Source code for dynamo.protocols.protocol_subBoxing

# **************************************************************************
# *
# * Authors:    David Herreros Calero (dherreros@cnb.csic.es)
# *
# *  BCU, Centro Nacional de Biotecnologia, CSIC
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# * This program is free software; you can redistribute it and/or modify
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# * the Free Software Foundation; either version 2 of the License, or
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# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# * GNU General Public License for more details.
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# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307  USA
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# *  All comments concerning this program package may be sent to the
# *  e-mail address 'scipion@cnb.csic.es'
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import os
import glob
import numpy as np

from pyworkflow import BETA
import pyworkflow.utils as pwutils
import pyworkflow.protocol.params as params
from pwem.protocols import EMProtocol

from tomo.protocols import ProtTomoBase
from tomo.objects import SetOfCoordinates3D
import tomo.constants as const

from dynamo import Plugin
from dynamo.convert import matrix2eulerAngles, readDynCoord


[docs]class DynamoSubBoxing(EMProtocol, ProtTomoBase): """SubBoxing using Dynamo""" _label = 'subBoxing' _devStatus = BETA def __init__(self, **kwargs): EMProtocol.__init__(self, **kwargs) # --------------------------- DEFINE param functions ---------------------- def _defineParams(self, form): form.addSection(label='Input') form.addParam('inputCoordinates', params.PointerParam, label="Input 3D Coordinates", important=True, pointerClass='SetOfCoordinates3D', help='Select the SetOfCoordinates3D.') form.addParam('inputAverage', params.PointerParam, label="Input Average", important=True, pointerClass='AverageSubTomogram', help='Select the AverageSubTomogram.') form.addParam('symmetry', params.StringParam, label='Point Group Symmetry', important=True, default='C2') # --------------------------- INSERT steps functions ---------------------- def _insertAllSteps(self): self._insertFunctionStep('writeSetOfCoordinates3D') self._insertFunctionStep('launchDynamoSubBoxingStep') self._insertFunctionStep('createOutputStep') # --------------------------- STEPS functions -----------------------------
[docs] def writeSetOfCoordinates3D(self): coords = self.inputCoordinates.get() tomos = coords.getPrecedents() samplingRateCoord = coords.getSamplingRate() samplingRateTomo = tomos.getFirstItem().getSamplingRate() self.factor = float(samplingRateCoord / samplingRateTomo) self.lines = [] inputSet = tomos.getFiles() self.coordsFileName = self._getExtraPath('coords.txt') self.anglesFileName = self._getExtraPath('angles.txt') outC = open(self.coordsFileName, "w") outA = open(self.anglesFileName, 'w') for idt, item in enumerate(inputSet): coordDict = [] for coord3DSet in coords.iterCoordinates(): if pwutils.removeBaseExt(item) == pwutils.removeBaseExt(coord3DSet.getVolName()): angles_coord = matrix2eulerAngles(coord3DSet.getMatrix()) x = round(self.factor * coord3DSet.getX(const.BOTTOM_LEFT_CORNER)) y = round(self.factor * coord3DSet.getY(const.BOTTOM_LEFT_CORNER)) z = round(self.factor * coord3DSet.getZ(const.BOTTOM_LEFT_CORNER)) outC.write("%d\t%d\t%d\t%d\n" % (x, y, z, idt + 1)) outA.write("%f\t%f\t%f\n" % (angles_coord[0], angles_coord[1], angles_coord[2])) coordDict.append(coord3DSet.getObjId()) if coordDict: self.lines.append(coordDict) outC.close() outA.close()
