|
|
@@ -0,0 +1,565 @@
|
|
|
+import sys
|
|
|
+import os
|
|
|
+import json
|
|
|
+import cv2
|
|
|
+import numpy as np
|
|
|
+from skimage.measure import find_contours
|
|
|
+
|
|
|
+import pydicom
|
|
|
+import zlib
|
|
|
+from PyQt5.QtWidgets import (
|
|
|
+ QApplication, QMainWindow, QLabel, QPushButton, QColorDialog, QInputDialog,
|
|
|
+ QFileDialog, QMessageBox, QVBoxLayout, QHBoxLayout, QWidget, QFrame, QSizePolicy
|
|
|
+)
|
|
|
+from PyQt5.QtGui import QImage, QPixmap, QPainter, QPen, QColor
|
|
|
+from PyQt5.QtCore import Qt, QPoint
|
|
|
+from PyQt5.QtWidgets import QSplitter, QGroupBox, QVBoxLayout
|
|
|
+from PyQt5.QtWidgets import QSlider
|
|
|
+
|
|
|
+# Тестирование для синовиальной оболочки
|
|
|
+# Добавлен подсчет объема в мл, вывод суммарного объема в отдельном виджете, использован SpacingBetweenSlices вместо Slice Thickness
|
|
|
+# Выводится номер среза и объем на каждом конкретном срезе
|
|
|
+
|
|
|
+
|
|
|
+
|
|
|
+class ImageLabel(QLabel):
|
|
|
+ def __init__(self, parent=None):
|
|
|
+ super().__init__(parent)
|
|
|
+ self.setMouseTracking(True)
|
|
|
+ self.image = QImage()
|
|
|
+ self.rois = {}
|
|
|
+ self.current_roi = []
|
|
|
+ self.drawing = False
|
|
|
+ self.current_color = QColor(Qt.red)
|
|
|
+ self.current_label = "ROI"
|
|
|
+ self.undo_stack = []
|
|
|
+ self.slice_index = 0
|
|
|
+ self.dicom_files = []
|
|
|
+ self.sag_pd_dicom_files = []
|
|
|
+ self.dataset = None
|
|
|
+ self.base_roi = None # новый общий ROI
|
|
|
+ self.spacing = (0, 0)
|
|
|
+ self.spacing_z = 0
|
|
|
+ self.volume_by_slice = {}
|
|
|
+
|
|
|
+
|
|
|
+ # Zoom parameters
|
|
|
+ self.zoom_factor = 1.0
|
|
|
+ self.zoom_step = 0.1
|
|
|
+ self.min_zoom = 0.1
|
|
|
+ self.max_zoom = 5.0
|
|
|
+
|
|
|
+ def load_dicom_series(self, folder_path):
|
|
|
+ # Load all DICOM files from the folder
|
|
|
+ self.dicom_files = [os.path.join(folder_path, f) for f in os.listdir(folder_path)
|
|
|
+ ] # if f.lower().endswith('.dcm')
|
|
|
+
|
|
|
+
|
|
|
+ if not self.dicom_files:
|
|
|
+ raise ValueError("No DICOM files found in the selected folder.")
