def write_vertex_measures(
table_file,
labels_or_file,
sulci=[],
fundi=[],
affine_transform_file="",
transform_format="itk",
area_file="",
mean_curvature_file="",
travel_depth_file="",
geodesic_depth_file="",
convexity_file="",
thickness_file="",
delimiter=",",
):
"""
Make a table of shape values per vertex.
Parameters
----------
table_file : output filename (without path)
labels_or_file : list or string
label number for each vertex or name of VTK file with index scalars
sulci : list of integers
indices to sulci, one per vertex, with -1 indicating no sulcus
fundi : list of integers
indices to fundi, one per vertex, with -1 indicating no fundus
affine_transform_file : string
affine transform file to standard space
transform_format : string
format for transform file
Ex: 'txt' for text, 'itk' for ITK, and 'mat' for Matlab format
area_file : string
name of VTK file with surface area scalar values
mean_curvature_file : string
name of VTK file with mean curvature scalar values
travel_depth_file : string
name of VTK file with travel depth scalar values
geodesic_depth_file : string
name of VTK file with geodesic depth scalar values
convexity_file : string
name of VTK file with convexity scalar values
thickness_file : string
name of VTK file with thickness scalar values
delimiter : string
delimiter between columns, such as ','
Returns
-------
shape_table : table file name for vertex shape values
Examples
--------
>>> import os
>>> from mindboggle.utils.io_vtk import read_scalars
>>> from mindboggle.tables.all_shapes import write_vertex_measures
>>> #
>>> table_file = 'vertex_shapes.csv'
>>> path = os.environ['MINDBOGGLE_DATA']
>>> labels_or_file = os.path.join(path, 'arno', 'labels', 'lh.labels.DKT25.manual.vtk')
>>> sulci_file = os.path.join(path, 'arno', 'features', 'sulci.vtk')
>>> fundi_file = os.path.join(path, 'arno', 'features', 'fundi.vtk')
>>> sulci, name = read_scalars(sulci_file)
>>> fundi, name = read_scalars(fundi_file)
>>> affine_transform_file = os.path.join(path, 'arno', 'mri',
>>> 't1weighted_brain.MNI152Affine.txt')
>>> transform_format = 'itk'
>>> area_file = os.path.join(path, 'arno', 'shapes', 'lh.pial.area.vtk')
>>> mean_curvature_file = os.path.join(path, 'arno', 'shapes', 'lh.pial.mean_curvature.vtk')
>>> travel_depth_file = os.path.join(path, 'arno', 'shapes', 'lh.pial.travel_depth.vtk')
>>> geodesic_depth_file = os.path.join(path, 'arno', 'shapes', 'lh.pial.geodesic_depth.vtk')
>>> convexity_file = ''
>>> thickness_file = ''
>>> delimiter = ','
>>> #
>>> write_vertex_measures(table_file, labels_or_file, sulci, fundi,
>>> affine_transform_file, transform_format, area_file,
>>> mean_curvature_file, travel_depth_file, geodesic_depth_file,
>>> convexity_file, thickness_file, delimiter)
"""
import os
import numpy as np
from mindboggle.utils.io_vtk import read_scalars, read_vtk, apply_affine_transform
from mindboggle.utils.io_table import write_columns
# Make sure inputs are lists:
if isinstance(labels_or_file, np.ndarray):
labels = labels_or_file.tolist()
elif isinstance(labels_or_file, list):
labels = labels_or_file
elif isinstance(labels_or_file, str):
labels, name = read_scalars(labels_or_file)
if isinstance(sulci, np.ndarray):
sulci = sulci.tolist()
if isinstance(fundi, np.ndarray):
fundi = fundi.tolist()
# Feature names and corresponding feature lists:
feature_names = ["label", "sulcus", "fundus"]
feature_lists = [labels, sulci, fundi]
# Shape names corresponding to shape files below:
shape_names = ["area", "mean curvature", "travel depth", "geodesic depth", "convexity", "thickness"]
# Load shape files as a list of numpy arrays of per-vertex shape values:
shape_files = [
area_file,
mean_curvature_file,
travel_depth_file,
geodesic_depth_file,
convexity_file,
thickness_file,
]
# Append columns of per-vertex scalar values:
columns = []
column_names = []
for ifeature, values in enumerate(feature_lists):
if values:
columns.append(values)
column_names.append(feature_names[ifeature])
first_pass = True
for ishape, shape_file in enumerate(shape_files):
if os.path.exists(shape_file):
if first_pass:
u1, u2, u3, points, u4, scalars, u5, u6 = read_vtk(shape_file)
columns.append(points)
column_names.append("coordinates")
first_pass = False
if affine_transform_file:
affine_points, foo1 = apply_affine_transform(affine_transform_file, points, transform_format)
columns.append(affine_points)
column_names.append("coordinates in standard space")
else:
scalars, name = read_scalars(shape_file)
if len(scalars):
columns.append(scalars)
column_names.append(shape_names[ishape])
# Prepend with column of indices and write table
shapes_table = os.path.join(os.getcwd(), table_file)
write_columns(range(len(columns[0])), "index", shapes_table, delimiter)
write_columns(columns, column_names, shapes_table, delimiter, quote=True, input_table=shapes_table)
return shapes_table
def write_vertex_measures(output_table, labels_or_file, sulci=[], fundi=[],
affine_transform_file='', transform_format='itk',
area_file='', mean_curvature_file='', travel_depth_file='',
geodesic_depth_file='', freesurfer_convexity_file='',
freesurfer_thickness_file='', delimiter=','):
"""
Make a table of shape values per vertex.
