def __init__(self, master, get_gain, set_gain, label=''):
Frame.__init__(self, master, width=FADER_WIDTH, height=FADER_HEIGHT)
self.get_gain = get_gain
self._set_gain = set_gain
if isinstance(label, StringVar):
Label(self, textvar=label, width=15).pack()
else:
Label(self, text=label, width=15).pack()
self.gain_label = Label(self)
gain_scale = Scale(self, from_=1, to=0, command=self.set_gain, orient='vertical')
gain_scale.set(self.get_gain())
gain_scale.pack()
self.gain_label.pack()
def __init__(self, master, sequencer):
Frame.__init__(self, master)
self.sequencer = sequencer
self.control_label = Label(self, text="Control")
self.start_button = Button(self, text="Start")
self.stop_button = Button(self, text="Stop")
self.start_button.config(command=self.sequencer.play)
self.stop_button.config(command=self.sequencer.stop)
self.control_label.pack()
self.start_button.pack()
self.stop_button.pack()
Label(self, text='Tempo').pack()
self.tempo_label = Label(self)
self.tempo_label.pack()
def set_tempo(v):
tempo = float(v)
self.sequencer.set_speed(tempo)
self.tempo_label.config(text='%3.0f' % tempo)
tempo_scale = Scale(self, from_=400, to=5, command=set_tempo, orient='vertical')
tempo_scale.set(self.sequencer.speed)
tempo_scale.pack()
measure_control_frame = Frame(self)
measure_control_frame.pack()
self.measure_resolution = StringVar(measure_control_frame)
self.measure_resolution.set(self.sequencer.measure_resolution)
self.beats_per_measure = StringVar(measure_control_frame)
self.beats_per_measure.set(self.sequencer.beats_per_measure)
Label(measure_control_frame, text='Resolution').grid(row=0, column=0, sticky='E')
measure_resolution_entry = Entry(measure_control_frame, textvariable=self.measure_resolution, width=3)
measure_resolution_entry.grid(row=0, column=1)
Label(measure_control_frame, text='Beats').grid(row=1, column=0, sticky='E')
beats_per_measure_entry = Entry(measure_control_frame, textvariable=self.beats_per_measure, width=3)
beats_per_measure_entry.grid(row=1, column=1)
change_measure_update = Button(measure_control_frame, text='Update Measure', command=self.change_measures)
change_measure_update.grid(row=2, columnspan=2)
def initUI(self):
self.parent.title("Gripper Demo")
self.style = Style()
self.style.theme_use("default")
self.pack(fill=BOTH, expand=1)
#scale1 - Gripper Pos
ScaleGripperPos = Scale(self,
from_=0,
to=100,
orient=HORIZONTAL,
length=300,
resolution=1,
command=self.onScaleGripperPos)
ScaleGripperPos.grid(row=1, column=2)
self.label = Label(self, text="Gripper Pos ")
self.label.grid(row=1, column=1)
self.GripperPos = IntVar()
self.labelScaleGripperPos = Label(self,
text=0,
textvariable=self.GripperPos)
self.labelScaleGripperPos.grid(row=1, column=3)
#scale2 - X ROTATION
scaleRotX = Scale(self,
from_=0,
to=650,
orient=HORIZONTAL,
length=300,
resolution=1,
command=self.onScaleXAxisRot)
scaleRotX.grid(row=2, column=2)
scaleRotX.set(450)
self.label = Label(self, text="X Axis Rotation ")
self.label.grid(row=2, column=1)
self.labelRotX = Label(self)
self.labelRotX.grid(row=2, column=3)
#Entry1 - Force
self.entryForce = Entry(self)
self.entryForce.grid(row=3, column=2)
self.entryForce.insert(0, "50") #35=700
#self.forceString = StringVar()
#self.forceString.set(1023);
self.labelForce = Label(self)
self.labelForce.grid(row=3, column=3)
#self.entryForce.insert(1023,self.force.get())
#self.entry1.delete(0,END) #delete entry text
#entry.bind("<Return>", callback) #calls callback function after hit "enter"
self.label = Label(self, text="Current (A)")
self.label.grid(row=6, column=1)
self.labelCurrent = Label(self)
self.labelCurrent.grid(row=6, column=3)
#Entry2 - Speed
self.entrySpeed = Entry(self)
self.entrySpeed.grid(row=4, column=2)
self.entrySpeed.insert(0, "4000")
self.labelSpeed = Label(self)
self.labelSpeed.grid(row=4, column=3)
#Entry2 - Active Distance
self.entryDistance = Entry(self)
self.entryDistance.grid(row=5, column=2)
#Entry3 - Send Command
self.entrySendCommand = Entry(self)
self.entrySendCommand.grid(row=8, column=2)
self.activeDistance = IntVar()
self.activeDistance.set(15)
self.labelActiveDistance = Label(self)
self.labelActiveDistance.grid(row=5, column=3)
self.entryDistance.insert(0, self.activeDistance.get())
#Button1 - close
self.button1 = Button(self, text="close", command=self.gripperClose)
self.button1.grid(row=7, column=1)
#Button2 - open
self.button2 = Button(self, text="open", command=self.gripperOpen)
self.button2.grid(row=7, column=2)
#Button3 - home
self.button3 = Button(self,
text="home",
command=self.gripperHomeRoutine)
self.button3.grid(row=7, column=3)
#Button4 - send command
self.button4 = Button(self, text="send", command=self.sendCommand)
self.button4.grid(row=8, column=3)
#Button3
self.buttonForce = Button(self,
text="forceSetPoint (mg)",
command=self.gripperSetForce)
self.buttonForce.grid(row=3, column=1)
#Button4
self.buttonSpeed = Button(self,
text="speedSetPoint (mseg/close)",
command=self.gripperSetSpeed)
#80degree each finger = to move 40 degree to close
self.buttonSpeed.grid(row=4, column=1)
#Button5
self.buttonDistance = Button(self,
text="distanceSetPoint (Cm)",
command=self.gripperSetDistance)
self.buttonDistance.grid(row=5, column=1)
class VisualVolumes(MyFrame):
#Paths need to be changed when used in a different environment
#Also segmentation accepts only one file now!
