# -*- coding: utf-8 -*-
# **************************************************************************
# *
# * Authors: Scipion Team
# *
# * National Center of Biotechnology, CSIC, Spain
# *
# * This program is free software; you can redistribute it and/or modify
# * it under the terms of the GNU General Public License as published by
# * the Free Software Foundation; either version 2 of the License, or
# * (at your option) any later version.
# *
# * 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.
# *
# * 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
# *
# * All comments concerning this program package may be sent to the
# * e-mail address 'scipion@cnb.csic.es'
# *
# **************************************************************************
from enum import Enum
from pwem.protocols import EMProtocol
from pyworkflow import BETA
from pyworkflow.protocol import PointerParam, BooleanParam, FloatParam, EnumParam
from pyworkflow.utils import Message
from reliontomo import Plugin
from reliontomo.constants import OUT_PARTICLES_STAR, COORD_X, COORD_Y, COORD_Z, SHIFTX_ANGST, SHIFTY_ANGST, \
SHIFTZ_ANGST, ROT, TILT, PSI
from reliontomo.objects import relionTomoMetadata
from reliontomo.utils import genEnumParamDict, genRelionParticles
# Operation labels and values
NO_OPERATION = 'No operation'
OP_ADDITION = 'Add'
OP_MULTIPLICATION = 'Multiply'
OP_SET_TO = 'Set to'
OPERATION_LABELS = [NO_OPERATION, OP_ADDITION, OP_MULTIPLICATION, OP_SET_TO]
# Labels to which apply the operation
COORDINATES = 'coordinates'
SHIFTS = 'shifts'
ANGLES = 'angles'
LABELS_TO_OPERATE_WITH = [COORDINATES, SHIFTS, ANGLES]
[docs]class outputObjects(Enum):
outputRelionParticles = relionTomoMetadata
[docs]class ProtRelionEditParticlesStar(EMProtocol):
"""Operate on the particles star file"""
_label = 'Apply operation to Relion particles'
_devStatus = BETA
_possibleOutputs = outputObjects
operationDict = genEnumParamDict(OPERATION_LABELS)
labelsDict = genEnumParamDict(LABELS_TO_OPERATE_WITH)
def __init__(self, **kargs):
super().__init__(**kargs)
self.label1 = None
self.label2 = None
self.label3 = None
# -------------------------- DEFINE param functions -----------------------
def _defineParams(self, form):
form.addSection(label=Message.LABEL_INPUT)
form.addParam('inOptSet', PointerParam,
pointerClass='relionTomoMetadata',
label='Input Relion Tomo Metadata',
important=True)
form.addSection(label='Center')
form.addParam('doRecenter', BooleanParam,
label='Perform centering of particles',
default=False,
help='Perform centering of particles according to a position in the reference.')
group = form.addGroup('Shift center', condition='doRecenter')
group.addParam('shiftX', FloatParam,
label='X (pix.)',
default=0,
help='X-coordinate in the reference to center particles on (in pix)')
group.addParam('shiftY', FloatParam,
label='Y (pix.)',
default=0,
help='Y-coordinate in the reference to center particles on (in pix)')
group.addParam('shiftZ', FloatParam,
label='Z (pix.)',
default=0,
help='Z-coordinate in the reference to center particles on (in pix)')
form.addSection(label='Operate')
form.addParam('chosenOperation', EnumParam,
choices=list(self.operationDict.keys()),
default=self.operationDict[NO_OPERATION],
label='Choose operation')
form.addParam('opValue', FloatParam,
default=1,
label='Value to operate the selected labels')
group = form.addGroup('Operation', condition='chosenOperation > 0')
group.addParam('operateWith', EnumParam,
choices=list(self.labelsDict.keys()),
default=self.labelsDict[COORDINATES],
label='Operate with')
group.addParam('label1x', BooleanParam,
label='X (pix.)',
condition='operateWith == %s' % self.labelsDict[COORDINATES],
