def padder(animal, bgcolor):
fileLocationManager = FileLocationManager(animal)
sqlController = SqlController()
sqlController.get_animal_info(animal)
INPUT = os.path.join(fileLocationManager.prep, 'thumbnail_masked')
OUTPUT = '/net/birdstore/Active_Atlas_Data/data_root/brains_info/masks/{}/prealigned'.format(animal)
files = sorted(os.listdir(INPUT))
width = sqlController.scan_run.width
height = sqlController.scan_run.height
max_width = int(width * SCALING_FACTOR)
max_height = int(height * SCALING_FACTOR)
for i, file in enumerate(tqdm(files)):
infile = os.path.join(INPUT, file)
try:
img = io.imread(infile)
except:
print('Could not open', infile)
continue
fixed = place_image(img, file, max_width, max_height, bgcolor)
outpath = os.path.join(OUTPUT, file)
cv2.imwrite(outpath, fixed.astype('uint8'))
print('Finished')
class GUICropBrainStem(QWidget):
def __init__(self, stack, parent=None):
super(GUICropBrainStem, self).__init__(parent)
self.stack = stack
self.fileLocationManager = FileLocationManager(self.stack)
self.sqlController = SqlController()
self.sqlController.get_animal_info(self.stack)
self.valid_sections = self.sqlController.get_valid_sections(stack)
self.valid_section_keys = sorted(list(self.valid_sections))
self.curr_section_index = 0
self.curr_section = None
self.active_selection = ''
self.img_width = 2001
self.img_height = 1001
self.rostral = -1
self.caudal = -1
self.ventral = -1
self.dorsal = -1
self.first_slice = -1
self.last_slice = -1
self.init_ui()
self.b_rostral.clicked.connect(
lambda: self.click_button(self.b_rostral))
self.b_caudal.clicked.connect(lambda: self.click_button(self.b_caudal))
self.b_dorsal.clicked.connect(lambda: self.click_button(self.b_dorsal))
self.b_ventral.clicked.connect(
lambda: self.click_button(self.b_ventral))
self.b_first_slice.clicked.connect(
lambda: self.click_button(self.b_first_slice))
self.b_last_slice.clicked.connect(
lambda: self.click_button(self.b_last_slice))
self.b_done.clicked.connect(lambda: self.click_button(self.b_done))
self.viewer.click.connect(self.click_photo)
def init_ui(self):
self.font_h1 = QFont("Arial", 32)
self.font_p1 = QFont("Arial", 16)
self.grid_top = QGridLayout()
self.grid_body_upper = QGridLayout()
self.grid_body = QGridLayout()
self.grid_body_lower = QGridLayout()
self.resize(1600, 1100)
# Grid Top
self.e_title = QLineEdit()
self.e_title.setAlignment(Qt.AlignCenter)
self.e_title.setFont(self.font_h1)
self.e_title.setReadOnly(True)
self.e_title.setText("Setup Sorted Filenames")
self.e_title.setFrame(False)
self.grid_top.addWidget(self.e_title, 0, 0)
self.b_help = QPushButton("HELP")
self.b_help.setDefault(True)
self.b_help.setEnabled(True)
self.grid_top.addWidget(self.b_help, 0, 1)
# Grid BODY UPPER
self.e_filename = QLineEdit()
self.e_filename.setAlignment(Qt.AlignCenter)
self.e_filename.setFont(self.font_p1)
self.e_filename.setReadOnly(True)
self.e_filename.setText("Filename: ")
self.grid_body_upper.addWidget(self.e_filename, 0, 2)
self.e_section = QLineEdit()
self.e_section.setAlignment(Qt.AlignCenter)
self.e_section.setFont(self.font_p1)
self.e_section.setReadOnly(True)
self.e_section.setText("Section: ")
self.grid_body_upper.addWidget(self.e_section, 0, 3)
# Grid BODY
self.viewer = ImageViewer(self)
self.grid_body.addWidget(self.viewer, 0, 0)
# Grid BODY LOWER
self.b_rostral = QPushButton("Rostral Limit:")
self.grid_body_lower.addWidget(self.b_rostral, 0, 0)
self.e_rostral = QLineEdit()
self.e_rostral.setAlignment(Qt.AlignCenter)
self.e_rostral.setFont(self.font_p1)
self.grid_body_lower.addWidget(self.e_rostral, 0, 1)
self.b_caudal = QPushButton("Caudal Limit:")
self.grid_body_lower.addWidget(self.b_caudal, 1, 0)
self.e_caudal = QLineEdit()
self.e_caudal.setAlignment(Qt.AlignCenter)
self.e_caudal.setFont(self.font_p1)
self.grid_body_lower.addWidget(self.e_caudal, 1, 1)
self.b_dorsal = QPushButton("Dorsal Limit:")
self.grid_body_lower.addWidget(self.b_dorsal, 0, 2)
self.e_dorsal = QLineEdit()
self.e_dorsal.setAlignment(Qt.AlignCenter)
self.e_dorsal.setFont(self.font_p1)
self.grid_body_lower.addWidget(self.e_dorsal, 0, 3)
self.b_ventral = QPushButton("Ventral Limit:")
self.grid_body_lower.addWidget(self.b_ventral, 1, 2)
self.e_ventral = QLineEdit()
self.e_ventral.setAlignment(Qt.AlignCenter)
self.e_ventral.setFont(self.font_p1)
self.grid_body_lower.addWidget(self.e_ventral, 1, 3)
self.b_first_slice = QPushButton("Mark as FIRST Slice With Brainstem:")
self.grid_body_lower.addWidget(self.b_first_slice, 0, 4)
self.e_first_slice = QLineEdit()
self.e_first_slice.setAlignment(Qt.AlignCenter)
self.e_first_slice.setFont(self.font_p1)
self.grid_body_lower.addWidget(self.e_first_slice, 0, 5)
self.b_last_slice = QPushButton("Mark as LAST Slice With Brainstem:")
self.grid_body_lower.addWidget(self.b_last_slice, 1, 4)
self.e_last_slice = QLineEdit()
self.e_last_slice.setAlignment(Qt.AlignCenter)
self.e_last_slice.setFont(self.font_p1)
self.grid_body_lower.addWidget(self.e_last_slice, 1, 5)
self.b_done = QPushButton("DONE")
self.grid_body_lower.addWidget(self.b_done, 1, 6)
# Super grid
self.supergrid = QGridLayout()
self.supergrid.addLayout(self.grid_top, 0, 0)
self.supergrid.addLayout(self.grid_body_upper, 1, 0)
self.supergrid.addLayout(self.grid_body, 2, 0)
self.supergrid.addLayout(self.grid_body_lower, 3, 0)
# Set layout and window title
self.setLayout(self.supergrid)
self.setWindowTitle("Q")
def set_curr_section(self, section_index=-1):
"""
Sets the current section to the section passed in.
Will automatically update curr_section, prev_section, and next_section.
Updates the header fields and loads the current section image.
"""
if section_index == -1:
section_index = self.curr_section_index
# Update curr, prev, and next section
self.curr_section_index = section_index
self.curr_section = self.valid_sections[self.valid_section_keys[
self.curr_section_index]]
# Update the section and filename at the top
self.e_filename.setText(self.curr_section['destination'])
self.e_section.setText(str(self.curr_section['section_number']))
# Get filepath of "curr_section" and set it as viewer's photo
img_fp = os.path.join(self.fileLocationManager.thumbnail_prep,
self.curr_section['destination'])
if os.path.isfile(img_fp):
img = cv2.imread(img_fp) * 3
self.img_height, self.img_width, channel = img.shape
if self.rostral != -1:
x_coordinate = int(self.rostral)
img[:, x_coordinate - 2:x_coordinate + 2, :] = np.ones(
(self.img_height, 4, 3)) * 255
if self.caudal != -1:
x_coordinate = int(self.caudal)
img[:, x_coordinate - 2:x_coordinate + 2, :] = np.ones(
(self.img_height, 4, 3)) * 255
if self.dorsal != -1:
y_coordinate = int(self.dorsal)
img[y_coordinate - 2:y_coordinate + 2, :, :] = np.ones(
(4, self.img_width, 3)) * 255
if self.ventral != -1:
y_coordinate = int(self.ventral)
img[y_coordinate - 2:y_coordinate + 2, :, :] = np.ones(
(4, self.img_width, 3)) * 255
qImg = QImage(img.data, self.img_width, self.img_height,
3 * self.img_width, QImage.Format_RGB888)
self.viewer.set_photo(QPixmap(qImg))
# Update the internal crop values based on text boxes
#self.updateCropVals()
def get_valid_section_index(self, section_index):
if section_index >= len(self.valid_sections):
return 0
elif section_index < 0:
return len(self.valid_sections) - 1
else:
return section_index
def click_button(self, button):
if button in [
self.b_rostral, self.b_caudal, self.b_dorsal, self.b_ventral
]:
self.viewer.set_drag_mode(0)
if button == self.b_rostral:
self.active_selection = 'rostral'
elif button == self.b_caudal:
self.active_selection = 'caudal'
elif button == self.b_dorsal:
self.active_selection = 'dorsal'
elif button == self.b_ventral:
self.active_selection = 'ventral'
# Prep2 section limits
elif button in [self.b_first_slice, self.b_last_slice]:
if button == self.b_first_slice:
self.first_slice = int(self.curr_section)
self.e_first_slice.setText(str(self.curr_section))
elif button == self.b_last_slice:
self.last_slice = int(self.curr_section)
self.e_last_slice.setText(str(self.curr_section))
elif button == self.b_done:
if -1 in [
self.rostral, self.caudal, self.dorsal, self.ventral,
self.first_slice, self.last_slice
]:
QMessageBox.about(self, "Popup Message",
"Make sure all six fields have values!")
