Source code for continuousflex.viewers.viewer_nma_alignment

# **************************************************************************
# *
# * Authors:     J.M. De la Rosa Trevin (jmdelarosa@cnb.csic.es)
# *              Slavica Jonic  (slavica.jonic@upmc.fr)
# *
# * 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'
# *
# **************************************************************************
"""
This module implement the wrappers aroung Xmipp CL2D protocol
visualization program.
"""

from os.path import basename

from pwem.emlib import MetaData, MDL_ORDER
from pyworkflow.protocol.params import StringParam
from pyworkflow.viewer import (ProtocolViewer, DESKTOP_TKINTER, WEB_DJANGO)
from pyworkflow.protocol import params
from continuousflex.protocols.data import Point, Data
from continuousflex.viewers.nma_plotter import FlexNmaPlotter
from continuousflex.protocols import FlexProtAlignmentNMA

FIGURE_LIMIT_NONE = 0
FIGURE_LIMITS = 1

X_LIMITS_NONE = 0
X_LIMITS = 1
Y_LIMITS_NONE = 0
Y_LIMITS = 1
Z_LIMITS_NONE = 0
Z_LIMITS = 1

[docs]class FlexAlignmentNMAViewer(ProtocolViewer): """ Visualization of results from the NMA protocol """ _label = 'viewer nma alignment' _targets = [FlexProtAlignmentNMA] _environments = [DESKTOP_TKINTER, WEB_DJANGO] def __init__(self, **kwargs): ProtocolViewer.__init__(self, **kwargs) self._data = None
[docs] def getData(self): if self._data is None: self._data = self.loadData() return self._data
def _defineParams(self, form): form.addSection(label='Visualization') form.addParam('displayRawDeformation', StringParam, default='7 8', label='Display the computed normal-mode amplitudes', help='Type 7 to see the histogram of amplitudes along mode 7; \n' 'type 8 to see the histogram of amplitudes along mode 8, etc.\n' 'Type 7 8 to see the 2D plot of amplitudes along modes 7 and 8.\n' 'Type 7 8 9 to see the 3D plot of amplitudes along modes 7, 8 and 9; etc.' ) form.addParam('limits_modes', params.EnumParam, choices=['Automatic (Recommended)', 'Set manually Use upper and lower values'], default=FIGURE_LIMIT_NONE, label='Error limits', display=params.EnumParam.DISPLAY_COMBO, help='If you want to use a range of Error in the color bar choose to set it manually.') form.addParam('LimitLow', params.FloatParam, default=None, condition='limits_modes==%d' % FIGURE_LIMITS, label='Lower Error value', help='The lower Error used in the graph') form.addParam('LimitHigh', params.FloatParam, default=None, condition='limits_modes==%d' % FIGURE_LIMITS, label='Upper Error value', help='The upper Error used in the graph') form.addParam('xlimits_mode', params.EnumParam, choices=['Automatic (Recommended)', 'Set manually x-axis limits'], default=X_LIMITS_NONE, label='x-axis limits', display=params.EnumParam.DISPLAY_COMBO, help='This allows you to use a specific range of x-axis limits') form.addParam('xlim_low', params.FloatParam, default=None, condition='xlimits_mode==%d' % X_LIMITS, label='Lower x-axis limit') form.addParam('xlim_high', params.FloatParam, default=None, condition='xlimits_mode==%d' % X_LIMITS, label='Upper x-axis limit') form.addParam('ylimits_mode', params.EnumParam, choices=['Automatic (Recommended)', 'Set manually y-axis limits'], default=Y_LIMITS_NONE, label='y-axis limits', display=params.EnumParam.DISPLAY_COMBO, help='This allows you to use a specific range of y-axis limits') form.addParam('ylim_low', params.FloatParam, default=None, condition='ylimits_mode==%d' % Y_LIMITS, label='Lower y-axis limit') form.addParam('ylim_high', params.FloatParam, default=None, condition='ylimits_mode==%d' % Y_LIMITS, label='Upper y-axis limit') form.addParam('zlimits_mode', params.EnumParam, choices=['Automatic (Recommended)', 'Set manually z-axis limits'], default=Z_LIMITS_NONE, label='z-axis limits', display=params.EnumParam.DISPLAY_COMBO, help='This allows you to use a specific range of z-axis limits') form.addParam('zlim_low', params.FloatParam, default=None, condition='zlimits_mode==%d' % Z_LIMITS, label='Lower z-axis limit') form.addParam('zlim_high', params.FloatParam, default=None, condition='zlimits_mode==%d' % Z_LIMITS, label='Upper z-axis limit') def _getVisualizeDict(self): return {'displayRawDeformation': self._viewRawDeformation, } def _viewRawDeformation(self, paramName): components = self.displayRawDeformation.get() return self._doViewRawDeformation(components) def _doViewRawDeformation(self, components): components = list(map(int, components.split())) dim = len(components) views = [] if dim > 0: modeList = [] modeNameList = [] missingList = [] for modeNumber in components: found = False md = MetaData(self.protocol._getExtraPath('modes.xmd')) for i, objId in enumerate(md): modeId = md.getValue(MDL_ORDER, objId) if modeNumber == modeId: modeNameList.append('Mode %d' % modeNumber) modeList.append(i) found = True break if not found: missingList.append(str(modeNumber)) if missingList: return [self.errorMessage("Invalid mode(s) *%s*\n." % (', '.join(missingList)), title="Invalid input")] # Actually plot if self.limits_modes == FIGURE_LIMIT_NONE: plotter = FlexNmaPlotter(data=self.getData(), xlim_low=self.xlim_low, xlim_high=self.xlim_high, ylim_low=self.ylim_low, ylim_high=self.ylim_high, zlim_low=self.zlim_low, zlim_high=self.zlim_high) else: plotter = FlexNmaPlotter(data=self.getData(), LimitL=self.LimitLow, LimitH=self.LimitHigh, xlim_low=self.xlim_low, xlim_high=self.xlim_high, ylim_low=self.ylim_low, ylim_high=self.ylim_high, zlim_low=self.zlim_low, zlim_high=self.zlim_high) baseList = [basename(n) for n in modeNameList] self.getData().XIND = modeList[0] if dim == 1: plotter.plotArray1D("Histogram of normal-mode amplitudes: %s" % baseList[0], "Amplitude", "Number of images") else: self.getData().YIND = modeList[1] if dim == 2: plotter.plotArray2D("Normal-mode amplitudes: %s vs %s" % tuple(baseList), *baseList) elif dim == 3: self.getData().ZIND = modeList[2] plotter.plotArray3D("Normal-mode amplitudes: %s %s %s" % tuple(baseList), *baseList) views.append(plotter) return views
[docs] def loadData(self): """ Iterate over the images and their deformations to create a Data object with theirs Points. """ particles = self.protocol.outputParticles data = Data() for i, particle in enumerate(particles): pointData = list(map(float, particle._xmipp_nmaDisplacements)) data.addPoint(Point(pointId=particle.getObjId(), data=pointData, weight=particle._xmipp_cost.get())) return data