Source code for medpy.metric.binary

# Copyright (C) 2013 Oskar Maier
#
# This program is free software: you can redistribute it and/or modify
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
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# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <http://www.gnu.org/licenses/>.
#
# author Oskar Maier
# version r0.1.1
# since 2014-03-13
# status Release

# build-in modules

# third-party modules
import numpy
from scipy.ndimage import _ni_support
from scipy.ndimage.morphology import distance_transform_edt, binary_erosion,\
generate_binary_structure
from scipy.ndimage.measurements import label, find_objects
from scipy.stats import pearsonr

# own modules

# code
[docs]def dc(result, reference): r""" Dice coefficient Computes the Dice coefficient (also known as Sorensen index) between the binary objects in two images. The metric is defined as .. math:: DC=\frac{2|A\cap B|}{|A|+|B|} , where :math:A is the first and :math:B the second set of samples (here: binary objects). Parameters ---------- result : array_like Input data containing objects. Can be any type but will be converted into binary: background where 0, object everywhere else. reference : array_like Input data containing objects. Can be any type but will be converted into binary: background where 0, object everywhere else. Returns ------- dc : float The Dice coefficient between the object(s) in result and the object(s) in reference. It ranges from 0 (no overlap) to 1 (perfect overlap). Notes ----- This is a real metric. The binary images can therefore be supplied in any order. """ result = numpy.atleast_1d(result.astype(numpy.bool)) reference = numpy.atleast_1d(reference.astype(numpy.bool)) intersection = numpy.count_nonzero(result & reference) size_i1 = numpy.count_nonzero(result) size_i2 = numpy.count_nonzero(reference) try: dc = 2. * intersection / float(size_i1 + size_i2) except ZeroDivisionError: dc = 0.0 return dc
[docs]def jc(result, reference): """ Jaccard coefficient Computes the Jaccard coefficient between the binary objects in two images. Parameters ---------- result: array_like Input data containing objects. Can be any type but will be converted into binary: background where 0, object everywhere else. reference: array_like Input data containing objects. Can be any type but will be converted into binary: background where 0, object everywhere else. Returns ------- jc: float The Jaccard coefficient between the object(s) in result and the object(s) in reference. It ranges from 0 (no overlap) to 1 (perfect overlap). Notes ----- This is a real metric. The binary images can therefore be supplied in any order. """ result = numpy.atleast_1d(result.astype(numpy.bool)) reference = numpy.atleast_1d(reference.astype(numpy.bool)) intersection = numpy.count_nonzero(result & reference) union = numpy.count_nonzero(result | reference) jc = float(intersection) / float(union) return jc
[docs]def precision(result, reference): """ Precison. Parameters ---------- result : array_like Input data containing objects. Can be any type but will be converted into binary: background where 0, object everywhere else. reference : array_like Input data containing objects. Can be any type but will be converted into binary: background where 0, object everywhere else. Returns ------- precision : float The precision between two binary datasets, here mostly binary objects in images, which is defined as the fraction of retrieved instances that are relevant. The precision is not symmetric. See also -------- :func:recall Notes ----- Not symmetric. The inverse of the precision is :func:recall. High precision means that an algorithm returned substantially more relevant results than irrelevant. References ---------- ..  http://en.wikipedia.org/wiki/Precision_and_recall ..  http://en.wikipedia.org/wiki/Confusion_matrix#Table_of_confusion """ result = numpy.atleast_1d(result.astype(numpy.bool)) reference = numpy.atleast_1d(reference.astype(numpy.bool)) tp = numpy.count_nonzero(result & reference) fp = numpy.count_nonzero(result & ~reference) try: precision = tp / float(tp + fp) except ZeroDivisionError: precision = 0.0 return precision
