class ImagePreviewDialog(PreviewDialog):
def _beforePreview(self):
self.dim = 256
self.previewLabel = ''
def _createPreview(self, frame):
""" Should be implemented by subclasses to
create the items preview.
"""
from pyworkflow.gui.matplotlib_image import ImagePreview
self.preview = ImagePreview(frame, self.dim, label=self.previewLabel)
self.preview.grid(row=0, column=0)
def _itemSelected(self, obj):
index = obj.getIndex()
filename = obj.getFileName()
if index:
filename = "%03d@%s" % (index, filename)
# self.image = xmipp.Image()
self.image = ImageHandler()._img
try:
self.image.readPreview(filename, self.dim)
if filename.endswith('.psd'):
self.image.convertPSD()
self.Z = self.image.getData()
except Exception, e:
from pyworkflow.gui.matplotlib_image import getPngData
self.Z = getPngData(findResource('no-image.png'))
dialog.showError("Input particles", "Error reading image <%s>" % filename, self)
self.preview.updateData(self.Z)
class ImagePreviewDialog(PreviewDialog):
def _beforePreview(self):
self.dim = 256
self.previewLabel = ''
def _createPreview(self, frame):
""" Should be implemented by subclasses to
create the items preview.
"""
from pyworkflow.gui.matplotlib_image import ImagePreview
self.preview = ImagePreview(frame, self.dim, label=self.previewLabel)
self.preview.grid(row=0, column=0)
def _itemSelected(self, obj):
index = obj.getIndex()
filename = obj.getFileName()
if index:
filename = "%03d@%s" % (index, filename)
# self.image = xmipp.Image()
self.image = ImageHandler()._img
try:
self.image.readPreview(filename, self.dim)
if filename.endswith('.psd'):
self.image.convertPSD()
self.Z = self.image.getData()
except Exception, e:
from pyworkflow.gui.matplotlib_image import getPngData
self.Z = getPngData(findResource('no-image.png'))
dialog.showError("Input particles",
"Error reading image <%s>" % filename, self)
self.preview.updateData(self.Z)
def getImgData(self, imgFile):
import numpy as np
img = ImageHandler().read(imgFile)
imgData = img.getData()
maxRes = np.amax(imgData)
imgData2 = np.ma.masked_where(imgData < 0.1, imgData, copy=True)
minRes = np.amin(imgData2)
return imgData2, minRes, maxRes
class BsoftFilterDialog(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):
pass #FIXME
# self.freqFrame = ttk.LabelFrame(frame, text="Frequencies", padding="5 5 5 5")
# self.freqFrame.grid(row=0, column=0)
# if self.protocolParent.filterType <= FILTER_SPACE_REAL:
# 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()
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
"""
from pyworkflow.em.packages.xmipp3 import locationToXmipp
# Copy image to filter to Tmp project folder
inputPath = os.path.join("Tmp", "bsoft_filter_input.spi")
outputPath = os.path.join("Tmp", "bsoft_filter_output.spi")
cleanPath(inputPath, outputPath)
ih = ImageHandler()
ih.convert(self.lastObj.getLocation(), inputPath)
self.protocolParent.runFilter(inputPath, outputPath)
# Get output image and update filtered image
img = ih._img
img.read(outputPath)
self.rightImage = img
self.updateFilteredImage()
class BsoftFilterDialog(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):
pass #FIXME
# self.freqFrame = ttk.LabelFrame(frame, text="Frequencies", padding="5 5 5 5")
# self.freqFrame.grid(row=0, column=0)
# if self.protocolParent.filterType <= FILTER_SPACE_REAL:
# 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()
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
"""
from pyworkflow.em.packages.xmipp3 import locationToXmipp
# Copy image to filter to Tmp project folder
inputPath = os.path.join("Tmp", "bsoft_filter_input.spi")
outputPath = os.path.join("Tmp", "bsoft_filter_output.spi")
cleanPath(inputPath, outputPath)
ih = ImageHandler()
ih.convert(self.lastObj.getLocation(), inputPath)
self.protocolParent.runFilter(inputPath, outputPath)
# Get output image and update filtered image
img = ih._img
img.read(outputPath)
self.rightImage = img
self.updateFilteredImage()
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_SPACE_REAL:
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()
def getRadius(self):
return self.radiusSlider.get()
def addFreqSlider(self, label, value, col):
slider = LabelSlider(self.freqFrame, label, from_=0, to=0.5, value=value, callback=None)
slider.grid(row=0, column=col, padx=5, pady=5)
return slider
def getLowFreq(self):
return self.lfSlider.get()
def getHighFreq(self):
return self.hfSlider.get()
def getTemperature(self):
return self.tempSlider.get()
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
"""
from pyworkflow.em.packages.xmipp3 import locationToXmipp
# 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 = {}
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_SPACE_REAL:
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 = locationToXmipp(1, outputPath)
img.read(locXmippStr)
self.rightImage = img
self.updateFilteredImage()
class BandPassFilterDialog(DownsampleDialog):
def _beforePreview(self):
ImagePreviewDialog._beforePreview(self)
self.lastObj = None
self.rightPreviewLabel = "Filtered"
self.message = "Computing filtered image..."
