- 优化dcm支持

Author: yatengLG

ISAT/annotation.py

@@ -6,56 +6,10 @@
 import numpy as np
 from json import load, dump
 from typing import List, Union
-import pydicom
+from ISAT.utils.dicom import load_dcm_as_image
 
 __all__ = ['Object', 'Annotation']
 
-
-def get_windowed_image(ds):
-    # Apply Rescale Slope and Rescale Intercept if they exist
-    pixel_array = ds.pixel_array.astype(float)
-    rescale_slope = ds.get("RescaleSlope", 1)
-    rescale_intercept = ds.get("RescaleIntercept", 0)
-    if rescale_slope != 1 or rescale_intercept != 0:
-        pixel_array = pixel_array * rescale_slope + rescale_intercept
-
-    # Check for windowing information in the DICOM metadata
-    window_center = ds.get("WindowCenter", None)
-    window_width = ds.get("WindowWidth", None)
-
-    if window_center is None or window_width is None:
-        # If no windowing info, use the full dynamic range
-        window_min = pixel_array.min()
-        window_max = pixel_array.max()
-    else:
-        # Handle possible multi-valued tags by taking the first value
-        if isinstance(window_center, pydicom.multival.MultiValue):
-            window_center = window_center[0]
-        if isinstance(window_width, pydicom.multival.MultiValue):
-            window_width = window_width[0]
-
-        window_min = window_center - window_width / 2
-        window_max = window_center + window_width / 2
-
-    # Apply windowing
-    pixel_array = np.clip(pixel_array, window_min, window_max)
-
-    # Normalize to 0-255
-    if window_max > window_min:
-        pixel_array = ((pixel_array - window_min) / (window_max - window_min)) * 255.0
-    else:  # Handle case where all pixels are the same
-        pixel_array.fill(128)
-
-    # Handle Photometric Interpretation
-    photometric_interpretation = ds.get("PhotometricInterpretation", "MONOCHROME2")
-    if photometric_interpretation == "MONOCHROME1":
-        pixel_array = 255.0 - pixel_array
-
-    # Convert to 8-bit unsigned integer
-    image_8bit = pixel_array.astype(np.uint8)
-
-    return image_8bit
-
 class Object:
     r"""A class to represent an annotation object.
 
@@ -104,48 +58,23 @@ def __init__(self, image_path:str, label_path:str):
         self.img_name = img_name
         self.label_path = label_path
         self.note = ''
-        self.image_path = image_path
-        self._img_data = None
 
-        # Defer image loading to get_img_data()
-        self.width = 0
-        self.height = 0
-        self.depth = 0
+        if image_path.lower().endswith('.dcm'):
+            image = np.array(load_dcm_as_image(image_path))
+        else:
+            image = np.array(Image.open(image_path))
+        if image.ndim == 3:
+            self.height, self.width, self.depth = image.shape
+        elif image.ndim == 2:
+            self.height, self.width = image.shape
+            self.depth = 0
+        else:
+            self.height, self.width, self.depth = image.shape[:, :3]
+            print('Warning: Except image has 2 or 3 ndim, but get {}.'.format(image.ndim))
+        del image
 
         self.objects:List[Object, ] = []
 
-    def get_img_data(self, to_rgb=False):
-        if self._img_data is None:
-            if self.image_path.lower().endswith('.dcm'):
-                ds = pydicom.dcmread(self.image_path)
-                image_data = get_windowed_image(ds)
-                self._img_data = np.stack([image_data, image_data, image_data], axis=-1)
-            else:
-                self._img_data = Image.open(self.image_path)
-
-        if self.width == 0 or self.height == 0:
-            if isinstance(self._img_data, np.ndarray):
-                image = self._img_data
-                if image.ndim == 3:
-                    self.height, self.width, self.depth = image.shape
-                elif image.ndim == 2:
-                    self.height, self.width = image.shape
-                    self.depth = 1
-            else: # PIL Image
-                self.width, self.height = self._img_data.size
-                self.depth = len(self._img_data.getbands())
-
-        if to_rgb:
-            if isinstance(self._img_data, np.ndarray):
-                return self._img_data # DICOM data is already RGB numpy array
-            else: # PIL Image
-                return np.array(self._img_data.convert('RGB'))
-        else:
-            if isinstance(self._img_data, np.ndarray):
-                 return self._img_data
-            else: # PIL Image
-                return np.array(self._img_data)
-
     def load_annotation(self):
         r"""
         Load annotation from self.label_path

