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"""Mayavi/traits GUI for averaging two sets of KIT marker points."""
# Authors: Christian Brodbeck <christianbrodbeck@nyu.edu>
#
# License: BSD (3-clause)
import os
import sys
import numpy as np
from mayavi.tools.mlab_scene_model import MlabSceneModel
from pyface.api import confirm, error, FileDialog, OK, YES
from traits.api import (HasTraits, HasPrivateTraits, on_trait_change,
cached_property, Instance, Property, Array, Bool,
Button, Enum, File, Float, List, Str)
from traitsui.api import View, Item, HGroup, VGroup, CheckListEditor
from traitsui.menu import Action, CancelButton
from ..transforms import apply_trans, rotation, translation
from ..coreg import fit_matched_points
from ..io.kit import read_mrk
from ..io.meas_info import _write_dig_points
from ._viewer import PointObject
backend_is_wx = False # is there a way to determine this?
if backend_is_wx:
mrk_wildcard = ['Supported Files (*.sqd, *.mrk, *.txt, *.pickled)|'
'*.sqd;*.mrk;*.txt;*.pickled',
'Sqd marker file (*.sqd;*.mrk)|*.sqd;*.mrk',
'Text marker file (*.txt)|*.txt',
'Pickled markers (*.pickled)|*.pickled']
mrk_out_wildcard = ["Tab separated values file (*.txt)|*.txt"]
else:
if sys.platform in ('win32', 'linux2'):
# on Windows and Ubuntu, multiple wildcards does not seem to work
mrk_wildcard = ["*.sqd", "*.mrk", "*.txt", "*.pickled"]
else:
mrk_wildcard = ["*.sqd;*.mrk;*.txt;*.pickled"]
mrk_out_wildcard = "*.txt"
out_ext = '.txt'
use_editor_v = CheckListEditor(cols=1, values=[(i, str(i)) for i in range(5)])
use_editor_h = CheckListEditor(cols=5, values=[(i, str(i)) for i in range(5)])
mrk_view_editable = View(
VGroup('file',
Item('name', show_label=False, style='readonly'),
HGroup(
Item('use', editor=use_editor_v, enabled_when="enabled",
style='custom'),
'points',
),
HGroup(Item('clear', enabled_when="can_save", show_label=False),
Item('save_as', enabled_when="can_save",
show_label=False)),
))
mrk_view_basic = View(
VGroup('file',
Item('name', show_label=False, style='readonly'),
Item('use', editor=use_editor_h, enabled_when="enabled",
style='custom'),
HGroup(Item('clear', enabled_when="can_save", show_label=False),
Item('edit', show_label=False),
Item('switch_left_right', label="Switch Left/Right",
show_label=False),
Item('reorder', show_label=False),
Item('save_as', enabled_when="can_save",
show_label=False)),
))
mrk_view_edit = View(VGroup('points'))
class ReorderDialog(HasPrivateTraits):
"""Dialog for reordering marker points."""
order = Str("0 1 2 3 4")
index = Property(List, depends_on='order')
is_ok = Property(Bool, depends_on='order')
view = View(
Item('order', label='New order (five space delimited numbers)'),
buttons=[CancelButton, Action(name='OK', enabled_when='is_ok')])
def _get_index(self):
try:
return [int(i) for i in self.order.split()]
except ValueError:
return []
def _get_is_ok(self):
return sorted(self.index) == [0, 1, 2, 3, 4]
class MarkerPoints(HasPrivateTraits):
"""Represent 5 marker points."""
points = Array(float, (5, 3))
can_save = Property(depends_on='points')
save_as = Button()
view = View(VGroup('points',
Item('save_as', enabled_when='can_save')))
@cached_property
def _get_can_save(self):
return np.any(self.points)
def _save_as_fired(self):
dlg = FileDialog(action="save as", wildcard=mrk_out_wildcard,
default_filename=self.name,
default_directory=self.dir)
dlg.open()
if dlg.return_code != OK:
return
path, ext = os.path.splitext(dlg.path)
if not path.endswith(out_ext) and len(ext) != 0:
ValueError("The extension '%s' is not supported." % ext)
path = path + out_ext
if os.path.exists(path):
answer = confirm(None, "The file %r already exists. Should it "
"be replaced?", "Overwrite File?")
if answer != YES:
return
self.save(path)
def save(self, path):
"""Save the marker points.
Parameters
----------
path : str
Path to the file to write. The kind of file to write is determined
based on the extension: '.txt' for tab separated text file,
'.pickled' for pickled file.
