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dvc_interface.py
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dvc_interface.py
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# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
# Author: Laura Murgatroyd (UKRI-STFC)
# Author: Edoardo Pasca (UKRI-STFC)
import os
import sys
import PySide2
from PySide2 import QtCore, QtGui, QtWidgets
from PySide2.QtCore import (QByteArray, QRegExp, QSettings, QSize, Qt,
QThreadPool)
from PySide2.QtGui import QCloseEvent, QKeySequence, QRegExpValidator
from PySide2.QtWidgets import (QAction, QCheckBox, QComboBox,
QDockWidget,
QDoubleSpinBox, QFileDialog, QFormLayout,
QFrame, QGroupBox, QLabel, QLineEdit,
QMainWindow, QMessageBox,
QProgressDialog, QPushButton, QSpinBox,
QTabWidget, QTabBar, QVBoxLayout,
QHBoxLayout, QSizePolicy,
QWidget)
import time
import numpy as np
import math
import matplotlib.pyplot as plt
from functools import partial
from datetime import datetime
import vtk
from ccpi.viewer import viewer2D, viewer3D
from ccpi.viewer.QCILViewerWidget import QCILViewerWidget
from ccpi.viewer.CILViewer2D import (SLICE_ORIENTATION_XY,
SLICE_ORIENTATION_XZ,
SLICE_ORIENTATION_YZ)
import ccpi.viewer.viewerLinker as vlink
# from ccpi.viewer.QtThreading import Worker, WorkerSignals, ErrorObserver #
from eqt.threading import Worker
from ccpi.viewer.utils.error_handling import ErrorObserver
from ccpi.viewer.utils.colormaps import CILColorMaps
from natsort import natsorted
import imghdr
import glob
# from vtk.numpy_interface import algorithms as algs
# from vtk.numpy_interface import dataset_adapter as dsa
# from vtk.util import numpy_support
working_directory = os.getcwd()
os.chdir(working_directory)
from ccpi.viewer.utils import (cilMaskPolyData, cilPlaneClipper, Converter)
import tempfile
import json
import shutil
import zipfile
from functools import reduce
import copy
from idvc.io import ImageDataCreator, getProgress, displayErrorDialogFromWorker, warningDialog
from idvc.pointcloud_conversion import cilRegularPointCloudToPolyData, cilNumpyPointCloudToPolyData, PointCloudConverter
from idvc.dvc_runner import DVC_runner
from eqt.ui import FormDialog
import qdarkstyle
from qdarkstyle.dark.palette import DarkPalette
from qdarkstyle.light.palette import LightPalette
from idvc import version as gui_version
from idvc.ui.widgets import *
from idvc.ui.dialogs import *
from idvc.ui.windows import *
from idvc.utilities import *
__version__ = gui_version.version
import logging
from idvc.utils.AutomaticRegistration import AutomaticRegistration
class MainWindow(QMainWindow):
def __init__(self):
QMainWindow.__init__(self)
self.threadpool = QThreadPool()
self.temp_folder = None
self.setWindowTitle("Digital Volume Correlation v{}".format(__version__))
DVCIcon = QtGui.QIcon()
file_dir = os.path.dirname(__file__)
DVCIcon.addFile(os.path.join(file_dir, "DVCIconSquare.png"))
self.setWindowIcon(DVCIcon)
self.InitialiseSessionVars()
self.setDockNestingEnabled(True)
self.CreateDockWindows()
# Menu
self.menu = self.menuBar()
self.file_menu = self.menu.addMenu("File")
#Settings QAction
settings_action = QAction("Settings", self)
#save_action.setShortcut(QKeySequence.Save)
settings_action.triggered.connect(self.OpenSettings)
self.file_menu.addAction(settings_action)
#Save QAction
save_action = QAction("Save", self)
save_action.triggered.connect(partial(self.CreateSaveWindow,"Cancel", lambda x: print(type(x))))
self.file_menu.addAction(save_action)
#New QAction
new_action = QAction("New Session", self)
new_action.triggered.connect(self.NewSession)
self.file_menu.addAction(new_action)
#Load QAction
load_action = QAction("Load Session", self)
#load_action.setShortcut(QKeySequence.Open)
load_action.triggered.connect(lambda: self.CreateSessionSelector("current window"))
self.file_menu.addAction(load_action)
#Export Session
export_action = QAction("Export Session", self)
export_action.triggered.connect(self.ExportSession)
self.file_menu.addAction(export_action)
# Exit QAction
exit_action = QAction("Exit", self)
exit_action.setShortcut(QKeySequence.Quit)
exit_action.triggered.connect(self.close)
self.file_menu.addAction(exit_action)
# # Window dimensions
geometry = qApp.desktop().availableGeometry(self)
border = 50
self.setGeometry(border, border, geometry.width()-2*border, geometry.height()-2*border)
self.e = ErrorObserver()
self.CreateWorkingTempFolder()
#Load Settings:
self.settings = QSettings("CCPi", "DVC Interface v20.7.2")
if self.settings.value("copy_files"):
self.copy_files = True
else:
self.copy_files = False
self.SetAppStyle()
if self.settings.value("first_app_load") != "False":
self.OpenSettings()
# self.settings.setValue("first_app_load", False)
else:
self.CreateSessionSelector("new window")
def createPopupMenu(self):
'''return an empty menu for the main window to use as a popup menu.
