cgse 2023.38.0__py3-none-any.whl → 2024.1.3__py3-none-any.whl

egse/coordinates/__init__.py

@@ -1,531 +0,0 @@
-import ast
-import logging
-import re
-from math import atan
-from math import atan2
-from math import cos
-from math import degrees
-from math import pow
-from math import radians
-from math import sin
-from math import sqrt
-from math import tan
-from typing import Dict
-from typing import List
-from typing import Optional
-from typing import Union
-
-import numpy as np
-from numpy.polynomial import Polynomial
-
-from egse.coordinates.referenceFrame import ReferenceFrame
-from egse.settings import Settings
-from egse.state import GlobalState
-from egse.setup import NavigableDict
-
-logger = logging.getLogger(__name__)
-
-FOV_SETTINGS = Settings.load("Field-Of-View")
-CCD_SETTINGS = Settings.load("CCD")
-
-
-def undistorted_to_distorted_focal_plane_coordinates(
-    x_undistorted, y_undistorted, distortion_coefficients, focal_length
-):
-    """
-    Conversion from undistorted to distorted focal-plane coordinates.  The distortion is a
-    radial effect and is defined as the difference in radial distance to the optical axis
-    between the distorted and undistorted coordinates, and can be expressed in terms of the
-    undistorted radial distance r as follows:
-
-        Δr = r * [(k1 * r**2) + (k2 * r**4) + (k3 * r**6)],
-
-    where the distortion and r are expressed in normalised focal-plane coordinates (i.e. divided
-    by the focal length, expressed in the same unit), and (k1, k2, k3) are the distortion
-    coefficients.
-
-    Args:
-        x_undistorted: Undistorted x-coordinate on the focal plane [mm].
-        y_undistorted: Undistorted y-coordinate on the focal plane [mm].
-        distortion_coefficients: List of polynomial coefficients for the field distortion.
-        focal_length: Focal length [mm].
-    Returns:
-        x_distorted: Distorted x-coordinate on the focal plane [mm].
-        y_distorted: Distorted y-coordinate on the focal plane [mm].
-    """
-
-    # Distortion coefficients -> (0, 0, 0, k1, 0, k2, 0, k3)
-
-    coefficients = [
-        0,
-        0,
-        0,
-        distortion_coefficients[0],
-        0,
-        distortion_coefficients[1],
-        0,
-        distortion_coefficients[2],
-    ]
-    distortion_polynomial = Polynomial(coefficients)
-
-    # Position on the focal plane:
-    #   - field angle [radians]
-    #   - radial distance from the optical axis [normalised pixels]
-
-    angle = atan2(y_undistorted, x_undistorted)
-    distance_undistorted = sqrt(pow(x_undistorted, 2) + pow(y_undistorted, 2)) / focal_length
-
-    # Distortion [mm]
-    # Source moves away from the optical axis (radially)
-
-    distortion = distortion_polynomial(distance_undistorted) * focal_length
-
-    # The field angle remains the same
-
-    x_distorted = x_undistorted + cos(angle) * distortion
-    y_distorted = y_undistorted + sin(angle) * distortion
-
-    return x_distorted, y_distorted
-
-
-def distorted_to_undistorted_focal_plane_coordinates(
-    x_distorted, y_distorted, inverse_distortion_coefficients, focal_length
-):
-    """
-    Conversion from distorted to undistorted focal-plane coordinates.  The inverse distortion is a
-    radial effect and is defined as the difference in radial distance to the optical axis
-    between the distorted and undistorted coordinates, and can be expressed in terms of the
-    undistorted radial distance r as follows:
-
-        Δr = r * [(k1 * r**2) + (k2 * r**4) + (k3 * r**6)],
-
-    where the inverse distortion and r are expressed in normalised focal-plane coordinates (i.e. divided
-    by the focal length, expressed in the same unit), and (k1, k2, k3) are the inverse distortion
-    coefficients.
-
-    Args:
-        x_distorted: Distorted x-coordinate on the focal plane [mm].
-        y_distorted: Distorted y-coordinate on the focal plane [mm].
