"""Peak direction (PAM) slicers for Skyline."""
import numpy as np
from dipy.utils.optpkg import optional_package
from dipy.viz.skyline.UI.elements import (
create_numeric_input,
render_group,
thin_slider,
toggle_button,
)
from dipy.viz.skyline.render.renderer import (
Visualization,
slice_slider_bounds,
slice_slider_values_from_state,
slice_state_from_slider_values,
)
fury_trip_msg = (
"Skyline requires Fury version 2.0.0 or higher."
" Please upgrade Fury by `pip install -U fury --pre` to use Skyline."
)
fury, has_fury_v2, _ = optional_package(
"fury",
min_version="2.0.0",
trip_msg=fury_trip_msg,
)
if has_fury_v2:
from fury.actor import peaks_slicer, set_group_opacity
from fury.transform import apply_transformation
imgui_bundle, has_imgui, _ = optional_package(
"imgui_bundle", min_version="1.92.600", max_version="1.92.801"
)
if has_imgui:
imgui = imgui_bundle.imgui
[docs]
def create_peak_visualization(
input,
idx,
*,
opacity=100,
render_callback=None,
sync_callabck=None,
):
"""Create peak visualization from input
Parameters
----------
input : tuple
Tuple of the (pam, filename) or (pam,)
idx : int
Index of the peak for naming purposes if filename is not provided.
opacity : int, optional
Opacity of the peak rendering.
render_callback : callable, optional
Callback function to be called after rendering.
sync_callabck : callable, optional
Callback function to synchronize slice positions across visualizations.
Returns
-------
Peak3D
The created Peak3D object.
"""
if not isinstance(input, tuple) or len(input) not in (1, 2):
raise ValueError(
"Input must be a tuple containing (pam, filename) or (pam,) "
"for peak visualization."
)
if len(input) == 1:
pam = input[0]
filename = f"Peaks_{idx}"
else:
pam, filename = input
peak_values = 1.0
if pam.peak_values is not None:
max = np.percentile(pam.peak_values, 99)
peak_values = np.clip(pam.peak_values, 0, max)
return Peak3D(
filename,
pam.peak_dirs,
affine=pam.affine,
peak_values=peak_values,
opacity=opacity,
render_callback=render_callback,
sync_callabck=sync_callabck,
)
[docs]
class Peak3D(Visualization):
"""Represent ``Peak3D`` in Skyline.
Parameters
----------
name : str
Display name used in the Skyline UI.
peaks : ndarray
Value for ``peaks``.
affine : ndarray, optional
Voxel-to-world affine used to position slices in world coordinates.
peak_values : ndarray or float, optional
Value for ``peak values``.
opacity : int, optional
Slice opacity in percent, expected in ``[0, 100]``.
render_callback : callable, optional
Callback used to request a render/update.
sync_callabck : callable, optional
Callback used to synchronize state across views.
"""
def __init__(
self,
name,
peaks,
*,
affine=None,
peak_values=1.0,
opacity=100,
render_callback=None,
sync_callabck=None,
):
"""Represent ``Peak3D`` in Skyline.
Parameters
----------
name : str
Display name used in the Skyline UI.
peaks : ndarray
Value for ``peaks``.
affine : ndarray, optional
Voxel-to-world affine used to position slices in world coordinates.
peak_values : ndarray or float, optional
Value for ``peak values``.
opacity : int, optional
Slice opacity in percent, expected in ``[0, 100]``.
render_callback : callable, optional
Callback used to request a render/update.
sync_callabck : callable, optional
Callback used to synchronize state across views.
"""
self.peaks = peaks
self.affine = affine
self.peak_values = peak_values
self._scale = 1.0
self.opacity = opacity
self._synchronize = True
self._sync_callabck = sync_callabck
self._slice_visibility = [True, True, True]
self._create_peak_actor()
super().__init__(name, render_callback)
def _create_peak_actor(self):
"""Handle create peak actor for ``Peak3D``.
None
"""
self._slicer = peaks_slicer(
self.peaks,
affine=self.affine,
peak_values=self.peak_values * self._scale,
visibility=self._slice_visibility,
)
self.state = self._get_cross_section()
self._cross_section_state = np.asarray(self.state, dtype=np.float32)
lower_bounds = np.zeros(3)
upper_bounds = np.array(self.peaks.shape[:3]) - 1
if self.affine is not None:
self.bounds = apply_transformation(
np.array([lower_bounds, upper_bounds]), self.affine
)
else:
self.bounds = np.asarray([lower_bounds, upper_bounds])
self._cross_section_space = self._infer_cross_section_space()
self._apply_cross_section_from_state()
def _populate_info(self):
"""Handle populate info for ``Peak3D``.
