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osirix.roi

Functionality for the regions of interest in 2D (ROI) and 3D (ROIVolume) viewers.

The following ROI types are available in pyOsiriX, seperated into 2 core groups:

  1. Brush ROIs: Described by a 2D array of boolean values (0 = outside ROI, 1 = within ROI).

    • tPlain: The only brush ROI type.

  2. Point-based ROIs: Described by a set of N 2-element vertices as a shape (N, 2) array.

    • tMeasure: A ruler measurement. N = 2.
    • tROI: A square ROI. N = 4. Created by rectangle.
    • tOval: An oval-based ROI. No limit on N. Created by rectangle.
    • tOPolygon: An open polygon. No limit on N.
    • tCPolygon: A closed polygon. No limit on N.
    • tAngle: An angle measurement. N = 3.
    • tText: A text box. Created by rectangle.
    • tArrow: An arrow. N = 2 (arrow head then tail).
    • tPencil: A closed polygon. No limit it N.
    • t2DPoint: A single point ROI. Created by rectangle.
    • tAxis: An axis-based ROI for bi-dimensional measurement. N = 4.
    • tDynAngle: The angle between two lines. N = 4.
    • tTAGT: A pair of oriented perpendicular lines for measuring distance. N = 6.
    • tBall: A circular ROI representing a slice of a 3D ball ROI. No limit on N. It is not possible to create a new tBall ROI with pyOsiriX.
    • tOvalAngle: An oval with an additional angle specifier. No limit on N. Created by rectangle.
Example usage 
import osirix
import matplotlib.pyplot as plt

viewer = osirix.frontmost_viewer()  # Raises GrpcException error if no viewer is available.
rois = viewer.selected_rois()  # Get the currently selected ROI object.
if len(rois) == 0:
    raise ValueError("No ROIs found.")
roi = rois[0]
roi_type = roi.itypes()[roi.itype]  # Get the selected ROI type.
if roi_type == "tPlain":
    raise ValueError("Cannot plot mask (brush) ROI vertices")
plt.plot(roi.points[:, 0], roi.points[:, 1], "ko")  # Plot the ROI vertices.
plt.show()

ROI

Bases: OsirixBase

Represents a single region of interest in a 2D viewer (ViewerController)

color property writable

The color of the volume ROI as a (r, g, b) tuple (each channel in range 0-255)

itype property

The ROI type as an integer

name property writable

The name of the ROI

opacity property writable

The opacity of the ROI, ranging from 0 (transparent) to 1 (opaque)

pix property

The DCMPix instance coupled with the ROI. This should be the one on which it is drawn.

points property writable

The vertices of any polygon-based ROI. An array with shape [N, 2].

stype property

The type of the ROI as a string

thickness property writable

The line thickness (in points) of any polygon-based ROI.

centroid()

The centroid of the ROI in format (column, row). Non-integer values are permitted.

delete()

Delete the ROI. This cannot be undone!

flip_horizontally()

Flip the ROI horizontally

flip_vertically()

Flip the ROI vertically

itypes(reverse_order=False) classmethod

A map between the integer ROI type (itype) and a text descriptor.

Parameters:

Name Type Description Default
reverse_order bool

If False then the mapping is provided in the form {itype: descriptor} else it is returned in reverse order: {descriptor: itype}.

 False

Returns:

Type Description
Dict

A mapping between ROI itype and textual descriptor.

roi_area()

The area of the ROI in squared centimeters.

roi_move(columns, rows)

Move the ROI by a specified number of columns and rows.

Parameters:

Name Type Description Default
columns int

The number of columns to move. positive = left → right, negative = right → left.

 required
rows int

The number of rows to move. positive = downwards, negative = upwards.

 required

rotate(theta, center=None)

Rotate the ROI by angle theta, about a given

Parameters:

Name Type Description Default
theta float

The angle by which to rotate (in degrees). Positive is clockwise.

 required
center Tuple[float, float]

The position (column, row) about which to rotate. These can be non-integer values. If None, then rotation is about the centroid of the ROI.

 None

ROIVolume

Bases: OsirixBase

Represents a single volumetric region of interest in a 3D viewer (VRController)

color property writable

The color of the volume ROI as a (r, g, b) tuple (each channel in range 0-1)

factor property writable

The factor of the ROI volume in the range 0-1

name property

The name of the ROI volume.

opacity property writable

The opacity of the ROI volume in the range 0-1

texture property writable

Whether the volume ROI is textured

visible property writable

Whether the volume ROI is visible in the 3D viewer

vr_controller property

The 3D volume render window in which this ROI is shown.

volume()

The volume of the ROI

Returns:

Type Description
float

The volume of the 3D ROI (in millilitres).