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scAnt.py
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import datetime
import time
import sys
import traceback
import os
import cgitb
from pathlib import Path
from PyQt5 import QtWidgets, QtGui, QtCore
from GUI.scAnt_GUI_mw import Ui_MainWindow # importing main window of the GUI
import scripts.project_manager as ymlRW
from scripts.Scanner_Controller import ScannerController
from scripts.processStack import getThreads, stack_images, mask_images
from scripts.write_meta_data import write_exif_to_img, get_default_values
"""
Locations of required executables and how to use them:
"""
# qt designer located at:
# C:\Users\PlumStation\Anaconda3\envs\tf-gpu\Lib\site-packages\pyqt5_tools\Qt\bin\designer.exe
# pyuic5 to convert UI to executable python code is located at:
# C:\Users\PlumStation\Anaconda3\envs\tf-gpu\Scripts\pyuic5.exe
# to convert the UI into the required .py file run:
# -x = generates extra code to make ui.py file executable -o = output
# pyuic5.exe -x "I:\3D_Scanner\scAnt\GUI\test.ui" -o "I:\3D_Scanner\scAnt\GUI\test.py"
# or alternatively on Ubuntu
# pyuic5 scAnt_GUI_mw.ui -o scAnt_GUI_mw.py
class WorkerSignals(QtCore.QObject):
'''
Defines the signals available from a running worker thread.
Supported signals are:
finished
No data
error
`tuple` (exctype, value, traceback.format_exc() )
result
`object` data returned from processing, anything
progress
`int` indicating % progress
'''
finished = QtCore.pyqtSignal()
error = QtCore.pyqtSignal(tuple)
result = QtCore.pyqtSignal(object)
progress = QtCore.pyqtSignal(int)
class Worker(QtCore.QRunnable):
'''
Worker thread
Inherits from QRunnable to handler worker thread setup, signals and wrap-up.
:param callback: The function callback to run on this worker thread. Supplied args and
kwargs will be passed through to the runner.
:type callback: function
:param args: Arguments to pass to the callback function
:param kwargs: Keywords to pass to the callback function
'''
def __init__(self, fn, *args, **kwargs):
super(Worker, self).__init__()
# Store constructor arguments (re-used for processing)
self.fn = fn
self.args = args
self.kwargs = kwargs
self.signals = WorkerSignals()
# Add the callback to our kwargs
self.kwargs['progress_callback'] = self.signals.progress
@QtCore.pyqtSlot()
def run(self):
'''
Initialise the runner function with passed args, kwargs.
'''
# Retrieve args/kwargs here; and fire processing using them
try:
result = self.fn(*self.args, **self.kwargs)
except:
traceback.print_exc()
exctype, value = sys.exc_info()[:2]
self.signals.error.emit((exctype, value, traceback.format_exc()))
else:
self.signals.result.emit(result) # Return the result of the processing
finally:
self.signals.finished.emit() # Done
class scAnt_mainWindow(QtWidgets.QMainWindow):
def __init__(self):
super(scAnt_mainWindow, self).__init__()
self.setWindowIcon(QtGui.QIcon(str(Path.cwd().joinpath("images", "scAnt_icon.png"))))
self.liveView = False
self.exit_program = False
self.ui = Ui_MainWindow()
self.ui.setupUi(self)
self.set_project_title()
self.ui.pushButton_startLiveView.pressed.connect(self.begin_live_view)
self.ui.pushButton_captureImage.pressed.connect(self.capture_image)
self.ui.lineEdit_projectName.textChanged.connect(self.set_project_title)
# start thread pool
self.threadpool = QtCore.QThreadPool()
# search for cameras connected to the computer and supported by installed drivers
self.camera_type = None
self.camera_model = None
self.file_format = ".tif"
self.DSLR_read_out = False
# Find FLIR cameras, if attached
try:
from GUI.Live_view_FLIR import customFLIR
self.FLIR = customFLIR()
# camera needs to be initialised before use (self.cam.initialise_camera)
# all detected FLIR cameras are listed in self.cam.device_names
# by default, use the first camera found in the list
self.cam = self.FLIR
self.cam.initialise_camera(select_cam=0)
# now retrieve the name of all found FLIR cameras and add them to the camera selection
for cam in self.cam.device_names:
self.ui.comboBox_selectCamera.addItem(str(cam[0] + " ID: " + cam[1]))
self.camera_type = "FLIR"
# cam.device_names contains both model and serial number
self.camera_model = self.cam.device_names[0][0]
self.FLIR_found = True
except IndexError:
message = "No FLIR camera found!"
self.log_info(message)
print(message)
self.FLIR_found = False
self.disable_FLIR_inputs()
try:
# TODO add support for the selection of multiple connected DSLR cameras
from GUI.Live_view_DSLR import customDSLR
self.DSLR_initialised = False
self.DSLR = customDSLR()
self.log_info("Found " + str(self.DSLR.camera_model))
self.ui.comboBox_selectCamera.addItem(str(self.DSLR.camera_model))
self.DSLR_found = True
if not self.FLIR_found:
self.ui.stacked_camera_settings.setCurrentIndex(1)
self.cam = self.DSLR
self.camera_type = "DSLR"
self.camera_model = self.DSLR.camera_model
# initialise DSLR by launching an instance of DigiCamControl
worker = Worker(self.launch_DCC_threaded)
worker.signals.finished.connect(self.finished_DCC_launch)
self.threadpool.start(worker)
except:
self.log_info("No DSLR camera found!")
