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diff --git a/modules/find_path.py b/modules/find_path.py
index 426563ddd4843ab49ab9c08f8424cbd21508d864..4ae9c7fa5afc77a9a29cf214956f55fbfd225fc7 100644
--- a/modules/find_path.py
+++ b/modules/find_path.py
@@ -1,17 +1,30 @@
from skimage.graph import route_through_array
-def find_path(cost_image, points):
+def find_path(cost_image: "numpy.ndarray", points: list) -> list:
+ """
+ Find the optimal path through a cost image between two points.
+ Parameters:
+ cost_image (numpy.ndarray): A 2D array representing the cost of traversing each pixel.
+ points (list): A list containing two tuples, each representing the
+ (row, column) coordinates of the seed and target points.
+
+ Returns:
+ list: A list of (row, column) tuples representing the path from the seed to the target point.
+
+ Raises:
+ ValueError: If the points list does not contain exactly two points.
+ """
if len(points) != 2:
raise ValueError("Points should be a list of 2 points: seed and target.")
seed_rc, target_rc = points
path_rc, cost = route_through_array(
- cost_image,
- start=seed_rc,
- end=target_rc,
+ cost_image,
+ start=seed_rc,
+ end=target_rc,
fully_connected=True
)
- return path_rc
\ No newline at end of file
+ return path_rc
diff --git a/modules/imageGraphicsView.py b/modules/imageGraphicsView.py
index c2c984755352faf36f90645adf1a771e9d306d6c..1855d717866a601eafe886b0e311da772f9322da 100644
--- a/modules/imageGraphicsView.py
+++ b/modules/imageGraphicsView.py
@@ -1,8 +1,8 @@
+import math
from scipy.signal import savgol_filter
from PyQt5.QtWidgets import QGraphicsScene, QGraphicsPixmapItem
from PyQt5.QtGui import QPixmap, QColor
-from PyQt5.QtCore import Qt, QRectF
-import math
+from PyQt5.QtCore import Qt, QRectF, QPoint
import numpy as np
from panZoomGraphicsView import PanZoomGraphicsView
from labeledPointItem import LabeledPointItem
@@ -10,6 +10,14 @@ from find_path import find_path
class ImageGraphicsView(PanZoomGraphicsView):
+ """
+ A custom QGraphicsView for displaying and interacting with an image.
+
+ This class extends PanZoomGraphicsView to provide additional functionality
+ for loading images, adding labeled anchor points, and computing paths
+ between points based on a cost image.
+ """
+
def __init__(self, parent=None):
super().__init__(parent)
self.scene = QGraphicsScene(self)
@@ -19,10 +27,10 @@ class ImageGraphicsView(PanZoomGraphicsView):
self.image_item = QGraphicsPixmapItem()
self.scene.addItem(self.image_item)
- self.anchor_points = [] # List[(x, y)]
- self.point_items = [] # LabeledPointItem
- self.full_path_points = [] # QGraphicsEllipseItems for path
- self._full_path_xy = [] # entire path coords (smoothed)
+ self.anchor_points = []
+ self.point_items = []
+ self.full_path_points = []
+ self._full_path_xy = []
self.dot_radius = 4
self.path_radius = 1
@@ -49,16 +57,18 @@ class ImageGraphicsView(PanZoomGraphicsView):
self._savgol_window_length = 7
def set_rainbow_enabled(self, enabled: bool):
+ """Enable rainbow coloring of the path."""
self._rainbow_enabled = enabled
self._rebuild_full_path()
def toggle_rainbow(self):
+ """Toggle rainbow coloring of the path."""
self._rainbow_enabled = not self._rainbow_enabled
self._rebuild_full_path()
def set_savgol_window_length(self, wlen: int):
- if wlen < 3:
- wlen = 3
+ """Set the window length for Savitzky-Golay smoothing."""
+ wlen = max(3, wlen)
if wlen % 2 == 0:
wlen += 1
self._savgol_window_length = wlen
@@ -68,7 +78,8 @@ class ImageGraphicsView(PanZoomGraphicsView):
# --------------------------------------------------------------------
# LOADING
# --------------------------------------------------------------------
- def load_image(self, path):
+ def load_image(self, path: str):
+ """Load an image from a file path."""
pixmap = QPixmap(path)
if not pixmap.isNull():
self.image_item.setPixmap(pixmap)
@@ -90,7 +101,9 @@ class ImageGraphicsView(PanZoomGraphicsView):
# --------------------------------------------------------------------
# ANCHOR POINTS
# --------------------------------------------------------------------
- def _insert_anchor_point(self, idx, x, y, label="", removable=True, z_val=0, radius=4):
+ def _insert_anchor_point(self, idx, x: float, y: float, label="", removable=True,
+ z_val=0, radius=4):
+ """Insert an anchor point at a specific index."""
