coralnet-toolbox 0.0.72__py2.py3-none-any.whl → 0.0.74__py2.py3-none-any.whl

coralnet_toolbox/Annotations/QtAnnotation.py

@@ -4,8 +4,8 @@ import warnings
 
 import numpy as np
 
-from PyQt5.QtCore import Qt, pyqtSignal, QObject, QPointF, QTimer, pyqtProperty
 from PyQt5.QtGui import QColor, QPolygonF, QPen, QBrush
+from PyQt5.QtCore import Qt, pyqtSignal, QObject, QPointF, QTimer, pyqtProperty
 from PyQt5.QtWidgets import (QMessageBox, QGraphicsEllipseItem, QGraphicsRectItem,
                              QGraphicsPolygonItem, QGraphicsScene, QGraphicsItemGroup)
 
@@ -54,12 +54,11 @@ class Annotation(QObject):
         self.annotation_size = None
         self.tolerance = 0.1  # Default detail level for simplification/densification
 
-        # Attributes to store the graphics items for center/centroid, bounding box, and polygon
+        # Attributes to store the graphics items for center/centroid and bounding box
         self.center_graphics_item = None
         self.bounding_box_graphics_item = None
-        self.polygon_graphics_item = None
 
-        # New: group for all graphics items
+        # Group for all graphics items
         self.graphics_item_group = None
         
         # Animation properties
@@ -87,6 +86,10 @@ class Annotation(QObject):
     def get_polygon(self):
         """Get the polygon representation of this annotation."""
         raise NotImplementedError("Subclasses must implement this method.")
+    
+    def get_painter_path(self):
+        """Get the QPainterPath representation of this annotation."""
+        raise NotImplementedError("Subclasses must implement this method.")
 
     def get_bounding_box_top_left(self):
         """Get the top-left corner of the annotation's bounding box."""
@@ -125,6 +128,11 @@ class Annotation(QObject):
     def cut(cls, annotations: list, cutting_points: list):
         """Cut multiple annotations using specified cutting points."""
         raise NotImplementedError("Subclasses must implement this method.")
+    
+    @classmethod
+    def subtract(cls, base_annotation, cutter_annotations: list):
+        """Subtract cutter annotations from a base annotation."""
+        raise NotImplementedError("Subclasses must implement this method.")
 
     def show_warning_message(self):
         """Display a warning message about removing machine suggestions when altering an annotation."""
@@ -171,45 +179,35 @@ class Annotation(QObject):
         self.graphics_item = None
         self.center_graphics_item = None
         self.bounding_box_graphics_item = None
-        self.polygon_graphics_item = None
 
     def create_graphics_item(self, scene: QGraphicsScene):
         """Create all graphics items for the annotation and add them to the scene as a group."""
         # Remove old group if it exists
         if self.graphics_item_group and self.graphics_item_group.scene():
             self.graphics_item_group.scene().removeItem(self.graphics_item_group)
-            # Clear references to deleted items
             self.center_graphics_item = None
             self.bounding_box_graphics_item = None
-            self.polygon_graphics_item = None
         self.graphics_item_group = QGraphicsItemGroup()
 
-        # Create the main graphics item based on the polygon
-        polygon = self.get_polygon()
-        self.graphics_item = QGraphicsPolygonItem(polygon)
-        
-        # Style the main graphics item with color and pen
-        color = QColor(self.label.color)
-        color.setAlpha(self.transparency)
-        self.graphics_item.setBrush(QBrush(color))
-        
-        # Use the consolidated pen creation method
-        self.graphics_item.setPen(self._create_pen(color))
-        
-        self.graphics_item.setData(0, self.id)
-        self.graphics_item_group.addToGroup(self.graphics_item)
+        # The subclass has already created self.graphics_item.
+        # This parent method is now only responsible for styling and grouping it.
+        if self.graphics_item:
+            color = QColor(self.label.color)
+            color.setAlpha(self.transparency)
+            self.graphics_item.setBrush(QBrush(color))
+            
+            self.graphics_item.setPen(self._create_pen(color))
+            
+            self.graphics_item.setData(0, self.id)
+            self.graphics_item_group.addToGroup(self.graphics_item)
 