def __init__(self,
image_paths=None,
segm_path=None,
supervoxel_id_path=None,
topframe=None):
MyFrame.__init__(self,
topframe=None)
Style().theme_use('clam')
self.set_title('Visualise Volumes')
self.set_variables(image_paths,
segm_path=segm_path,
supervoxel_id_path=supervoxel_id_path)
self.create_ui(image_paths=image_paths,
supervoxel_id_path=supervoxel_id_path)
########## variable setting ###########################F
def set_variables(self,
image_paths,
segm_path=None,
supervoxel_id_path=None):
"""Set initial alpha for opacity, boundaries, undo-redo stacks,
and paths for modalities, segmentation and supervoxels"""
#Alpha value for opacity initialization
self.alpha = 0.2
self._axis = 0
self.show_supervoxels = True
self._set_images(segm_path, image_paths, supervoxel_id_path)
# set boundaries for all images:
self.boundaries = ms.get_boundaries_series(image_paths)
# set stacks for CTRL+Z and CTRL+Y
# CTRL+Z to undo
# CTRL+Y to redo
self.undo_stack = []
self.redo_stack = []
self.image_nb = len(image_paths)
self.selected_id_list = []
#Keybindings for undo and redo actions
self.bind('<Control-z>', self.undo_action)
self.bind('<Control-y>', self.redo_action)
self.bind('<t>', self.toggle_segm)
self.bind("<h>", self.set_healthy)
self.bind("<r>", self.unselect_all)
self.bind("<c>", self.print_com)
self.bind("<i>", self.inverse_selection)
for j in range(len(label_hot_keys)):
self.bind("<%s>" % label_hot_keys[j],
lambda event, arg0=j : self.change_label(arg0))
self.bind("<Right>", self.slice_up)
self.bind("<Left>", self.slice_down)
self.focus_set()
def _set_images(self, segm_path, image_paths, supervoxel_id_path):
""" Set and check image and segmentation arrays and dimensions. """
# Shapes for all modalities
shapes = [oitk.get_itk_array(path).shape \
for path in image_paths]
if len(set(shapes)) != 1:
err = 'Images are not of same dimension'
raise ValueError(err)
self.dim = shapes[0]
# set the images and the image paths
self.images = [oitk.get_itk_array(path) \
for path in image_paths]
self.images_original = np.copy(self.images)
# Get segmentation from segmentation path if given
self.segm = None
self.segm_path = None
if segm_path is not None:
self.segm = oitk.get_itk_array(segm_path)
self.segm_path = segm_path
# Get supervoxels from supervoxel path if given
self.supervoxel_border = None
self.supervoxel_id = None
if supervoxel_id_path is not None:
# get supervoxels and adapt if segmentation is at hand
self.supervoxel_id = oitk.get_itk_array(supervoxel_id_path)
if self.segm is not None:
self.supervoxel_id = utils.adapt_borders(self.segm,
self.supervoxel_id)
# get borders of the supervoxels
self.supervoxel_border = utils.get_borders(self.supervoxel_id)
########## Frame setting ############
def create_ui(self, image_paths, supervoxel_id_path):
"""This function creates the UI elements."""
sub_frame = Frame(self)
sub_frame.grid(column=1,
row=0,
columnspan=self.image_nb)
# create a sub frame to select the image slices that are displayed
slice_frame = Frame(sub_frame)
slice_frame.grid(column=0,
row=1,
columnspan=self.image_nb)
pic_frame = Frame(sub_frame)
pic_frame.grid(column=0,
row=0,
columnspan=self.image_nb)
self.configure_images(pic_frame, image_paths)
self.add_slice_bar(slice_frame)
self.set_optional_buttons(supervoxel_id_path)
def configure_images(self,
pic_frame,
image_paths):
"""Create widgets to place images, descriptions and slice scrollers."""
# create a sub frame to display the images
self._imagelabel = [None for _ in range(self.image_nb)]
self._image_view = [None for _ in range(self.image_nb)]
_descrlabel = [None for _ in range(self.image_nb)]
# descriptions of the images defaults to their path basenames
descriptions = [os.path.basename(image_paths[i])
for i in range(self.image_nb)]
self.histogram_sliders = []
for i in range(self.image_nb):
_sub_pic_frame = Frame(pic_frame)
_sub_pic_frame.grid(column=int(i%2),
row=int(i/2),
pady=5)
# set Label for a description above the images
_descrlabel[i] = Label(_sub_pic_frame,
text=descriptions[i])
_descrlabel[i].grid(column=0, row=0)
# set Label to depict the images
self._imagelabel[i] = Label(_sub_pic_frame)
self._imagelabel[i].grid(column=0, row=1)
# set Scales for the intensity slides
_sub_sub_frame = Frame(_sub_pic_frame)
_sub_sub_frame.grid(column=0,
row=2)
min_val = np.min(self.images_original[i])
max_val = np.max(self.images_original[i])
intensity_scale1 = Scale(_sub_sub_frame,
from_=min_val,
to=max_val/2,
orient=HORIZONTAL)
intensity_scale1.set(min_val)
intensity_scale1.grid(column=0,
row=0,
sticky=['e', 'w', 's'])
intensity_scale2 = Scale(_sub_sub_frame,
from_=max_val/2,
to=max_val,
orient=HORIZONTAL)
intensity_scale2.set(max_val)
intensity_scale2.grid(column=1,
row=0,
sticky=['e', 'w', 's'])
self.histogram_sliders.append(intensity_scale1)
self.histogram_sliders.append(intensity_scale2)
intensity_scale1.bind("<B1-Motion>", self.change_intensity)
intensity_scale2.bind("<B1-Motion>", self.change_intensity)
# Attach commands to the image frames
self._imagelabel[i].bind("<Button-1>", self.click_image)
self._imagelabel[i].bind("<Button-3>", self.label_dropdown)
self._imagelabel[i].bind("<Button 4>", self.slice_up)
self._imagelabel[i].bind("<Button 5>", self.slice_down)
self._imagelabel[i].bind("<B1-Motion>", self.motion_image)
self._imagelabel[i].bind("<Double-Button-1>", self.select_connected)
def add_slice_bar(self, slice_frame):
"""Add a slice selection options to slice_frame.