ISAT/widgets/canvas.py

@@ -4,11 +4,11 @@
 from PyQt5 import QtWidgets, QtGui, QtCore
 from ISAT.widgets.polygon import Polygon, Vertex, PromptPoint, Line, Rect
 from ISAT.configs import STATUSMode, DRAWMode, CONTOURMode
+from ISAT.utils.dicom import load_dcm_as_image
 import numpy as np
 import cv2
 import time  # 拖动鼠标描点
 import shapely
-import pydicom
 
 
 class AnnotationScene(QtWidgets.QGraphicsScene):
@@ -90,8 +90,13 @@ def load_image(self, image_path: str):
         if self.mainwindow.use_segment_anything:
             self.mainwindow.segany.reset_image()
 
-        self.image_data = self.mainwindow.current_label.get_img_data(to_rgb=True)
-
+        if image_path.lower().endswith('.dcm'):
+            image = load_dcm_as_image(image_path)
+        else:
+            image = Image.open(image_path)
+        if self.mainwindow.can_be_annotated:
+            image = image.convert('RGB')
+        self.image_data = np.array(image)
         self.image_item = QtWidgets.QGraphicsPixmapItem()
         self.image_item.setZValue(0)
         self.addItem(self.image_item)
@@ -101,9 +106,10 @@ def load_image(self, image_path: str):
 
         height, width, channel = self.image_data.shape
         bytes_per_line = channel * width
-        q_image = QtGui.QImage(self.image_data.data, width, height, bytes_per_line,
+        q_image = QtGui.QImage(self.image_data.tobytes(), width, height, bytes_per_line,
                                QtGui.QImage.Format_RGB888)
         self.image_item.setPixmap(QtGui.QPixmap.fromImage(q_image))
+        # self.image_item.setPixmap(QtGui.QPixmap(image_path))
         self.setSceneRect(self.image_item.boundingRect())
         self.change_mode_to_view()
 
@@ -599,7 +605,7 @@ def copy_item(self):
                     x, y = point.x(), point.y()
                     self.current_graph.addPoint(QtCore.QPointF(x, y))
 
-                self.current_graph.set_drawed(item.category, item.group, item.iscrowd, item.note, item.color, item.zValue())
+                self.current_graph.set_drawed(item.category, item.group, item.iscrowd, item.note, item.color, int(item.zValue()))
                 self.mainwindow.polygons.insert(index, self.current_graph)
                 self.mainwindow.annos_dock_widget.listwidget_add_polygon(self.current_graph)
                 item.setSelected(False)
@@ -1087,7 +1093,7 @@ def update_mask(self):
         else:
             mask_image = np.zeros(self.image_data.shape, dtype=np.uint8)
             mask_image = cv2.addWeighted(self.image_data, 1, mask_image, 0, 0)
-        mask_image = QtGui.QImage(mask_image[:], mask_image.shape[1], mask_image.shape[0], mask_image.shape[1] * 3,
+        mask_image = QtGui.QImage(mask_image.tobytes(), mask_image.shape[1], mask_image.shape[0], mask_image.shape[1] * 3,
                                   QtGui.QImage.Format_RGB888)
         mask_pixmap = QtGui.QPixmap(mask_image)
         if self.mask_item is not None:

ISAT/widgets/mainwindow.py

@@ -25,6 +25,7 @@
 from ISAT.configs import STATUSMode, MAPMode, load_config, save_config, CONFIG_FILE, SOFTWARE_CONFIG_FILE, CHECKPOINT_PATH, ISAT_ROOT, CONTOURMode
 from ISAT.annotation import Object, Annotation
 from ISAT.widgets.polygon import Polygon, PromptPoint
+from ISAT.utils.dicom import load_dcm_as_image
 import os
 from PIL import Image
 import functools
@@ -39,8 +40,6 @@
 from skimage.draw.draw import polygon
 import requests
 import orjson
-import pydicom
-from ISAT.annotation import get_windowed_image
 
 
 class QtBoxStyleProgressBar(QtWidgets.QProgressBar):
@@ -209,7 +208,10 @@ def run(self):
 
                     image_path = os.path.join(self.mainwindow.image_root, self.mainwindow.files_list[index])
 
