xmipp3.utils module

This module contains utils functions for Xmipp protocols

class xmipp3.utils.Data(**kwargs)[source]

Bases: object

Store data points.

addPoint(point, position=None)[source]

clear()[source]

getDiscardedSize()[source]

getPoint(index)[source]

getSelectedSize()[source]

getSize()[source]

getWeights()[source]

getXData()[source]

getYData()[source]

getZData()[source]

iterAll()[source]: Iterate over all points, including the discarded ones.

class xmipp3.utils.PathData(**kwargs)[source]

Bases: Data

Just contains two list of x and y coordinates.

createEmptyPoint()[source]

removeLastPoint()[source]

splitLongestSegment()[source]: Split the longest segment by adding the midpoint.

class xmipp3.utils.Point(pointId, data, weight, state=0)[source]

Bases: object

Return x, y 2d coordinates and some other properties such as weight and state.

DISCARDED = -1

NORMAL = 0

SELECTED = 1

eval(expression)[source]

getData()[source]

getId()[source]

getState()[source]

getWeight()[source]

getX()[source]

getY()[source]

getZ()[source]

isDiscarded()[source]

isSelected()[source]

setDiscarded()[source]

setSelected()[source]

setState(newState)[source]

setX(value)[source]

setY(value)[source]

setZ(value)[source]

xmipp3.utils.applyTransform(imag_array, M, shape)[source]: Apply a transformation(M) to a np array(imag) and return it in a given shape

xmipp3.utils.copy_image(imag)[source]: Return a copy of a xmipp_image

xmipp3.utils.flipYImage(inFn, outFn=None, outDir=None)[source]: Flips an image in the Y axis

xmipp3.utils.matmul_serie(mat_list, size=4)[source]: Return the matmul of several numpy arrays

xmipp3.utils.normalize_array(ar)[source]: Normalize values in an array with mean 0 and std deviation 1

xmipp3.utils.readImage(fn)[source]

xmipp3.utils.rotation(imag, angle, shape, P)[source]: Rotate a np.array and return also the transformation matrix #imag: np.array #angle: angle in degrees #shape: output shape #P: transform matrix (further transformation in addition to the rotation)

xmipp3.utils.surrounding_values(a, ii, jj, depth=1)[source]: Return a list with the surrounding elements, given the indexs of the center, from an 2D numpy array

xmipp3.utils.validateXmippGpuBins()[source]

xmipp3.utils.writeImageFromArray(array, fn)[source]