Returns
-------
this_slice_label_number : Label
the field displaying the current slice number
this_new_slice : Entry
the field allowing the user to fill in a slice number
new_value : int
the initial slice number to be set
"""
# Have a line displaying slice number
_slice_label = Label(slice_frame, text='Slice displayed : ')
_slice_label.grid(column=0, row=0, sticky=['w', 'e'])
this_slice_label_number = Label(slice_frame)
this_slice_label_number.grid(column=1, row=0,
sticky=['w', 'e'])
# Allow to change slice number
_goto = Label(slice_frame, text=' - go to slice :')
_goto.grid(column=2, row=0, sticky=['w', 'e'])
this_new_slice = Entry(slice_frame, width=6)
this_new_slice.bind('<Return>', self.goto_slice)
this_new_slice.bind('<KP_Enter>', self.goto_slice)
this_new_slice.grid(column=3, row=0, sticky=['w', 'e'])
self.image_scale = (self.screen_width - 200) / 4
# Allow to scroll through the slices
self._slice_scroll = lsb.LinkedScrollBar(master=slice_frame,
command=self.disp_im,
minVal=self._get_min_slice(),
maxVal=self._get_max_slice(),
step=1,
orient='horizontal')
self._slice_scroll.grid(column=0,
row=1,
columnspan=self.image_nb,
sticky=['e', 'w', 's'])
self._slice_label_number = this_slice_label_number
self._new_slice = this_new_slice
self.reset_slice_scroll()
##### allow to show segmentations, change axis and quit #########
def set_optional_buttons(self, supervoxel_id_path=None):
""" Set bottoms to quit, change axis, show and hide segmentation, ...
at the upper row of the main frame.
"""
_sub_frame1 = Frame(self)
_sub_frame1.grid(column=0,
row=0,
padx=10,
sticky=['n', 'e', 'w'])
_sub_sub_frame1 = Frame(_sub_frame1)
_sub_sub_frame1.grid(column=0,
row=0,
sticky=['e', 'w'],
pady=10)
ind = 0
self.button_axis = Button(_sub_sub_frame1,
text="Change axis",
command=self.change_axis)
self.button_axis.grid(column=0, row=ind, pady=3)
ind += 1
self.button_axis = Button(_sub_sub_frame1,
text="Mirror Images",
command=self.mirror_image)
self.button_axis.grid(column=0, row=ind, pady=3)
ind = 0
if self.segm is not None:
_sub_sub_frame2 = Frame(_sub_frame1)
_sub_sub_frame2.grid(column=0,
row=1,
sticky=['e', 'w'],
pady=10)
_sub_sub_frame3 = Frame(_sub_frame1)
_sub_sub_frame3.grid(column=0,
row=2,
sticky=['e', 'w'],
pady=10)
self.button_supervoxels = Button(_sub_sub_frame2,
text="Show/Hide supervoxels",
command=self.change_supervoxels)
self.button_supervoxels.grid(column=0,
row=ind,
sticky=['w', 'n', 'e'])
if supervoxel_id_path is None:
self.button_supervoxels['state'] = 'disabled'
ind += 1
self.tumor_checkbox_label = Label(_sub_sub_frame2,
text="Display tumor type: ",
relief=FLAT)
self.tumor_checkbox_label.grid(column=0, row=ind)
ind += 1
self.tumor_cb = []
for i in range(len(labels)):
tumor_button = IntVar()
this_text = '%s (%s <%s>)' % (labels[i],
label_colors_d[i],
label_hot_keys[i+1])
button = Checkbutton(_sub_sub_frame2,
text=this_text,
variable=tumor_button,
command=lambda arg0=i: self.change_segm(arg0))
button.grid(column=0, row=ind, sticky=['w', 'n', 'e'])
self.tumor_cb.append(tumor_button)
ind += 1
self.all_tumor_bc = IntVar()
button = Checkbutton(_sub_sub_frame2,
text="All tumors",
variable=self.all_tumor_bc,
command=lambda : self.change_segm(3))
button.grid(column=0,
row=ind,
sticky=['w', 'n', 'e'])
ind += 1
self.no_tumor_bc = IntVar()
button = Checkbutton(_sub_sub_frame2,
text="No tumors",
variable=self.no_tumor_bc,
command=lambda : self.change_segm(4))
button.grid(column=0,
row=ind,
sticky=['w', 'n', 'e'])
ind += 1
alpha_label = Label(_sub_sub_frame2, text="Opacity:")
alpha_label.grid(column=0, row=ind)
self.alpha_scale = Scale(_sub_sub_frame2,
from_=0.0,
to=1.0,
command=self.set_alpha,
orient=HORIZONTAL)
ind += 1
self.alpha_scale.set(self.alpha)
self.alpha_scale.grid(column=0,
row=ind,
columnspan=self.image_nb,
sticky=['w', 'n', 'e'])
ind = 0
self.button_save_segm = Button(_sub_sub_frame3,
text="Save segmentation",
command=self.save_segm)
self.button_save_segm.grid(column=0, row=ind, sticky=['w', 'n', 'e'])
ind += 1
self.button_open_segm = Button(_sub_sub_frame3,
text="Open segmentation",
command=self.open_segm)
self.button_open_segm.grid(column=0, row=ind, sticky=['w', 'n', 'e'])
#################### Display images ###########################
def disp_im(self):
"""use the size, slice and zoom to display the image"""
self.focus_set()
slice_index = int(self._slice_scroll.val)
for i in range(self.image_nb):
pix = np.array(\
ms.get_slice(self.images[i],
boundaries=self.boundaries,
visual_center=slice_index,
axis=self._axis),
dtype='float')
temp_im, im_size = pil.get_image_pil(pix,
self.image_scale,
return_image_size=True)
self.image_size = im_size