Note ::
This function is tailored for Mindboggle outputs.
Parameters
----------
output_table : string
output file (full path)
labels_or_file : list or string
label number for each vertex or name of VTK file with index scalars
sulci : list of integers
indices to sulci, one per vertex, with -1 indicating no sulcus
fundi : list of integers
indices to fundi, one per vertex, with -1 indicating no fundus
affine_transform_file : string
affine transform file to standard space
transform_format : string
format for transform file
Ex: 'txt' for text, 'itk' for ITK, and 'mat' for Matlab format
area_file : string
name of VTK file with surface area scalar values
mean_curvature_file : string
name of VTK file with mean curvature scalar values
travel_depth_file : string
name of VTK file with travel depth scalar values
geodesic_depth_file : string
name of VTK file with geodesic depth scalar values
freesurfer_convexity_file : string
name of VTK file with FreeSurfer convexity scalar values
freesurfer_thickness_file : string
name of VTK file with FreeSurfer thickness scalar values
delimiter : string
delimiter between columns, such as ','
Returns
-------
output_table : table file name for vertex shape values
Examples
--------
>>> import os
>>> from mindboggle.utils.io_vtk import read_scalars
>>> from mindboggle.utils.io_table import write_vertex_measures
>>> #
>>> output_table = ''#vertex_shapes.csv'
>>> path = os.environ['MINDBOGGLE_DATA']
>>> labels_or_file = os.path.join(path, 'arno', 'labels', 'lh.labels.DKT25.manual.vtk')
>>> sulci_file = os.path.join(path, 'arno', 'features', 'sulci.vtk')
>>> fundi_file = os.path.join(path, 'arno', 'features', 'fundi.vtk')
>>> sulci, name = read_scalars(sulci_file)
>>> fundi, name = read_scalars(fundi_file)
>>> affine_transform_file = os.path.join(path, 'arno', 'mri',
>>> 't1weighted_brain.MNI152Affine.txt')
>>> transform_format = 'itk'
>>> area_file = os.path.join(path, 'arno', 'shapes', 'lh.pial.area.vtk')
>>> mean_curvature_file = os.path.join(path, 'arno', 'shapes', 'lh.pial.mean_curvature.vtk')
>>> travel_depth_file = os.path.join(path, 'arno', 'shapes', 'lh.pial.travel_depth.vtk')
>>> geodesic_depth_file = os.path.join(path, 'arno', 'shapes', 'lh.pial.geodesic_depth.vtk')
>>> freesurfer_convexity_file = ''
>>> freesurfer_thickness_file = ''
>>> delimiter = ','
>>> #
>>> write_vertex_measures(output_table, labels_or_file, sulci, fundi,
>>> affine_transform_file, transform_format, area_file,
>>> mean_curvature_file, travel_depth_file, geodesic_depth_file,
>>> freesurfer_convexity_file, freesurfer_thickness_file, delimiter)
"""
import os
import numpy as np
from mindboggle.utils.io_vtk import read_scalars, read_vtk, \
apply_affine_transform
from mindboggle.utils.io_table import write_columns
# Make sure inputs are lists:
if isinstance(labels_or_file, np.ndarray):
labels = [int(x) for x in labels_or_file]
elif isinstance(labels_or_file, list):
labels = labels_or_file
elif isinstance(labels_or_file, str):
labels, name = read_scalars(labels_or_file)
if isinstance(sulci, np.ndarray):
sulci = [int(x) for x in sulci]
if isinstance(fundi, np.ndarray):
fundi = [int(x) for x in fundi]
if not labels and not sulci and not fundi:
import sys
sys.exit('No feature data to tabulate in write_vertex_measures().')