https://doc.qt.io/qt-6/qmainwindow.html#createPopupMenu
'''
return QtWidgets.QMenu(self) # Create a new menu
def SetAppStyle(self):
if self.settings.value("dark_mode") is None:
self.settings.setValue("dark_mode", True)
if self.settings.value("dark_mode") == "true":
style = qdarkstyle.load_stylesheet(palette=DarkPalette)
else:
style = qdarkstyle.load_stylesheet(palette=LightPalette)
self.setStyleSheet(style)
#Setting up the session:
def CreateWorkingTempFolder(self):
temp_folder = os.path.join(working_directory, 'DVC_Sessions')
if not os.path.isdir(temp_folder):
os.mkdir("DVC_Sessions")
temp_folder = os.path.join(working_directory, "DVC_Sessions")
self.temp_folder = os.path.abspath(temp_folder)
tempfile.tempdir = tempfile.mkdtemp(dir = self.temp_folder)
os.chdir(tempfile.tempdir)
# Creates folder in tempdir to save mask files in
os.mkdir("Masks")
os.mkdir("Results")
def OpenSettings(self):
self.settings_window = SettingsWindow(self)
self.settings_window.show()
def InitialiseSessionVars(self):
self.config={}
self.image=[[],[]]
self.dvc_input_image = [[],[]]
self.roi = None
self.run_folder = [None]
self.results_folder = [None]
self.pointCloudCreated = False
self.eroded_mask = False
self.pointCloudLoaded = False
self.orientation = 2 #z orientation is default
self.mask_reader = None
self.current_slice = None
self.mask_details = {}
self.pointCloud_details = {}
self.image_copied = [False,False]
self.runs_completed = 0
self.run_config_file = None
self.mask_load = False
self.raw_import_dialog = None
self.reg_load = False
self.loading_session = False
self.dvc_input_image_in_session_folder = False
if hasattr(self, 'ref_image_data'):
del self.ref_image_data
#Loading the DockWidgets:
def CreateDockWindows(self):
self.setTabPosition(QtCore.Qt.AllDockWidgetAreas, QTabWidget.North)
#Create widgets to view images in 2D and 3D and link them:
self.vis_widget_2D = VisualisationWidget(self, viewer=viewer2D, interactorStyle=vlink.Linked2DInteractorStyle)#interactorStyle= CILInteractorStyle2D) #previously unliked for testing
self.vis_widget_3D = VisualisationWidget(self, viewer=viewer3D, interactorStyle=vlink.Linked3DInteractorStyle) #interactorStyle= CILInteractorStyle3D)#previously unlinked for testing
self.CreateViewerSettingsPanel()
self.CreateHelpPanel()
self.CreateSelectImagePanel()
self.CreateRegistrationPanel()
self.CreateMaskPanel()
self.CreatePointCloudPanel()
self.CreateRunDVCPanel()
self.CreateViewDVCResultsPanel()
self.viewer2D_dock = self.vis_widget_2D
self.viewer3D_dock = QDockWidget("3D View")
self.viewer3D_dock.setObjectName("3DImageView")
self.viewer3D_dock.setWidget(self.vis_widget_3D)
self.viewer3D_dock.setAllowedAreas(Qt.LeftDockWidgetArea)
self.viewer3D_dock.setFeatures(QDockWidget.NoDockWidgetFeatures)
#Tabifies dockwidgets in LeftDockWidgetArea:
prev = None
first_dock = None
docks = []
for current_dock in self.findChildren(QDockWidget):
if self.dockWidgetArea(current_dock) == QtCore.Qt.LeftDockWidgetArea:
if prev:
self.tabifyDockWidget(prev,current_dock)
else:
first_dock = current_dock
prev= current_dock
docks.append(current_dock)