-        # Create the center graphics item
+        # Create and group the helper graphics (center, bbox, etc.)
         self.create_center_graphics_item(self.center_xy, scene, add_to_group=True)
-        # Create the bounding box graphics item
         self.create_bounding_box_graphics_item(self.get_bounding_box_top_left(),
                                                self.get_bounding_box_bottom_right(),
                                                scene, add_to_group=True)
-        # Create the polygon graphics item
-        points = [polygon.at(i) for i in range(polygon.count())]
-        self.create_polygon_graphics_item(points, scene, add_to_group=True)
-
-        # Add the group to the scene
+        
+        # Add the final group to the scene
         scene.addItem(self.graphics_item_group)
         
     def set_visibility(self, visible):
@@ -289,8 +287,6 @@ class Annotation(QObject):
             self.center_graphics_item.setPen(pen)
         if self.bounding_box_graphics_item:
             self.bounding_box_graphics_item.setPen(pen)
-        if self.polygon_graphics_item:
-            self.polygon_graphics_item.setPen(pen)
 
     def create_center_graphics_item(self, center_xy, scene, add_to_group=False):
         """Create a graphical item representing the annotation's center point."""
@@ -345,32 +341,6 @@ class Annotation(QObject):
             self.graphics_item_group.addToGroup(self.bounding_box_graphics_item)
         else:
             scene.addItem(self.bounding_box_graphics_item)
-    
-    def create_polygon_graphics_item(self, points, scene, add_to_group=False):
-        """Create a graphical item representing the annotation's polygon outline."""
-        try:
-            has_scene = self.polygon_graphics_item and self.polygon_graphics_item.scene()
-        except RuntimeError:
-            self.polygon_graphics_item = None
-            has_scene = False
-    
-        if has_scene:
-            self.polygon_graphics_item.scene().removeItem(self.polygon_graphics_item)
-    
-        color = QColor(self.label.color)
-        color.setAlpha(self.transparency)
-    
-        polygon = QPolygonF(points)
-        self.polygon_graphics_item = QGraphicsPolygonItem(polygon)
-        self.polygon_graphics_item.setBrush(color)
-    
-        # Use the consolidated pen creation method
-        self.polygon_graphics_item.setPen(self._create_pen(color))
-    
-        if add_to_group and self.graphics_item_group:
-            self.graphics_item_group.addToGroup(self.polygon_graphics_item)
-        else:
-            scene.addItem(self.polygon_graphics_item)
 
     def get_center_xy(self):
         """Get the center coordinates of the annotation."""
@@ -405,9 +375,11 @@ class Annotation(QObject):
         try:
             if self.graphics_item_group and self.graphics_item_group.scene():
                 scene = self.graphics_item_group.scene()
+                
         except RuntimeError:
             self.graphics_item_group = None
             scene = None
+            
         if scene is not None:
             # Remove the old group from the scene
             scene.removeItem(self.graphics_item_group)
@@ -440,19 +412,6 @@ class Annotation(QObject):
             # Use the consolidated pen creation method
             self.bounding_box_graphics_item.setPen(self._create_pen(color))
     
-    def update_polygon_graphics_item(self, points):
-        """Update the shape and appearance of the polygon graphics item."""
-        if self.polygon_graphics_item:
-            color = QColor(self.label.color)
-            color.setAlpha(self.transparency)
-    
-            polygon = QPolygonF(points)
-            self.polygon_graphics_item.setPolygon(polygon)
-            self.polygon_graphics_item.setBrush(color)
-    
-            # Use the consolidated pen creation method
-            self.polygon_graphics_item.setPen(self._create_pen(color))
-    
     def update_transparency(self, transparency: int):
         """Update the transparency value of the annotation's graphical representation."""
         if self.transparency != transparency:

coralnet_toolbox/Annotations/QtMaskAnnotation.py

@@ -0,0 +1,408 @@
+import warnings
+
+import zlib
+import base64
+import rasterio
+
+import numpy as np
+
+from scipy.ndimage import label as ndimage_label
+from skimage.measure import find_contours
+
+from PyQt5.QtCore import Qt, QPointF, QRectF, QPolygonF
+from PyQt5.QtWidgets import QGraphicsScene, QGraphicsPixmapItem
+from PyQt5.QtGui import QPixmap, QColor, QImage, QPainter, QBrush
+
+from coralnet_toolbox.Annotations.QtAnnotation import Annotation
+from coralnet_toolbox.Annotations.QtPolygonAnnotation import PolygonAnnotation
+
+warnings.filterwarnings("ignore", category=DeprecationWarning)
+
+
+# ----------------------------------------------------------------------------------------------------------------------
+# Helper Functions for Serialization
+# ----------------------------------------------------------------------------------------------------------------------
+
+
+def rle_encode(mask):
+    """
+    Encodes a 2D numpy array using Run-Length Encoding.
+    Returns a compressed string representation.
+    """
+    pixels = mask.flatten()
+    pixels = np.append(pixels, -1)  # Append a sentinel value
+    runs = np.where(pixels[1:] != pixels[:-1])[0] + 1
+    runs[1:] = runs[1:] - runs[:-1]
+    values = pixels[np.cumsum(np.append(0, runs[:-1]))]
+    
+    # Pair values and runs, then convert to a string
+    rle_pairs = ",".join([f"{v},{r}" for v, r in zip(values, runs)])
+    
+    # Further compress with zlib and encode in base64 for JSON compatibility
+    compressed = zlib.compress(rle_pairs.encode('utf-8'))
+    return base64.b64encode(compressed).decode('ascii')
+
+
+def rle_decode(rle_string, shape):
+    """
+    Decodes a Run-Length Encoded string back into a 2D numpy array.
+    """
+    # Decode from base64 and decompress with zlib
+    decoded_b64 = base64.b64decode(rle_string)
+    decompressed = zlib.decompress(decoded_b64).decode('utf-8')
+    
+    # Parse the value,run pairs
+    pairs = decompressed.split(',')
+    values = [int(v) for v in pairs[0::2]]
+    runs = [int(r) for r in pairs[1::2]]
+    
+    # Reconstruct the pixel array
+    pixels = np.repeat(values, runs)
+    
+    # Reshape to the original 2D mask dimensions
+    return pixels.reshape(shape)
+
+
+# ----------------------------------------------------------------------------------------------------------------------
+# Classes
+# ----------------------------------------------------------------------------------------------------------------------
+
+
+class MaskAnnotation(Annotation):
+    def __init__(self,
+                 image_path: str,
+                 mask_data: np.ndarray,
+                 label_map: dict,
+                 transparency: int = 128,
+                 show_msg: bool = False,
+                 rasterio_src=None):
+        """
+        Initialize a full-image semantic segmentation annotation.
+        There should only be one MaskAnnotation per image.
+
+        Args:
+            image_path (str): Path to the source image.
+            mask_data (np.ndarray): 2D numpy array of integer class IDs, matching image dimensions.
+            label_map (dict): A map of {class_id: Label_object}.
+            transparency (int): The alpha value for displaying the mask overlay.
+            rasterio_src: Optional rasterio dataset object for the source image.
+        """
+        # For a full-image mask, the concept of a single "primary label" is ambiguous.
+        # We'll use the first available label as a placeholder to satisfy the base class.
+        if not label_map:
+            raise ValueError("label_map cannot be empty.")
+        placeholder_label = next(iter(label_map.values()))
+
+        super().__init__(
+            short_label_code=placeholder_label.short_label_code,
+            long_label_code=placeholder_label.long_label_code,
+            color=placeholder_label.color,
+            image_path=image_path,
+            label_id=placeholder_label.id,
+            transparency=transparency,
+            show_msg=show_msg
+        )
+        
+        self.mask_data = mask_data
+        self.label_map = label_map
