ts_obj2 = TimeSeries3DObj('TS2', ts_data, xyz_2, select=ts_select)
# ---------------- Pictures ----------------
pic_data = 100. * np.random.rand(10, 20, 17)
p_obj1 = Picture3DObj('P1', pic_data, xyz_1)
p_obj2 = Picture3DObj('P2', 2 * pic_data, xyz_2)
# ---------------- ROI // Volume // Cross-sections ----------------
# ROI :
roi_obj = RoiObj('brodmann')
roi_obj.select_roi([4, 6])
# Volume :
vol_obj = VolumeObj('aal')
# Cross-sections :
cs_obj = CrossSecObj('aal')
cs_obj.cut_coords((50, 60, 70))
# ---------------- Application ----------------
vb = Brain(source_obj=[s_obj1, s_obj2], connect_obj=[c_obj, c_obj2],
time_series_obj=[ts_obj1, ts_obj2], picture_obj=[p_obj1, p_obj2],
roi_obj=roi_obj, vol_obj=vol_obj, cross_sec_obj=cs_obj,
verbose='debug')
class TestBrain(_TestVisbrain):
"""Test brain.py."""
###########################################################################
# BRAIN
###########################################################################
ts_obj2 = TimeSeries3DObj('TS2', ts_data, xyz_2, select=ts_select)
# ---------------- Pictures ----------------
pic_data = 100. * np.random.rand(10, 20, 17)
p_obj1 = Picture3DObj('P1', pic_data, xyz_1)
p_obj2 = Picture3DObj('P2', 2 * pic_data, xyz_2)
# ---------------- ROI // Volume // Cross-sections ----------------
# ROI :
roi_obj = RoiObj('brodmann')
roi_obj.select_roi([4, 6])
# Volume :
vol_obj = VolumeObj('aal')
# Cross-sections :
cs_obj = CrossSecObj('aal')
cs_obj.cut_coords((50, 60, 70))
# ---------------- Application ----------------
vb = Brain(source_obj=[s_obj1, s_obj2], connect_obj=[c_obj, c_obj2],
time_series_obj=[ts_obj1, ts_obj2], picture_obj=[p_obj1, p_obj2],
roi_obj=roi_obj, vol_obj=vol_obj, cross_sec_obj=cs_obj,
verbose='debug')
class TestBrain(_TestVisbrain):
"""Test brain.py."""
###########################################################################
# BRAIN
###########################################################################
print("""
# =============================================================================
# Connectivity
# =============================================================================
""")
arch = np.load(download_file('phase_sync_delta.npz'))
nodes, edges = arch['nodes'], arch['edges']
c_count = ConnectObj('default', nodes, edges, select=edges > .7,
color_by='count', antialias=True, line_width=2.,
dynamic=(.1, 1.))
s_obj_c = SourceObj('sources', nodes, color='#ab4642', radius_min=5.)
sc.add_to_subplot(c_count, row=2, col=0, row_span=2, title='3D connectivity')
sc.add_to_subplot(s_obj_c, row=2, col=0)
sc.add_to_subplot(BrainObj('B3'), use_this_cam=True, row=2, col=0)
print("""
=============================================================================
Cross-sections
=============================================================================
""")
cs_brod = CrossSecObj('brodmann', interpolation='nearest',
coords=(70, 80, 90), cmap='viridis')
cs_brod.localize_source((-10., -15., 20.))
sc.add_to_subplot(cs_brod, row=2, col=1, col_span=2, row_span=2,
title='Cross-sections')
sc.preview()
def __init__(self, canvas, **kwargs):
"""Init."""
