def plot(self, **kwargs):
self.configure()
if self.figure is None:
self.create_figure()
self.create_axis()
data = self.data_function(axes_manager=self.axes_manager)
if rgb_tools.is_rgbx(data):
self.colorbar = False
data = rgb_tools.rgbx2regular_array(data, plot_friendly=True)
self.optimize_contrast(data)
if (not self.axes_manager or self.axes_manager.navigation_size == 0):
self.plot_indices = False
if self.plot_indices is True:
if self._text is not None:
self._text.remove()
self._text = self.ax.text(
*self._text_position,
s=str(self.axes_manager.indices),
transform=self.ax.transAxes,
fontsize=12,
color='red',
animated=self.figure.canvas.supports_blit)
for marker in self.ax_markers:
marker.plot()
self.update(**kwargs)
if self.scalebar is True:
if self.pixel_units is not None:
self.ax.scalebar = widgets.ScaleBar(
ax=self.ax,
units=self.pixel_units,
animated=self.figure.canvas.supports_blit,
color=self.scalebar_color,
)
if self.colorbar is True:
self._colorbar = plt.colorbar(self.ax.images[0], ax=self.ax)
self._colorbar.set_label(self.quantity_label,
rotation=-90,
va='bottom')
self._colorbar.ax.yaxis.set_animated(
self.figure.canvas.supports_blit)
self._set_background()
self.figure.canvas.draw_idle()
if hasattr(self.figure, 'tight_layout'):
try:
if self.axes_ticks == 'off' and not self.colorbar:
plt.subplots_adjust(0, 0, 1, 1)
else:
self.figure.tight_layout()
except:
# tight_layout is a bit brittle, we do this just in case it
# complains
pass
self.connect()
def plot(self, **kwargs):
self.configure()
if self.figure is None:
self.create_figure()
self.create_axis()
data = self.data_function(axes_manager=self.axes_manager)
if rgb_tools.is_rgbx(data):
self.colorbar = False
data = rgb_tools.rgbx2regular_array(data, plot_friendly=True)
if self.vmin is not None or self.vmax is not None:
warnings.warn('vmin or vmax value given, hence '
'auto_contrast is set to False')
self.auto_contrast = False
self.optimize_contrast(data)
if (not self.axes_manager or self.axes_manager.navigation_size == 0):
self.plot_indices = False
if self.plot_indices is True:
if self._text is not None:
self._text.remove()
self._text = self.ax.text(*self._text_position,
s=str(self.axes_manager.indices),
transform=self.ax.transAxes,
fontsize=12,
color='red',
animated=True)
for marker in self.ax_markers:
marker.plot()
self.update(**kwargs)
if self.scalebar is True:
if self.pixel_units is not None:
self.ax.scalebar = widgets.ScaleBar(
ax=self.ax,
units=self.pixel_units,
animated=True,
color=self.scalebar_color,
)
if self.colorbar is True:
self._colorbar = plt.colorbar(self.ax.images[0], ax=self.ax)
self._colorbar.ax.yaxis.set_animated(True)
self.figure.canvas.draw()
if hasattr(self.figure, 'tight_layout'):
try:
self.figure.tight_layout()
except:
# tight_layout is a bit brittle, we do this just in case it
# complains
pass
self.connect()
def plot(self, data_function_kwargs={}, **kwargs):
self.data_function_kwargs = data_function_kwargs
self.configure()
if self.figure is None:
self.create_figure()
self.create_axis()
if (not self.axes_manager or self.axes_manager.navigation_size == 0):
self.plot_indices = False
if self.plot_indices is True:
if self._text is not None:
self._text.remove()
self._text = self.ax.text(
*self._text_position,
s=str(self.axes_manager.indices),
transform=self.ax.transAxes,
fontsize=12,
color='red',
animated=self.figure.canvas.supports_blit)
for marker in self.ax_markers:
marker.plot()
for attribute in ['vmin', 'vmax']:
if attribute in kwargs.keys():
setattr(self, attribute, kwargs.pop(attribute))
self.update(data_changed=True, auto_contrast=True, **kwargs)
if self.scalebar is True:
if self.pixel_units is not None:
self.ax.scalebar = widgets.ScaleBar(
ax=self.ax,
units=self.pixel_units,
animated=self.figure.canvas.supports_blit,
color=self.scalebar_color,
)
if self.colorbar:
self._add_colorbar()
if hasattr(self.figure, 'tight_layout'):
try:
if self.axes_ticks == 'off' and not self.colorbar:
plt.subplots_adjust(0, 0, 1, 1)
else:
self.figure.tight_layout()
except BaseException:
# tight_layout is a bit brittle, we do this just in case it
# complains
pass
self.connect()
self.figure.canvas.draw()
ax = fig.add_subplot(1,1,1)
# save corrected image as png and hdf5. The 'hdf5' file contains original intensity information an can be used for the quantification of intensity.
