def showmask(self, show_mask):
MainDisplay.init_canvas(self)
if self.skfilterButton.cget('text') == 'Hide':
MainDisplay.show_filter(self)
elif self.skfilterButton.cget('text') == 'Filter':
MainDisplay.show_image(self)
if show_mask == 0:
if self.skmaskButton.cget('text') == 'Hide':
self.skmaskButton.config(text='Mask')
elif self.skmaskButton.cget('text') == 'Mask':
MainDisplay.show_mask(self)
self.skmaskButton.config(text='Hide')
elif show_mask == 1:
MainDisplay.show_mask(self)
self._canvas.draw()
self.eshowButton.config(text='Show')
self.skskeletonButton.config(text='Skeleton')
self.tshowlabelButton.config(text='Show Labels')
self.tshowfitButton.config(text='Show Fit')
self._overedge['enable'].set(0)
self._overskel['enable'].set(0)
self._overlabel['enable'].set(0)
self._overfit['enable'].set(0)
def text_load(self, filename):
with open(filename, 'r') as f:
init_header = f.readline()
if 'Channel' in init_header:
self._img_info = FileOpen.initvar_img(self)
self._img_info['type'].set('AFM')
FileOpen.import_afm(self, filename)
MainDisplay.init_canvas(self)
MainDisplay.show_image(self)
def clearall_roiList(self): MainDisplay.show_overlay(self) ROIdisplay.noshow_roi(self) del self._roipath del self._roilabel self.roiListbox.delete(0, 'end') self._canvas.draw()
def reset(self):
self._mat_img = 1 * self._source_img
self._img_info['xmin'].set(0)
self._img_info['xmax'].set(int(self._img_info['sizepix_x'].get()))
self._img_info['ymin'].set(0)
self._img_info['ymax'].set(int(self._img_info['sizepix_y'].get()))
self._img_info['vmin'].set(np.min(self._mat_img.flatten()))
self._img_info['vmax'].set(np.max(self._mat_img.flatten()))
MainDisplay.init_canvas(self)
MainDisplay.show_image(self)
def show_localfit(self):
if self.tshowfitButton.cget('text') == 'Show Fit':
self._overfit['enable'].set(1)
self.tshowfitButton.config(text='Hide Fit')
elif self.tshowfitButton.cget('text') == 'Hide Fit':
self._overfit['enable'].set(0)
self.tshowfitButton.config(text='Show Fit')
MainDisplay.show_overlay(self)
self.skfilterButton.config(text='Filter')
self.skmaskButton.config(text='Mask')
def show_track(self):
if self.tshowlabelButton.cget('text') == 'Show Labels':
self._overlabel['enable'].set(1)
self.tshowlabelButton.config(text='Hide Labels')
elif self.tshowlabelButton.cget('text') == 'Hide Labels':
self._overlabel['enable'].set(0)
self.tshowlabelButton.config(text='Show Labels')
MainDisplay.show_overlay(self)
self.skfilterButton.config(text='Filter')
self.skmaskButton.config(text='Mask')
def showskeleton(self):
if self.skskeletonButton.cget('text') == 'Skeleton':
self._overskel['enable'].set(1)
self.skskeletonButton.config(text='Hide')
elif self.skskeletonButton.cget('text') == 'Hide':
self._overskel['enable'].set(0)
self.skskeletonButton.config(text='Skeleton')
MainDisplay.show_overlay(self)
self.skfilterButton.config(text='Filter')
self.skmaskButton.config(text='Mask')
def show(self):
if self.eshowButton.cget('text') == 'Show':
self._overedge['enable'].set(1)
self.eshowButton.config(text='Hide')
elif self.eshowButton.cget('text') == 'Hide':
self._overedge['enable'].set(0)
self.eshowButton.config(text='Show')
MainDisplay.show_overlay(self)
self.skfilterButton.config(text='Filter')
self.skmaskButton.config(text='Mask')
def keepdelall_roi(self, keep): self.roiListbox.selection_clear(0, 'end') self.roiListbox.selection_set(0, 'end') if keep == 0: ROImanager.deldata_inroi(self) elif keep == 1: ROImanager.keepdata_inroi(self) ROIdisplay.noshow_roi(self) del self._roipath; del self._roilabel self.roiListbox.delete(0, 'end') MainDisplay.show_overlay(self)