# makes first panel the one that is open by default.
first_dock.raise_()
self.addDockWidget(QtCore.Qt.LeftDockWidgetArea, self.viewer3D_dock)
# Make a window to house the right dockwidgets
# This ensures the 2D viewer is large and allows us to position the help and settings below it
self.RightDockWindow = VisualisationWindow(self)
self.setCentralWidget(self.RightDockWindow)
self.RightDockWindow.setCentralWidget(self.viewer2D_dock)
self.RightDockWindow.addDockWidget(QtCore.Qt.BottomDockWidgetArea,self.help_dock)
self.RightDockWindow.addDockWidget(QtCore.Qt.BottomDockWidgetArea,self.viewer_settings_dock)
# Stop the widgets in the tab to be moved around
for wdg in self.findChildren(QTabBar):
wdg.setMovable(False)
def CreateViewerSettingsPanel(self):
self.viewer_settings_panel = generateUIDockParameters(self, "Viewer Settings")
dockWidget = self.viewer_settings_panel[0]
dockWidget.setObjectName("ViewerSettingsPanel")
groupBox = self.viewer_settings_panel[5]
formLayout = self.viewer_settings_panel[6]
self.viewer_settings_dock = dockWidget
vs_widgets = {}
widgetno = 0
vs_widgets['coords_info_label'] = QLabel(groupBox)
vs_widgets['coords_info_label'].setText("The viewer displays a downsampled image for visualisation purposes: ")
vs_widgets['coords_info_label'].setVisible(False)
formLayout.setWidget(widgetno, QFormLayout.SpanningRole, vs_widgets['coords_info_label'])
widgetno+=1
vs_widgets['loaded_image_dims_label'] = QLabel(groupBox)
vs_widgets['loaded_image_dims_label'].setText("Loaded Image Size: ")
vs_widgets['loaded_image_dims_label'].setVisible(True)
formLayout.setWidget(widgetno, QFormLayout.LabelRole, vs_widgets['loaded_image_dims_label'])
vs_widgets['loaded_image_dims_value'] = QLabel(groupBox)
vs_widgets['loaded_image_dims_value'].setText("")
vs_widgets['loaded_image_dims_value'].setVisible(False)
formLayout.setWidget(widgetno, QFormLayout.FieldRole, vs_widgets['loaded_image_dims_value'])
widgetno+=1
vs_widgets['displayed_image_dims_label'] = QLabel(groupBox)
vs_widgets['displayed_image_dims_label'].setText("Displayed Image Size: ")
vs_widgets['displayed_image_dims_label'].setVisible(False)
formLayout.setWidget(widgetno, QFormLayout.LabelRole, vs_widgets['displayed_image_dims_label'])
vs_widgets['displayed_image_dims_value'] = QLabel(groupBox)
vs_widgets['displayed_image_dims_value'].setText("")
vs_widgets['displayed_image_dims_value'].setVisible(False)
formLayout.setWidget(widgetno, QFormLayout.FieldRole, vs_widgets['displayed_image_dims_value'])
widgetno+=1
vs_widgets['coords_label'] = QLabel(groupBox)
vs_widgets['coords_label'].setText("Display viewer coordinates in: ")
formLayout.setWidget(widgetno, QFormLayout.LabelRole, vs_widgets['coords_label'])
vs_widgets['coords_combobox'] = QComboBox(groupBox)
vs_widgets['coords_combobox'].addItems(["Loaded Image", "Downsampled Image"])
vs_widgets['coords_combobox'].setEnabled(False)
vs_widgets['coords_combobox'].currentIndexChanged.connect(self.updateCoordinates)
formLayout.setWidget(widgetno, QFormLayout.FieldRole, vs_widgets['coords_combobox'])
widgetno +=1
vs_widgets['coords_warning_label'] = QLabel(groupBox)
vs_widgets['coords_warning_label'].setText("Warning: These coordinates are approximate.")
vs_widgets['coords_warning_label'].setVisible(False)
formLayout.setWidget(widgetno, QFormLayout.FieldRole, vs_widgets['coords_warning_label'])
self.visualisation_setting_widgets = vs_widgets
def updateCoordinates(self):
viewers_2D = [self.vis_widget_2D.frame.viewer]
vs_widgets = self.visualisation_setting_widgets
if hasattr(self, 'vis_widget_reg'):
viewers_2D.append(self.vis_widget_reg.frame.viewer)
for viewer in viewers_2D:
if hasattr(viewer, 'img3D'):
if viewer.img3D is not None:
viewer.setVisualisationDownsampling(self.resample_rate)
shown_resample_rate = self.resample_rate
vs_widgets['loaded_image_dims_label'].setVisible(True)
vs_widgets['loaded_image_dims_value'].setVisible(True)
if vs_widgets['coords_combobox'].currentIndex() == 0:
viewer.setDisplayUnsampledCoordinates(True)
if shown_resample_rate != [1,1,1]:
vs_widgets['coords_warning_label'].setVisible(True)
else:
vs_widgets['coords_warning_label'].setVisible(False)
else:
viewer.setDisplayUnsampledCoordinates(False)
vs_widgets['coords_warning_label'].setVisible(False)
if hasattr(self, 'point0_world_coords'):
self.SetPoint0Text()
viewer.updatePipeline()
def CreateHelpPanel(self):
help_panel = generateUIDockParameters(self, "Help")
dockWidget = help_panel[0]
dockWidget.setObjectName("HelpPanel")
groupBox = help_panel[5]
formLayout = help_panel[6]
self.help_dock = dockWidget
self.help_text = ["Please use 'raw' or 'npy' images.\n"
"You can view the shortcuts for the viewer by clicking on the 2D image and then pressing the 'h' key."]
