Source code for spider.wizards

# **************************************************************************
# *
# * Authors:     J.M. De la Rosa Trevin (
# *              Jose Gutierrez (
# *
# * 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 3 of the License, or
# * (at your option) any later version.
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# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * 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 ''
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# **************************************************************************

import os
import tkinter as tk
from tkinter import ttk

from pyworkflow.utils.path import cleanPath
import pyworkflow.gui.dialog as dialog
from pyworkflow.gui.widgets import LabelSlider, HotButton
from pwem.constants import UNIT_PIXEL
from pwem.emlib.image import ImageHandler
from pwem.wizards import (EmWizard, ParticleMaskRadiusWizard,
                          FilterParticlesWizard, DownsampleDialog,
                          ImagePreviewDialog, ListTreeProvider,

from . import Plugin
from .utils import SpiderShell, runCustomMaskScript
from .constants import FILTER_FERMI
from .convert import locationToSpider
from .protocols import (SpiderProtCAPCA, SpiderProtAlignAPSR,
                        SpiderProtAlignPairwise, SpiderProtFilter,
                        SpiderProtCustomMask, SpiderProtRefinement)

# =============================================================================
# =============================================================================

[docs]class SpiderProtMaskWizard(ParticleMaskRadiusWizard): _targets = [(SpiderProtCAPCA, ['radius']), (SpiderProtRefinement, ['radius'])] def _getParameters(self, protocol): label, value = self._getInputProtocol(self._targets, protocol) protParams = dict() if protocol.getClassName().endswith('Refinement'): protParams['input'] = protocol.input3DReference else: protParams['input'] = protocol.inputParticles protParams['label'] = label protParams['value'] = value return protParams def _getProvider(self, protocol): _objs = self._getParameters(protocol)['input'] return ParticleMaskRadiusWizard._getListProvider(self, _objs)
[docs] def show(self, form, *args): params = self._getParameters(form.protocol) _value = params['value'] _label = params['label'], form, _value, _label)
[docs]class SpiderParticlesMaskRadiiWizard(ParticlesMaskRadiiWizard): _targets = [(SpiderProtAlignAPSR, ['innerRadius', 'outerRadius']), (SpiderProtAlignPairwise, ['innerRadius', 'outerRadius'])] def _getParameters(self, protocol): label, value = self._getInputProtocol(self._targets, protocol) protParams = dict() protParams['input'] = protocol.inputParticles protParams['label'] = label protParams['value'] = value return protParams def _getProvider(self, protocol): _objs = self._getParameters(protocol)['input'] return ParticlesMaskRadiiWizard._getListProvider(self, _objs)
[docs] def show(self, form, *args): params = self._getParameters(form.protocol) value = params['value'] label = params['label'] protocol = form.protocol provider = self._getProvider(protocol) if provider is not None: d = MaskRadiiPreviewDialog(form.root, provider, innerRadius=value[0], outerRadius=value[1], unit=UNIT_PIXEL) if d.resultYes(): form.setVar(label[0], int(d.getRadius(d.radiusSliderIn))) form.setVar(label[1], int(d.getRadius(d.radiusSliderOut))) else: dialog.showWarning("Empty input", "Select elements first", form.root)
# ============================================================================= # FILTERS # =============================================================================
[docs]class SpiderFilterParticlesWizard(FilterParticlesWizard): _targets = [(SpiderProtFilter, ['filterRadius', 'lowFreq', 'highFreq', 'temperature'])] def _getParameters(self, protocol): label, value = self._getInputProtocol(self._targets, protocol) protParams = dict() protParams['input'] = protocol.inputParticles protParams['label'] = label protParams['value'] = value protParams['mode'] = [protocol.filterType.get(), protocol.filterMode.get(), protocol.usePadding.get()] return protParams def _getProvider(self, protocol): _objs = self._getParameters(protocol)['input'] return FilterParticlesWizard._getListProvider(self, _objs)