x_clamped = self._clamp(x, radius, self._img_w - radius)
y_clamped = self._clamp(y, radius, self._img_h - radius)
@@ -110,7 +123,7 @@ class ImageGraphicsView(PanZoomGraphicsView):
self.scene.addItem(item)
def _add_guide_point(self, x, y):
- # Ensure we clamp properly
+ """Add a guide point to the path."""
x_clamped = self._clamp(x, self.dot_radius, self._img_w - self.dot_radius)
y_clamped = self._clamp(y, self.dot_radius, self._img_h - self.dot_radius)
@@ -125,7 +138,8 @@ class ImageGraphicsView(PanZoomGraphicsView):
self._apply_all_guide_points_to_cost()
self._rebuild_full_path()
- def _insert_anchor_between_subpath(self, x_new, y_new):
+ def _insert_anchor_between_subpath(self, x_new: float, y_new: float ):
+ """Insert an anchor point between existing anchor points."""
# If somehow we have no path yet
if not self._full_path_xy:
self._insert_anchor_point(-1, x_new, y_new)
@@ -147,9 +161,11 @@ class ImageGraphicsView(PanZoomGraphicsView):
return
def approx_equal(xa, ya, xb, yb, tol=1e-3):
+ """Check if two points are approximately equal."""
return (abs(xa - xb) < tol) and (abs(ya - yb) < tol)
def is_anchor(coord):
+ """Check if a point is an anchor point."""
cx, cy = coord
for (ax, ay) in self.anchor_points:
if approx_equal(ax, ay, cx, cy):
@@ -158,23 +174,23 @@ class ImageGraphicsView(PanZoomGraphicsView):
# Walk left
left_anchor_pt = None
- iL = best_idx
- while iL >= 0:
- px, py = self._full_path_xy[iL]
+ i_l = best_idx
+ while i_l >= 0:
+ px, py = self._full_path_xy[i_l]
if is_anchor((px, py)):
left_anchor_pt = (px, py)
break
- iL -= 1
+ i_l -= 1
# Walk right
right_anchor_pt = None
- iR = best_idx
- while iR < len(self._full_path_xy):
- px, py = self._full_path_xy[iR]
+ i_r = best_idx
+ while i_r < len(self._full_path_xy):
+ px, py = self._full_path_xy[i_r]
if is_anchor((px, py)):
right_anchor_pt = (px, py)
break
- iR += 1
+ i_r += 1
# If we can't find distinct anchors on left & right,
# just insert before E.
@@ -221,7 +237,8 @@ class ImageGraphicsView(PanZoomGraphicsView):
if self.point_items[i].is_removable():
self._lower_cost_in_circle(ax, ay, self.radius_cost_image)
- def _lower_cost_in_circle(self, x_f, y_f, radius):
+ def _lower_cost_in_circle(self, x_f: float, y_f: float, radius: int):
+ """Lower the cost in a circle centered at (x_f, y_f)."""
if self.cost_image is None:
return
h, w = self.cost_image.shape
@@ -244,6 +261,7 @@ class ImageGraphicsView(PanZoomGraphicsView):
# PATH BUILDING
# --------------------------------------------------------------------
def _rebuild_full_path(self):
+ """Rebuild the full path based on the anchor points."""
for item in self.full_path_points:
self.scene.removeItem(item)
self.full_path_points.clear()
@@ -295,7 +313,8 @@ class ImageGraphicsView(PanZoomGraphicsView):
if p_item._text_item:
p_item.setZValue(100)
- def _compute_subpath_xy(self, xA, yA, xB, yB):
+ def _compute_subpath_xy(self, xA: float, yA: float, xB: float, yB: float):
+ """Compute a subpath between two points."""
if self.cost_image is None:
return []
h, w = self.cost_image.shape
@@ -313,7 +332,8 @@ class ImageGraphicsView(PanZoomGraphicsView):
# Convert from (row, col) to (x, y)
return [(c, r) for (r, c) in path_rc]
- def _rainbow_color(self, fraction):
+ def _rainbow_color(self, fraction: float):
+ """Get a rainbow color."""
hue = int(300 * fraction)
saturation = 255
value = 255
@@ -322,7 +342,8 @@ class ImageGraphicsView(PanZoomGraphicsView):
# --------------------------------------------------------------------
# MOUSE EVENTS
# --------------------------------------------------------------------
- def mousePressEvent(self, event):
+ def mouse_press_event(self, event):
+ """Handle mouse press events for dragging a point or adding a point."""