return
elif self.rostral >= self.caudal:
QMessageBox.about(
self, "Popup Message",
"Rostral Limit must be smaller than caudal limit!")
return
elif self.dorsal >= self.ventral:
QMessageBox.about(
self, "Popup Message",
"Dorsal Limit must be smaller than Ventral limit!")
return
elif self.first_slice >= self.last_slice:
QMessageBox.about(self, "Popup Message",
"Last slice must be after the first slice!")
return
try:
QMessageBox.about(
self, "Popup Message",
"This operation will take roughly 1.5 minutes per image.")
self.setCurrSection(self.curr_section)
stain = stack_metadata[stack]['stain']
os.subprocess.call([
'python', 'a_script_preprocess_6.py', stack, stain, '-l',
str(self.rostral),
str(self.caudal),
str(self.dorsal),
str(self.ventral),
str(self.first_slice),
str(self.last_slice)
])
sys.exit(app.exec_())
except Exception as e:
sys.stderr.write('\n ********************************\n')
sys.stderr.write(str(e))
sys.stderr.write('\n ********************************\n')
def click_photo(self, pos):
if self.viewer.dragMode() == QGraphicsView.NoDrag:
x = pos.x()
y = pos.y()
print('%d, %d' % (pos.x(), pos.y()))
scale_factor = 1.0 / self.viewer.scale_factor
if self.active_selection == '':
pass
elif self.active_selection == 'rostral':
self.rostral = int(x * scale_factor)
self.rostral = min(self.rostral, self.img_width - 5)
self.rostral = max(self.rostral, 5)
self.e_rostral.setText(str(self.rostral))
elif self.active_selection == 'caudal':
self.caudal = int(x * scale_factor)
self.caudal = min(self.caudal, self.img_width - 5)
self.caudal = max(self.caudal, 5)
self.e_caudal.setText(str(self.caudal))
elif self.active_selection == 'dorsal':
self.dorsal = int(y * scale_factor)
self.dorsal = min(self.dorsal, self.img_height - 5)
self.dorsal = max(self.dorsal, 5)
self.e_dorsal.setText(str(self.dorsal))
elif self.active_selection == 'ventral':
self.ventral = int(y * scale_factor)
self.ventral = min(self.ventral, self.img_height - 5)
self.ventral = max(self.ventral, 5)
self.e_ventral.setText(str(self.ventral))
self.active_selection = ''
self.viewer.set_drag_mode(1)
def updateCropVals(self):
if self.e_rostral.text() != '':
try:
self.rostral = int(self.e_rostral.text())
except:
self.rostral = -1
self.e_rostral.setText("")
if self.e_caudal.text() != '':
try:
self.caudal = int(self.e_caudal.text())
except:
self.caudal = -1
self.e_caudal.setText("")
if self.e_dorsal.text() != '':
try:
self.dorsal = int(self.e_dorsal.text())
except:
self.dorsal = -1
self.e_dorsal.setText("")
if self.e_ventral.text() != '':
try:
self.ventral = int(self.e_ventral.text())
except:
self.ventral = -1
self.e_ventral.setText("")
if self.e_first_slice.text() != '':
try:
self.first_slice = int(self.e_first_slice.text())
except:
self.first_slice = -1
self.e_first_slice.setText("")
if self.e_last_slice.text() != '':
try:
self.last_slice = int(self.e_last_slice.text())
except:
self.last_slice = -1
self.e_last_slice.setText("")
def keyPressEvent(self, event):
try:
key = event.key()
except AttributeError:
key = event
if key == 91: # [
index = self.get_valid_section_index(self.curr_section_index - 1)
self.set_curr_section(index)
elif key == 93: # ]
index = self.get_valid_section_index(self.curr_section_index + 1)
self.set_curr_section(index)
elif key == 16777220: # Enter
index = self.get_valid_section_index(self.curr_section_index)
self.set_curr_section(index)
else:
print(key)
def closeEvent(self, event):
sys.exit(app.exec_())
class GUISetupMain(QWidget):
def __init__(self, stack, parent=None):
super(GUISetupMain, self).__init__(parent)
# Stack specific info, determined from dropdown menu selection
self.stack = stack
self.fileLocationManager = FileLocationManager(self.stack)
self.sqlController = SqlController()
self.sqlController.get_animal_info(self.stack)
self.stain = self.sqlController.histology.counterstain
self.curr_step = self.sqlController.get_current_step_from_progress_ini(self.stack)
# Init UI
self.init_ui()
# Set buttons functionality
self.b_1_4.clicked.connect(lambda: self.click_button(self.b_1_4))
self.b_1_6.clicked.connect(lambda: self.click_button(self.b_1_6))
self.b_exit.clicked.connect(lambda: self.click_button(self.b_exit))
# Update buttons
self.update_buttons()
# Center the GUI
self.center()
def init_ui(self):
self.grid_buttons = QGridLayout()
self.grid_bottom = QGridLayout()
# Grid buttons
self.b_1_4 = QPushButton("Setup Sorted Filenames")
self.grid_buttons.addWidget(self.b_1_4)
self.b_1_6 = QPushButton("Run automatic setup scripts")
self.grid_buttons.addWidget(self.b_1_6)
# Grid bottom
self.progress = QProgressBar(self)
self.progress.hide()
self.grid_bottom.addWidget(self.progress)
self.b_exit = QPushButton("Exit")
self.b_exit.setDefault(True)
self.grid_bottom.addWidget(self.b_exit)
# Super grid
self.super_grid = QGridLayout()
self.super_grid.addLayout(self.grid_buttons, 1, 0)
self.super_grid.addLayout(self.grid_bottom, 2, 0)
self.setLayout(self.super_grid)
self.setWindowTitle("Align to Active Brainstem Atlas - Setup Page")
self.resize(1000, 450)
def update_buttons(self):
"""
Locates where you are in the pipeline by reading the brains_info/STACK_progress.ini
Buttons corresponding to previous steps are marked as "completed", buttons corresponding
to future steps are marked as "unpressable" and are grayed out.
"""
self.stain = self.sqlController.histology.counterstain
try:
self.curr_step = self.sqlController.get_current_step_from_progress_ini(self.stack)
print('format grid buttons current step is', self.curr_step)
curr_step_index = ['1-4', '1-5', '1-6'].index(self.curr_step[:3])
for index, button in enumerate([self.b_1_4, self.b_1_6]):
if index <= curr_step_index + 1:
button.setEnabled(True)
else:
button.setEnabled(False)
# If there are no stacks/brains that have been started
except KeyError:
for button in [self.b_1_4, self.b_1_6]:
button.setEnabled(False)
def click_button(self, button):
"""
If any of the "grid" buttons are pressed, this is the callback function.
In this case, "grid" buttons have a one-to_one correspondance to the steps in the pipeline.
The completion of each step means you move onto the next one.
"""
# Setup/Create sorted filenames
if button == self.b_1_4:
try:
subprocess.call(['python', 'a_GUI_setup_sorted_filenames.py', self.stack])
self.update_buttons()
except Exception as e:
sys.stderr.write(str(e))
# Run automatic scripts
elif button == self.b_1_6:
message = "This operation will take a long time."
message += " Several minutes per image."
QMessageBox.about(self, "Popup Message", message)
preprocess_setup(self.stack, self.stain)
#subprocess.call(['python', 'utilities/a_script_preprocess_1.py', self.stack, self.stain])
subprocess.call(['python', 'a_script_preprocess_2.py', self.stack, self.stain])
self.sqlController.set_step_completed_in_progress_ini(self.stack, '1-6_setup_scripts')
"""
pipeline_status = get_pipeline_status(self.stack)
if not 'preprocess_1' in pipeline_status and \
not 'preprocess_2' in pipeline_status and not 'setup' in pipeline_status:
self.sqlController.set_step_completed_in_progress_ini(self.stack, '1-6_setup_scripts')
sys.exit(app.exec_())
pipeline_status = get_pipeline_status(self.stack)
if pipeline_status == 'a_script_preprocess_3':
self.sqlController.set_step_completed_in_progress_ini(self.stack, '1-6_setup_scripts')
sys.exit(app.exec_())
# else:
# print '\n\n\n\n'
# print 'pipeline_status:'
## print pipeline_status
# print '\n\n\n\n'
# #set_step_completed_in_progress_ini( self.stack, '1-6_setup_scripts')
print('finished in button 4')
"""
elif button == self.b_exit:
self.closeEvent(None)
self.update_buttons()
def center(self):
"""
This function simply aligns the GUI to the center of your monitor.