self.previewLabel = "Image"
self.rightImage = ImageHandler()._img
def _createControls(self, frame):
self.freqFrame = ttk.LabelFrame(frame,
text="Frequencies (%s)" % self.unit,
padding="5 5 5 5")
self.freqFrame.grid(row=0, column=0)
self.showLowFreq = getattr(self, 'showLowFreq', True)
self.showHighFreq = getattr(self, 'showHighFreq', True)
self.showDecay = getattr(self, 'showDecay', True)
if (not self.showLowFreq) or (not self.showHighFreq):
label_high = 'Freq'
label_low = 'Freq'
else:
label_high = 'High freq'
label_low = 'Low freq'
self.samplingRate = 1.0
self.sliTo = 0.5
self.sliFrom = 0.
if self.unit == UNIT_ANGSTROM:
self.samplingRate = self.firstItem.getSamplingRate()
self.itemDim, _, _ = self.firstItem.getDim()
self.sliFrom = 2. * self.samplingRate
self.sliTo = 2. * self.itemDim * self.samplingRate
self.step = self.sliTo / 1000
if self.showLowFreq:
self.lfSlider = self.addFreqSlider(label_low, self.lowFreq, col=0)
if self.showHighFreq:
self.hfSlider = self.addFreqSlider(label_high,
self.highFreq,
col=1)
if self.showDecay:
self.freqDecaySlider = self.addFreqSlider('Decay',
self.freqDecay,
col=2)
def addFreqSlider(self, label, value, col):
fromValue = self.sliFrom
toValue = self.sliTo
if self.unit == UNIT_ANGSTROM:
fromValue = self.sliTo
toValue = self.sliFrom
slider = LabelSlider(
self.freqFrame,
label,
from_=fromValue,
to=toValue,
step=self.step,
value=value,
callback=lambda a, b, c: self.updateFilteredImage())
slider.grid(row=0, column=col, padx=5, pady=5)
return slider
def updateFilteredImage(self):
self._computeRightPreview()
self.rightPreview.updateData(self.rightImage.getData())
def _computeRightPreview(self):
""" This function should compute the right preview
using the self.lastObj that was selected
"""
from pyworkflow.em.packages.xmipp3.convert import getImageLocation
xmipp.bandPassFilter(self.rightImage, getImageLocation(self.lastObj),
self.getLowFreq(), self.getHighFreq(),
self.getFreqDecay(), self.dim)
def getLowFreq(self):
if self.showLowFreq:
if self.unit == UNIT_ANGSTROM:
return self.samplingRate / self.lfSlider.get()
else:
return self.lfSlider.get()
return 0.
def getHighFreq(self):
if self.showHighFreq:
if self.unit == UNIT_ANGSTROM:
return self.samplingRate / self.hfSlider.get()
else:
return self.hfSlider.get()
return 1.0
def getFreqDecay(self):
if self.showDecay:
if self.unit == UNIT_ANGSTROM:
return self.samplingRate / self.freqDecaySlider.get()
else:
return self.freqDecaySlider.get()
return 0.
class DownsampleDialog(ImagePreviewDialog):
def _beforePreview(self):
ImagePreviewDialog._beforePreview(self)
self.lastObj = None
self.rightPreviewLabel = "PSD"
self.message = "Computing PSD..."
self.previewLabel = "Micrograph"
self.rightImage = ImageHandler()._img
def _createPreview(self, frame):
""" Should be implemented by subclasses to
create the items preview.