self.DSLR_found = False
# connect camera selection combo box to respective function
self.ui.comboBox_selectCamera.currentTextChanged.connect(self.select_camera)
try:
self.scanner = ScannerController()
self.scanner_initialised = True
except IndexError:
self.scanner_initialised = False
self.disable_stepper_inputs()
warning = "No Stepper Controller found!"
self.log_info(warning)
print(warning)
# FLIR settings
self.ui.checkBox_exposureAuto.stateChanged.connect(self.check_exposure)
self.ui.doubleSpinBox_exposureTime.valueChanged.connect(self.set_exposure_manual)
self.ui.checkBox_gainAuto.stateChanged.connect(self.check_gain)
self.ui.doubleSpinBox_gainLevel.valueChanged.connect(self.set_gain_manual)
self.ui.doubleSpinBox_gamma.valueChanged.connect(self.set_gamma)
self.ui.doubleSpinBox_balanceRatioRed.valueChanged.connect(self.set_balance_ratio)
self.ui.doubleSpinBox_balanceRatioBlue.valueChanged.connect(self.set_balance_ratio)
# TODO Add support for Black level selection
# self.ui.doubleSpinBox_blackLevel.valueChanged.connect(self.set_black_level)
# DSLR settings
self.ui.comboBox_shutterSpeed.currentTextChanged.connect(self.set_shutterspeed)
self.ui.comboBox_aperture.currentTextChanged.connect(self.set_aperture)
self.ui.comboBox_iso.currentTextChanged.connect(self.set_iso)
self.ui.comboBox_whiteBalance.currentTextChanged.connect(self.set_whitebalance)
self.ui.comboBox_compression.currentTextChanged.connect(self.set_compression)
# Stepper settings
self.ui.pushButton_xHome.pressed.connect(self.homeX)
self.ui.pushButton_yReset.pressed.connect(self.resetY)
self.ui.pushButton_zHome.pressed.connect(self.homeZ)
self.ui.pushButton_stepperDeEnergise.pressed.connect(self.deEnergise)
self.ui.pushButton_Energise.pressed.connect(self.energise)
self.ui.horizontalSlider_xAxis.sliderReleased.connect(self.moveStepperX)
self.ui.horizontalSlider_xAxis.valueChanged.connect(self.updateDisplayX)
self.ui.horizontalSlider_yAxis.sliderReleased.connect(self.moveStepperY)
self.ui.horizontalSlider_yAxis.valueChanged.connect(self.updateDisplayY)
self.ui.horizontalSlider_zAxis.sliderReleased.connect(self.moveStepperZ)
self.ui.horizontalSlider_zAxis.valueChanged.connect(self.updateDisplayZ)
if self.scanner_initialised:
# disable stepper control before they have been homed (except for y axis)
self.deEnergise()
self.homed_X = False
self.homed_Z = False
self.ui.horizontalSlider_xAxis.setEnabled(False)
self.ui.horizontalSlider_zAxis.setEnabled(False)
self.resetY()
# get default scanner Range
self.ui.doubleSpinBox_xMin.setValue(self.scanner.scan_pos[0][0])
self.ui.doubleSpinBox_xMax.setValue(self.scanner.scan_pos[0][-1] + self.scanner.scan_stepSize[0])
self.ui.doubleSpinBox_yMin.setValue(self.scanner.scan_pos[1][0])
self.ui.doubleSpinBox_yMax.setValue(self.scanner.scan_pos[1][-1] + self.scanner.scan_stepSize[1])
self.ui.doubleSpinBox_zMin.setValue(self.scanner.scan_pos[2][0])
self.ui.doubleSpinBox_zMax.setValue(self.scanner.scan_pos[2][-1] + self.scanner.scan_stepSize[2])
# adjust scanner range on input
self.ui.doubleSpinBox_xMin.valueChanged.connect(self.setScannerRange)
self.ui.doubleSpinBox_xStep.valueChanged.connect(self.setScannerRange)
self.ui.doubleSpinBox_xMax.valueChanged.connect(self.setScannerRange)
self.ui.doubleSpinBox_yMin.valueChanged.connect(self.setScannerRange)
self.ui.doubleSpinBox_yStep.valueChanged.connect(self.setScannerRange)
self.ui.doubleSpinBox_yMax.valueChanged.connect(self.setScannerRange)
self.ui.doubleSpinBox_zMin.valueChanged.connect(self.setScannerRange)
self.ui.doubleSpinBox_zStep.valueChanged.connect(self.setScannerRange)
self.ui.doubleSpinBox_zMax.valueChanged.connect(self.setScannerRange)
self.images_to_take = len(self.scanner.scan_pos[0]) * len(self.scanner.scan_pos[1]) * len(
self.scanner.scan_pos[2])
self.images_taken = 0
self.progress = 0
self.ui.pushButton_startScan.pressed.connect(self.runScanAndReport)
self.xMoving = False
self.yMoving = False
self.zMoving = False
self.posX = 0
self.posY = 0
self.posZ = 0
self.abortScan = False
self.scanInProgress = False
self.showExposure = False
# Scanner output setup
self.output_location = str(Path.cwd())
self.update_output_location()
self.ui.pushButton_browseOutput.pressed.connect(self.set_output_location)
self.output_location_folder = Path(self.output_location).joinpath(self.ui.lineEdit_projectName.text())
# processing
self.stackImages = False
self.stackMethod = "Default"
self.stackFocusThreshold = 10.0
self.stackDisplayFocus = False
self.stackSharpen = False