"""
frameGm = self.frameGeometry()
screen = QApplication.desktop().screenNumber(QApplication.desktop().cursor().pos())
centerPoint = QApplication.desktop().screenGeometry(screen).center()
frameGm.moveCenter(centerPoint)
self.move(frameGm.topLeft())
def closeEvent(self, event):
sys.exit(app.exec_())
class init_GUI(QWidget):
def __init__(self, stack, parent=None):
super(init_GUI, self).__init__(parent)
self.font_h1 = QFont("Arial", 32)
self.font_p1 = QFont("Arial", 16)
self.stack = stack
self.fileLocationManager = FileLocationManager(self.stack)
self.sqlController = SqlController()
self.sqlController.get_animal_info(self.stack)
self.valid_sections = self.sqlController.get_valid_sections(stack)
self.valid_section_keys = sorted(list(self.valid_sections))
section_length = len(self.valid_section_keys)
self.curr_section_index = section_length // 2
self.prev_section_index = self.curr_section_index
self.next_section_index = self.curr_section_index
self.curr_section = self.valid_sections[self.valid_section_keys[
self.curr_section_index]]['destination']
self.prev_section = self.getPrevValidSection(self.curr_section_index)
self.next_section = self.getNextValidSection(self.curr_section_index)
self.curr_T = None
self.mode = 'view'
# self.mode = 'align'
self.transform_type = 'pairwise' # Can toggle to 'anchor'
# Increasing this number will brighten the images
self.curr_img_multiplier = 1
self.prev_img_multiplier = 1
self.initUI()
def initUI(self):
# Set Layout and Geometry of Window
self.grid_top = QGridLayout()
self.grid_body_upper = QGridLayout()
self.grid_body = QGridLayout()
self.grid_body_lower_align_mode = QGridLayout()
self.grid_bottom = QGridLayout()
self.grid_blank = QGridLayout()
# self.setFixedSize(1600, 1100)
self.resize(1600, 1100)
### VIEWER ### (Grid Body)
self.viewer = ImageViewer(self)
self.viewer.photoClicked.connect(self.photoClicked)
### Grid TOP ###
# Static Text Field (Title)
self.e1 = QLineEdit()
self.e1.setValidator(QIntValidator())
self.e1.setAlignment(Qt.AlignCenter)
self.e1.setFont(self.font_h1)
self.e1.setReadOnly(True)
self.e1.setText("Quality Checker")
self.e1.setFrame(False)
self.grid_top.addWidget(self.e1, 0, 0)
# Button Text Field
self.b_help = QPushButton("HELP")
self.b_help.setDefault(True)
self.b_help.setEnabled(True)
self.b_help.clicked.connect(
lambda: self.help_button_press(self.b_help))
self.b_help.setStyleSheet(
"color: rgb(0,0,0); background-color: rgb(250,250,250);")
self.grid_top.addWidget(self.b_help, 0, 1)
### Grid BODY UPPER ###
# Static Text Field
self.e2 = QLineEdit()
self.e2.setAlignment(Qt.AlignCenter)
self.e2.setFont(self.font_p1)
self.e2.setReadOnly(True)
self.e2.setText("Filename: ")
self.e2.setStyleSheet(
"color: rgb(50,50,250); background-color: rgb(250,250,250);")
self.grid_body_upper.addWidget(self.e2, 0, 0)
# Static Text Field
self.e3 = QLineEdit()
self.e3.setAlignment(Qt.AlignCenter)
self.e3.setFont(self.font_p1)
self.e3.setReadOnly(True)
self.e3.setText("Section: ")
self.e3.setStyleSheet(
"color: rgb(50,50,250); background-color: rgb(250,250,250);")
self.grid_body_upper.addWidget(self.e3, 0, 1)
# Static Text Field
self.e4 = QLineEdit()
self.e4.setAlignment(Qt.AlignCenter)
self.e4.setFont(self.font_p1)
self.e4.setReadOnly(True)
self.e4.setText("Filename: ")
self.e4.setStyleSheet(
"color: rgb(250,50,50); background-color: rgb(250,250,250);")
self.grid_body_upper.addWidget(self.e4, 0, 2)
# Static Text Field
self.e5 = QLineEdit()
self.e5.setAlignment(Qt.AlignCenter)
self.e5.setFont(self.font_p1)
self.e5.setReadOnly(True)
self.e5.setText("Section: ")
self.e5.setStyleSheet(
"color: rgb(250,50,50); background-color: rgb(250,250,250);")
self.grid_body_upper.addWidget(self.e5, 0, 3)
### Grid BODY ###
# Custom VIEWER
self.grid_body.addWidget(self.viewer, 0, 0)
### Grid BODY LOWER (align mode only) ###
# Button Text Field
self.b1 = QPushButton("Brighten blue image")
self.b1.setDefault(True)
self.b1.setEnabled(False)
self.b1.clicked.connect(lambda: self.buttonPress(self.b1))
self.b1.setStyleSheet(
"color: rgb(50,50,250); background-color: rgb(250,250,250);")
self.grid_body_lower_align_mode.addWidget(self.b1, 0, 0)
# Button Text Field
self.b2 = QPushButton("Brighten red image")
self.b2.setDefault(True)
self.b2.setEnabled(False)
self.b2.clicked.connect(lambda: self.buttonPress(self.b2))
self.b2.setStyleSheet(
"color: rgb(250,50,50); background-color: rgb(250,250,250);")
self.grid_body_lower_align_mode.addWidget(self.b2, 1, 0)
# Button Text Field
self.b_up = QPushButton("/\\")
self.b_up.setDefault(True)
self.b_up.setEnabled(False)
self.b_up.clicked.connect(lambda: self.buttonPress(self.b_up))
self.b_up.setStyleSheet(
"color: rgb(250,50,50); background-color: rgb(250,250,250);")
self.grid_body_lower_align_mode.addWidget(self.b_up, 0, 3)
# Button Text Field
self.b_left = QPushButton("<=")
self.b_left.setDefault(True)
self.b_left.setEnabled(False)
self.b_left.clicked.connect(lambda: self.buttonPress(self.b_left))
self.b_left.setStyleSheet(
"color: rgb(250,50,50); background-color: rgb(250,250,250);")
self.grid_body_lower_align_mode.addWidget(self.b_left, 1, 2)
# Button Text Field
self.b_down = QPushButton("\/")
self.b_down.setDefault(True)
self.b_down.setEnabled(False)
self.b_down.clicked.connect(lambda: self.buttonPress(self.b_down))
self.b_down.setStyleSheet(
"color: rgb(250,50,50); background-color: rgb(250,250,250);")
self.grid_body_lower_align_mode.addWidget(self.b_down, 1, 3)
# Button Text Field
self.b_right = QPushButton("=>")
self.b_right.setDefault(True)
self.b_right.setEnabled(False)
self.b_right.clicked.connect(lambda: self.buttonPress(self.b_right))
self.b_right.setStyleSheet(
"color: rgb(250,50,50); background-color: rgb(250,250,250);")
self.grid_body_lower_align_mode.addWidget(self.b_right, 1, 4)
# Button Text Field
self.b_clockwise = QPushButton("^--'")
self.b_clockwise.setDefault(True)
self.b_clockwise.setEnabled(False)
self.b_clockwise.clicked.connect(
lambda: self.buttonPress(self.b_clockwise))
self.b_clockwise.setStyleSheet(
"color: rgb(250,50,50); background-color: rgb(250,250,250);")
self.grid_body_lower_align_mode.addWidget(self.b_clockwise, 0, 6)
# Button Text Field
self.b_cclockwise = QPushButton("'--^")
self.b_cclockwise.setDefault(True)
self.b_cclockwise.setEnabled(False)
self.b_cclockwise.clicked.connect(
lambda: self.buttonPress(self.b_cclockwise))
self.b_cclockwise.setStyleSheet(
"color: rgb(250,50,50); background-color: rgb(250,250,250);")
self.grid_body_lower_align_mode.addWidget(self.b_cclockwise, 0, 7)
# Button Text Field
self.b_save_transform = QPushButton("Save Transformation")
self.b_save_transform.setDefault(True)
self.b_save_transform.setEnabled(False)
self.b_save_transform.clicked.connect(
lambda: self.buttonPress(self.b_save_transform))
self.b_save_transform.setStyleSheet(
"color: rgb(0,0,0); background-color: rgb(250,200,250);")
self.grid_body_lower_align_mode.addWidget(self.b_save_transform, 1, 9)
# Button Text Field
self.b_done = QPushButton("DONE")
self.b_done.setDefault(True)
self.b_done.setEnabled(True)
self.b_done.clicked.connect(lambda: self.buttonPress(self.b_done))
self.b_done.setStyleSheet(
"color: rgb(0,0,0); background-color: rgb(200,250,250);")
self.grid_body_lower_align_mode.addWidget(self.b_done, 1, 10)
# Grid stretching
self.grid_body_upper.setColumnStretch(0, 2)
self.grid_body_upper.setColumnStretch(2, 2)
### SUPERGRID ###
self.supergrid = QGridLayout()
self.supergrid.addLayout(self.grid_top, 0, 0)
self.supergrid.addLayout(self.grid_body_upper, 1, 0)
self.supergrid.addLayout(self.grid_body, 2, 0)
self.supergrid.addLayout(self.grid_body_lower_align_mode, 3, 0)
self.supergrid.addLayout(self.grid_bottom, 4, 0)
# Set layout and window title
self.setLayout(self.supergrid)
self.setWindowTitle("Q")
# Loads self.curr_section as the current image and sets all fields appropriatly
self.setCurrSection(self.curr_section_index)
def help_button_press(self, button):
info_text = "This GUI is used to align slices to each other. The shortcut commands are as follows: \n\n\
- `m`: Toggle between view mode (grayscale) and alignment mode (red & blue).\n\
- `[`: Go back one section. \n\
- `]`: Go forward one section. \n\n\
\
All changes must be done in alignment mode. Alignment mode will display the pairwise alignment between the current \
active section (red) and the previous section (blue). Using the buttons at the foot of the GUI, you can translate and \
rotate the active section (red) as well as brighten either the active or previous section. Adjust the red slice such \
that it is aligned to the blue slice as well as possible and press \"Save Transformation\".\n\n\
\
The grayscale images should all be aligned to one another. Please verify that all sections are aligned properly \
before you finish this step."