"""
leftFrame = tk.Frame(frame)
leftFrame.grid(row=0, column=0)
rightFrame = tk.Frame(frame)
rightFrame.grid(row=0, column=1)
ImagePreviewDialog._createPreview(self, leftFrame)
self.rightPreview = self._createRightPreview(rightFrame)
self.rightPreview.grid(row=0, column=0)
def _createRightPreview(self, rightFrame):
from pyworkflow.gui.matplotlib_image import ImagePreview
return ImagePreview(rightFrame, self.dim, label=self.rightPreviewLabel)
def _createControls(self, frame):
self.downVar = tk.StringVar()
self.downVar.set(getattr(self, 'downsample', 1))
downFrame = tk.Frame(frame)
downFrame.grid(row=0, column=0, sticky='nw')
downLabel = tk.Label(downFrame, text='Downsample')
downLabel.grid(row=0, column=0, padx=5, pady=5)
downEntry = tk.Entry(downFrame, width=10, textvariable=self.downVar)
downEntry.grid(row=0, column=1, padx=5, pady=5)
downButton = tk.Button(downFrame,
text='Preview',
command=self._doPreview)
downButton.grid(row=0, column=2, padx=5, pady=5)
def getDownsample(self):
return float(self.downVar.get())
def _itemSelected(self, obj):
self.lastObj = obj
ImagePreviewDialog._itemSelected(self, obj)
dialog.FlashMessage(self, self.message, func=self._computeRightPreview)
self.rightPreview.updateData(self.rightImage.getData())
def _doPreview(self, e=None):
if self.lastObj is None:
dialog.showError("Empty selection",
"Select an item first before preview", self)
else:
self._itemSelected(self.lastObj)
def _computeRightPreview(self):
""" This function should compute the right preview
using the self.lastObj that was selected
"""
xmipp.fastEstimateEnhancedPSD(self.rightImage,
self.lastObj.getFileName(),
self.getDownsample(), self.dim, 2)
class BandPassFilterDialog(DownsampleDialog):
def _beforePreview(self):
ImagePreviewDialog._beforePreview(self)
self.lastObj = None
self.rightPreviewLabel = "Filtered"
self.message = "Computing filtered image..."
self.previewLabel = "Image"
self.rightImage = ImageHandler()._img
def _createControls(self, frame):
self.freqFrame = ttk.LabelFrame(frame, text="Frequencies ("+self.unit+")",
padding="5 5 5 5")
self.freqFrame.grid(row=0, column=0)
self.showLowFreq = getattr(self, 'showLowFreq', True)
self.showHighFreq = getattr(self, 'showHighFreq', True)
self.showDecay = getattr(self, 'showDecay', True)
if (not self.showLowFreq) or (not self.showHighFreq):
label_high = 'Freq'
label_low = 'Freq'
else:
label_high = 'High freq'
label_low = 'Low freq'
self.samplingRate = 1.0
self.sliTo = 0.5
self.sliFrom = 0.
if self.unit == UNIT_ANGSTROM:
self.samplingRate = self.firstItem.getSamplingRate()
self.itemDim,_,_ = self.firstItem.getDim()
self.sliFrom = 2.*self.samplingRate
self.sliTo = 2.*self.itemDim*self.samplingRate
self.step = self.sliTo/1000
if self.showLowFreq:
self.lfSlider = self.addFreqSlider(label_low, self.lowFreq, col=0)
if self.showHighFreq:
self.hfSlider = self.addFreqSlider(label_high, self.highFreq, col=1)
if self.showDecay:
self.freqDecaySlider = self.addFreqSlider('Decay', self.freqDecay, col=2)
def addFreqSlider(self, label, value, col):
fromValue = self.sliFrom
toValue = self.sliTo
if self.unit == UNIT_ANGSTROM:
fromValue = self.sliTo
toValue = self.sliFrom
slider = LabelSlider(self.freqFrame, label, from_=fromValue, to=toValue,
step=self.step , value=value, callback=lambda a, b, c:self.updateFilteredImage())
slider.grid(row=0, column=col, padx=5, pady=5)
return slider
def updateFilteredImage(self):
self._computeRightPreview()
self.rightPreview.updateData(self.rightImage.getData())
def _computeRightPreview(self):
""" This function should compute the right preview
using the self.lastObj that was selected
"""
from pyworkflow.em.packages.xmipp3.convert import getImageLocation
xmipp.bandPassFilter(self.rightImage, getImageLocation(self.lastObj), self.getLowFreq(), self.getHighFreq(), self.getFreqDecay(), self.dim)
def getLowFreq(self):
if self.showLowFreq:
if self.unit == UNIT_ANGSTROM:
return self.samplingRate/self.lfSlider.get()
else:
return self.lfSlider.get()
return 0.
