Source code for dynamo.protocols.protocol_import_subtomos

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# * Authors:     Estrella Fernandez Gimenez (
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# *  BCU, Centro Nacional de Biotecnologia, CSIC
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from os.path import basename, isfile

from pyworkflow import BETA
from pyworkflow.protocol.params import PathParam, PointerParam
from pyworkflow.utils.path import createAbsLink, copyFile
from pwem.emlib.image import ImageHandler

from tomo.protocols.protocol_base import ProtTomoImportFiles
from tomo.objects import SubTomogram
from tomo.utils import _getUniqueFileName

from ..convert import readDynTable

[docs]class DynamoImportSubtomos(ProtTomoImportFiles): """ This protocol imports subtomograms with metadata generated by a Dynamo table. A Dynamo catalogue can be also imported in order to relate subtomograms with their original tomograms. """ _label = 'import subtomos from Dynamo' _devStatus = BETA # -------------------------- DEFINE param functions ---------------------- def _defineParams(self, form): ProtTomoImportFiles._defineParams(self, form) form.addParam('tablePath', PathParam, label="Dynamo table file:", help='Select dynamo table (.tbl) to link dynamo metadata to the subtomograms that will be ' 'imported to Scipion. ') form.addParam('tomoSet', PointerParam, pointerClass='SetOfTomograms', label="Tomograms:", help="Select the Tomograms used to extract the SubTomograms") # --------------------------- STEPS functions ------------------------------ def _insertAllSteps(self): self._insertFunctionStep('importSubTomogramsStep', self.getPattern(), self.samplingRate.get()) self._insertFunctionStep('createOutputStep') # --------------------------- STEPS functions -----------------------------
[docs] def importSubTomogramsStep(self, pattern, samplingRate):"Using pattern: '%s'" % pattern) subtomo = SubTomogram() subtomo.setSamplingRate(samplingRate) imgh = ImageHandler() self.subtomoSet = self._createSetOfSubTomograms() self.subtomoSet.setSamplingRate(samplingRate) dynTable = self._getExtraPath('dynamo_table.tbl') copyFile(self.tablePath.get(), dynTable) self.fhTable = open(dynTable, 'r') for fileName, fileId in self.iterFiles(): _, _, _, n = imgh.getDimensions(fileName) newFileName = _getUniqueFileName(self.getPattern(), fileName) if fileName.endswith(':mrc'): fileName = fileName[:-4] createAbsLink(fileName, newFileName) if n == 1: self._addSubtomogram(subtomo, fileName, newFileName) else: for index in range(1, n + 1): self._addSubtomogram(subtomo, newFileName, index=index) self.fhTable.close()
def _addSubtomogram(self, subtomo, newFileName, index=None): """ adds a subtomogram to a set """ tomoSet = self.tomoSet.get() subtomo.cleanObjId() if index is None: subtomo.setFileName(newFileName) else: subtomo.setLocation(index, newFileName) readDynTable(self, subtomo, tomoSet) self.subtomoSet.append(subtomo)
[docs] def createOutputStep(self): self._defineOutputs(outputSubTomograms=self.subtomoSet)
# --------------------------- INFO functions ------------------------------ def _hasOutput(self): return self.hasAttribute('outputSubTomograms') def _getSubTomMessage(self): return "SubTomograms %s" % self.getObjectTag('outputSubTomograms') def _summary(self): summary = [] if self._hasOutput(): summary.append("%s imported from:\n%s" % (self._getSubTomMessage(), self.getPattern())) if self.samplingRate.get(): summary.append(u"Sampling rate: *%0.2f* (Å/px)" % self.samplingRate.get()) return summary def _methods(self): methods = [] if self._hasOutput(): methods.append(" %s imported with a sampling rate *%0.2f*" % (self._getSubTomMessage(), self.samplingRate.get())) return methods def _getVolumeFileName(self, fileName, extension=None): if extension is not None: baseFileName = "import_" + str(basename(fileName)).split(".")[0] + ".%s" % extension else: baseFileName = "import_" + str(basename(fileName)).split(":")[0] return self._getExtraPath(baseFileName) def _validate(self): errors = [] try: next(self.iterFiles()) except StopIteration: errors.append('No files matching the pattern %s were found.' % self.getPattern()) if not self.tablePath.get() or not isfile(self.tablePath.get()): errors.append("Could not find specified dynamo catalogue file") return errors