self.ui.checkBox_stackImages.stateChanged.connect(self.enableStacking)
self.maskImages = False
self.maskThreshMin = 215
self.maskThreshMax = 240
self.maskArtifactSizeBlack = 1000
self.maskArtifactSizeWhite = 2000
self.ui.checkBox_maskImages.stateChanged.connect(self.enableMasking)
# once the scan has been started check if new sets of images are available for stacking
self.timerStack = QtCore.QTimer(self)
self.timerStack.timeout.connect(self.checkActiveStackThreads)
self.exif = get_default_values()
self.createCutout = True
# use config file
self.loadedConfig = False
self.ui.pushButton_browsePresets.pressed.connect(self.loadConfig)
self.ui.pushButton_saveConfig.pressed.connect(self.writeConfig)
# stack and mask images
self.maxStackThreads = int(getThreads() / 6)
self.activeThreads = 0
self.stackList = []
"""
Stepper Control
"""
def setScannerRange(self):
self.scanner.setScanRange(stepper=0, min=self.ui.doubleSpinBox_xMin.value(),
max=self.ui.doubleSpinBox_xMax.value() + self.ui.doubleSpinBox_xStep.value(),
step=self.ui.doubleSpinBox_xStep.value())
self.scanner.setScanRange(stepper=1, min=self.ui.doubleSpinBox_yMin.value(),
max=self.ui.doubleSpinBox_yMax.value() + self.ui.doubleSpinBox_yStep.value(),
step=self.ui.doubleSpinBox_yStep.value())
self.scanner.setScanRange(stepper=2, min=self.ui.doubleSpinBox_zMin.value(),
max=self.ui.doubleSpinBox_zMax.value() + self.ui.doubleSpinBox_zStep.value(),
step=self.ui.doubleSpinBox_zStep.value())
def updateDisplayX(self):
pos = self.ui.horizontalSlider_xAxis.value()
self.ui.lcdNumber_xAxis.display(pos)
def updateDisplayY(self):
pos = self.ui.horizontalSlider_yAxis.value()
self.ui.lcdNumber_yAxis.display(pos)
def updateDisplayZ(self):
pos = self.ui.horizontalSlider_zAxis.value()
self.ui.lcdNumber_zAxis.display(pos)
def energise(self):
self.scanner.resume()
self.log_info("Energised steppers")
def deEnergise(self):
self.scanner.deEnergise()
self.log_info("De-energised steppers")
self.ui.horizontalSlider_xAxis.setEnabled(False)
self.ui.horizontalSlider_zAxis.setEnabled(False)
self.homed_X = False
self.homed_Z = False
def homeX_threaded(self, progress_callback):
self.ui.horizontalSlider_xAxis.setEnabled(False)
self.scanner.home(0)
self.log_info("Homed X Axis")
self.ui.horizontalSlider_xAxis.setEnabled(True)
self.scanner.getStepperPosition(0)
self.ui.lcdNumber_xAxis.display(self.scanner.stepper_position[0])
self.ui.horizontalSlider_xAxis.setValue(self.scanner.stepper_position[0])
self.homed_X = True
self.posX = 0
def homeZ_threaded(self, progress_callback):
self.ui.horizontalSlider_zAxis.setEnabled(False)
self.scanner.home(2)
self.log_info("Homed Z Axis")
self.ui.horizontalSlider_zAxis.setEnabled(True)
self.scanner.getStepperPosition(2)
self.ui.lcdNumber_zAxis.display(self.scanner.stepper_position[2])
self.ui.horizontalSlider_zAxis.setValue(self.scanner.stepper_position[2])
self.homed_Z = True
self.posZ = 0
def homeX(self):
worker = Worker(self.homeX_threaded)
self.threadpool.start(worker)
def resetY(self):
self.ui.horizontalSlider_yAxis.setValue(0)
self.updateDisplayY()
self.scanner.home(1)
self.log_info("Reset Y Axis")
def homeZ(self):
worker = Worker(self.homeZ_threaded)
self.threadpool.start(worker)
def moveStepperX_threaded(self, progress_callback):
self.ui.horizontalSlider_xAxis.setEnabled(False)
self.ui.pushButton_xHome.setEnabled(False)
pos = self.ui.horizontalSlider_xAxis.value()
self.scanner.moveToPosition(stepper=0, pos=pos)
self.ui.horizontalSlider_xAxis.setEnabled(True)
self.ui.pushButton_xHome.setEnabled(True)
self.posX = pos
self.xMoving = False
def moveStepperX(self):
self.xMoving = True
worker = Worker(self.moveStepperX_threaded)
self.threadpool.start(worker)
def moveStepperY_threaded(self, progress_callback):
self.ui.pushButton_yReset.setEnabled(False)
self.ui.horizontalSlider_yAxis.setEnabled(False)
pos = self.ui.horizontalSlider_yAxis.value()
self.scanner.moveToPosition(stepper=1, pos=pos)
self.ui.horizontalSlider_yAxis.setEnabled(True)
self.ui.pushButton_yReset.setEnabled(True)
self.posY = pos
self.yMoving = False
def moveStepperY(self):
self.yMoving = True
worker = Worker(self.moveStepperY_threaded)
self.threadpool.start(worker)
def moveStepperZ_threaded(self, progress_callback):
self.ui.pushButton_zHome.setEnabled(False)
self.ui.horizontalSlider_zAxis.setEnabled(False)
pos = self.ui.horizontalSlider_zAxis.value()
self.scanner.moveToPosition(stepper=2, pos=pos)
self.ui.horizontalSlider_zAxis.setEnabled(True)
self.ui.pushButton_zHome.setEnabled(True)
self.posZ = pos
self.zMoving = False
def moveStepperZ(self):