def apply(self): self._overedge['size'].set(self.ove_szSpinbox.get()) self._overedge['ecolor'].set(self.ove_ecCombobox.get()) self._overedge['fcolor'].set(self.ove_fcCombobox.get()) self._overskel['size'].set(self.ovs_szSpinbox.get()) self._overskel['ecolor'].set(self.ovs_ecCombobox.get()) self._overskel['fcolor'].set(self.ovs_fcCombobox.get()) self._overlabel['size'].set(self.ovl_szSpinbox.get()) self._overlabel['ecolor'].set(self.ovl_ecCombobox.get()) self._overfit['lwidth'].set(self.ovf_lwSpinbox.get()) self._overfit['color'].set(self.ovf_lcCombobox.get()) MainDisplay.show_overlay(self) try: ROIdisplay.show_roi(self) except AttributeError: pass ImageOverlay.setstate_cpanel(self)
def crop_infostrip(self):
if self._img_info['sizepix_y'].get() == 2207: size_infostrip = 175
elif self._img_info['sizepix_y'].get() == 1103: size_infostrip = 85
try:
self._mat_img = self._source_img[:-size_infostrip, :]
self._img_info['xmin'].set(0)
self._img_info['xmax'].set(int(self._img_info['sizepix_x'].get()))
self._img_info['ymin'].set(0)
self._img_info['ymax'].set(
int(int(self._img_info['sizepix_y'].get()) - size_infostrip))
self._img_info['vmin'].set(np.min(self._mat_img.flatten()))
self._img_info['vmax'].set(np.max(self._mat_img.flatten()))
self._tracking_step = 2
except NameError:
self.imgcropinfoButton.config(text='Size not known')
self.imgcropinfoButton.state(['disabled'])
MainDisplay.init_canvas(self)
MainDisplay.show_image(self)
def crop_selection(self):
x1, x2 = self._a_img.get_xlim()
y2, y1 = self._a_img.get_ylim()
if int(x1) < 0: x1 = 0
if int(y1) < 0: y1 = 0
if int(x2) > self._mat_img.shape[1]: x2 = self._mat_img.shape[1]
if int(y2) > self._mat_img.shape[0]: y2 = self._mat_img.shape[0]
self._img_info['xmin'].set(int(x1))
self._img_info['xmax'].set(int(x2))
self._img_info['ymin'].set(int(y1))
self._img_info['ymax'].set(int(y2))
self._mat_img = self._mat_img[int(y1):int(y2), int(x1):int(x2)]
self._img_info['vmin'].set(np.min(self._mat_img.flatten()))
self._img_info['vmax'].set(np.max(self._mat_img.flatten()))
MainDisplay.init_canvas(self)
MainDisplay.show_image(self)
self._tracking_step = 2
def image_load(self, filename):
self._img_info = FileOpen.initvar_img(self)
self._img_info['type'].set('STEM')
source_image = np.array(Image.open(filename))
self._img_info['sizepix_x'].set(source_image.shape[1])
self._img_info['sizepix_y'].set(source_image.shape[0])
self._colormap_options['Source'] = 'gray'
self._menucheckCO.set(0)
try: self._source_img = source_image[:,:,0];
except IndexError: self._source_img = source_image[:,:]
self._img_info['vmin'].set(np.min(source_image.flatten()))
self._img_info['vmax'].set(np.max(source_image.flatten()))
self._mat_img = 1*self._source_img
MainDisplay.init_canvas(self)
MainDisplay.show_image(self)
self._canvas.draw()
def keepdelsel_roi(self, keep): if keep == 0: ROImanager.deldata_inroi(self) list_del = self.roiListbox.curselection() elif keep == 1: ROImanager.keepdata_inroi(self) list_del = [item for item in np.arange(self.roiListbox.size()) if item not in self.roiListbox.curselection()] ROIdisplay.noshow_roi(self) for item in sorted(list_del, reverse=True): del self._roipath[item] del self._roilabel[item] for n, item in enumerate(self._roilabel): item.set_text(str(n+1)) MainDisplay.show_overlay(self) ROIdisplay.show_roi(self) ROImanager.update_roiList(self)