QMessageBox.information(self, "Empty Field", info_text)
def loadImage(self):
# Get filepath of "curr_section" and set it as viewer's photo
#fp = get_fp(self.curr_section, prep_id=1)
input_tif = os.path.join(self.fileLocationManager.thumbnail_prep,
self.curr_section)
print('input_tif', input_tif)
#fp = io.imread(input_tif)
self.viewer.setPhoto(QPixmap(input_tif))
self.curr_T = None
#
# img, T = get_transformed_image( self.curr_section,
# transformation='anchor',
# prev_section=self.prev_section )
# T = get_comulative_pairwise_transform( stack,
# DataManager.metadata_cache['sections_to_filenames'][stack][self.curr_section] )
# img = apply_transform( stack, T,
# DataManager.metadata_cache['sections_to_filenames'][stack][self.curr_section])
# height, width, channel = img.shape
# bytesPerLine = 3 * width
# qImg = QImage(img.data, width, height, bytesPerLine, QImage.Format_RGB888)
#
# self.viewer.setPhoto( QPixmap( qImg ) )
def loadImageThenNormalize(self):
# Get filepath of "curr_section" and set it as viewer's photo
input_tif = os.path.join(self.fileLocationManager.oriented,
self.curr_section)
#fp = imread(input_tif)
img = io.imread(input_tif) * 3
height, width, channel = img.shape
bytesPerLine = 3 * width
qImg = QImage(img.data, width, height, bytesPerLine,
QImage.Format_RGB888)
self.viewer.setPhoto(QPixmap(qImg))
def loadImagesColored(self):
# we want to load RED (current section) and BLUE (previous section) channels overlayed
curr_tif = os.path.join(self.fileLocationManager.oriented,
self.curr_section)
img_curr_red = io.imread(curr_tif)
prev_tif = os.path.join(self.fileLocationManager.oriented,
self.prev_section)
img_prev_blue = io.imread(prev_tif)
# Load the untransformed images
# img_curr_red = cv2.imread( fp_curr_red )
# img_prev_blue = cv2.imread( fp_prev_blue )
if self.transform_type == 'anchor':
# Load anchor-transformed images
img_curr_red, T = get_transformed_image(self.curr_section,
transformation='anchor')
img_prev_blue, Tb = get_transformed_image(self.prev_section,
transformation='anchor')
self.curr_T = T
elif self.transform_type == 'pairwise' and self.curr_section > self.prev_section:
# Load pairwise-transformed images
# The current red image is transformed to the previous blue image
img_curr_red, T = get_transformed_image(
self.curr_section,
transformation='pairwise',
prev_section=self.prev_section)
self.curr_T = T
# Blue image does not change
prev_tif = os.path.join(self.fileLocationManager.oriented,
self.prev_section)
img_prev_blue = io.imread(prev_tif)
elif self.transform_type == 'pairwise' and self.curr_section < self.prev_section:
# In the case of wrapping (prev_section wrapps to the last section when curr_section is 0)
# We just load the red ad blue channels of curr_section making it appear purple
self.curr_T = None
curr_tif = os.path.join(self.fileLocationManager.oriented,
self.curr_section)
img_curr_red = io.imread(curr_tif)
prev_tif = os.path.join(self.fileLocationManager.oriented,
self.prev_section)
img_prev_blue = io.imread(prev_tif)
height_r, width_r, _ = img_curr_red.shape
height_b, width_b, _ = img_prev_blue.shape
new_height = max(height_r, height_b)
new_width = max(width_r, width_b)
img_combined = np.ones((new_height, new_width, 3))
img_combined[0:height_r, 0:width_r, 0] += img_curr_red[:, :, 0]
img_combined[0:height_b, 0:width_b, 2] += img_prev_blue[:, :, 0]
img_combined = np.array(
img_combined,
dtype=np.uint8) # This line only change the type, not values
# Create a "qImg" which allows you to create a QPixmap from a matrix
bytesPerLine = 3 * new_width
qImg = QImage(img_combined.data * 2, new_width, new_height,
bytesPerLine, QImage.Format_RGB888)
pixmap = QPixmap(qImg)
# pixmap = pixmap.scaled(640,400, Qt.KeepAspectRatio)
self.viewer.setPhoto(pixmap)
def transformImagesColored(self):
# we want to load RED (current section) and BLUE (previous section) channels overlayed
#fp_curr_red = get_fp(self.curr_section)
#fp_prev_blue = get_fp(self.prev_section)
curr_tif = os.path.join(self.fileLocationManager.oriented,
self.curr_section)
fp_curr_red = io.imread(curr_tif)
prev_tif = os.path.join(self.fileLocationManager.oriented,
self.prev_section)
fp_prev_blue = io.imread(prev_tif)
if self.transform_type == 'anchor':
# Load anchor-transformed images
img_curr_red = apply_transform(stack, self.curr_T,
self.curr_section)
img_prev_blue, Tb = get_transformed_image(self.prev_section,
transformation='anchor')
elif self.transform_type == 'pairwise':
# Load pairwise-transformed images
# The current red image is transformed to the previous blue image
img_curr_red = apply_transform(stack, self.curr_T,
self.curr_section)
# Blue image does not change
img_prev_blue = io.imread(fp_prev_blue)
height_r, width_r, _ = img_curr_red.shape
height_b, width_b, _ = img_prev_blue.shape
new_height = max(height_r, height_b)
new_width = max(width_r, width_b)
img_combined = np.ones((new_height, new_width, 3))
img_combined[0:height_r, 0:width_r,
0] += img_curr_red[:, :, 0] * self.curr_img_multiplier
img_combined[0:height_b, 0:width_b,
2] += img_prev_blue[:, :, 0] * self.prev_img_multiplier
img_combined = np.array(
img_combined,
dtype=np.uint8) # This line only change the type, not values
# Create a "qImg" which allows you to create a QPixmap from a matrix
bytesPerLine = 3 * new_width
qImg = QImage(img_combined.data * 2, new_width, new_height,
bytesPerLine, QImage.Format_RGB888)
pixmap = QPixmap(qImg)
# pixmap = pixmap.scaled(640,400, Qt.KeepAspectRatio)
self.viewer.setPhoto(pixmap)
def photoClicked(self, pos):
if self.viewer.dragMode() == QGraphicsView.NoDrag:
print('%d, %d' % (pos.x(), pos.y()))
def pixInfo(self):
self.viewer.toggleDragMode()
def keyPressEvent(self, event):
try:
key = event.key()
except AttributeError:
key = event
if key == 91: # [
self.getPrevValidSection(self.curr_section_index)
self.setCurrSection(self.prev_section_index)
elif key == 93: # ]
self.getNextValidSection(self.curr_section_index)
self.setCurrSection(self.next_section_index)
elif key == 81: # Q
self.pixInfo()
elif key == 77: # M
self.toggleMode()
else:
print(key)
def setCurrSection(self, section_index=-1):
"""
Sets the current section to the section passed in.
Will automatically update curr_section, prev_section, and next_section.
Updates the header fields and loads the current section image.
