def get_scan_name(self):
def set_scan_name(event=None):
if self.scan_in.get().strip() == "":
tkMessageBox.showerror("Classify", "Enter a scan name.")
elif self.ext_in.get().strip() == "":
tkMessageBox.showerror("Classify",
"Enter an image file extension.")
else:
self.scan = self.scan_in.get().strip()
self.ext = self.ext_in.get().strip()
print 'Scan name set to \'' + self.scan + '\''
print 'File extension set to \'' + self.ext + '\''
self.frame.destroy()
self.frame2.destroy()
del self.scan_in, self.ext_in, self.submit
self.setup_data_entry()
# Get the scan name from the user
self.frame = tk.Frame(self.root)
self.frame.pack()
self.scan_input_text = mtk.Title(self.frame, text='Enter scan name:')
self.scan_input_text.pack()
self.scan_in = mtk.Entry(self.frame)
self.scan_in.insert(0, self.scan)
self.scan_in.pack()
# Get file extension from user
self.frame2 = tk.Frame(self.root)
self.frame2.pack()
self.ext_input_text = mtk.Title(self.frame2,
text="Enter file extension:")
self.ext_input_text.pack()
self.ext_in = mtk.Entry(self.frame2)
self.ext_in.insert(0, self.ext)
self.ext_in.pack()
# Confirm button
self.submit = mtk.Button(self.frame2,
text='Done',
command=set_scan_name)
self.submit.pack()
def initialize_objects(self):
def set_init_objects(event=None):
self.complete_f = self.complete.get()
self.fragment_f = self.fragment.get()
self.damaged_f = self.damaged.get()
self.all_objects_f = self.all_objects.get()
if not any([self.complete_f, self.fragment_f, self.damaged_f, self.all_objects_f]):
tkMessageBox.showerror('Specify','Pick objects to load.')
else:
print 'Objects loaded: ' + self.complete_f * 'Complete' + self.complete_f * ', ' + self.fragment_f * 'Fragment' + self.fragment_f * ', ' + self.damaged_f * 'Damaged' + self.all_objects_f * ', ' + self.all_objects_f * 'All Objects'
self.frame.destroy()
del self.submit
self.read_data()
if self.restart:
self.complete_f = int(self.checkpoint_codes[1])
self.fragment_f = int(self.checkpoint_codes[2])
self.damaged_f = int(self.checkpoint_codes[3])
self.all_objects_f = int(self.checkpoint_codes[4])
print 'Objects loaded: ' + self.complete_f * 'Complete' + self.complete_f * ', ' + self.fragment_f * 'Fragment' + self.fragment_f * ', ' + self.damaged_f * 'Damaged' + self.all_objects_f * ', ' + self.all_objects_f * 'All Objects'
self.read_data()
else:
self.frame = tk.Frame(self.root)
self.frame.pack()
self.init_obj_text = mtk.Title(self.frame,text='Load which objects?')
self.init_obj_text.pack()
self.complete = tk.IntVar()
self.fragment = tk.IntVar()
self.damaged = tk.IntVar()
self.all_objects = tk.IntVar()
self.complete_check = tk.Checkbutton(self.frame,text="Complete",variable=self.complete,onvalue=1,offvalue=0)
self.complete_check.pack()
self.fragment_check = tk.Checkbutton(self.frame,text="Fragment",variable=self.fragment,onvalue=1,offvalue=0)
self.fragment_check.pack()
self.damaged_check = tk.Checkbutton(self.frame,text="Damaged",variable=self.damaged,onvalue=1,offvalue=0)
self.damaged_check.pack()
self.all_check = tk.Checkbutton(self.frame,text="All",variable=self.all_objects,onvalue=1,offvalue=0)
self.all_check.pack()
self.submit = mtk.Button(self.frame,text='Done',command=set_init_objects)
self.submit.pack()
def set_ages(self):
def set_species_options_by_age(event=None):
try:
self.start_number = float(self.start_date_entry.get())
except ValueError:
self.start_number = ''
try:
self.end_number = float(self.end_date_entry.get())
except ValueError:
self.end_number = ''
if (self.start_number == '') and (self.end_number == '') and (self.no_fossils.get() == 0):
print 'No age range set; using full species list for autocomplete.'