+        self.offset = QPointF(0, 0)  # A full-image mask has no offset
+        self.rasterio_src = rasterio_src  # Store rasterio source if provided
+        
+        # Set geometric properties from mask
+        self.set_centroid()
+        self.set_cropped_bbox()
+
+    def set_centroid(self):
+        """Set the centroid to the center of the image."""
+        height, width = self.mask_data.shape
+        self.center_xy = QPointF(width / 2.0, height / 2.0)
+
+    def set_cropped_bbox(self):
+        """Set the bounding box to the full dimensions of the image."""
+        height, width = self.mask_data.shape
+        self.cropped_bbox = (0, 0, width, height)
+        self.annotation_size = int(max(width, height))
+
+    def _render_mask_to_pixmap(self) -> QPixmap:
+        """Converts the numpy mask_data into a colored QPixmap for display."""
+        height, width = self.mask_data.shape
+        
+        # Create a color map for fast lookup from class ID to RGBA color
+        max_id = max(self.label_map.keys()) if self.label_map else 0
+        color_map = np.zeros((max_id + 1, 4), dtype=np.uint8)
+        for class_id, label in self.label_map.items():
+            color = label.color
+            color_map[class_id] = [color.red(), color.green(), color.blue(), self.transparency]
+
+        colored_mask = color_map[self.mask_data]
+        q_image = QImage(colored_mask.data, width, height, QImage.Format_RGBA8888)
+        
+        return QPixmap.fromImage(q_image)
+
+    def contains_point(self, point: QPointF) -> bool:
+        """Check if a point is within the mask's classified area."""
+        x, y = int(point.x()), int(point.y())
+        height, width = self.mask_data.shape
+        if 0 <= y < height and 0 <= x < width:
+            return self.mask_data[y, x] > 0
+        return False
+
+    def get_area(self):
+        """Return the total number of non-background pixels."""
+        return np.count_nonzero(self.mask_data)
+
+    def get_bounding_box_top_left(self):
+        """Get the top-left corner of the annotation's bounding box (always 0,0)."""
+        return QPointF(0, 0)
+
+    def get_bounding_box_bottom_right(self):
+        """Get the bottom-right corner of the annotation's bounding box."""
+        height, width = self.mask_data.shape
+        return QPointF(width, height)
+
+    def create_graphics_item(self, scene: QGraphicsScene):
+        """Create a QGraphicsPixmapItem to display the mask."""
+        pixmap = self._render_mask_to_pixmap()
+        self.graphics_item = QGraphicsPixmapItem(pixmap)
+        self.graphics_item.setPos(self.offset)
+        super().create_graphics_item(scene)
+
+    def update_graphics_item(self):
+        """Update the pixmap if the mask data has changed."""
+        if self.graphics_item:
+            pixmap = self._render_mask_to_pixmap()
+            self.graphics_item.setPixmap(pixmap)
+        super().update_graphics_item()
+
+    def update_mask(self, brush_location: QPointF, brush_mask: np.ndarray, new_class_id: int):
+        """Modify the mask data based on a brush stroke."""
+        x_start, y_start = int(brush_location.x()), int(brush_location.y())
+        brush_h, brush_w = brush_mask.shape
+        mask_h, mask_w = self.mask_data.shape
+
+        x_end = min(x_start + brush_w, mask_w)
+        y_end = min(y_start + brush_h, mask_h)
+        clipped_x_start = max(x_start, 0)
+        clipped_y_start = max(y_start, 0)
+
+        if clipped_x_start >= x_end or clipped_y_start >= y_end:
+            return
+
+        target_slice = self.mask_data[clipped_y_start:y_end, clipped_x_start:x_end]
+        brush_x_offset = clipped_x_start - x_start
+        brush_y_offset = clipped_y_start - y_start
+        clipped_brush_mask = brush_mask[brush_y_offset:brush_y_offset + target_slice.shape[0],
+                                        brush_x_offset:brush_x_offset + target_slice.shape[1]]
+
+        target_slice[clipped_brush_mask] = new_class_id
+
+        self.update_graphics_item()
+        self.annotationUpdated.emit(self)
+
+    # --- Data Manipulation & Editing Methods ---
+
+    def fill_region(self, point: QPointF, new_class_id: int):