"""
if section_index == -1:
section_index = self.curr_section_index
# Update curr, prev, and next section
self.curr_section_index = section_index
self.curr_section = self.valid_sections[self.valid_section_keys[
self.curr_section_index]]['destination']
self.prev_section = self.getPrevValidSection(self.curr_section_index)
self.next_section = self.getNextValidSection(self.curr_section_index)
self.updateCurrHeaderFields()
self.updatePrevHeaderFields()
self.curr_img_multiplier = 1
self.prev_img_multiplier = 1
if self.mode == 'view':
self.loadImage()
self.toggle_align_buttons(enabled=False)
elif self.mode == 'align':
self.loadImagesColored()
self.toggle_align_buttons(enabled=True)
def toggleMode(self):
if self.mode == 'view':
self.mode = 'align'
elif self.mode == 'align':
self.mode = 'view'
self.setCurrSection()
def buttonPress(self, button):
# Brighten an image
if button in [self.b1, self.b2]:
if button == self.b1:
self.prev_img_multiplier += 1
if self.prev_img_multiplier > 5:
self.prev_img_multiplier = 1
if button == self.b2:
self.curr_img_multiplier += 1
if self.curr_img_multiplier > 5:
self.curr_img_multiplier = 1
# Translate the red image and update T matrix
if button in [self.b_right, self.b_left, self.b_up, self.b_down]:
if button == self.b_right:
self.curr_T[0, 2] += 3
if button == self.b_left:
self.curr_T[0, 2] -= 3
if button == self.b_up:
self.curr_T[1, 2] -= 3
if button == self.b_down:
self.curr_T[1, 2] += 3
# self.transformImagesColored()
# Rotate the red image and update T matrix
if button in [self.b_clockwise, self.b_cclockwise]:
if button == self.b_clockwise:
degrees = 0.3
if button == self.b_cclockwise:
degrees = -0.3
# Update matrix's rotation fields
self.curr_T[0, 0] = math.cos(
math.acos(self.curr_T[0, 0]) + degrees * (math.pi / 180))
self.curr_T[1, 1] = math.cos(
math.acos(self.curr_T[1, 1]) + degrees * (math.pi / 180))
self.curr_T[0, 1] = -math.sin(
math.asin(-self.curr_T[0, 1]) + degrees * (math.pi / 180))
self.curr_T[1, 0] = math.sin(
math.asin(self.curr_T[1, 0]) + degrees * (math.pi / 180))
if button == self.b_save_transform:
self.saveCurrTransform()
self.update_prep1_images()
if button == self.b_done:
sys.exit(app.exec_())
self.transformImagesColored()
def getNextValidSection(self, section_index):
self.next_section_index = section_index + 1
if self.next_section_index > len(self.valid_sections) - 1:
self.next_section_index = 0
self.next_section = self.valid_sections[self.valid_section_keys[
self.next_section_index]]['destination']
return self.next_section
def getPrevValidSection(self, section_index):
self.prev_section_index = int(section_index) - 1
if self.prev_section_index < 0:
self.prev_section_index = len(self.valid_sections) - 1
self.prev_section = self.valid_sections[self.valid_section_keys[
self.prev_section_index]]['destination']
return self.prev_section
def toggle_align_buttons(self, enabled):
self.b1.setEnabled(enabled)
self.b2.setEnabled(enabled)
self.b_right.setEnabled(enabled)
self.b_left.setEnabled(enabled)
self.b_up.setEnabled(enabled)
self.b_down.setEnabled(enabled)
self.b_clockwise.setEnabled(enabled)
self.b_cclockwise.setEnabled(enabled)
self.b_save_transform.setEnabled(enabled)
def updateCurrHeaderFields(self):
label = self.valid_sections[self.valid_section_keys[
self.curr_section_index]]['source']
self.e4.setText(label)
self.e5.setText(self.curr_section)
def updatePrevHeaderFields(self):
label = self.valid_sections[self.valid_section_keys[
self.prev_section_index]]['source']
self.e2.setText(label)
self.e3.setText(self.prev_section)
def update_prep1_images(self):
version = stain_to_metainfo[self.stain]['img_version_1']
create_input_spec_ini_all(name='input_spec.ini', \
stack=stack, prep_id='None', version=version, resol='thumbnail')
# Call "compose" to regenerate the csv file
command = [
'python', 'compose_v3.py', 'input_spec.ini', '--op',
'from_none_to_aligned'
]
completion_message = 'Finished creating transforms to anchor csv file.'
call_and_time(command, completion_message=completion_message)
# Apply transformations from csv and save as prep1 images
command = [
'python', 'warp_crop_v3.py', '--input_spec', 'input_spec.ini',
'--op_id', 'from_none_to_padded', '--njobs', '8', '--pad_color',
get_padding_color(stack)
]
completion_message = 'Finished transformation to padded (prep1).'
call_and_time(command, completion_message=completion_message)
def saveCurrTransform(self):
if self.transform_type == 'pairwise':
curr_section_fn = self.sections_to_filenames[self.curr_section]
prev_section_fn = self.sections_to_filenames[self.prev_section]
custom_transform_txt_name = '{}_to_{}.txt'.format(
curr_section_fn, prev_section_fn)
custom_transform_txt_file = os.path.join(
self.fileLocationManager.custom_transform,
custom_transform_txt_name)
custom_transform_img_name = '{}_{}.txt'.format(
curr_section_fn, prev_section_fn)
custom_transform_img_file = os.path.join(
self.fileLocationManager.aligned_to, custom_transform_img_name)
T = self.curr_T
# Saves the transformed image since we gave a specific output_fp
apply_transform(stack, self.curr_T, self.curr_section,
custom_transform_img_file)
with open(custom_transform_txt_file, 'w') as file:
file.write(str(T[0, 0]) + ' ' + str(T[0, 1]) + ' ' + str(T[0, 2]) + ' ' + \
str(T[1, 0]) + ' ' + str(T[1, 1]) + ' ' + str(T[1, 2]))
else:
pass
class init_GUI(QWidget):
def __init__(self, stack, parent=None):
super(init_GUI, self).__init__(parent)
self.font_h1 = QFont("Arial", 32)
self.font_p1 = QFont("Arial", 16)
self.queued_transformations = []
# create a dataManager object
self.sqlController = SqlController()
self.stack = stack
self.fileLocationManager = FileLocationManager(self.stack)
self.sqlController.get_animal_info(self.stack)
self.valid_sections = self.sqlController.get_valid_sections(stack)
self.valid_section_keys = sorted(list(self.valid_sections))
section_length = len(self.valid_section_keys)
self.curr_section_index = section_length // 2
self.prev_section_index = self.curr_section_index
self.next_section_index = self.curr_section_index
self.curr_section = self.valid_sections[self.valid_section_keys[
self.curr_section_index]]['destination']
self.prev_section = self.getPrevValidSection(self.curr_section_index)
self.next_section = self.getNextValidSection(self.curr_section_index)
self.initUI()
def initUI(self):
# Set Layout and Geometry of Window
self.grid_top = QGridLayout()
self.grid_body_upper = QGridLayout()
self.grid_body = QGridLayout()
self.grid_body_lower = QGridLayout()
self.grid_bottom = QGridLayout()
self.grid_blank = QGridLayout()
# self.setFixedSize(1600, 1000)
self.resize(1600, 1000)
### VIEWER ### (Grid Body)
self.viewer = ImageViewer(self)
self.viewer.photoClicked.connect(self.photoClicked)
### Grid TOP ###
# Static Text Field (Title)
self.e1 = QLineEdit()
self.e1.setValidator(QIntValidator())
self.e1.setAlignment(Qt.AlignCenter)
self.e1.setFont(self.font_h1)
self.e1.setReadOnly(True)
self.e1.setText("Orient Images")
self.e1.setFrame(False)
self.grid_top.addWidget(self.e1, 0, 0)
# Button Text Field
self.b_help = QPushButton("HELP")
self.b_help.setDefault(True)
self.b_help.setEnabled(True)
self.b_help.clicked.connect(
lambda: self.help_button_press(self.b_help))
self.b_help.setStyleSheet(
"color: rgb(0,0,0); background-color: rgb(250,250,250);")
self.grid_top.addWidget(self.b_help, 0, 1)
### Grid BODY UPPER ###
# Static Text Field
self.e4 = QLineEdit()
self.e4.setAlignment(Qt.AlignCenter)
self.e4.setFont(self.font_p1)
self.e4.setReadOnly(True)
self.e4.setText("Filename: ")
# self.e4.setStyleSheet("color: rgb(250,50,50); background-color: rgb(250,250,250);")
self.grid_body_upper.addWidget(self.e4, 0, 2)
# Static Text Field
self.e5 = QLineEdit()
self.e5.setAlignment(Qt.AlignCenter)
self.e5.setFont(self.font_p1)
self.e5.setReadOnly(True)
self.e5.setText("Section: ")
# self.e5.setStyleSheet("color: rgb(250,50,50); background-color: rgb(250,250,250);")
self.grid_body_upper.addWidget(self.e5, 0, 3)
### Grid BODY ###
# Custom VIEWER
self.grid_body.addWidget(self.viewer, 0, 0)
### Grid BODY LOWER ###
# Button Text Field
self.b1 = QPushButton("Flip image(s) across central vertical line")
self.b1.setDefault(True)
self.b1.setEnabled(True)
self.b1.clicked.connect(lambda: self.buttonPress(self.b1))
self.b1.setStyleSheet(
"color: rgb(0,0,0); background-color: rgb(250,250,200);")
self.grid_body_lower.addWidget(self.b1, 0, 0)
# Button Text Field
self.b2 = QPushButton("Flop image(s) across central horozontal line")
self.b2.setDefault(True)
self.b2.setEnabled(True)
self.b2.clicked.connect(lambda: self.buttonPress(self.b2))
self.b2.setStyleSheet(
"color: rgb(0,0,0); background-color: rgb(250,250,200);")
self.grid_body_lower.addWidget(self.b2, 1, 0)
# Button Text Field
self.b3 = QPushButton("Rotate Image(s)")
self.b3.setDefault(True)
self.b3.setEnabled(True)
self.b3.clicked.connect(lambda: self.buttonPress(self.b3))
self.b3.setStyleSheet(
"color: rgb(0,0,0); background-color: rgb(250,200,250);")
self.grid_body_lower.addWidget(self.b3, 0, 1, 1, 2)
# Checkbox
self.cb_1 = QCheckBox("Apply transformation to ALL images")
self.cb_1.setChecked(True)
self.cb_1.setEnabled(False)
self.grid_body_lower.addWidget(self.cb_1, 0, 3)
# Static Text Field
self.e6 = QLineEdit()
self.e6.setMaximumWidth(250)
self.e6.setAlignment(Qt.AlignRight)
self.e6.setReadOnly(True)
self.e6.setText("Degrees to rotate (clockwise!): ")
self.grid_body_lower.addWidget(self.e6, 1, 1)
# Dropbown Menu (ComboBox) for selecting Stack
self.cb = QComboBox()
self.cb.addItems(['90', '180', '270'])
# self.cb.addItems( ['Rotate by 90 degrees', 'Rotate by 180 degrees', 'Rotate by 270 degrees'] )
# self.cb.addItems( ['45', '90', '135', '180', '225', '270', '315'] )
self.grid_body_lower.addWidget(self.cb, 1, 2)
# Button Text Field
self.b_done = QPushButton("Done orienting")
self.b_done.setDefault(True)
self.b_done.setEnabled(True)
self.b_done.clicked.connect(lambda: self.buttonPress(self.b_done))
self.b_done.setStyleSheet(
"color: rgb(0,0,0); background-color: #dfbb19;")
self.grid_body_lower.addWidget(self.b_done, 1, 3)
# Grid stretching
# self.grid_body_upper.setColumnStretch(0, 2)
self.grid_body_upper.setColumnStretch(2, 2)
# self.grid_body_lower.setColumnStretch(3, 1)
### SUPERGRID ###
self.supergrid = QGridLayout()
self.supergrid.addLayout(self.grid_top, 0, 0)
self.supergrid.addLayout(self.grid_body_upper, 1, 0)
self.supergrid.addLayout(self.grid_body, 2, 0)
# self.supergrid.addLayout( self.grid_body_lower, 4, 0)
self.supergrid.addWidget(QHLine(), 6, 0, 1, 2)
# self.supergrid.addLayout( self.grid_bottom, 6, 0)
self.supergrid.addLayout(self.grid_body_lower, 7, 0)
self.supergrid.addWidget(QHLine(), 8, 0, 1, 2)
# Set layout and window title
self.setLayout(self.supergrid)
self.setWindowTitle("Q")
# Loads self.curr_section as the current image and sets all fields appropriatly
self.setCurrSection(self.curr_section_index)
def help_button_press(self, button):
info_text = "This GUI is used to align slices to each other. The shortcut commands are as follows: \n\n\
- `[`: Go back one section. \n\
- `]`: Go forward one section."