def finalstep(self):
MainDisplay.init_canvas(self)
MainDisplay.show_image(self)
self.progressBar.config(mode='determinate',
maximum=np.max(self._im.flatten()) + 1)
self.progressBar['value'] = 1
self.progressBar.update()
ascale = self._tracking_settings['edge_ascale_current'].get()
xm = 1 * self._xmm[self._im > 0]
ym = 1 * self._ymm[self._im > 0]
im = 1 * self._im[self._im > 0]
m = self._m[self._im > 0]
int_profile = []
pos_profile = []
full_profile = []
full_position = []
fiber_xc = []
fiber_yc = []
fiber_x1 = []
fiber_x2 = []
fiber_y1 = []
fiber_y2 = []
fiber_e1 = []
fiber_e2 = []
fiber_number = []
fiber_slope = []
xprofile = []
yprofile = []
pix_edge = int(self._tracking_settings['pixels_edge_img'].get())
pix_back = int(
self._tracking_settings['pixels_background_profile'].get())
nc = 0
for icn in np.unique(im):
self.progressBar['value'] = icn
self.progressBar.update()
xcn = xm[np.where(im == icn)]
ycn = ym[np.where(im == icn)]
mcn = m[np.where(im == icn)]
nc = nc + 1
for ix in range(len(xcn)):
print('Filament: ' + str(icn) + ' (' + str(np.unique(im)[-1]) +
') Profile: ' + str(ix + 1) + ' (' + str(len(xcn)) + ')')
if (ycn[ix] >= pix_edge) and (
xcn[ix] >= pix_edge
): # if the point lies inside the confidence area determined by the picture edge to discard
if mcn[ix] >= 1e6: # if the skeleton line is vertical
direction = 0
x_interp = np.arange(0, self._mat_img.shape[1])
y_interp = np.array(
[int(x) for x in ycn[ix] * np.ones(len(x_interp))])
offset_edge = int(ascale) + int(pix_back)
elif np.abs(mcn[ix]) < 1 / self._mat_img.shape[
1]: # if the skeleton line is horizontal
direction = 1
y_interp = np.arange(0, self._mat_img.shape[0])
x_interp = np.array(
[int(x) for x in xcn[ix] * np.ones(len(y_interp))])
offset_edge = int(ascale) + int(pix_back)
else: # if the skeleton line is diagonal
direction = 2
x_pline = np.arange(0, self._mat_img.shape[1])
y_pline = ycn[ix] + 1 / mcn[ix] * (xcn[ix] - x_pline)
if y_pline[1] > y_pline[-1]:
if np.max(y_pline) >= self._mat_img.shape[0]:
ind_y1 = np.where(y_pline >= self._mat_img.
shape[0])[0][-1] + 1
else:
ind_y1 = 1
if np.min(y_pline) < 0:
ind_y2 = np.where(y_pline < 0)[0][0] - 1
else:
ind_y2 = len(y_pline)
else:
if np.max(y_pline) >= self._mat_img.shape[0]:
ind_y2 = np.where(y_pline >= self._mat_img.
shape[0])[0][0] - 1
else:
ind_y2 = len(y_pline)
if np.min(y_pline) < 0:
ind_y1 = np.where(y_pline < 0)[0][-1] - 1
else:
ind_y1 = 1
x_profile = [int(x) for x in x_pline[ind_y1:ind_y2]]
y_profile = [int(x) for x in y_pline[ind_y1:ind_y2]]
try:
f_interp = interp1d(x_profile, y_profile)
x_interp = np.arange(np.min(x_profile),
np.max(x_profile),
step=0.1)
offset_edge = 10 * (int(ascale) + int(pix_back))
y_interp = f_interp(x_interp)
except ValueError:
x_interp = x_profile
y_interp = y_profile
offset_edge = int(ascale) + int(pix_back)
x_profile_int = [int(x) for x in x_interp]
y_profile_int = [int(x) for x in y_interp]
x_profile = np.array(x_profile_int)
y_profile = np.array(y_profile_int)
try:
xms = np.mean(
np.where(np.abs(x_profile - xcn[ix]) < 2))
yms = np.mean(
np.where(np.abs(y_profile - ycn[ix]) < 2))
if direction == 0: posx = int(xms)
elif direction == 1: posx = int(yms)
elif direction == 2: posx = int(np.mean([xms, yms]))
sign_position = 0 * x_profile
sign_position[:posx] = -1
sign_position[posx:] = 1
mask_profile = 0 * self._mask_edge
mask_profile[y_profile[posx:], x_profile[posx:]] = 1
