AnalyseMorphologique/utils/files/input.py

"""
Created on Thu Apr 20 2023
@name:   input.py
@desc:   This module contains the functions to parse the input files, and create a ScannedObject.
@auth:   Djalim Simaila
@e-mail: djalim.simaila@inrae.fr
"""
import numpy as np
import os
from utils.files.output import save_output_file
from utils.settings.SettingManager import SettingManager


class FacesNotGiven(Exception):
    """
    Exception raised when no faces was given.
    """

class ResultFileNotGiven(Exception):
    """
    Exception raised when no faces was given.
    """

class InvalidFileFormat(Exception):
    """
    Exception raised when the file format is not supported.
    """

class ScannedObject:
    """
    This class is used to manage the data of the 3D object.

    :param vertices: List of verticesm Ndarray of shape (n,2)
    :param faces: List of faces, Ndarray of shape (n,2)
    
    :ivar vertices: List of vertices, Ndarray of shape (n,2)
    :ivar faces: List of faces, Ndarray of shape (n,2)
    :ivar x: List of x values of the vertices
    :ivar y: List of y values of the vertices
    :ivar z: List of z values of the vertices

    :static method from_xyz_file(): Creates a ScannedObject from a .xyz file
    :static method from_obj_file(): Creates a ScannedObject from a .obj file
    :method get_x(): Returns the x values of the vertices
    :method get_y(): Returns the y values of the vertices
    :method get_z(): Returns the z values of the vertices
    :method get_vertices(): Returns the vertices
    :method get_faces(): Returns the faces
    :method get_discrete_vertices(): Returns the discrete vertices
    :method get_data(): Returns the data
    :method export: Exports the data to a file

    :raises FacesNotGiven: If no faces was given
    :raises ResultFileNotGiven: If no result file was given
    """
    def __init__(self, vertices, faces=None):
        self.vertices = np.asarray(vertices)
        self.faces = np.asarray(faces) if faces is not None else None
        self.old_delta = None
        self.old_discrete = None
        self.old_discrete_type = None
        self.x = np.asarray([vertex[0] for vertex in vertices])
        self.y = np.asarray([vertex[1] for vertex in vertices])
        self.z = np.asarray([vertex[2] for vertex in vertices])


    @staticmethod
    def from_file(file_path:str, ratio:float = 1,normalised:str = '')->'ScannedObject':
        """
        Create an Object from a file.

        :param file_path: Path to the file
        :param ratio: Ratio to apply to the vertices
        :param normalised: the axis to normalise
        :return: A ScannedObject
        """
        if os.path.splitext(file_path)[1].lower() == ".xyz":
            return ScannedObject.from_xyz_file(file_path, ' ',ratio, normalised)
        elif os.path.splitext(file_path)[1].lower() == ".obj":
            return ScannedObject.from_obj_file(file_path, ratio, normalised)
        else:
            raise InvalidFileFormat("The file format is not supported.")


    @staticmethod
    def from_obj_file(file_path:str, ratio:float = 1,normalised:str = '')->'ScannedObject':
        """
        Create an Object from an OBJ file.

        :param file_path: Path to the OBJ file
        :param ratio: Ratio to apply to the vertices
        :param normalised: the axis to normalise
        :return: A ScannedObject
        """
        with open(file_path, 'r', encoding='utf-8') as f:
            x, y, z = [], [], []
            triangles = []
            data = f.readlines()
            for line in data :
                if line.startswith('f'):
                    # Ignore the normals and textures
                    if "//" in line:
                        triangles.append([int(line.split()[1].split("//")[0])-1, int(line.split()[2].split("//")[0])-1, int(line.split()[3].split("//")[0])-1])
                    elif "/" in line:
                        triangles.append([int(line.split()[1].split("/")[0])-1, int(line.split()[2].split("/")[0])-1, int(line.split()[3].split("/")[0])-1])
                    else:
                        triangles.append([int(line.split()[1])-1, int(line.split()[2])-1, int(line.split()[3])-1])
                