# Create a root node :
self._vbNode = scene.Node(name='Brain')
self._vbNode.transform = vist.STTransform(scale=[self._gl_scale] * 3)
logger.debug("Brain rescaled " + str([self._gl_scale] * 3))
PROFILER("Root node", level=1)
# ========================= SOURCES =========================
self.sources = CombineSources(kwargs.get('source_obj', None))
if self.sources.name is None:
self._obj_type_lst.model().item(4).setEnabled(False)
# Disable menu :
self.menuDispSources.setChecked(False)
self.menuTransform.setEnabled(False)
self.sources.parent = self._vbNode
PROFILER("Sources object", level=1)
# ========================= CONNECTIVITY =========================
self.connect = CombineConnect(kwargs.get('connect_obj', None))
if self.connect.name is None:
self._obj_type_lst.model().item(5).setEnabled(False)
self.menuDispConnect.setEnabled(False)
self.connect.parent = self._vbNode
PROFILER("Connect object", level=1)
# ========================= TIME-SERIES =========================
self.tseries = CombineTimeSeries(kwargs.get('time_series_obj', None))
if self.tseries.name is None:
self._obj_type_lst.model().item(6).setEnabled(False)
self.tseries.parent = self._vbNode
PROFILER("Time-series object", level=1)
# ========================= PICTURES =========================
self.pic = CombinePictures(kwargs.get('picture_obj', None))
if self.pic.name is None:
self._obj_type_lst.model().item(7).setEnabled(False)
self.pic.parent = self._vbNode
PROFILER("Pictures object", level=1)
# ========================= VECTORS =========================
self.vectors = CombineVectors(kwargs.get('vector_obj', None))
if self.vectors.name is None:
self._obj_type_lst.model().item(8).setEnabled(False)
self.vectors.parent = self._vbNode
PROFILER("Vectors object", level=1)
# ========================= VOLUME =========================
# ----------------- Volume -----------------
if kwargs.get('vol_obj', None) is None:
self.volume = VolumeObj('brodmann')
self.volume.visible_obj = False
else:
self.volume = kwargs.get('vol_obj')
if self.volume.name not in self.volume.list():
self.volume.save(tmpfile=True)
self.volume.parent = self._vbNode
PROFILER("Volume object", level=1)
# ----------------- ROI -----------------
if kwargs.get('roi_obj', None) is None:
self.roi = RoiObj('brodmann')
self.roi.visible_obj = False
else:
self.roi = kwargs.get('roi_obj')
if self.roi.name not in self.roi.list():
self.roi.save(tmpfile=True)
self.roi.parent = self._vbNode
PROFILER("ROI object", level=1)
# ----------------- Cross-sections -----------------
if kwargs.get('cross_sec_obj', None) is None:
self.cross_sec = CrossSecObj('brodmann')
else:
self.cross_sec = kwargs.get('cross_sec_obj')
if self.cross_sec.name not in self.cross_sec.list():
self.cross_sec.save(tmpfile=True)
self.cross_sec.visible_obj = False
self.cross_sec.text_size = 2.
self.cross_sec.parent = self._csView.wc.scene
self._csView.camera = self.cross_sec._get_camera()
self.cross_sec.set_shortcuts_to_canvas(self._csView)
PROFILER("Cross-sections object", level=1)
# ========================= BRAIN =========================
if kwargs.get('brain_obj', None) is None:
self.atlas = BrainObj('B1')
else:
self.atlas = kwargs['brain_obj']
if self.atlas.name not in self.atlas.list():
self.atlas.save(tmpfile=True)
self.atlas.scale = self._gl_scale
self.atlas.parent = self._vbNode
PROFILER("Brain object", level=1)
from visbrain.objects import VolumeObj, CrossSecObj, SourceObj
from visbrain.io import download_file
"""Download two NIFTI files
"""
path_1 = download_file('GG-853-GM-0.7mm.nii.gz')
path_2 = download_file('GG-853-WM-0.7mm.nii.gz')
"""Define four sources sources and a Source object
"""
s_xyz = np.array([[29.9, -37.3, -19.3],
[-5.33, 14.00, 20.00],
[25.99, 14.00, 34.66],
[0., -1.99, 10.66]])
s_obj = SourceObj('MySources', s_xyz)
"""Define a volume object and a cross-section object
"""
vol_obj = VolumeObj(path_1)
cross_sec_obj = CrossSecObj(path_2)
"""Localize a source in the cross-section object
"""
cross_sec_obj.localize_source(s_xyz[2, :])
"""Define a Brain instance and pass the source, volume and cross-section
object
"""
vb = Brain(source_obj=s_obj, vol_obj=vol_obj, cross_sec_obj=cross_sec_obj)
vb.show()
def __init__(self, canvas, **kwargs):
"""Init."""