self.final_data = species_data
else:
if self.no_fossils.get() == 1:
self.final_data = species_data[['specName','End','Start']].query('End >= 0')
else:
self.query = 'End >= ' + str(self.end_date_entry.get()) + ' and Start <= ' + str(self.start_date_entry.get())
self.final_data = species_data[['specName','End','Start']].query(self.query)
self.frame.destroy()
self.setup_data_entry()
self.frame = tk.Frame(self.root)
self.frame.pack(side="left")
self.date_label = mtk.Title(self.frame,text='Age Range (Inclusive):')
self.date_label.pack()
self.end_default = tk.StringVar()
self.end_date_entry = tk.Entry(self.frame, textvariable = self.end_default, width = 5)
self.end_default.set('End')
self.end_date_entry.pack()
self.start_default = tk.StringVar()
self.start_date_entry = tk.Entry(self.frame, textvariable = self.start_default, width = 5)
self.start_default.set('Start')
self.start_date_entry.pack()
self.no_fossils = tk.IntVar()
self.no_fossils_check = tk.Checkbutton(self.frame,text="No fossils",variable=self.no_fossils,onvalue=1,offvalue=0)
self.no_fossils_check.pack()
self.set_ages = mtk.Button(self.frame,text='Set Ages',command=set_species_options_by_age)
self.set_ages.pack()
def confirm_species(self,event=None):
print 'Species set as: ' + self.species_entry._hits[self.species_entry._hit_index]
self.entry_name_split = self.species_entry._hits[self.species_entry._hit_index].split('_')
self.species_only = self.entry_name_split[0]
if len(self.entry_name_split) == 1:
self.genus_only = ''
self.note = ''
elif len(self.entry_name_split) == 2:
self.genus_only = self.entry_name_split[1]
self.note = ''
elif len(self.entry_name_split) == 3:
self.genus_only = self.entry_name_split[1]
self.note = self.entry_name_split[2]
self.conf_window = tk.Toplevel()
self.conf_window_label = mtk.Title(self.conf_window,text='Confidence Level:')
self.conf_window_label.pack()
self.conf_window.wm_attributes("-topmost", 1)
self.conf_window.focus_force()
def set_confidence_level(confidence_level):
def _f(event=None):
if self.species_confidence is not None:
self.buttons[confidence_level].unSet()
self.species_confidence = confidence_level
self.update_database()
return _f
self.species_confidence = None
self.buttons = {}
confidence = ['very','somewhat','not']
conf_keys = ['1','2','3']
for i,c in enumerate(confidence):
self.buttons[c] = mtk.Button(self.conf_window,text=conf_keys[i] + '. ' + c,color='light gray',command=set_confidence_level(c),staydown=True)
self.conf_window.bind(conf_keys[i],set_confidence_level(c))
self.buttons[c].pack()
def convert_csv(self):
def write_converted_csv(event=None):
if self.v.get() == 1:
self.temp_csv = pandas.read_csv(data_file)
self.temp_csv_subset = self.temp_csv.ix[:,1:4]
for i in range(len(self.temp_csv_subset.ix[:,0])):
self.old_entry = self.temp_csv_subset.ix[i,0]
self.new_entry = 'obj' + '0' * (5 - len(str(self.old_entry))) + str(self.old_entry)
self.temp_csv_subset.ix[i,0] = self.new_entry
self.temp_csv_subset.columns = ['object','id','confidence']
self.new_filename = self.output_base + '_converted.csv'
self.temp_csv_subset.to_csv(self.new_filename, mode='w', index=False)
self.data_todb = self.new_filename
elif self.v.get() == 2:
self.temp_csv = pandas.read_csv(data_file)
self.temp_csv.columns = ['object','id','confidence']
self.new_filename = self.output_base + '_converted.csv'
self.temp_csv.to_csv(self.new_filename, mode='w', index=False)
self.data_todb = self.new_filename
else:
self.data_todb = data_file
self.frame.destroy()
self.initialize_objects()
self.frame = tk.Frame(self.root)
self.frame.pack()
self.convert_csv_text = mtk.Title(self.frame,text='Convert CSV format?')