temp_im = temp_im.convert('RGB')
if self.segm is not None:
temp_im = self.add_segmentation(temp_im, slice_index)
if self.show_supervoxels and type(self.supervoxel_border) is np.ndarray:
temp_im = self.add_supervoxels(temp_im, slice_index)
# create the 2d view with or without the bounding box
self._image_view[i] = ImageTk.PhotoImage(temp_im)
self._imagelabel[i]['image'] = self._image_view[i]
# update slice label
self._slice_label_number['text'] = str(int(self._slice_scroll.val))
def add_segmentation(self, image, slice_ind=None):
""" Add a segmentation to the image (colors will be overlaid). """
#Segmentation is separated into binary segmentations
#Also, segm contains 3 binary segmentations
if len(self.selected_id_list) > 0:
segm = utils.get_separate_labels(self.segm_disp, length=len(labels)+1)
else:
segm = utils.get_separate_labels(self.segm, length=len(labels))
r, g, b = image.convert('RGB').split()
rgb = [r, g, b]
#Variable that contains selected colors
colors = [None for _ in range(len(segm))]
#Add labels if their check box is selected
if hasattr(self, 'tumor_cb'):
for i in range(len(labels)):
if self.tumor_cb[i].get() == 1:
colors[i] = label_colors[i]
if len(colors)==4:
colors[3] = selected
#Do the painting with respect to colors variable
for i in range(len(segm)):
if colors[i] is None:
continue
pix = np.array(ms.get_slice(segm[i],
boundaries=self.boundaries,
visual_center=slice_ind,
axis=self._axis))
pix[pix > 0.5] = 1
pix = pix.astype('uint8')
if np.any(pix):
color_region = pil.get_image_pil(pix, self.image_scale)
rgb = pil.set_color_custom(color_region, colors[i], rgb=rgb)
#Merge operation for all
segm_im = ImagePIL.merge("RGB", rgb)
return ImagePIL.blend(image, segm_im, self.alpha)
def add_supervoxels(self, image, slice_ind=None):
""" Add supervoxels to the image (boundaries will be drawn)."""
r, g, b = image.convert('RGB').split()
pix = np.array(ms.get_slice(self.supervoxel_id,
boundaries=self.boundaries,
visual_center=slice_ind,
axis=self._axis))
self.supervoxel_id_slice = pix
if np.any(pix):
pix = pix *50000
#Get image with supervoxels that has borders calculated with contours
sup_im = pil.get_image_pil(pix, self.image_scale)\
.convert("RGB")\
.filter(ImageFilter.CONTOUR)\
.filter(ImageFilter.EDGE_ENHANCE_MORE)\
.filter(ImageFilter.EDGE_ENHANCE_MORE)
r_border, g_border, b_border = sup_im.split()
r = pil.set_color_empty(r, r_border)
g = pil.set_color_empty(g, g_border)
b = pil.set_color_empty(b, b_border)
#Merge operation for all colors
sup_im = ImagePIL.merge("RGB", (r, g, b))
return ImagePIL.blend(image, sup_im, self.alpha)
#################### EVENTS: Change slice ######################
def reset_slice_scroll(self):
max_slice = self._get_max_slice()
min_slice = self._get_min_slice()
diff = max_slice - min_slice
new_value = int(min_slice + np.floor(diff / 2))
self._slice_scroll.set_value(new_value)
def slice_up(self, *args):
"""increase slice number"""
new_value = self._slice_scroll.val + 1
if new_value <= self._get_max_slice(in_boundaries=True):
self._slice_scroll.set_value(new_value)
def slice_down(self, *args):
"""decrease slice number"""
new_value = self._slice_scroll.val - 1
if new_value >= self._get_min_slice(in_boundaries=True):
self._slice_scroll.set_value(new_value)
def _get_max_slice(self, in_boundaries=True):
"""Gets the maximum slice of the numpy array."""
if in_boundaries:
return self.boundaries[self._axis][1]
else:
return self.dim[self._axis] - 1
def _get_min_slice(self, in_boundaries=True):
"""Gets the minimum slice of the numpy array."""
if in_boundaries:
return self.boundaries[self._axis][0]
else:
return 0
def change_axis(self):
"""It changes the axis of the image."""
self._axis = (self._axis + 1) % 3
self.reset_slice_scroll()
self.disp_im()
def mirror_image(self):
"""It mirrors the image."""
for i in range(self.image_nb):
self.images[i] = np.flip(self.images[i], axis=(self._axis + 1) % 3)
self.images_original[i] = np.flip(self.images_original[i], axis=(self._axis + 1) % 3)
if self.segm is not None:
self.segm = np.flip(self.segm, axis=(self._axis + 1) % 3)
if self.show_supervoxels and type(self.supervoxel_border) is np.ndarray:
self.supervoxel_id = np.flip(self.supervoxel_id, axis=(self._axis + 1) % 3)
self.boundaries = ms.get_boundaries_series(self.images)
self.disp_im()
def goto_slice(self, *args):
"""moves to the desired slice"""
z = self._new_slice.get()
max_valid_z = self._get_max_slice(in_boundaries=True)
min_valid_z = self._get_min_slice(in_boundaries=True)
# if not an integer
try:
z = int(z)
# if out of range
if z < 0:
msg = 'Please select a positive slice index. ' +\
'Lowest non-zero slice is shown.'
