def plot(self, img):
"""
Plots and call auxfun_drag class for moving and removing points.
"""
self.drs = []
self.updatedCoords = []
for bpindex, bp in enumerate(self.bodyparts):
color = self.colormap(self.norm(self.colorIndex[bpindex]))
self.points = [
self.dataFrame[self.scorer][bp]["x"].values[self.iter],
self.dataFrame[self.scorer][bp]["y"].values[self.iter],
]
circle = [
patches.Circle(
(self.points[0], self.points[1]),
radius=self.markerSize,
fc=color,
alpha=self.alpha,
)
]
self.axes.add_patch(circle[0])
self.dr = auxfun_drag.DraggablePoint(circle[0],
self.bodyparts[bpindex])
self.dr.connect()
self.dr.coords = MainFrame.getLabels(self, self.iter)[bpindex]
self.drs.append(self.dr)
self.updatedCoords.append(self.dr.coords)
if not np.isnan(self.points)[0]:
self.buttonCounter.append(bpindex)
self.figure.canvas.draw()
return self.buttonCounter
def add_point(self, center, animal, bodypart, **kwargs):
circle = patches.Circle(center, **kwargs)
self.ax1.add_patch(circle)
dp = auxfun_drag.DraggablePoint(
circle, bodypart, animal,
)
dp.connect()
self.dps.append(dp)
def onClick(self, event):
"""
This function adds labels and auto advances to the next label.
"""
x1 = event.xdata
y1 = event.ydata
if event.button == 3:
if self.rdb.GetSelection() in self.buttonCounter:
wx.MessageBox(
"%s is already annotated. \n Select another body part to annotate."
% (str(self.bodyparts[self.rdb.GetSelection()])),
"Error!",
wx.OK | wx.ICON_ERROR,
)
else:
color = self.colormap(
self.norm(self.colorIndex[self.rdb.GetSelection()])
)
circle = [
patches.Circle(
(x1, y1), radius=self.markerSize, fc=color, alpha=self.alpha
)
]
self.num.append(circle)
self.axes.add_patch(circle[0])
self.dr = auxfun_drag.DraggablePoint(
circle[0], self.bodyparts[self.rdb.GetSelection()]
)
self.dr.connect()
self.buttonCounter.append(self.rdb.GetSelection())
self.dr.coords = [
[
x1,
y1,
self.bodyparts[self.rdb.GetSelection()],
self.rdb.GetSelection(),
]
]
self.drs.append(self.dr)
self.updatedCoords.append(self.dr.coords)
if self.rdb.GetSelection() < len(self.bodyparts) - 1:
self.rdb.SetSelection(self.rdb.GetSelection() + 1)
self.figure.canvas.draw()
self.canvas.mpl_disconnect(self.onClick)
self.canvas.mpl_disconnect(self.onButtonRelease)
def plot(self, im):
"""
Plots and call auxfun_drag class for moving and removing points.
"""
# small hack in case there are any 0 intensity images!
im = io.imread(im)
maxIntensity = np.max(im)
if maxIntensity == 0:
maxIntensity = np.max(im) + 255
self.drs = []
for bpindex, bp in enumerate(self.bodyparts):
color = self.colormap(self.norm(self.colorIndex[bpindex]))
if "CollectedData_" in self.fileName:
self.points = [
self.Dataframe[self.scorer][bp]["x"].values[self.iter],
self.Dataframe[self.scorer][bp]["y"].values[self.iter],
1.0,
]
self.likelihood = self.points[2]
else:
self.points = [
self.Dataframe[self.scorer][bp]["x"].values[self.iter],
self.Dataframe[self.scorer][bp]["y"].values[self.iter],
self.Dataframe[self.scorer][bp]["likelihood"].values[
self.iter],
]
self.likelihood = self.points[2]
if self.move2corner:
ny, nx = np.shape(im)[0], np.shape(im)[1]
if self.points[0] > nx or self.points[0] < 0:
self.points[0] = self.center[0]
if self.points[1] > ny or self.points[1] < 0:
self.points[1] = self.center[1]
if (not ("CollectedData_" in self.fileName)
and self.likelihood < self.threshold):
circle = [
patches.Circle(
(self.points[0], self.points[1]),
radius=self.markerSize,
facecolor="None",
edgecolor=color,
)
]
else:
circle = [
patches.Circle(
(self.points[0], self.points[1]),
radius=self.markerSize,
fc=color,
alpha=self.alpha,
)
]
self.axes.add_patch(circle[0])
self.dr = auxfun_drag.DraggablePoint(circle[0],
bp,
likelihood=self.likelihood)
self.dr.connect()
self.dr.coords = MainFrame.getLabels(self, self.iter)[bpindex]
self.drs.append(self.dr)
self.updatedCoords.append(self.dr.coords)
self.figure.canvas.draw()
def plot(self, im):
"""
Plots and call auxfun_drag class for moving and removing points.