self.convert_csv_text.pack()
self.v = tk.IntVar()
tk.Radiobutton(self.frame,text='Convert old Classify to new Classify format',variable=self.v,value=1).pack()
tk.Radiobutton(self.frame,text='Convert Classify column names',variable=self.v,value=2).pack()
tk.Radiobutton(self.frame,text='No conversion',variable=self.v,value=0).pack()
self.submit_csv = mtk.Button(self.frame,text='Done',command=write_converted_csv)
self.submit_csv.pack()
def setup_data_entry(self):
self.image_list = [
x for x in listdir('.')
if splitext(x)[1] == self.ext or splitext(x)[1][1:] == self.ext
]
self.num_objects = len(self.image_list)
self.display_image()
self.display_object_name()
self.display_undo_button()
#root.wm_attributes("-topmost", 1)
#root.focus_force()
def make_selection_fn(new_selection):
def _f(event=None):
if self.selection is not None:
self.buttons[self.selection].unSet()
self.selection = new_selection
if self.buttons[self.selection].state != 'down':
self.buttons[self.selection].set()
return _f
self.selection = None
self.confidence = None
self.frame = tk.Frame(self.root)
self.frame.pack(side="left")
self.buttons = {}
planktonic = ['complete', 'fragment', 'damaged']
nonplankton = ['benthic', 'mollusk', 'ostracod', 'rock', 'junk image']
other = [
'echinoid spine', 'radiolarian', 'spicule', 'tooth',
'clipped image', 'unknown'
]
colors = ['green', 'gray', 'dark blue']
keys = lowercase
button_count = 0
for m, lst in enumerate([planktonic, nonplankton, other]):
for n, name in enumerate(lst):
self.buttons[name] = mtk.Button(
self.frame,
text=keys[button_count] + '. ' + name,
command=make_selection_fn(name),
color=colors[m],
staydown=True)
self.buttons[name].pack()
# attach key to button
self.frame.bind_all(keys[button_count],
make_selection_fn(name))
button_count += 1
self.confidence_label = mtk.Title(self.frame, text='Confidence:')
self.confidence_label.pack()
def make_confidence_callback(conf):
def _f(event=None):
if not self.selection:
tkMessageBox.showerror("Fragment", "Choose a type first!")
if self.confidence is not None:
self.buttons[conf].unSet()
self.confidence = conf
self.next_image()
return _f
confidence = ['very', 'somewhat', 'not']
conf_keys = ['1', '2', '3']
for n, name in enumerate(confidence):
# fix command here
self.buttons[name] = mtk.Button(
self.frame,
text=conf_keys[n] + '. ' + name,
color='light gray',
command=make_confidence_callback(name),
staydown=True)
self.frame.bind_all(conf_keys[n], make_confidence_callback(name))
self.buttons[name].pack()
def setup_data_entry(self):
def make_selection(new_selection):
def _f(event=None):
if self.selection is not None:
self.buttons[self.selection].unSet()
self.checking_data[self.objects_list[self.image_ind]] = new_selection
print '{:s}: {:s}\n'.format(self.objects_list[self.image_ind],new_selection)
self.next_image()
return _f
if self.mode.get() == 1:
self.display_windows()
self.frame = tk.Frame(self.root)
self.frame.pack(side="left")
self.selection = None
self.buttons = {}
options = [('correct','1. Correct as marked'),('change','2. Needs change'),('remove','3. Remove from dataset')]
for i,option in enumerate(options):
self.buttons[option[0]] = mtk.Button(self.frame,
text=option[1],
command=make_selection(option[0]))
self.buttons[option[0]].pack()
self.frame.bind_all(str(i+1),make_selection(option[0]))
# Checkpoint button
self.checkpoint_button = mtk.Button(self.frame,text='Checkpoint',color='dark blue',command=self.check_checkpoint)
self.checkpoint_button.pack()
# Undo button
self.undo_button = tk.Button(self.frame,text='Undo',width=20,pady=2,height=1,bd=2,command=self.previous_image)
self.undo_button.pack()
else:
self.objects_list = [x[0] for x in self.all_rows]
