Source code for deepfinder.protocols.protocol_import_coordinates

# -*- coding: utf-8 -*-
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# *
# * Authors: Emmanuel Moebel (emmanuel.moebel@inria.fr)
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# * Inria - Centre de Rennes Bretagne Atlantique, France
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import os
from os.path import basename

from pyworkflow import BETA
from pyworkflow.object import String

from tomo.objects import SetOfCoordinates3D, Coordinate3D
from tomo.protocols.protocol_base import ProtTomoImportFiles

import pyworkflow.protocol.params as params

import deepfinder.convert as cv


[docs]class ImportCoordinates3D(ProtTomoImportFiles): """Protocol to import a DeepFinder object list as a set of 3D coordinates in Scipion""" _outputClassName = 'SetOfCoordinates3D' _label = 'import coordinates' _devStatus = BETA def _defineParams(self, form): ProtTomoImportFiles._defineImportParams(self, form) form.addParam('importTomograms', params.PointerParam, pointerClass='SetOfTomograms', label='Input tomograms', help='Select the tomograms/tomogram for which you ' 'want to import coordinates. The file names of the tomogram and ' 'coordinate files must be the same.') def _insertAllSteps(self): self._insertFunctionStep('importCoordinatesStep') # --------------------------- STEPS functions -----------------------------
[docs] def importCoordinatesStep(self): importTomograms = self.importTomograms.get() suffix = self._getOutputSuffix(SetOfCoordinates3D) coord3DSet = self._createSetOfCoordinates3D(importTomograms, suffix) #coord3DSet.setBoxSize(self.boxSize.get()) # ?? I (emoebel) dont understand this param coord3DSet.setPrecedents(importTomograms) coordCounter = 1 for tomoInd,tomo in enumerate(importTomograms.iterItems()): tomoName = basename(os.path.splitext(tomo.getFileName())[0]) samplingRate = tomo.getSamplingRate() for coordFile, fileId in self.iterFiles(): fileName = basename(os.path.splitext(coordFile)[0]) if tomo is not None and tomoName == fileName: objl = cv.objl_read(coordFile) for idx in range(len(objl)): x = objl[idx]['x'] y = objl[idx]['y'] z = objl[idx]['z'] lbl = objl[idx]['label'] coord = Coordinate3D() coord.setObjId(coordCounter) coord.setPosition(x, y, z) coord.setVolume(tomo) coord.setVolId(tomoInd + 1) coord._dfLabel = String(str(lbl)) coord3DSet.append(coord) coordCounter += 1 coord3DSet.setSamplingRate(samplingRate) self._defineOutputs(outputCoordinates=coord3DSet) self._defineSourceRelation(self.importTomograms, coord3DSet)