"""
# small hack in case there are any 0 intensity images!
img = io.imread(im)
maxIntensity = np.max(img)
if maxIntensity == 0:
maxIntensity = np.max(img) + 255
divider = make_axes_locatable(self.axes)
cax = divider.append_axes("right", size="5%", pad=0.05)
self.drs = []
if (self.visualization_rdb.GetSelection() == 0
): # i.e. for color scheme for individuals
self.Colorscheme = visualization.get_cmap(
len(self.individual_names), self.cfg["colormap"])
self.norm, self.colorIndex = self.image_panel.getColorIndices(
im, self.individual_names)
cbar = self.figure.colorbar(self.ax,
cax=cax,
spacing="proportional",
ticks=self.colorIndex)
cbar.set_ticklabels(self.individual_names)
else: # i.e. for color scheme for all bodyparts
self.Colorscheme = visualization.get_cmap(len(self.all_bodyparts),
self.cfg["colormap"])
self.norm, self.colorIndex = self.image_panel.getColorIndices(
im, self.all_bodyparts)
cbar = self.figure.colorbar(self.ax,
cax=cax,
spacing="proportional",
ticks=self.colorIndex)
cbar.set_ticklabels(self.all_bodyparts)
for ci, ind in enumerate(self.individual_names):
col_idx = (
0 # variable for iterating through the colorscheme for all bodyparts
)
image_points = []
if ind == "single":
if self.visualization_rdb.GetSelection() == 0:
for c, bp in enumerate(self.uniquebodyparts):
self.points = [
self.Dataframe[self.scorer][ind][bp]["x"].values[
self.iter],
self.Dataframe[self.scorer][ind][bp]["y"].values[
self.iter],
self.Dataframe[self.scorer][ind][bp]
["likelihood"].values[self.iter],
]
self.likelihood = self.points[2]
# fix move to corner
if self.move2corner:
ny, nx = np.shape(img)[0], np.shape(img)[1]
if self.points[0] > nx or self.points[0] < 0:
print("fixing x for ", bp)
self.points[0] = self.center[0]
if self.points[1] > ny or self.points[1] < 0:
print("fixing y for ", bp)
self.points[1] = self.center[1]
if self.likelihood < self.threshold:
self.circle = [
patches.Circle(
(self.points[0], self.points[1]),
radius=self.markerSize,
facecolor="None",
edgecolor=self.Colorscheme(ci),
alpha=self.alpha,
)
]
else:
self.circle = [
patches.Circle(
(self.points[0], self.points[1]),
radius=self.markerSize,
fc=self.Colorscheme(ci),
alpha=self.alpha,
)
]
self.axes.add_patch(self.circle[0])
self.dr = auxfun_drag.DraggablePoint(
self.circle[0],
bp,
individual_names=ind,
likelihood=self.likelihood,
)
self.dr.connect()
self.dr.coords = MainFrame.getLabels(
self, self.iter, ind, self.uniquebodyparts)[c]
self.drs.append(self.dr)
self.updatedCoords.append(self.dr.coords)
else:
for c, bp in enumerate(self.uniquebodyparts):
self.points = [
self.Dataframe[self.scorer][ind][bp]["x"].values[
self.iter],
self.Dataframe[self.scorer][ind][bp]["y"].values[
self.iter],
self.Dataframe[self.scorer][ind][bp]
["likelihood"].values[self.iter],
]
self.likelihood = self.points[2]
# fix move to corner
if self.move2corner:
ny, nx = np.shape(img)[0], np.shape(img)[1]
if self.points[0] > nx or self.points[0] < 0:
print("fixing x for ", bp)
self.points[0] = self.center[0]
if self.points[1] > ny or self.points[1] < 0:
print("fixing y for ", bp)
self.points[1] = self.center[1]
if self.likelihood < self.threshold:
self.circle = [
patches.Circle(
(self.points[0], self.points[1]),