# Feature names and corresponding feature lists:
feature_names = ['Label', 'Sulcus', 'Fundus']
feature_lists = [labels, sulci, fundi]
# Shape names corresponding to shape files below:
shape_names = ['area', 'mean curvature', 'travel depth', 'geodesic depth',
'FreeSurfer convexity', 'FreeSurfer thickness']
# Load shape files as a list of numpy arrays of per-vertex shape values:
shape_files = [area_file, mean_curvature_file, travel_depth_file,
geodesic_depth_file, freesurfer_convexity_file,
freesurfer_thickness_file]
# Append columns of per-vertex scalar values:
columns = []
column_names = []
for ifeature, values in enumerate(feature_lists):
if values:
columns.append(values)
column_names.append(feature_names[ifeature])
first_pass = True
for ishape, shape_file in enumerate(shape_files):
if os.path.exists(shape_file):
if first_pass:
u1, u2, u3, points, u4, scalars, u5, u6 = read_vtk(shape_file)
columns.append(points)
column_names.append('coordinates')
first_pass = False
if affine_transform_file and transform_format:
affine_points, \
foo1 = apply_affine_transform(affine_transform_file,
points, transform_format,
vtk_file_stem='')
columns.append(affine_points)
column_names.append('coordinates in standard space')
else:
scalars, name = read_scalars(shape_file)
if len(scalars):
columns.append(scalars)
column_names.append(shape_names[ishape])
# Prepend with column of indices and write table
if not output_table:
output_table = os.path.join(os.getcwd(), 'vertices.csv')
write_columns(range(len(columns[0])), 'Index', delimiter, quote=True,
input_table='', output_table=output_table)
write_columns(columns, column_names, delimiter, quote=True,
input_table=output_table, output_table=output_table)
if not os.path.exists(output_table):
raise(IOError(output_table + " not found"))
return output_table
def write_shape_stats(
labels_or_file,
sulci=[],
fundi=[],
affine_transform_file="",
transform_format="itk",
area_file="",
mean_curvature_file="",
travel_depth_file="",
geodesic_depth_file="",
convexity_file="",
thickness_file="",
labels_spectra=[],
labels_spectra_IDs=[],
sulci_spectra=[],
sulci_spectra_IDs=[],
exclude_labels=[-1],
delimiter=",",
):
"""
Make tables of shape statistics per label, fundus, and/or sulcus.
Parameters
----------
labels_or_file : list or string
label number for each vertex or name of VTK file with index scalars
sulci : list of integers
indices to sulci, one per vertex, with -1 indicating no sulcus
fundi : list of integers
indices to fundi, one per vertex, with -1 indicating no fundus
affine_transform_file : string
affine transform file to standard space
transform_format : string
format for transform file
Ex: 'txt' for text, 'itk' for ITK, and 'mat' for Matlab format
area_file : string
name of VTK file with surface area scalar values
mean_curvature_file : string
name of VTK file with mean curvature scalar values
travel_depth_file : string
name of VTK file with travel depth scalar values
geodesic_depth_file : string
name of VTK file with geodesic depth scalar values
convexity_file : string
name of VTK file with convexity scalar values
thickness_file : string
name of VTK file with thickness scalar values
labels_spectra : list of lists of floats
Laplace-Beltrami spectra for labeled regions
labels_spectra_IDs : list of integers
unique ID numbers (labels) for labels_spectra
sulci_spectra : list of lists of floats
Laplace-Beltrami spectra for sulci
sulci_spectra_IDs : list of integers
unique ID numbers (labels) for sulci_spectra
exclude_labels : list of lists of integers
indices to be excluded (in addition to -1)
delimiter : string
delimiter between columns, such as ','
Returns
-------
label_table : string
output table filename for label shapes
sulcus_table : string
output table filename for sulcus shapes
fundus_table : string
output table filename for fundus shapes
Examples
--------
>>> import os
>>> from mindboggle.utils.io_vtk import read_scalars
>>> from mindboggle.utils.io_table import write_shape_stats
>>> path = os.environ['MINDBOGGLE_DATA']
>>> labels_or_file = os.path.join(path, 'arno', 'labels', 'lh.labels.DKT25.manual.vtk')
>>> sulci_file = os.path.join(path, 'arno', 'features', 'sulci.vtk')
>>> fundi_file = os.path.join(path, 'arno', 'features', 'fundi.vtk')
>>> sulci, name = read_scalars(sulci_file)
>>> fundi, name = read_scalars(fundi_file)
>>> affine_transform_file = os.path.join(path, 'arno', 'mri',