self.zMoving = True
worker = Worker(self.moveStepperZ_threaded)
self.threadpool.start(worker)
"""
Camera Settings
"""
def select_camera(self):
self.disable_FLIR_inputs()
self.disable_DSLR_inputs()
selected_camera = self.ui.comboBox_selectCamera.currentText()
self.log_info("Selected camera: " + str(selected_camera))
# stop the live view if currently in use
if self.liveView:
self.begin_live_view() # sets live view false if already running
# de-initialised previous FLIR, if it was in use
if self.camera_type == "FLIR":
# de-initialise the previous camera before setting up the newly selected one
self.cam.deinitialise_camera()
# new camera -> FLIR
if selected_camera.split(" ")[0] == "Blackfly":
for ID, FLIR in enumerate(self.FLIR.device_names):
if self.ui.comboBox_selectCamera.currentText() == str(FLIR[0] + " ID: " + FLIR[1]):
self.cam = self.FLIR
self.cam.initialise_camera(select_cam=ID)
self.log_info("Camera in use: " + str(FLIR[0] + " ID: " + FLIR[1]))
self.camera_type = "FLIR"
self.begin_live_view()
self.camera_model = self.FLIR.device_names[ID][0]
self.enable_FLIR_inputs()
self.file_format = ".tif"
# new camera -> DSLR
else:
self.cam = self.DSLR
self.camera_type = "DSLR"
self.camera_model = self.DSLR.camera_model
# initialise DSLR by launching an instance of DigiCamControl
worker = Worker(self.launch_DCC_threaded)
worker.signals.finished.connect(self.finished_DCC_launch)
self.threadpool.start(worker)
def launch_DCC_threaded(self, progress_callback):
self.cam.initialise_camera()
self.DSLR_initialised = True
def finished_DCC_launch(self):
self.log_info("Launched DCC and retrieved camera settings")
self.enable_DSLR_inputs()
# FLIR Settings
def check_exposure(self):
if self.ui.checkBox_exposureAuto.isChecked():
self.set_exposure_auto()
else:
self.set_exposure_manual()
def set_exposure_auto(self):
self.cam.reset_exposure()
self.ui.label_exposureTime.setEnabled(False)
self.ui.doubleSpinBox_exposureTime.setEnabled(False)
self.log_info("Enabled automatic exposure")
def set_exposure_manual(self):
self.ui.label_exposureTime.setEnabled(True)
self.ui.doubleSpinBox_exposureTime.setEnabled(True)
value = self.ui.doubleSpinBox_exposureTime.value()
if value is not None:
self.log_info("Exposure time set to " + str(value) + " [us]")
self.cam.configure_exposure(float(value))
def check_gain(self):
if self.ui.checkBox_gainAuto.isChecked():
self.set_gain_auto()
else:
self.set_gain_manual()
def set_gain_auto(self):
self.cam.reset_gain()
self.ui.label_gainLevel.setEnabled(False)
self.ui.doubleSpinBox_gainLevel.setEnabled(False)
self.log_info("Enabled automatic exposure")
def set_gain_manual(self):
self.ui.label_gainLevel.setEnabled(True)
self.ui.doubleSpinBox_gainLevel.setEnabled(True)
value = self.ui.doubleSpinBox_gainLevel.value()
if value is not None:
self.log_info("Gain level set to " + str(value) + " [dB]")
self.cam.set_gain(float(value))
def set_gamma(self):
value = self.ui.doubleSpinBox_gamma.value()
if value is not None:
self.log_info("Gain set to " + str(value))
self.cam.set_gamma(float(value))
def set_balance_ratio(self):
value_red = self.ui.doubleSpinBox_balanceRatioRed.value()
value_blue = self.ui.doubleSpinBox_balanceRatioBlue.value()
if value_red is not None and value_blue is not None:
self.log_info("White balance ratio set to " + str(value_red) + " and " + str(value_blue))
self.cam.set_white_balance(float(value_red), float(value_blue))
def set_black_level(self):
# TODO -> not yet functional, error thrown from PySpin
value = self.ui.doubleSpinBox_blackLevel.value()
if value is not None:
self.log_info("Gain set to " + str(value))
self.cam.set_black_level(float(value))
def update_live_view(self, progress_callback):
while self.liveView and self.camera_type == "FLIR":
try:
img = self.cam.live_view()
# if enabled, display exposure as histogram and highlight over exposed areas
if self.ui.checkBox_highlightExposure.isChecked():
img = self.cam.showExposure(img)
live_img = QtGui.QImage(img, img.shape[1], img.shape[0], QtGui.QImage.Format_RGB888).rgbSwapped()
live_img_pixmap = QtGui.QPixmap.fromImage(live_img)
# Setup pixmap with the acquired image
live_img_scaled = live_img_pixmap.scaled(self.ui.label_liveView.width(),
self.ui.label_liveView.height(),
QtCore.Qt.KeepAspectRatio)
# Set the pixmap onto the label
self.ui.label_liveView.setPixmap(live_img_scaled)
# Align the label to center
self.ui.label_liveView.setAlignment(QtCore.Qt.AlignCenter)
except AttributeError:
print("Live view ended")
self.ui.label_liveView.setText("Live view disabled.")