[docs] def show(self, form, *args): protocol = form.protocol provider = self._getProvider(protocol) installErrors = Plugin.validateInstallation() if installErrors: dialog.showError("SPIDER not properly installed.", "\n".join(installErrors), form.root) return if provider is not None: d = SpiderFilterDialog(form.root, provider, protocolParent=protocol) if d.resultYes(): if protocol.filterType <= FILTER_FERMI: form.setVar('filterRadius', d.getRadius()) else: form.setVar('lowFreq', d.getLowFreq()) form.setVar('highFreq', d.getHighFreq()) if protocol.filterType == FILTER_FERMI: form.setVar('temperature', d.getTemperature()) else: dialog.showWarning("Input particles", "Select particles first", form.root)
# ============================================================================= # UTILS # =============================================================================
[docs]class SpiderFilterDialog(DownsampleDialog): def _beforePreview(self): ImagePreviewDialog._beforePreview(self) self.lastObj = None self.rightPreviewLabel = "Filtered particle" self.message = "Filtering particle..." self.previewLabel = "Particle" self.rightImage = ImageHandler()._img def _createControls(self, frame): self.freqFrame = ttk.LabelFrame(frame, text="Frequencies", padding="5 5 5 5") self.freqFrame.grid(row=0, column=0) if self.protocolParent.filterType <= FILTER_FERMI: self.radiusSlider = self.addFreqSlider('Radius', self.protocolParent.filterRadius.get(), col=0) else: self.lfSlider = self.addFreqSlider('Low freq', self.protocolParent.lowFreq.get(), col=0) self.hfSlider = self.addFreqSlider('High freq', self.protocolParent.highFreq.get(), col=1) if self.protocolParent.filterType == FILTER_FERMI: self.tempSlider = self.addFreqSlider('Temperature', self.protocolParent.temperature.get(), col=2) radiusButton = tk.Button(self.freqFrame, text='Preview', command=self._doPreview) radiusButton.grid(row=0, column=3, padx=5, pady=5) def _doPreview(self, e=None): if self.lastObj is None: dialog.showError("Empty selection", "Select an item first before preview", self) else: self._computeRightPreview()
[docs] def getRadius(self): return self.radiusSlider.get()
[docs] def addFreqSlider(self, label, value, col): slider = LabelSlider(self.freqFrame, label, to=0.5, value=value) slider.grid(row=0, column=col, padx=5, pady=5) return slider
[docs] def getLowFreq(self): return self.lfSlider.get()
[docs] def getHighFreq(self): return self.hfSlider.get()
[docs] def getTemperature(self): return self.tempSlider.get()
[docs] def updateFilteredImage(self): self.rightPreview.updateData(self.rightImage.getData())
def _computeRightPreview(self): """ This function should compute the right preview using the self.lastObj that was selected """ # Copy image to filter to Tmp project folder outputName = os.path.join("Tmp", "filtered_particle") outputPath = outputName + ".spi" cleanPath(outputPath) outputLoc = (1, outputPath) ih = ImageHandler() ih.convert(self.lastObj.getLocation(), outputLoc) outputLocSpiStr = locationToSpider(1, outputName) pars = dict() pars["filterType"] = self.protocolParent.filterType.get() pars["filterMode"] = self.protocolParent.filterMode.get() pars["usePadding"] = self.protocolParent.usePadding.get() pars["op"] = "FQ" if self.protocolParent.filterType <= FILTER_FERMI: pars['filterRadius'] = self.getRadius() else: pars['lowFreq'] = self.getLowFreq() pars['highFreq'] = self.getHighFreq() if self.protocolParent.filterType == FILTER_FERMI: pars['temperature'] = self.getTemperature() filter_spider(outputLocSpiStr, outputLocSpiStr, **pars) # Get output image and update filtered image img = ImageHandler()._img locXmippStr = ImageHandler.locationToXmipp((1, outputPath)) self.rightImage = img self.updateFilteredImage()
