ai_ct_scans.GUI.viewer_widget module
- class ai_ct_scans.GUI.viewer_widget.SliceDirection(value)
Bases:
EnumEnum assigning identifier to slice orientation.
- AXIAL = 0
- CORONAL = 1
- SAGITTAL = 2
- class ai_ct_scans.GUI.viewer_widget.ViewerWidget(number_of_scans=0)
Bases:
QWidgetWidget to handle displaying scan data.
- ui
UI class containing UI elements for this widget.
- Type
- data
data for display.
- Type
dict
- blank_frames
blank frame for each scan of correct size.
- Type
dict of np.ndarray
- phase_correlation_shift
Phase correlation shift values in each of 3 axes.
- Type
tuple of int
- orientation
Orientation of scan view slicing.
- Type
- local_region
Local region for phase correlation alignment. 2D coordinates.
- Type
list of int
- cpd_aligned_scan
Aligned 3D scan (using loaded CPD alignment)
- Type
np.ndarray
- class Ui(widget, number_of_scans=0)
Bases:
object
- calculate_non_rigid_alignment()
Calculate the non-rigid alignment, store the offset and trigger an update to the display.
- change_orientation(index)
Update orientation setting and displays.
- Parameters
index (int) – index of orientation to change to
- detect_ellipses()
Method for triggering ellipse detection on each scan.
- display_results(slice_index)
Method to display results using the results display.
- Parameters
slice_index (int) – slice index
- display_sectioned_slice(slice_index)
Method to display results of tissue sectioning.
- Parameters
slice_index (int) – slice index
- display_slice(slice_index)
Display axial slice of full scan.
- Parameters
slice_index (int) – slice index
- extract_centre_coordinates_from_string(info_string)
- Extract slice coordinates as floats from string data in form “[x , y, z]”.
Removes any leading or trailing spaces inserted by PyQtTableWidgets.
- Parameters
info_string (string) – list values formatted as single string.
- Returns
list of centre coordinates from string.
- Return type
(list)
- extract_ellipse_overlay_info(scan_label, slice_index)
- Extract closest match for ellipse in current axis from ellipsoid
contributing ellipses.
- Parameters
scan_label (str) – string label for which scan to refer to. e.g. scan_1 or scan_2
slice_index (int) – current slice index.
- Returns
- dictionary describing ellipse to overlay, or None if no matches in current
orientation.
- Return type
(dict)
- handle_item_selection(table_index)
Detect the selected table item in the scan ellipse table and move the slice view to the relevant slice.
- set_data(data, cpd_alignment=None, sectioning_model=None)
Set data for displaying. If CPD alignment is present, calculate the 3D transform for second scan.
- Parameters
data (dictionary of np.ndarray) – dictionary with two or more full scan arrays
cpd_alignment (sklearn.pipeline.Pipeline) – CPD alignment pipeline object
sectioning_model (sectioning.TextonSectioner) – A trained tissue sectioning model
- setup_orientation(orientation)
Configure class attributes specific to the currently selected orientation.
- Parameters
orientation (SliceDirection) – Enum value for slice orientation
- show_phase_correlation()
Perform phase correlation based around the local region defined.
- staticMetaObject = <PySide2.QtCore.QMetaObject object>
- toggle_ellipse_table()
If toggle button pressed, either hide or show detection table.
- toggle_ellipse_table_button()
Programatically hide or show detection table toggle button.
- toggle_non_rigid_2d_controls()
Hide or show the controls used for non-rigid alignment.
- toggle_phase_correlation_controls()
Hide or show the controls used for phase correlation alignment.
- toggle_tissue_sectioning()
Display or hide the tissue sectioning controls and display.
- toggle_warp_display()
Display or hide the warp display.
- update_ellipse_table(scan_1_ellipses=None, scan_2_ellipses=None)
Method for updating the detection table with ellipse data.
- Parameters
scan_1_ellipses (list) – List of ellipse dictionaries for scan 1
scan_2_ellipses (list) – List of ellipse dictionaries for scan 2
- update_local_region()
Update the local region that has been defined for phase correlation alignment, as (x, y) coordinates.
- update_scan(slice_index)
Update 3D scan view with updated slice index or orientation.
- update_scan_toggle()
Update scan display visibility depending on toggle value.