-        inverse_distortion_coefficients: List of polynomial coefficients for the inverse field distortion.
-        focal_length: Focal length [mm].
-    Returns:
-        x_undistorted: Undistorted x-coordinate on the focal plane [mm].
-        y_undistorted: Undistorted y-coordinate on the focal plane [mm].
-    """
-
-    # Inverse distortion coefficients -> (0, 0, 0, k1, 0, k2, 0, k3)
-
-    coefficients = [
-        0,
-        0,
-        0,
-        inverse_distortion_coefficients[0],
-        0,
-        inverse_distortion_coefficients[1],
-        0,
-        inverse_distortion_coefficients[2],
-    ]
-    inverse_distortion_polynomial = Polynomial(coefficients)
-
-    # Position on the focal plane:
-    #   - field angle [radians]
-    #   - radial distance from the optical axis [normalised pixels]
-
-    angle = atan2(y_distorted, x_distorted)
-    distance_distorted = sqrt(pow(x_distorted, 2) + pow(y_distorted, 2)) / focal_length
-
-    # Inverse distortion [mm]
-    # Source moves towards the optical axis (radially) -> negative!
-
-    inverse_distortion = inverse_distortion_polynomial(distance_distorted) * focal_length
-
-    # The field angle remains the same
-
-    x_undistorted = x_distorted + cos(angle) * inverse_distortion
-    y_undistorted = y_distorted + sin(angle) * inverse_distortion
-
-    return x_undistorted, y_undistorted
-
-
-def focal_plane_to_ccd_coordinates(x_fp, y_fp):
-    """
-    Conversion from focal-plane to pixel coordinates on the appropriate CCD.
-
-    Args:
-        x_fp: Focal-plane x-coordinate [mm].
-        y_fp: Focal-plane y-coordinate [mm].
-    Returns:
-        Pixel coordinates (row, column) and the corresponding CCD.  If the given
-        focal-plane coordinates do not fall on any CCD, (None, None, None) is
-        returned.
-    """
-    setup = GlobalState.setup
-
-    if setup is not None:
-        num_rows = setup.camera.ccd.num_rows
-        num_cols = setup.camera.ccd.num_column
-    else:
-        num_rows = CCD_SETTINGS.NUM_ROWS
-        num_cols = CCD_SETTINGS.NUM_COLUMNS
-
-    for ccd_code in range(1, 5):
-
-        (row, column) = __focal_plane_to_ccd_coordinates__(x_fp, y_fp, ccd_code)
-
-        if (row < 0) or (column < 0):
-            continue
-
-        if (row >= num_rows) or (column >= num_cols):
-                continue
-
-        return row, column, ccd_code
-
-    return None, None, None
-
-
-def __focal_plane_to_ccd_coordinates__(x_fp, y_fp, ccd_code):
-    """
-    Conversion from focal-plane coordinates to pixel coordinates on the given CCD.
-
-    Args:
-        x_fp: Focal-plane x-coordinate [mm].
-        y_fp: Focal-plane y-coordinate [mm].
-        ccd_code: Code of the CCD for which to calculate the pixel coordinates [1, 2, 3, 4].
-    Returns:
-        Pixel coordinates (row, column) on the given CCD.
-    """
-
-    setup = GlobalState.setup
-
-    if setup is not None:
-        ccd_orientation = setup.camera.ccd.orientation[int(ccd_code) - 1]
-        pixel_size      = setup.camera.ccd.pixel_size / 1000.0  # [mm]
-        ccd_origin_x    = GlobalState.setup.camera.ccd.origin_offset_x[int(ccd_code) - 1]
-        ccd_origin_y    = GlobalState.setup.camera.ccd.origin_offset_y[int(ccd_code) - 1]
-    else:
-        ccd_orientation = CCD_SETTINGS.ORIENTATION[int(ccd_code) - 1]
-        pixel_size      = CCD_SETTINGS.PIXEL_SIZE / 1000  # Pixel size [mm]
-        ccd_origin_x    = CCD_SETTINGS.ZEROPOINT[0]
-        ccd_origin_y    = CCD_SETTINGS.ZEROPOINT[1]
-
-    ccd_angle = radians(ccd_orientation)
-
-    # CCD coordinates [mm]
-
-    row    = ccd_origin_y - x_fp * sin(ccd_angle) + y_fp * cos(ccd_angle)
-    column = ccd_origin_x + x_fp * cos(ccd_angle) + y_fp * sin(ccd_angle)
-
-    row /= pixel_size
-    column /= pixel_size
-
-    return row, column
-
-
-def focal_plane_coordinates_to_angles(x_fp, y_fp):
-    """
-    Conversion from focal-plane coordinates to the gnomonic distance from the optical axis and
-    the in-field angle.