QMessageBox.information(self, "Empty Field", info_text)
def loadImage(self):
curr_fn = self.valid_sections[self.valid_section_keys[
self.curr_section_index]]['destination']
# Get filepath of "curr_section" and set it as viewer's photo
img_fp = os.path.join(self.fileLocationManager.thumbnail_prep, curr_fn)
self.viewer.setPhoto(QPixmap(img_fp))
def photoClicked(self, pos):
if self.viewer.dragMode() == QGraphicsView.NoDrag:
print('%d, %d' % (pos.x(), pos.y()))
def pixInfo(self):
self.viewer.toggleDragMode()
def keyPressEvent(self, event):
try:
key = event.key()
except AttributeError:
key = event
if key == 91: # [
self.getPrevValidSection(self.curr_section_index)
self.setCurrSection(self.prev_section_index)
elif key == 93: # ]
self.getNextValidSection(self.curr_section_index)
self.setCurrSection(self.next_section_index)
else:
print(key)
def setCurrSection(self, section_index=-1):
"""
Sets the current section to the section passed in.
Will automatically update curr_section, prev_section, and next_section.
Updates the header fields and loads the current section image.
"""
if section_index == -1:
section_index = self.curr_section_index
# Update curr, prev, and next section
self.curr_section_index = section_index
self.curr_section = self.valid_sections[self.valid_section_keys[
self.curr_section_index]]['destination']
self.prev_section = self.getPrevValidSection(self.curr_section_index)
self.next_section = self.getNextValidSection(self.curr_section_index)
# Update the section and filename at the top
self.updateCurrHeaderFields()
# Update the quality selection in the bottom left
self.loadImage()
def getNextValidSection(self, section_index):
self.next_section_index = section_index + 1
if self.next_section_index > len(self.valid_sections) - 1:
self.next_section_index = 0
self.next_section = self.valid_sections[self.valid_section_keys[
self.next_section_index]]['destination']
return self.next_section
def getPrevValidSection(self, section_index):
self.prev_section_index = int(section_index) - 1
if self.prev_section_index < 0:
self.prev_section_index = len(self.valid_sections) - 1
self.prev_section = self.valid_sections[self.valid_section_keys[
self.prev_section_index]]['destination']
return self.prev_section
def buttonPress(self, button):
# Brighten an image
if button in [self.b1, self.b2, self.b3]:
# "Flip image(s) across central vertical line"
if button == self.b1:
self.transform_thumbnails('flip')
# "Flop image(s) across central horozontal line"
elif button == self.b2:
self.transform_thumbnails('flop')
# "Rotate Image(s)"
elif button == self.b3:
self.transform_thumbnails('rotate',
degrees=str(self.cb.currentText()))
# Update the Viewer info and displayed image
self.setCurrSection(self.curr_section_index)
elif button == self.b_done:
QMessageBox.about(
self, "Popup Message",
"All selected operations will now be performed on the\
full sized raw images. This may take an hour or two, depending on how many operations are queued."
)
self.apply_queued_transformations()
self.finished()
def updateCurrHeaderFields(self):
label = self.valid_sections[self.valid_section_keys[
self.curr_section_index]]['source']
self.e4.setText(label)
self.e5.setText(str(self.curr_section))
def transform_thumbnails(self, transform_type, degrees=0):
"""
Transform_type must be "rotate", "flip", or "flop".
These transformations get applied to all the active sections. The actual
conversions take place on the thumbnails and the raw files.
The transformed raw files get placed in the preps/oriented dir.
"""
if transform_type == 'rotate':
base_cmd = ['convert', '-' + transform_type, str(degrees)]
else:
base_cmd = ['convert', '-' + transform_type]
self.queued_transformations.append(base_cmd)
# Apply transforms to just the thumbnails
THUMBNAIL = self.fileLocationManager.prep_thumbnail
for k, v in self.valid_sections.items():
thumbnail = os.path.join(THUMBNAIL, v['destination'])
subprocess.call(base_cmd + [thumbnail, thumbnail])
def finished(self):
self.sqlController.set_step_completed_in_progress_ini(
self.stack, '1-5_setup_orientations')
# close_main_gui( ex )
sys.exit(app.exec_())
def apply_queued_transformations(self):
print('queued_transformations', self.queued_transformations)
if self.queued_transformations == []:
print('No transformations to do. Exit stage left ...')
else:
# Apply to "raw" images
RAW = self.fileLocationManager.tif
ORIENTED = self.fileLocationManager.oriented
for base_cmd in tqdm(self.queued_transformations):
for k, v in self.valid_sections.items():
raw = os.path.join(RAW, v['source'])
oriented = os.path.join(ORIENTED, v['destination'])
subprocess.call(base_cmd + [raw, oriented])
#print(base_cmd + [raw, oriented])
# Clear the queued transformations
self.queued_transformations = []
class GUISortedFilenames(QWidget):
def __init__(self, stack, parent=None):
super(GUISortedFilenames, self).__init__(parent)
self.stack = stack
self.fileLocationManager = FileLocationManager(self.stack)
self.sqlController = SqlController()
self.sqlController.get_animal_info(self.stack)
self.valid_sections = self.sqlController.get_valid_sections(stack)
self.valid_section_keys = sorted(list(self.valid_sections))
self.curr_section_index = 0
self.curr_section = None
self.init_ui()
self.b_rotate_left.clicked.connect(
lambda: self.click_button(self.b_rotate_left))
self.b_rotate_right.clicked.connect(
lambda: self.click_button(self.b_rotate_right))
self.b_flip_vertical.clicked.connect(
lambda: self.click_button(self.b_flip_vertical))
self.b_flip_horozontal.clicked.connect(
lambda: self.click_button(self.b_flip_horozontal))
self.b_move_left.clicked.connect(
lambda: self.click_button(self.b_move_left))
self.b_move_right.clicked.connect(
lambda: self.click_button(self.b_move_right))
self.b_quality.currentIndexChanged.connect(
lambda: self.click_button(self.b_quality))
self.b_remove.clicked.connect(lambda: self.click_button(self.b_remove))
self.b_help.clicked.connect(lambda: self.click_button(self.b_help))
self.b_done.clicked.connect(lambda: self.click_button(self.b_done))
self.set_curr_section(self.curr_section_index)
def init_ui(self):
self.font_h1 = QFont("Arial", 32)
self.font_p1 = QFont("Arial", 16)
self.grid_top = QGridLayout()
self.grid_body_upper = QGridLayout()
self.grid_body = QGridLayout()
self.grid_body_lower = QGridLayout()
self.resize(1600, 1100)
# Grid Top
self.e_title = QLineEdit()
self.e_title.setAlignment(Qt.AlignCenter)
self.e_title.setFont(self.font_h1)
self.e_title.setReadOnly(True)
self.e_title.setText("Setup Sorted Filenames")
self.e_title.setFrame(False)
self.grid_top.addWidget(self.e_title, 0, 0)
self.b_help = QPushButton("HELP")
self.b_help.setDefault(True)
self.b_help.setEnabled(True)
self.grid_top.addWidget(self.b_help, 0, 1)
# Grid BODY UPPER
self.e_filename = QLineEdit()
self.e_filename.setAlignment(Qt.AlignCenter)
self.e_filename.setFont(self.font_p1)
self.e_filename.setReadOnly(True)
self.e_filename.setText("Filename: ")
self.grid_body_upper.addWidget(self.e_filename, 0, 2)
self.e_section = QLineEdit()
self.e_section.setAlignment(Qt.AlignCenter)
self.e_section.setFont(self.font_p1)
self.e_section.setReadOnly(True)
self.e_section.setText("Section: ")
self.grid_body_upper.addWidget(self.e_section, 0, 3)
# Grid BODY
self.viewer = ImageViewer(self)
self.grid_body.addWidget(self.viewer, 0, 0)
# Grid BODY LOWER
self.b_flip_vertical = QPushButton("Flip vertically")
self.grid_body_lower.addWidget(self.b_flip_vertical, 0, 0)
self.b_flip_horozontal = QPushButton("Flop horizontally")
self.grid_body_lower.addWidget(self.b_flip_horozontal, 0, 1)
self.b_rotate_left = QPushButton("Rotate Left")
self.grid_body_lower.addWidget(self.b_rotate_left, 0, 2)
self.b_rotate_right = QPushButton("Rotate Right")
self.grid_body_lower.addWidget(self.b_rotate_right, 0, 3)
self.b_move_left = QPushButton("<-- Move Section Left <--")
#self.grid_body_lower.addWidget(self.b_move_left, 1, 0)
self.b_move_right = QPushButton("--> Move Section Right -->")
#self.grid_body_lower.addWidget(self.b_move_right, 1, 1)
self.b_quality = QComboBox()
self.b_quality.addItems([
'Section quality: unusable', 'Section quality: blurry',
'Section quality: good'
])
#self.grid_body_lower.addWidget(self.b_quality, 1, 2)
self.b_remove = QPushButton("Remove section")
#self.grid_body_lower.addWidget(self.b_remove, 1, 3)
self.progress = QProgressBar(self)
self.grid_body_lower.addWidget(self.progress, 2, 0, 1, 3)
self.progress.hide()
self.b_done = QPushButton("Finished")
self.grid_body_lower.addWidget(self.b_done, 2, 3)
# Super grid
self.supergrid = QGridLayout()
self.supergrid.addLayout(self.grid_top, 0, 0)
self.supergrid.addLayout(self.grid_body_upper, 1, 0)
self.supergrid.addLayout(self.grid_body, 2, 0)
self.supergrid.addLayout(self.grid_body_lower, 3, 0)
# Set layout and window title
self.setLayout(self.supergrid)
self.setWindowTitle("Q")
def set_curr_section(self, section_index=-1):
"""
Sets the current section to the section passed in.