def getHighFreq(self):
if self.showHighFreq:
if self.unit == UNIT_ANGSTROM:
return self.samplingRate/self.hfSlider.get()
else:
return self.hfSlider.get()
return 1.0
def getFreqDecay(self):
if self.showDecay:
if self.unit == UNIT_ANGSTROM:
return self.samplingRate/self.freqDecaySlider.get()
else:
return self.freqDecaySlider.get()
return 0.
class DownsampleDialog(ImagePreviewDialog):
def _beforePreview(self):
ImagePreviewDialog._beforePreview(self)
self.lastObj = None
self.rightPreviewLabel = "PSD"
self.message = "Computing PSD..."
self.previewLabel = "Micrograph"
self.rightImage = ImageHandler()._img
def _createPreview(self, frame):
""" Should be implemented by subclasses to
create the items preview.
"""
leftFrame = tk.Frame(frame)
leftFrame.grid(row=0, column=0)
rightFrame = tk.Frame(frame)
rightFrame.grid(row=0, column=1)
ImagePreviewDialog._createPreview(self, leftFrame)
self.rightPreview = self._createRightPreview(rightFrame)
self.rightPreview.grid(row=0, column=0)
def _createRightPreview(self, rightFrame):
from pyworkflow.gui.matplotlib_image import ImagePreview
return ImagePreview(rightFrame, self.dim, label=self.rightPreviewLabel)
def _createControls(self, frame):
self.downVar = tk.StringVar()
self.downVar.set(getattr(self, 'downsample', 1))
downFrame = tk.Frame(frame)
downFrame.grid(row=0, column=0, sticky='nw')
downLabel = tk.Label(downFrame, text='Downsample')
downLabel.grid(row=0, column=0, padx=5, pady=5)
downEntry = tk.Entry(downFrame, width=10, textvariable=self.downVar)
downEntry.grid(row=0, column=1, padx=5, pady=5)
downButton = tk.Button(downFrame, text='Preview', command=self._doPreview)
downButton.grid(row=0, column=2, padx=5, pady=5)
def getDownsample(self):
return float(self.downVar.get())
def _itemSelected(self, obj):
self.lastObj = obj
ImagePreviewDialog._itemSelected(self, obj)
dialog.FlashMessage(self, self.message, func=self._computeRightPreview)
#self._computeRightPreview(obj)
self.rightPreview.updateData(self.rightImage.getData())
def _doPreview(self, e=None):
if self.lastObj is None:
dialog.showError("Empty selection", "Select an item first before preview", self)
else:
self._itemSelected(self.lastObj)
def _computeRightPreview(self):
""" This function should compute the right preview
using the self.lastObj that was selected
"""
xmipp.fastEstimateEnhancedPSD(self.rightImage, self.lastObj.getFileName(), self.getDownsample(), self.dim, 2)
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()
def getRadius(self):
return self.radiusSlider.get()
def addFreqSlider(self, label, value, col):
slider = LabelSlider(self.freqFrame,
label,
from_=0,
to=0.5,
value=value,
callback=None)
slider.grid(row=0, column=col, padx=5, pady=5)
return slider
def getLowFreq(self):
return self.lfSlider.get()
def getHighFreq(self):
return self.hfSlider.get()
def getTemperature(self):
return self.tempSlider.get()
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
"""
from pyworkflow.em.packages.xmipp3 import locationToXmipp
# 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 = {}
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 = locationToXmipp(1, outputPath)
img.read(locXmippStr)
self.rightImage = img
self.updateFilteredImage()