# DSLR settings
def set_shutterspeed(self):
if not self.DSLR_read_out:
self.cam.set_shutterspeed(self.ui.comboBox_shutterSpeed.currentText())
self.log_info("Set shutter speed to " + self.ui.comboBox_shutterSpeed.currentText())
def set_aperture(self):
if not self.DSLR_read_out:
self.cam.set_aperture(self.ui.comboBox_aperture.currentText())
self.log_info("Set aperture to " + self.ui.comboBox_aperture.currentText())
def set_iso(self):
if not self.DSLR_read_out:
self.cam.set_iso(self.ui.comboBox_iso.currentText())
self.log_info("Set iso to " + self.ui.comboBox_iso.currentText())
def set_whitebalance(self):
if not self.DSLR_read_out:
self.cam.set_whitebalance(self.ui.comboBox_whiteBalance.currentText())
self.log_info("Set white balance to " + self.ui.comboBox_whiteBalance.currentText())
def set_compression(self):
if not self.DSLR_read_out:
self.cam.set_compression(self.ui.comboBox_compression.currentText())
self.log_info("Set compression to " + self.ui.comboBox_compression.currentText())
def get_DSLR_file_ending(self):
# first get the current compression setting
compression_setting = self.cam.get_current_setting("compressionsetting")
if compression_setting.split(" ")[0] == "JPEG":
self.file_format = ".jpg"
elif compression_setting.split(" ")[0] == "RAW":
# different cameras use different RAW format endings
brand = self.camera_model.split(" ")[0]
# Nikon cameras are simply named D###
if brand[0] == "D":
self.file_format = ".nef"
# Canon cameras use their brand name directly
elif brand == "Canon":
self.file_format = ".CR2"
else:
self.file_format = ".jpg"
self.log_warning("Unknown image file format! Using JPEG as default!")
# Info & Threading functions
def log_info(self, info):
now = datetime.datetime.now()
self.ui.listWidget_log.addItem(now.strftime("%H:%M:%S") + " [INFO] " + info)
self.ui.listWidget_log.sortItems(QtCore.Qt.DescendingOrder)
def log_warning(self, warning):
now = datetime.datetime.now()
self.ui.listWidget_log.addItem(now.strftime("%H:%M:%S") + " [ERROR] " + warning)
self.ui.listWidget_log.sortItems(QtCore.Qt.DescendingOrder)
def thread_complete(self):
self.ui.pushButton_startScan.setText("Start Scan")
self.scanInProgress = False
self.changeInputState()
self.log_info("Scanning completed!")
def begin_live_view(self):
if not self.liveView:
self.log_info("Began camera live view")
self.ui.pushButton_startLiveView.setText("Stop Live View")
self.liveView = True
if self.camera_type == "FLIR":
worker = Worker(self.update_live_view)
self.threadpool.start(worker)
else:
# starts live view in external Window
self.ui.label_liveView.setText("Live view opened in external DCC window!")
self.cam.start_live_view()
else:
self.ui.label_liveView.setText("Live view disabled.")
