
self.artist.set_visible(self.state.visible)
self.artist.set_zorder(self.state.zorder)
self.lc.set_color(self.state.color)
self.lc.set_linewidth(self.state.linewidth)
#self.artist.set_markeredgecolor(self.state.color)
# if self.state.fill:
# self.artist.set_markerfacecolor(self.state.color)
# else:
# self.artist.set_markerfacecolor('white')
self.artist.set_alpha(self.state.alpha)
self.redraw()
def _on_attribute_change(self, value=None):
if self._viewer_state.x_att is None or self._viewer_state.y_att is None:
return
#parent
x = self.state.layer[self._viewer_state.x_att]
#height
y = self.state.layer[self._viewer_state.y_att]
orientation = self._viewer_state.orientation
### sorty by
##### sorby_array = None for using the orignal order
sortby_array = y ### sort by height
x, y = sort1Darrays(x, y, sortby_array)
verts, verts_horiz = dendro_layout(x, y, orientation=orientation)
nleaf = calculate_nleaf(x)
### Fix the input!
color_code = 'linear'
color_code_by = y ## height
color_code_cmap = cm.Reds
####
if color_code == 'fixed':
verts_final = np.concatenate([verts, verts_horiz])
colors_final = list(np.ones(len(verts_final)))
elif color_code == 'linear':
cmap = color_code_cmap
normalize = mplcolors.Normalize(np.nanmin(y), np.nanmax(y))
colors = [cmap(normalize(yi)) for yi in y]
colors_horiz = []
for i in range(len(verts_horiz)):
colors_horiz.append((0., 0., 0., 1.))
verts_final = np.concatenate([verts, verts_horiz])
colors_final = np.concatenate([colors, colors_horiz])
#self.artist.set_data(x, y)
self.lc.set_segments(verts_final)
self.lc.set_color(colors_final)
# parent
xmin = (-.5)
xmax = nleaf + 1.5
# height
ymin = np.nanmin(y) - .05 * (np.nanmax(y) - np.nanmin(y))
ymax = np.nanmax(y) + .05 * (np.nanmax(y) - np.nanmin(y))
if orientation == 'bottom-up':
self.axes.set_xlim(xmin, xmax)
self.axes.set_ylim(ymin, ymax)
elif orientation == 'top-down':
self.axes.set_xlim(xmin, xmax)
self.axes.set_ylim(ymax, ymin)
elif orientation == 'left-right':
self.axes.set_ylim(xmin, xmax)
self.axes.set_xlim(ymin, ymax)
elif orientation == 'right-left':
self.axes.set_ylim(xmin, xmax)
self.axes.set_xlim(ymax, ymin)
self.redraw()
def update(self):
self._on_attribute_change()
self._on_visual_change()
def set_segments(self, segments):
'''
Set 3D segments
'''
self._segments3d = np.asanyarray(segments)
LineCollection.set_segments(self, [])
class SpikeBrowserUI(object):
def __init__(self, window):
self.window = window
self.sp_win = [-0.8, 1]
self.spike_collection = None
self.fig = Figure((9, 5), 75)
self.canvas = window.get_canvas(self.fig)
self._mpl_init()
self.canvas.mpl_connect('key_press_event', self._zoom_key_handler)
self.canvas.mpl_connect(
'key_press_event', self._browse_spikes_key_handler)
self.window.set_scroll_handler(self.OnScrollEvt)
def _mpl_init(self):
self.fig.clf()
self.axes = self.fig.add_axes([0.02, 0.1, 0.96, 0.85])
self.fancyyaxis = FancyYAxis(self, 0.05)
self.ax_prev = self.fig.add_axes([0.8, 0.0, 0.1, 0.05])
self.ax_next = self.fig.add_axes([0.9, 0.0, 0.1, 0.05])
self.b_next = Button(self.ax_next, 'Next')
self.b_prev = Button(self.ax_prev, "Prev")
self.b_next.on_clicked(self._next_spike)
self.b_prev.on_clicked(self._prev_spike)
self.i_spike = 0
self.i_start = 0
self.line_collection = None
def _next_spike(self, event):
try:
if self.i_spike < len(self.spt) - 1:
self.i_spike += 1
t_spk = self.spt[self.i_spike]
i_start = int(
np.ceil(t_spk / 1000. * self.FS - self.i_window / 2.))
i_start = np.maximum(self.i_min, i_start)
i_start = np.minimum(self.i_max, i_start)
self.i_start = i_start
self.i_end = self.i_start + self.i_window
self.window.set_scroll_pos(self.i_start)
self.draw_plot()
except IndexError:
pass
def _prev_spike(self, event):
try:
if self.i_spike > 0:
self.i_spike -= 1
t_spk = self.spt[self.i_spike]
i_start = int(
np.ceil(t_spk / 1000. * self.FS - self.i_window / 2.))
