class CustomColormap(HasTraits):
lut_list = lut_manager.lut_mode_list()
lut_list.remove('black-white')
lut_list.remove('blue-red')
lut_list.append('custom_heat')
imgs_path = 'cmap_images'
map_type = Enum('default', 'scalar', 'activation', 'connmat')
cmap = Enum(lut_list)
reverse = Bool
fname = File
label = Str
threshold = Range(0.0, 0.5, 0.2)
_pl = Property(Instance(LinearSegmentedColormap))
def __init__(self, type):
self.map_type = type
def _cmap_default(self):
if self.map_type == 'scalar': return 'BuGn'
elif self.map_type == 'activation': return 'YlOrRd'
elif self.map_type == 'connmat': return 'RdYlBu'
else: return 'cool' #return default
def _reverse_default(self):
if self.map_type == 'connmat': return True
else: return False
def _label_default(self):
if self.map_type == 'scalar': return 'Scalars Colormap'
elif self.map_type == 'activation': return 'Conns Colormap'
elif self.map_type == 'connmat': return 'Matrix Colormap'
else: return 'Default Colormap'
def _get__pl(self):
'''return the LinearSegmentedColormap describing this CustomColormap'''
if self.cmap == 'file' and self.fname:
colors = lut_manager.parse_lut_file(self.fname)
if self.reverse:
colors.reverse()
return LinearSegmentedColormap.from_list('file', colors)
elif self.cmap == 'custom_heat':
return gen_heatmap(t=self.threshold, reverse=self.reverse)
elif self.reverse:
return get_cmap(self.cmap + '_r')
else:
return get_cmap(self.cmap)
class DataModuleFactory(ModuleFactory):
""" Base class for all the module factories operating on data (ie not
text and outline) """
reset_zoom = true(help="""Reset the zoom to accomodate the data newly
added to the scene. Defaults to True.""")
extent = CArray(shape=(6,),
help="""[xmin, xmax, ymin, ymax, zmin, zmax]
Default is the x, y, z arrays extent. Use
this to change the extent of the object
created.""", )
def _extent_changed(self):
tools.set_extent(self._target, self.extent)
transparent = false(help="""make the opacity of the actor depend on the
scalar.""")
def _transparent_changed(self):
if self.transparent:
data_range = \
self._target.module_manager.scalar_lut_manager.data_range
self._target.module_manager.scalar_lut_manager.lut.alpha_range = \
(0.2, 0.8)
data_range = ( numpy.mean(data_range)
+ 0.4 * ( data_range.max() - data_range.min())
* numpy.array([-1, 1]))
self._target.module_manager.scalar_lut_manager.data_range = \
data_range
colormap = Trait('blue-red', lut_mode_list(),
help="""type of colormap to use.""")
def _colormap_changed(self):
colormap = self.colormap
if colormap[-2:] == "_r":
colormap = colormap[:-2]
self._target.module_manager.scalar_lut_manager.reverse_lut = True
self._target.module_manager.vector_lut_manager.reverse_lut = True
self._target.module_manager.scalar_lut_manager.lut_mode = colormap
self._target.module_manager.vector_lut_manager.lut_mode = colormap
vmin = Trait(None, None, CFloat,
help="""vmin is used to scale the colormap.
If None, the min of the data will be used""")
vmax = Trait(None, None, CFloat,
help="""vmax is used to scale the colormap.
If None, the max of the data will be used""")
def _vmin_changed(self):
if self.vmin == None and self.vmax == None:
self._target.module_manager.scalar_lut_manager.use_default_range\
= True
return
self._target.module_manager.scalar_lut_manager.use_default_range \
= False
vmin, vmax = \
self._target.module_manager.scalar_lut_manager.data_range
if self.vmin is not None:
vmin = self.vmin
if self.vmax is not None:
vmax = self.vmax
self._target.module_manager.scalar_lut_manager.data_range = \
(vmin, vmax)
_vmax_changed = _vmin_changed
def __init__(self, *args, **kwargs):
super(DataModuleFactory, self).__init__(*args, **kwargs)
# We are adding data to the scene, reset the zoom:
scene = self._scene.scene
if scene is not None and self.reset_zoom:
scene.reset_zoom()
cortex = "classic"
# get colors
cortex_map = {
"classic": ("Greys", -1, 2, False),
"high_contrast": ("Greys", -.1, 1.3, False),
"low_contrast": ("Greys", -5, 5, False),
"bone": ("bone", -.2, 2, True)
}
# 在这里解释一下为什么"low_contrast"对应的是("Greys", -5, 5, False)，其它的举一反三都改知道是什么含义了
# 首先colormap是颜色映射的意思，也就是将颜色和scalar value做映射。"Grey"指定了颜色映射表用的是灰色，
# -5~5指定了映射表映射的值的范围，这里是将灰色映射到-5~5宽度为10的值域，而二值化的曲率的值只是0和1，它们之间
# 的灰度差只占了整体的1/10，所以对比度较低，然而high_contrast的值域是-.1~1.3，宽度为1.4，可想而知！
if cortex in cortex_map.keys():
color_data = cortex_map[cortex]
elif cortex in lut_manager.lut_mode_list():
color_data = cortex, -1, 2, False
else:
color_data = cortex
# collect key-word args
colormap, vmin, vmax, reverse = color_data
meshargs = dict(figure=figure, scalars=bin_curv) # 第二个参数是取了0,1两个标量
surfargs = dict(colormap=colormap, vmin=vmin, vmax=vmax)
# 获取坐标信息
x = coords[:, 0]
y = coords[:, 1]
z = coords[:, 2]
geo_mesh = mayavi.mlab.pipeline.triangular_mesh_source(x, y, z, faces, **meshargs) # 返回一个二维网格
# 再根据顶点法向量调整成surface？
"""
Script to generate the preview images for the mayavi2 LUTs.