self.help_text.append(
"1. Click 'Select point 0' to choose a point and region for the registration.\n"
"2. Adjust the registration box size as needed.\n"
"3. Click 'Start Registration' to begin the registration process.\n"
"4. The suggested registration will be displayed, and the difference volume of the registered image will be shown in the viewer.\n"
"5. Use the mouse wheel to navigate in the third direction, and the 'x', 'y', or 'z' keys to control the slicing orientation.\n"
"6. To manually adjust the registration, click on the image and move the two images relative to each other using the 'j' (up), 'n' (down), 'b' (right), and 'm' (left) keys.\n"
"7. You can 'Reset' the registration values or 'Set to Automatic Registration'.\n"
"8. You can 'Confirm Registration' or 'Cancel'.\n"
"9. Once satisfied with the registration, move to the next tab. Be aware that point 0 is the point from which DVC will start."
)
self.help_text.append("To create a mask you need to create a selection. Start tracing a freehand region for the selection by clicking 'Start Tracing' button.\n"
"When you are happy with your region click 'Create Mask'.")
self.help_text.append("Dense point clouds that accurately reflect sample geometry and reflect measurement objectives yield the best results.\n"
"The first point in the cloud is significant, as it is used as a global starting point and reference for the rigid translation between the two images.\n"
"If the point 0 you selected in image registration falls inside the mask, then the pointcloud will be created with the first point at the location of point 0.\n"
"If you load a pointcloud from a file, you must still specify the subvolume size on this panel, which will later be input to the DVC code.\n"
"It will be the first point in the file that is used as the reference point.")
self.help_text.append("Once the code is run it is recommended that you save or export your session, to back up your results."
"You can access these options under 'File'.")
self.help_text.append("Vectors can be displayed for the displacement of points either including or excluding the rigid body offset."
"You may also scale the vectors to make them larger and easier to view.")
self.help_label = QLabel(groupBox)
self.help_label.setWordWrap(True)
self.help_label.setText(self.help_text[0])
formLayout.setWidget(1, QFormLayout.SpanningRole, self.help_label)
def displayHelp(self, open, panel_no = None):
if open:
self.help_label.setText(self.help_text[panel_no])
#Select Image Panel:
def CreateSelectImagePanel(self):
self.select_image_panel = generateUIDockParameters(self, "1 - Select Image")
dockWidget = self.select_image_panel[0]
dockWidget.setObjectName("SelectImagePanel")
groupBox = self.select_image_panel[5]
groupBox.setTitle('Image Selection')
formLayout = self.select_image_panel[6]
self.select_image_dock = dockWidget
dockWidget.visibilityChanged.connect(partial(self.displayHelp,panel_no = 0))
#Create the widgets:
widgetno = 1
si_widgets = {}
si_widgets['ref_vol_label'] = QLabel(groupBox)
si_widgets['ref_vol_label'].setText("Reference Volume:")
formLayout.setWidget(widgetno, QFormLayout.LabelRole, si_widgets['ref_vol_label'])
si_widgets['ref_file_label'] = QLabel(groupBox)
si_widgets['ref_file_label'].setText("")
formLayout.setWidget(widgetno, QFormLayout.FieldRole, si_widgets['ref_file_label'])
widgetno += 1
si_widgets['ref_browse'] = QPushButton(groupBox)
si_widgets['ref_browse'].setText("Browse..")
formLayout.setWidget(widgetno, QFormLayout.FieldRole, si_widgets['ref_browse'])
widgetno += 1
separators = []
separators.append(QFrame(groupBox))
separators[-1].setFrameShape(QFrame.HLine)
separators[-1].setFrameShadow(QFrame.Raised)
formLayout.setWidget(widgetno, QFormLayout.SpanningRole, separators[-1])
widgetno += 1
si_widgets['cor_vol_label'] = QLabel(groupBox)
si_widgets['cor_vol_label'].setText("Correlate Volume:")
formLayout.setWidget(widgetno, QFormLayout.LabelRole, si_widgets['cor_vol_label'])
si_widgets['cor_file_label'] = QLabel(groupBox)
si_widgets['cor_file_label'].setText("")
formLayout.setWidget(widgetno, QFormLayout.FieldRole, si_widgets['cor_file_label'])
widgetno += 1
si_widgets['cor_browse'] = QPushButton(groupBox)
si_widgets['cor_browse'].setText("Browse..")
