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.DeprecatedParam(newParamName, prot)[source]¶

Bases: object

Deprecated param. To be used when you want to rename an existing param and still be able to recover old param value. It acts like a redirector, passing the value received when its value is set to the new renamed parameter

getObjValue()[source]¶

isPointer()[source]¶

set(value)[source]¶

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]¶