-
-    Args:
-        x_fp: Focal-plane x-coordinate [mm].
-        y_fp: Focal-plane y-coordinate [mm].
-    Returns:
-        Gnomonic distance from the optical axis and in-field angle [degrees].
-    """
-
-    setup = GlobalState.setup
-
-    if setup is not None:
-        focal_length_mm = GlobalState.setup.camera.fov.focal_length_mm
-    else:
-        focal_length_mm = FOV_SETTINGS.FOCAL_LENGTH
-
-    theta = degrees(atan(sqrt(pow(x_fp, 2) + pow(y_fp, 2)) / focal_length_mm))
-    phi = degrees(atan2(y_fp, x_fp))
-
-    return theta, phi
-
-
-def ccd_to_focal_plane_coordinates(row, column, ccd_code):
-    """
-    Conversion from pixel-coordinates on the given CCD to focal-plane coordinates.
-
-    Args:
-        row: Row coordinate [pixels].
-        column: Column coordinate [pixels].
-        ccd_code: Code of the CCD for which the pixel coordinates are given.
-    Returns:
-        Focal-plane coordinates (x, y) [mm].
-    """
-
-    setup = GlobalState.setup
-
-    if setup is not None:
-        ccd_orientation = setup.camera.ccd.orientation[int(ccd_code) - 1]
-        pixel_size_mm   = setup.camera.ccd.pixel_size / 1000.0  # [mm]
-        ccd_origin_x    = GlobalState.setup.camera.ccd.origin_offset_x[int(ccd_code) - 1]
-        ccd_origin_y    = GlobalState.setup.camera.ccd.origin_offset_y[int(ccd_code) - 1]
-    else:
-        ccd_orientation = CCD_SETTINGS.ORIENTATION[int(ccd_code) - 1]
-        pixel_size_mm   = CCD_SETTINGS.PIXEL_SIZE / 1000  # Pixel size [mm]
-        ccd_origin_x    = CCD_SETTINGS.ZEROPOINT[0]
-        ccd_origin_y    = CCD_SETTINGS.ZEROPOINT[1]
-
-    # Convert the pixel coordinates into [mm] coordinates
-
-    row_mm = row * pixel_size_mm
-    column_mm = column * pixel_size_mm
-
-    # Convert the CCD coordinates into FP coordinates [mm]
-
-    ccd_angle = radians(ccd_orientation)
-
-    x_fp = (column_mm - ccd_origin_x) * cos(ccd_angle) - (row_mm - ccd_origin_y) * sin(ccd_angle)
-    y_fp = (column_mm - ccd_origin_x) * sin(ccd_angle) + (row_mm - ccd_origin_y) * cos(ccd_angle)
-
-    # That's it
-
-    return x_fp, y_fp
-
-def angles_to_focal_plane_coordinates(theta, phi):
-    """
-    Conversion from the gnomonic distance from the optical axis and
-    the in-field angle to focal-plane coordinates.
-
-    Args:
-        theta: Gnomonic distance from the optical axis [degrees].
-        phi: In-field angle [degrees].
-    Returns:
-        Focal-plane coordinates (x, y) [mm].