# Create a root node :
self._vbNode = scene.Node(name='Engram')
self._vbNode.transform = vist.STTransform(scale=[self._gl_scale] * 3)
logger.debug("Engram rescaled " + str([self._gl_scale] * 3))
PROFILER("Root node", level=1)
# ========================= SOURCES =========================
self.sources = CombineSources(kwargs.get('source_obj', None))
if self.sources.name is None:
self._obj_type_lst.model().item(4).setEnabled(False)
# Disable menu :
self.menuDispSources.setChecked(False)
self.menuTransform.setEnabled(False)
self.sources.parent = self._vbNode
PROFILER("Sources object", level=1)
# ========================= CONNECTIVITY =========================
self.connect = CombineConnect(kwargs.get('connect_obj', None))
if self.connect.name is None:
self._obj_type_lst.model().item(5).setEnabled(False)
self.menuDispConnect.setEnabled(False)
self.connect.parent = self._vbNode
PROFILER("Connect object", level=1)
# ========================= TIME-SERIES =========================
self.tseries = CombineTimeSeries(kwargs.get('time_series_obj', None))
if self.tseries.name is None:
self._obj_type_lst.model().item(6).setEnabled(False)
self.tseries.parent = self._vbNode
PROFILER("Time-series object", level=1)
# ========================= PICTURES =========================
self.pic = CombinePictures(kwargs.get('picture_obj', None))
if self.pic.name is None:
self._obj_type_lst.model().item(7).setEnabled(False)
self.pic.parent = self._vbNode
PROFILER("Pictures object", level=1)
# ========================= VECTORS =========================
self.vectors = CombineVectors(kwargs.get('vector_obj', None))
if self.vectors.name is None:
self._obj_type_lst.model().item(8).setEnabled(False)
self.vectors.parent = self._vbNode
PROFILER("Vectors object", level=1)
# ========================= VOLUME =========================
# ----------------- Volume -----------------
if kwargs.get('vol_obj', None) is None:
self.volume = VolumeObj('brodmann')
self.volume.visible_obj = False
else:
self.volume = kwargs.get('vol_obj')
if self.volume.name not in self.volume.list():
self.volume.save(tmpfile=True)
self.volume.parent = self._vbNode
PROFILER("Volume object", level=1)
# ----------------- ROI -----------------
if kwargs.get('roi_obj', None) is None:
self.roi = RoiObj('brodmann')
self.roi.visible_obj = False
else:
self.roi = kwargs.get('roi_obj')
if self.roi.name not in self.roi.list():
self.roi.save(tmpfile=True)
self.roi.parent = self._vbNode
PROFILER("ROI object", level=1)
# ----------------- Cross-sections -----------------
if kwargs.get('cross_sec_obj', None) is None:
self.cross_sec = CrossSecObj('brodmann')
else:
self.cross_sec = kwargs.get('cross_sec_obj')
if self.cross_sec.name not in self.cross_sec.list():
self.cross_sec.save(tmpfile=True)
self.cross_sec.visible_obj = False
self.cross_sec.text_size = 2.
self.cross_sec.parent = self._csView.wc.scene
self._csView.camera = self.cross_sec._get_camera()
self.cross_sec.set_shortcuts_to_canvas(self._csView)
PROFILER("Cross-sections object", level=1)
# ========================= ENGRAM =========================
if kwargs.get('engram_obj', None) is None:
self.atlas = BrainObj('B1')
else:
self.atlas = kwargs['engram_obj']
if self.atlas.name not in self.atlas.list():
self.atlas.save(tmpfile=True)
self.atlas.scale = self._gl_scale
self.atlas.parent = self._vbNode
PROFILER("Engram object", level=1)
pic_height=21., cmap='viridis')
sc.add_to_subplot(pic_obj, row=1, col=2, title='3D pictures')
sc.add_to_subplot(BrainObj('B2'), use_this_cam=True, row=1, col=2)
###############################################################################
# Connectivity
###############################################################################
arch = np.load(download_file('phase_sync_delta.npz', astype='example_data'))
nodes, edges = arch['nodes'], arch['edges']
c_count = ConnectObj('default', nodes, edges, select=edges > .7,
color_by='count', antialias=True, line_width=2.,
dynamic=(.1, 1.))
s_obj_c = SourceObj('sources', nodes, color='#ab4642', radius_min=5.)