"""
_write_dig_points(path, self.points)
class MarkerPointSource(MarkerPoints): # noqa: D401
"""MarkerPoints subclass for source files."""
file = File(filter=mrk_wildcard, exists=True)
name = Property(Str, depends_on='file')
dir = Property(Str, depends_on='file')
use = List(list(range(5)), desc="Which points to use for the interpolated "
"marker.")
enabled = Property(Bool, depends_on=['points', 'use'])
clear = Button(desc="Clear the current marker data")
edit = Button(desc="Edit the marker coordinates manually")
switch_left_right = Button(
desc="Switch left and right marker points; this is intended to "
"correct for markers that were attached in the wrong order")
reorder = Button(desc="Change the order of the marker points")
view = mrk_view_basic
@cached_property
def _get_enabled(self):
return np.any(self.points)
@cached_property
def _get_dir(self):
if self.file:
return os.path.dirname(self.file)
@cached_property
def _get_name(self):
if self.file:
return os.path.basename(self.file)
@on_trait_change('file')
def load(self, fname):
if not fname:
self.reset_traits(['points'])
return
try:
pts = read_mrk(fname)
except Exception as err:
error(None, str(err), "Error Reading mrk")
self.reset_traits(['points'])
else:
self.points = pts
def _clear_fired(self):
self.reset_traits(['file', 'points', 'use'])
def _edit_fired(self):
self.edit_traits(view=mrk_view_edit)
def _reorder_fired(self):
dlg = ReorderDialog()
ui = dlg.edit_traits(kind='modal')
if not ui.result: # user pressed cancel
return
self.points = self.points[dlg.index]
def _switch_left_right_fired(self):
self.points = self.points[[1, 0, 2, 4, 3]]
class MarkerPointDest(MarkerPoints): # noqa: D401
"""MarkerPoints subclass that serves for derived points."""
src1 = Instance(MarkerPointSource)
src2 = Instance(MarkerPointSource)
name = Property(Str, depends_on='src1.name,src2.name')
dir = Property(Str, depends_on='src1.dir,src2.dir')
points = Property(Array(float, (5, 3)),
depends_on=['method', 'src1.points', 'src1.use',
'src2.points', 'src2.use'])
enabled = Property(Bool, depends_on=['points'])
method = Enum('Transform', 'Average', desc="Transform: estimate a rotation"
"/translation from mrk1 to mrk2; Average: use the average "
"of the mrk1 and mrk2 coordinates for each point.")
view = View(VGroup(Item('method', style='custom'),
Item('save_as', enabled_when='can_save',
show_label=False)))
@cached_property
def _get_dir(self):
return self.src1.dir
@cached_property
def _get_name(self):
n1 = self.src1.name
n2 = self.src2.name
if not n1:
if n2:
return n2
else:
return ''
elif not n2:
return n1
if n1 == n2:
return n1
i = 0
l1 = len(n1) - 1
l2 = len(n1) - 2
while n1[i] == n2[i]:
if i == l1:
return n1
elif i == l2:
return n2
i += 1
return n1[:i]
@cached_property
def _get_enabled(self):
return np.any(self.points)
@cached_property
def _get_points(self):
# in case only one or no source is enabled
if not (self.src1 and self.src1.enabled):
if (self.src2 and self.src2.enabled):
return self.src2.points
else:
return np.zeros((5, 3))
elif not (self.src2 and self.src2.enabled):
return self.src1.points
# Average method
if self.method == 'Average':
if len(np.union1d(self.src1.use, self.src2.use)) < 5:
error(None, "Need at least one source for each point.",
"Marker Average Error")
return np.zeros((5, 3))
pts = (self.src1.points + self.src2.points) / 2.
for i in np.setdiff1d(self.src1.use, self.src2.use):
pts[i] = self.src1.points[i]
for i in np.setdiff1d(self.src2.use, self.src1.use):
pts[i] = self.src2.points[i]
return pts
# Transform method
idx = np.intersect1d(np.array(self.src1.use),
np.array(self.src2.use), assume_unique=True)
if len(idx) < 3:
error(None, "Need at least three shared points for trans"
"formation.", "Marker Interpolation Error")
return np.zeros((5, 3))
src_pts = self.src1.points[idx]
tgt_pts = self.src2.points[idx]
est = fit_matched_points(src_pts, tgt_pts, out='params')
rot = np.array(est[:3]) / 2.
tra = np.array(est[3:]) / 2.
