AvtomatskaPoravnavaMarkerjev/SeekTransformModule/SeekTransformModule.py

import os
import numpy as np
import scipy
from scipy.spatial.distance import cdist
from scipy.spatial.transform import Rotation as R
import slicer
from DICOMLib import DICOMUtils
from collections import deque
import vtk
from slicer.ScriptedLoadableModule import *
import qt

#exec(open("C:/Users/lkomar/Documents/Prostata/FirstTryRegister.py").read())

class SeekTransformModule(ScriptedLoadableModule):
    """
    Module description shown in the module panel.
    """
    def __init__(self, parent):
        ScriptedLoadableModule.__init__(self, parent)
        self.parent.title = "Seek Transform module"
        self.parent.categories = ["Image Processing"]
        self.parent.contributors = ["Luka Komar (Onkološki Inštitut Ljubljana, Fakulteta za Matematiko in Fiziko Ljubljana)"]
        self.parent.helpText = "This module applies rigid transformations to CBCT volumes based on reference CT volumes."
        self.parent.acknowledgementText = "Supported by doc. Primož Peterlin & prof. Andrej Studen"

class SeekTransformModuleWidget(ScriptedLoadableModuleWidget):
    """
    GUI of the module.
    """
    def setup(self):
        ScriptedLoadableModuleWidget.setup(self)

        # Dropdown menu za izbiro metode
        self.rotationMethodComboBox = qt.QComboBox()
        self.rotationMethodComboBox.addItems(["Kabsch", "Horn", "Iterative Closest Point (Kabsch)"])
        self.layout.addWidget(self.rotationMethodComboBox)
        
        # Load button
        self.applyButton = qt.QPushButton("Find markers and transform")
        self.applyButton.toolTip = "Finds markers, computes optimal rigid transform and applies it to CBCT volumes."
        self.applyButton.enabled = True
        self.layout.addWidget(self.applyButton)

        # Connect button to logic
        self.applyButton.connect('clicked(bool)', self.onApplyButton)

        self.layout.addStretch(1)

    def onApplyButton(self):
        logic = MyTransformModuleLogic()
        selectedMethod = self.rotationMethodComboBox.currentText #izberi metodo izračuna rotacije
        logic.run(selectedMethod)

class MyTransformModuleLogic(ScriptedLoadableModuleLogic):
    """
    Core logic of the module.
    """
    def run(self, selectedMethod):
        print("Calculating...")
        def group_points(points, threshold):
            # Function to group points that are close to each other
            grouped_points = []
            while points:
                point = points.pop()  # Take one point from the list
                group = [point]  # Start a new group
                
                # Find all points close to this one
                distances = cdist([point], points)  # Calculate distances from this point to others
                close_points = [i for i, dist in enumerate(distances[0]) if dist < threshold]
                
                # Add the close points to the group
                group.extend([points[i] for i in close_points])
                
                # Remove the grouped points from the list
                points = [point for i, point in enumerate(points) if i not in close_points]
                
                # Add the group to the result
                grouped_points.append(group)
            
            return grouped_points

        def region_growing(image_data, seed, intensity_threshold, max_distance):
            dimensions = image_data.GetDimensions()
            visited = set()
            region = []
            queue = deque([seed])

            while queue:
                x, y, z = queue.popleft()
                if (x, y, z) in visited:
                    continue

                visited.add((x, y, z))
                voxel_value = image_data.GetScalarComponentAsDouble(x, y, z, 0)
                
                if voxel_value >= intensity_threshold:
                    region.append((x, y, z))
                    # Add neighbors within bounds
                    for dx, dy, dz in [(1, 0, 0), (-1, 0, 0), (0, 1, 0), (0, -1, 0), (0, 0, 1), (0, 0, -1)]:
                        nx, ny, nz = x + dx, y + dy, z + dz
                        if 0 <= nx < dimensions[0] and 0 <= ny < dimensions[1] and 0 <= nz < dimensions[2]:
                            if (nx, ny, nz) not in visited:
                                queue.append((nx, ny, nz))

            return region

        def detect_points_region_growing(volume_name, yesCbct, intensity_threshold=3000, x_min=90, x_max=380, y_min=190, y_max=380, z_min=80, z_max=140, max_distance=9, centroid_merge_threshold=5):
            volume_node = slicer.util.getNode(volume_name)
            if not volume_node:
                raise RuntimeError(f"Volume {volume_name} not found.")
            