|
|
|
+
|
|
|
+ for i in range(len(self.dicom_files)):
|
|
|
+ dataset = pydicom.dcmread(self.dicom_files[i])
|
|
|
+ # 'Sag PD'
|
|
|
+ if 'T1 Cube' in dataset['0008', '103e'][0:]:
|
|
|
+ self.sag_pd_dicom_files.append(self.dicom_files[i])
|
|
|
+
|
|
|
+
|
|
|
+
|
|
|
+ # Sort files by InstanceNumber or SliceLocation
|
|
|
+ self.sag_pd_dicom_files.sort(key=lambda f: int(pydicom.dcmread(f).InstanceNumber))
|
|
|
+
|
|
|
+ self.slice_index = len(self.sag_pd_dicom_files) // 2
|
|
|
+ self.rois.clear()
|
|
|
+ self.load_slice()
|
|
|
+
|
|
|
+ def load_slice(self):
|
|
|
+ if 0 <= self.slice_index < len(self.sag_pd_dicom_files):
|
|
|
+ self.dataset = pydicom.dcmread(self.sag_pd_dicom_files[self.slice_index])
|
|
|
+ self.spacing = self.dataset.PixelSpacing
|
|
|
+ self.spacing_z = self.dataset.SpacingBetweenSlices
|
|
|
+ #print(self.dicom_files[self.slice_index])
|
|
|
+ #print(self.dataset['0008', '103e'])
|
|
|
+ #if 'Sag PD frFSE FS' in self.dataset['0008', '103e'][0:]:
|
|
|
+ pixel_array = self.dataset.pixel_array
|
|
|
+ print(f'This file comprises {pixel_array.shape[0]} slices. File"s name is ', self.dataset['0008', '103e'],self.dicom_files[self.slice_index])
|
|
|
+ image_normalized = cv2.normalize(pixel_array, None, alpha=0, beta=255, norm_type=cv2.NORM_MINMAX)
|
|
|
+ image_normalized = image_normalized.astype(np.uint8)
|
|
|
+
|
|
|
+ # # Normalize pixel array to 8-bit
|
|
|
+ image = QImage(image_normalized.data, pixel_array.shape[1], pixel_array.shape[0],
|
|
|
+ QImage.Format_Grayscale8)
|
|
|
+ self.image = image
|
|
|
+ if self.base_roi is not None:
|
|
|
+ if self.slice_index not in self.rois:
|
|
|
+ self.rois[self.slice_index] = [self.base_roi.copy()]
|
|
|
+ self.setPixmap(QPixmap.fromImage(self.image))
|
|
|
+ self.update()
|
|
|
+ # else:
|
|
|
+ # pass
|
|
|
+
|
|
|
+
|
|
|
+ def next_slice(self):
|
|
|
+ if self.slice_index < len(self.sag_pd_dicom_files) - 1:
|
|
|
+ self.slice_index += 1
|
|
|
+ self.load_slice()
|
|
|
+
|
|
|
+
|
|
|
+ def previous_slice(self):
|
|
|
+ if self.slice_index > 0:
|
|
|
+ self.slice_index -= 1
|
|
|
+ self.load_slice()
|
|
|
+
|
|
|
+ def set_current_color(self, color):
|
|
|
+ self.current_color = color
|
|
|
+
|
|
|
+ def set_current_label(self, label):
|
|
|
+ self.current_label = label
|
|
|
+
|
|
|
+ def mousePressEvent(self, event):
|
|
|
+ if event.button() == Qt.LeftButton:
|
|
|
+ self.drawing = True
|
|
|
+ self.current_roi = [event.pos()]
|
|
|
+ self.update()
|
|
|
+
|
|
|
+ def mouseMoveEvent(self, event):
|
|
|
+ if self.drawing:
|
|
|
+ self.current_roi.append(event.pos())
|
|
|
+ self.update()
|
|
|
+
|
|
|
+ def mouseReleaseEvent(self, event):
|
|
|
+ if event.button() == Qt.LeftButton and self.drawing:
|
|
|
+ self.drawing = False
|
|
|
+ if len(self.current_roi) > 2:
|
|
|
+ if self.slice_index not in self.rois:
|
|
|
+ self.rois[self.slice_index] = []
|
|
|
+ roi = {
|
|
|
+ 'label': self.current_label,
|
|
|
+ 'color': self.current_color,
|
|
|
+ 'points': self.current_roi
|
|
|
+ }
|
|
|
+ # если ещё нет базового ROI — сохранить
|
|
|
+ if self.base_roi is None:
|
|
|
