Source code for cryocare.utils

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from os.path import join, exists

from pyworkflow.utils import createLink

from cryocare.constants import TRAIN_DATA_FN, VALIDATION_DATA_FN


def makeDatasetSymLinks(prot, trainDataDir):
    # The prediction is expecting the training and validation datasets to be in the same place as the training
    # model, but they are located in the training data generation extra directory. Hence, a symbolic link will
    # be created for each one
    linkedTrainingDataFile = prot._getExtraPath(TRAIN_DATA_FN)
    linkedValidationDataFile = prot._getExtraPath(VALIDATION_DATA_FN)
    if not exists(linkedTrainingDataFile):
        createLink(join(trainDataDir, TRAIN_DATA_FN), linkedTrainingDataFile)
    if not exists(linkedValidationDataFile):
        createLink(join(trainDataDir, VALIDATION_DATA_FN), linkedValidationDataFile)

class CryocareUtils:
    @staticmethod
    def checkInputTomoSetsSize(evenTomoSet, oddTomoSet):
        message = ''
        xe, ye, ze = evenTomoSet.getDimensions()
        xo, yo, zo = oddTomoSet.getDimensions()
        ne = evenTomoSet.getSize()
        no = oddTomoSet.getSize()
        if (xe, ye, ze, ne) != (xo, yo, zo, no):
            message = ('Size of even and odd set of tomograms must be the same:\n'
                       'Even --> (x, y, z, n) = ({xe}, {ye}, {ze}, {ne})\n'
                       'Odd  --> (x, y, z, n) = ({xo}, {yo}, {zo}, {no})'.format(
                        xe=xe, ye=ye, ze=ze, ne=ne, xo=xo, yo=yo, zo=zo, no=no))

        return message