Source code for spider.viewers.viewer_classify

# **************************************************************************
# *
# * Authors:     J.M. De la Rosa Trevin (
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# * Unidad de  Bioinformatica of 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 3 of the License, or
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# * You should have received a copy of the GNU General Public License
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from os.path import join

import tkinter as tk

from pwem.protocols import ProtUserSubSet
from pwem.objects import SetOfClasses2D
from pwem.viewers import EmPlotter, ClassesView
from pyworkflow.protocol.params import IntParam, FloatParam, LabelParam
from pyworkflow.protocol.constants import STATUS_FINISHED
from import Icon
from pyworkflow.viewer import ProtocolViewer, DESKTOP_TKINTER, WEB_DJANGO
from pyworkflow.utils.graph import Graph
from pyworkflow.utils.path import cleanPath
from pyworkflow.gui import Window
from pyworkflow.gui.widgets import HotButton
from pyworkflow.gui.graph import LevelTree
from pyworkflow.gui.canvas import Canvas, Item
from pyworkflow.gui.dialog import askString

from ..utils import SpiderDocFile
from ..protocols import SpiderProtClassifyWard, SpiderProtClassifyDiday

[docs]class SpiderViewerClassify(ProtocolViewer): """ Visualization of Spider classification results. """ _environments = [DESKTOP_TKINTER, WEB_DJANGO] def _defineParams(self, form): form.addSection(label='Visualization') group1 = form.addGroup('Dendrogram') group1.addParam('doShowDendrogram', LabelParam, label="Show dendrogram", default=True, help='In a dendrogram larger vertical bars signify a ' 'greater difference between classes. Many small ' 'differences at the bottom can be eliminated with ' 'an increase of the "Minimum height" setting.') group1.addParam('minHeight', FloatParam, default=0.5, label='Minimum height', help='The dendrogram will be cut at this level') self.groupClass = form.addGroup('Classes') self.groupClass.addParam('doShowClasses', LabelParam, label="Visualize class averages", default=True, help='Display class averages') def _getVisualizeDict(self): return {'doShowDendrogram': self._plotDendrogram, 'doShowClasses': self.visualizeClasses } def _plotDendrogram(self, e=None): xplotter = EmPlotter() self.plt = xplotter.createSubPlot("Dendrogram", "", "") self.step = 0.25 self.rightMost = 0.0 # Used to arrange leaf nodes at the bottom node = self.protocol.buildDendrogram() self.plotNode(node, self.minHeight.get()) self.plt.set_xlim(0., self.rightMost + self.step) self.plt.set_ylim(-10, 105) return [xplotter]
[docs] def plotNode(self, node, minHeight=-1): childs = node.getChilds() h = node.height if h > minHeight and len(childs) > 1: x1, y1 = self.plotNode(childs[0], minHeight) x2, y2 = self.plotNode(childs[1], minHeight) xm = (x1 + x2)/2 x = [x1, x1, x2, x2] y = [y1, h, h, y2] self.plt.plot(x, y, color='b') point = (xm, h) else: self.rightMost += self.step point = (self.rightMost, 0.) length = node.length index = node.index self.plt.annotate("%d(%d)" % (index, length), point, xytext=(0, -5), textcoords='offset points', va='top', ha='center', size='x-small') self.plt.plot(point[0], point[1], 'ro') return point
def _createNode(self, canvas, node, y): node.selected = False = SpiderImageBox(canvas, node, y) return
[docs]class SpiderViewerWard(SpiderViewerClassify): """ Visualization of Spider - classify Ward protocol results. """ _targets = [SpiderProtClassifyWard] _label = "viewer ward" def _defineParams(self, form): SpiderViewerClassify._defineParams(self, form) self.groupClass.addParam('maxLevel', IntParam, default=4, label='Maximum level', help='Maximum level of classes to show')
[docs] def visualizeClasses(self, e=None): classTemplate = "class_%03d" averages = '%03d@' + self.protocol._getFileName('averages') def getInfo2(level, classNo): return classTemplate % classNo, averages % classNo node = self.protocol.buildDendrogram(writeAverages=False) g = Graph(root=node) self.graph = g = Window("Select classes", self.formWindow, minsize=(1000, 600)) root = canvas = Canvas(root) canvas.grid(row=0, column=0, sticky='nsew') root.grid_columnconfigure(0, weight=1) root.grid_rowconfigure(0, weight=1) self.buttonframe = tk.Frame(root) self.buttonframe.grid(row=2, column=0, columnspan=2), column=0, sticky='n', padx=5, pady=5) saveparticlesbtn = HotButton(self.buttonframe, "Particles", Icon.PLUS_CIRCLE, command=self._askCreateParticles) saveparticlesbtn.grid(row=0, column=1, sticky='n', padx=5, pady=5) btn = HotButton(self.buttonframe, "Classes", Icon.PLUS_CIRCLE, command=self._askCreateClasses) btn.grid(row=0, column=2, sticky='n', padx=5, pady=5) lt = LevelTree(g) lt.DY = 135 # TODO: change in percent of the image size lt.setCanvas(canvas) lt.paint(self._createNode, maxLevel=self.maxLevel.get()-1) canvas.updateScrollRegion() return []
