geometric_calibration package¶
Top-level package for Geometric Calibration.
Submodules¶
geometric_calibration.cli module¶
geometric_calibration.geometric_calibration module¶
Main module.
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geometric_calibration.geometric_calibration.
calibrate_2d
(projection_dir, bbs_3d, sad, sid)[source]¶ Main 2D Calibration routines.
Parameters: - projection_dir (str) – path to directory containing .raw files
- bbs_3d (numpy.array) – array containing 3D coordinates of BBs
- sad (float) – nominal source to isocenter (A) distance
- sid (float) – nominal source to image distance
Returns: dictionary with calibration results
Return type: dict
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geometric_calibration.geometric_calibration.
calibrate_cbct
(projection_dir, bbs_3d, sad, sid)[source]¶ Main CBCT Calibration routines.
Parameters: - projection_dir (str) – path to directory containing .raw files
- bbs_3d (numpy.array) – array containing 3D coordinates of BBs
- sad (float) – nominal source to isocenter (A) distance
- sid (float) – nominal source to image distance
Returns: dictionary with calibration results
Return type: dict
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geometric_calibration.geometric_calibration.
calibrate_projection
(projection_file, bbs_3d, sad, sid, angle, angle_offset=0, img_dim=[1024, 768], pixel_size=[0.388, 0.388], search_area=7, resolution_factor=1, image_center=None, drag_and_drop=True)[source]¶ Calibration of a single projection.
Parameters: - projection_file (str) – path to file
- bbs_3d (numpy.array) – 3D coordinates of phantom’s reference points
- sad (float) – nominal source to isocenter (A) distance
- sid (float) – nominal source to image distance
- angle (float) – gantry angle for current projection
- angle_offset (int, optional) – angle offset for panel, defaults to 0
- img_dim (list, optional) – image dimensions in pixels, defaults to [1024, 768]
- pixel_size (list, optional) – pixel dimensions in mm, defaults to [0.388, 0.388]
- search_area (int, optional) – dimension of reference point’s searching area, defaults to 7
- resolution_factor (int, optional :param image_center: [description], defaults to None) – resolution factor, when mode is “cbct” this parameter equals to 1, in 2D mode is 2 (because resolution is doubled), defaults to 1
- image_center (list, optional) – center of image, defaults to None
- drag_and_drop (bool, optional) – whether or not perform Drag&Drop correction routines, typically set to True for first projection. Defaults to True
Raises: Exception – if less than 5 BBs centroids are recognized, optimizer automatically fails since calibration can’t be consider reliable
Returns: dictionary with calibration results for current projection
Return type: dict
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geometric_calibration.geometric_calibration.
calibration_cost_function
(param, bbs_3d, pixel_size, bbs_2d, isocenter)[source]¶ Cost Function for calibration optimizers.
Parameters: - param (list) – parameters to be optimized
- bbs_3d (numpy.array) – 3D coordinates of reference BBs
- pixel_size (list) – pixel dimensions in mm
- bbs_2d (numpy.array) – 2D coordinates of BBs projected on the current image
- isocenter (numpy.array) – coordinates of isocenter
Returns: cost function value to be minimized
Return type: float
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geometric_calibration.geometric_calibration.
plot_calibration_results
(calib_results)[source]¶ Plot source/panel position after calibration.
Parameters: calib_results (dict) – dictionary containing results of a calibration
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geometric_calibration.geometric_calibration.
save_lut
(path, calib_results, mode)[source]¶ Save LUT file for a calibration.
Parameters: - path (str) – path to .raw file directory, where LUT will be saved
- calib_results (string) – dictionary containing results for a calibration
- calib_results – acquisition modality for calibration
geometric_calibration.reader module¶
This module contains some function for I/O purposes.
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geometric_calibration.reader.
read_bbs_ref_file
(filename)[source]¶ Read phantom reference file with bbs coordinates
Parameters: filename (str) – path to file Returns: Array containing bbs coordinates [x,y,z] Return type: numpy.array
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geometric_calibration.reader.
read_img_label_file
(filename)[source]¶ Read imgLabels.txt file contained in .raw projection’s directory. This File contains information about path and the gantry angle of every .raw projection.
Parameters: filename (str) – path to file Returns: list with path and list with angles for every row in imgLabels.txt file Return type: list
geometric_calibration.utils module¶
Utilities module.
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class
geometric_calibration.utils.
DraggablePoints
(artists, tolerance=10)[source]¶ Bases:
object
Draggable points on matplotlibe figure.
- Returns:
- DraggablePoints – DraggablePoints object
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get_coord
()[source]¶ Obtain current coordinates of points.