>>> # 'affine_to_template.mat')
>>> 't1weighted_brain.MNI152Affine.txt')
>>> #transform_format = 'mat'
>>> transform_format = 'itk'
>>> area_file = os.path.join(path, 'arno', 'shapes', 'lh.pial.area.vtk')
>>> mean_curvature_file = os.path.join(path, 'arno', 'shapes', 'lh.pial.mean_curvature.vtk')
>>> travel_depth_file = os.path.join(path, 'arno', 'shapes', 'lh.pial.travel_depth.vtk')
>>> geodesic_depth_file = os.path.join(path, 'arno', 'shapes', 'lh.pial.geodesic_depth.vtk')
>>> convexity_file = ''
>>> thickness_file = ''
>>> delimiter = ','
>>> #
>>> import numpy as np
>>> labels, name = read_scalars(labels_or_file)
>>> labels_spectra = [[1,2,3] for x in labels]
>>> labels_spectra_IDs = np.unique(labels).tolist()
>>> sulci_spectra = [[1,2,3] for x in sulci]
>>> sulci_spectra_IDs = np.unique(sulci).tolist()
>>> exclude_labels = [-1]
>>> #
>>> write_shape_stats(labels_or_file, sulci, fundi,
>>> affine_transform_file, transform_format, area_file,
>>> mean_curvature_file, travel_depth_file, geodesic_depth_file,
>>> convexity_file, thickness_file, labels_spectra,
>>> labels_spectra_IDs, sulci_spectra,
>>> sulci_spectra_IDs, exclude_labels, delimiter)
"""
import os
import numpy as np
from mindboggle.shapes.measure import means_per_label, stats_per_label, sum_per_label
from mindboggle.utils.io_vtk import read_scalars, read_vtk, apply_affine_transform
from mindboggle.utils.io_table import write_columns
# Make sure inputs are lists:
if isinstance(labels_or_file, np.ndarray):
labels = labels_or_file.tolist()
elif isinstance(labels_or_file, list):
labels = labels_or_file
elif isinstance(labels_or_file, str):
labels, name = read_scalars(labels_or_file)
if isinstance(sulci, np.ndarray):
sulci = sulci.tolist()
if isinstance(fundi, np.ndarray):
fundi = fundi.tolist()
# -------------------------------------------------------------------------
# Feature lists, shape names, and shape files:
# -------------------------------------------------------------------------
# Feature lists:
feature_lists = [labels, sulci, fundi]
feature_names = ["label", "sulcus", "fundus"]
spectra_lists = [labels_spectra, sulci_spectra]
spectra_ID_lists = [labels_spectra_IDs, sulci_spectra_IDs]
spectra_names = ["label spectrum", "sulcus spectrum"]
table_names = ["label_shapes.csv", "sulcus_shapes.csv", "fundus_shapes.csv"]
# Shape names corresponding to shape files below:
shape_names = ["area", "mean curvature", "travel depth", "geodesic depth", "convexity", "thickness"]
# Load shape files as a list of numpy arrays of per-vertex shape values:
shape_files = [
area_file,
mean_curvature_file,
travel_depth_file,
geodesic_depth_file,
convexity_file,
thickness_file,
]
shape_arrays = []
column_names = []
first_pass = True
area_array = []
for ishape, shape_file in enumerate(shape_files):
if os.path.exists(shape_file):
if first_pass:
faces, lines, indices, points, npoints, scalars_array, name, input_vtk = read_vtk(
shape_file, True, True
)
points = np.array(points)
first_pass = False
if affine_transform_file:
affine_points, foo1 = apply_affine_transform(
affine_transform_file, points, transform_format, save_file=False
)
affine_points = np.array(affine_points)
else:
scalars_array, name = read_scalars(shape_file, True, True)
if scalars_array.size:
shape_arrays.append(scalars_array)
# Store area array:
if ishape == 0:
area_array = scalars_array.copy()
# Initialize table file names:
sulcus_table = None
fundus_table = None
# Loop through features / tables:
for itable, feature_list in enumerate(feature_lists):
table_column_names = []
# ---------------------------------------------------------------------
# For each feature, construct a table of average shape values:
# ---------------------------------------------------------------------
table_file = os.path.join(os.getcwd(), table_names[itable])
if feature_list:
feature_name = feature_names[itable]
columns = []
# -----------------------------------------------------------------
# Mean positions in the original space:
# -----------------------------------------------------------------
# Compute mean position per feature:
positions, sdevs, label_list, foo = means_per_label(points, feature_list, exclude_labels, area_array)
# Append mean position per feature to columns:
table_column_names.append("mean position")
columns.append(positions)