[docs]def recall(result, reference): """ Recall. Parameters ---------- result : array_like Input data containing objects. Can be any type but will be converted into binary: background where 0, object everywhere else. reference : array_like Input data containing objects. Can be any type but will be converted into binary: background where 0, object everywhere else. Returns ------- recall : float The recall between two binary datasets, here mostly binary objects in images, which is defined as the fraction of relevant instances that are retrieved. The recall is not symmetric. See also -------- :func:precision Notes ----- Not symmetric. The inverse of the recall is :func:precision. High recall means that an algorithm returned most of the relevant results. References ---------- ..  http://en.wikipedia.org/wiki/Precision_and_recall ..  http://en.wikipedia.org/wiki/Confusion_matrix#Table_of_confusion """ result = numpy.atleast_1d(result.astype(numpy.bool)) reference = numpy.atleast_1d(reference.astype(numpy.bool)) tp = numpy.count_nonzero(result & reference) fn = numpy.count_nonzero(~result & reference) try: recall = tp / float(tp + fn) except ZeroDivisionError: recall = 0.0 return recall
[docs]def sensitivity(result, reference): """ Sensitivity. Same as :func:recall, see there for a detailed description. See also -------- :func:specificity """ return recall(result, reference)
[docs]def specificity(result, reference): """ Specificity. Parameters ---------- result : array_like Input data containing objects. Can be any type but will be converted into binary: background where 0, object everywhere else. reference : array_like Input data containing objects. Can be any type but will be converted into binary: background where 0, object everywhere else. Returns ------- specificity : float The specificity between two binary datasets, here mostly binary objects in images, which denotes the fraction of correctly returned negatives. The specificity is not symmetric. See also -------- :func:sensitivity Notes ----- Not symmetric. The completment of the specificity is :func:sensitivity. High recall means that an algorithm returned most of the irrelevant results. References ---------- ..  https://en.wikipedia.org/wiki/Sensitivity_and_specificity ..  http://en.wikipedia.org/wiki/Confusion_matrix#Table_of_confusion """ result = numpy.atleast_1d(result.astype(numpy.bool)) reference = numpy.atleast_1d(reference.astype(numpy.bool)) tn = numpy.count_nonzero(~result & ~reference) fp = numpy.count_nonzero(result & ~reference) try: specificity = tn / float(tn + fp) except ZeroDivisionError: specificity = 0.0 return specificity
[docs]def true_negative_rate(result, reference): """ True negative rate. Same as :func:specificity, see there for a detailed description. See also -------- :func:true_positive_rate :func:positive_predictive_value """ return specificity(result, reference)
[docs]def true_positive_rate(result, reference): """ True positive rate. Same as :func:recall and :func:sensitivity, see there for a detailed description. See also -------- :func:positive_predictive_value :func:true_negative_rate """ return recall(result, reference)
[docs]def positive_predictive_value(result, reference): """ Positive predictive value. Same as :func:precision, see there for a detailed description. See also -------- :func:true_positive_rate :func:true_negative_rate """ return precision(result, reference)
[docs]def hd(result, reference, voxelspacing=None, connectivity=1): """ Hausdorff Distance. Computes the (symmetric) Hausdorff Distance (HD) between the binary objects in two images. It is defined as the maximum surface distance between the objects. Parameters ---------- result : array_like Input data containing objects. Can be any type but will be converted into binary: background where 0, object everywhere else. reference : array_like Input data containing objects. Can be any type but will be converted into binary: background where 0, object everywhere else. voxelspacing : float or sequence of floats, optional The voxelspacing in a distance unit i.e. spacing of elements along each dimension. If a sequence, must be of length equal to the input rank; if a single number, this is used for all axes. If not specified, a grid spacing of unity is implied. connectivity : int The neighbourhood/connectivity considered when determining the surface of the binary objects. This value is passed to scipy.ndimage.morphology.generate_binary_structure and should usually be :math:> 1. Note that the connectivity influences the result in the case of the Hausdorff distance. Returns ------- hd : float The symmetric Hausdorff Distance between the object(s) in result and the object(s) in reference. The distance unit is the same as for the spacing of elements along each dimension, which is usually given in mm. See also -------- :func:assd :func:asd Notes ----- This is a real metric. The binary images can therefore be supplied in any order. """ hd1 = __surface_distances(result, reference, voxelspacing, connectivity).max() hd2 = __surface_distances(reference, result, voxelspacing, connectivity).max() hd = max(hd1, hd2) return hd