+ self.base_roi = roi.copy()
|
|
|
+ # добавить сразу ко всем срезам
|
|
|
+ for idx in range(len(self.sag_pd_dicom_files)):
|
|
|
+ self.rois.setdefault(idx, []).append(self.base_roi.copy())
|
|
|
+
|
|
|
+ # добавить на текущем срезе если изменили вручную
|
|
|
+ self.rois.setdefault(self.slice_index, []).append(roi)
|
|
|
+ self.undo_stack.append((self.slice_index, roi))
|
|
|
+ self.current_roi = []
|
|
|
+ self.update()
|
|
|
+
|
|
|
+
|
|
|
+ def paintEvent(self, event):
|
|
|
+ super().paintEvent(event)
|
|
|
+ if not self.image.isNull():
|
|
|
+ painter = QPainter(self)
|
|
|
+ # Apply zoom transformation
|
|
|
+ transform = painter.transform()
|
|
|
+ transform.scale(self.zoom_factor, self.zoom_factor)
|
|
|
+ painter.setTransform(transform)
|
|
|
+
|
|
|
+ painter.drawImage(self.rect(), self.image, self.image.rect())
|
|
|
+ pen = QPen(Qt.red, 2, Qt.SolidLine)
|
|
|
+ painter.setPen(pen)
|
|
|
+ if self.slice_index in self.rois:
|
|
|
+ for roi in self.rois[self.slice_index]:
|
|
|
+ pen.setColor(roi['color'])
|
|
|
+ painter.setPen(pen)
|
|
|
+ points = [QPoint(p.x(), p.y()) for p in roi['points']]
|
|
|
+ painter.drawPolygon(*points)
|
|
|
+ if self.current_roi:
|
|
|
+ pen.setColor(Qt.blue)
|
|
|
+ painter.setPen(pen)
|
|
|
+ points = [QPoint(p.x(), p.y()) for p in self.current_roi]
|
|
|
+ painter.drawPolyline(*points)
|
|
|
+ painter.end()
|
|
|
+
|
|
|
+ def undo(self):
|
|
|
+ #if self.undo_stack:
|
|
|
+ #slice_idx, last_roi = self.undo_stack.pop()
|
|
|
+ #if slice_idx in self.rois and last_roi in self.rois[slice_idx]:
|
|
|
+ #self.rois[slice_idx].remove(last_roi)
|
|
|
+ #if not self.rois[slice_idx]:
|
|
|
+ #del self.rois[slice_idx]
|
|
|
+ #self.update()
|
|
|
+
|
|
|
+
|
|
|
+ self.rois[self.slice_index] = []
|
|
|
+
|
|
|
+ self.update()
|
|
|
+
|
|
|
+ def save_rois(self, file_path):
|
|
|
+ roi_data = {}
|
|
|
+ for slice_idx, rois in self.rois.items():
|
|
|
+ roi_data[slice_idx] = []
|
|
|
+ for roi in rois:
|
|
|
+ roi_data[slice_idx].append({
|
|
|
+ 'label': roi['label'],
|
|
|
+ 'color': roi['color'].name(),
|
|
|
+ 'points': [(point.x(), point.y()) for point in roi['points']]
|
|
|
+ })
|
|
|
+ with open(file_path, 'w') as file:
|
|
|
+ json.dump(roi_data, file, indent=4)
|
|
|
+
|
|
|
+
|
|
|
+
|
|
|
+ def wheelEvent(self, event):
|
|
|
+ if event.modifiers() & Qt.ControlModifier:
|
|
|
+ # Zooming
|
|
|
+ angle = event.angleDelta().y()
|
|
|
+ factor = 1.1 if angle > 0 else 0.9
|
|
|
+ self.zoom_factor *= factor
|
|
|
+ self.update()
|
|
|
+ else:
|
|
|
+ # Slice navigation
|
|
|
+ angle = event.angleDelta().y()
|
|
|
+ if angle > 0:
|
|
|
+ self.previous_slice()
|
|
|
+ else:
|
|
|
+ self.next_slice()
|
|
|
+
|
|
|
+ def zoom_in(self):
|
|
|
+ if self.zoom_factor < self.max_zoom:
|
|
|
+ self.zoom_factor += self.zoom_step
|
|
|
+ self.update()
|
|
|
+
|
|
|
+ def zoom_out(self):
|
|
|
+ if self.zoom_factor > self.min_zoom:
|
|
|
+ self.zoom_factor -= self.zoom_step
|
|
|
+ self.update()
|
|
|
+
|
|
|
+
|
|
|
+class ROIDrawer(QMainWindow):
|
|
|
+ def __init__(self):
|
|
|
+ super().__init__()
|
|
|
+ self.initUI()
|
|
|