Will automatically update curr_section, prev_section, and next_section.
Updates the header fields and loads the current section image.
"""
if section_index == -1:
section_index = self.curr_section_index
# Update curr, prev, and next section
self.curr_section_index = section_index
self.curr_section = self.valid_sections[self.valid_section_keys[
self.curr_section_index]]
# Update the section and filename at the top
self.e_filename.setText(self.curr_section['destination'])
self.e_section.setText(str(self.curr_section['section_number']))
# Get filepath of "curr_section" and set it as viewer's photo
img_fp = os.path.join(self.fileLocationManager.thumbnail_prep,
self.curr_section['destination'])
self.viewer.set_photo(img_fp)
# Update the quality selection in the bottom left
index = self.b_quality.findText(self.curr_section['quality'],
Qt.MatchFixedString)
if index >= 0:
self.b_quality.setCurrentIndex(index)
def get_valid_section_index(self, section_index):
if section_index >= len(self.valid_sections):
return 0
elif section_index < 0:
return len(self.valid_sections) - 1
else:
return section_index
def click_button(self, button):
if button == self.b_quality:
curr_section = self.valid_sections[self.valid_section_keys[
self.curr_section_index]]
curr_section['quality'] = self.b_quality.currentText()
self.sqlController.save_valid_sections(self.valid_sections)
elif button in [self.b_move_left, self.b_move_right, self.b_remove]:
if button == self.b_move_left:
self.sqlController.move_section(
self.stack, self.curr_section['section_number'], -1)
elif button == self.b_move_right:
self.sqlController.move_section(
self.stack, self.curr_section['section_number'], 1)
elif button == self.b_remove:
result = self.message_box(
'Are you sure you want to totally remove this section from this brain?\n\n'
+
'Warning: The image will be marked as irrelevant to the current brain!',
True)
# The answer is Yes
if result == 2:
# Remove the current section from "self.valid_sections
self.sqlController.inactivate_section(
self.stack, self.curr_section['section_number'])
self.valid_sections = self.sqlController.get_valid_sections(
self.stack)
self.valid_section_keys = sorted(list(self.valid_sections))
if self.curr_section_index == 0:
self.curr_section_index = len(
self.valid_section_keys) - 1
else:
self.curr_section_index = self.curr_section_index - 1
else:
pass
# Update the Viewer info and displayed image
self.valid_sections = self.sqlController.get_valid_sections(
self.stack)
self.valid_section_keys = sorted(list(self.valid_sections))
self.set_curr_section(self.curr_section_index)
elif button in [
self.b_flip_vertical, self.b_flip_horozontal,
self.b_rotate_right, self.b_rotate_left
]:
"""
Transform_type must be "rotate", "flip", or "flop".
These transformations get applied to all the active sections. The actual
conversions take place on the thumbnails and the raw files.
The transformed raw files get placed in the preps/oriented dir.
"""
index = [
self.b_flip_vertical, self.b_flip_horozontal,
self.b_rotate_right, self.b_rotate_left
].index(button)
op = ['flip', 'flop', 'right', 'left'][index]
size = len(self.valid_sections.values()) - 1
self.progress_bar(True, size)
for index, section in enumerate(self.valid_sections.values()):
thumbnail_path = os.path.join(
self.fileLocationManager.thumbnail_prep,
section['destination'])
if os.path.isfile(thumbnail_path):
self.transform_image(thumbnail_path, op)
self.progress.setValue(index)
self.progress_bar(False, size)
self.set_curr_section(section_index=-1)
elif button == self.b_help:
self.message_box(
'This GUI is used to align slices to each other. The shortcut commands are as follows: \n\n'
+ '- `[`: Go back one section. \n' +
'- `]`: Go forward one section. \n\n' +
'Use the buttons on the bottom panel to move', False)
elif button == self.b_done:
self.message_box(
"All selected operations will now be performed on the full sized raw images"
+
"This may take an hour or two, depending on how many operations are queued.",
False)
# Apply the transformations to the real images
self.apply_queued_transformations()
self.sqlController.set_step_completed_in_progress_ini(
self.stack, '1-4_setup_sorted_filenames')
self.sqlController.set_step_completed_in_progress_ini(
self.stack, '1-5_setup_orientations')
sys.exit(app.exec_())
def transform_image(self, filename, op):
def get_last_2d(data):
if data.ndim <= 2:
return data
m, n = data.shape[-2:]
return data.flat[:m * n].reshape(m, n)
img = io.imread(filename)
img = get_last_2d(img)
# Rotating a multidimensional image has to be done backwards.
# To rotate right, do np.rot(img, 3), to rotate left, do np.rot(img, 1)
if op == 'left':
img = np.rot90(img, 3)
elif op == 'right':
img = np.rot90(img, 1)
elif op == 'flip':
img = np.flipud(img)
elif op == 'flop':
img = np.fliplr(img)
os.unlink(filename)
io.imsave(filename, img)
self.save_to_web_thumbnail(filename, img)
def save_to_web_thumbnail(self, filename, img):
filename = os.path.basename(filename)
png_file = os.path.splitext(filename)[0] + '.png'
png_path = os.path.join(self.fileLocationManager.thumbnail_web,
png_file)
if os.path.exists(png_path):
os.unlink(png_path)
io.imsave(png_path, img)
def apply_queued_transformations(self):
pass
def progress_bar(self, show, max_value):
if show:
self.progress.setMaximum(max_value)
self.progress.show()
else:
self.progress.hide()
self.b_quality.setDisabled(show)
self.b_move_left.setDisabled(show)
self.b_move_right.setDisabled(show)
self.b_flip_vertical.setDisabled(show)
self.b_flip_horozontal.setDisabled(show)
self.b_rotate_right.setDisabled(show)
self.b_rotate_left.setDisabled(show)
self.b_remove.setDisabled(show)
self.b_done.setDisabled(show)
def message_box(self, text, is_warn):
msg_box = QMessageBox()
msg_box.setText(text)
if is_warn:
msg_box.addButton(QPushButton('Cancel'), QMessageBox.RejectRole)
msg_box.addButton(QPushButton('No'), QMessageBox.NoRole)
msg_box.addButton(QPushButton('Yes'), QMessageBox.YesRole)
return msg_box.exec_()
def keyPressEvent(self, event):
try:
key = event.key()
except AttributeError:
key = event
if key == 91: # [
index = self.get_valid_section_index(self.curr_section_index - 1)
self.set_curr_section(index)
elif key == 93: # ]
index = self.get_valid_section_index(self.curr_section_index + 1)
self.set_curr_section(index)
else:
print(key)
def closeEvent(self, event):
sys.exit(app.exec_())
class init_GUI(QWidget):
def __init__(self, stack, parent = None):
super(init_GUI, self).__init__(parent)
self.font1 = QFont("Arial",16)
self.font2 = QFont("Arial",12)
# Stack specific info, determined from dropdown menu selection
self.stack = stack
self.curr_step = ""
self.sqlController = SqlController()
self.sqlController.get_animal_info(self.stack)
self.initUI()
def initUI(self):
# Set Layout and Geometry of Window
self.grid_top = QGridLayout()
self.grid_buttons = QGridLayout()
self.grid_bottom = QGridLayout()
#self.setFixedSize(1000, 450)
self.resize(1000, 450)
### Grid Top (1 row) ###
# Static Text Field
self.e1 = QLineEdit()
self.e1.setValidator( QIntValidator() )
self.e1.setAlignment(Qt.AlignCenter)
self.e1.setFont( self.font1 )
self.e1.setReadOnly( True )
self.e1.setText( "Align Step: Main Page" )
self.e1.setFrame( False )
self.grid_top.addWidget( self.e1, 0, 0)
### Grid Buttons ###
# Button
self.b_1 = QPushButton("1) Correct automatic alignments")
format_grid_button_initial( self.b_1 )
self.b_1.clicked.connect( lambda:self.button_grid_push(self.b_1) )
self.grid_buttons.addWidget( self.b_1, 0, 0)
### Grid Bottom ###
# Button Text Field
self.b_exit = QPushButton("Exit")
self.b_exit.setDefault(True)
self.b_exit.clicked.connect(lambda:self.button_push(self.b_exit))
self.grid_bottom.addWidget(self.b_exit, 0, 4)
#self.grid_buttons.setColumnStretch(1, 3)
#self.grid_buttons.setRowStretch(1, 2)
### SUPERGRID ###
self.supergrid = QGridLayout()
self.supergrid.addLayout( self.grid_top, 0, 0)
self.supergrid.addLayout( self.grid_buttons, 1, 0)
self.supergrid.addLayout( self.grid_bottom, 2, 0)
# Set layout and window title
self.setLayout( self.supergrid )
self.setWindowTitle("Align to Active Brainstem Atlas - Aligning Slices Page")
# Update interactive windows
self.updateFields()
# Center the GUI
self.center()
def updateFields(self):
# Set stack-specific variables
try:
self.stain = self.sqlController.histology.counterstain
# Check the brains_info/STACK_progress.ini file for which step we're on
self.curr_step = self.sqlController.get_current_step_from_progress_ini(self.stack)
# Disable all grid buttons except for the one corresponding to our current step
self.format_grid_buttons()
# If there are no stacks/brains that have been started
except KeyError:
for grid_button in [self.b_1]:
format_grid_button_cantStart( grid_button )
def format_grid_buttons(self):
"""
Locates where you are in the pipeline by reading the brains_info/STACK_progress.ini
Buttons corresponding to previous steps are marked as "completed", buttons corresponding
to future steps are marked as "unpressable" and are grayed out.