sc.add_to_subplot(c_count, row=2, col=0, row_span=2, title='3D connectivity')
sc.add_to_subplot(s_obj_c, row=2, col=0)
sc.add_to_subplot(BrainObj('B3'), use_this_cam=True, row=2, col=0)
###############################################################################
# Cross-sections
###############################################################################
cs_brod = CrossSecObj('brodmann', interpolation='nearest',
coords=(70, 80, 90), cmap='viridis')
cs_brod.localize_source((-10., -15., 20.))
sc.add_to_subplot(cs_brod, row=2, col=1, col_span=2, row_span=2,
title='Cross-sections')
sc.preview()
"""Test CrossSecObj."""
import numpy as np
from visbrain.objects import CrossSecObj
from visbrain.objects.tests._testing_objects import _TestObjects
from visbrain.io import download_file, clean_tmp
cs_obj = CrossSecObj('brodmann')
class TestCrossSecObj(_TestObjects):
"""Test CrossSecObj."""
OBJ = cs_obj
def test_definition(self):
"""Test class definition."""
for k in ['brodmann', 'aal', 'talairach']:
CrossSecObj(k)
CrossSecObj('test', vol=np.random.rand(100, 100, 100))
def test_cut_coords(self):
"""Test method cut_coords."""
cs_obj.cut_coords((14, 15, 50))
def test_localize_source(self):
"""Test function localize_source."""
cs_obj.localize_source((15., 12., 23.))
def test_nii_definition(self):
def test_definition(self):
"""Test class definition."""
for k in ['brodmann', 'aal', 'talairach']:
CrossSecObj(k)
CrossSecObj('test', vol=np.random.rand(100, 100, 100))
def test_remove(self):
"""Test function remove."""
v_obj = CrossSecObj('GG-853-GM-0.7mm')
v_obj.remove()
clean_tmp()
Illustration and main functionalities and inputs of the cross-section object.
.. image:: ../../picture/picobjects/ex_cs_obj.png
"""
from visbrain.objects import CrossSecObj, SceneObj
from visbrain.io import download_file
sc = SceneObj()
print("""
# =============================================================================
# Brodmann area
# =============================================================================
""")
cs_brod = CrossSecObj('brodmann',
interpolation='nearest',
coords=(70., 80., 90.))
cs_brod.localize_source((-10., -15., 20.))
sc.add_to_subplot(cs_brod, row=0, col=0, title='Brodmann area')
print("""
# =============================================================================
# Nii.gz file
# =============================================================================
""")
path = download_file('GG-853-GM-0.7mm.nii.gz')
cs_cust = CrossSecObj(path, coords=(0., 0., 0.), cmap='gist_stern')
sc.add_to_subplot(cs_cust, row=0, col=1, title='Nii.gz file')
sc.preview()
def test_save(self):
"""Test function save."""
v_obj = CrossSecObj(download_file('GG-853-GM-0.7mm.nii.gz',
astype='example_data'))
v_obj.save()
v_obj.save(tmpfile=True)
def test_nii_definition(self):
"""Test function nii_definition."""
CrossSecObj(
download_file('GG-853-GM-0.7mm.nii.gz', astype='example_data'))
ts_obj2 = TimeSeries3DObj('TS2', ts_data, xyz_2, select=ts_select)
# ---------------- Pictures ----------------
pic_data = 100. * np.random.rand(10, 20, 17)
p_obj1 = Picture3DObj('P1', pic_data, xyz_1)
p_obj2 = Picture3DObj('P2', 2 * pic_data, xyz_2)
# ---------------- ROI // Volume // Cross-sections ----------------
# ROI :
roi_obj = RoiObj('brodmann')
roi_obj.select_roi([4, 6])
# Volume :
vol_obj = VolumeObj('aal')
# Cross-sections :
cs_obj = CrossSecObj('aal')
cs_obj.set_data((50, 60, 70))
# ---------------- Application ----------------
vb = Brain(source_obj=[s_obj1, s_obj2],
connect_obj=[c_obj, c_obj2],
time_series_obj=[ts_obj1, ts_obj2],
picture_obj=[p_obj1, p_obj2],
roi_obj=roi_obj,
vol_obj=vol_obj,
cross_sec_obj=cs_obj,
verbose='debug')
class TestBrain(_TestVisbrain):
"""Test brain.py."""