self.ui.pushButton_startLiveView.setText("Start Live View")
self.log_info("Ended camera live view")
self.liveView = False
if self.camera_type == "DSLR":
self.cam.stop_live_view()
def capture_image(self):
now = datetime.datetime.now()
self.create_output_folders()
# create unique filename
file_name = str(self.output_location_folder.joinpath(now.strftime("%Y-%m-%d_%H-%M-%S-%MS_" + self.file_format)))
self.cam.capture_image(file_name)
self.log_info("Captured " + file_name)
def create_output_folders(self):
self.output_location_folder = Path(self.output_location).joinpath(self.ui.lineEdit_projectName.text())
if not os.path.exists(self.output_location_folder):
os.makedirs(self.output_location_folder)
self.log_info("Created folder at:" + str(self.output_location_folder))
if not os.path.exists(self.output_location_folder.joinpath("RAW")):
os.makedirs(self.output_location_folder.joinpath("RAW"))
if not os.path.exists(self.output_location_folder.joinpath("stacked")):
os.makedirs(self.output_location_folder.joinpath("stacked"))
"""
Scanner Setup
"""
def getProgress(self):
self.progress = min(int(100 * (self.images_taken / self.images_to_take)), 100)
def set_project_title(self):
name = self.ui.lineEdit_projectName.text()
self.setWindowTitle("scAnt V 1.0 : " + name)
def set_output_location(self):
new_location = QtWidgets.QFileDialog.getExistingDirectory(self, "Choose output location",
str(Path.cwd()))
if new_location:
self.output_location = new_location
self.update_output_location()
def loadConfig(self):
file = QtWidgets.QFileDialog.getOpenFileName(self, "Load existing config file",
str(Path.cwd()), "config file (*.yaml)")
config_location = file[0]
if config_location:
# if a file has been selected, convert it into a Path object
config_location = Path(config_location)
config = ymlRW.read_config_file(config_location)
# check if the camera type in the config file matches the connected/selected camera type
if config["general"]["camera_type"] != self.camera_type:
self.log_warning("The selected config file was generated for a different camera type!")
QtWidgets.QMessageBox.critical(self, "Failed to load " + str(config_location.name),
"The selected config file was generated for a different camera type!")
return
# camera_settings:
if config["general"]["camera_type"] == "FLIR":
# FLIR
self.ui.doubleSpinBox_exposureTime.setValue(config["camera_settings"]["exposure_time"])
if config["camera_settings"]["exposure_auto"]:
self.ui.checkBox_exposureAuto.setChecked(True)
else:
self.set_exposure_manual()
self.ui.doubleSpinBox_gainLevel.setValue(config["camera_settings"]["gain_level"])
if config["camera_settings"]["gain_auto"]:
self.ui.checkBox_gainAuto.setChecked(True)
else:
self.ui.checkBox_gainAuto.setChecked(False)
self.ui.doubleSpinBox_gamma.setValue(config["camera_settings"]["gamma"])
self.set_gamma()
self.ui.doubleSpinBox_balanceRatioRed.setValue(config["camera_settings"]["balance_ratio_red"])
self.ui.doubleSpinBox_balanceRatioBlue.setValue(config["camera_settings"]["balance_ratio_blue"])
self.set_balance_ratio()
# self.ui.doubleSpinBox_blackLevel.setValue(config["camera_settings"]["black_level"])
# self.set_black_level()
else:
# DSLR
self.ui.comboBox_shutterSpeed.setCurrentIndex(
self.ui.comboBox_shutterSpeed.findText(str(config["camera_settings"]["shutterspeed"])))
self.ui.comboBox_aperture.setCurrentIndex(
self.ui.comboBox_aperture.findText(str(config["camera_settings"]["aperture"])))
self.ui.comboBox_iso.setCurrentIndex(
self.ui.comboBox_iso.findText(str(config["camera_settings"]["iso"])))
self.ui.comboBox_whiteBalance.setCurrentIndex(
self.ui.comboBox_whiteBalance.findText(str(config["camera_settings"]["whitebalance"])))
self.ui.comboBox_compression.setCurrentIndex(
self.ui.comboBox_compression.findText(str(config["camera_settings"]["compression"])))
if self.scanner_initialised:
# scanner_settings
self.ui.doubleSpinBox_xMin.setValue(config["scanner_settings"]["x_min"])
self.ui.doubleSpinBox_yMin.setValue(config["scanner_settings"]["y_min"])
self.ui.doubleSpinBox_zMin.setValue(config["scanner_settings"]["z_min"])
self.ui.doubleSpinBox_xMax.setValue(config["scanner_settings"]["x_max"])
self.ui.doubleSpinBox_yMax.setValue(config["scanner_settings"]["y_max"])
self.ui.doubleSpinBox_zMax.setValue(config["scanner_settings"]["z_max"])
self.ui.doubleSpinBox_xStep.setValue(config["scanner_settings"]["x_step"])
self.ui.doubleSpinBox_yStep.setValue(config["scanner_settings"]["y_step"])
self.ui.doubleSpinBox_zStep.setValue(config["scanner_settings"]["z_step"])
self.setScannerRange()
else:
self.log_warning("Stepper controllers are not connected!")
# stacking
self.ui.checkBox_stackImages.setChecked(config["stacking"]["stack_images"])
if config["stacking"]["stacking_method"] == "default":
self.ui.comboBox_stackingMethod.setCurrentIndex(0)
elif config["stacking"]["stacking_method"] == "1-star":
self.ui.comboBox_stackingMethod.setCurrentIndex(1)
elif config["stacking"]["stacking_method"] == "masks":
self.ui.comboBox_stackingMethod.setCurrentIndex(2)
self.stackFocusThreshold = config["stacking"]["threshold"]
self.ui.spinBox_thresholdFocus.setValue(self.stackFocusThreshold)
self.stackDisplayFocus = config["stacking"]["display_focus_check"]
self.stackSharpen = config["stacking"]["additional_sharpening"]
# masking
self.ui.checkBox_maskImages.setChecked(config["masking"]["mask_images"])
self.maskThreshMin = config["masking"]["mask_thresh_min"]
self.ui.spinBox_thresholdMin.setValue(self.maskThreshMin)
self.maskThreshMax = config["masking"]["mask_thresh_max"]
self.ui.spinBox_thresholdMax.setValue(self.maskThreshMax)
self.maskArtifactSizeBlack = config["masking"]["min_artifact_size_black"]
self.maskArtifactSizeWhite = config["masking"]["min_artifact_size_white"]
# meta data (exif)
self.exif = config["exif_data"]
self.loadedConfig = True
self.log_info("Loaded config-file successfully!")