-    """
-
-    setup = GlobalState.setup
-
-    if setup is not None:
-        focal_length_mm = GlobalState.setup.camera.fov.focal_length_mm
-    else:
-        focal_length_mm = FOV_SETTINGS.FOCAL_LENGTH
-
-    distance = focal_length_mm * tan(radians(theta))  # [mm]
-
-    phi_radians = radians(phi)
-
-    x_fp = distance * cos(phi_radians)
-    y_fp = distance * sin(phi_radians)
-
-    return x_fp, y_fp
-
-
-def dict_to_ref_model(model_def: Union[Dict, List]) -> NavigableDict:
-    """
-    Creates a reference frames model from a dictionary or list of reference frame definitions.
-
-    When a list is provided, the items in the list must be ReferenceFrames.
-
-    The reference frame definitions are usually read from a YAML file or returned by a Setup,
-    but can also be just ReferenceFrame objects.
-
-    ReferenceFrame definitions have the following format:
-
-    ```
-    ReferenceFrame://(<definition>)
-    ```
-    where `<definition>` has the following elements, separated by '` | `':
-    * a translation matrix
-    * a rotation matrix
-    * the name of the reference frame
-    * the name of the reference for this reference frame
-    * a dictionary of links
-
-    Args:
-        model_def (dict or list): the definition of the reference model
-
-    Returns:
-        A dictionary representing the reference frames model.
-    """
-
-    ref_model = NavigableDict({})
-    ref_links = {}
-
-    def create_ref_frame(name, data) -> Union[ReferenceFrame, str]:
-
-        # This is a recursive function that creates a reference frame based on the given data.
-        # * When the data is already a ReferenceFrame, it just returns data
-        # * When data starts with the special string `ReferenceFrame//`, the data string is parsed
-        #   and a corresponding ReferenceFrame is returned
-        # * When there is no match, the data is returned unaltered.
-        #
-        # SIDE EFFECT:
-        # * In the process, the outer ref-model and ref_links are updated.
-
-        if isinstance(data, ReferenceFrame):
-            return data
-
-        match = re.match(r"ReferenceFrame//\((.*)\)$", data)
-        if not match:
-            return data
-
-        translation, rotation, name, ref_name, links = match[1].split(" | ")
-
-        # all links are processed later..
-
-        ref_links[name] = ast.literal_eval(links)
-
-        if ref_name == name == "Master":
-            ref_model.add(ref_name, ReferenceFrame.createMaster())
-            return ref_model["Master"]
-
-        if ref_name not in ref_model:
-            ref_model.add(ref_name, create_ref_frame(ref_name, model_def[ref_name]))
-
-        ref_frame = ReferenceFrame.fromTranslationRotation(
-            deserialize_array(translation),
-            deserialize_array(rotation),
-            name=name,
-            ref=ref_model[ref_name],
-        )
-
-        return ref_frame
-
-    # if the given model_def is a list, turn it into a dict
-
-    if isinstance(model_def, list):
-        model_def = {frame.name: frame for frame in model_def}
-
-    for key, value in model_def.items():
-        if key not in ref_model:
-            ref_model.add(key, create_ref_frame(key, value))
-
-    # Process all the links
-
-    for ref_name, link_names in ref_links.items():
-        ref = ref_model[ref_name]
-        for link_name in link_names:
-            if link_name not in ref.linkedTo:
-                ref.addLink(ref_model[link_name])
-
-    return ref_model
-
-
-def ref_model_to_dict(ref_model) -> NavigableDict:
-    """Creates a dictionary with reference frames definitions that define a reference model.
-
-    Args:
-        ref_model: A dictionary representing the reference frames model or a list of reference
-            frames.
-    Returns:
-        A dictionary of reference frame definitions.
-    """
-
-    if isinstance(ref_model, dict):
-        ref_model = ref_model.values()
-
-    # take each key (which is a reference frame) and serialize it
-
-    model_def = {}
-
-    for ref in ref_model:
-        translation, rotation = ref.getTranslationRotationVectors()
-        links = [ref.name for ref in ref.linkedTo]
-        model_def[ref.name] = (
-            f"ReferenceFrame//("
-            f"{serialize_array(translation, precision=6)} | "
-            f"{serialize_array(rotation, precision=6)} | "
-            f"{ref.name} | "
-            f"{ref.ref.name} | "
-            f"{links})"
-        )
-
-    return NavigableDict(model_def)
-
-
-def serialize_array(arr: Union[np.ndarray, list], precision: int = 4) -> str:
-    """Returns a string representation of a numpy array.