+ self.threshold_brightness = 0.5 # Default values
|
|
|
+ self.contours_thr = 0.3
|
|
|
+
|
|
|
+ def initUI(self):
|
|
|
+ self.setWindowTitle("KneeSeg")
|
|
|
+ screen_geometry = QApplication.desktop().availableGeometry()
|
|
|
+ screen_width = screen_geometry.width()
|
|
|
+ screen_height = screen_geometry.height()
|
|
|
+ # Set window to 70% of the screen size
|
|
|
+ self.resize(int(screen_width * 0.97), int(screen_height * 0.97))
|
|
|
+ self.setFixedSize(self.size())
|
|
|
+
|
|
|
+ # Central widget
|
|
|
+ central_widget = QWidget(self)
|
|
|
+ self.setCentralWidget(central_widget)
|
|
|
+
|
|
|
+ # Create threshold sliders
|
|
|
+ self.brightness_slider = QSlider(Qt.Horizontal)
|
|
|
+ self.brightness_slider.setMinimum(1) # 1 corresponds to 0.01
|
|
|
+ self.brightness_slider.setMaximum(99) # 99 corresponds to 0.99
|
|
|
+ self.brightness_slider.setValue(50) # Default to 0.50
|
|
|
+ self.brightness_slider.setTickInterval(1)
|
|
|
+ self.brightness_slider.valueChanged.connect(self.update_thresholds)
|
|
|
+
|
|
|
+ self.contour_slider = QSlider(Qt.Horizontal)
|
|
|
+ self.contour_slider.setMinimum(1)
|
|
|
+ self.contour_slider.setMaximum(99)
|
|
|
+ self.contour_slider.setValue(30) # Default to 0.30
|
|
|
+ self.contour_slider.setTickInterval(1)
|
|
|
+ self.contour_slider.valueChanged.connect(self.update_thresholds)
|
|
|
+
|
|
|
+ # Add sliders to the UI layout
|
|
|
+ threshold_layout = QVBoxLayout()
|
|
|
+ brightness_label = QLabel("Порог яркости")
|
|
|
+ brightness_label.setStyleSheet("font-size: 14px;font-weight: bold;")
|
|
|
+
|
|
|
+ contour_label = QLabel("Порог площали")
|
|
|
+ contour_label.setStyleSheet("font-size: 14px;font-weight: bold;")
|
|
|
+
|
|
|
+ threshold_layout.addWidget(brightness_label)
|
|
|
+ threshold_layout.addWidget(self.brightness_slider)
|
|
|
+ threshold_layout.addWidget(contour_label)
|
|
|
+ threshold_layout.addWidget(self.contour_slider)
|
|
|
+
|
|
|
+ # threshold_layout = QVBoxLayout()
|
|
|
+ # threshold_layout.addWidget(QLabel("Brightness Threshold"))
|
|
|
+ # threshold_layout.addWidget(self.brightness_slider)
|
|
|
+ # threshold_layout.addWidget(QLabel("Contour Threshold"))
|
|
|
+ # threshold_layout.addWidget(self.contour_slider)
|
|
|
+
|
|
|
+ # Layouts
|
|
|
+ main_layout = QVBoxLayout(central_widget)
|
|
|
+ main_layout.addLayout(threshold_layout)
|
|
|
+
|
|
|
+ # top_layout = QHBoxLayout()
|
|
|
+ # bottom_layout = QHBoxLayout()
|
|
|
+
|
|
|
+ # Splitter
|
|
|
+ splitter = QSplitter(Qt.Horizontal)
|
|
|
+
|
|
|
+ self.pixel_count_label = QLabel("Суммарный объем: 0")
|
|
|
+ self.pixel_count_label.setStyleSheet("font-size: 16pt; font-weight: bold;")
|
|
|
+ main_layout.addWidget(self.pixel_count_label)
|
|
|
+
|
|
|
+ # Image display with ROI drawing
|
|
|
+ self.image_label = ImageLabel(self)
|
|
|
+ self.image_label.setAlignment(Qt.AlignCenter)
|
|
|
+ image_frame = self.create_labeled_frame("Image", self.image_label)
|
|
|
+ splitter.addWidget(image_frame)
|
|
|
+
|
|
|
+ # Filtration result display
|
|
|
+ self.filtration_label = ImageLabel(self) #QLabel("Filtration results will be displayed here.")