filename = img.metadata.General.original_filename
img.mean(0).save("%s.png" %(filename), overwrite=True)
img.mean(0).save("%s.hdf5" %(filename), overwrite=True)
np.savetxt('%s.csv' %(filename), shift, delimiter=',')
#print("%s is aligned" %(filename))
# Save images with scale bar in a different folder.
os.chdir('scalebar')
imgplot = ax.imshow(img.mean(0).data, extent=[0,cal*resx,0,cal*resy])
#imgplot.set_clim(min, max)
#scalebar = widgets.Scale_Bar(ax=ax, units='%s' %(unit), lw=4, color='white', max_size_ratio=0.12)
scalebar = widgets.ScaleBar(ax=ax, units=unit, lw=4, color='white', max_size_ratio=0.15)
#cbar = fig.colorbar(imgplot)
ax.set_frame_on(False)
ax.axes.get_yaxis().set_visible(False)
ax.axes.get_xaxis().set_visible(False)
filename = img.metadata.General.original_filename
plt.rcParams['mathtext.fontset'] = "stix"
plt.subplots_adjust(bottom=0, left=0, right=1, top=1)
plt.savefig("%s.tiff" %(filename), frameon=False, overwrite=True, dpi=dpx)
plt.close()
print("%s is aligned and converted" %(filename))
os.chdir('../')
print("Batch convert mission is completed")
cal = img.original_metadata.ImageList.TagGroup0.ImageData.Calibrations.Dimension.TagGroup0.Scale
unit = img.original_metadata.ImageList.TagGroup0.ImageData.Calibrations.Dimension.TagGroup0.Units
dpx = res * 100.0 / 480.0
## scale bar for 2nm
#scale = 2/cal/res
#print scale
fig = plt.figure()
ax = fig.add_subplot(1, 1, 1)
imgplot = ax.imshow(img.data, extent=[0, cal * res, 0, cal * res])
imgplot.set_clim(min, max)
scalebar = widgets.ScaleBar(ax=ax,
units='%s' % (unit),
lw=4,
color='white',
max_size_ratio=0.12)
#cbar = fig.colorbar(imgplot)
ax.set_frame_on(False)
ax.axes.get_yaxis().set_visible(False)
ax.axes.get_xaxis().set_visible(False)
#plt.axhline(y=res*(1-0.05), xmin=0.05, xmax=0.05+scale, linewidth=4, color='w')
#ax.set_title("Sample")
#plt.show()
filename = img.metadata.General.get_item('title')
plt.rcParams['mathtext.fontset'] = "stix"
# plt.savefig("%s.png" %(filename), frameon=False, overwrite=True, dpi=dpx)
def plot(self, **kwargs):
self.configure()
if self.figure is None:
self.create_figure()
self.create_axis()
data = self.data_function(axes_manager=self.axes_manager)
if rgb_tools.is_rgbx(data):
self.colorbar = False
data = rgb_tools.rgbx2regular_array(data, plot_friendly=True)
self.optimize_contrast(data)
if (not self.axes_manager or
self.axes_manager.navigation_size == 0):
self.plot_indices = False
if self.plot_indices is True:
if self._text is not None:
self._text.remove()
self._text = self.ax.text(
*self._text_position,
s=str(self.axes_manager.indices),
transform=self.ax.transAxes,
fontsize=12,
color='red',
animated=self.figure.canvas.supports_blit)
for marker in self.ax_markers:
marker.plot()
self.update(**kwargs)
if self.scalebar is True:
if self.pixel_units is not None:
self.ax.scalebar = widgets.ScaleBar(
ax=self.ax,
units=self.pixel_units,
animated=self.figure.canvas.supports_blit,
color=self.scalebar_color,
)
if self.colorbar is True:
self._colorbar = plt.colorbar(self.ax.images[0], ax=self.ax)
self._colorbar.set_label(
self.quantity_label, rotation=-90, va='bottom')
self._colorbar.ax.yaxis.set_animated(
self.figure.canvas.supports_blit)
self._set_background()
if hasattr(self.figure, 'tight_layout'):
try:
if self.axes_ticks == 'off' and not self.colorbar:
plt.subplots_adjust(0, 0, 1, 1)
else:
self.figure.tight_layout()
except BaseException:
# tight_layout is a bit brittle, we do this just in case it
# complains
pass
self.connect()
# ask the canvas to re-draw itself the next time it
# has a chance.
# For most of the GUI backends this adds an event to the queue
# of the GUI frameworks event loop.
self.figure.canvas.draw_idle()
try:
# make sure that the GUI framework has a chance to run its event loop
# and clear any GUI events. This needs to be in a try/except block
# because the default implementation of this method is to raise
# NotImplementedError
self.figure.canvas.flush_events()
except NotImplementedError:
pass