-
-    >>> serialize_array([1,2,3])
-    '[1, 2, 3]'
-    >>> serialize_array([[1,2,3], [4,5,6]])
-    '[[1, 2, 3], [4, 5, 6]]'
-    >>> serialize_array([[1,2.2,3], [4.3,5,6]])
-    '[[1.0000, 2.2000, 3.0000], [4.3000, 5.0000, 6.0000]]'
-    >>> serialize_array([[1,2.2,3], [4.3,5,6]], precision=2)
-    '[[1.00, 2.20, 3.00], [4.30, 5.00, 6.00]]'
-
-    Args:
-        arr: a one or two dimensional numpy array or list.
-        precision (int): number of digits of precision
-    Returns:
-        A string representing the input array.
-    """
-    if isinstance(arr, list):
-        arr = np.array(arr)
-    msg = np.array2string(
-        arr,
-        separator=", ",
-        suppress_small=True,
-        formatter={"float_kind": lambda x: f"{x:.{precision}f}"},
-    ).replace("\n", "")
-    return msg
-
-
-def deserialize_array(arr_str: str) -> Optional[np.ndarray]:
-    """Returns a numpy array from the given string.
-
-    The input string is interpreted as a one or two-dimensional array, with commas or spaces
-    separating the columns, and semi-colons separating the rows.
-
-    >>> deserialize_array('1,2,3')
-    array([1, 2, 3])
-    >>> deserialize_array('1 2 3')
-    array([1, 2, 3])
-    >>> deserialize_array('1,2,3;4,5,6')
-    array([[1, 2, 3],
-           [4, 5, 6]])
-    >>> deserialize_array("[[1,2,3], [4,5,6]]")
-    array([[1, 2, 3],
-           [4, 5, 6]])
-
-    Args:
-        arr_str: string representation of a numpy array
-    Returns:
-        A one or two-dimensional numpy array or `None` when input string cannot be parsed into a
-        numpy array.
-    """
-
-    import re
-
-    arr_str = re.sub(r"\],\s*\[", "];[", arr_str)
-    try:
-        arr = np.array(_convert_from_string(arr_str))
-        return arr if ";" in arr_str else arr.flatten()
-    except ValueError as exc:
-        logger.error(f"Input string could not be parsed into a numpy array: {exc}")
-    return None
-
-
-def _convert_from_string(data):
-
-    # This function was copied from:
-    #   https://github.com/numpy/numpy/blob/v1.19.0/numpy/matrixlib/defmatrix.py#L14
-    # We include the function here because the np.matrix class is deprecated and will be removed.
-    # This function is what we actually needed from np.matrix.
-
-    for char in "[]":
-        data = data.replace(char, "")
-
-    rows = data.split(";")
-    new_data = []
-    count = 0
-    for row in rows:
-        trow = row.split(",")
-        new_row = []
-        for col in trow:
-            temp = col.split()
-            new_row.extend(map(ast.literal_eval, temp))
-        if count == 0:
-            n_cols = len(new_row)
-        elif len(new_row) != n_cols:
-            raise ValueError("Rows not the same size.")