                # if it is a vertex, the line starts with a 'v ',
                # taking only 'v' would cause to take the textures coordinates('vt'),
                # vertex normals ('vn') and space vertices ('vp')
                elif line.startswith('v '):
                    x.append(float(line.split()[1]) * ratio)
                    y.append(float(line.split()[2]) * ratio)
                    z.append(float(line.split()[3]) * ratio)

            if 'x' in normalised: 
                xmin = min(x)
                for count,_ in enumerate(x):
                    x[count] -= xmin

            if 'y' in normalised: 
                ymin = min(y)
                for count,_ in enumerate(y):
                    y[count] -= ymin

            if 'z' in normalised: 
                zmin = min(z)
                for count,_ in enumerate(z):
                    z[count] -= zmin

        return ScannedObject(list(zip(x,y,z)), triangles, )

    @staticmethod
    def from_xyz_file(file_path:str, delimiter:str = ' ', ratio:float=1, normalised:str = '')->'ScannedObject':
        """
        Create an Object from an XYZ file.

        :param file_path: Path to the XYZ file
        :param delimiter: The delimiter used in the xyz file.
        :param normalised: the axis to normalise
        :return: A ScannedObject
        """
        x , y , z = [], [], []
        with open(file_path, 'r',encoding='utf-8') as f:
            data = f.readlines()
            for line in data:
                x.append(float(line.split(delimiter)[0])* ratio)
                y.append(float(line.split(delimiter)[1])* ratio)
                z.append(float(line.split(delimiter)[2])* ratio)

        if 'x' in normalised:
            xmin = min(x)
            for count,_ in enumerate(x):
                x[count] -= xmin

        if 'y' in normalised:
            ymin = min(y)
            for count,_ in enumerate(y):
                y[count] -= ymin

        if 'z' in normalised:
            zmin = min(z)
            for count,_ in enumerate(z):
                z[count] -= zmin
        return ScannedObject(list(zip(x,y,z)))

    def get_x(self)->list:
        """
        Get the x coordinates of the object.
        return: x coordinates
        """
        return self.x

    def get_y(self)->list:
        """
        Get the y coordinates of the object.
        return: y coordinates
        """
        return self.y

    def get_z(self)->list:
        """
        Get the z coordinates of the object.
        return: z coordinates
        """
        return self.z

    def get_vertices(self, sort:bool = False)->list:
        """
        Get the vertices of the object.
        :param sort: Sort the vertices by z coordinate

        :return: vertices
        """
        vertices = self.vertices if not sort else sorted(self.vertices, key=lambda vertex: vertex[2])
        return vertices

    def get_discrete_vertices(self, step:float = 1)->list:
        """
        Discretize the vertices using the method specified in the settings.

        :param step: Step of the discretization
        :return: Discretized vertices
        """
        if SettingManager.get_instance().get_setting("discretisation_method") == "Z0-Zi < DeltaZ":
            return self.get_discrete_vertices_1(step)
        return self.get_discrete_vertices_2(step)

    def get_discrete_vertices_1(self, step:float = 1)->list:
        """
        Discretize the vertices of the object using a split method.
        This implementation will split the object at every step interval.

        :param step: Step of the discretization
        :return: Discretized vertices
        """

        # if it has already been calculated with the same method and parametters
        # dont do it again
        if self.old_delta == step and self.old_discrete_type == 0:
            return self.old_discrete
        self.old_delta = step
        self.old_discrete_type = 0

        current_interval = int(min(self.get_z()))
        splitted_data = [[]]
        for line in self.get_vertices(sort=True):
            # TODO check distance instead of equality
            if line[2] >= current_interval + step:
                splitted_data.append([])
                current_interval += step
            splitted_data[-1].append(line)
        self.old_discrete = splitted_data
        return splitted_data

    def get_discrete_vertices_2(self, step:float = 1)->list:
        """
        Discretize the vertices of the object using a length method.
        This implementation will split the object when difference between the
        first and last point of a slice is greater or equal then the step interval.