            image_data = volume_node.GetImageData()
            matrix = vtk.vtkMatrix4x4()
            volume_node.GetIJKToRASMatrix(matrix)

            dimensions = image_data.GetDimensions()
            #detected_regions = []

            if yesCbct: #je cbct ali ct?
                valid_x_min, valid_x_max = 0, dimensions[0] - 1
                valid_y_min, valid_y_max = 0, dimensions[1] - 1
                valid_z_min, valid_z_max = 0, dimensions[2] - 1
            else:
                valid_x_min, valid_x_max = max(x_min, 0), min(x_max, dimensions[0] - 1)
                valid_y_min, valid_y_max = max(y_min, 0), min(y_max, dimensions[1] - 1)
                valid_z_min, valid_z_max = max(z_min, 0), min(z_max, dimensions[2] - 1)

            visited = set()

            def grow_region(x, y, z):
                if (x, y, z) in visited:
                    return None

                voxel_value = image_data.GetScalarComponentAsDouble(x, y, z, 0)
                if voxel_value < intensity_threshold:
                    return None

                region = region_growing(image_data, (x, y, z), intensity_threshold, max_distance=max_distance)
                if region:
                    for point in region:
                        visited.add(tuple(point))
                    return region
                return None

            regions = []
            for z in range(valid_z_min, valid_z_max + 1):
                for y in range(valid_y_min, valid_y_max + 1):
                    for x in range(valid_x_min, valid_x_max + 1):
                        region = grow_region(x, y, z)
                        if region:
                            regions.append(region)

            # Collect centroids using intensity-weighted average
            centroids = []
            for region in regions:
                points = np.array([matrix.MultiplyPoint([*point, 1])[:3] for point in region])
                intensities = np.array([image_data.GetScalarComponentAsDouble(*point, 0) for point in region])
                
                if intensities.sum() > 0:
                    weighted_centroid = np.average(points, axis=0, weights=intensities)
                    max_intensity = intensities.max()
                    centroids.append((np.round(weighted_centroid, 2), max_intensity))

            unique_centroids = []
            for centroid, intensity in centroids:
                if not any(np.linalg.norm(centroid - existing_centroid) < centroid_merge_threshold for existing_centroid, _ in unique_centroids):
                    unique_centroids.append((centroid, intensity))
                    
            markups_node = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLMarkupsFiducialNode", f"Markers_{volume_name}")
            for centroid, intensity in unique_centroids:
                markups_node.AddControlPoint(*centroid)
                #print(f"Detected Centroid (RAS): {centroid}, Max Intensity: {intensity}")

            return unique_centroids

        def compute_Kabsch_rotation(moving_points, fixed_points):
            """
            Computes the optimal rotation matrix to align moving_points to fixed_points.
            
            Parameters:
            moving_points (list or ndarray): List of points to be rotated CBCT
            fixed_points (list or ndarray): List of reference points CT

            Returns:
            ndarray: Optimal rotation matrix.
            """
            assert len(moving_points) == len(fixed_points), "Point lists must be the same length."

            # Convert to numpy arrays
            moving = np.array(moving_points)
            fixed = np.array(fixed_points)

            # Compute centroids
            centroid_moving = np.mean(moving, axis=0)
            centroid_fixed = np.mean(fixed, axis=0)

            # Center the points
            moving_centered = moving - centroid_moving
            fixed_centered = fixed - centroid_fixed

            # Compute covariance matrix
            H = np.dot(moving_centered.T, fixed_centered)

            # SVD decomposition
            U, _, Vt = np.linalg.svd(H)
            Rotate_optimal = np.dot(Vt.T, U.T)

            # Correct improper rotation (reflection)
            if np.linalg.det(Rotate_optimal) < 0:
                Vt[-1, :] *= -1
                Rotate_optimal = np.dot(Vt.T, U.T)

            return Rotate_optimal


        def compute_Horn_rotation(moving_points, fixed_points):
            """
            Computes the optimal rotation matrix using quaternions.