def hd95(result, reference, voxelspacing=None, connectivity=1): """ 95th percentile of the Hausdorff Distance. Computes the 95th percentile of the (symmetric) Hausdorff Distance (HD) between the binary objects in two images. Compared to the Hausdorff Distance, this metric is slightly more stable to small outliers and is commonly used in Biomedical Segmentation challenges. Parameters ---------- result : array_like Input data containing objects. Can be any type but will be converted into binary: background where 0, object everywhere else. reference : array_like Input data containing objects. Can be any type but will be converted into binary: background where 0, object everywhere else. voxelspacing : float or sequence of floats, optional The voxelspacing in a distance unit i.e. spacing of elements along each dimension. If a sequence, must be of length equal to the input rank; if a single number, this is used for all axes. If not specified, a grid spacing of unity is implied. connectivity : int The neighbourhood/connectivity considered when determining the surface of the binary objects. This value is passed to scipy.ndimage.morphology.generate_binary_structure and should usually be :math:> 1. Note that the connectivity influences the result in the case of the Hausdorff distance. Returns ------- hd : float The symmetric Hausdorff Distance between the object(s) in result and the object(s) in reference. The distance unit is the same as for the spacing of elements along each dimension, which is usually given in mm. See also -------- :func:hd Notes ----- This is a real metric. The binary images can therefore be supplied in any order. """ hd1 = __surface_distances(result, reference, voxelspacing, connectivity) hd2 = __surface_distances(reference, result, voxelspacing, connectivity) hd95 = numpy.percentile(numpy.hstack((hd1, hd2)), 95) return hd95
[docs]def assd(result, reference, voxelspacing=None, connectivity=1): """ Average symmetric surface distance. Computes the average symmetric surface distance (ASD) between the binary objects in two images. Parameters ---------- result : array_like Input data containing objects. Can be any type but will be converted into binary: background where 0, object everywhere else. reference : array_like Input data containing objects. Can be any type but will be converted into binary: background where 0, object everywhere else. voxelspacing : float or sequence of floats, optional The voxelspacing in a distance unit i.e. spacing of elements along each dimension. If a sequence, must be of length equal to the input rank; if a single number, this is used for all axes. If not specified, a grid spacing of unity is implied. connectivity : int The neighbourhood/connectivity considered when determining the surface of the binary objects. This value is passed to scipy.ndimage.morphology.generate_binary_structure and should usually be :math:> 1. The decision on the connectivity is important, as it can influence the results strongly. If in doubt, leave it as it is. Returns ------- assd : float The average symmetric surface distance between the object(s) in result and the object(s) in reference. The distance unit is the same as for the spacing of elements along each dimension, which is usually given in mm. See also -------- :func:asd :func:hd Notes ----- This is a real metric, obtained by calling and averaging >>> asd(result, reference) and >>> asd(reference, result) The binary images can therefore be supplied in any order. """ assd = numpy.mean( (asd(result, reference, voxelspacing, connectivity), asd(reference, result, voxelspacing, connectivity)) ) return assd
[docs]def asd(result, reference, voxelspacing=None, connectivity=1): """ Average surface distance metric. Computes the average surface distance (ASD) between the binary objects in two images. Parameters ---------- result : array_like Input data containing objects. Can be any type but will be converted into binary: background where 0, object everywhere else. reference : array_like Input data containing objects. Can be any type but will be converted into binary: background where 0, object everywhere else. voxelspacing : float or sequence of floats, optional The voxelspacing in a distance unit i.e. spacing of elements along each dimension. If a sequence, must be of length equal to the input rank; if a single number, this is used for all axes. If not specified, a grid spacing of unity is implied. connectivity : int The neighbourhood/connectivity considered when determining the surface of the binary objects. This value is passed to scipy.ndimage.morphology.generate_binary_structure and should usually be :math:> 1. The decision on the connectivity is important, as it can