# TODO: Refactor this function to be used also by method filterParticles
[docs]def filter_spider(inputLocStr, outputLocStr, **pars): """ Function to filter an image located on inputLocStr and write it to outputLocStr. """ spi = SpiderShell() # Create the Spider process to send commands filterNumber = pars["filterType"] * 2 + 1 # Consider low-pass or high-pass filterNumber += pars["filterMode"] OP = pars["op"] if not pars["usePadding"]: OP += ' NP' args = [] if pars["filterType"] <= FILTER_FERMI: args.append(pars['filterRadius']) else: args.append('%f %f' % (pars['lowFreq'], pars['highFreq'])) if pars["filterType"] == FILTER_FERMI: args.append(pars['temperature']) spi.runFunction(OP, inputLocStr, outputLocStr, filterNumber, *args) spi.close()
# -------------- Custom mask Wizard ------------------------------------------- CUSTOMMASK_VARS = {'filterRadius1': 'First radius', 'sdFactor': 'First threshold', 'filterRadius2': 'Second radius', 'maskThreshold': 'Max threshold'} # and the label to the given image MASKRESULT_LABELS = ['input image', 'filtered', 'thresholded', 'filtered mask', 'final mask', 'mask * image', 'inverted mask', 'inverted \nmask * image', ]
[docs]class SpiderCustomMaskWizard(EmWizard): _targets = [(SpiderProtCustomMask, CUSTOMMASK_VARS.keys())] def _getParameters(self, protocol): protParams = dict() protParams['input'] = protocol.inputImage protParams['label'] = CUSTOMMASK_VARS.keys() protParams['labelText'] = MASKRESULT_LABELS protParams['value'] = [protocol.getAttributeValue(a) for a in protParams['label']] return protParams def _getProvider(self, protocol): return ListTreeProvider([self._getParameters(protocol)['input'].get()])
[docs] def show(self, form, *args): protocol = form.protocol provider = self._getProvider(protocol) if protocol.inputImage.get(): d = CustomMaskDialog(form.root, provider, protocolParent=protocol) if d.resultYes(): for varName in CUSTOMMASK_VARS: form.setVar(varName, d.getVarValue(varName)) else: dialog.showWarning("Input error", "Select the input image first", form.root)
[docs]class CustomMaskDialog(ImagePreviewDialog): def _beforePreview(self): imgLocation = self.protocolParent.inputImage.get().getLocation() self.dim = ImageHandler().getDimensions(imgLocation)[0] self.lastObj = None self.rightPreviewLabel = "Final mask" self.message = "Generating mask..." self.ih = ImageHandler() self.rightImage = self.ih.createImage() def _createPreview(self, frame): """ Should be implemented by subclasses to create the items preview. """ self._previews = [] for i, label in enumerate(MASKRESULT_LABELS): self.previewLabel = label previewFrame = tk.Frame(frame) ImagePreviewDialog._createPreview(self, previewFrame) self._previews.append(self.preview) # store all previews created previewFrame.grid(row=i//4, column=i % 4) def _itemSelected(self, obj): self.lastObj = obj dialog.FlashMessage(self, self.message, func=self._computeRightPreview) def _createVarWidgets(self, parent, varName, varLabel, row, col): var = tk.StringVar() self._vars[varName] = var var.set(self.protocolParent.getAttributeValue(varName)) varLabel = tk.Label(parent, text=varLabel) varLabel.grid(row=row, column=col*2, padx=5, pady=5) varEntry = tk.Entry(parent, width=10, textvariable=var) varEntry.grid(row=row, column=col*2+1, padx=5, pady=5) def _createControls(self, frame): self._vars = {} inputFrame = tk.Frame(frame) inputFrame.grid(row=0, column=0) for i, varName in enumerate(CUSTOMMASK_VARS): self._createVarWidgets(inputFrame, varName, CUSTOMMASK_VARS[varName], i % 2, i//2) previewBtn = HotButton(frame, text='Preview', command=self._computeRightPreview) previewBtn.grid(row=1, column=1, padx=5, pady=5)
[docs] def getVarValue(self, varName): return self._vars[varName].get()
def _computeRightPreview(self, e=None): """ This function should compute the right preview using the self.lastObj that was selected """ prot = self.protocolParent # short notation tmp = prot.getProject().getTmpPath() ext = prot.getExt() # Convert input image to spider imgPrefix = 'inputImage' imgName = '%s.%s' % (imgPrefix, ext) imgFn = os.path.join(tmp, imgName) self.ih.convert(self.lastObj, (1, imgFn)) runCustomMaskScript(self.getVarValue('filterRadius1'), self.getVarValue('sdFactor'), self.getVarValue('filterRadius2'), self.getVarValue('maskThreshold'), workingDir=tmp, ext=ext, inputImage=imgPrefix+'@1') for i, preview in enumerate(self._previews): if i == 0: else:'%d@%s/stkmask.%s' % (i, tmp, ext)) preview.updateData(self.rightImage.getData())