|
|
|
+ self.filtration_label.setAlignment(Qt.AlignCenter)
|
|
|
+ filtration_frame = self.create_labeled_frame("Filtration", self.filtration_label)
|
|
|
+ splitter.addWidget(filtration_frame)
|
|
|
+
|
|
|
+ # Segmentation result display
|
|
|
+ self.segmentation_label = ImageLabel(self) # QLabel("Segmentation results will be displayed here.")
|
|
|
+ self.segmentation_label.setAlignment(Qt.AlignCenter)
|
|
|
+ # segmentation_frame = self.create_labeled_frame("Image Segmentation ", self.segmentation_label)
|
|
|
+ segmentation_frame = self.create_labeled_frame("Segmentation", self.segmentation_label)
|
|
|
+ splitter.addWidget(segmentation_frame)
|
|
|
+
|
|
|
+ #Enable Scaled Contents for Each
|
|
|
+ self.image_label.setScaledContents(True)
|
|
|
+ self.filtration_label.setScaledContents(True)
|
|
|
+ self.segmentation_label.setScaledContents(True)
|
|
|
+
|
|
|
+ # # Set size policies to allow resizing
|
|
|
+ self.image_label.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
|
|
|
+ self.filtration_label.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
|
|
|
+ self.segmentation_label.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
|
|
|
+ #
|
|
|
+ # # Set initial sizes for splitter sections to be equal
|
|
|
+ splitter.setSizes([1, 1, 1])
|
|
|
+ splitter.setStretchFactor(0, 1) # First widget
|
|
|
+ splitter.setStretchFactor(1, 1) # Second widget
|
|
|
+ splitter.setStretchFactor(2, 1) # Third widget
|
|
|
+
|
|
|
+ # Buttons layout
|
|
|
+ button_layout = QHBoxLayout()
|
|
|
+
|
|
|
+ # Add splitter to the main layout
|
|
|
+ main_layout.addWidget(splitter)
|
|
|
+ main_layout.addLayout(button_layout)
|
|
|
+
|
|
|
+ # Buttons
|
|
|
+ load_button = QPushButton('Load DICOM ', self)
|
|
|
+ load_button.setFixedSize(150, 50)
|
|
|
+ load_button.setStyleSheet('QPushButton { font-size: 20px;}')
|
|
|
+ load_button.clicked.connect(self.load_dicom_series)
|
|
|
+ load_button.clicked.connect(lambda: (self.apply_segmentation(), self.apply_filtration()))
|
|
|
+ button_layout.addWidget(load_button)
|
|
|
+
|
|
|
+ color_button = QPushButton('Select Color', self)
|
|
|
+ color_button.setFixedSize(150, 50)
|
|
|
+ color_button.setStyleSheet('QPushButton { font-size: 20px; }')
|
|
|
+ color_button.clicked.connect(self.select_color)
|
|
|
+ button_layout.addWidget(color_button)
|
|
|
+
|
|
|
+ label_button = QPushButton('Set Label', self)
|
|
|
+ label_button.setFixedSize(100, 50)