radius=self.markerSize,
fc="None",
edgecolor=self.Colorscheme(col_idx),
alpha=self.alpha,
)
]
else:
self.circle = [
patches.Circle(
(self.points[0], self.points[1]),
radius=self.markerSize,
fc=self.Colorscheme(col_idx),
alpha=self.alpha,
)
]
self.axes.add_patch(self.circle[0])
col_idx = col_idx + 1
self.dr = auxfun_drag.DraggablePoint(
self.circle[0],
bp,
individual_names=ind,
likelihood=self.likelihood,
)
self.dr.connect()
self.dr.coords = MainFrame.getLabels(
self, self.iter, ind, self.uniquebodyparts)[c]
self.drs.append(self.dr)
self.updatedCoords.append(self.dr.coords)
else:
if self.visualization_rdb.GetSelection() == 0:
for c, bp in enumerate(self.multianimalbodyparts):
self.points = [
self.Dataframe[self.scorer][ind][bp]["x"].values[
self.iter],
self.Dataframe[self.scorer][ind][bp]["y"].values[
self.iter],
self.Dataframe[self.scorer][ind][bp]
["likelihood"].values[self.iter],
]
self.likelihood = self.points[2]
# fix move to corner
if self.move2corner:
ny, nx = np.shape(img)[0], np.shape(img)[1]
if self.points[0] > nx or self.points[0] < 0:
print("fixing x for ", bp)
self.points[0] = self.center[0]
if self.points[1] > ny or self.points[1] < 0:
print("fixing y for ", bp)
self.points[1] = self.center[1]
if self.likelihood < self.threshold:
self.circle = [
patches.Circle(
(self.points[0], self.points[1]),
radius=self.markerSize,
fc="None",
edgecolor=self.Colorscheme(ci),
alpha=self.alpha,
)
]
else:
self.circle = [
patches.Circle(
(self.points[0], self.points[1]),
radius=self.markerSize,
fc=self.Colorscheme(ci),
alpha=self.alpha,
)
]
self.axes.add_patch(self.circle[0])
self.dr = auxfun_drag.DraggablePoint(
self.circle[0],
bp,
individual_names=ind,
likelihood=self.likelihood,
)
self.dr.connect()
self.dr.coords = MainFrame.getLabels(
self, self.iter, ind, self.multianimalbodyparts)[c]
self.drs.append(self.dr)
self.updatedCoords.append(self.dr.coords)
else:
for c, bp in enumerate(self.multianimalbodyparts):
self.points = [
self.Dataframe[self.scorer][ind][bp]["x"].values[
self.iter],
self.Dataframe[self.scorer][ind][bp]["y"].values[
self.iter],
self.Dataframe[self.scorer][ind][bp]
["likelihood"].values[self.iter],
]
self.likelihood = self.points[2]
# fix move to corner
if self.move2corner:
ny, nx = np.shape(img)[0], np.shape(img)[1]
if self.points[0] > nx or self.points[0] < 0:
print("fixing x for ", bp)
self.points[0] = self.center[0]
if self.points[1] > ny or self.points[1] < 0:
print("fixing y for ", bp)
self.points[1] = self.center[1]
if self.likelihood < self.threshold:
self.circle = [
patches.Circle(
(self.points[0], self.points[1]),
radius=self.markerSize,
fc="None",
edgecolor=self.Colorscheme(col_idx),
alpha=self.alpha,
)
]
else:
self.circle = [
patches.Circle(
(self.points[0], self.points[1]),
radius=self.markerSize,
fc=self.Colorscheme(col_idx),
alpha=self.alpha,
)
]
self.axes.add_patch(self.circle[0])
col_idx = col_idx + 1
self.dr = auxfun_drag.DraggablePoint(
self.circle[0],
bp,
individual_names=ind,
likelihood=self.likelihood,
)
self.dr.connect()
self.dr.coords = MainFrame.getLabels(
self, self.iter, ind, self.multianimalbodyparts)[c]
self.drs.append(self.dr)
self.updatedCoords.append(self.dr.coords)
self.figure.canvas.draw()