if event.button() == Qt.LeftButton:
self._mouse_pressed = True
self._was_dragging = False
@@ -341,9 +362,10 @@ class ImageGraphicsView(PanZoomGraphicsView):
elif event.button() == Qt.RightButton:
self._remove_point_by_click(event.pos())
- super().mousePressEvent(event)
+ super().mouse_press_event(event)
- def mouseMoveEvent(self, event):
+ def mouse_move_event(self, event):
+ """Handle mouse move events for dragging a point or dragging the view"""
if self._dragging_idx is not None:
scene_pos = self.mapToScene(event.pos())
x_new = scene_pos.x() - self._drag_offset[0]
@@ -368,10 +390,11 @@ class ImageGraphicsView(PanZoomGraphicsView):
if dist > self._drag_threshold:
self._was_dragging = True
- super().mouseMoveEvent(event)
+ super().mouse_move_event(event)
- def mouseReleaseEvent(self, event):
- super().mouseReleaseEvent(event)
+ def mouse_release_event(self, event):
+ """Handle mouse release events for dragging a point or adding a point."""
+ super().mouse_release_event(event)
if event.button() == Qt.LeftButton and self._mouse_pressed:
self._mouse_pressed = False
self.setCursor(Qt.ArrowCursor)
@@ -394,7 +417,8 @@ class ImageGraphicsView(PanZoomGraphicsView):
self._was_dragging = False
- def _remove_point_by_click(self, view_pos):
+ def _remove_point_by_click(self, view_pos: QPoint):
+ """Remove a point by clicking on it."""
idx = self._find_item_near(view_pos, threshold=10)
if idx is None:
return
@@ -409,7 +433,8 @@ class ImageGraphicsView(PanZoomGraphicsView):
self._apply_all_guide_points_to_cost()
self._rebuild_full_path()
- def _find_item_near(self, view_pos, threshold=10):
+ def _find_item_near(self, view_pos: QPoint, threshold=10):
+ """Find the index of an item near a given position."""
scene_pos = self.mapToScene(view_pos)
x_click, y_click = scene_pos.x(), scene_pos.y()
@@ -431,6 +456,7 @@ class ImageGraphicsView(PanZoomGraphicsView):
return max(mn, min(val, mx))
def _clear_all_points(self):
+ """Clear all anchor points and guide points."""
for it in self.point_items:
self.scene.removeItem(it)
self.point_items.clear()
@@ -442,6 +468,7 @@ class ImageGraphicsView(PanZoomGraphicsView):
self._full_path_xy.clear()
def clear_guide_points(self):
+ """Clear all guide points."""
i = 0
while i < len(self.anchor_points):
if self.point_items[i].is_removable():
@@ -461,4 +488,5 @@ class ImageGraphicsView(PanZoomGraphicsView):
self._rebuild_full_path()
def get_full_path_xy(self):
- return self._full_path_xy
\ No newline at end of file
+ """Returns the entire path as a list of (x, y) coordinates."""
+ return self._full_path_xy
diff --git a/modules/labeledPointItem.py b/modules/labeledPointItem.py
index ff9e263fd112579b1cb5e3467acb3b684effbcbf..f96bb8ff7875daead14c7ada43dc899e6ebad4b3 100644
--- a/modules/labeledPointItem.py
+++ b/modules/labeledPointItem.py
@@ -1,10 +1,20 @@
+import math
from PyQt5.QtWidgets import QGraphicsEllipseItem, QGraphicsTextItem
from PyQt5.QtGui import QPen, QBrush, QColor, QFont
from PyQt5.QtCore import Qt
-import math
+
class LabeledPointItem(QGraphicsEllipseItem):
- def __init__(self, x, y, label="", radius=4, color=Qt.red, removable=True, z_value=0, parent=None):
+ """
+ A QGraphicsEllipseItem subclass that represents a labeled point in a 2D space.
+
+ This class creates a circular point.
+ The point can be customized with different colors, sizes, and labels, and can
+ be marked as removable.
+ """
+
+ def __init__(self, x: float, y: float, label: str ="", radius:int =4,
+ color=Qt.red, removable=True, z_value=0, parent=None):
super().__init__(0, 0, 2*radius, 2*radius, parent)
self._x = x
self._y = y
@@ -30,6 +40,7 @@ class LabeledPointItem(QGraphicsEllipseItem):
self.set_pos(x, y)
def _scale_text_to_fit(self):
+ """Scales the text to fit inside the circle."""
if not self._text_item:
return
self._text_item.setScale(1.0)
@@ -43,6 +54,7 @@ class LabeledPointItem(QGraphicsEllipseItem):
self._center_label()
def _center_label(self):
+ """Centers the text inside the circle."""
if not self._text_item:
return
ellipse_w = 2 * self._r
@@ -62,10 +74,14 @@ class LabeledPointItem(QGraphicsEllipseItem):
self.setPos(x - self._r, y - self._r)
def get_pos(self):
+ """Returns the (x, y) coordinates of the center of the circle."""
return (self._x, self._y)
def distance_to(self, x_other, y_other):
+ """Returns the Euclidean distance from the center
+ of the circle to another circle."""
return math.sqrt((self._x - x_other)**2 + (self._y - y_other)**2)
def is_removable(self):
- return self._removable
\ No newline at end of file
+ """Returns True if the point is removable, False otherwise."""
