Source code for dynamo.protocols.protocol_import_tomograms

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# * Authors:     David Herreros Calero (
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# *  BCU, Centro Nacional de Biotecnologia, CSIC
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import numpy as np
from pyworkflow import BETA
import pyworkflow.protocol.params as params
from pyworkflow.utils import Message

from pwem.objects import Transform

from tomo.protocols.protocol_base import ProtTomoImportFiles
from tomo.objects import Tomogram
from tomo.protocols.protocol_base import ProtTomoImportAcquisition

from ..convert import readDynCatalogue

[docs]class DynamoImportTomograms(ProtTomoImportFiles, ProtTomoImportAcquisition): '''This protocols imports a series of Tomogram stored in a Dynamo catalogue into Scipion. In order to avoid handling a MatLab binary, the script relies on MatLab itself to turn a binary MatLab object into an Structure which can be afterwards read by Python.''' _label = 'import tomograms from Dynamo' _devStatus = BETA # -------------------------- DEFINE param functions ---------------------- def _defineParams(self, form): form.addSection('Import') form.addParam('ctgPath', params.PathParam, label="Dynamo catalogue file", help='Path to Dynamo catalogues.') # form.addParam('filesPattern', params.StringParam, # label='Pattern', # help="Pattern of the files to be imported.\n\n" # "The pattern can contain standard wildcards such as\n" # "*, ?, etc, or special ones like ### to mark some\n" # "digits in the filename as ID.\n\n" # "NOTE: wildcards and special characters " # "('*', '?', '#', ':', '%') cannot appear in the " # "actual path.") form.addParam('samplingRate', params.FloatParam, label=Message.LABEL_SAMP_RATE) form.addSection('Origin Info') form.addParam('setOrigCoord', params.BooleanParam, label="Set origin of coordinates", help="Option YES:\nA new volume will be created with " "the " "given ORIGIN of coordinates. This ORIGIN will be " "set in the map file header.\nThe ORIGIN of " "coordinates will be placed at the center of the " "whole volume if you select n(x)/2, n(y)/2, " "n(z)/2 as " "x, y, z coordinates (n(x), n(y), n(z) are the " "dimensions of the whole volume). However, " "selecting " "0, 0, 0 as x, y, z coordinates, the volume will be " "placed at the upper right-hand corner.\n\n" "Option NO:\nThe ORIGIN of coordinates will be " "placed at the center of the whole volume (" "coordinates n(x)/2, n(y)/2, n(z)/2 by default). " "This " "ORIGIN will NOT be set in the map file header.\n\n" "WARNING: In case you want to process " "the volume with programs requiring a specific " "symmetry regarding the origin of coordinates, " "for example the protocol extract unit " "cell, check carefully that the coordinates of the " "origin preserve the symmetry of the whole volume. " "This is particularly relevant for loading " "fragments/subunits of the whole volume.\n", default=False) form.addLine('Offset', help="A wizard will suggest you possible " "coordinates for the ORIGIN. In MRC volume " "files, the ORIGIN coordinates will be " "obtained from the file header.\n " "In case you prefer set your own ORIGIN " "coordinates, write them here. You have to " "provide the map center coordinates in " "Angstroms (pixels x sampling).\n", condition='setOrigCoord') # line.addParam would produce a nicer looking form # but them the wizard icon is drawn outside the visible # window. Until this bug is fixed form is a better option form.addParam('x', params.FloatParam, condition='setOrigCoord', label="x", help="offset along x axis (Angstroms)") form.addParam('y', params.FloatParam, condition='setOrigCoord', label="y", help="offset along y axis (Angstroms)") form.addParam('z', params.FloatParam, condition='setOrigCoord', label="z", help="offset along z axis (Angstroms)") ProtTomoImportAcquisition._defineParams(self, form) # ----------------------- INSERT STEPS functions -------------------------- def _insertAllSteps(self): self._insertFunctionStep('importDynamoTomogramsStep', self.samplingRate.get()) # --------------------------- STEPS functions -----------------------------
[docs] def importDynamoTomogramsStep(self, samplingRate): """ Copy images matching the filename pattern. Register other parameters.""" #"Using pattern: '%s'" % pattern) self._parseAcquisitionData() # Create a Volume template object tomo = Tomogram() tomo.setSamplingRate(samplingRate) tomoSet = self._createSetOfTomograms() tomoSet.setSamplingRate(samplingRate) # for fileName, fileId in self.iterFiles(): # Convert the catalogue bynary into a Python readable file tdb = readDynCatalogue(self.ctgPath.get(), self._getExtraPath()) # Append Catalogue Tomograms to output set volumes_structs = tdb.volumes if isinstance(tdb.volumes, np.ndarray) else [tdb.volumes] for idv, volume in enumerate(volumes_structs): tomo.cleanObjId() tomo.setLocation(volume.file) x, y, z = tomo.getDim() origin = Transform() origin.setShifts(x / -2. * samplingRate, y / -2. * samplingRate, z / -2. * samplingRate) tomo.setOrigin(origin) tomo.setAcquisition(self._extractAcquisitionParameters(tomo.getFileName())) tomoSet.append(tomo) self._defineOutputs(outputTomograms=tomoSet)
# --------------------------- INFO functions ------------------------------ def _hasOutput(self): return self.hasAttribute('outputTomograms') def _getTomMessage(self): return "Tomograms %s" % self.getObjectTag('outputTomograms') def _summary(self): try: summary = [] if self._hasOutput(): summary.append("%s imported from:\n%s" % (self._getTomMessage(), self.ctgPath.get())) if self.samplingRate.get(): summary.append(u"Sampling rate: *%0.2f* (Å/px)" % self.samplingRate.get()) x, y, z = self.outputTomograms.getFirstItem().getShiftsFromOrigin() summary.append(u"Tomograms Origin (x,y,z):\n" u" x: *%0.2f* (Å/px)\n" u" y: *%0.2f* (Å/px)\n" u" z: *%0.2f* (Å/px)" % (x, y, z)) except Exception as e: print(e) return summary def _methods(self): methods = [] if self._hasOutput(): methods.append(" %s imported with a sampling rate *%0.2f*" % (self._getTomMessage(), self.samplingRate.get()),) return methods