# -----------------------------------------------------------------
# Mean positions in standard space:
# -----------------------------------------------------------------
if affine_transform_file:
# Compute standard space mean position per feature:
standard_positions, sdevs, label_list, foo = means_per_label(
affine_points, feature_list, exclude_labels, area_array
)
# Append standard space mean position per feature to columns:
table_column_names.append("mean position in standard space")
columns.append(standard_positions)
# -----------------------------------------------------------------
# Loop through shape measures:
# -----------------------------------------------------------------
table_column_names.extend(column_names[:])
for ishape, shape_array in enumerate(shape_arrays):
shape_name = shape_names[ishape]
print(" Compute statistics on {0} {1}".format(feature_name, shape_name))
# Append shape names and values per feature to columns:
pr = feature_name + ": " + shape_name + ": "
if np.size(area_array):
po = " (weighted)"
else:
po = ""
# -------------------------------------------------------------
# Append total feature areas to columns:
# -------------------------------------------------------------
if ishape == 0 and np.size(area_array):
sums, label_list = sum_per_label(shape_array, feature_list, exclude_labels)
table_column_names.append(pr + "total")
columns.append(sums)
# -------------------------------------------------------------
# Append feature shape statistics to columns:
# -------------------------------------------------------------
else:
medians, mads, means, sdevs, skews, kurts, lower_quarts, upper_quarts, label_list = stats_per_label(
shape_array, feature_list, exclude_labels, area_array, precision=1
)
table_column_names.append(pr + "median" + po)
table_column_names.append(pr + "median absolute deviation" + po)
table_column_names.append(pr + "mean" + po)
table_column_names.append(pr + "standard deviation" + po)
table_column_names.append(pr + "skew" + po)
table_column_names.append(pr + "kurtosis" + po)
table_column_names.append(pr + "lower quartile" + po)
table_column_names.append(pr + "upper quartile" + po)
columns.append(medians)
columns.append(mads)
columns.append(means)
columns.append(sdevs)
columns.append(skews)
columns.append(kurts)
columns.append(lower_quarts)
columns.append(upper_quarts)
# -----------------------------------------------------------------
# Laplace-Beltrami spectra:
# -----------------------------------------------------------------
if itable in [0, 1]:
spectra = spectra_lists[itable]
spectra_name = spectra_names[itable]
spectra_IDs = spectra_ID_lists[itable]
# Order spectra into a list:
spectrum_list = []
for label in label_list:
if label in spectra_IDs:
spectrum = spectra[spectra_IDs.index(label)]
spectrum_list.append(spectrum)
else:
spectrum_list.append("")
# Append spectral shape name and values to relevant columns:
columns.append(spectrum_list)
table_column_names.append(spectra_name)
# -----------------------------------------------------------------
# Write labels/IDs and values to table:
# -----------------------------------------------------------------
# Write labels/IDs to table:
write_columns(label_list, feature_name, table_file, delimiter)
# Append columns of shape values to table:
if columns:
write_columns(columns, table_column_names, table_file, delimiter, quote=True, input_table=table_file)
else:
# Write something to table:
write_columns([], "", table_file, delimiter)
# ---------------------------------------------------------------------
# Return correct table file name:
# ---------------------------------------------------------------------
if itable == 0:
label_table = table_file
elif itable == 1:
sulcus_table = table_file
elif itable == 2:
fundus_table = table_file
return label_table, sulcus_table, fundus_table
def write_shape_stats(labels_or_file=[], sulci=[], fundi=[],
affine_transform_file='', transform_format='itk',
area_file='', normalize_by_area=True, mean_curvature_file='',
travel_depth_file='', geodesic_depth_file='',
freesurfer_convexity_file='', freesurfer_thickness_file='',
labels_spectra=[], labels_spectra_IDs=[],
sulci_spectra=[], sulci_spectra_IDs=[],
labels_zernike=[], labels_zernike_IDs=[],
sulci_zernike=[], sulci_zernike_IDs=[],
exclude_labels=[-1], delimiter=','):
"""
Make tables of shape statistics per label, sulcus, and/or fundus.
