osirix.viewer_controller

Functionality for the 2D viewer.

Example usage

import osirix

viewer = osirix.frontmost_viewer()  # Raises GrpcException error if no viewer is available.
n_slices = len(viewer.pix_list(0))  # pix_list(n) returns array of DCMPix instances for nth frame.
viewer.idx = int(n_slices / 2)  # Move display to the central slice.
viewer.wlww = (50, 100)  # Set the displayed window level and width..
viewer.needs_display_update()  #Get the viewer to re-draw itself.

ViewerController

Bases: OsirixBase

Represents one of the displayed volume render windows.

displayed_idx: int property writable

The data slice index currently being displayed to the viewer (starting at 0).

Note that this may not be equal to the index displayed on the viewer when data_flipped is True.

flipped_data: int property

Whether the slices data are flipped in the viewer.

idx: int property writable

The slice index currently being displayed to the viewer (starting at 0).

Note that the index displayed on the viewer is this value plus one.

max_movie_index: int property

The maximum movie index in the viewer.

modality: str property

The modality of the displayed data.

movie_idx: int property writable

The frame currently being displayed by the viewer.

title: str property

The title of the 2D viewing window.

wlww: Tuple[float, float] property writable

The window level and window width of the viewer.

blending_controller()

Return the viewer controller instance that is being fused with this one.

Returns:

Type	Description
ViewerController	The blending viewer instance.

Example usage

frontmost_viewer = osirix.frontmost_viewer()
blending_controller = frontmost_viewer.blending_controller()

close()

Close the viewer.

Note: This will close any associated viewers (e.g. VRControllers).

close_viewer()

Close the viewer

copy_viewer_window()

Create a copy of the viewer.

This can be useful for image processing when you want to keep a copy of the original and a processed version.

Returns:

Type	Description
ViewerController	The new osirix.viewer_controller.ViewerController instance.

Example usage

frontmost_viewer = osirix.frontmost_viewer()
acopy = frontmost_viewer.copy_viewer_window()

cur_dcm()

Return the currently displayed DCMPix instance.

Returns:

Type	Description
DCMPix	The currently displayed DCMPix instance.

Example usage

frontmost_viewer = osirix.frontmost_viewer()
pix = frontmost_viewer.cur_dcm()

fuse_with_viewer(viewer)

Fuse another viewer onto this one.

Parameters:

Name	Type	Description	Default
viewer	ViewerController	The viewer to fuse onto the present one.	required

Example usage

frontmost_viewer = osirix.frontmost_viewer()
frontmost_viewer.fuse_with_viewer(another_viewer_controller)

is_data_volumic(in_4d=False)

Does the underlying data have sufficient geometric properties for volume rendering.

Parameters:

Name	Type	Description	Default
in_4d	bool	Determine for all frames.	False

Returns:

Type	Description
bool	Is the data volumic?

needs_display_update()

Tell the viewer it should update its display.

This is particularly important if you want to see changes to pixel values in real time.

new_angle_roi(p1, p2, p3, **kwargs)

Create a new angle ROI within the viewer.

This draws two connected vectors:

- v = p2 → p1
- u = p2 → p3

The displayed angle is the angle between these two vectors.

Parameters:

Name	Type	Description	Default
p1	(float, float)	The (column, row) position of the first angle vertex.	required
p2	(float, float)	The (column, row) position of the second angle vertex.	required
p3	(float, float)	The (column, row) position of the third angle vertex.	required
**kwargs		See new_roi for all additional parameters.	{}

Returns:

Type	Description
ROI	The created ROI instance.

new_arrow_roi(tail, head, **kwargs)

Create a new text-box ROI within the viewer.

Parameters:

Name	Type	Description	Default
tail	(float, float)	The (column, row) position of the arrow tail.	required
head	(float, float)	The (column, row) position of the arrow hear.	required
**kwargs		See new_roi for all additional parameters.	{}

Returns:

Type	Description
ROI	The created ROI instance.

new_axis_roi(p1, p2, p3, p4, **kwargs)

Create a new axis ROI within the viewer.

Parameters:

Name	Type	Description	Default
p1	(float, float)	The (column, row) position of the first vertex.	required
p2	(float, float)	The (column, row) position of the second vertex.	required
p3	(float, float)	The (column, row) position of the third vertex.	required
p4	(float, float)	The (column, row) position of the fourth vertex.	required
**kwargs		See new_roi for all additional parameters.	{}

Returns:

Type	Description
ROI	The created ROI instance.

new_dynamic_angle_roi(p1, p2, p3, p4, **kwargs)

Create a new dynamic angle ROI within the viewer.