mask_profile[y_profile[:posx], x_profile[:posx]] = -1
mask_overlap = mask_profile * binary_dilation(
self._mask_edge)
try:
ymatch = np.where(mask_overlap < 0)[0]
xmatch = np.where(mask_overlap < 0)[1]
dmatch = np.sqrt((xmatch - xcn[ix])**2 +
(ymatch - ycn[ix])**2)
ind_x1 = xmatch[np.argmin(dmatch)]
ind_y1 = ymatch[np.argmin(dmatch)]
ymatch = np.where(mask_overlap > 0)[0]
xmatch = np.where(mask_overlap > 0)[1]
dmatch = np.sqrt((xmatch - xcn[ix])**2 +
(ymatch - ycn[ix])**2)
ind_x2 = xmatch[np.argmin(dmatch)]
ind_y2 = ymatch[np.argmin(dmatch)]
ind_xmatch = [ind_x1, ind_x2]
ind_ymatch = [ind_y1, ind_y2]
try:
if direction == 0:
ind_1 = np.where(x_profile == ind_x1)[0][0]
ind_2 = np.where(x_profile == ind_x2)[0][0]
else:
ind_1 = np.where(y_profile == ind_y1)[0][0]
ind_2 = np.where(y_profile == ind_y2)[0][0]
xmatch = x_profile[ind_1 - offset_edge:ind_2 +
offset_edge]
ymatch = y_profile[ind_1 - offset_edge:ind_2 +
offset_edge]
full_profile.append(
np.array(self._mat_img[y_profile,
x_profile]))
int_profile.append(
np.array(self._mat_img[ymatch, xmatch]))
fiber_xc.append(
np.mean(
[x_profile[ind_1], x_profile[ind_2]]))
fiber_yc.append(
np.mean(
[y_profile[ind_1], y_profile[ind_2]]))
fiber_x1.append(x_profile[ind_1])
fiber_x2.append(x_profile[ind_2])
fiber_y1.append(y_profile[ind_1])
fiber_y2.append(y_profile[ind_2])
fiber_e1.append(self._WT_m1[fiber_y1[-1],
fiber_x1[-1]])
fiber_e2.append(self._WT_m1[fiber_y2[-1],
fiber_x2[-1]])
fiber_number.append(nc)
fiber_slope.append(mcn[ix])
dist_full = np.sqrt(
(x_profile - fiber_xc[-1])**2 +
(y_profile -
fiber_yc[-1])**2) * sign_position
full_position.append(dist_full)
pos_profile.append(
dist_full[ind_1 - offset_edge:ind_2 +
offset_edge])
except IndexError as e:
print('error 182: ' + str(e))
except ValueError as e:
print('error 183: ' + str(e))
except ValueError as e:
print('error 184: ' + str(e))
mask_newlabel = 0 * self._mat_img
fx = [int(x) for x in fiber_xc]
fy = [int(x) for x in fiber_yc]
mask_newlabel[np.array(fy), np.array(fx)] = 1
labelled_filaments = remove_small_objects(label(mask_newlabel),
min_size=3)
[yl, xl] = np.where(labelled_filaments)
xy_l = [[xl[ix], yl[ix]] for ix in range(len(xl))]
new_ind = [0 for x in fiber_xc]
for ix in range(0, len(fiber_xc)):
if [fx[ix], fy[ix]] in xy_l: new_ind[ix] = 1
new_ind = np.array(new_ind)
ind_del = np.where(new_ind == 0)[0]
self.progressBar['value'] = icn + 1
self.progressBar.update()
self._full_int_profile = np.delete(np.array(full_profile),
ind_del,
axis=0)
self._full_position = np.delete(np.array(full_position),
ind_del,
axis=0)
self._int_profile = np.delete(np.array(int_profile), ind_del, axis=0)
self._fiber_xc = np.delete(np.array(fiber_xc), ind_del, axis=0)
self._fiber_yc = np.delete(np.array(fiber_yc), ind_del, axis=0)
self._fiber_x1 = np.delete(np.array(fiber_x1), ind_del, axis=0)
self._fiber_x2 = np.delete(np.array(fiber_x2), ind_del, axis=0)
self._fiber_y1 = np.delete(np.array(fiber_y1), ind_del, axis=0)
self._fiber_y2 = np.delete(np.array(fiber_y2), ind_del, axis=0)
self._fiber_e1 = np.delete(np.array(fiber_e1), ind_del, axis=0)
self._fiber_e2 = np.delete(np.array(fiber_e2), ind_del, axis=0)
self._fiber_number = np.delete(np.array(fiber_number), ind_del, axis=0)
self._fiber_slope = np.delete(np.array(fiber_slope), ind_del, axis=0)
self._pos_profile = np.delete(np.array(pos_profile), ind_del, axis=0)
self.progressBar['value'] = 0
self.progressBar.update()