[docs] def launchDynamoSubBoxingStep(self): matlabFile = self.writeMatlabCode() args = ' %s' % matlabFile self.runJob(Plugin.getDynamoProgram(), args, env=Plugin.getEnviron()) pwutils.cleanPattern('*.m')
[docs] def createOutputStep(self): inputCoords = self.inputCoordinates.get() tomos = inputCoords.getPrecedents() suffix = self._getOutputSuffix(SetOfCoordinates3D) outSet = self._createSetOfCoordinates3D(tomos, suffix) outSet.setBoxSize(np.loadtxt(self._getExtraPath('recBoxSize.txt'))) outSet.setSamplingRate(inputCoords.getSamplingRate()) outSet.setPrecedents(tomos) for coordFile in glob.glob(self._getExtraPath('*.tbl')): idt = int(''.join(filter(str.isdigit, pwutils.removeBaseExt(coordFile)))) readDynCoord(coordFile, outSet, tomos[idt].clone()) args = {} args['outputCoordinates3D'] = outSet self._defineOutputs(**args) self._defineSourceRelation(inputCoords, outSet) self._defineSourceRelation(self.inputAverage, outSet)
# --------------------------- DEFINE utils functions ----------------------
[docs] def writeMatlabCode(self): # Initialization params average = self.inputAverage.get() codeFilePath = self._getExtraPath("DynamoSubBoxing.m") # Write code to Matlab code file codeFid = open(codeFilePath, 'w') content = "box=%d\n" \ "aux=readmatrix('%s')\n" \ "angles=readmatrix('%s')\n" \ "coords=aux(:,1:3)\n" \ "tags=aux(:,4)'\n" \ "dynamo_mapview('%s')\n" \ "hGUI = findobj(0)\n" \ "hGUI.ShowHiddenHandles=true\n" \ "h=findobj(0,'type','figure')\n" \ "click_panel=findobj(h.Children,'tag','uipanel_clicks')\n" \ "north_ui=findobj(click_panel.Children,'tag','edit_anchor_north')\n" \ "distance_ui=findobj(click_panel.Children,'tag','text_anchor_distance')\n" \ "while ishandle(h)\n" \ "north=str2num(north_ui.String)\n" \ "distance=2*floor(str2num(distance_ui.String))\n" \ "pause(0.01)\n" \ "end\n" \ "rSubunitFromCenter=north-box/2\n" \ "writematrix(distance,'%s')\n" \ "for tag=unique(tags)\n" \ "tomoCoords=coords(tags==tag,:)\n" \ "tomoAngles=angles(tags==tag,:)\n" \ "t=dynamo_table_blank(size(tomoCoords,1),'r',tomoCoords,'angles',tomoAngles)\n" \ "ts=dynamo_subboxing_table(t,rSubunitFromCenter,'sym','%s')\n" \ "dynamo_write(ts,['%s','_ID',num2str(tag),'.tbl'])\n" \ "end\n" \ % (average.getXDim(), os.path.abspath(self.coordsFileName), os.path.abspath(self.anglesFileName), os.path.abspath(average.getFileName()), os.path.abspath(self._getExtraPath('recBoxSize.txt')), self.symmetry.get(), os.path.abspath(self._getExtraPath('subBoxTable'))) codeFid.write(content) codeFid.close() return codeFilePath
# --------------------------- DEFINE info functions ---------------------- def _validate(self): pass def _methods(self): methodsMsgs = [] boxSize = np.loadtxt(self._getExtraPath('recBoxSize.txt')) if self.getOutputsSize() >= 1: methodsMsgs.append("Particle box size: *%s*" % boxSize) methodsMsgs.append("Total particles found: *%s*" % self.outputCoordinates3D.getSize()) methodsMsgs.append("Symmetry: *%s*" % self.symmetry.get()) else: methodsMsgs.append("Output coordinates not ready yet.") return methodsMsgs def _summary(self): summary = [] boxSize = np.loadtxt(self._getExtraPath('recBoxSize.txt')) if self.getOutputsSize() >= 1: summary.append("Particle box size: *%s*" % boxSize) summary.append("Total particles found: *%s*" % self.outputCoordinates3D.getSize()) summary.append("Symmetry: *%s*" % self.symmetry.get()) else: summary.append("Output coordinates not ready yet.") return summary