-        count += 1
-        new_data.append(new_row)
-    return new_data

egse/coordinates/avoidance.py

@@ -1,103 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-"""
-Created on Wed Sep  9 17:19:47 2020
-
-@author: pierre
-"""
-import numpy as np
-from egse.state import GlobalState
-from egse.coordinates.point import Points
-
-
-def is_avoidance_ok(hexusr,hexobj,setup=None,verbose=False):
-    """
-    is_avoidance_ok(hexusr,hexobj,setup=None)
-    
-    INPUT
-    hexusr : ReferenceFrame 
-             xy plane = maximal height of the FPA_SEN
-             z axis  pointing away from the FPA
-             
-    hexobj : ReferenceFrame
-             xy plane = FPA_SEN
-             z axis pointing towards L6
-             
-    setup  : GlobalSetup.setup, optional
-             if not provided, GlobalState.setup is used
-    
-    
-    OUTPUT :  Boolean indicating wheather or not the FPA is outside of the avoidance volume around L6
-    """
-        
-    if setup is None:
-        setup = GlobalState.setup
-    
-    """
-    A. HORIZONTAL AVOIDANCE
-    Ensure that the center of L6, materialised by HEX_USR (incl. z-direction security wrt TOU_L6)
-    stays within a given radius of the origin of FPA_SEN
-    """
-
-    # Clearance = the tolerance in every horizontal direction (3 mm; PLATO-KUL-PL-ICD-0001 v1.2)
-    clearance_xy = setup.camera.fpa.avoidance.clearance_xy
-    
-    # l6xy = the projection of the origin of HEX_USR on the X-Y plane of FPA_SEN
-    l6xy = hexusr.getOrigin().expressIn(hexobj)[:2]
-    
-    # !! This is a verification of the current situation --> need to replace by a simulation of the forthcoming movement in the building block
-    horizontal_check = ((l6xy[0]**2.+l6xy[1]**2.) < clearance_xy*clearance_xy)
-    
-    
-    """
-    B. VERTICAL AVOIDANCE
-    Ensure that the CCD never hits L6.
-    The definition of HEX_USR includes a tolerance below L6 (1.65 mm)
-    We include a tolerance above FPA_SEN here (0.3 mm)
-    We define a collection of points to act at the vertices of the avoidance volume above the FPA
-    """
-
-    # Clearance = vertical uncertainty on the CCD location (0.3 mm; PLATO-KUL-PL-ICD-0001 v1.2)
-    clearance_z = setup.camera.fpa.avoidance.clearance_z
-    
-    # Vertices = Points representing the vertices of the avoidance volume above the FPA (60)
-    vertices_nb     = setup.camera.fpa.avoidance.vertices_nb
-    # All vertices are on a circle of radius 'vertices_radius' (100 mm)
-    vertices_radius = setup.camera.fpa.avoidance.vertices_radius
-    
-    angles = np.linspace(0,np.pi * 2,vertices_nb,endpoint=False)
-    vertices_x = np.cos(angles) * vertices_radius
-    vertices_y = np.sin(angles) * vertices_radius
-    vertices_z = np.ones_like(angles) * clearance_z
-    
-    # The collection of Points defining the avoidance volume around FPA_SEN
-    vert_obj = Points(coordinates=np.array([vertices_x,vertices_y,vertices_z]),ref=hexobj,name="vert_obj")
-    
-    # Their coordinates in HEX_USR
-    # NB: vert_obj is a Points, vert_usr is an array
-    vert_usr = vert_obj.expressIn(hexusr)
-    
-    
-    # !! Same as above : this is verifying the current situation, not the one after a planned movement
-    # Verify that all vertices ("protecting" FPA_SEN) are below the x-y plane of HEX_USR ("protecting" L6)
-    vertical_check = (np.all(vert_usr[2,:] < 0.))
-    
-    if verbose:
-        printdict = {True:"OK", False:"NOT OK"}
-        print(f"HORIZONTAL AVOIDANCE: {printdict[horizontal_check]}")
-        print(f" VERTICAL  AVOIDANCE: {printdict[vertical_check]}")
-    
-    if verbose > 1:
-        print(f"Points Coordinates")
-        coobj = vert_obj.coordinates
-        for i in range(vertices_nb):
-            print(f"{i} OBJ {np.round(coobj[:3,i],6)} --> USR {np.round(vert_usr[:3,i],6)}")
-        vert_z = vert_usr[2,:]
-        vert_zi = np.where(vert_z==np.max(vert_z))
-        print(f"#vertices at max z : {len(vert_zi[0])}")
-        print(f"First one: vertex {vert_zi[0][0]} : {np.round(vert_usr[:3,vert_zi[0][0]],6)}")
-
-    return horizontal_check and vertical_check
-
-
-