See : https://brainder.org/download/flair/ .. image:: ../../picture/picbrain/ex_crossec_and_volume.png """ from visbrain import Brain from visbrain.objects import CrossSecObj, VolumeObj from visbrain.io import download_file """Import the volume and the associated affine transformation """ volume_name = 'GG-853-WM-0.7mm.nii.gz' # 'GG-853-GM-0.7mm.nii.gz' """Download the file. """ path = download_file(volume_name) """Define a cross-section object Go to the Objects tab and select 'Cross-section' in the combo box. You can also press x to display the cross-section panel. """ cs_obj = CrossSecObj(path, coords=(0., 0., 0.), cmap='gist_stern') """Define a volume object. Go to the Objects tab and select 'Volume' in the combo box. You can also press x to display the volume panel. """ v_obj = VolumeObj(path) """Create the GUI and pass the cross-section and the volume object """ vb = Brain(cross_sec_obj=cs_obj, vol_obj=v_obj) vb.show()
def test_nii_definition(self):
"""Test function nii_definition."""
CrossSecObj(download_file('GG-853-GM-0.7mm.nii.gz'))
from visbrain.objects import VolumeObj, CrossSecObj, SourceObj
from visbrain.io import download_file
"""Download two NIFTI files
"""
path_1 = download_file('GG-853-GM-0.7mm.nii.gz', astype='example_data')
path_2 = download_file('GG-853-WM-0.7mm.nii.gz', astype='example_data')
"""Define four sources sources and a Source object
"""
s_xyz = np.array([[29.9, -37.3, -19.3],
[-5.33, 14.00, 20.00],
[25.99, 14.00, 34.66],
[0., -1.99, 10.66]])
s_obj = SourceObj('MySources', s_xyz)
"""Define a volume object and a cross-section object
"""
vol_obj = VolumeObj(path_1)
cross_sec_obj = CrossSecObj(path_2)
"""Localize a source in the cross-section object
"""
cross_sec_obj.localize_source(s_xyz[2, :])
"""Define a Brain instance and pass the source, volume and cross-section
object
"""
vb = Brain(source_obj=s_obj, vol_obj=vol_obj, cross_sec_obj=cross_sec_obj)
vb.show()
def test_save(self):
"""Test function save."""
v_obj = CrossSecObj(download_file('GG-853-GM-0.7mm.nii.gz'))
v_obj.save()
v_obj.save(tmpfile=True)
See : https://brainder.org/download/flair/ .. image:: ../../picture/picbrain/ex_crossec_and_volume.png """ from visbrain import Brain from visbrain.objects import CrossSecObj, VolumeObj from visbrain.io import download_file """Import the volume and the associated affine transformation """ volume_name = 'GG-853-WM-0.7mm.nii.gz' # 'GG-853-GM-0.7mm.nii.gz' """Download the file. """ path = download_file(volume_name) """Define a cross-section object Go to the Objects tab and select 'Cross-section' in the combo box. You can also press x to display the cross-section panel. """ cs_obj = CrossSecObj(path, section=(70, 171, 80), cmap='gist_stern') """Define a volume object. Go to the Objects tab and select 'Volume' in the combo box. You can also press x to display the volume panel. """ v_obj = VolumeObj(path) """Create the GUI and pass the cross-section and the volume object """ vb = Brain(cross_sec_obj=cs_obj, vol_obj=v_obj) vb.show()
def test_remove(self):
"""Test function remove."""
v_obj = CrossSecObj('GG-853-GM-0.7mm')
v_obj.remove()
clean_tmp()
Illustration and main functionalities and inputs of the cross-section object.
.. image:: ../../picture/picobjects/ex_cs_obj.png
"""
from visbrain.objects import CrossSecObj, SceneObj
from visbrain.io import download_file
sc = SceneObj()
print("""
# =============================================================================
# Brodmann area
# =============================================================================
""")
cs_brod = CrossSecObj('brodmann',
interpolation='nearest',
section=(70, 80, 90))
cs_brod.localize_source((-10., -15., 20.))
sc.add_to_subplot(cs_brod, row=0, col=0, title='Brodmann area')
print("""
# =============================================================================
# Nii.gz file
# =============================================================================
""")
path = download_file('GG-853-GM-0.7mm.nii.gz')
cs_cust = CrossSecObj(path, section=(90, 80, 100), cmap='gist_stern')
sc.add_to_subplot(cs_cust, row=0, col=1, title='Nii.gz file')
sc.preview()
class Visuals(object):
"""Initialize Brain objects.
