surfa.Overlay#

class surfa.Overlay(data, labels=None, metadata=None)#

1D mesh overlay class defining an array with data frames.

Parameters

  • data (array_like) – Image data array.

  • labels (dict or LabelLookup, optional) – Label-name lookup for segmentation indices.

  • metadata (dict, optional) – Dictionary containing arbitrary array metadata.

Attributes

basedim

Base spatial dimensionality of the array (always excludes frame dimension).

baseshape

Base spatial shape of the data array (always excludes the frame dimension).

data

Core data numpy ndarray.

dtype

Data type.

framed_data

Core data array reshaped to include the frame dimension, regardless of nframes.

labels

Label-name lookup for segmentation indices.

metadata

Dictionary to store various metadata associated with the image.

nframes

Number of data frames.

shape

True shape of the internal data array.

size

Total number of elements in the data array.

Methods

astype(dtype, copy=True, order='K')#

Copy of the array, casted to a specified type.

Parameters

  • dtype (np.dtype) – Target datatype.

  • copy (bool) – Return copy if array already has matching datatype.

  • order ({‘C’, ‘F’, ‘A’, ‘K’}) – Controls the memory layout order of the result. ‘C’ means C order, ‘F’ means Fortran order, ‘A’ means ‘F’ order if all the arrays are Fortran contiguous, ‘C’ order otherwise, and ‘K’ means as close to the order the array elements appear in memory as possible.

Returns

arr – Array with target datatype.

Return type

Overlay

ceil()#

Ceil the array to integer values.

clip(a_min, a_max)#

Clip the array between low and high values.

Parameters

  • a_min (array_like or None) – Minimum and maximum value. If None, clipping is not performed on the corresponding edge

  • a_max (array_like or None) – Minimum and maximum value. If None, clipping is not performed on the corresponding edge

collapse(mapping=None)#

Collapse a one-hot encoded probabilistic map to discrete labels.

Parameters

mapping (array_like of int) – List of label indices that correspond to probabilistic data frames encoded.

Returns

arr – Collapsed, discrete segmentation array.

Return type

Overlay

copy()#

Return a deep copy of the object.

floor()#

Floor the array to integer values.

max(frames=False)#

Compute the maximum.

Parameters

frames (bool) – Compute max along frame axis.

Returns

Returns scalar max value, unless frames=True, in which case a new Overlay is returned.

Return type

scalar or Overlay

mean(nonzero=False, frames=False)#

Compute the mean.

Parameters

  • nonzero (bool) – If enabled, only consider nonzero elements. This is ignored if frames=True.

  • frames (bool) – Compute mean along frame axis.

Returns

Returns scalar mean value, unless frames is set to true, in which case a new Overlay is returned.

Return type

scalar or Overlay

min(nonzero=False, frames=False)#

Compute the minimum.

Parameters

  • nonzero (bool) – If enabled, only consider nonzero elements. This is ignored if frames=True.

  • frames (bool) – Compute min along frame axis.

Returns

Returns scalar min value, unless frames is set to true, in which case a new Overlay is returned.

Return type

scalar or Overlay

new(data)#

Return a new instance of the array with updated data. Metadata is preserved.

onehot(mapping, dtype=<class 'numpy.int32'>)#

Convert discrete labels to a one-hot encoded probabilistic map.

Parameters

  • mapping (array_like of int) – List of label indices to one-hot encode. Label order is preserved.

  • dtype (np.dtype) – Output segmentation datatype.

Returns

arr – Multi-frame one-hot segmentation array.

Return type

Overlay

percentile(percentiles, method='linear', nonzero=False)#

Compute the q-th percentile of the data.

Parameters

  • percentiles (array_like of float) – Percentile or sequence of percentiles to compute, which must be between 0 and 100 inclusive.

  • method (str) – Method to use for estimating the percentile. View numpy percentile doc for more information.

  • nonzero (bool) – If enabled, only consider nonzero elements.

Returns

percentile – Computes percentiles.

Return type

scalar or ndarray

round()#

Round the array to the nearest integer value.

save(filename, fmt=None, intent=0)#

Write array to file.

Parameters

  • filename (str) – Target filename to write array to.

  • fmt (str) – Optional file format to force.

unique()#

Find all unique elements of an array, sorted.

zeros(dtype=None, frames=None, order='K')#

Return a copy of the framed array with all elements set to zero.

Parameters

  • dtype (np.dtype) – Data type of new array.

  • frames (int) – Number of frames to allocate. If None, the number of frames is determined from the source array.

  • order ({‘C’, ‘F’, ‘K’}) – Controls the memory layout order of the result. ‘C’ means C order, ‘F’ means Fortran order, and ‘K’ means as close to the order the array elements appear in memory as possible.

Returns

arr – Array with zero values.

Return type

Overlay