+ return self._removable
diff --git a/modules/load_image.py b/modules/load_image.py
index 5bded2a55ebbc1a93d8f42d587920948d779965f..d2fa7eadf42d6098f0cc14bee50a4f015d9d0240 100644
--- a/modules/load_image.py
+++ b/modules/load_image.py
@@ -1,4 +1,13 @@
import cv2
-def load_image(path):
+def load_image(path: str) -> "numpy.ndarray":
+ """
+ Loads an image from the specified file path in grayscale mode.
+
+ Args:
+ path (str): The file path to the image.
+
+ Returns:
+ numpy.ndarray: The loaded grayscale image.
+ """
return cv2.imread(path, cv2.IMREAD_GRAYSCALE)
\ No newline at end of file
diff --git a/modules/panZoomGraphicsView.py b/modules/panZoomGraphicsView.py
index 85d5e1ac297ad469c8ff6416b9b6fc869df8aa5d..dc86430cf0f11138094e72876f8ec4aed95eacc0 100644
--- a/modules/panZoomGraphicsView.py
+++ b/modules/panZoomGraphicsView.py
@@ -1,8 +1,10 @@
from PyQt5.QtWidgets import QGraphicsView, QSizePolicy
from PyQt5.QtCore import Qt
-# A pan & zoom QGraphicsView
class PanZoomGraphicsView(QGraphicsView):
+ """
+ A QGraphicsView subclass that supports panning and zooming with the mouse.
+ """
def __init__(self, parent=None):
super().__init__(parent)
self.setDragMode(QGraphicsView.NoDrag) # We'll handle panning manually
@@ -10,10 +12,10 @@ class PanZoomGraphicsView(QGraphicsView):
self._panning = False
self._pan_start = None
- # Let it expand in layouts
+ # Expands layout
self.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
- def wheelEvent(self, event):
+ def wheel_event(self, event):
""" Zoom in/out with mouse wheel. """
zoom_in_factor = 1.25
zoom_out_factor = 1 / zoom_in_factor
@@ -23,25 +25,25 @@ class PanZoomGraphicsView(QGraphicsView):
self.scale(zoom_out_factor, zoom_out_factor)
event.accept()
- def mousePressEvent(self, event):
+ def mouse_press_event(self, event):
""" If left button: Start panning (unless overridden). """
if event.button() == Qt.LeftButton:
self._panning = True
self._pan_start = event.pos()
self.setCursor(Qt.ClosedHandCursor)
- super().mousePressEvent(event)
+ super().mouse_press_event(event)
- def mouseMoveEvent(self, event):
+ def mouse_move_event(self, event):
""" If panning, translate the scene. """
if self._panning and self._pan_start is not None:
delta = event.pos() - self._pan_start
self._pan_start = event.pos()
self.translate(delta.x(), delta.y())
- super().mouseMoveEvent(event)
+ super().mouse_move_event(event)
- def mouseReleaseEvent(self, event):
+ def mouse_release_event(self, event):
""" End panning. """
if event.button() == Qt.LeftButton:
self._panning = False
self.setCursor(Qt.ArrowCursor)
- super().mouseReleaseEvent(event)
+ super().mouse_release_event(event)
diff --git a/modules/preprocess_image.py b/modules/preprocess_image.py
index 403323faacb81a18905b08eb53a0a80bae6614e4..351988f1b00389c592d35e1913a0ca1221cb7224 100644
--- a/modules/preprocess_image.py
+++ b/modules/preprocess_image.py
@@ -1,11 +1,23 @@
from skimage.filters import gaussian
from skimage import exposure
-def preprocess_image(image, sigma=3, clip_limit=0.01):
- # Apply histogram equalization
- image_contrasted = exposure.equalize_adapthist(image, clip_limit=clip_limit)
- # Apply smoothing
+def preprocess_image(image: "np.ndarray", sigma: int = 3, clip_limit: float = 0.01) -> "np.ndarray":
+ """
+ Preprocess the input image by applying histogram equalization and Gaussian smoothing.
+
+ Args:
+ image: (ndarray): Input image to be processed.
+ sigma: (float, optional): Standard deviation for Gaussian kernel. Default is 3.
+ clip_limit: (float, optional): Clipping limit for contrast enhancement. Default is 0.01.
+ Returns:
+ ndarray: The preprocessed image.
+ """
+ # Applies histogram equalization to enhance contrast
+ image_contrasted = exposure.equalize_adapthist(
+ image, clip_limit=clip_limit)
+
+ # Applies smoothing
smoothed_img = gaussian(image_contrasted, sigma=sigma)
- return smoothed_img
\ No newline at end of file
+ return smoothed_img