|
|
|
+ label_button.setStyleSheet('QPushButton { font-size: 20px; }')
|
|
|
+ label_button.clicked.connect(self.set_label)
|
|
|
+ button_layout.addWidget(label_button)
|
|
|
+
|
|
|
+ undo_button = QPushButton('Undo', self)
|
|
|
+ undo_button.setFixedSize(100, 50)
|
|
|
+ undo_button.setStyleSheet('QPushButton { font-size: 20px; }')
|
|
|
+ undo_button.clicked.connect(self.image_label.undo)
|
|
|
+ button_layout.addWidget(undo_button)
|
|
|
+
|
|
|
+ prev_button = QPushButton('>>', self) # Previous Slice
|
|
|
+ prev_button.setFixedSize(50, 50)
|
|
|
+ prev_button.setStyleSheet('QPushButton { font-size: 20px; }')
|
|
|
+ prev_button.clicked.connect(self.image_label.previous_slice)
|
|
|
+ prev_button.clicked.connect(lambda: (self.apply_segmentation(), self.apply_filtration()))
|
|
|
+ button_layout.addWidget(prev_button)
|
|
|
+
|
|
|
+ next_button = QPushButton('<<', self) # Next Slice
|
|
|
+ next_button.setFixedSize(50, 50)
|
|
|
+ next_button.setStyleSheet('QPushButton { font-size: 20px; }')
|
|
|
+ next_button.clicked.connect(self.image_label.next_slice)
|
|
|
+ next_button.clicked.connect(lambda: (self.apply_segmentation(), self.apply_filtration()))
|
|
|
+ button_layout.addWidget(next_button)
|
|
|
+
|
|
|
+ # Filtration and Segmentation Buttons
|
|
|
+ # filtration_button = QPushButton(' Filtration', self)
|
|
|
+ # filtration_button.setFixedSize(150, 50)
|
|
|
+ # filtration_button.setStyleSheet('QPushButton { font-size: 20px; }')
|
|
|
+ # filtration_button.clicked.connect(self.apply_filtration)
|
|
|
+ # button_layout.addWidget(filtration_button)
|
|
|
+
|
|
|
+ segmentation_button = QPushButton('Segmentation', self)
|
|
|
+ segmentation_button.setFixedSize(150, 50)
|
|
|
+ segmentation_button.setStyleSheet('QPushButton { font-size: 20px; }')
|
|
|
+ segmentation_button.clicked.connect(lambda: (self.apply_segmentation(), self.apply_filtration()))
|
|
|
+ button_layout.addWidget(segmentation_button)
|
|
|
+
|
|
|
+ save_button = QPushButton('Save ROIs', self)
|
|
|
+ save_button.setFixedSize(150, 50)
|
|
|
+ save_button.setStyleSheet('QPushButton { font-size: 20px; }')
|
|
|
+ save_button.clicked.connect(self.save_rois)
|
|
|
+ button_layout.addWidget(save_button)
|
|
|
+
|
|
|
+ button_layout.addStretch(1) # Push buttons to the top
|
|
|
+
|
|
|
+ def update_thresholds(self):
|
|
|
+ """Update segmentation thresholds based on slider values."""