def _askCreateParticles(self): self._askCreateSubset('Particles', self.getSelectedNodesCount(2)) def _askCreateClasses(self): self._askCreateSubset('Classes', self.getSelectedNodesCount(1)) def _askCreateSubset(self, output, size): if self._selectionOverlap():"Classes could not overlap in the tree.") return s = '' if size == 1 else 's' headerLabel = 'Are you sure you want to create a new set of ' \ ' %s with %s element%s?' % (output, size, s) runname = askString('Question', 'Run name:',, 30, defaultValue='ProtUserSubSet', headerLabel=headerLabel) if runname: createFunc = getattr(self, 'save' + output) createFunc(runname) def _createSubsetProtocol(self, createOutputFunc, label=None): """ Create a subset of classes or particles. """ try: project = self.getProject() prot = project.newProtocol(ProtUserSubSet) prot.setObjLabel(label) prot.inputObject.set(self.protocol) project._setupProtocol(prot) prot.makePathsAndClean() createOutputFunc(prot) prot.setStatus(STATUS_FINISHED) project._storeProtocol(prot) # self.project.launchProtocol(prot, wait=True) except Exception as ex:
[docs] def getSelectedNodesCount(self, depth): if depth == 1: return len([node for node in self.graph.getNodes() if node.selected]) else: count = 0 for node in self.graph.getNodes(): if node.selected: count += len(node.imageList) return count
def _selectionOverlap(self): """ Check if selected classes do overlap. """ allImages = set() for n in self._selectedNodes(): for i in n.imageList: if i in allImages: return True allImages.add(i) return False def _selectedNodes(self): return [node for node in self.graph.getNodes() if node.selected]
[docs] def saveClasses(self, runname=None): """ Store selected classes. """ def createClasses(prot): classes = prot._createSetOfClasses2D(self.protocol.inputParticles.get(), suffix='Selection') self.protocol._fillClassesFromNodes(classes, self._selectedNodes()) prot._defineOutputs(outputClasses=classes) self._createSubsetProtocol(createClasses, runname)
[docs] def saveParticles(self, runname=None): """ Store particles from selected classes. """ def createParticles(prot): inputParticles = self.protocol.inputParticles.get() particles = prot._createSetOfParticles(suffix='Selection') particles.copyInfo(inputParticles) self.protocol._fillParticlesFromNodes(inputParticles, particles, self._selectedNodes()) prot._defineOutputs(outputParticles=particles) self._createSubsetProtocol(createParticles, runname)
[docs]class ImageBox(Item): # copied from pw/gui/, still depends on xmippLib def __init__(self, canvas, imgPath, x=0, y=0, text=None): Item.__init__(self, canvas, x, y) # Create the image from pyworkflow.gui import getImage from pwem.viewers.filehandlers import getImageFromPath if imgPath is None: self.image = getImage('no-image.gif') else: self.image = getImageFromPath(imgPath) if text is not None: self.label = tk.Label(canvas, image=self.image, text=text, compound=tk.TOP, bg='gray') = self.canvas.create_window(x, y, window=self.label) self.label.bind('<Button-1>', self._onClick) else: = self.canvas.create_image(x, y, image=self.image)
[docs] def setSelected(self, value): # Ignore selection highlight pass
def _onClick(self, e=None): pass
[docs]class SpiderImageBox(ImageBox): def __init__(self, canvas, node, y): ImageBox.__init__(self, canvas, node.path, text=node.getName(), y=y) def _onClick(self, e=None): if self.node.path is None: return # On click change the selection state self.node.selected = not self.node.selected if self.node.selected: self.label.config(bd=2, bg='green') else: self.label.config(bd=0, bg='grey')
[docs]class SpiderViewerDiday(SpiderViewerClassify): """ Visualization of Spider - classify Diday protocol results. """ _targets = [SpiderProtClassifyDiday] _label = "viewer diday" def _defineParams(self, form): SpiderViewerClassify._defineParams(self, form) self.groupClass.addParam('numberOfClasses', IntParam, default=4, label='Number of classes', help='Desired number of classes.')
[docs] def visualizeClasses(self, e=None): prot = self.protocol classDir = prot.getClassDir() classAvg = 'classavg' classVar = 'classvar' classDoc = 'docclass' params = {'[class_dir]': classDir, '[desired-classes]': self.numberOfClasses.get(), '[particles]': prot._params['particles'] + '@******', '[class_doc]': join(classDir, classDoc + '***'), '[class_avg]': join(classDir, classAvg + '***'), '[class_var]': join(classDir, classVar + '***'), } prot.runTemplate('mda/classavg.msa', prot.getExt(), params) particles = prot.inputParticles.get() particles.load() sampling = particles.getSamplingRate() setFn = prot._getTmpPath('classes2D.sqlite') cleanPath(setFn) classes2D = SetOfClasses2D(filename=setFn) classes2D.setImages(particles) # We need to first create a map between the particles index and # the assigned class number classDict = {} for classId in range(1, self.numberOfClasses.get()+1): docClass = prot._getPath(classDir, classDoc + '%03d.stk' % classId) doc = SpiderDocFile(docClass) for values in doc.iterValues(): imgIndex = int(values[0]) classDict[imgIndex] = classId doc.close() updateItem = lambda p, i: p.setClassId(classDict[i]) def updateClass(cls): rep = cls.getRepresentative() rep.setSamplingRate(particles.getSamplingRate()) avgFn = prot._getPath(classDir, classAvg + '%03d.stk' % cls.getObjId()) rep.setLocation(1, avgFn) particlesRange = range(1, particles.getSize()+1) classes2D.classifyItems(updateItemCallback=updateItem, updateClassCallback=updateClass, itemDataIterator=iter(particlesRange)) classes2D.write() classes2D.close() return [ClassesView(self.getProject(), prot.strId(), classes2D.getFileName(), particles.strId())]