Returns: An array nx2 containing coordinates for every point [x,y] Return type: numpy.array
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on_close
(event)[source]¶ Event Handler for closure of figure.
- Arguments:
- event – Event that triggers the method
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on_key_pressed
(event)[source]¶ Event Handler for “enter” key pression.
- Arguments:
- event – Event that triggers the method
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on_motion
(event)[source]¶ Event Handler for mouse movement during dragging of points.
- Arguments:
- event – Event that triggers the method
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geometric_calibration.utils.
adjust_image
(img, new_grayscale_range)[source]¶ Translate image data to the appropriate lower bound of the default data range. This translation is needed to show properly .raw images.
Parameters: - img (numpy.array) – Array containing the loaded .raw image
- new_grayscale_range (list) – Grayscale range to apply to image
Returns: Image corrected with new grayscale range
Return type: numpy.array
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geometric_calibration.utils.
angle2rotm
(rot_x, rot_y, rot_z)[source]¶ Generate a rototranslator (only rotation) starting from Euler angles
NB: Convention is ‘XYZ’
Parameters: - rot_x (int or float) – Rotation along x
- rot_y (int or float) – Rotation along y
- rot_z (int or float) – Rotation along z
Returns: 4x4 Rototranslation matrix in homogeneous form
Return type: numpy.array
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geometric_calibration.utils.
create_camera_matrix
(panel_orientation, sid, sad, pixel_size, isocenter)[source]¶ Generate projection matrix starting from extrinsic and intrinsic parameters.
Parameters: - panel_orientation (numpy.array) – Array nx3 containing rotations of the image’s plane [rot_x, rot_y, rot_z]
- sid (float) – SID distance
- sad (float) – SAD distance
- pixel_size (list) – Pixel Dimensions in mm
- isocenter (numpy.array) – Coordinates of isocenter
Returns: 3x4 Camera Matrix
Return type: numpy.array
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geometric_calibration.utils.
deg2rad
(angle_deg)[source]¶ Convert angles from degrees to radians.
Parameters: angle_deg (int or float) – Angle to convert Returns: Angle converted in radians Return type: float
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geometric_calibration.utils.
drag_and_drop_bbs
(projection_path, bbs_projected, grayscale_range)[source]¶ Drag&Drop Routines for bbs position’s correction.
Parameters: - projection_path (str) – Path to the projection .raw file
- bbs_projected (numpy.array) – Array nx2 with bbs yet projected
- grayscale_range (list) – Grayscale range for current projection
Returns: Array nx2 containing the updated coordinates for bbs
Return type: numpy.array
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geometric_calibration.utils.
get_grayscale_range
(img)[source]¶ New grayscale range for .raw images, since original values are too bright. New range is computed between min of image and one order of magnitude less than original image. Worst case scenario [0, 6553.5] (since im is loaded as uint16)
Parameters: img (numpy.array) – Array containing the loaded .raw image Returns: Grayscale range for current projection Return type: list
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geometric_calibration.utils.
project_camera_matrix
(r3d, image_center, camera_matrix, resolution_scale=1)[source]¶ Project 3D data starting from camera matrix based on intrinsic and extrinsic parameters
Parameters: - r3d (numpy.array) – Array nx3 containing 3d coordinates of points [x,y,z]
- image_center (list) – Center of the image
- camera_matrix (numpy.array) – Projection matrix obtained combining extrinsic and intrinsic parameters
- resolution_scale – resolution factor, when mode is “cbct” this
- parameter equals to 1, in 2D mode is 2 (because resolution is doubled),
- defaults to 1
Returns: Array nx2 containing 2D coordinates of points projected on image plane [x,y] Return type: numpy.array
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geometric_calibration.utils.
search_bbs_centroids
(img, ref_2d, search_area, dim_img, grayscale_range)[source]¶ Search bbs based on projection.
Starting from the updated coordinates, define a search area around them and identify the bbs as black pixels inside these areas (brandis are used as probes). Search for the bbs in the image (basically very low intensity surrounding by higher intensity pixel. Centroids coordinates are the mean pixels that have an intensity that is lower than the lowest nominal intensity plus a tollerance.
Parameters: - img (numpy.array) – Array containing the loaded .raw file
- ref_2d (numpy.array) – Array nx2 containing the coordinates for bbs projected on img
- search_area (int) – Size of the region in which to search for centroids. Actual dimension of the area is a square with dimension (2*search_area, 2*search_area)
- dim_img (list) – Dimension of img
- grayscale_range (list) – Grayscale range for current projection
Raises: Exception – if the function does not find any centroid, an exception is thrown
Returns: Array nx2 containing coordinates for every centroids found [x,y]
Return type: numpy.array