si_widgets['cor_browse'].setEnabled(False)
formLayout.setWidget(widgetno, QFormLayout.FieldRole, si_widgets['cor_browse'])
widgetno += 1
separators.append(QFrame(groupBox))
separators[-1].setFrameShape(QFrame.HLine)
separators[-1].setFrameShadow(QFrame.Raised)
formLayout.setWidget(widgetno, QFormLayout.SpanningRole, separators[-1])
widgetno += 1
si_widgets['view_button'] = QPushButton(groupBox)
si_widgets['view_button'].setText("View Image")
si_widgets['view_button'].setEnabled(False)
formLayout.setWidget(widgetno, QFormLayout.SpanningRole, si_widgets['view_button'])
widgetno += 1
#button functions:
si_widgets['ref_browse'].clicked.connect(lambda: self.SelectImage(0, self.image, label=si_widgets['ref_file_label'], next_button=si_widgets['cor_browse']))
si_widgets['cor_browse'].clicked.connect(lambda: self.SelectImage(1, self.image, label=si_widgets['cor_file_label'], next_button=si_widgets['view_button']))
si_widgets['view_button'].clicked.connect(self.view_and_load_images)
self.addDockWidget(QtCore.Qt.LeftDockWidgetArea,dockWidget)
self.si_widgets = si_widgets
def view_and_load_images(self):
self.view_image()
self.resetRegistration()
def SelectImage(self, image_var, image, label=None, next_button=None):
#print("In select image")
dialogue = QFileDialog()
files = dialogue.getOpenFileNames(self,"Load Images")[0]
if len(files) > 0:
if self.copy_files:
new_file_name = 'reference'
if image_var == 1:
new_file_name = 'correlate'
# first of all we need to remove the files that were copied in the previous run
self.create_progress_window("Copying", "Copying files", 100, None)
# self.progress_window.setValue(1)
self.image_copied[image_var] = True
new_file_dest = []
for file_num, f in enumerate(files):
file_name = os.path.basename(f)
file_ext = file_name.split(".")[-1]
if len(files) == 1:
if file_ext == "mhd":
new_file_dest.append( os.path.join(new_file_name + "." + "mha") )
else:
new_file_dest.append( os.path.join(new_file_name + "." + file_ext) )
else:
new_file_dest.append( os.path.join(new_file_name + "_" + str(file_num) + "." + file_ext) )
# files[file_num] = new_file_dest[-1]
copy_worker = Worker(self.copy_file, start_location=files, end_location=new_file_dest, image_var=image_var)
copy_worker.signals.progress.connect(self.progress_window.setValue)
copy_worker.signals.finished.connect(partial(self.update_interface_on_copy_complete, image, image_var, label, next_button))
copy_worker.signals.error.connect(partial(self.worker_error, progress_dialog=self.progress_window))
self.threadpool.start(copy_worker)
else:
self.image_copied[image_var] = False
self.update_interface_no_copy(files, image, image_var, label, next_button)
def worker_error(self, error, **kwargs):
if 'progress_dialog' in kwargs.keys():
kwargs['progress_dialog'].close()
dialog_retval = warningDialog(self, str(error[1]), "Error", str(error[2]))
def update_interface_on_copy_complete(self, image, image_var, label, next_button):
new_file_name = 'reference'
if image_var == 1:
new_file_name = 'correlate'
files = glob.glob(new_file_name+"*")
self.update_interface_no_copy(files, image, image_var, label, next_button)
def update_interface_no_copy(self, files, image, image_var, label, next_button):
if len(files) == 1: #@todo
if(image[image_var]):
image[image_var]= files
else:
image[image_var].append(files[0])
if label is not None:
label.setText(os.path.basename(files[0]))
elif len(files) > 1:
# Make sure that the files are sorted 0 - end
filenames = natsorted(files)
image[image_var] = filenames
if label is not None:
label.setText(
os.path.dirname(self.image[image_var][0]) + "\n" +\
os.path.basename(self.image[image_var][0]) + " + " + str(len(files)-1) + " more files.")
