def _populate_experiment_table(self):
self.treeview.delete(*self.treeview.get_children())
if not self.experiments:
return
# Populate the table with saved experiments.
for exp in self.experiments:
n_imgs = -1
if not os.path.exists(exp.img_path):
print("Can't find this path...", exp.img_path)
messagebox.showwarning(
"Experiment problem",
"Can't find directory {} for experiment {}.".format(
exp.img_path, exp.name))
exp.status = "Error"
else:
imgs = get_images_from_dir(exp.img_path)
n_imgs = len(imgs)
if not n_imgs:
messagebox.showwarning(
"Experiment problem",
"Problem with images for experiment {}.".format(
exp.name))
exp.status = "Error"
values = [exp.name, exp.species, exp.panel_n, n_imgs, exp.status]
e_item = self.treeview.insert('', 'end', values=values)
self.exp_treeview_ids[exp.eid] = e_item
def _save_masks_function(exp, sev_dir):
scatter_f = os.path.join(exp.get_results_dir(), "panel_seed_idxs.json")
if not os.path.exists(scatter_f):
return
with open(scatter_f) as fh:
panel_seed_idxs = json.load(fh)
exp_masks_dir_frame = os.path.join(exp.get_masks_dir(), "frame_%d")
for idx in range(exp.start_img,
len(get_images_from_dir(exp.img_path))):
masks = np.load(exp_masks_dir_frame % idx)
for curr_panel, mask in enumerate(masks):
fig = plt.figure()
ax = fig.add_subplot(111)
ax.imshow(mask)
m, n = mask.shape
ys, xs = [], []
for i, y, x in panel_seed_idxs[str(curr_panel)]:
if i == -1:
continue
if idx >= i:
ys.append(y)
xs.append(x)
if len(ys) and len(xs):
ax.scatter(xs, ys, c='r', s=40)
ax.set_xlim(0, n)
ax.set_ylim(m, 0)
fig.canvas.draw()
fig.savefig(
os.path.join(
sev_dir,
'panel_%d_frame_%d.jpg' % (curr_panel, idx)))
plt.close(fig)
messagebox.showinfo("", "Masks Finished Saving.")
def __init__(self, exp):
Tkinter.Toplevel.__init__(self)
self.title("View masks")
self.iconbitmap('logo.ico')
self.exp = exp
self.imgs = get_images_from_dir(self.exp.img_path)
self.exp_masks_dir = pj(self.exp.exp_path, "masks")
self.exp_masks_dir_frame = pj(self.exp_masks_dir, "frame_%d.npy")
self.exp_results_dir = pj(self.exp.exp_path, "results")
self.showing_scatter = False
self.panel_seed_idxs = None
self.scatter = None
scatter_f = pj(self.exp_results_dir, "panel_seed_idxs.json")
if os.path.exists(scatter_f):
with open(scatter_f) as fh:
self.panel_seed_idxs = json.load(fh)
self.showing_scatter = True
self.num_images = len(self.imgs)
self.curr_panel = 0
self.pan_btns = []
self.playing = False
self.fig = plt.Figure()
self.ax = self.fig.add_subplot(111)
for tic in self.ax.xaxis.get_major_ticks():
tic.tick1On = tic.tick2On = False
tic.label1On = tic.label2On = False
for tic in self.ax.yaxis.get_major_ticks():
tic.tick1On = tic.tick2On = False
tic.label1On = tic.label2On = False
self.tk_fig_canvas = FigureCanvasTkAgg(self.fig, master=self)
self.tk_fig_canvas.draw()
self.tk_fig_canvas_widget = self.tk_fig_canvas.get_tk_widget()
self.fn_label_var = Tkinter.StringVar()
self.fn_label_var.set("")
self.filename_label = Tkinter.Label(master=self,
textvariable=self.fn_label_var)
#img = imread(img_path)
self.curr_img = self.exp.start_img
print(self.curr_img)
self.img_plot = self.ax.imshow(self._get_image(self.curr_img))
self.panel_frame = Tkinter.Frame(self)
self._add_panel_selectors()
self.prev_button = Tkinter.Button(master=self,
text="Previous",
command=self._prev_click)
