Source code for dynamo.protocols.protocol_boxing

# **************************************************************************
# *
# * 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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# * 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
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# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
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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 numpy as np

import pyworkflow.utils as pwutils
from pyworkflow.protocol.params import PointerParam, IntParam, EnumParam
from pyworkflow.utils.properties import Message
from pyworkflow.gui.dialog import askYesNo

from tomo.protocols import ProtTomoPicking
from tomo.viewers.views_tkinter_tree import TomogramsTreeProvider

from dynamo import Plugin
from dynamo.viewers.views_tkinter_tree import DynamoTomoDialog
from dynamo.convert import textFile2Coords, matrix2eulerAngles

[docs]class DynamoBoxing(ProtTomoPicking): """Manual vectorial picker from Dynamo. After choosing the Tomogram to be picked, the tomo slicer from Dynamo will be direclty loaded with all the models previously saved in the disk (if any). This picking will only save the "user points" defined in a set of models. It is possible to create several models at once in a given tomogram. Once the coordinates are defined, the models are automatically saved in the catalogue and registered. Currently the following Dynamo models are supported: - Ellipsoidal Vesicle""" _label = 'vectorial picking' OUTPUT_PREFIX = 'outputMeshes' def __init__(self, **kwargs): ProtTomoPicking.__init__(self, **kwargs) # --------------------------- DEFINE param functions ---------------------- def _defineParams(self, form): ProtTomoPicking._defineParams(self, form) form.addParam('boxSize', IntParam, label="Box Size") form.addParam('selection', EnumParam, choices=['Yes', 'No'], default=1, label='Modify previous meshes?', display=EnumParam.DISPLAY_HLIST, help='This option allows to add and/or remove coordinates to a previous SetOfMeshes') form.addParam('inputMeshes', PointerParam, label="Input Meshes", condition='selection == 0', allowsNull=True, pointerClass='SetOfMeshes', help='Select the previous SetOfMeshes you want to modify') # --------------------------- INSERT steps functions ---------------------- def _insertAllSteps(self): # Copy input coordinates to Extra Path self._insertFunctionStep('copyInputMeshes') # Launch Boxing GUI self._insertFunctionStep('launchDynamoBoxingStep', interactive=True) # --------------------------- STEPS functions -----------------------------
[docs] def copyInputMeshes(self): # Initialize the catalogue listTomosFile = self._getExtraPath("tomos.vll") catalogue = os.path.abspath(self._getExtraPath("tomos")) # Create list of tomos file tomoFid = open(listTomosFile, 'w') for tomo in self.inputTomograms.get().iterItems(): tomoPath = os.path.abspath(tomo.getFileName()) tomoFid.write(tomoPath + '\n') tomoFid.close() # Save coordinates into .txt file for each tomogram codeFile = self._getExtraPath('coords2model.m') if self.selection.get() == 0: inputMeshes = self.inputMeshes.get() inputTomograms = self.inputTomograms.get() for tomo in inputTomograms.iterItems(iterate=False): outFileCoord = self._getExtraPath(pwutils.removeBaseExt(tomo.getFileName())) + ".txt" coords_tomo = [] for coord in inputMeshes.iterCoordinates(tomo.getObjId()): coords_tomo.append(list(coord.getPosition()) + [coord.getGroupId()]) if coords_tomo: np.savetxt(outFileCoord, np.asarray(coords_tomo), delimiter=' ') # Create small program to tell Dynamo to save the inputMeshes in a Ellipsoidal Vesicle Model contents = "dcm -create %s -fromvll %s\n" \ "path='%s'\n" \ "catalogue=dread(['%s' '.ctlg'])\n" \ "nVolumes=length(catalogue.volumes)\n" \ "for idv=1:nVolumes\n" \ "tomoPath=catalogue.volumes{idv}.fullFileName()\n" \ "tomoIndex=catalogue.volumes{idv}.index\n" \ "[~,tomoName,~]=fileparts(tomoPath)\n" \ "coordFile=[path '/' tomoName '.txt']\n" \ "if ~isfile(coordFile)\n" \ "continue\n" \ "end\n" \ "coords_ids=readmatrix(coordFile,'Delimiter',' ')\n" \ "idm_vec=unique(coords_ids(:,4))'\n" \ "for idm=idm_vec\n" \ "model_name=['model_',num2str(idm)]\n" \ "coords=coords_ids(coords_ids(:,4)==idm,1:3)\n" \ "vesicle=dmodels.ellipsoidalVesicle()\n" \ "vesicle.name=model_name\n" \ "addPoint(vesicle,coords(:,1:3),coords(:,3))\n" \ "vesicle.linkCatalogue('%s','i',tomoIndex,'s',1)\n" \ "vesicle.saveInCatalogue()\n" \ "end\n" \ "end\n" \ "exit\n" % (catalogue, listTomosFile, os.path.abspath(self._getExtraPath()), catalogue, catalogue) else: contents = "dcm -create %s -fromvll %s\n" % (catalogue, listTomosFile) codeFid = open(codeFile, 'w') codeFid.write(contents) codeFid.close() # Tell Dynamo to create the catalogue with the models args = ' %s' % codeFile self.runJob(Plugin.getDynamoProgram(), args, env=Plugin.getEnviron())
[docs] def launchDynamoBoxingStep(self): tomoList = [tomo.clone() for tomo in self.inputTomograms.get().iterItems()] tomoProvider = TomogramsTreeProvider(tomoList, self._getExtraPath(), "txt") self.dlg = DynamoTomoDialog(None, self._getExtraPath(), provider=tomoProvider) # Open dialog to request confirmation to create output import tkinter as tk if askYesNo(Message.TITLE_SAVE_OUTPUT, Message.LABEL_SAVE_OUTPUT, tk.Frame()): self._createOutput() pwutils.cleanPattern(self._getExtraPath('*.m'))
def _createOutput(self): textFile2Coords(self, self.inputTomograms.get(), self._getExtraPath(), False, True) # --------------------------- DEFINE info functions ----------------------
[docs] def getMethods(self, output): msg = 'User picked %d particles ' % output.getSize() msg += 'with a particle size of %s.' % output.getBoxSize() return msg
def _methods(self): methodsMsgs = [] if self.getOutputsSize() >= 1: for key, output in self.iterOutputAttributes(): msg = self.getMethods(output) methodsMsgs.append("%s: %s" % (self.getObjectTag(output), msg)) else: methodsMsgs.append(Message.TEXT_NO_OUTPUT_CO) return methodsMsgs