else:
raise ValueError('Something went wrong with the file copy')
if next_button is not None:
next_button.setEnabled(True)
def copy_file(self, start_location, end_location, image_var, **kwargs):
progress_callback = kwargs.get('progress_callback', PrintCallback())
# message_callback = kwargs.get('message_callback', PrintCallback())
# first of all we need to remove the files that were copied in the previous run
new_file_name = 'reference'
if image_var == 1:
new_file_name = 'correlate'
files_to_remove = glob.glob(new_file_name+"*")
N = len(files_to_remove)
for i,f in enumerate(files_to_remove):
progress_callback.emit(i/N*100)
os.remove(f)
self.image_copied[image_var] = True
file_extension = os.path.splitext(start_location[0])[1]
# if the file is a mhd file we have a header and the data blob, i.e. 2 files
if file_extension == '.mhd':
progress_callback.emit(0)
reader = vtk.vtkMetaImageReader()
reader.SetFileName(start_location[0])
reader.Update()
progress_callback.emit(50)
writer = vtk.vtkMetaImageWriter()
# tmpdir = tempfile.gettempdir()
writer.SetFileName(end_location[0])
writer.SetCompression(False)
writer.SetInputData(reader.GetOutput())
writer.Write()
progress_callback.emit(100)
else:
N = len(start_location)
for i,fs in enumerate(zip(start_location, end_location)):
if N > 1:
ftype = imghdr.what(fs[0])
if ftype != 'tiff':
raise ValueError('File type not supported: {}'.format(fs[0]))
progress_callback.emit(i/N*100)
shutil.copyfile(fs[0], fs[1])
progress_callback.emit(100)
def show_copy_progress(self, _file, new_file_dest,ratio, file_type, num_files):
while not os.path.exists(new_file_dest):
time.sleep(0.001)
if(file_type != "mhd"):
while os.path.getsize(_file) != os.path.getsize(new_file_dest):
self.progress_window.setValue(int((float(os.path.getsize(new_file_dest))/float(os.path.getsize(_file)*ratio))*100))
time.sleep(0.1)
self.progress_window.setValue(100)
def displayFileErrorDialog(self, message, title, action_button=None):
msg = QMessageBox(self)
msg.setIcon(QMessageBox.Critical)
msg.setWindowTitle(title)
msg.setText(message)
try:
msg.setDetailedText(self.e.ErrorMessage())
except:
pass
if action_button is not None:
msg.addButton(action_button, msg.ActionRole)
msg.exec_()
def view_image(self):
self.ref_image_data = vtk.vtkImageData()
self.image_info = dict()
if self.settings.value("gpu_size") is not None and self.settings.value("volume_mapper") == "gpu":
if self.settings.value("vis_size"):
if float(self.settings.value("vis_size")) < float(self.settings.value("gpu_size")):
target_size = float(self.settings.value("vis_size"))
else:
target_size = (float(self.settings.value("gpu_size")))
else:
target_size = (float(self.settings.value("gpu_size")))
else:
if self.settings.value("vis_size"):
target_size = float(self.settings.value("vis_size"))
else:
target_size = 0.125
self.target_image_size = target_size
ImageDataCreator.createImageData(self, self.image[0], self.ref_image_data, info_var = self.image_info, convert_raw = True,
finish_fn = partial(self.save_image_info, "ref"), resample= True, target_size = target_size, output_dir='.')
def save_image_info(self, image_type):
if 'vol_bit_depth' in self.image_info:
self.vol_bit_depth = self.image_info['vol_bit_depth']
maximum_value = round((self.target_image_size**(1/3))*1024/3*int(self.vol_bit_depth)/8)
minimum_image_dimension = np.min(self.ref_image_data.GetDimensions())-1
if maximum_value > minimum_image_dimension:
maximum_value = minimum_image_dimension
#Update registration box size according to target size and vol bit depth
self.registration_parameters['registration_box_size_entry'].setMaximum(maximum_value)
self.registration_parameters['registration_box_size_entry'].setValue(maximum_value)
#Update mask slices above/below to be max extent of downsampled image
self.mask_parameters['mask_extend_above_entry'].setMaximum(np.max(self.ref_image_data.GetDimensions()))
self.mask_parameters['mask_extend_below_entry'].setMaximum(np.max(self.ref_image_data.GetDimensions()))
#Update max subvolume size to be min dimension of image
#TODO: fix so that this works
validatorint = QtGui.QIntValidator()
validatorint.setTop(np.min(self.ref_image_data.GetDimensions()))
self.rdvc_widgets['subvol_size_range_max_value'].setValidator(validatorint)
self.rdvc_widgets['subvol_size_range_min_value'].setValidator(validatorint)
self.isoValueEntry.setValidator(validatorint)
if 'header_length' in self.image_info:
self.vol_hdr_lngth = self.image_info['header_length']
else:
self.vol_hdr_lngth = 0
self.resample_rate = [1,1,1]
if 'shape' in self.image_info:
self.unsampled_image_dimensions = self.image_info['shape']
#print("Unsampled dims: ", self.unsampled_image_dimensions)
#print("current dims: ", self.ref_image_data.GetDimensions())
for i, value in enumerate(self.resample_rate):
self.resample_rate[i] = self.unsampled_image_dimensions[i]/(self.ref_image_data.GetDimensions()[i])
self.visualisation_setting_widgets['coords_warning_label'].setVisible(True)
else:
self.unsampled_image_dimensions = list(self.ref_image_data.GetDimensions())
self.visualisation_setting_widgets['coords_warning_label'].setVisible(False)
if 'raw_file' in self.image_info:
image_file = [self.image_info['raw_file']]
if image_type == "ref":
self.dvc_input_image[0] = image_file
if os.path.splitext(self.image[0][0])[1] in ['.mhd', '.mha']: #need to call create image data so we read header and save image to file w/o header
self.temp_image_data = vtk.vtkImageData()
ImageDataCreator.createImageData(self, self.image[1], self.temp_image_data, info_var=self.image_info, convert_raw=True, finish_fn=partial(
self.save_image_info, "corr"), output_dir='.')