self._slice_scroll.set_value(min_valid_z)
self._new_slice.delete(0, END)
elif z < min_valid_z:
msg = 'Slice %d has only zeros. ' % z
msg += 'Lowest non-zero slice is shown.'
self._slice_scroll.set_value(min_valid_z)
self._new_slice.delete(0, END)
elif z > self._get_max_slice(in_boundaries=False):
msg = 'Slice %d exceeds the image dimension. ' % z
msg += 'Highest non-zero slice is shown.'
self._slice_scroll.set_value(max_valid_z)
self._new_slice.delete(0, END)
elif z > max_valid_z:
msg = 'Slice %d consists of zeros. ' % z
msg += 'Highest non-zero slice is shown.'
self._slice_scroll.set_value(max_valid_z)
self._new_slice.delete(0, END)
else:
self._slice_scroll.set_value(z)
self._new_slice.delete(0, END)
except ValueError as e:
print e
self._new_slice.delete(0, END)
############### EVENTS : select and change #########################
def click_image(self, event):
""" Select a supervoxel and color it in blue.
Called when clicked on an image. """
supervoxel_id = self._get_supervoxel_id(event.x, event.y)
self._update_selected_id_list(supervoxel_id)
def motion_image(self, event):
""" Select multiple supervoxels and color it in blue.
Called when clicked and motioned on an image. """
supervoxel_id = self._get_supervoxel_id(event.x, event.y)
self._update_selected_id_list(supervoxel_id, unselect=False)
def select_connected(self, event):
supervoxel_id = self._get_supervoxel_id(event.x, event.y)
label = self.segm[self.supervoxel_id == supervoxel_id][0]
im = sitk.GetImageFromArray((self.segm==label).astype(np.int))
connected = sitk.GetArrayFromImage(sitk.ConnectedComponent(im))
clabel = connected[self.supervoxel_id == supervoxel_id][0]
supervoxel_ids = list(np.unique(self.supervoxel_id[connected==clabel]))
self._update_selected_id_list(supervoxel_ids)
def unselect_all(self, *args):
""" Unselect all selected supervoxels. """
print 'Emptying selection'
self.selected_id_list = []
self.disp_im()
def set_healthy(self, *args):
""" Select all supervoxels in this slice and set them to
background. """
print 'Setting all supervoxels in slice to background'
supervoxel_ids = list(np.unique(self.supervoxel_id_slice))
if 0 in supervoxel_ids:
supervoxel_ids.remove(0)
self.change_label(0, supervoxel_ids=supervoxel_ids)
def inverse_selection(self, *args):
all_ids = np.unique(self.supervoxel_id)
new_ids = [sup_id for sup_id in all_ids
if id not in self.selected_id_list]
self.selected_id_list = new_ids
self.update_segm_display()
def _get_supervoxel_id(self, eventx, eventy):
""" Get the supervoxel id of the given mouse position. """
#the size of the image:
#0 element of image corresponds to 1 element
#of supervoxel_id_slice and vice versa
#converting the coordinates on the clicked image into the
#coordinates of the voxel
#Since the displayed pixels range from 1 to lenght+1,
#need to subtract 1 from the coordinates
# print self.supervoxel_id_slice.shape
x_coordinate_supervoxel = (eventx - 1) *\
len(self.supervoxel_id_slice[0]) /\
self.image_size[0]
y_coordinate_supervoxel = (eventy - 1) *\
len(self.supervoxel_id_slice) /\
self.image_size[1]
z_coordinate_supervoxel = int(self._slice_scroll.val)
coordinates = [x_coordinate_supervoxel,
y_coordinate_supervoxel,
z_coordinate_supervoxel]
selected_id = self.supervoxel_id_slice[coordinates[1], coordinates[0]]
return selected_id
def _update_selected_id_list(self, selected_id, add_to_undo=True, unselect=True):
""" Depending whether this supervoxel is already selected, mark
or unmark the supervoxel. """
if isinstance(selected_id, list):
if unselect:
if all([sid in self.selected_id_list for sid in selected_id]):
map(self.selected_id_list.remove, selected_id)
else:
self.selected_id_list.extend(selected_id)
else:
if not all([sid in self.selected_id_list for sid in selected_id]):
self.selected_id_list.extend(selected_id)
else:
return #nothing changed
else:
if unselect:
if selected_id in self.selected_id_list:
self.selected_id_list.remove(selected_id)
else:
self.selected_id_list.append(selected_id)
else:
if selected_id not in self.selected_id_list:
self.selected_id_list.append(selected_id)
else:
return #nothing changed
print 'Selected supervoxels: %s' % str(self.selected_id_list)
if add_to_undo:
action = selected_id, None, None
self.undo_stack.append(action)
self.update_segm_display()
def update_segm_display(self):
""" Color all supervoxels with ids in self.selected_id_list blue
in self.segm_disp. """
#Selection is updated for visualisation
self.segm_disp = self.segm.copy()
if len(self.selected_id_list) == 1:
mask = self.supervoxel_id == self.selected_id_list[0]
elif len(self.selected_id_list) > 1:
ind1d = np.in1d(self.supervoxel_id.flatten(), self.selected_id_list)
mask = np.reshape(ind1d, self.supervoxel_id.shape)
else:
mask = np.zeros_like(self.supervoxel_id)
selected_idx = np.where(mask)
self.segm_disp[selected_idx[0], selected_idx[1], selected_idx[2]] = 4
self.disp_im()
def print_com(self, *args):
ind1d = np.in1d(self.supervoxel_id.flatten(), self.selected_id_list)
ind3d = np.reshape(ind1d, self.supervoxel_id.shape)
com = spim.measurements.center_of_mass(ind3d)
print 'Center of mass'
print '\t com : %s' % str(com)
if self.segm_path is not None:
ID = os.path.basename(self.segm_path).split('.')[0]
print '\t path : %s' % ID
print 'com_dict["%s"] = %s' % (ID, str(com))
def label_dropdown(self, event):
"""When clicking right on a supervoxel, give a drop-down list
with labels to change to."""