+        """Fills a contiguous region with a new class ID (paint bucket tool)."""
+        x, y = int(point.x()), int(point.y())
+        height, width = self.mask_data.shape
+        if not (0 <= y < height and 0 <= x < width):
+            return
+
+        old_class_id = self.mask_data[y, x]
+        if old_class_id == new_class_id:
+            return
+
+        labeled_array, num_features = ndimage_label(self.mask_data == old_class_id)
+        region_label = labeled_array[y, x]
+        
+        self.mask_data[labeled_array == region_label] = new_class_id
+        
+        self.update_graphics_item()
+        self.annotationUpdated.emit(self)
+
+    def replace_class(self, old_class_id: int, new_class_id: int):
+        """Replaces all pixels of one class ID with another across the entire mask."""
+        self.mask_data[self.mask_data == old_class_id] = new_class_id
+        self.update_graphics_item()
+        self.annotationUpdated.emit(self)
+
+    def import_annotations(self, annotations: list, class_id: int):
+        """Burns a list of vector annotations into the mask with a given class ID."""
+        height, width = self.mask_data.shape
+        # Use Format_Alpha8 for an efficient 8-bit stencil mask
+        stencil = QImage(width, height, QImage.Format_Alpha8)
+        stencil.fill(Qt.transparent)
+
+        painter = QPainter(stencil)
+        painter.setPen(Qt.NoPen)
+        painter.setBrush(QBrush(QColor("white")))  # Opaque white
+        
+        for anno in annotations:
+            path = anno.get_painter_path()
+            painter.drawPath(path)
+        painter.end()
+
+        # Convert the QImage stencil to a boolean numpy array
+        ptr = stencil.bits()
+        ptr.setsize(stencil.byteCount())
+        stencil_np = np.array(ptr).reshape(height, width) > 0  # True where painted
+
+        # Update the mask data where the stencil is True
+        self.mask_data[stencil_np] = class_id
+        
+        self.update_graphics_item()
+        self.annotationUpdated.emit(self)
+
+    # --- Analysis & Information Retrieval Methods ---
+
+    def get_class_statistics(self) -> dict:
+        """Returns a dictionary with pixel counts and percentages for each class."""
+        stats = {}
+        total_pixels = self.get_area()
+        if total_pixels == 0:
+            return stats
+
+        class_ids, counts = np.unique(self.mask_data[self.mask_data > 0], return_counts=True)
+        
+        for cid, count in zip(class_ids, counts):
+            label = self.label_map.get(int(cid))
+            if label:
+                stats[label.short_label_code] = {
+                    "pixel_count": int(count),
+                    "percentage": (count / total_pixels) * 100
+                }
+        return stats
+
+    def get_class_at_point(self, point: QPointF) -> int:
+        """Returns the class ID at a specific point."""
+        x, y = int(point.x()), int(point.y())
+        height, width = self.mask_data.shape
+        if 0 <= y < height and 0 <= x < width:
+            return self.mask_data[y, x]
+        return 0  # Return background class if outside bounds
+
+    # --- Conversion & Exporting Methods ---
+    
+    def get_binary_mask(self, class_id: int) -> np.ndarray:
+        """Returns a boolean numpy array where True corresponds to the given class ID."""
+        return self.mask_data == class_id
+
+    def to_instance_polygons(self, class_id: int) -> list:
+        """Converts all contiguous regions of a class ID into PolygonAnnotations."""
+        binary_mask = self.get_binary_mask(class_id)
+        # Add padding to handle contours touching the border
+        padded_mask = np.pad(binary_mask, pad_width=1, mode='constant', constant_values=0)
+        
+        # Level is 0.5 to find contours between 0 and 1 values
+        contours = find_contours(padded_mask, level=0.5)
+        
+        annotations = []
+        for contour in contours:
+            # Remove padding offset and swap (row, col) to (x, y)
+            points = [QPointF(p[1] - 1, p[0] - 1) for p in contour]
+            if len(points) > 2:  # Must have at least 3 points for a valid polygon