elif image_type == "corr":
self.dvc_input_image[1] = image_file
if hasattr(self, 'temp_image_data'):
del self.temp_image_data
self.dvc_input_image_in_session_folder = True
else:
self.dvc_input_image = self.image
self.dvc_input_image_in_session_folder = False
if image_type == "ref":
self.visualise()
def visualise(self):
if self.ref_image_data is None:
#self.progress_window.setValue(100)
self.warningDialog('Unable to load image.','Error', 'Image is in incorrect format to perform run of DVC. Please load a different image.')
return
time.sleep(0.1)
self.create_progress_window("Loading", "Loading Image")
self.progress_window.setValue(10)
self.vis_widget_2D.setImageData(self.ref_image_data)
self.vis_widget_2D.displayImageData()
self.progress_window.setValue(50)
self.vis_widget_3D.setImageData(self.ref_image_data) #3D)
self.vis_widget_3D.displayImageData()
self.progress_window.setValue(80)
# observe mouse events and keypress events and invoke the plane clipper
self.vis_widget_2D.frame.viewer.style.AddObserver("MouseWheelForwardEvent",
self.vis_widget_2D.PlaneClipper.UpdateClippingPlanes, 0.9)
self.vis_widget_2D.frame.viewer.style.AddObserver("MouseWheelBackwardEvent",
self.vis_widget_2D.PlaneClipper.UpdateClippingPlanes, 0.9)
self.vis_widget_2D.frame.viewer.style.AddObserver("KeyPressEvent",
self.vis_widget_2D.PlaneClipper.UpdateClippingPlanes, 0.9)
# handles vectors updating when switching orientation)
self.vis_widget_2D.frame.viewer.style.AddObserver("KeyPressEvent", self.OnKeyPressEventForVectors, 0.95)
#Link Viewers:
self.link2D3D = vlink.ViewerLinker(self.vis_widget_2D.frame.viewer,
self.vis_widget_3D.frame.viewer)
self.link2D3D.setLinkPan(False)
self.link2D3D.setLinkZoom(False)
self.link2D3D.setLinkWindowLevel(True)
self.link2D3D.setLinkSlice(True)
self.link2D3D.setLinkOrientation(True)
self.link2D3D.enable()
#reset these so they aren't remembered for next image load
self.current_slice = None
self.orientation = None
self.progress_window.setValue(100)
time.sleep(0.1)
#self.LoadCorrImageForReg()
self.pointCloudCreated = False
self.pointCloudLoaded = False
self.eroded_mask = False
if(self.mask_load):
self.MaskWorker("load session")
self.mask_load = False # so it does not reload next time
if hasattr(self, 'no_mask_pc_load'):
if(self.no_mask_pc_load):
self.PointCloudWorker("load pointcloud file")
self.pointCloudLoaded = True
self.no_mask_pc_load = False
self.pointcloud_is = 'loaded'
if(self.reg_load):
self.displayRegistrationViewer(registration_open = True)
#first we need to set the z slice -> go to slice self.config['point0'][2]
v = self.vis_widget_2D.frame.viewer
if v.img3D is not None:
self.createPoint0(self.config['point0'])
rp = self.registration_parameters
if self.config['reg_translation'] is not None:
rp['translate_X_entry'].setText(str(self.config['reg_translation'][0]*-1))
rp['translate_Y_entry'].setText(str(self.config['reg_translation'][1]*-1))
rp['translate_Z_entry'].setText(str(self.config['reg_translation'][2]*-1))
self.translate = vtk.vtkImageTranslateExtent()
self.translate.SetTranslation(self.config['reg_translation'])
self.registration_parameters['registration_box_size_entry'].setValue(self.config['reg_sel_size'])
self.registration_parameters['registration_box_size_entry'].setEnabled(True)
self.reg_viewer_dock.setVisible(False)
self.viewer2D_dock.setVisible(True)
self.viewer3D_dock.setVisible(True)
self.reg_load = False
#bring image loading panel to front if it isnt already:
self.select_image_dock.raise_()
def create_progress_window(self, title, text, max = 100, cancel = None):
self.progress_window = QProgressDialog(text, "Cancel", 0,max, self, QtCore.Qt.Dialog)
self.progress_window.setWindowTitle(title)
self.progress_window.setWindowModality(QtCore.Qt.ApplicationModal) #This means the other windows can't be used while this is open
self.progress_window.setMinimumDuration(0.01)
self.progress_window.setWindowFlag(QtCore.Qt.WindowCloseButtonHint, True)
self.progress_window.setWindowFlag(QtCore.Qt.WindowMaximizeButtonHint, False)
self.progress_window.setAutoClose(True)
if cancel is None:
self.progress_window.setCancelButton(None)
else:
self.progress_window.canceled.connect(cancel)
def setup2DPointCloudPipeline(self):
self.vis_widget_2D.PlaneClipper.AddDataToClip('pc_actor', self.polydata_masker.GetOutputPort())
mapper = vtk.vtkPolyDataMapper()
# save reference
self.pointmapper = mapper
mapper.SetInputConnection(self.vis_widget_2D.PlaneClipper.GetClippedData('pc_actor').GetOutputPort())
# create an actor for the points as point
actor = vtk.vtkLODActor()
# save reference
self.pointactor = actor
actor.SetMapper(mapper)
actor.GetProperty().SetPointSize(3)
actor.GetProperty().SetColor(0., 1., 1.)
