def _visualizeHistogram(self, e=None):
views = []
numberOfBins = self.visualizeHistogram.get()
if hasattr(self.protocol, "outputCTF"):
numberOfBins = min(numberOfBins, self.protocol.outputCTF.getSize())
plotter = EmPlotter()
plotter.createSubPlot("Resolution Discrepancies histogram",
"Resolution (A)", "# of Comparisons")
resolution = [
ctf.getResolution() for ctf in self.protocol.outputCTF
]
plotter.plotHist(resolution, nbins=numberOfBins)
views.append(plotter)
if hasattr(self.protocol, "outputCTFDiscarded"):
numberOfBins = min(numberOfBins,
self.protocol.outputCTFDiscarded.getSize())
plotter = EmPlotter()
plotter.createSubPlot(
"Resolution Discrepancies histogram (discarded)",
"Resolution (A)", "# of Comparisons")
resolution = [
ctf.getResolution() for ctf in self.protocol.outputCTFDiscarded
]
plotter.plotHist(resolution, nbins=numberOfBins)
views.append(plotter)
return views
def _plotHistogram(self, param=None):
imageFile = self.protocol._getFileName(FN_RESOLMAP)
img = ImageHandler().read(imageFile)
imgData = img.getData()
imgList = imgData.flatten()
imgListNoZero = filter(lambda x: x > 0, imgList)
nbins = 30
plotter = EmPlotter(x=1, y=1, mainTitle=" ")
plotter.createSubPlot("Resolution histogram",
"Resolution (A)", "# of Counts")
plotter.plotHist(list(imgListNoZero), nbins)
return [plotter]
def _plotHistogram(self, param=None):
imageFile = self.protocol._getFileName(RESMAP_VOL)
img = ImageHandler().read(imageFile)
imgData = img.getData()
imgList = imgData.flatten()
imgDataMax = self.getBackGroundValue(imgList)
imgListNoZero = filter(lambda x: 0 < x < imgDataMax, imgList)
nbins = 30
plotter = EmPlotter(x=1, y=1, mainTitle=" ")
plotter.createSubPlot("Resolution histogram", "Resolution (A)",
"# of Counts")
plotter.plotHist(imgListNoZero, nbins)
return [plotter]
def _showHistogram(self, param=None):
fn = self.protocol._getFileName('output_hist')
with open(fn) as f:
views = []
numberOfBins = 10
plotter = EmPlotter()
plotter.createSubPlot("PSF Resolution histogram", "Resolution (A)",
"Ang (str)")
resolution = [float(line.strip()) for line in f]
plotter.plotHist(resolution, nbins=numberOfBins)
plotter.show()
return views.append(plotter)
def plotMultiHistogram(valuesList,
colors=None,
legend=None,
numOfBins=100,
plotter=None,
views=None,
includeEmpties=False):
""" Values list must be a n-list of list,
where n is the number of the subhistograms to plot.
Multiple histograms will be plot in the same chart
If no views is passed, a new list-views will be returned with the hist.
If no plotter is passed, a new generic one will be created.
"""
if not all([isinstance(x, list) for x in valuesList]):
print("Not all items in values list are lists. Returning...")
return
if colors is None:
from matplotlib import colors
from random import shuffle
colors = colors.cnames.keys()
shuffle(colors)
if any([len(x) for x in valuesList]):
if plotter is None:
plotter = EmPlotter()
plotter.createSubPlot("Histogram", "Score", "# of Items")
w1 = None
finalLegend = []
for idx, values in enumerate(valuesList):
if values or includeEmpties:
if w1 is None:
w1 = (max(values) - min(values)) / numOfBins
else:
numOfBins = int((max(values) - min(values)) / w1)
plotter.plotHist(values, nbins=numOfBins, color=colors[idx])
if legend:
finalLegend.append(legend[idx])
if finalLegend:
plotter.legend(labels=finalLegend)
if views is None:
views = [plotter]
else:
views.append(plotter)
return views
def _visualizeHistogram(self, e=None):
views = []
numberOfBins = self.visualizeHistogram.get()
outCoords = self.protocol.getOutput()
if outCoords:
mdLabel = emlib.MDL_GOOD_REGION_SCORE
if getXmippAttribute(outCoords.getFirstItem(), mdLabel):
plotter = EmPlotter()
plotter.createSubPlot("Deep micrograph score",
"Deep micrograph score",
"Number of Coordinates")
cScores = [getXmippAttribute(coord, mdLabel).get()
for coord in outCoords]
plotter.plotHist(cScores, nbins=numberOfBins)
views.append(plotter)
else:
print(" > 'outputCoordinates' don't have 'xmipp_zScoreDeepLearning2' label.")
else:
print(" > Output not ready yet.")
return views