Initialize sources / connectivity / areas / colorbar / projections.
Organize them at diffrent levels and make the link with the graphical
user interface (if no object is detected, the corresponding panel in the
GUI has to be deactivate).
"""
def __init__(self, canvas, **kwargs):
"""Init."""
# Create a root node :
self._vbNode = scene.Node(name='Brain')
self._vbNode.transform = vist.STTransform(scale=[self._gl_scale] * 3)
logger.debug("Brain rescaled " + str([self._gl_scale] * 3))
PROFILER("Root node", level=1)
# ========================= SOURCES =========================
self.sources = CombineSources(kwargs.get('source_obj', None))
if self.sources.name is None:
self._obj_type_lst.model().item(4).setEnabled(False)
# Disable menu :
self.menuDispSources.setChecked(False)
self.menuTransform.setEnabled(False)
self.sources.parent = self._vbNode
PROFILER("Sources object", level=1)
# ========================= CONNECTIVITY =========================
self.connect = CombineConnect(kwargs.get('connect_obj', None))
if self.connect.name is None:
self._obj_type_lst.model().item(5).setEnabled(False)
self.menuDispConnect.setEnabled(False)
self.connect.parent = self._vbNode
PROFILER("Connect object", level=1)
# ========================= TIME-SERIES =========================
self.tseries = CombineTimeSeries(kwargs.get('time_series_obj', None))
if self.tseries.name is None:
self._obj_type_lst.model().item(6).setEnabled(False)
self.tseries.parent = self._vbNode
PROFILER("Time-series object", level=1)
# ========================= PICTURES =========================
self.pic = CombinePictures(kwargs.get('picture_obj', None))
if self.pic.name is None:
self._obj_type_lst.model().item(7).setEnabled(False)
self.pic.parent = self._vbNode
PROFILER("Pictures object", level=1)
# ========================= VECTORS =========================
self.vectors = CombineVectors(kwargs.get('vector_obj', None))
if self.vectors.name is None:
self._obj_type_lst.model().item(8).setEnabled(False)
self.vectors.parent = self._vbNode
PROFILER("Vectors object", level=1)
# ========================= VOLUME =========================
# ----------------- Volume -----------------
if kwargs.get('vol_obj', None) is None:
self.volume = VolumeObj('brodmann')
self.volume.visible_obj = False
else:
self.volume = kwargs.get('vol_obj')
if self.volume.name not in self.volume.list():
self.volume.save(tmpfile=True)
self.volume.parent = self._vbNode
PROFILER("Volume object", level=1)
# ----------------- ROI -----------------
if kwargs.get('roi_obj', None) is None:
self.roi = RoiObj('brodmann')
self.roi.visible_obj = False
else:
self.roi = kwargs.get('roi_obj')
if self.roi.name not in self.roi.list():
self.roi.save(tmpfile=True)
self.roi.parent = self._vbNode
PROFILER("ROI object", level=1)
# ----------------- Cross-sections -----------------
if kwargs.get('cross_sec_obj', None) is None:
self.cross_sec = CrossSecObj('brodmann')
else:
self.cross_sec = kwargs.get('cross_sec_obj')
if self.cross_sec.name not in self.cross_sec.list():
self.cross_sec.save(tmpfile=True)
self.cross_sec.visible_obj = False
self.cross_sec.text_size = 2.
self.cross_sec.parent = self._csView.wc.scene
self._csView.camera = self.cross_sec._get_camera()
self.cross_sec.set_shortcuts_to_canvas(self._csView)
PROFILER("Cross-sections object", level=1)
# ========================= BRAIN =========================
if kwargs.get('brain_obj', None) is None:
self.atlas = BrainObj('B1')
else:
self.atlas = kwargs['brain_obj']
if self.atlas.name not in self.atlas.list():
self.atlas.save(tmpfile=True)
self.atlas.scale = self._gl_scale
self.atlas.parent = self._vbNode
PROFILER("Brain object", level=1)