print(config)
def writeConfig(self):
if self.ui.comboBox_stackingMethod.currentIndex() == 0:
stacking_method = "default"
elif self.ui.comboBox_stackingMethod.currentIndex() == 1:
stacking_method = "1-star"
elif self.ui.comboBox_stackingMethod.currentIndex() == 2:
stacking_method = "mask"
if self.camera_type == "DSLR":
self.get_DSLR_file_ending()
config = {'general': {'project_name': self.ui.lineEdit_projectName.text(),
'camera_type': self.camera_type,
'camera_model': self.camera_model,
},
'camera_settings': {'exposure_auto': self.ui.checkBox_exposureAuto.isChecked(),
'exposure_time': self.ui.doubleSpinBox_exposureTime.value(),
'gain_auto': self.ui.checkBox_gainAuto.isChecked(),
'gain_level': self.ui.doubleSpinBox_gainLevel.value(),
'gamma': self.ui.doubleSpinBox_gamma.value(),
'balance_ratio_red': self.ui.doubleSpinBox_balanceRatioRed.value(),
'balance_ratio_blue': self.ui.doubleSpinBox_balanceRatioBlue.value(),
# values specific to DSLR cameras
'shutterspeed': self.ui.comboBox_shutterSpeed.currentText(),
'aperture': self.ui.comboBox_aperture.currentText(),
'iso': self.ui.comboBox_iso.currentText(),
'whitebalance': self.ui.comboBox_whiteBalance.currentText(),
'compression': self.ui.comboBox_compression.currentText()
},
'scanner_settings': {'x_min': self.ui.doubleSpinBox_xMin.value(),
'x_max': self.ui.doubleSpinBox_xMax.value(),
'x_step': self.ui.doubleSpinBox_xStep.value(),
'y_min': self.ui.doubleSpinBox_yMin.value(),
'y_max': self.ui.doubleSpinBox_yMax.value(),
'y_step': self.ui.doubleSpinBox_yStep.value(),
'z_min': self.ui.doubleSpinBox_zMin.value(),
'z_max': self.ui.doubleSpinBox_zMax.value(),
'z_step': self.ui.doubleSpinBox_zStep.value()},
'stacking': {'stack_images': self.ui.checkBox_stackImages.isChecked(),
'stacking_method': stacking_method,
'threshold': self.ui.spinBox_thresholdFocus.value(),
'display_focus_check': self.stackDisplayFocus,
'additional_sharpening': self.stackSharpen},
'masking': {'mask_images': self.ui.checkBox_maskImages.isChecked(),
'mask_thresh_min': self.ui.spinBox_thresholdMin.value(),
'mask_thresh_max': self.ui.spinBox_thresholdMax.value(),
'min_artifact_size_black': self.maskArtifactSizeBlack,
'min_artifact_size_white': self.maskArtifactSizeWhite},
"exif_data": self.exif}
self.create_output_folders()
ymlRW.write_config_file(config, Path(self.output_location_folder))
self.log_info("Exported config_file successfully!")
def update_output_location(self):
self.ui.lineEdit_outputLocation.setText(self.output_location)
def enableStacking(self, set_to=False):
self.stackImages = self.ui.checkBox_stackImages.isChecked()
self.ui.label_stackingMethod.setEnabled(self.stackImages)
self.ui.comboBox_stackingMethod.setEnabled(self.stackImages)
self.ui.label_thresholdFocus.setEnabled(self.stackImages)
self.ui.spinBox_thresholdFocus.setEnabled(self.stackImages)
self.ui.label_maskImages.setEnabled(self.stackImages)
self.ui.checkBox_maskImages.setEnabled(self.stackImages)
def enableMasking(self, set_to=False):
self.maskImages = self.ui.checkBox_maskImages.isChecked()
self.ui.label_thresholdMasking.setEnabled(self.maskImages)
self.ui.label_thresholdMaskingMin.setEnabled(self.maskImages)
self.ui.label_thresholdMaskingMax.setEnabled(self.maskImages)
self.ui.spinBox_thresholdMin.setEnabled(self.maskImages)
self.ui.spinBox_thresholdMax.setEnabled(self.maskImages)
def displayProgress(self, progress):
print("Displaying progress!")
