def plot_surfaces(vtk_files, use_colormap=False, colormap_file=''):
"""
Use vtkviewer to visualize one or more VTK surface files.
Optionally provide colormap file or set $COLORMAP environment variable.
Parameters
----------
vtk_files : string or list of strings
name of VTK surface mesh file or list of file names
use_colormap : Boolean
use Paraview-style XML colormap file?
colormap_file : string
use colormap in given file if use_colormap==True? if empty and
use_colormap==True, use file set by $COLORMAP environment variable
Examples
--------
>>> import os
>>> from mindboggle.utils.plots import plot_surfaces
>>> path = os.environ['MINDBOGGLE_DATA']
>>> vtk_files = os.path.join(path, 'arno', 'labels', 'lh.labels.DKT31.manual.vtk')
>>> #vtk_files = [os.path.join(path, 'cube.vtk'), os.path.join(path, 'test_one_label.vtk')]
>>> use_colormap = True
>>> colormap_file = '/software/mindboggle_tools/colormap.xml'
>>> plot_surfaces(vtk_files, use_colormap, colormap_file)
"""
import os
import sys
import mindboggle.thirdparty.vtkviewer as vtkviewer
if isinstance(vtk_files, str):
vtk_files = [vtk_files]
vv = vtkviewer.VTKViewer()
colormap = None
if use_colormap:
if colormap_file and os.path.isfile(colormap_file):
colormap = vv.LoadColorMap(colormap_file)
elif "COLORMAP" in os.environ:
colormap = vv.LoadColorMap(os.environ["COLORMAP"])
for vtk_file in vtk_files:
if os.path.isfile(vtk_file):
vv.AddFile(vtk_file, colormap)
else:
sys.exit("Huh?: {0}".format(vtk_file))
vv.Start()
def plot_surfaces(vtk_files, use_colormap=False, colormap_file=''):
"""
Use vtkviewer to visualize one or more VTK surface files.
Optionally provide colormap file or set $COLORMAP environment variable.
Parameters
----------
vtk_files : string or list of strings
name of VTK surface mesh file or list of file names
use_colormap : bool
use Paraview-style XML colormap file?
colormap_file : string
use colormap in given file if use_colormap==True? if empty and
use_colormap==True, use file set by $COLORMAP environment variable
Examples
--------
>>> import os
>>> from mindboggle.mio.plots import plot_surfaces
>>> from mindboggle.mio.fetch_data import prep_tests
>>> urls, fetch_data = prep_tests()
>>> label_file = fetch_data(urls['freesurfer_labels'])
>>> use_colormap = True
>>> colormap_file = '/software/vtk_cpp_tools/colormap.xml' # doctest: +SKIP
>>> plot_surfaces(vtk_files, use_colormap, colormap_file) # doctest: +SKIP
"""
import os
import sys
import mindboggle.thirdparty.vtkviewer as vtkviewer
if isinstance(vtk_files, str):
vtk_files = [vtk_files]
vv = vtkviewer.VTKViewer()
colormap = None
if use_colormap:
if colormap_file and os.path.isfile(colormap_file):
colormap = vv.LoadColorMap(colormap_file)
elif "COLORMAP" in os.environ:
colormap = vv.LoadColorMap(os.environ["COLORMAP"])
for vtk_file in vtk_files:
if os.path.isfile(vtk_file):
vv.AddFile(vtk_file, colormap)
else:
sys.exit("Huh?: {0}".format(vtk_file))
vv.Start()
def plot_surfaces(vtk_files, use_colormap=False, colormap_file=''):
"""
Use vtkviewer to visualize one or more VTK surface files.
Optionally provide colormap file or set $COLORMAP environment variable.
Parameters
----------
vtk_files : string or list of strings
name of VTK surface mesh file or list of file names
use_colormap : bool
use Paraview-style XML colormap file?
colormap_file : string
use colormap in given file if use_colormap==True? if empty and
use_colormap==True, use file set by $COLORMAP environment variable
Examples
--------
>>> from mindboggle.mio.plots import plot_surfaces
>>> from mindboggle.mio.fetch_data import prep_tests
>>> urls, fetch_data = prep_tests()
>>> labels_file = fetch_data(urls['left_manual_labels'], '', '.vtk') #'left_freesurfer_labels'
>>> use_colormap = True
>>> colormap_file = '/software/vtk_cpp_tools/colormap.xml' # doctest: +SKIP
>>> plot_surfaces(labels_file, use_colormap, colormap_file) # doctest: +SKIP
Plot manual labels on folds of the left hemisphere:
>>> from mindboggle.mio.vtks import read_scalars
>>> from mindboggle.mio.fetch_data import prep_tests
>>> from mindboggle.mio.vtks import rewrite_scalars
>>> from mindboggle.mio.plots import plot_surfaces
>>> urls, fetch_data = prep_tests()
>>> labels_file = fetch_data(urls['left_manual_labels'], '', '.vtk') #'left_freesurfer_labels'
>>> folds_file = fetch_data(urls['left_folds'], '', '.vtk')
>>> labels, name = read_scalars(labels_file, True, True)
>>> folds, name = read_scalars(folds_file, True, True)
>>> background_value = -1
>>> # Limit number of folds to speed up the test:
>>> limit_folds = False
>>> if limit_folds:
... fold_numbers = [4] #[4, 6]
... indices = [i for i,x in enumerate(folds) if x in fold_numbers]
... i0 = [i for i,x in enumerate(folds) if x not in fold_numbers]
... folds[i0] = background_value
... else:
... indices = [i for i,x in enumerate(folds) if x != background_value]
>>> folds[indices] = labels[indices]
>>> rewrite_scalars(labels_file, 'labeled_folds.vtk',
... folds, 'skeleton', folds, background_value) # doctest: +SKIP
>>> plot_surfaces('labeled_folds.vtk') # doctest: +SKIP
"""
import os
import sys
import mindboggle.thirdparty.vtkviewer as vtkviewer
if isinstance(vtk_files, str):
vtk_files = [vtk_files]
vv = vtkviewer.VTKViewer()
colormap = None
if use_colormap:
if colormap_file and os.path.isfile(colormap_file):
colormap = vv.LoadColorMap(colormap_file)
elif "COLORMAP" in os.environ:
colormap = vv.LoadColorMap(os.environ["COLORMAP"])
for vtk_file in vtk_files:
if os.path.isfile(vtk_file):
vv.AddFile(vtk_file, colormap)
else:
sys.exit("Huh?: {0}".format(vtk_file))
vv.Start()