actor.VisibilityOn()
# create a mapper/actor for the point cloud with a CubeSource and with vtkGlyph3D
# which copies oriented and scaled glyph geometry to every input point
subv_glyph = vtk.vtkGlyph3D()
subv_glyph.OrientOn()
# save reference
self.cubesphere = subv_glyph
subv_glyph.SetScaleFactor(1.)
v = self.vis_widget_2D.frame.viewer
spacing = v.img3D.GetSpacing()
# pointCloud = self.pointCloud
subvol_size = self.pointCloud_subvol_size
# # Spheres may be a bit complex to visualise if the spacing of the image is not homogeneous
sphere_source = vtk.vtkSphereSource()
# # save reference
self.sphere_source = sphere_source
sphere_source.SetRadius(self.pointCloud_subvol_size/2) # * v.img3D.GetSpacing()[0])
sphere_source.SetThetaResolution(12)
sphere_source.SetPhiResolution(12)
# # Cube source
cube_source = vtk.vtkCubeSource()
# print("IMAGE SPACING", v.img3D.GetSpacing())
cube_source.SetXLength(self.pointCloud_subvol_size)
cube_source.SetYLength(self.pointCloud_subvol_size)
cube_source.SetZLength(self.pointCloud_subvol_size)
self.cube_source = cube_source
rotate= self.pointCloud_rotation
# print("Rotate", self.pointCloud_rotation)
transform = vtk.vtkTransform()
# save reference
self.transform = transform
# rotate around the center of the image data
# print("ROTATE: ", self.pointCloud_rotation[2])
self.transform.RotateX(self.pointCloud_rotation[0])
self.transform.RotateY(self.pointCloud_rotation[1])
self.transform.RotateZ(self.pointCloud_rotation[2])
t_filter = vtk.vtkTransformPolyDataFilter()
t_filter.SetInputConnection(self.cube_source.GetOutputPort())
t_filter.SetTransform(self.transform)
self.cube_transform_filter = t_filter
self.cube_transform_filter.Update()
self.cube_source.Update()
#cube_source.SetRadius(spacing[0])
# # mapper for the glyphs
sphere_mapper = vtk.vtkPolyDataMapper()
# # save reference
self.cubesphere_mapper = sphere_mapper
# # sphere_mapper.SetInputConnection( subv_glyph.GetOutputPort() )
subv_glyph.SetInputConnection( self.polydata_masker.GetOutputPort() )
if self.pointCloud_shape == cilRegularPointCloudToPolyData.CUBE:
#print("CUBE")
self.glyph_source = self.cube_transform_filter #self.cube_source
self.cubesphere.SetSourceConnection(self.cube_transform_filter.GetOutputPort())
else:
#print("SPHERE")
self.glyph_source = self.sphere_source
self.cubesphere.SetSourceConnection(self.sphere_source.GetOutputPort())
#self.cubesphere.SetSourceConnection( self.glyph_source.GetOutputPort() )
self.cubesphere.Update()
self.vis_widget_2D.PlaneClipper.AddDataToClip('subvol_actor', self.cubesphere.GetOutputPort())
sphere_mapper.SetInputConnection( self.vis_widget_2D.PlaneClipper.GetClippedData('subvol_actor').GetOutputPort())
self.cubesphere.Update()
self.cubesphere.SetVectorModeToUseNormal()
# # actor for the glyphs
sphere_actor = vtk.vtkActor()
# # save reference
self.cubesphere_actor = sphere_actor
sphere_actor.SetMapper(sphere_mapper)
sphere_actor.GetProperty().SetColor(1, 0, 0)
#sphere_actor.GetProperty().SetColor(1, .2, .2)
sphere_actor.GetProperty().SetOpacity(0.5)
sphere_actor.GetProperty().SetLineWidth(2.0)
sphere_actor.GetProperty().SetEdgeVisibility(True)
sphere_actor.GetProperty().SetEdgeColor(1, .2, .2)
sphere_actor.GetProperty().SetRenderLinesAsTubes(True)
sphere_actor.GetProperty().SetRepresentationToWireframe()
self.vis_widget_2D.frame.viewer.AddActor(actor, 'pc_actor')
self.vis_widget_2D.frame.viewer.AddActor(sphere_actor, 'subvol_actor')
self.cubesphere.Update()
def setup3DPointCloudPipeline(self):
#polydata_masker = self.polydata_masker
mapper = vtk.vtkPolyDataMapper()
# save reference
self.pointmapper = mapper
mapper.SetInputConnection(self.polydata_masker.GetOutputPort())
# create an actor for the points as point
actor = vtk.vtkLODActor()