if len(self.selected_id_list) == 0:
return
# Adding the selection menu with radio buttons.
self.menu = Menu(self, tearoff=0)
self.menu\
.add_radiobutton(label="Background",
value=0,
command=lambda arg0=0: \
self.change_label(arg0))
self.menu\
.add_radiobutton(label=labels[0],
value=3,
command=lambda arg0=1: \
self.change_label(arg0))
self.menu\
.add_radiobutton(label=labels[1],
value=2,
command=lambda arg0=2: \
self.change_label(arg0))
self.menu\
.add_radiobutton(label=labels[2],
value=1,
command=lambda arg0=3: \
self.change_label(arg0))
self.menu.tk_popup(event.x_root, event.y_root)
def change_label(self, new_label, supervoxel_ids=None):
"""Changing the label of the supervoxel
new label is the type of pixel 0 - background,
#3 - edema, 2 - Non-active tumor and 1 - Active tumor
self.segm is the array with segmentations
self.supervoxel_ids is the the array with the supervoxels
"""
empty_selected_id_list = False
if supervoxel_ids is None:
empty_selected_id_list = True
supervoxel_ids = self.selected_id_list
#Empty the redo_stack whenever segmentation is changed by user
self.redo_stack = []
for selected_id in (supervoxel_ids):
#Segmentation is updated with new labels
#Old label is saved for undo and redo actions
region = self.supervoxel_id == selected_id
old_label = self.segm[region]
old_label = old_label[0]
self.segm[region] = new_label
# if the checkboxes are unselected but changed, they are automatically checked.
if new_label > 0:
self.tumor_cb[new_label-1].set(1)
self.no_tumor_bc.set(0)
#Actions as coordinates, old_label and new_label to go switch between segmentation states
action = selected_id, old_label, new_label
self.undo_stack.append(action)
if empty_selected_id_list:
self.selected_id_list = []
self.disp_im()
def change_intensity(self, event):
""" Change the intensity of the images based on the hist slider."""
slider = event.widget
i = self.histogram_sliders.index(slider)
# find the image index based on the slider
image_i = 3
if i == 0 or i == 1:
image_i = 0
elif i == 2 or i == 3:
image_i = 1
elif i == 4 or i == 5:
image_i = 2
original_image = self.images_original[image_i]
image = self.images[image_i]
if (i + 1) % 2 == 0:
slider_upper = slider
slider_lower = self.histogram_sliders[i - 1]
else:
slider_lower = slider
slider_upper = self.histogram_sliders[i + 1]
lower = slider_lower.get()
upper = slider_upper.get()
lower = np.float(lower)
upper = np.float(upper)
np.clip(original_image, lower, upper, image)
np.subtract(image, lower, out=image, casting='unsafe')
self.disp_im()
def change_segm(self, button_ind):
""" Show or hide the segmentation from the images."""
# if tumor type is (un)selected, set all_tumors and no_tumors
# accordingly
if button_ind <= 2:
checked = [self.tumor_cb[i].get() for i in range(len(labels))]
checked_sum = sum(checked)
if checked_sum < len(labels):
self.all_tumor_bc.set(0)
else:
self.all_tumor_bc.set(1)
if checked_sum > 0:
self.no_tumor_bc.set(0)
else:
self.no_tumor_bc.set(1)
# if all_tumors or no_tumors is (un)selected, allign the other
# buttons
if button_ind == 3:
for i in range(len(labels)):
self.tumor_cb[i].set(1)
self.all_tumor_bc.set(1)
self.no_tumor_bc.set(0)
if button_ind == 4:
for i in range(len(labels)):
self.tumor_cb[i].set(0)
self.all_tumor_bc.set(0)
self.no_tumor_bc.set(1)
self.disp_im()
def toggle_segm(self, *args):
# if at least one tumor type is visualized,
# remove all tumors (set no_tumors) and supervoxels
checked = [self.tumor_cb[i].get() for i in range(len(labels))]
checked_sum = sum(checked)
if checked_sum > 0:
print 'Visualizing no tumors'
self.change_segm(4)
# if no tumor type is visualized, set all_tumors
# visualize all tumors (set all_tumors) and supervoxels
else:
print 'Visualizing all tumors'
self.change_segm(3)
def change_supervoxels(self):
""" Toggle between showing supervoxels or not."""
self.show_supervoxels = not self.show_supervoxels
self.disp_im()
def set_alpha(self, *args):
""" Change the opacity level."""
self.alpha = self.alpha_scale.get()
self.disp_im()
def undo_action(self, *args):
""" Execute undo action on CTRL-Z."""
#If respective stack is not empty
#Go to the last state of segmentation
#and update the redo_stack
print 'undo!'
if len(self.undo_stack) > 0:
action = self.undo_stack.pop()
self.redo_stack.append(action)
selected_id, old_label, _ = action
if old_label is not None:
self._change_label_supervoxel(old_label, selected_id)
else:
self._update_selected_id_list(selected_id, add_to_undo=False)
self.disp_im()
def redo_action(self, *args):
"""Execute redo action on CTRL-Y"""
#If respective stack is not empty
#Go to the last state of segmentation
#and update the undo_stack
print 'redo!'
if len(self.redo_stack) > 0:
action = self.redo_stack.pop()
self.undo_stack.append(action)
selected_id, _, new_label = action
if new_label is not None:
self._change_label_supervoxel(new_label, selected_id)
else:
self._update_selected_id_list(selected_id, add_to_undo=False)
self.disp_im()
def _change_label_supervoxel(self, new_label, selected_id):
""" Change the label of the supervoxel
cooordinates is a list of the ids of the selected voxel.