influence the results strongly. If in doubt, leave it as it is. Returns ------- asd : float The average surface distance between the object(s) in result and the object(s) in reference. The distance unit is the same as for the spacing of elements along each dimension, which is usually given in mm. See also -------- :func:assd :func:hd Notes ----- This is not a real metric, as it is directed. See assd for a real metric of this. The method is implemented making use of distance images and simple binary morphology to achieve high computational speed. Examples -------- The connectivity determines what pixels/voxels are considered the surface of a binary object. Take the following binary image showing a cross >>> from scipy.ndimage.morphology import generate_binary_structure >>> cross = generate_binary_structure(2, 1) array([[0, 1, 0], [1, 1, 1], [0, 1, 0]]) With connectivity set to 1 a 4-neighbourhood is considered when determining the object surface, resulting in the surface .. code-block:: python array([[0, 1, 0], [1, 0, 1], [0, 1, 0]]) Changing connectivity to 2, a 8-neighbourhood is considered and we get: .. code-block:: python array([[0, 1, 0], [1, 1, 1], [0, 1, 0]]) , as a diagonal connection does no longer qualifies as valid object surface. This influences the results asd returns. Imagine we want to compute the surface distance of our cross to a cube-like object: >>> cube = generate_binary_structure(2, 1) array([[1, 1, 1], [1, 1, 1], [1, 1, 1]]) , which surface is, independent of the connectivity value set, always .. code-block:: python array([[1, 1, 1], [1, 0, 1], [1, 1, 1]]) Using a connectivity of 1 we get >>> asd(cross, cube, connectivity=1) 0.0 while a value of 2 returns us >>> asd(cross, cube, connectivity=2) 0.20000000000000001 due to the center of the cross being considered surface as well. """ sds = __surface_distances(result, reference, voxelspacing, connectivity) asd = sds.mean() return asd
[docs]def ravd(result, reference): """ Relative absolute volume difference. Compute the relative absolute volume difference between the (joined) binary objects in the two images. Parameters ---------- result : array_like Input data containing objects. Can be any type but will be converted into binary: background where 0, object everywhere else. reference : array_like Input data containing objects. Can be any type but will be converted into binary: background where 0, object everywhere else. Returns ------- ravd : float The relative absolute volume difference between the object(s) in result and the object(s) in reference. This is a percentage value in the range :math:[-1.0, +inf] for which a :math:0 denotes an ideal score. Raises ------ RuntimeError If the reference object is empty. See also -------- :func:dc :func:precision :func:recall Notes ----- This is not a real metric, as it is directed. Negative values denote a smaller and positive values a larger volume than the reference. This implementation does not check, whether the two supplied arrays are of the same size. Examples -------- Considering the following inputs >>> import numpy >>> arr1 = numpy.asarray([[0,1,0],[1,1,1],[0,1,0]]) >>> arr1 array([[0, 1, 0], [1, 1, 1], [0, 1, 0]]) >>> arr2 = numpy.asarray([[0,1,0],[1,0,1],[0,1,0]]) >>> arr2 array([[0, 1, 0], [1, 0, 1], [0, 1, 0]]) comparing arr1 to arr2 we get >>> ravd(arr1, arr2) -0.2 and reversing the inputs the directivness of the metric becomes evident >>> ravd(arr2, arr1) 0.25 It is important to keep in mind that a perfect score of 0 does not mean that the binary objects fit exactely, as only the volumes are compared: >>> arr1 = numpy.asarray([1,0,0]) >>> arr2 = numpy.asarray([0,0,1]) >>> ravd(arr1, arr2) 0.0 """ result = numpy.atleast_1d(result.astype(numpy.bool)) reference = numpy.atleast_1d(reference.astype(numpy.bool)) vol1 = numpy.count_nonzero(result) vol2 = numpy.count_nonzero(reference) if 0 == vol2: raise RuntimeError('The second supplied array does not contain any binary object.') return (vol1 - vol2) / float(vol2)
[docs]def volume_correlation(results, references): r""" Volume correlation. Computes the linear correlation in binary object volume between the contents of the successive binary images supplied. Measured through the Pearson product-moment correlation coefficient. Parameters ---------- results : sequence of array_like Ordered list of input data containing objects. Each array_like will be converted into binary: background where 0, object everywhere else. references : sequence of array_like Ordered list of input data containing objects. Each array_like will be converted into binary: background where 0, object everywhere else. The order must be the same as for results. Returns ------- r : float The correlation coefficient between -1 and 1. p : float The two-side p value. """ results = numpy.atleast_2d(numpy.array(results).astype(numpy.bool)) references = numpy.atleast_2d(numpy.array(references).astype(numpy.bool)) results_volumes = [numpy.count_nonzero(r) for r in results] references_volumes = [numpy.count_nonzero(r) for r in references] return pearsonr(results_volumes, references_volumes) # returns (Pearson'
