def run(self):
""" runs the kymograph aligner """
# show the images
self.fig = plt.figure()
self.ax = plt.gca()
plt.subplots_adjust(bottom=0.2)
# prepare image to work with
image = self.kymograph._make_image(self.kymograph.offsets)
height, width = image.shape
window = self.window_margin
self.data = np.empty((height, width + 2*window), np.double) + np.nan
self.data[:, window:width + window] = image
self.image = self.ax.imshow(self.data, interpolation='none',
aspect='auto', cmap=plt.get_cmap('gray'))
self.ax.set_title(self.title)
# internal data
self.active = True
self.result = 'cancel'
self._ax_points = None
# create the widget for selecting the range
useblit = graphics.backend_supports_blitting()
self.selector = \
widgets.RectangleSelector(self.ax, self.select_callback,
drawtype='box',
useblit=useblit,
button=[1]) # only use the left button
# the rectangle marking the selected area
self.selected = slice(0, 0)
self.selected_marker = patches.Rectangle((0, -5), self.data.shape[1], 0,
color='y', alpha=0.5)
self.ax.add_patch(self.selected_marker)
# add buttons
ax_align = plt.axes([0.5, 0.05, 0.1, 0.075])
bn_align = widgets.Button(ax_align, 'Align All')
bn_align.on_clicked(self.clicked_align)
ax_ok = plt.axes([0.7, 0.05, 0.1, 0.075])
bn_ok = widgets.Button(ax_ok, 'Save')
bn_ok.on_clicked(self.clicked_ok)
ax_cancel = plt.axes([0.81, 0.05, 0.1, 0.075])
bp_cancel = widgets.Button(ax_cancel, 'Cancel')
bp_cancel.on_clicked(self.clicked_cancel)
# initialize the interaction with the image
self.fig.canvas.mpl_connect('key_release_event', self.key_callback)
# process result
plt.show()
return self.result
def measure_lines(self):
""" shows an interface for measuring lines """
# create the widget for selecting the range
useblit = graphics.backend_supports_blitting()
self.selector = \
widgets.RectangleSelector(self.ax, self.select_callback,
drawtype='line', lineprops=self.lineprops,
useblit=useblit, button=[1])
self.line = self.ax.plot([-1, -1], [-1, -1], **self.lineprops)[0]
plt.show()
def __init__(self, ax=None):
if ax is None:
self.ax = plt.gca()
else:
self.ax = ax
self.width = self.ax.get_xlim()[1]
self.height = self.ax.get_ylim()[1]
# create the widget for selecting the range
useblit = graphics.backend_supports_blitting()
self.selector = \
widgets.RectangleSelector(self.ax, self.select_callback,
drawtype='box',
useblit=useblit,
button=[1]) # left button
# the rectangle marking the selected area
self.selected = None
self.selected_marker = patches.Rectangle((0, -5), 0, 0, color='y',
alpha=0.5)
self.ax.add_patch(self.selected_marker)
def run(self):
""" runs the segment picker """
# show the images
self.fig, self.axes = plt.subplots(nrows=1, ncols=2, sharex=True,
sharey=True, squeeze=True)
plt.subplots_adjust(bottom=0.2)
ax_img, ax_feat = self.axes
imshow_args = {'interpolation': 'none', 'aspect': 1,
'cmap': plt.get_cmap('gray')}
ax_img.imshow(self._frame, **imshow_args)
ax_img.set_title('First _frame of video')
ax_img.set_autoscale_on(False)
ax_feat.imshow(self.features, **imshow_args)
ax_feat.set_title('Automatic feature extraction')
ax_feat.set_autoscale_on(False)
# internal data
self.active = True
self.result = 'cancel'
self.bounds = self._frame.shape
self._ax_segments = [[] for _ in xrange(len(self.axes))]
# initialize data
if self.segments:
segments = self.segments
self.segments = []
for segment in segments:
self._add_segment(segment)
# drawtype is 'box' or 'line' or 'none'
useblit = graphics.backend_supports_blitting()
self.selectors = [
widgets.RectangleSelector(ax, self.select_callback,
drawtype='line',
lineprops=self.lineprops,
useblit=useblit,
button=[1], # don't use middle button
minspanx=5, minspany=5,
spancoords='pixels')
for ax in (ax_img, ax_feat)]
# add buttons
ax_active = plt.axes([0.5, 0.05, 0.1, 0.075])
check = widgets.CheckButtons(ax_active, ['active'], [self.active])
check.on_clicked(self.clicked_check)
ax_ok = plt.axes([0.7, 0.05, 0.1, 0.075])
bn_ok = widgets.Button(ax_ok, 'Ok')
bn_ok.on_clicked(self.clicked_ok)
ax_cancel = plt.axes([0.81, 0.05, 0.1, 0.075])
bp_cancel = widgets.Button(ax_cancel, 'Cancel')
bp_cancel.on_clicked(self.clicked_cancel)
self.msg()
# initialize the interaction with the image
self.fig.canvas.mpl_connect('button_press_event', self.click_image)
# process result
plt.show()
return self.result
def run(self):
""" runs the segment picker """
# show the images
self.fig, self.axes = plt.subplots(nrows=1,
ncols=2,
sharex=True,
sharey=True,
squeeze=True)
plt.subplots_adjust(bottom=0.2)
ax_img, ax_feat = self.axes
imshow_args = {
'interpolation': 'none',
'aspect': 1,
'cmap': plt.get_cmap('gray')
}
ax_img.imshow(self._frame, **imshow_args)
ax_img.set_title('First _frame of video')
ax_img.set_autoscale_on(False)
ax_feat.imshow(self.features, **imshow_args)
ax_feat.set_title('Automatic feature extraction')
ax_feat.set_autoscale_on(False)
# internal data
self.active = True
self.result = 'cancel'
self.bounds = self._frame.shape
self._ax_segments = [[] for _ in xrange(len(self.axes))]
# initialize data
if self.segments:
segments = self.segments
self.segments = []
for segment in segments:
self._add_segment(segment)
# drawtype is 'box' or 'line' or 'none'
useblit = graphics.backend_supports_blitting()
self.selectors = [
widgets.RectangleSelector(
ax,
self.select_callback,
drawtype='line',
lineprops=self.lineprops,
useblit=useblit,
button=[1], # don't use middle button
minspanx=5,
minspany=5,
spancoords='pixels') for ax in (ax_img, ax_feat)
]
# add buttons
ax_active = plt.axes([0.5, 0.05, 0.1, 0.075])
check = widgets.CheckButtons(ax_active, ['active'], [self.active])
check.on_clicked(self.clicked_check)
ax_ok = plt.axes([0.7, 0.05, 0.1, 0.075])
bn_ok = widgets.Button(ax_ok, 'Ok')
bn_ok.on_clicked(self.clicked_ok)
ax_cancel = plt.axes([0.81, 0.05, 0.1, 0.075])
bp_cancel = widgets.Button(ax_cancel, 'Cancel')
bp_cancel.on_clicked(self.clicked_cancel)
self.msg()
# initialize the interaction with the image
self.fig.canvas.mpl_connect('button_press_event', self.click_image)
# process result
plt.show()
return self.result