default=False)
group.addParam('label2y', BooleanParam,
label='Y (pix.)',
condition='operateWith == %s' % self.labelsDict[COORDINATES],
default=False)
group.addParam('label3z', BooleanParam,
label='Z (pix.)',
condition='operateWith == %s' % self.labelsDict[COORDINATES],
default=False)
group.addParam('label1sx', BooleanParam,
label='Shift X (pix.)',
condition='operateWith == %s' % self.labelsDict[SHIFTS],
default=False)
group.addParam('label2sy', BooleanParam,
label='Shift Y (pix.)',
condition='operateWith == %s' % self.labelsDict[SHIFTS],
default=False)
group.addParam('label3sz', BooleanParam,
label='Shift Z (pix.)',
condition='operateWith == %s' % self.labelsDict[SHIFTS],
default=False)
group.addParam('label1rot', BooleanParam,
label='Rot (deg.)',
condition='operateWith == %s' % self.labelsDict[ANGLES],
default=False)
group.addParam('label2tilt', BooleanParam,
label='Tilt (deg.)',
condition='operateWith == %s' % self.labelsDict[ANGLES],
default=False)
group.addParam('label3psi', BooleanParam,
label='Psi (deg.)',
condition='operateWith == %s' % self.labelsDict[ANGLES],
default=False)
# -------------------------- INSERT steps functions -----------------------
def _insertAllSteps(self):
self._initialize()
self._insertFunctionStep(self._operateStep)
self._insertFunctionStep(self.createOutputStep)
def _initialize(self):
self._manageOperateLabels()
def _operateStep(self):
Plugin.runRelionTomo(self, 'relion_star_handler', self._getOperateCommand())
[docs] def createOutputStep(self):
# Output RelionParticles
relionParticles = genRelionParticles(self._getExtraPath(), self.inOptSet.get())
self._defineOutputs(**{outputObjects.outputRelionParticles.name: relionParticles})
# -------------------------- INFO functions -------------------------------
def _validate(self):
valMsg = []
if not self.doRecenter.get() and self.chosenOperation.get() == self.operationDict[NO_OPERATION]:
valMsg.append('No recentering or operation was chosen.')
return valMsg
# --------------------------- UTILS functions -----------------------------
def _manageOperateLabels(self):
if self.chosenOperation.get() != self.operationDict[NO_OPERATION]:
labelGroup = self.operateWith.get()
if labelGroup == self.labelsDict[COORDINATES]:
self.label1 = (COORD_X, self.label1x.get())
self.label2 = (COORD_Y, self.label2y.get())
self.label3 = (COORD_Z, self.label3z.get())
elif labelGroup == self.labelsDict[SHIFTS]:
self.label1 = (SHIFTX_ANGST, self.label1sx.get())
self.label2 = (SHIFTY_ANGST, self.label2sy.get())
self.label3 = (SHIFTZ_ANGST, self.label3sz.get())
else:
self.label1 = (ROT, self.label1rot.get())
self.label2 = (TILT, self.label2tilt.get())
self.label3 = (PSI, self.label3psi.get())
def _getOperateCommand(self):
cmd = ''
cmd += '--i %s ' % self.inOptSet.get().getParticles()
cmd += '--o %s ' % self._getExtraPath(OUT_PARTICLES_STAR)
if self.doRecenter.get():
cmd += '--center '
if self.shiftX.get() != 0:
cmd += '--center_X %.2f ' % self.shiftX.get()
if self.shiftY.get() != 0:
cmd += '--center_Y %.2f ' % self.shiftY.get()
if self.shiftZ.get() != 0:
cmd += '--center_Z %.2f ' % self.shiftZ.get()
if self.chosenOperation.get() != self.operationDict[NO_OPERATION]:
opValue = self.opValue.get()
if self.chosenOperation.get() == self.operationDict[OP_ADDITION]:
cmd += '--add_to %.2f ' % opValue
elif self.chosenOperation.get() == self.operationDict[OP_MULTIPLICATION]:
cmd += '--multiply_by %.2f ' % opValue
else:
cmd += '--set_to %.2f ' % opValue
if self.label1.get()[1]:
cmd += 'operate %.2f ' % self.label1.get()[0]
if self.label2.get()[1]:
cmd += 'operate2 %.2f ' % self.label2.get()[0]
if self.label3.get()[1]:
cmd += 'operate3 %.2f ' % self.label3.get()[0]
return cmd