Note ::
This function is tailored for Mindboggle outputs.
Parameters
----------
labels_or_file : list or string
label number for each vertex or name of VTK file with index scalars
sulci : list of integers
indices to sulci, one per vertex, with -1 indicating no sulcus
fundi : list of integers
indices to fundi, one per vertex, with -1 indicating no fundus
affine_transform_file : string
affine transform file to standard space
transform_format : string
format for transform file
Ex: 'txt' for text, 'itk' for ITK, and 'mat' for Matlab format
area_file : string
name of VTK file with surface area scalar values
normalize_by_area : Boolean
normalize all shape measures by area of label/feature?
mean_curvature_file : string
name of VTK file with mean curvature scalar values
travel_depth_file : string
name of VTK file with travel depth scalar values
geodesic_depth_file : string
name of VTK file with geodesic depth scalar values
freesurfer_convexity_file : string
name of VTK file with FreeSurfer convexity scalar values
freesurfer_thickness_file : string
name of VTK file with FreeSurfer thickness scalar values
labels_zernike : list of lists of floats
Laplace-Beltrami spectra for labeled regions
labels_spectra_IDs : list of integers
unique ID numbers (labels) for labels_spectra
sulci_spectra : list of lists of floats
Laplace-Beltrami spectra for sulci
sulci_spectra_IDs : list of integers
unique ID numbers (labels) for sulci_spectra
labels_zernike : list of lists of floats
Zernike moments for labeled regions
labels_zernike_IDs : list of integers
unique ID numbers (labels) for labels_zernike
sulci_zernike : list of lists of floats
Zernike moments for sulci
sulci_zernike_IDs : list of integers
unique ID numbers (labels) for sulci_zernike
exclude_labels : list of lists of integers
indices to be excluded (in addition to -1)
delimiter : string
delimiter between columns, such as ','
Returns
-------
label_table : string
output table filename for label shapes
sulcus_table : string
output table filename for sulcus shapes
fundus_table : string
output table filename for fundus shapes
Examples
--------
>>> import os
>>> from mindboggle.utils.io_vtk import read_scalars
>>> from mindboggle.utils.io_table import write_shape_stats
>>> path = os.environ['MINDBOGGLE_DATA']
>>> labels_or_file = os.path.join(path, 'arno', 'labels', 'lh.labels.DKT25.manual.vtk')
>>> sulci_file = os.path.join(path, 'arno', 'features', 'sulci.vtk')
>>> fundi_file = os.path.join(path, 'arno', 'features', 'fundi.vtk')
>>> sulci, name = read_scalars(sulci_file)
>>> fundi, name = read_scalars(fundi_file)
>>> affine_transform_file = os.path.join(path, 'arno', 'mri', 't1weighted_brain.MNI152Affine.txt')
>>> #transform_format = 'mat'
>>> transform_format = 'itk'
>>> area_file = os.path.join(path, 'arno', 'shapes', 'lh.pial.area.vtk')
>>> normalize_by_area = True
>>> mean_curvature_file = os.path.join(path, 'arno', 'shapes', 'lh.pial.mean_curvature.vtk')
>>> travel_depth_file = os.path.join(path, 'arno', 'shapes', 'lh.pial.travel_depth.vtk')
>>> geodesic_depth_file = os.path.join(path, 'arno', 'shapes', 'lh.pial.geodesic_depth.vtk')
>>> freesurfer_convexity_file = ''
>>> freesurfer_thickness_file = ''
>>> delimiter = ','
>>> #
>>> labels, name = read_scalars(labels_or_file)
>>> labels_spectra = []
>>> labels_spectra_IDs = []
>>> sulci_spectra = []
>>> sulci_spectra_IDs = []
>>> labels_zernike = []
>>> labels_zernike_IDs = []
>>> sulci_zernike = []
>>> sulci_zernike_IDs = []
>>> exclude_labels = [-1]
>>> #
>>> write_shape_stats(labels_or_file, sulci, fundi,
>>> affine_transform_file, transform_format, area_file, normalize_by_area,
