Source code for xmipp3.viewers.viewer_cl2d

# **************************************************************************
# *
# * Authors:     L. del Cano (ldelcano@cnb.csic.es)
# *
# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
# *
# * 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.
"""

import os
from pyworkflow.viewer import ProtocolViewer, DESKTOP_TKINTER, WEB_DJANGO
from pyworkflow.protocol.params import LabelParam, LEVEL_ADVANCED
from pyworkflow.protocol.params import EnumParam, StringParam

from xmipp3.protocols.protocol_cl2d import XmippProtCL2D
from pwem.viewers import DataView, ClassesView

CLASSES = 0
CLASS_CORES = 1
CLASS_STABLE_CORES = 2   

LEVEL_LAST = 0
LEVEL_SEL = 1
LEVEL_CHOICES = ['last', 'selection']
        
        
[docs]class XmippCL2DViewer(ProtocolViewer): """ Visualization of Xmipp CL2D protocol results. """ _label = 'viewer cl2d' _targets = [XmippProtCL2D] _environments = [DESKTOP_TKINTER, WEB_DJANGO] def __init__(self, **kwargs): ProtocolViewer.__init__(self, **kwargs) def _defineParams(self, form): form.addSection(label='Visualization') # Select the level to show form.addParam('doShowLastLevel', EnumParam, default=LEVEL_LAST, choices=LEVEL_CHOICES, display=EnumParam.DISPLAY_HLIST, label="Level to visualize") form.addParam('showSeveralLevels', StringParam, default='', label='Levels selection', condition='doShowLastLevel==%d' % LEVEL_SEL, help='Specify a list of levels like: 0,1,3 or 0-3 ') # TO-DO; All commented code is for revision with @cossorzano # Sorted or not # form.addParam('doSorted', BooleanParam, default=False, # label="Display sorted classes", # help="Note that the average of the images assigned to " # "the sorted class are not, in general, aligned with " # "the sorted class, because the sorted class " # "representatives have been realigned to be shown " # "all in the same orientation") # Classes CLASS_CHOICES = ['classes'] if self.protocol.doCore: CLASS_CHOICES.append('cores') if self.protocol.doStableCore: CLASS_CHOICES.append('stable cores') form.addParam('classesToShow', EnumParam, choices=CLASS_CHOICES, label="What to show", default=CLASSES, display=EnumParam.DISPLAY_HLIST) # Convergence form.addParam('showConvergence', LabelParam, label="Visualize convergence", help="It shows per iteration the similarity " "(cl2dSimilarity) between experimental images and " "the references as well as the number experimental " "images changing class.") form.addParam('showClassHierarchy', LabelParam, expertLevel=LEVEL_ADVANCED, hidden=not self.protocol.computeHierarchy, label="Visualize class hierarchy.") def _getVisualizeDict(self): self.protocol._defineFileNames() # Load filename templates return {'classesToShow': self._viewLevelFiles, 'showConvergence': self._viewConvergence, 'showClassHierarchy': self._viewClassHierarchy, } # ============================================================================== # showClasses # ============================================================================== def _viewLevelFiles(self, e=None): views = [] fnSubset = self._getSubset() viewFinalClasses = False # TO-DO; All commented code is for revision with @cossorzano viewParams = {} # if self.doSorted: # suffix = '_sorted' # viewParams[showj.SORT_BY] = '_xmipp_cl2dOrder' if self.doShowLastLevel == LEVEL_LAST: fn = self.protocol._getFileName("final_classes", sub=fnSubset) if os.path.exists(fn): viewFinalClasses = True levList = [self.protocol._lastLevel()] else: levList = self._getListFromRangeString(self.showSeveralLevels.get()) for level in levList: if viewFinalClasses: fn = self.protocol._getFileName("final_classes", sub=fnSubset) else: fn = self.protocol._getFileName("level_classes", level=level, sub=fnSubset) if level <= self.protocol._lastLevel() and os.path.exists(fn): fn = self.protocol._getLevelClasses(level, fnSubset) if os.path.exists(fn): inputParts = self.protocol.inputParticles.get() views.append(ClassesView(self.getProject(), self.protocol.strId(), fn, inputParts.strId())) return views # ============================================================================== # showConvergence # ============================================================================== def _viewConvergence(self, e=None): views = [] if self.doShowLastLevel == LEVEL_LAST: fn = self.protocol._getFileName('level_classes', level=self.protocol._lastLevel(), sub='') views.append(self._viewInfo(fn)) else: levList = self._getListFromRangeString(self.showSeveralLevels.get()) if len(levList) > 0: for level in levList: if level <= self.protocol._lastLevel(): fn = self.protocol._getFileName('level_classes', level=level, sub='') views.append(self._viewInfo(fn)) return views def _viewInfo(self, fn): """ Display the info block in the metadata for a level convergence. """ return DataView('info@' + fn) # ============================================================================== # showClassHierarchy # ============================================================================== def _viewClassHierarchy(self, e=None): fnSubset = self._getSubset() fnHierarchy = self.protocol._getFileName('classes_hierarchy', sub=fnSubset) if os.path.exists(fnHierarchy): return [self.textView([fnHierarchy])] #=============================================================================== # Utils Functions #=============================================================================== def _getSubset(self): fnSubset = "" classesToShow = self.classesToShow.get() if classesToShow == CLASSES: fnSubset = "" elif classesToShow == CLASS_CORES: fnSubset = "_core" elif classesToShow == CLASS_STABLE_CORES: fnSubset = "_stable_core" return fnSubset
# TO-DO; All commented code is for revision with @cossorzano # def _setClassOrder(self, classItem, classRow): # """ Set the class order for display the classes sorted. """ # lastOrder = getattr(self, 'lastOrder', 0) + 1 # classItem._xmipp_cl2dOrder = Integer(lastOrder) # setattr(self, 'lastOrder', lastOrder)