self.play_stop_button = Tkinter.Button(master=self,
text="Start",
command=self._play_stop_click)
self.next_button = Tkinter.Button(master=self,
text="Next",
command=self._next_click)
self.filename_label.grid(in_=self,
column=1,
row=0,
columnspan=3,
sticky='news')
self.tk_fig_canvas_widget.grid(in_=self,
column=1,
row=1,
columnspan=3,
sticky='news')
self.prev_button.grid(
in_=self,
column=1,
row=2,
#sticky='
)
self.play_stop_button.grid(
in_=self,
column=2,
row=2,
)
self.next_button.grid(
in_=self,
column=3,
row=2,
)
self.panel_frame.grid(
in_=self,
column=4,
row=1,
rowspan=3,
)
def _add(self):
name = self.name_entry.get()
dir_ = self.dir_entry.get()
panel_n = self.panel_num_entry.get()
seeds_row_n = self.seeds_per_panel_row_entry.get()
seeds_col_n = self.seeds_per_panel_col_entry.get()
species = self.species_var.get()
bg_remover = self.removers_var.get()
start_img = self.start_image_entry.get()
end_img = self.end_image_entry.get()
if len(end_img) < 1:
end_img = '-1'
if len(start_img) < 1:
start_img = '-1'
use_colour = self.use_colour.get()
use_delta = self.use_delta.get()
pre_conditions = [
(len(name) < 1, "Experiment name is too short"),
(len(dir_) < 1, "Need to enter a directory"),
(len(panel_n) < 1, "Need to enter the number of panels"),
(len(seeds_col_n) < 1, "Need to enter the number of seeds per column"),
(len(seeds_row_n) < 1, "Need to enter the number of seeds per row"),
(len(start_img) < 1, "Need to enter start image index"),
(len(end_img) < 1, "Need to enter end image index")
]
if not self._warning_conditions(pre_conditions):
self.app.lift()
return
post_conditions = [
(self.db.get(where("name") == name) is not None,
"Experiment with this name already exists"),
(not os.path.exists(dir_), "Cannot find experiment directory"),
(len(os.listdir(dir_)) < 1,
"Directory does not contain any files"),
(not self._is_int(panel_n), "Panel value needs to be an integer"),
(not self._is_int(seeds_row_n), "Seeds row value needs to be an integer"),
(not self._is_int(seeds_col_n), "Seeds column value needs to be an integer"),
(not self._is_int(start_img), "Start image index needs to be an integer"),
(not self._is_int(end_img), "End image index needs to be an integer")
]
if not self._warning_conditions(post_conditions):
self.app.lift()
return
panel_n = int(panel_n)
seeds_col_n = int(seeds_col_n)
seeds_row_n = int(seeds_row_n)
start_img = int(start_img)
end_img = int(end_img)
imgs = get_images_from_dir(dir_)
if end_img == -1:
end_img = len(imgs)
if start_img == -1:
start_img = 0
if not imgs:
messagebox.showwarning("Warning",
"Cannot find images in directory: {}".format(dir_))
self.app.lift()
return
exp_path = "./data/experiments/%s" % (slugify(name))
exp = Experiment(name=name,
img_path=dir_,
panel_n=panel_n,
seeds_col_n=seeds_col_n,
seeds_row_n=seeds_row_n,
species=species,
exp_path=exp_path,
start_img=start_img,
end_img=end_img,
bg_remover=bg_remover,
use_colour=use_colour,
use_delta=use_delta,
panel_labelled=False,
_yuv_ranges_set=False,
_status="")
exp.create_directories()
exp.insert_into_database()
self.app.experiments.append(exp)
self.destroy()
self.app._populate_experiment_table()
self.app.lift()
def _view_images(self):
exp = self._get_exp()
imgs = get_images_from_dir(exp.img_path)
self.image_viewer = ImageViewer(exp.img_path,
imgs[exp.start_img:exp.end_img])