>>> mean_curvature_file, travel_depth_file, geodesic_depth_file,
>>> freesurfer_convexity_file, freesurfer_thickness_file,
>>> labels_spectra, labels_spectra_IDs,
>>> sulci_spectra, sulci_spectra_IDs,
>>> labels_zernike, labels_zernike_IDs,
>>> sulci_zernike, sulci_zernike_IDs,
>>> exclude_labels, delimiter)
"""
import os
import numpy as np
from mindboggle.utils.compute import means_per_label, stats_per_label, \
sum_per_label
from mindboggle.utils.io_vtk import read_scalars, read_vtk, \
apply_affine_transform
from mindboggle.utils.io_table import write_columns
from mindboggle.LABELS import DKTprotocol
dkt = DKTprotocol()
# Make sure inputs are lists:
if isinstance(labels_or_file, np.ndarray):
labels = [int(x) for x in labels_or_file]
elif isinstance(labels_or_file, list):
labels = labels_or_file
elif isinstance(labels_or_file, str):
labels, name = read_scalars(labels_or_file)
if isinstance(sulci, np.ndarray):
sulci = [int(x) for x in sulci]
if isinstance(fundi, np.ndarray):
fundi = [int(x) for x in fundi]
if not labels and not sulci and not fundi:
import sys
sys.exit('No feature data to tabulate in write_shape_stats().')
#-------------------------------------------------------------------------
# Feature lists, shape names, and shape files:
#-------------------------------------------------------------------------
# Feature lists:
feature_lists = [labels, sulci, fundi]
feature_names = ['Label', 'Sulcus', 'Fundus']
spectra_lists = [labels_spectra, sulci_spectra]
spectra_ID_lists = [labels_spectra_IDs, sulci_spectra_IDs]
zernike_lists = [labels_zernike, sulci_zernike]
zernike_ID_lists = [labels_zernike_IDs, sulci_zernike_IDs]
table_names = ['label_shapes.csv', 'sulcus_shapes.csv',
'fundus_shapes.csv']
# Shape names corresponding to shape files below:
shape_names = ['area', 'mean curvature', 'travel depth', 'geodesic depth',
'FreeSurfer convexity', 'FreeSurfer thickness']
# Load shape files as a list of numpy arrays of per-vertex shape values:
shape_files = [area_file, mean_curvature_file, travel_depth_file,
geodesic_depth_file, freesurfer_convexity_file,
freesurfer_thickness_file]
shape_arrays = []
first_pass = True
area_array = []
for ishape, shape_file in enumerate(shape_files):
if os.path.exists(shape_file):
if first_pass:
faces, lines, indices, points, npoints, scalars_array, name, \
input_vtk = read_vtk(shape_file, True, True)
points = np.array(points)
first_pass = False
if affine_transform_file and transform_format:
affine_points, \
foo1 = apply_affine_transform(affine_transform_file,
points, transform_format,
vtk_file_stem='')
affine_points = np.array(affine_points)
else:
scalars_array, name = read_scalars(shape_file, True, True)
if scalars_array.size:
shape_arrays.append(scalars_array)
# Store area array:
if ishape == 0:
area_array = scalars_array.copy()
if normalize_by_area:
use_area = area_array
else:
use_area = []
# Initialize table file names:
label_table = ''
sulcus_table = ''
fundus_table = ''
# Loop through features / tables:
for itable, feature_list in enumerate(feature_lists):
column_names = []
#---------------------------------------------------------------------
# For each feature, construct a table of average shape values:
#---------------------------------------------------------------------
if feature_list:
feature_name = feature_names[itable]
columns = []
#-----------------------------------------------------------------
# Loop through shape measures:
#-----------------------------------------------------------------
column_names.extend(column_names[:])
for ishape, shape_array in enumerate(shape_arrays):
shape = shape_names[ishape]
print(' Compute statistics on {0} {1}...'.