            Parameters:
            moving_points (list or ndarray): List of points to be rotated.
            fixed_points (list or ndarray): List of reference points.

            Returns:
            ndarray: Optimal rotation matrix.
            """
            assert len(moving_points) == len(fixed_points), "Point lists must be the same length."
            
            moving = np.array(moving_points)
            fixed = np.array(fixed_points)
            
            # Compute centroids
            centroid_moving = np.mean(moving, axis=0)
            centroid_fixed = np.mean(fixed, axis=0)
            
            # Center the points
            moving_centered = moving - centroid_moving
            fixed_centered = fixed - centroid_fixed
            
            # Construct the cross-dispersion matrix
            M = np.dot(moving_centered.T, fixed_centered)
            
            # Construct the N matrix for quaternion solution
            A = M - M.T
            delta = np.array([A[1, 2], A[2, 0], A[0, 1]])
            trace = np.trace(M)
            
            N = np.zeros((4, 4))
            N[0, 0] = trace
            N[1:, 0] = delta
            N[0, 1:] = delta
            N[1:, 1:] = M + M.T - np.eye(3) * trace
            
            # Compute the eigenvector corresponding to the maximum eigenvalue
            eigvals, eigvecs = np.linalg.eigh(N)
            q_optimal = eigvecs[:, np.argmax(eigvals)]  # Optimal quaternion
            
            # Convert quaternion to rotation matrix
            w, x, y, z = q_optimal
            R = np.array([
                [1 - 2*(y**2 + z**2), 2*(x*y - z*w), 2*(x*z + y*w)],
                [2*(x*y + z*w), 1 - 2*(x**2 + z**2), 2*(y*z - x*w)],
                [2*(x*z - y*w), 2*(y*z + x*w), 1 - 2*(x**2 + y**2)]
            ])
            
            return R

        def icp_algorithm(moving_points, fixed_points, max_iterations=100, tolerance=1e-5):
            """
            Iterative Closest Point (ICP) algorithm to align moving_points to fixed_points.
            
            Parameters:
            moving_points (list or ndarray): List of points to be aligned.
            fixed_points (list or ndarray): List of reference points.
            max_iterations (int): Maximum number of iterations.
            tolerance (float): Convergence tolerance.

            Returns:
            ndarray: Transformed moving points.
            ndarray: Optimal rotation matrix.
            ndarray: Optimal translation vector.
            """
            # Convert to numpy arrays
            moving = np.array(moving_points)
            fixed = np.array(fixed_points)

            # Initialize transformation
            R = np.eye(3)  # Identity matrix for rotation
            t = np.zeros(3)  # Zero vector for translation

            prev_error = np.inf  # Initialize previous error to a large value

            for iteration in range(max_iterations):
                # Step 1: Find the nearest neighbors (correspondences)
                distances = np.linalg.norm(moving[:, np.newaxis] - fixed, axis=2)
                nearest_indices = np.argmin(distances, axis=1)
                nearest_points = fixed[nearest_indices]

                # Step 2: Compute the optimal rotation and translation
                R_new = compute_Kabsch_rotation(moving, nearest_points)
                centroid_moving = np.mean(moving, axis=0)
                centroid_fixed = np.mean(nearest_points, axis=0)
                t_new = centroid_fixed - np.dot(R_new, centroid_moving)

                # Step 3: Apply the transformation
                moving = np.dot(moving, R_new.T) + t_new

                # Update the cumulative transformation
                R = np.dot(R_new, R)
                t = np.dot(R_new, t) + t_new

                # Step 4: Check for convergence
                mean_error = np.mean(np.linalg.norm(moving - nearest_points, axis=1))
                if np.abs(prev_error - mean_error) < tolerance:
                    print(f"ICP converged after {iteration + 1} iterations.")
                    break
                prev_error = mean_error

            else:
                print(f"ICP reached maximum iterations ({max_iterations}).")

            return moving, R, t


        def compute_translation(moving_points, fixed_points, rotation_matrix):
            """
            Computes the translation vector to align moving_points to fixed_points given a rotation matrix.
            