Requires ImageMagick.
"""
import os
from mayavi import mlab
from mayavi.core.lut_manager import lut_mode_list, lut_image_dir
import numpy as np
# Create some data
X = np.arange(0, 255)
X = X * np.ones((200, 1))
mlab.clf()
image = mlab.imshow(X.T)
mlab.view(0, 0, 118)
# Make a preview for each possible lut
for lut in lut_mode_list():
filebasename = os.path.join(lut_image_dir, lut.lower())
if not lut == 'file':
image.module_manager.scalar_lut_manager.lut_mode = lut
mlab.savefig(filebasename + '.png', size=(80, 20))
#os.system('convert %s.png %s.gif &' %(filebasename, filebasename))
os.system('montage -geometry -0-0 -label "%s" %s.png %s.gif &' %
(lut, filebasename, filebasename))
"""
Script to generate the preview images for the mayavi2 LUTs.
Requires ImageMagick.
"""
import os
from mayavi import mlab
from mayavi.core.lut_manager import lut_mode_list, lut_image_dir
import numpy as np
# Create some data
X = np.arange(0, 255)
X = X * np.ones((200, 1))
mlab.clf()
image = mlab.imshow(X.T)
mlab.view(0, 0, 118)
# Make a preview for each possible lut
for lut in lut_mode_list():
filebasename = os.path.join(lut_image_dir, lut.lower())
if not lut == 'file':
image.module_manager.scalar_lut_manager.lut_mode = lut
mlab.savefig(filebasename + '.png', size=(80, 20))
#os.system('convert %s.png %s.gif &' %(filebasename, filebasename))
os.system('montage -geometry -0-0 -label "%s" %s.png %s.gif &'
% (lut, filebasename, filebasename) )
from traits.etsconfig.api import ETSConfig
from traitsui.api \
import Item, Group, View, ImageEnumEditor, InstanceEditor, HGroup
from mayavi.core.lut_manager import lut_mode_list, \
lut_image_dir
def _number_of_lut_cols():
return 1 if ETSConfig.toolkit == 'qt4' else 6
# The view of the LUT Manager object.
view = View(
Group(
Item(name='lut_mode',
editor=ImageEnumEditor(values=lut_mode_list(),
cols=_number_of_lut_cols(),
path=lut_image_dir)),
Item(name='file_name', visible_when="lut_mode=='file'"),
Item(name='number_of_colors'),
Item(name='reverse_lut'),
Item(name='lut',
show_label=False,
editor=InstanceEditor(label='Edit LUT properties',
id='mayavi.core.lut_manager.edit_lut')),
Item(name='scalar_bar_representation',
show_label=False,
visible_when='scalar_bar_representation is not None',
editor=InstanceEditor(
label='Edit Legend representation',
id='mayavi.core.lut_manager.edit_represetation')),
# Judah De Paula <*****@*****.**>
# Copyright (c) 2005-2015, Enthought, Inc.
# License: BSD Style.
from traits.etsconfig.api import ETSConfig
from traitsui.api \
import Item, Group, View, ImageEnumEditor, InstanceEditor, HGroup
from mayavi.core.lut_manager import lut_mode_list, \
lut_image_dir
def _number_of_lut_cols():
return 1 if ETSConfig.toolkit == 'qt4' else 6
# The view of the LUT Manager object.
view = View(Group(Item(name='lut_mode',
editor=ImageEnumEditor(values=lut_mode_list(),
cols=_number_of_lut_cols(),
path=lut_image_dir)),
Item(name='file_name', visible_when="lut_mode=='file'"),
Item(name='number_of_colors'),
Item(name='reverse_lut'),
Item(name='lut',
show_label=False,
editor=InstanceEditor(label='Edit LUT properties',
id='mayavi.core.lut_manager.edit_lut')),
Item(name='scalar_bar_representation',
show_label=False,
visible_when='scalar_bar_representation is not None',
editor=InstanceEditor(label='Edit Legend representation',
id='mayavi.core.lut_manager.edit_represetation')),
Item(name='create_lut', show_label=False),
#!/usr/bin/env python3 # # Copyright 2014 Simone Campagna # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. # __author__ = "Simone Campagna" __all__ = ['COLORMAPS'] from mayavi.core.lut_manager import lut_mode_list COLORMAPS = lut_mode_list()