+                # Use the label associated with the class_id for the new annotation
+                label = self.label_map[class_id]
+                anno = PolygonAnnotation(
+                    points=points,
+                    short_label_code=label.short_label_code,
+                    long_label_code=label.long_label_code,
+                    color=label.color,
+                    image_path=self.image_path,
+                    label_id=label.id
+                )
+                annotations.append(anno)
+        return annotations
+
+    def export_as_png(self, path: str, use_label_colors: bool = True):
+        """Saves the mask to a PNG file."""
+        if use_label_colors:
+            # Use rendering logic to create a colored image
+            pixmap = self._render_mask_to_pixmap()
+            pixmap.toImage().save(path)
+        else:
+            # Save the raw class IDs as a grayscale image
+            height, width = self.mask_data.shape
+            # Ensure data is in a format QImage can handle (e.g., 8-bit grayscale)
+            if self.mask_data.max() < 256:
+                img_data = self.mask_data.astype(np.uint8)
+                q_image = QImage(img_data.data, width, height, QImage.Format_Grayscale8)
+                q_image.save(path)
+            else:
+                warnings.warn("Mask contains class IDs > 255; cannot save as 8-bit grayscale PNG.")
+
+    def export_as_raster(self, path: str):
+        """Saves the mask data to a raster file (e.g., GeoTIFF) using rasterio."""
+        profile = {
+            'driver': 'GTiff',
+            'height': self.mask_data.shape[0],
+            'width': self.mask_data.shape[1],
+            'count': 1,
+            'dtype': self.mask_data.dtype
+        }
+        
+        # If the original image was opened with rasterio, copy its spatial metadata
+        if self.rasterio_src:
+            profile['crs'] = self.rasterio_src.crs
+            profile['transform'] = self.rasterio_src.transform
+
+        with rasterio.open(path, 'w', **profile) as dst:
+            dst.write(self.mask_data, 1)
+
+    # --- Serialization & Deserialization ---
+
+    def to_dict(self):
+        """Serialize the annotation to a dictionary, with RLE for the mask."""
+        base_dict = super().to_dict()
+        rle_string = rle_encode(self.mask_data)
+        base_dict.update({
+            'shape': self.mask_data.shape,
+            'rle_mask': rle_string,
+            'label_map': {cid: label.short_label_code for cid, label in self.label_map.items()}
+        })
+        return base_dict
+
+    @classmethod
+    def from_dict(cls, data, label_window):
+        """Instantiate a MaskAnnotation from a dictionary."""
+        label_map = {}
+        for cid_str, short_code in data['label_map'].items():
+            label = label_window.get_label_by_short_code(short_code)
+            if label:
+                label_map[int(cid_str)] = label
+
+        mask_data = rle_decode(data['rle_mask'], data['shape'])
+
+        annotation = cls(
+            image_path=data['image_path'],
+            mask_data=mask_data,
+            label_map=label_map
+        )
+        annotation.id = data.get('id', annotation.id)
+        annotation.data = data.get('data', {})
+        return annotation
+
+    @classmethod
+    def from_rasterio(cls, file_path: str, image_path: str, label_map: dict):
+        """Creates a MaskAnnotation instance by loading data from a raster file."""
+        with rasterio.open(file_path) as src:
+            mask_data = src.read(1)
+            return cls(
+                image_path=image_path,
+                mask_data=mask_data,
+                label_map=label_map,
+                rasterio_src=src
+            )
+
+    # --- Compatibility Methods ---
+    def get_perimeter(self):
+        height, width = self.mask_data.shape
+        return 2 * (width + height)
+    
+    def get_polygon(self):
+        height, width = self.mask_data.shape
+        return QPolygonF(QRectF(0, 0, width, height))
+
+    def __repr__(self):
+        return (f"MaskAnnotation(id={self.id}, image_path={self.image_path}, "
+                f"shape={self.mask_data.shape})")