            Parameters:
            moving_points (list or ndarray): List of points to be translated.
            fixed_points (list or ndarray): List of reference points.
            rotation_matrix (ndarray): Rotation matrix.

            Returns:
            ndarray: Translation vector.
            """
            # Convert to numpy arrays
            moving = np.array(moving_points)
            fixed = np.array(fixed_points)

            # Compute centroids
            centroid_moving = np.mean(moving, axis=0)
            centroid_fixed = np.mean(fixed, axis=0)

            # Compute translation
            translation = centroid_fixed - np.dot(centroid_moving, rotation_matrix)

            return translation

        def create_vtk_transform(rotation_matrix, translation_vector):
            """
            Creates a vtkTransform from a rotation matrix and a translation vector.
            """
            # Create a 4x4 transformation matrix
            transform_matrix = np.eye(4)  # Start with an identity matrix
            transform_matrix[:3, :3] = rotation_matrix  # Set rotation part
            transform_matrix[:3, 3] = translation_vector  # Set translation part

            # Convert to vtkMatrix4x4
            vtk_matrix = vtk.vtkMatrix4x4()
            for i in range(4):
                for j in range(4):
                    vtk_matrix.SetElement(i, j, transform_matrix[i, j])
            #print("Transform matrix:")
            #for i in range(4):
            #    print(" ".join(f"{vtk_matrix.GetElement(i, j):.6f}" for j in range(4)))
            # Create vtkTransform and set the matrix
            transform = vtk.vtkTransform()
            transform.SetMatrix(vtk_matrix)
            return transform


        # Initialize lists and dictionary
        cbct_list = []
        ct_list = []
        volume_points_dict = {}

        # Process loaded volumes
        for volumeNode in slicer.util.getNodesByClass("vtkMRMLScalarVolumeNode"):
            volumeName = volumeNode.GetName()
            #print(volumeName)
            shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(slicer.mrmlScene)
            imageItem = shNode.GetItemByDataNode(volumeNode)
            
               # Pridobi vse atribute za ta element
            #attributeNames = shNode.GetItemAttributeNames(imageItem)
            
            #modality = shNode.GetItemAttribute(imageItem, 'DICOM.Modality')
            #manufacturer = shNode.GetItemAttribute(imageItem, 'DICOM.Manufacturer')
            #print(modality)
            
            # Check if the volume is loaded into the scene
            if not slicer.mrmlScene.IsNodePresent(volumeNode):
                print(f"Volume {volumeName} not present in the scene.")
                continue
            
            manufacturer = shNode.GetItemAttribute(imageItem, 'DICOM.Manufacturer')
            #print(manufacturer.lower())
            # Determine scan type
            if "varian" in manufacturer.lower() or "elekta" in manufacturer.lower():
                cbct_list.append(volumeName)
                scan_type = "CBCT"
                yesCbct = True
            else: #Siemens or phillips imamo CTje
                ct_list.append(volumeName)
                scan_type = "CT"
                yesCbct = False
            
            # Detect points using region growing
            grouped_points = detect_points_region_growing(volumeName, yesCbct, intensity_threshold=3000)
            volume_points_dict[(scan_type, volumeName)] = grouped_points

        # Print the results
        # print(f"\nCBCT Volumes: {cbct_list}")
        # print(f"CT Volumes: {ct_list}")
        # print("\nDetected Points by Volume:")
        # for (scan_type, vol_name), points in volume_points_dict.items():
        #     print(f"{scan_type} Volume '{vol_name}': {len(points)} points detected.")