        :param step: Step of the discretization
        :return: Discretized vertices
        """

        # if it has already been calculated with the same method and parametters
        # dont do it again
        if self.old_delta == step and self.old_discrete_type == 1:
            return self.old_discrete
        self.old_delta = step
        self.old_discrete_type = 1

        splitted_data = [[]]
        z = min(self.get_z())
        sorted_vertices = self.get_vertices(sort=True)
        for index,_ in enumerate(sorted_vertices):
            splitted_data[-1].append(sorted_vertices[index])
            if sorted_vertices[index][2] - z > step:
                z = sorted_vertices[index+1][2]
                splitted_data.append([])
        self.old_discrete = splitted_data
        return splitted_data

    def has_faces(self)->bool:
        """
        Check if the object has faces.

        :return: True if the object has faces, False otherwise
        """
        return self.faces is not None

    def get_faces(self,resolved:bool = False)->list:
        """
        Get the faces of the object.
        If the faces are not resolved, the faces will be returned as a list of
        indices of the vertices. else, the faces will be returned as a list of
        vertices.

        :param resolved: If the faces should be resolved
        :return: faces
        """
        if self.faces is None:
            raise FacesNotGiven('No faces were given')
        if resolved:
            return self.vertices[self.faces]
        return self.faces

    def update_from_faces(self,faces:list):
        """
        Update the object from the faces. This will reconstruct the vertices
        from the faces, it is assumed that the faces are given as a list of
        vertices.

        :param faces: Faces to update the object from
        """
        cpt = 0
        vertex_dict = {}
        new_vertices = []
        new_faces = []
        for face in faces:
            new_faces.append([])
            for vertex in face:
                vertex = tuple(vertex)
                if vertex not in vertex_dict:
                    vertex_dict[vertex] = cpt
                    cpt += 1
                    new_vertices.append(vertex)
                new_faces[-1].append(vertex_dict[vertex])

        self.vertices = np.asarray(new_vertices)
        self.faces = np.asarray(new_faces)
        self.x = self.vertices[:,0]
        self.y = self.vertices[:,1]
        self.z = self.vertices[:,2]
        self.normalise()

    def normalise(self, axis:str = 'z'):
        """
        Normalise the object.

        :param axis: Axis to normalise
        """
        if 'x' in axis:
            self.x -= min(self.x)
        if 'y' in axis:
            self.y -= min(self.y)
        if 'z' in axis:
            self.z -= min(self.z)
        self.vertices = np.asarray(list(zip(self.x,self.y,self.z))) 

    def get_data(self)->dict:
        """
        Get the data of the object.

        :return: Data of the object
        """
        return {'verticies': self.vertices,
                'faces': self.faces,
                'x': self.x,
                'y': self.y,
                'z': self.z
                }

    def export_xyz(self, file_path:str,separator:str="\t"):
        """
        Export the object in a file.

        :param file_path: Path of the file
        :param separator: chars used to separate the values
        """
        string = ''
        for vertex in self.get_vertices(sort=True):
            x = round(vertex[0], 6)
            y = round(vertex[1], 6)
            z = round(vertex[2], 6)
            string+=f"{x}{separator}{y}{separator}{z}\n"
        save_output_file(file_path,string)

    def export_obj(self,file_path):
        """
        Export the object in a file.

        :param file_path: Path of the file
        """
        string = ''
        for vertex in self.get_vertices():
            x = round(vertex[0], 6)
            y = round(vertex[1], 6)
            z = round(vertex[2], 6)
            string+=f"v {x} {y} {z}\n"
        for face in self.get_faces():
            string+="f "
            for vertex in face:
                string+=f"{vertex+1} "
            string+="\n"
        save_output_file(file_path,string)


def parse_result_file(file_path: str, separator: str = "\t")-> tuple:
    """
    This functions parses the discretised output file to retreive the first
    three colunms. It is used to extract the means of x y z for the consistency
    check.

    :param file_path: Path of the file  
    :param separator: chars used to separate the values
    :return: x, y, z

    :Example:
    >>> parse_result_file("test.txt")
    ([1.0, 2.0, 3.0], [1.0, 2.0, 3.0], [1.0, 2.0, 3.0])
    """
    lines = []
    x, y, z = [], [], []
    with open(file_path, "r") as f:
        lines = f.readlines()[1:]
    for line in lines:
        line = line.replace(",", ".")
        values = line.split(separator)
        x.append(float(values[0]))
        y.append(float(values[1]))
        z.append(float(values[2]))
    return x, y, z