coordinates[0] - x coordinate, coordinate[1] - y coordinate, coordinate[2] - z coordinate
new label is the type of pixel 0 - background,
3 - edema, 2 - Non-active tumor and 1 - Active tumor
self.segms is the array with segmentations
self.supervoxel_ids is the the array with the supervoxels"""
#Segmentation is updated with new labels
self.segm[self.supervoxel_id == selected_id] = new_label
self.disp_im()
#################### Save or load a segmentation ###################
def save_segm(self):
""" Save the current custom segmentation into a file."""
kwargs = {}
if self.segm_path is not None:
dirname, basename = os.path.split(self.segm_path)
if not basename.startswith('corrected_'):
basename = 'corrected_'+basename
kwargs['initialfile'] = basename
kwargs['initialdir'] = dirname
path = asksaveasfilename(title="Please select a path to save your segmentation",
filetypes=[('Image files',
('.nii',
'.mha',
'.nii.gz'))],
**kwargs)
#TODO: change here self.segm_path
if self.segm_path is not None:
old_segm = oitk.get_itk_image(self.segm_path)
image = oitk.make_itk_image(self.segm, old_segm)
oitk.write_itk_image(image, path)
def open_segm(self):
""" Open a new custom segmentation from a file."""
kwargs = {}
kwargs['initialdir'] = os.environ.get('HOME')
if self.segm_path is not None:
dirname, basename = os.path.split(self.segm_path)
if not basename.startswith('corrected_'):
basename = 'corrected_'+basename
kwargs['initialfile'] = basename
kwargs['initialdir'] = dirname
msg = 'Please select a segmentation'
segm_path = askopenfilename(title=msg,
filetypes=[('Image files',
('.nii',
'.mha',
'.nii.gz'))],
**kwargs)
if os.path.exists(segm_path):
self.segm_path = segm_path
self.segm = oitk.get_itk_array(self.segm_path)
self.disp_im()
def configure_images(self,
pic_frame,
image_paths):
"""Create widgets to place images, descriptions and slice scrollers."""
# create a sub frame to display the images
self._imagelabel = [None for _ in range(self.image_nb)]
self._image_view = [None for _ in range(self.image_nb)]
_descrlabel = [None for _ in range(self.image_nb)]
# descriptions of the images defaults to their path basenames
descriptions = [os.path.basename(image_paths[i])
for i in range(self.image_nb)]
self.histogram_sliders = []
for i in range(self.image_nb):
_sub_pic_frame = Frame(pic_frame)
_sub_pic_frame.grid(column=int(i%2),
row=int(i/2),
pady=5)
# set Label for a description above the images
_descrlabel[i] = Label(_sub_pic_frame,
text=descriptions[i])
_descrlabel[i].grid(column=0, row=0)
# set Label to depict the images
self._imagelabel[i] = Label(_sub_pic_frame)
self._imagelabel[i].grid(column=0, row=1)
# set Scales for the intensity slides
_sub_sub_frame = Frame(_sub_pic_frame)
_sub_sub_frame.grid(column=0,
row=2)
min_val = np.min(self.images_original[i])
max_val = np.max(self.images_original[i])
intensity_scale1 = Scale(_sub_sub_frame,
from_=min_val,
to=max_val/2,
orient=HORIZONTAL)
intensity_scale1.set(min_val)
intensity_scale1.grid(column=0,
row=0,
sticky=['e', 'w', 's'])
intensity_scale2 = Scale(_sub_sub_frame,
from_=max_val/2,
to=max_val,
orient=HORIZONTAL)
intensity_scale2.set(max_val)
intensity_scale2.grid(column=1,
row=0,
sticky=['e', 'w', 's'])
self.histogram_sliders.append(intensity_scale1)
self.histogram_sliders.append(intensity_scale2)
intensity_scale1.bind("<B1-Motion>", self.change_intensity)
intensity_scale2.bind("<B1-Motion>", self.change_intensity)
# Attach commands to the image frames
self._imagelabel[i].bind("<Button-1>", self.click_image)
self._imagelabel[i].bind("<Button-3>", self.label_dropdown)
self._imagelabel[i].bind("<Button 4>", self.slice_up)
self._imagelabel[i].bind("<Button 5>", self.slice_down)
self._imagelabel[i].bind("<B1-Motion>", self.motion_image)
self._imagelabel[i].bind("<Double-Button-1>", self.select_connected)
class qual_window(Frame):
def __init__(self, parent):
Frame.__init__(self, parent)
self.parent = parent
self.initUI(parent)
def initUI(self, parent):
# initalising some variables
self.Quality_e = None
self.scale = None
self.fmemory_e = None
self.memory_e = None
self.style = Style()
self.style.theme_use("classic")
Style().configure("TEntry", font='serif 10')
Style().configure("TLabel", font='serif 10')
# creating menubar
menubar = Menu(self.parent)
self.parent.config(menu=menubar)
fileMenu = Menu(menubar)
fileMenu.add_command(label="Restart", command=self.re_start)
menubar.add_cascade(label="Options", menu=fileMenu)
# creating layout from frames
self.frame3 = Frame(parent, relief="sunken")
self.frame3.pack(side="bottom", fill=X)
self.frame1 = Frame(parent, relief="sunken")
self.frame1.pack(side="left", fill=Y)
self.frame2 = Frame(parent,
width=gbl.x2 - gbl.x1,
height=max(gbl.y2 - gbl.y1, 200),
relief="flat",
bg="#333")
self.frame2.pack(side="right", fill="both", expand="True")
# creating canvas in frame 2
self.canvas = Canvas(self.frame2)
self.canvas.pack(fill="both", expand="True")
# creating save and next Button
self.b9 = Button(self.frame1,