        if cbct_list and ct_list:
            # Izberi prvi CT volumen kot referenco
            ct_volume_name = ct_list[0]
            ct_points = [centroid for centroid, _ in volume_points_dict[("CT", ct_volume_name)]]

            if len(ct_points) < 3:
                print("CT volumen nima dovolj točk za registracijo.")
            else:
                #print("CT points: ", np.array(ct_points))
                
                for cbct_volume_name in cbct_list:
                    # Izvleci točke za trenutni CBCT volumen
                    cbct_points = [centroid for centroid, _ in volume_points_dict[("CBCT", cbct_volume_name)]]

                    print(f"\nProcessing CBCT Volume: {cbct_volume_name}")
                    if len(cbct_points) < 3:
                        print(f"CBCT Volume '{cbct_volume_name}' nima dovolj točk za registracijo.")
                        continue

                    #print("CBCT points: ", np.array(cbct_points))

                    # Display the results for the current CBCT volume
                    # print("\nSVD Method:")
                    # print("Rotation Matrix:\n", svd_rotation_matrix)
                    # print("Translation Vector:\n", svd_translation_vector)

                    # print("\nHorn Method:")
                    # print("Rotation Matrix:\n", horn_rotation_matrix)
                    # print("Translation Vector:\n", horn_translation_vector)

                    # print("\nQuaternion Method:")
                    # print("Rotation Matrix:\n", quaternion_rotation_matrix)
                    # print("Translation Vector:\n", quaternion_translation_vector)

                    
                    
                    # Izberi metodo glede na uporabnikov izbor
                    if selectedMethod == "Kabsch":
                        chosen_rotation_matrix = compute_Kabsch_rotation(cbct_points, ct_points)
                        chosen_translation_vector = compute_translation(cbct_points, ct_points, chosen_rotation_matrix)
                        print("\nKabsch Method:")
                        print("Rotation Matrix:\n", chosen_rotation_matrix)
                        print("Translation Vector:\n", chosen_translation_vector)
                    elif selectedMethod == "Horn":
                        chosen_rotation_matrix = compute_Horn_rotation(cbct_points, ct_points)
                        chosen_translation_vector = compute_translation(cbct_points, ct_points, chosen_rotation_matrix)
                        print("\nHorn Method:")
                        print("Rotation Matrix:\n", chosen_rotation_matrix)
                        print("Translation Vector:\n", chosen_translation_vector)
                    elif selectedMethod == "Iterative Closest Point (Kabsch)":
                        new_points, chosen_rotation_matrix, chosen_translation_vector = icp_algorithm(cbct_points, ct_points)
                        #chosen_translation_vector = compute_translation(cbct_points, ct_points, chosen_rotation_matrix)
                        print("\Iterative Closest Point Method:")
                        print("Rotation Matrix:\n", chosen_rotation_matrix)
                        print("Translation Vector:\n", chosen_translation_vector)

                    imeTransformNoda = cbct_volume_name + " Transform"
                    # Ustvari vtkTransformNode in ga poveži z CBCT volumenom
                    transform_node = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLTransformNode", imeTransformNoda)
                    # Kliči funkcijo, ki uporabi matriki
                    vtk_transform = create_vtk_transform(chosen_rotation_matrix, chosen_translation_vector)
                    # Dodaj transform v node
                    transform_node.SetAndObserveTransformToParent(vtk_transform)

                    # Pridobi CBCT volumen in aplikacijo transformacije
                    cbct_volume_node = slicer.util.getNode(cbct_volume_name)
                    cbct_volume_node.SetAndObserveTransformNodeID(transform_node.GetID()) # Pripni transform node na volumen

                    # Uporabi transformacijo na volumnu (fizična aplikacija)
                    slicer.vtkSlicerTransformLogic().hardenTransform(cbct_volume_node) # Uporabi transform na volumen
                    print("Transform uspešen na", cbct_volume_name)
                    
                    
                    #transformed_cbct_image = create_vtk_transform(cbct_image_sitk, chosen_rotation_matrix, chosen_translation_vector)

        else:
            print("CBCT ali CT volumen ni bil najden.")