-                    image_data = self.mainwindow.current_label.get_img_data(to_rgb=True)
+                    if image_path.lower().endswith('.dcm'):
+                        image_data = np.array(load_dcm_as_image(image_path).convert('RGB'))
+                    else:
+                        image_data = np.array(Image.open(image_path).convert('RGB'))
                     try:
                         features, original_size, input_size = self.sam_encoder(image_data)
                     except Exception as e:
@@ -1182,31 +1184,16 @@ def show_image(self, index: int, zoomfit: bool=True):
             self.plugin_manager_dialog.trigger_before_image_open(file_path)
 
             if file_path.lower().endswith('.dcm'):
-                self.can_be_annotated = True
+                image_data = load_dcm_as_image(file_path)
             else:
-                try:
-                    image = Image.open(file_path)
-                    png_palette = image.getpalette()
-                    if png_palette is not None and file_path.endswith('.png'):
-                        self.statusbar.showMessage('This image might be a label image in VOC format.')
-                        self.can_be_annotated = False
-                    else:
-                        self.can_be_annotated = True
-                except Exception as e:
-                    # stausbar show error
-                    self.statusbar.showMessage(str(e), 5000)
-                    return
+                image_data = Image.open(file_path)
 
-            # load label
-            if self.can_be_annotated:
-                self.current_group = 1
-                _, name = os.path.split(file_path)
-                label_path = os.path.join(self.label_root, '.'.join(name.split('.')[:-1]) + '.json')
-                self.current_label = Annotation(file_path, label_path)
-                # 载入数据
-                self.current_label.load_annotation()
-                # get image data and info
-                self.current_label.get_img_data()
+            png_palette = image_data.getpalette()
+            if png_palette is not None and file_path.endswith('.png'):
+                self.statusbar.showMessage('This image might be a label image in VOC format.')
+                self.can_be_annotated = False
+            else:
+                self.can_be_annotated = True
 
             if self.can_be_annotated:
                 self.actionPolygon.setEnabled(True)
@@ -1231,22 +1218,28 @@ def show_image(self, index: int, zoomfit: bool=True):
                 self.view.zoomfit()
 
             # 判断图像是否旋转
-            if not file_path.lower().endswith('.dcm'):
-                image_data = Image.open(file_path)
-                exif_info = image_data.getexif()
-                if exif_info and exif_info.get(274, 1) != 1:
-                    warning_info = '这幅图像包含EXIF元数据，且图像的方向已被旋转.\n建议去除EXIF信息后再进行标注\n你可以使用[菜单栏]-[工具]-[处理exif标签]功能处理图像的旋转问题。'\
-                        if self.cfg['software']['language'] == 'zh' \
-                        else 'This image has EXIF metadata, and the image orientation is rotated.\nSuggest labeling after removing the EXIF metadata.\nYou can use the function of [Process EXIF tag] in [Tools] in [Menu bar] to deal with the problem of images.'
-                    QtWidgets.QMessageBox.warning(self, 'Warning', warning_info, QtWidgets.QMessageBox.Ok)
+            exif_info = image_data.getexif()
+            if exif_info and exif_info.get(274, 1) != 1:
+                warning_info = '这幅图像包含EXIF元数据，且图像的方向已被旋转.\n建议去除EXIF信息后再进行标注\n你可以使用[菜单栏]-[工具]-[处理exif标签]功能处理图像的旋转问题。'\
+                    if self.cfg['software']['language'] == 'zh' \
+                    else 'This image has EXIF metadata, and the image orientation is rotated.\nSuggest labeling after removing the EXIF metadata.\nYou can use the function of [Process EXIF tag] in [Tools] in [Menu bar] to deal with the problem of images.'
+                QtWidgets.QMessageBox.warning(self, 'Warning', warning_info, QtWidgets.QMessageBox.Ok)
 
             if self.use_segment_anything and self.can_be_annotated:
                 self.segany.reset_image()
                 self.seganythread.index = index
                 self.seganythread.start()
                 self.SeganyEnabled()
 
+            # load label
             if self.can_be_annotated:
+                self.current_group = 1
+                _, name = os.path.split(file_path)
+                label_path = os.path.join(self.label_root, '.'.join(name.split('.')[:-1]) + '.json')
+                self.current_label = Annotation(file_path, label_path)
+                # 载入数据
+                self.current_label.load_annotation()
+
                 for object in self.current_label.objects:
                     try:
                         group = int(object.group)

requirements.txt

@@ -16,4 +16,4 @@ fuzzywuzzy
 python-Levenshtein
 iopath
 orjson
-pydicom
+pydicom