[docs]def volume_change_correlation(results, references): r""" Volume change correlation. Computes the linear correlation of change in binary object volume between the contents of the successive binary images supplied. Measured through the Pearson product-moment correlation coefficient. Parameters ---------- results : sequence of array_like Ordered list of input data containing objects. Each array_like will be converted into binary: background where 0, object everywhere else. references : sequence of array_like Ordered list of input data containing objects. Each array_like will be converted into binary: background where 0, object everywhere else. The order must be the same as for results. Returns ------- r : float The correlation coefficient between -1 and 1. p : float The two-side p value. """ results = numpy.atleast_2d(numpy.array(results).astype(numpy.bool)) references = numpy.atleast_2d(numpy.array(references).astype(numpy.bool)) results_volumes = numpy.asarray([numpy.count_nonzero(r) for r in results]) references_volumes = numpy.asarray([numpy.count_nonzero(r) for r in references]) results_volumes_changes = results_volumes[1:] - results_volumes[:-1] references_volumes_changes = references_volumes[1:] - references_volumes[:-1] return pearsonr(results_volumes_changes, references_volumes_changes) # returns (Pearson's correlation coefficient, 2-tailed p-value)
[docs]def obj_assd(result, reference, voxelspacing=None, connectivity=1): """ Average symmetric surface distance. Computes the average symmetric surface distance (ASSD) between the binary objects in two images. Parameters ---------- result : array_like Input data containing objects. Can be any type but will be converted into binary: background where 0, object everywhere else. reference : array_like Input data containing objects. Can be any type but will be converted into binary: background where 0, object everywhere else. voxelspacing : float or sequence of floats, optional The voxelspacing in a distance unit i.e. spacing of elements along each dimension. If a sequence, must be of length equal to the input rank; if a single number, this is used for all axes. If not specified, a grid spacing of unity is implied. connectivity : int The neighbourhood/connectivity considered when determining what accounts for a distinct binary object as well as when determining the surface of the binary objects. This value is passed to scipy.ndimage.morphology.generate_binary_structure and should usually be :math:> 1. The decision on the connectivity is important, as it can influence the results strongly. If in doubt, leave it as it is. Returns ------- assd : float The average symmetric surface distance between all mutually existing distinct binary object(s) in result and reference. The distance unit is the same as for the spacing of elements along each dimension, which is usually given in mm. See also -------- :func:obj_asd Notes ----- This is a real metric, obtained by calling and averaging >>> obj_asd(result, reference) and >>> obj_asd(reference, result) The binary images can therefore be supplied in any order. """ assd = numpy.mean( (obj_asd(result, reference, voxelspacing, connectivity), obj_asd(reference, result, voxelspacing, connectivity)) ) return assd
[docs]def obj_asd(result, reference, voxelspacing=None, connectivity=1): """ Average surface distance between objects. First correspondences between distinct binary objects in reference and result are established. Then the average surface distance is only computed between corresponding objects. Correspondence is defined as unique and at least one voxel overlap. Parameters ---------- result : array_like Input data containing objects. Can be any type but will be converted into binary: background where 0, object everywhere else. reference : array_like Input data containing objects. Can be any type but will be converted into binary: background where 0, object everywhere else. voxelspacing : float or sequence of floats, optional The voxelspacing in a distance unit i.e. spacing of elements along each dimension. If a sequence, must be of length equal to the input rank; if a single number, this is used for all axes. If not specified, a grid spacing of unity is implied. connectivity : int The neighbourhood/connectivity considered when determining what accounts for a distinct binary object as well as when determining the surface of the binary objects. This value is passed to scipy.ndimage.morphology.generate_binary_structure and should usually be :math:> 1. The decision on the connectivity is important, as it can influence the results strongly. If in doubt, leave it as it is. Returns ------- asd : float The average surface distance between all mutually existing distinct binary object(s) in result and reference. The distance unit is the same as for the spacing of elements along each dimension, which is usually given in mm. See also -------- :func:obj_assd :func:obj_tpr :func:obj_fpr Notes ----- This is not a real metric, as it is directed. See obj_assd for a real metric of this. For the understanding of this metric, both the notions of connectedness and surface distance are essential. Please see :func:obj_tpr and :func:obj_fpr for more information on the first and :func:asd on the second. Examples -------- >>> arr1 = numpy.asarray([[1,1,1],[1,1,1],[1,1,1]]) >>> arr2 = numpy.asarray([[0,1,0],[0,1,0],[0,1,0]]) >>> arr1 array([[1, 1, 1], [1, 1, 1], [1, 1, 1]]) >>> arr2 array([[0, 1, 0], [0, 1, 0], [0, 1, 0]]) >>> obj_asd(arr1, arr2) 1.5 >>> obj_asd(arr2, arr1) 0.333333333333 With the voxelspacing parameter, the distances between the voxels can be set for each dimension separately: >>> obj_asd(arr1, arr2, voxelspacing=(1,2)) 1.5 >>> obj_asd(arr2, arr1, voxelspacing=(1,2)) 0.333333333333 More examples depicting the notion of object connectedness: >>> arr1 = numpy.asarray([[1,0,1],[1,0,0],[0,0,0]]) >>> arr2 = numpy.asarray([[1,0,1],[1,0,0],[0,0,1]]) >>> arr1 array([[1, 0, 1], [1, 0, 0], [0, 0, 0]]) >>> arr2 array([[1, 0, 1], [1, 0, 0], [0, 0, 1]]) >>> obj_asd(arr1, arr2) 0.0 >>> obj_asd(arr2, arr1) 0.0 >>> arr1 = numpy.asarray([[1,0,1],[1,0,1],[0,0,1]]) >>> arr2 = numpy.asarray([[1,0,1],[1,0,0],[0,0,1]]) >>> arr1 array([[1, 0, 1], [1, 0, 1], [0, 0, 1]]) >>> arr2 array([[1, 0, 1], [1, 0, 0], [0, 0, 1]]) >>> obj_asd(arr1, arr2) 0.6 >>> obj_asd(arr2, arr1) 0.0 Influence of connectivity parameter can be seen in the following example, where with the (default) connectivity of 1 the first array is considered to contain two objects, while with an increase connectivity of 2, just one large object is detected. >>> arr1 = numpy.asarray([[1,0,0],[0,1,1],[0,1,1]]) >>> arr2 = numpy.asarray([[1,0,0],[0,0,0],[0,0,0]]) >>> arr1 array([[1, 0, 0], [0, 1, 1], [0, 1, 1]]) >>> arr2 array([[1, 0, 0], [0, 0, 0], [0, 0, 0]]) >>> obj_asd(arr1, arr2) 0.0 >>> obj_asd(arr1, arr2, connectivity=2) 1.742955328 Note that the connectivity also influence the notion of what is considered an object surface voxels. """ sds = list() labelmap1, labelmap2, _a, _b, mapping = __distinct_binary_object_correspondences(result, reference, connectivity) slicers1 = find_objects(labelmap1) slicers2 = find_objects(labelmap2) for lid2, lid1 in list(mapping.items()): window = __combine_windows(slicers1[lid1 - 1], slicers2[lid2 - 1]) object1 = labelmap1[window] == lid1 object2 = labelmap2[window] == lid2 sds.extend(__surface_distances(object1, object2, voxelspacing, connectivity)) asd = numpy.mean(sds) return asd
[docs]def obj_fpr(result, reference, connectivity=1): """ The false positive rate of distinct binary object detection. The false positive rates gives a percentage measure of how many distinct binary objects in the second array do not exists in the first array. A partial overlap (of minimum one voxel) is here considered sufficient. In cases where two distinct binary object in the second array overlap with a single distinct object in the first array, only one is considered to have been detected successfully and the other is added to the count of false positives. Parameters ---------- result : array_like Input data containing objects. Can be any type but will be converted into binary: background where 0, object everywhere else. reference : array_like Input data containing objects. Can be any type but will be converted into binary: background where 0, object everywhere else. connectivity : int The neighbourhood/connectivity considered when determining what accounts for a distinct binary object. This value is passed to scipy.ndimage.morphology.generate_binary_structure and should usually be :math:> 1. The decision on the connectivity is important, as it can influence the results strongly. If in doubt, leave it as it is. Returns ------- tpr : float A percentage measure of how many distinct binary objects in results have no corresponding binary object in reference. It has the range :math:[0, 1], where a :math:0 denotes an ideal score. Raises ------ RuntimeError If the second array is empty. See also -------- :func:obj_tpr Notes ----- This is not a real metric, as it is directed. Whatever array is considered as reference should be passed second. A perfect score of :math:0 tells that there are no distinct binary objects in the second array that do not exists also in the reference array, but does not reveal anything about objects in the reference array also existing in the second array (use :func:obj_tpr for this). Examples -------- >>> arr2 = numpy.asarray([[1,0,0],[1,0,1],[0,0,1]]) >>> arr1 = numpy.asarray([[0,0,1],[1,0,1],[0,0,1]]) >>> arr2 array([[1, 0, 0], [1, 0, 1], [0, 0, 1]]) >>> arr1 array([[0, 0, 1], [1, 0, 1], [0, 0, 1]]) >>> obj_fpr(arr1, arr2) 0.0 >>> obj_fpr(arr2, arr1) 0.0 Example of directedness: >>> arr2 = numpy.asarray([1,0,1,0,1]) >>> arr1 = numpy.asarray([1,0,1,0,0]) >>> obj_fpr(arr1, arr2) 0.0 >>> obj_fpr(arr2, arr1) 0.3333333333333333 Examples of multiple overlap treatment: >>> arr2 = numpy.asarray([1,0,1,0,1,1,1]) >>> arr1 = numpy.asarray([1,1,1,0,1,0,1]) >>> obj_fpr(arr1, arr2) 0.3333333333333333 >>> obj_fpr(arr2, arr1) 0.3333333333333333 >>> arr2 = numpy.asarray([1,0,1,1,1,0,1]) >>> arr1 = numpy.asarray([1,1,1,0,1,1,1]) >>> obj_fpr(arr1, arr2) 0.0 >>> obj_fpr(arr2, arr1) 0.3333333333333333 >>> arr2 = numpy.asarray([[1,0,1,0,0], [1,0,0,0,0], [1,0,1,1,1], [0,0,0,0,0], [1,0,1,0,0]]) >>> arr1 = numpy.asarray([[1,1,1,0,0], [0,0,0,0,0], [1,1,1,0,1], [0,0,0,0,0], [1,1,1,0,0]]) >>> obj_fpr(arr1, arr2) 0.0 >>> obj_fpr(arr2, arr1) 0.2 """ _, _, _, n_obj_reference, mapping = __distinct_binary_object_correspondences(reference, result, connectivity) return (n_obj_reference - len(mapping)) / float(n_obj_reference)
[docs]def obj_tpr(result, reference, connectivity=1): """ The true positive rate of distinct binary object detection. The true positive rates gives a percentage measure of how many distinct binary objects in the first array also exists in the second array. A partial overlap (of minimum one voxel) is here considered sufficient. In cases where two distinct binary object in the first array overlaps with a single distinct object in the second array, only one is considered to have been detected successfully. Parameters ---------- result : array_like Input data containing objects. Can be any type but will be converted into binary: background where 0, object everywhere else. reference : array_like Input data containing objects. Can be any type but will be converted into binary: background where 0, object everywhere else. connectivity : int The neighbourhood/connectivity considered when determining what accounts for a distinct binary object. This value is passed to scipy.ndimage.morphology.generate_binary_structure and should usually be :math:> 1. The decision on the connectivity is important, as it can influence the results strongly. If in doubt, leave it as it is. Returns ------- tpr : float A percentage measure of how many distinct binary objects in result also exists in reference. It has the range :math:[0, 1], where a :math:1 denotes an ideal score. Raises ------ RuntimeError If the reference object is empty. See also -------- :func:obj_fpr Notes ----- This is not a real metric, as it is directed. Whatever array is considered as reference should be passed second. A perfect score of :math:1 tells that all distinct binary objects in the reference array also exist in the result array, but does not reveal anything about additional binary objects in the result array (use :func:obj_fpr for this). Examples -------- >>> arr2 = numpy.asarray([[1,0,0],[1,0,1],[0,0,1]]) >>> arr1 = numpy.asarray([[0,0,1],[1,0,1],[0,0,1]]) >>> arr2 array([[1, 0, 0], [1, 0, 1], [0, 0, 1]]) >>> arr1 array([[0, 0, 1], [1, 0, 1], [0, 0, 1]]) >>> obj_tpr(arr1, arr2) 1.0 >>> obj_tpr(arr2, arr1) 1.0 Example of directedness: >>> arr2 = numpy.asarray([1,0,1,0,1]) >>> arr1 = numpy.asarray([1,0,1,0,0]) >>> obj_tpr(arr1, arr2) 0.6666666666666666 >>> obj_tpr(arr2, arr1) 1.0 Examples of multiple overlap treatment: >>> arr2 = numpy.asarray([1,0,1,0,1,1,1]) >>> arr1 = numpy.asarray([1,1,1,0,1,0,1]) >>> obj_tpr(arr1, arr2) 0.6666666666666666 >>> obj_tpr(arr2, arr1) 0.6666666666666666 >>> arr2 = numpy.asarray([1,0,1,1,1,0,1]) >>> arr1 = numpy.asarray([1,1,1,0,1,1,1]) >>> obj_tpr(arr1, arr2) 0.6666666666666666 >>> obj_tpr(arr2, arr1) 1.0 >>> arr2 = numpy.asarray([[1,0,1,0,0], [1,0,0,0,0], [1,0,1,1,1], [0,0,0,0,0], [1,0,1,0,0]]) >>> arr1 = numpy.asarray([[1,1,1,0,0], [0,0,0,0,0], [1,1,1,0,1], [0,0,0,0,0], [1,1,1,0,0]]) >>> obj_tpr(arr1, arr2) 0.8 >>> obj_tpr(arr2, arr1) 1.0 """ _, _, n_obj_result, _, mapping = __distinct_binary_object_correspondences(reference, result, connectivity) return len(mapping) / float(n_obj_result)