text="Save and Next>>",
state="active",
font='serif 10',
command=self.save_next)
self.b9.pack(side="bottom", pady=5)
self.b9.bind('<Return>', self.save_next)
self.b8 = Button(self.frame1,
text="<<Back",
state="active",
font='serif 10',
command=self.go_back)
self.b8.pack(side="bottom", pady=5)
self.b8.bind('<Return>', self.go_back)
self.parent.bind('<Return>', self.save_next)
# track for editable entries
self.e1s = StringVar(self.frame1)
self.e2s = StringVar(self.frame1)
self.e1s.trace("w", self.check)
self.e2s.trace("w", self.check)
# creating editable format and quality entries
# self.format_e = self.make_entry(gbl.out_format, "Format (Default JPEG)")
self.format_e = Entry(self.frame1,
textvariable=self.e1s,
bg="white",
bd=4,
cursor="xterm",
fg="Black",
justify="center",
relief="ridge")
self.format_e.insert(0, "JPEG")
self.format_e.pack(side="top")
Label(self.frame1, text="Format (Default JPEG)").pack(side="top")
# self.Quality_e = self.make_entry(gbl.Quality, "Format (Default 80)")
self.Quality_e = Entry(self.frame1,
textvariable=self.e2s,
bg="white",
bd=4,
cursor="xterm",
fg="Black",
justify="center",
relief="ridge")
self.Quality_e.insert(0, gbl.Quality)
self.Quality_e.pack(side="top")
Label(self.frame1, text="Quality (Default 80)").pack(side="top")
# self.format_e.config(textvariable=self.e1s)
# self.Quality_e.config(textvariable=self.e2s)
# creating sliding bar
self.var = IntVar()
self.scale = Scale(self.frame1,
from_=1,
to=100,
orient="horizontal",
length=168,
command=self.onScale)
self.scale.set(gbl.Quality)
self.scale.pack(side="top")
self.l1 = Label(self.frame1, textvariable=self.var)
self.l1.pack(side="top")
self.var.set(gbl.Quality)
# saving and putting PIL.Image in canvas
self.save_put_image()
# creating memory entries
self.fmemory_e = self.set_memory_entry(self.frame1, "Final",
gbl.output_file)
self.memory_e = self.set_memory_entry(self.frame1, "Initial",
gbl.input_file)
# creating status bar
Label(self.frame3, text=gbl.output_file).pack(side="left", anchor="w")
Label(self.frame3, text=str(gbl.cu_ind) + "/" +
str(gbl.total_files)).pack(side="right", anchor="e")
# def make_entry(self, data, text_):
# temp_entry = Entry(self.frame1, textvariable=None, bg="white", bd=4, cursor="xterm", fg="Black", justify="center", relief="ridge")
# temp_entry.insert(0,data)
# temp_entry.pack(side="top")
# Label(self.frame1, text=text_).pack(side="top")
# return temp_entry
def quality_entered(self):
gbl.out_format = str(self.format_e.get())
gbl.Quality = int(self.Quality_e.get())
if (self.scale != None):
self.scale.set(gbl.Quality)
self.var.set(gbl.Quality)
self.save_put_image()
def onScale(self, val):
v = int(float(val))
self.var.set(v)
self.Quality_e.delete(0, 'end')
self.Quality_e.insert(0, v)
def check(self, *args):
if (self.Quality_e != None):
e1_data = self.e1s.get()
e2_data = self.e2s.get()
if (e1_data in ["JPEG", "PNG"]) and e2_data.isdigit(
) and int(e2_data) <= 100 and int(e2_data) > 0:
self.b9.config(state="active")
self.b9.bind('<Return>', self.save_next)
self.quality_entered()
else:
self.b9.config(state="disabled")
self.b9.unbind('<Return>')
def save_next(self, *args):
if (os.path.isfile(gbl.output_file + "temp")):
os.remove(gbl.output_file + "temp")
self.quit()
def go_back(self, *args):
if (os.path.isfile(gbl.output_file + "temp")):
os.remove(gbl.output_file + "temp")
gbl.back = 1
gbl.cu_ind -= 1
self.quit()
def save_put_image(self):
if (os.path.isfile(gbl.output_file)):
os.remove(gbl.output_file)
if (os.path.isfile(gbl.output_file + "temp")):
os.remove(gbl.output_file + "temp")
gbl.crop_im.save(gbl.output_file + "temp",
gbl.out_format,
quality=gbl.Quality,
progressive=True,
optimize=True)
gbl.main_crop_im.save(gbl.output_file,
gbl.out_format,
quality=gbl.Quality,
progressive=True,
optimize=True)
self.temp_im = PIL.Image.open(gbl.output_file + "temp")
self.fc_im = PIL.ImageTk.PhotoImage(self.temp_im)
gbl.crop_im_canv = self.canvas.create_image(
(gbl.x2 - gbl.x1) / 2,
max(gbl.y2 - gbl.y1, 600) / 2,
image=self.fc_im)
if (self.fmemory_e != None):
self.memory = (os.path.getsize(gbl.output_file) * 1.0) / 1024
self.fmemory_e.config(state="normal")
self.fmemory_e.delete(0, 'end')
self.fmemory_e.insert(0, self.memory)
self.fmemory_e.config(state="readonly")
def set_memory_entry(self, framei, text_, file_name):
temp_entry = Entry(framei,
bg="white",
bd=4,
cursor="xterm",
fg="Black",
justify="center",
relief="ridge")
memory = (os.path.getsize(file_name) * 1.0) / 1024
temp_entry.insert(0, memory)
temp_entry.config(state="readonly")
temp_entry.pack(side="top")
Label(framei, text=text_ + " Memory (KB)").pack(side="top")
return temp_entry
def crop_size(self):
if ((gbl.w * 1.0) / gbl.h >= (int(gbl.width) * 1.0) / int(gbl.height)):
cropx = ((gbl.height * gbl.w) -
(gbl.width * gbl.h)) / (gbl.height * 2)
cropy = 0
else:
cropx = 0
cropy = ((gbl.width * gbl.h) -
(gbl.height * gbl.w)) / (gbl.width * 2)
return cropx, cropy
def re_start(self):
gbl.go_restart = 1
self.quit()