|
|
|
+ self.threshold_brightness = self.brightness_slider.value() / 100
|
|
|
+ self.contours_thr = self.contour_slider.value() / 100
|
|
|
+
|
|
|
+ def create_labeled_frame(self, title, widget):
|
|
|
+ frame = QFrame()
|
|
|
+ layout = QVBoxLayout()
|
|
|
+ label = QLabel(f"<b>{title}</b>")
|
|
|
+ label.setAlignment(Qt.AlignCenter)
|
|
|
+ layout.addWidget(label)
|
|
|
+ layout.addWidget(widget)
|
|
|
+ frame.setLayout(layout)
|
|
|
+ return frame
|
|
|
+ def load_dicom_series(self):
|
|
|
+ options = QFileDialog.Options()
|
|
|
+ folder_path = QFileDialog.getExistingDirectory(
|
|
|
+ self, "Select DICOM Series Folder", options=options)
|
|
|
+ if folder_path:
|
|
|
+ try:
|
|
|
+ self.image_label.load_dicom_series(folder_path)
|
|
|
+ except ValueError as e:
|
|
|
+ QMessageBox.critical(self, "Error", str(e))
|
|
|
+
|
|
|
+ def select_color(self):
|
|
|
+ color = QColorDialog.getColor()
|
|
|
+ if color.isValid():
|
|
|
+ self.image_label.set_current_color(color)
|
|
|
+
|
|
|
+ def set_label(self):
|
|
|
+ label, ok = QInputDialog.getText(self, 'Set ROI Label', 'Enter label for ROI:')
|
|
|
+ if ok and label:
|
|
|
+ self.image_label.set_current_label(label)
|
|
|
+
|
|
|
+ def save_rois(self):
|
|
|
+ options = QFileDialog.Options()
|
|
|
+ file_path, _ = QFileDialog.getSaveFileName(
|
|
|
+ self, "Save ROIs", "", "JSON Files (*.json);;All Files (*)", options=options)
|
|
|
+ if file_path:
|
|
|
+ self.image_label.save_rois(file_path)
|
|
|
+
|
|
|
+ def wheelEvent(self, event):
|
|
|
+
|
|
|
+ # Slice navigation
|
|
|
+ angle = event.angleDelta().y()
|
|
|
+ if angle > 0:
|
|
|
+ self.image_label.previous_slice()
|
|
|
+ self.apply_segmentation(), self.apply_filtration()
|
|
|
+ else:
|
|
|
+ self.image_label.next_slice()
|
|
|
+ self.apply_segmentation(), self.apply_filtration()
|
|
|
+
|
|
|
+
|
|
|
+ def apply_filtration(self):
|
|
|
+ if self.image_label.image.isNull():
|
|
|
+ QMessageBox.warning(self, "Warning", "No image loaded.")
|
|
|
+ return
|
|
|
+
|
|
|
+ # Convert QImage to numpy array
|
|
|
+ image = self.image_label.image
|
|
|
+ width = image.width()
|
|
|
+ height = image.height()
|
|
|
+ ptr = image.bits()
|
|
|
+ ptr.setsize(image.byteCount())
|
|
|
+ arr = np.array(ptr).reshape(height, width, 1) # Assuming grayscale
|
|
|
+
|
|
|
+ mask = np.zeros((height, width, 1), dtype=np.uint8)
|
|
|
+ rois = self.image_label.rois.get(self.image_label.slice_index, [])
|
|
|
+ # print(rois)
|
|
|
+ for roi in rois:
|
|
|
+ pts = np.array([[p.x(), p.y()] for p in roi['points']])
|
|
|
+ # print(pts)
|
|
|
+ cv2.fillPoly(mask, [pts], 255)
|
|
|
+
|
|
|
+ masked_arr = arr.copy()
|
|
|
+ masked_arr[mask != 255] = 0
|
|
|
+
|
|
|
+ thr = self.threshold_brightness * masked_arr.max()
|
|
|
+ seg = np.zeros_like(arr)
|
|
|
+ seg[(mask == 255) & (arr >= thr)] = 255
|
|
|
+
|
|
|
+ contours, _ = cv2.findContours(seg, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
|
|
|
+
|
|
|
+ # Convert grayscale image to BGR for color overlay
|
|
|
+ color_image = cv2.cvtColor(arr, cv2.COLOR_GRAY2BGR)
|
|
|
+
|
|
|
+ # Draw contours on the color image
|
|
|
+ cv2.drawContours(color_image, contours, -1, (255, 0, 0), 2) # Red color, thickness 2
|
|
|
+
|
|
|
+ # Convert back to QImage
|
|
|
+ q_image = QImage(color_image.data, color_image.shape[1], color_image.shape[0], QImage.Format_RGB888)
|
|
|
+ self.filtration_label.setPixmap(QPixmap.fromImage(q_image))
|
|
|
+
|
|
|
+
|
|
|
+
|
|
|
+ def apply_segmentation(self):
|
|
|
+ if self.image_label.image.isNull():
|
|
|
+ QMessageBox.warning(self, "Warning", "No image loaded.")