format(feature_name, shape))
#-------------------------------------------------------------
# Append feature areas to columns:
#-------------------------------------------------------------
if ishape == 0 and np.size(area_array):
sums, label_list = sum_per_label(shape_array,
feature_list, exclude_labels)
column_names.append(shape)
columns.append(sums)
#-------------------------------------------------------------
# Append feature shape statistics to columns:
#-------------------------------------------------------------
else:
medians, mads, means, sdevs, skews, kurts, \
lower_quarts, upper_quarts, \
label_list = stats_per_label(shape_array,
feature_list, exclude_labels, area_array, precision=1)
column_names.append(shape + ': median')
column_names.append(shape + ': MAD')
column_names.append(shape + ': mean')
column_names.append(shape + ': SD')
column_names.append(shape + ': skew')
column_names.append(shape + ': kurtosis')
column_names.append(shape + ': 25%')
column_names.append(shape + ': 75%')
columns.append(medians)
columns.append(mads)
columns.append(means)
columns.append(sdevs)
columns.append(skews)
columns.append(kurts)
columns.append(lower_quarts)
columns.append(upper_quarts)
#-----------------------------------------------------------------
# Mean positions in the original space:
#-----------------------------------------------------------------
# Compute mean position per feature:
positions, sdevs, label_list, foo = means_per_label(points,
feature_list, exclude_labels, use_area)
# Append mean position per feature to columns:
column_names.append('mean position')
columns.append(positions)
#-----------------------------------------------------------------
# Mean positions in standard space:
#-----------------------------------------------------------------
if affine_transform_file and transform_format:
# Compute standard space mean position per feature:
standard_positions, sdevs, label_list, \
foo = means_per_label(affine_points,
feature_list, exclude_labels, use_area)
# Append standard space mean position per feature to columns:
column_names.append('mean position in standard space')
columns.append(standard_positions)
#-----------------------------------------------------------------
# Label names:
#-----------------------------------------------------------------
if itable == 0:
label_numbers = dkt.label_numbers
label_names = dkt.label_names
name_list = []
for label in label_list:
name_list.append(label_names[label_numbers.index(label)])
#-----------------------------------------------------------------
# Laplace-Beltrami spectra:
#-----------------------------------------------------------------
if itable in [0, 1]:
spectra = spectra_lists[itable]
if spectra:
spectra_IDs = spectra_ID_lists[itable]
# Order spectra into a list:
spectrum_list = []
for label in label_list:
if label in spectra_IDs:
spectrum = spectra[spectra_IDs.index(label)]
spectrum_list.append(spectrum)
else:
spectrum_list.append('')
# Append spectral shape name and values to relevant columns:
columns.append(spectrum_list)
column_names.append('Laplace-Beltrami spectra')
#-----------------------------------------------------------------
# Zernike moments:
#-----------------------------------------------------------------
if itable in [0, 1]:
zernike = zernike_lists[itable]
if zernike:
zernike_IDs = zernike_ID_lists[itable]
# Order zernike into a list:
spectrum_list = []
for label in label_list:
if label in zernike_IDs:
spectrum = zernike[zernike_IDs.index(label)]
spectrum_list.append(spectrum)
else:
spectrum_list.append('')
# Append Zernike shape name and values to relevant columns:
columns.append(spectrum_list)
column_names.append('Zernike moments')
#-----------------------------------------------------------------
# Write labels/IDs and values to table:
#-----------------------------------------------------------------
# Write labels/IDs to table:
output_table = os.path.join(os.getcwd(), table_names[itable])
output_table = write_columns(label_list, feature_name, delimiter,
quote=True, input_table='',
output_table=output_table)
if itable == 0:
write_columns(name_list, 'Label name', delimiter,
quote=True, input_table=output_table,
output_table=output_table)
# Append columns of shape values to table:
if columns:
write_columns(columns, column_names, delimiter,
quote=True, input_table=output_table,
output_table=output_table)
if not os.path.exists(output_table):
raise(IOError(output_table + " not found"))
#-----------------------------------------------------------------
# Return correct table file name:
#-----------------------------------------------------------------
if itable == 0:
label_table = output_table
elif itable == 1:
sulcus_table = output_table
elif itable == 2:
fundus_table = output_table
return label_table, sulcus_table, fundus_table