self.image_list = [x for y in self.objects_list for x in os.listdir('.') if y in x]
self.display_windows()
self.species_entry_label = mtk.Title(root,text='Species ID:')
self.species_entry_label.pack()
self.species_entry = AutocompleteEntry(root)
self.species_entry.set_completion_list(self.final_data['specName'])
self.species_entry.pack()
self.species_entry.focus()
self.submit_species = mtk.Button(root,text='Confirm Species',command=self.confirm_species)
root.bind('<Return>',self.confirm_species)
self.submit_species.pack()
# Checkpoint button
self.checkpoint_button = mtk.Button(root,text='Checkpoint',color='dark blue',command=self.checkpoint)
self.checkpoint_button.pack()
# Undo button
self.undo_button = tk.Button(self.frame,text='Undo',width=20,pady=2,height=1,bd=2,command=self.previous_image)
self.undo_button.pack()
def __init__(self,root):
def start(event=None):
self.frame.destroy() # Remove mode selection screen
# Checking mode
if self.mode.get() == 1:
self.image_dir = tkFileDialog.askdirectory() # Get input directory containing images to check
self.image_ext = ['.jpg','.tif'] # All acceptable image extensions
self.all_files = glob.glob(os.path.join(self.image_dir,'*')) # All files in selected directory
self.image_list = [x for x in self.all_files if os.path.splitext(x)[1] in self.image_ext] # All image files in selected directory
self.num_objects = len(self.image_list)
self.objects_list = map(os.path.basename,self.image_list)
# Check if CSV output file already exists
self.csv_check = glob.glob(os.path.join(self.image_dir,'specify*csv'))
if self.csv_check:
if tkMessageBox.askyesno('Specify','Specify output file exists; overwrite?'):
self.overwrite = True
else:
self.overwrite = False
else:
self.overwrite = False
# Check if checkpoint file exists
if 'checkpoint.txt' in [os.path.basename(x) for x in self.all_files]:
self.restart = True
self.checkpoint_file = os.path.join(self.image_dir,'checkpoint.txt')
print 'Restarting from checkpoint file.'
with open(self.checkpoint_file,'rb') as f:
lines = f.readlines()
self.image_ind = int(lines[0].strip())
self.checking_data = ast.literal_eval(lines[1].strip())
# Clean start setup
else:
self.restart = False
self.image_ind = 0
self.checking_data = dict.fromkeys(self.objects_list)
self.setup_data_entry()
# Naming mode (standard)
else:
# Set species list
species_data = pandas.read_csv('app_species_list.csv')
species_data['specName'] = [x.lower() for x in species_data.specName]
species_list = species_data['specName']
# Convert dates
species_data['End'] = species_data['End'].convert_objects(convert_numeric=True)
species_data['Start'] = species_data['Start'].convert_objects(convert_numeric=True)
# Get directory of images from user
data_file = tkFileDialog.askopenfilename()
os.chdir(os.path.dirname(data_file))
self.data = os.path.basename(data_file)
# Checkpoint restart
if 'checkpoint' in data_file:
self.restart = True
self.checkpoint_data_tr = pandas.read_csv(data_file)
self.checkpoint_codes = map(list,self.checkpoint_data_tr.tail(1).values)[0]
self.output_base = '_'.join(self.data.split('_')[:-1])
self.data_todb = data_file
self.image_ind = int(self.checkpoint_codes[0])
self.initialize_objects()
print 'Restarting from checkpoint file.'
# Normal start
else:
self.restart = False
self.output_base = self.data[:-4]
self.image_ind = 0
self.convert_csv()
self.root = root
# Set mode
self.frame = tk.Frame(self.root)
self.frame.pack()
self.mode_select = mtk.Title(self.frame,text='Select mode:')
self.mode_select.pack()
self.mode = tk.IntVar()
tk.Radiobutton(self.frame,text='Checking mode',variable=self.mode,value=1).pack()
tk.Radiobutton(self.frame,text='Naming mode',variable=self.mode,value=2).pack()
mtk.Button(self.frame,text='Start',command=start).pack()