This draws two vectors:

- v = p2 → p1
- u = p3 → p4

The displayed angle is the angle between these two vectors. The vector p2 -> p3 is also drawn.

Parameters:

Name	Type	Description	Default
p1	(float, float)	The (column, row) position of the first angle vertex.	required
p2	(float, float)	The (column, row) position of the second angle vertex.	required
p3	(float, float)	The (column, row) position of the third angle vertex.	required
p4	(float, float)	The (column, row) position of the fourth angle vertex.	required
**kwargs		See new_roi for all additional parameters.	{}

Returns:

Type	Description
ROI	The created ROI instance.

new_mask_roi(buffer, **kwargs)

Create a new mask ROI within the viewer.

Parameters:

Name	Type	Description	Default
buffer	NDArray	The buffer mask as a 2D boolean Numpy array.	required
**kwargs		See new_roi for all additional parameters.	{}

Returns:

Type	Description
ROI	The created ROI instance.

new_measurement_roi(start, end, **kwargs)

Create a new length measurement ROI within the viewer.

Parameters:

Name	Type	Description	Default
start	(float, float)	The starting position of the ROI (column, row).	required
end	(float, float)	The ending position of the ROI (column, row).	required
**kwargs		See new_roi for all additional parameters.	{}

Returns:

Type	Description
ROI	The created ROI instance.

new_oval_angle_roi(center, width, height, **kwargs)

Create a new angle oval ROI within the viewer.

Note: At present we are not aware that it is possible to pre-determine the angle part of this ROI. This method defines only the oval that will be drawn; the angle appears to have a default value of 113 degrees that can then be adapted by the user.

Parameters:

Name	Type	Description	Default
center	(float, float)	The (column, row) center of the oval ROI.	required
width	float	The width of the oval ROI.	required
height	float	The height of the oval ROI.	required
**kwargs		See new_roi for all additional parameters.	{}

Returns:

Type	Description
ROI	The created ROI instance.

new_oval_roi(center, width, height, **kwargs)

Create a new oval ROI within the viewer.

Parameters:

Name	Type	Description	Default
center	(float, float)	The (column, row) center of the oval ROI.	required
width	float	The width of the oval ROI.	required
height	float	The height of the oval ROI.	required
**kwargs		See new_roi for all additional parameters.	{}

Returns:

Type	Description
ROI	The created ROI instance.

new_point_roi(column, row, **kwargs)

Create a new 2D point ROI within the viewer.

Parameters:

Name	Type	Description	Default
column	float	The column position of the ROI	required
row	float	The row position of the ROI	required
**kwargs		See new_roi for all additional parameters.	{}

Returns:

Type	Description
ROI	The created ROI instance.

new_polygon_roi(points, closed=True, **kwargs)

Create a new polygon ROI within the viewer.

Parameters:

Name	Type	Description	Default
points	NDArray	The vertices of the ROI. Must have shape (N, 2).	required
closed	bool	Whether the polygon is closed.	True
**kwargs		See new_roi for all additional parameters.	{}

Returns:

Type	Description
ROI	The created ROI instance.

new_rectangle_roi(center, width, height, **kwargs)

Create a new rectangle ROI within the viewer.

Parameters:

Name	Type	Description	Default
center	(float, float)	The (column, row) center of the rectangle ROI.	required
width	float	The width of the rectangle ROI.	required
height	float	The height of the rectangle ROI.	required
**kwargs		See new_roi for all additional parameters.	{}

Returns:

Type	Description
ROI	The created ROI instance.

new_roi(itype=15, name='', idx=0, movie_idx=0, buffer_position_column=0, buffer_position_row=0, color=(0, 255, 0), thickness=1.0, opacity=1.0, buffer=None, rect=None, points=None)

Create a new ROI within the viewer.

Important: It is safer to create a new ROI using one of the utility functions as they provide better checking on input parameters in certain contexts, and ensure the right ROI type is created. This is meant as a parent function that performs the heavy lifting. It is made public for transparency.