def __distinct_binary_object_correspondences(reference, result, connectivity=1): """ Determines all distinct (where connectivity is defined by the connectivity parameter passed to scipy's generate_binary_structure) binary objects in both of the input parameters and returns a 1to1 mapping from the labelled objects in reference to the corresponding (whereas a one-voxel overlap suffices for correspondence) objects in result. All stems from the problem, that the relationship is non-surjective many-to-many. @return (labelmap1, labelmap2, n_lables1, n_labels2, labelmapping2to1) """ result = numpy.atleast_1d(result.astype(numpy.bool)) reference = numpy.atleast_1d(reference.astype(numpy.bool)) # binary structure footprint = generate_binary_structure(result.ndim, connectivity) # label distinct binary objects labelmap1, n_obj_result = label(result, footprint) labelmap2, n_obj_reference = label(reference, footprint) # find all overlaps from labelmap2 to labelmap1; collect one-to-one relationships and store all one-two-many for later processing slicers = find_objects(labelmap2) # get windows of labelled objects mapping = dict() # mappings from labels in labelmap2 to corresponding object labels in labelmap1 used_labels = set() # set to collect all already used labels from labelmap2 one_to_many = list() # list to collect all one-to-many mappings for l1id, slicer in enumerate(slicers): # iterate over object in labelmap2 and their windows l1id += 1 # labelled objects have ids sarting from 1 bobj = (l1id) == labelmap2[slicer] # find binary object corresponding to the label1 id in the segmentation l2ids = numpy.unique(labelmap1[slicer][bobj]) # extract all unique object identifiers at the corresponding positions in the reference (i.e. the mapping) l2ids = l2ids[0 != l2ids] # remove background identifiers (=0) if 1 == len(l2ids): # one-to-one mapping: if target label not already used, add to final list of object-to-object mappings and mark target label as used l2id = l2ids if not l2id in used_labels: mapping[l1id] = l2id used_labels.add(l2id) elif 1 < len(l2ids): # one-to-many mapping: store relationship for later processing one_to_many.append((l1id, set(l2ids))) # process one-to-many mappings, always choosing the one with the least labelmap2 correspondences first while True: one_to_many = [(l1id, l2ids - used_labels) for l1id, l2ids in one_to_many] # remove already used ids from all sets one_to_many = [x for x in one_to_many if x] # remove empty sets one_to_many = sorted(one_to_many, key=lambda x: len(x)) # sort by set length if 0 == len(one_to_many): break l2id = one_to_many.pop() # select an arbitrary target label id from the shortest set mapping[one_to_many] = l2id # add to one-to-one mappings used_labels.add(l2id) # mark target label as used one_to_many = one_to_many[1:] # delete the processed set from all sets return labelmap1, labelmap2, n_obj_result, n_obj_reference, mapping def __surface_distances(result, reference, voxelspacing=None, connectivity=1): """ The distances between the surface voxel of binary objects in result and their nearest partner surface voxel of a binary object in reference. """ result = numpy.atleast_1d(result.astype(numpy.bool)) reference = numpy.atleast_1d(reference.astype(numpy.bool)) if voxelspacing is not None: voxelspacing = _ni_support._normalize_sequence(voxelspacing, result.ndim) voxelspacing = numpy.asarray(voxelspacing, dtype=numpy.float64) if not voxelspacing.flags.contiguous: voxelspacing = voxelspacing.copy() # binary structure footprint = generate_binary_structure(result.ndim, connectivity) # test for emptiness if 0 == numpy.count_nonzero(result): raise RuntimeError('The first supplied array does not contain any binary object.') if 0 == numpy.count_nonzero(reference): raise RuntimeError('The second supplied array does not contain any binary object.') # extract only 1-pixel border line of objects result_border = result ^ binary_erosion(result, structure=footprint, iterations=1) reference_border = reference ^ binary_erosion(reference, structure=footprint, iterations=1) # compute average surface distance # Note: scipys distance transform is calculated only inside the borders of the # foreground objects, therefore the input has to be reversed dt = distance_transform_edt(~reference_border, sampling=voxelspacing) sds = dt[result_border] return sds def __combine_windows(w1, w2): """ Joins two windows (defined by tuple of slices) such that their maximum combined extend is covered by the new returned window. """ res = [] for s1, s2 in zip(w1, w2): res.append(slice(min(s1.start, s2.start), max(s1.stop, s2.stop))) return tuple(res)