i_start = np.maximum(self.i_min, i_start)
i_start = np.minimum(self.i_max, i_start)
self.i_start = i_start
self.i_end = self.i_start + self.i_window
self.window.set_scroll_pos(self.i_start)
self.draw_plot()
except IndexError:
pass
def _zoom_key_handler(self, event):
if event.key == '+' or event.key == '=':
self.scale_y(0.5)
elif event.key == '-':
self.scale_y(2)
elif event.key == 'ctrl++' or event.key == 'ctrl+=':
self.scale_x(0.5)
elif event.key == 'ctrl+-':
self.scale_x(2)
self.draw_plot()
def _browse_spikes_key_handler(self, event):
if event.key == 'right':
self._next_spike(event)
elif event.key == 'left':
self._prev_spike(event)
else:
return
def set_spiketimes(self, spk_idx, labels=None, all_labels=None):
if spk_idx:
self.spt = spk_idx['data']
if labels is not None:
self.labels = labels
if all_labels is None:
self.color_func = label_color(np.unique(labels))
else:
self.color_func = label_color(all_labels)
else:
self.labels = None
self.ax_next.set_visible(True)
self.ax_prev.set_visible(True)
self.update_i_sipke()
else:
self.spt = None
self.ax_next.set_visible(False)
self.ax_prev.set_visible(False)
def set_data(self, data):
self.x = data['data']
self.FS = data['FS']
n_chans, n_pts = self.x.shape
# reset spike times data/hide buttons
self.set_spiketimes(None)
self.i_window = int(self.winsz / 1000. * self.FS)
# Extents of data sequence:
self.i_min = 0
self.i_max = n_pts - self.i_window
self.n_chans = n_chans
self.window.set_scroll_max(self.i_max, self.i_window)
# Indices of data interval to be plotted:
self.i_end = self.i_start + self.i_window
curr_slice = self.x[:, self.i_start:self.i_end]
ylims = (curr_slice.min(), curr_slice.max())
offset = ylims[1] - ylims[0]
self.ylims = np.array(ylims)
self.offsets = np.arange(n_chans) * offset
# will be filled in draw_plot
self.segs = np.empty((n_chans, self.i_window, 2))
if self.line_collection:
self.line_collection.remove()
self.line_collection = LineCollection(self.segs,
offsets=None,
transform=self.axes.transData,
color='k')
self.axes.add_collection(self.line_collection)
self.fancyyaxis.reset()
self.draw_plot()
def draw_plot(self):
self.time = np.arange(self.i_start, self.i_end) * 1. / self.FS
self.segs[:, :, 0] = self.time[np.newaxis, :]
y_signal = self.x[:, self.i_start:self.i_end]
y_signal = y_signal - np.mean(y_signal, 1)[:, None]
self.segs[:, :, 1] = y_signal + self.offsets[:, np.newaxis]
self.line_collection.set_segments(self.segs)
# Adjust plot limits:
self.axes.set_xlim((self.time[0], self.time[-1]))
ygap = np.max(np.abs(self.ylims))
self.axes.set_ylim((- ygap + self.offsets.min(),
ygap + self.offsets.max()))
self.fancyyaxis.update()
if self.spt is not None:
self.draw_spikes()
# Redraw:
self.canvas.draw()
def draw_spikes(self):
if self.spike_collection is not None:
self.spike_collection.remove()
self.spike_collection = None
sp_win = self.sp_win
time = self.segs[0, :, 0] * 1000.
t_min, t_max = time[0] - sp_win[0], time[-1] - sp_win[1]
spt = self.spt[(self.spt > t_min) & (self.spt < t_max)]
if len(spt) > 0:
n_pts = int((sp_win[1] - sp_win[0]) / 1000. * self.FS)
sp_segs = np.empty((len(spt), self.n_chans, n_pts, 2))
for i in range(len(spt)):
start, = np.nonzero(time >= (spt[i] + sp_win[0]))
start = start[0]
stop = start + n_pts
sp_segs[i, :, :, 0] = (time[np.newaxis, start:stop] / 1000.)
sp_segs[i, :, :, 1] = self.segs[:, start:stop, 1]
sp_segs = sp_segs.reshape(-1, n_pts, 2)
if self.labels is not None:
labs = self.labels[(self.spt > t_min) & (self.spt < t_max)]
colors = np.repeat(self.color_func(labs), self.n_chans, 0)
else:
colors = 'r'
self.spike_collection = LineCollection(sp_segs,
offsets=None,
color=colors,
transform=self.axes.transData)
self.axes.add_collection(self.spike_collection)
def scale_y(self, factor):
self.ylims *= factor
offset = self.ylims[1] - self.ylims[0]
self.offsets = np.arange(self.n_chans) * offset
def scale_x(self, factor):
i_center = self.i_start + self.i_window / 2
self.i_window = int(self.i_window * factor)
self.i_start = i_center - self.i_window / 2
self.i_start = self.i_start >= 0 and self.i_start or 0
self.i_end = self.i_start + self.i_window
self.segs = np.empty((self.n_chans, self.i_window, 2))
def OnScrollEvt(self, pos):
# Update the indices of the plot:
self.i_start = self.i_min + pos
self.i_end = self.i_min + self.i_window + pos
self.update_i_sipke()
self.draw_plot()
def update_i_sipke(self):
'''
Finds a spike index which is near or inside the current data
window (between i_start and i_end). The i_spike variable is then
updated with this index.
'''
t_center = (self.i_start + self.i_window / 2.) * 1000. / self.FS
idx, = np.where(self.spt < t_center)
if len(idx) > 0:
self.i_spike = idx[-1]
else:
self.i_spike = 0