Parameters:

Name	Type	Description	Default
itype	int	The index of the roi type (see osirix.roi.ROI.itypes for details).	15
name	str	The name of the ROI.	''
idx	int	The slice index on which to create the new ROI.	0
movie_idx	int	The frame on which to create the new ROI.	0
buffer_position_column	int	The column offset of a mask ROI in pixel coordinates.	0
buffer_position_row	int	The row offset of a mask ROI in pixel coordinates.	0
color	tuple	The RGB color of the ROI (values from 0-255 in each channel).	(0, 255, 0)
thickness	float	The thickness of the ROI. Value between 1-20 as per OsiriX.	1.0
opacity	float	The opacity on a scale from 0 (transparent) to 1 (opaque).	1.0
buffer	NDArray	The buffer mask as a 2D boolean Numpy array. If None, then ignored.	None
rect	NDArray	The rectangle defining the ROI. Must be shape (4,).	None
points	NDArray	The points defining the ROI. Must be shape (N, 2) for N vertices. If None or buffer is not None or rect is not None then ignored.	None

Returns:

Type	Description
ROI	The created ROI instance.

Raises:

Type	Description
ValueError	When buffer, points and rect are all None.
ValueError	When the input data is of invalid format.

new_tagt_roi(a, b, c, d, **kwargs)

Create a new tTAGT ROI within the viewer.

ROI displays:

- The length of vector DA.
- The perpendicular distance from B to DA
- The perpendicular distance from C to DA
- The distance between B and C, parallel to DA.

Parameters:

Name	Type	Description	Default
a	(float, float)	The (column, row) position of point A.	required
b	(float, float)	The (column, row) position of point B.	required
c	(float, float)	The (column, row) position of point C.	required
d	(float, float)	The (column, row) position of point D.	required
**kwargs		See new_roi for all additional parameters.	{}

Returns:

Type	Description
ROI	The created ROI instance.

new_text_roi(column, row, name, **kwargs)

Create a new text-box ROI within the viewer.

Parameters:

Name	Type	Description	Default
column	float	The column position of the ROI	required
row	float	The row position of the ROI	required
name	str	The text to show	required
**kwargs		See new_roi for all additional parameters.	{}

Returns:

Type	Description
ROI	The created ROI instance.

open_vr_viewer(mode='VR')

Open a new 3D viewer for the enclosed data.

Parameters:

Name	Type	Description	Default
mode	str	Either 'VR' for volume render, or 'MIP' for a maximum intensity projection.	'VR'

Returns:

Type	Description
VRController	A VRController instance.

Example usage

frontmost_viewer = osirix.frontmost_viewer()
vr_controller = frontmost_viewer.open_vr_viewer(mode="VR")

pix_list(movie_idx=None)

Access the list of DCMPix objects contained within the 2D viewer.

Parameters:

Name	Type	Description	Default
movie_idx	int	The frame from which to extract the DCMPix instances. If None, then use the currently displayed movie_idx.	None

Returns:

Type	Description
List[DCMPix]	The list of osirix.dcm_pix.DCMPix instances requested for a particular frame.

resample_viewer_controller(vc)

Resample this (moving) ViewerController based on another (fixed) ViewerController.

Note that the original moving viewer is closed, so a reference to the new one is returned. This means it is generally advised to the call the method in the following manner:

moving_viewer = moving_viewer.resample_viewer_controller(fixed_viewer)

Parameters:

Name	Type	Description	Default
vc	ViewerController	The fixed viewer.	required

Returns:

Type	Description
ViewerController	The resampled viewer window.

roi_list(movie_idx=None)

Access a list of lists of ROI objects contained within the 2D viewer.

The length of the outer list is the same as the number of slices in the viewer. Note that some inner lists will be empty if no ROIs are drawn on that slice.

Parameters:

Name	Type	Description	Default
movie_idx	int	The frame from which to extract the ROI instances. If None, then use the currently displayed movie_idx.	None

Returns:

Type	Description
List[List[ROI]]	A list of lists of osirix.roi.ROI instances requested for a particular frame.

rois_with_name(name, movie_idx=None, in_4d=False)

Return a list of ROIs with a given name. Args: name (str): The name of ROIs to look for. movie_idx (int): The frame from which to extract the ROI instances. If None, then use the currently displayed movie_idx. in_4d (bool): Whether to look through all frames.

Returns:

Type	Description
List[ROI]	A list of ROIs with the given name.

selected_rois()

Return a list of the user-selected ROIs

Returns:

Type	Description
List[ROI]	A list of selected ROIs.

vr_controllers()

Return the list of currently displayed 3D viewers associates with this 2D window.

Returns:

Type	Description
List[VRController]	Any VRController instances associated with this 2D window.

Example usage

frontmost_viewer = osirix.frontmost_viewer()
vr_controllers = frontmost_viewer.vr_controllers()