if len(self.src1.use) == 5:
trans = np.dot(translation(*tra), rotation(*rot))
pts = apply_trans(trans, self.src1.points)
elif len(self.src2.use) == 5:
trans = np.dot(translation(* -tra), rotation(* -rot))
pts = apply_trans(trans, self.src2.points)
else:
trans1 = np.dot(translation(*tra), rotation(*rot))
pts = apply_trans(trans1, self.src1.points)
trans2 = np.dot(translation(* -tra), rotation(* -rot))
for i in np.setdiff1d(self.src2.use, self.src1.use):
pts[i] = apply_trans(trans2, self.src2.points[i])
return pts
class CombineMarkersModel(HasPrivateTraits):
"""Combine markers model."""
mrk1_file = Instance(File)
mrk2_file = Instance(File)
mrk1 = Instance(MarkerPointSource)
mrk2 = Instance(MarkerPointSource)
mrk3 = Instance(MarkerPointDest)
clear = Button(desc="Clear the current marker data")
# stats
distance = Property(Str, depends_on=['mrk1.points', 'mrk2.points'])
def _clear_fired(self):
self.mrk1.clear = True
self.mrk2.clear = True
self.mrk3.reset_traits(['method'])
def _mrk1_default(self):
return MarkerPointSource()
def _mrk1_file_default(self):
return self.mrk1.trait('file')
def _mrk2_default(self):
return MarkerPointSource()
def _mrk2_file_default(self):
return self.mrk2.trait('file')
def _mrk3_default(self):
return MarkerPointDest(src1=self.mrk1, src2=self.mrk2)
@cached_property
def _get_distance(self):
if (self.mrk1 is None or self.mrk2 is None or
(not np.any(self.mrk1.points)) or
(not np.any(self.mrk2.points))):
return ""
ds = np.sqrt(np.sum((self.mrk1.points - self.mrk2.points) ** 2, 1))
desc = '\t'.join('%.1f mm' % (d * 1000) for d in ds)
return desc
class CombineMarkersPanel(HasTraits): # noqa: D401
"""Has two marker points sources and interpolates to a third one."""
model = Instance(CombineMarkersModel, ())
# model references for UI
mrk1 = Instance(MarkerPointSource)
mrk2 = Instance(MarkerPointSource)
mrk3 = Instance(MarkerPointDest)
distance = Str
# Visualization
scene = Instance(MlabSceneModel)
scale = Float(5e-3)
mrk1_obj = Instance(PointObject)
mrk2_obj = Instance(PointObject)
mrk3_obj = Instance(PointObject)
trans = Array()
view = View(VGroup(VGroup(Item('mrk1', style='custom'),
Item('mrk1_obj', style='custom'),
show_labels=False,
label="Source Marker 1", show_border=True),
VGroup(Item('mrk2', style='custom'),
Item('mrk2_obj', style='custom'),
show_labels=False,
label="Source Marker 2", show_border=True),
VGroup(Item('distance', style='readonly'),
label='Stats', show_border=True),
VGroup(Item('mrk3', style='custom'),
Item('mrk3_obj', style='custom'),
show_labels=False,
label="New Marker", show_border=True),
))
def _mrk1_default(self):
return self.model.mrk1
def _mrk2_default(self):
return self.model.mrk2
def _mrk3_default(self):
return self.model.mrk3
def __init__(self, *args, **kwargs): # noqa: D102
super(CombineMarkersPanel, self).__init__(*args, **kwargs)
self.model.sync_trait('distance', self, 'distance', mutual=False)
self.mrk1_obj = PointObject(scene=self.scene,
color=(0.608, 0.216, 0.216),
point_scale=self.scale)
self.model.mrk1.sync_trait(
'enabled', self.mrk1_obj, 'visible', mutual=False)
self.mrk2_obj = PointObject(scene=self.scene,
color=(0.216, 0.608, 0.216),
point_scale=self.scale)
self.model.mrk2.sync_trait(
'enabled', self.mrk2_obj, 'visible', mutual=False)
self.mrk3_obj = PointObject(scene=self.scene,
color=(0.588, 0.784, 1.),
point_scale=self.scale)
self.model.mrk3.sync_trait(
'enabled', self.mrk3_obj, 'visible', mutual=False)
@on_trait_change('model:mrk1:points,trans')
def _update_mrk1(self):
if self.mrk1_obj is not None:
self.mrk1_obj.points = apply_trans(self.trans,
self.model.mrk1.points)
@on_trait_change('model:mrk2:points,trans')
def _update_mrk2(self):
if self.mrk2_obj is not None:
self.mrk2_obj.points = apply_trans(self.trans,
self.model.mrk2.points)
@on_trait_change('model:mrk3:points,trans')
def _update_mrk3(self):
if self.mrk3_obj is not None:
self.mrk3_obj.points = apply_trans(self.trans,
self.model.mrk3.points)
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