"""
curr_step = self.curr_step
if '2_align' in curr_step:
active_button = self.b_1
else:
active_button = None
print(curr_step)
passed_curr_step = False
for grid_button in [self.b_1]:
if not passed_curr_step and grid_button != active_button:
format_grid_button_completed( grid_button )
elif grid_button == active_button:
passed_curr_step = True
format_grid_button_initial(active_button)
elif passed_curr_step and grid_button != active_button:
format_grid_button_cantStart( grid_button )
def button_grid_push(self, button):
"""
If any of the "grid" buttons are pressed, this is the callback function.
In this case, "grid" buttons have a one-to_one correspondance to the steps in the pipeline.
The completion of each step means you move onto the next one.
"""
# Alignment Correction GUI
if button == self.b_1:
subprocess.call(['python','a_GUI_correct_alignments.py', self.stack])
self.sqlController.set_step_completed_in_progress_ini(self.stack, '2_align')
self.updateFields()
def button_push(self, button):
"""
Secondary button callback function
"""
if button == self.b_exit:
sys.exit( app.exec_() )
def center(self):
"""
This function simply aligns the GUI to the center of your monitor.
"""
frameGm = self.frameGeometry()
screen = QApplication.desktop().screenNumber( QApplication.desktop().cursor().pos())
centerPoint = QApplication.desktop().screenGeometry(screen).center()
frameGm.moveCenter(centerPoint)
self.move(frameGm.topLeft())
def closeEvent(self, event):
sys.exit( app.exec_() )
class init_GUI(QWidget):
def __init__(self, parent=None):
super(init_GUI, self).__init__(parent)
self.font1 = QFont("Arial", 16)
self.font2 = QFont("Arial", 12)
self.stack = stack
self.fileLocationManager = FileLocationManager(self.stack)
self.sqlController = SqlController()
self.sqlController.get_animal_info(self.stack)
self.stain = self.sqlController.histology.counterstain
self.curr_step = self.sqlController.get_current_step_from_progress_ini(
self.stack)
self.initUI()
def initUI(self):
# Set Layout and Geometry of Window
self.grid_top = QGridLayout()
self.grid_buttons = QGridLayout()
self.grid_bottom = QGridLayout()
#self.setFixedSize(1000, 450)
self.resize(1000, 450)
### Grid Top (1 row) ###
# Static Text Field
self.e1 = QLineEdit()
self.e1.setValidator(QIntValidator())
self.e1.setAlignment(Qt.AlignCenter)
self.e1.setFont(self.font1)
self.e1.setReadOnly(True)
self.e1.setText("Global Atlas Fit Step: Main Page")
self.e1.setFrame(False)
self.grid_top.addWidget(self.e1, 0, 0)
### Grid Buttons ###
# Button
self.b_1 = QPushButton("1) Select centers of 12N and 3N")
format_grid_button_initial(self.b_1)
self.b_1.clicked.connect(lambda: self.button_grid_push(self.b_1))
self.grid_buttons.addWidget(self.b_1, 0, 0)
### Grid Bottom ###
# Button Text Field
self.b_exit = QPushButton("Exit")
self.b_exit.setDefault(True)
self.b_exit.clicked.connect(lambda: self.button_push(self.b_exit))
self.grid_bottom.addWidget(self.b_exit, 0, 4)
#self.grid_buttons.setColumnStretch(1, 3)
#self.grid_buttons.setRowStretch(1, 2)
### SUPERGRID ###
self.supergrid = QGridLayout()
self.supergrid.addLayout(self.grid_top, 0, 0)
self.supergrid.addLayout(self.grid_buttons, 1, 0)
self.supergrid.addLayout(self.grid_bottom, 2, 0)
# Set layout and window title
self.setLayout(self.supergrid)
self.setWindowTitle("Global Atlas fit")
# Update interactive windows
self.updateFields()
# Center the GUI
self.center()
def updateFields(self):
self.stain = self.sqlController.histology.counterstain
try:
self.curr_step = self.sqlController.get_current_step_from_progress_ini(
self.stack)
# Disable all grid buttons except for the one corresponding to our current step
self.format_grid_buttons()
# Disable all grid buttons except for the one corresponding to our current step
self.format_grid_buttons()
# If there are no stacks/brains that have been started
except KeyError:
for grid_button in [self.b_1]:
format_grid_button_cantStart(grid_button)
def format_grid_buttons(self):
"""
Locates where you are in the pipeline by reading the brains_info/STACK_progress.ini
Buttons corresponding to previous steps are marked as "completed", buttons corresponding
to future steps are marked as "unpressable" and are grayed out.
"""
curr_step = self.curr_step
if '5_fit_atlas_global' in curr_step:
active_button = self.b_1
else:
active_button = None
print(curr_step)
passed_curr_step = False
for grid_button in [self.b_1]:
if not passed_curr_step and grid_button != active_button:
format_grid_button_completed(grid_button)
elif grid_button == active_button:
passed_curr_step = True
format_grid_button_initial(active_button)
elif passed_curr_step and grid_button != active_button:
format_grid_button_cantStart(grid_button)
def button_grid_push(self, button):
"""
If any of the "grid" buttons are pressed, this is the callback function.
In this case, "grid" buttons have a one-to_one correspondance to the steps in the pipeline.
The completion of each step means you move onto the next one.
"""
# Alignment Correction GUI
if button == self.b_1:
subprocess.call(
['python', 'a_GUI_atlas_global_select_centers.py', self.stack])
"""
TODO, fix this get_pipelinestatus
progress = get_pipeline_status( self.stack )
if not progress=='a_script_preprocess_7':
fp1 = os.path.join(os.environ['ROOT_DIR'], 'CSHL_simple_global_registration',
self.stack+'_T_atlas_wrt_canonicalAtlasSpace_subject_wrt_wholebrain_atlasResol.txt')
#fp2 = os.path.join(os.environ['ROOT_DIR'], 'CSHL_simple_global_registration',
# self.stack+'_T_atlas_wrt_canonicalAtlasSpace_subject_wrt_wholebrain_atlasResol.bp')
#fp2_v2 = os.path.join(os.environ['ROOT_DIR'], 'CSHL_simple_global_registration',
# self.stack+'_T_atlas_wrt_canonicalAtlasSpace_subject_wrt_wholebrain_atlasResol.npy')
if os.path.exists( fp1 ):# and ( os.path.exists( fp2 ) or os.path.exists( fp2_v2 ) ):
set_step_completed_in_progress_ini( self.stack, '5_fit_atlas_global')
"""
self.updateFields()
def button_push(self, button):
"""
Secondary button callback function
"""
if button == self.b_exit:
sys.exit(app.exec_())
def center(self):
"""
This function simply aligns the GUI to the center of your monitor.
"""
frameGm = self.frameGeometry()
screen = QApplication.desktop().screenNumber(
QApplication.desktop().cursor().pos())
centerPoint = QApplication.desktop().screenGeometry(screen).center()
frameGm.moveCenter(centerPoint)
self.move(frameGm.topLeft())
def closeEvent(self, event):
sys.exit(app.exec_())