Returns
-------
str
The information of the peak visualization.
"""
info = f"Peaks shape: {self.peaks.shape}\n"
info += f"Peaks dtype: {self.peaks.dtype}\n"
if self.affine is not None:
affine_str = np.array2string(
np.round(self.affine, 2), separator=" ", prefix=""
)
info += f"Affine:\n{affine_str}\n"
return info
@property
def actor(self):
"""Handle actor for ``Peak3D``.
Returns
-------
Group
The actor of the peak visualization.
"""
return self._slicer
def _get_cross_section(self):
"""Handle get cross section for ``Peak3D``.
``peaks_slicer`` returns a ``Group`` of chunked ``VectorField`` actors and
only the chunks carry the ``cross_section`` property, so read it off the
first chunk. Every chunk is kept at the same cross section.
Returns
-------
np.ndarray
The cross section of the peak visualization.
"""
return np.asarray(self._slicer.children[0].cross_section, dtype=np.float32)
def _set_cross_section(self, cross_section):
"""Handle set cross section for ``Peak3D``.
Parameters
----------
cross_section : array-like
Cross section to propagate to every chunk of the slicer.
"""
for chunk in self._slicer.children:
chunk.cross_section = cross_section
def _infer_cross_section_space(self):
"""Handle infer cross section space for ``Peak3D``.
Returns
-------
str
The cross section space of the peak visualization.
"""
if self.affine is None:
return "voxel"
cross_section = self._get_cross_section()
voxel_center = (np.array(self.peaks.shape[:3], dtype=np.float32) - 1.0) * 0.5
world_center = apply_transformation(
np.array([voxel_center], dtype=np.float32), self.affine
)[0]
world_dist = np.linalg.norm(cross_section - world_center)
voxel_dist = np.linalg.norm(cross_section - voxel_center)
return "world" if world_dist <= voxel_dist else "voxel"
def _voxel_from_world_state(self, world_state):
"""Handle voxel from world state for ``Peak3D``.
Parameters
----------
world_state : array-like
World-space state vector to map into local slice coordinates.
Returns
-------
np.ndarray
The voxel state of the peak visualization.
"""
voxel_state = apply_transformation(
np.array([world_state], dtype=np.float32), np.linalg.inv(self.affine)
)[0]
voxel_state = np.round(voxel_state).astype(np.int16)
max_idx = np.array(self.peaks.shape[:3], dtype=np.int16) - 1
return np.clip(voxel_state, 0, max_idx)
def _apply_cross_section_from_state(self):
"""Handle apply cross section from state for ``Peak3D``.
None
"""
if self.affine is None:
voxel_state = np.round(self.state).astype(np.int16)
self._cross_section_state = voxel_state.astype(np.float32)
self._set_cross_section(voxel_state)
return
voxel_state = self._voxel_from_world_state(self.state)
if self._cross_section_space == "world":
world_state = apply_transformation(
np.array([voxel_state], dtype=np.float32), self.affine
)[0]
self._cross_section_state = np.asarray(world_state, dtype=np.float32)
self._set_cross_section(self._cross_section_state)
else:
self._cross_section_state = voxel_state.astype(np.float32)
self._set_cross_section(voxel_state)
[docs]
def update_state(self, new_state):
"""Handle update state for ``Peak3D``.
Parameters
----------
new_state : array-like
New synchronized state for this visualization.
"""
if self._synchronize:
self.state = np.asarray(new_state[:3], dtype=np.float32)
self.apply_scene_op(self._apply_cross_section_from_state)
def _set_opacity(self, opacity):
"""Handle set opacity for ``Peak3D``.
Parameters
----------
opacity : float
Slice opacity, expected in ``[0, 1]``.
"""
set_group_opacity(self._slicer, opacity)
def _set_slice_visibility(self, visibility):
"""Handle set slice visibility for ``Peak3D``.
``peaks_slicer`` returns a ``Group`` whose ``material`` is ``None``; the
per-axis visibility flags live on the material of each chunk.
Parameters
----------
visibility : tuple(bool, bool, bool)
Per-axis visibility flags for X/Y/Z slices.
"""
for chunk in self._slicer.children:
chunk.material.visibility = visibility
if not has_fury_v2:
create_peak_visualization = Peak3D = fury