|
|
|
+ return
|
|
|
+ image = self.image_label.image
|
|
|
+ spacing = self.image_label.spacing
|
|
|
+ spacing_z = self.image_label.spacing_z
|
|
|
+ slice_indx = self.image_label.slice_index
|
|
|
+ vol_by_slice = self.image_label.volume_by_slice
|
|
|
+ width, height = image.width(), image.height()
|
|
|
+ ptr = image.bits()
|
|
|
+ ptr.setsize(image.byteCount())
|
|
|
+ arr = np.array(ptr).reshape(height, width, 1)#[:, :, 0]
|
|
|
+
|
|
|
+ mask = np.zeros((height, width, 1), dtype=np.uint8)
|
|
|
+ #print(type(mask))
|
|
|
+ rois = self.image_label.rois.get(self.image_label.slice_index, [])
|
|
|
+ #print(rois)
|
|
|
+ for roi in rois:
|
|
|
+ pts = np.array([[p.x(), p.y()] for p in roi['points']])
|
|
|
+ #print(pts)
|
|
|
+ cv2.fillPoly(mask, [pts], 255)
|
|
|
+
|
|
|
+ masked_arr = arr.copy()
|
|
|
+ masked_arr[mask != 255] = 0
|
|
|
+
|
|
|
+ thr = self.threshold_brightness * masked_arr.max()
|
|
|
+ seg = np.zeros_like(arr)
|
|
|
+ seg[(mask == 255) & (arr >= thr)] = 255
|
|
|
+ #pixel_count = int(np.count_nonzero(seg))
|
|
|
+
|
|
|
+ contours, _ = cv2.findContours(seg, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
|
|
|
+ area_thr = self.contours_thr * max((cv2.contourArea(c) for c in contours), default=0)
|
|
|
+ filtered = [c for c in contours if cv2.contourArea(c) > area_thr]
|
|
|
+
|
|
|
+ pixel_count = 0
|
|
|
+ for c in contours:
|
|
|
+ if cv2.contourArea(c) > area_thr:
|
|
|
+ pixel_count += cv2.contourArea(c)
|
|
|
+
|
|
|
+ voxel_vol = float(spacing[0]) * float(spacing[1]) * float(spacing_z) # мм³
|
|
|
+ volume_ml = pixel_count * voxel_vol / 1000.0
|
|
|
+
|
|
|
+ color_image = cv2.cvtColor(arr, cv2.COLOR_GRAY2BGR)
|
|
|
+ cv2.drawContours(color_image, filtered, -1, (0, 255, 255), 2)
|
|
|
+ vol_by_slice[slice_indx] = volume_ml
|
|
|
+ sum_volume = sum(vol_by_slice.values())
|
|
|
+
|
|
|
+ cv2.putText(color_image,
|
|
|
+ f"Slice number: {slice_indx} Volume (ml): {volume_ml:.3f}",
|
|
|
+ (10, 20), cv2.FONT_HERSHEY_SIMPLEX,
|
|
|
+ 0.7, (0, 255, 255), 1)
|
|
|
+ self.pixel_count_label.setText(f"Суммарный объем (мл): {sum_volume:.2f}")
|
|
|
+
|
|
|
+ # Convert back to QImage
|
|
|
+ q_image = QImage(color_image.data, color_image.shape[1], color_image.shape[0], QImage.Format_RGB888)
|
|
|
+ self.segmentation_label.setPixmap(QPixmap.fromImage(q_image))
|
|
|
+
|
|
|
+
|
|
|
+
|
|
|
+if __name__ == '__main__':
|
|
|
+ app = QApplication(sys.argv)
|
|
|
+ drawer = ROIDrawer()
|
|
|
+ drawer.show()
|
|
|
+ sys.exit(app.exec_())
|
spacexerq