self.ui.progressBar_total.setValue(int(progress))
self.ui.horizontalSlider_xAxis.setValue(self.posX)
self.ui.horizontalSlider_yAxis.setValue(self.posY)
self.ui.horizontalSlider_zAxis.setValue(self.posZ)
self.ui.lcdNumber_xAxis.display(self.posX)
self.ui.lcdNumber_yAxis.display(self.posY)
self.ui.lcdNumber_zAxis.display(self.posZ)
def disable_stepper_inputs(self):
self.ui.horizontalSlider_xAxis.setEnabled(False)
self.ui.horizontalSlider_yAxis.setEnabled(False)
self.ui.horizontalSlider_zAxis.setEnabled(False)
self.ui.pushButton_xHome.setEnabled(False)
self.ui.pushButton_yReset.setEnabled(False)
self.ui.pushButton_zHome.setEnabled(False)
self.ui.doubleSpinBox_xMin.setEnabled(False)
self.ui.doubleSpinBox_yMin.setEnabled(False)
self.ui.doubleSpinBox_zMin.setEnabled(False)
self.ui.doubleSpinBox_xStep.setEnabled(False)
self.ui.doubleSpinBox_yStep.setEnabled(False)
self.ui.doubleSpinBox_zStep.setEnabled(False)
self.ui.doubleSpinBox_xMax.setEnabled(False)
self.ui.doubleSpinBox_yMax.setEnabled(False)
self.ui.doubleSpinBox_zMax.setEnabled(False)
self.ui.pushButton_Energise.setEnabled(False)
self.ui.pushButton_stepperDeEnergise.setEnabled(False)
self.ui.pushButton_startScan.setEnabled(False)
self.ui.lcdNumber_xAxis.setEnabled(False)
self.ui.lcdNumber_yAxis.setEnabled(False)
self.ui.lcdNumber_zAxis.setEnabled(False)
def disable_FLIR_inputs(self):
self.ui.checkBox_exposureAuto.setEnabled(False)
self.ui.doubleSpinBox_exposureTime.setEnabled(False)
self.ui.checkBox_gainAuto.setEnabled(False)
self.ui.doubleSpinBox_gainLevel.setEnabled(False)
self.ui.doubleSpinBox_gamma.setEnabled(False)
self.ui.doubleSpinBox_balanceRatioBlue.setEnabled(False)
self.ui.doubleSpinBox_balanceRatioRed.setEnabled(False)
self.ui.pushButton_startLiveView.setEnabled(False)
self.ui.pushButton_startScan.setEnabled(False)
self.ui.pushButton_captureImage.setEnabled(False)
self.ui.checkBox_highlightExposure.setEnabled(False)
# self.ui.doubleSpinBox_blackLevel.setEnabled(False)
def enable_FLIR_inputs(self):
self.ui.stacked_camera_settings.setCurrentIndex(0)
self.ui.checkBox_exposureAuto.setEnabled(True)
self.ui.doubleSpinBox_exposureTime.setEnabled(True)
self.ui.checkBox_gainAuto.setEnabled(True)
self.ui.doubleSpinBox_gainLevel.setEnabled(True)
self.ui.doubleSpinBox_gamma.setEnabled(True)
self.ui.doubleSpinBox_balanceRatioBlue.setEnabled(True)
self.ui.doubleSpinBox_balanceRatioRed.setEnabled(True)
self.ui.pushButton_startLiveView.setEnabled(True)
self.ui.pushButton_startScan.setEnabled(True)
self.ui.pushButton_captureImage.setEnabled(True)
self.ui.checkBox_highlightExposure.setEnabled(True)
# self.ui.doubleSpinBox_blackLevel.setEnabled(False)
def enable_DSLR_inputs(self):
# disable setting changes based on read out values:
self.DSLR_read_out = True
# set the index of the stacked widget to 1 to access DSLR settings
self.ui.stacked_camera_settings.setCurrentIndex(1)
# set retrieved values as combo box entries for each setting.
# Clear each combo box in case different options are available for different cameras
self.ui.comboBox_shutterSpeed.clear()
for shutterspeed in self.cam.all_shutterspeed_vals:
self.ui.comboBox_shutterSpeed.addItem(shutterspeed)
# set current value to the selected item
self.ui.comboBox_shutterSpeed.setCurrentIndex(
self.ui.comboBox_shutterSpeed.findText(self.cam.shutterspeed))
self.ui.comboBox_aperture.clear()
for aperture in self.cam.all_aperture_vals:
self.ui.comboBox_aperture.addItem(aperture)
# set current value to the selected item
self.ui.comboBox_aperture.setCurrentIndex(
self.ui.comboBox_aperture.findText(self.cam.aperture))
self.ui.comboBox_iso.clear()
for iso in self.cam.all_iso_vals:
self.ui.comboBox_iso.addItem(iso)
# set current value to the selected item
self.ui.comboBox_iso.setCurrentIndex(
self.ui.comboBox_iso.findText(self.cam.iso))
self.ui.comboBox_whiteBalance.clear()
for whitebalance in self.cam.all_whitebalance_vals:
self.ui.comboBox_whiteBalance.addItem(whitebalance)
# set current value to the selected item
self.ui.comboBox_whiteBalance.setCurrentIndex(
self.ui.comboBox_whiteBalance.findText(self.cam.whitebalance))
self.ui.comboBox_compression.clear()
for compression in self.cam.all_compression_vals:
self.ui.comboBox_compression.addItem(compression)
# set current value to the selected item
self.ui.comboBox_compression.setCurrentIndex(
self.ui.comboBox_compression.findText(self.cam.compression))