def createAlignmentPlot(meanX, meanY):
""" Create a plotter with the cumulative shift per frame. """
figureSize = (8, 6)
plotter = Plotter(*figureSize)
figure = plotter.getFigure()
ax = figure.add_subplot(111)
ax.grid()
ax.axis('equal')
ax.set_title('Cartesian representation')
ax.set_xlabel('Drift x (pixels)')
ax.set_ylabel('Drift y (pixels)')
# Max range of the plot of the two coordinates
plotRange = max(max(meanX) - min(meanX), max(meanY) - min(meanY))
i = 1
skipLabels = ceil(len(meanX) / 10.0)
for x, y in izip(meanX, meanY):
if i % skipLabels == 0:
ax.text(x - 0.02 * plotRange, y + 0.02 * plotRange, str(i))
i += 1
ax.plot(meanX, meanY, color='b')
ax.plot(meanX, meanY, 'yo')
# setting the plot windows to properly see the data
ax.axis([min(meanX) - 0.1 * plotRange, max(meanX) + 0.1 * plotRange,
min(meanY) - 0.1 * plotRange, max(meanY) + 0.1 * plotRange])
plotter.tightLayout()
return plotter
def _showBFactorPlot(self, key):
if key == 'guinier':
label = 'rlnFittedInterceptGuinierPlot'
title = "Polishing scale-factors"
else: # bfactor
label = 'rlnBfactorUsedForSharpening'
title = "Polishing B-factors"
modelStar = self.protocol._getFileName('bfactors')
if os.path.exists(modelStar):
table = Table(fileName=modelStar, tableName='perframe_bfactors')
frame = table.getColumnValues('rlnMovieFrameNumber')
bfactor = map(float, table.getColumnValues(label))
plotter = Plotter()
figure = plotter.getFigure()
a = figure.add_subplot(111)
a.grid(True)
a.set_xlabel('Movie frame number')
a.set_ylabel(label)
a.invert_yaxis()
a.plot(frame, list(bfactor))
a.set_title(title)
plotter.tightLayout()
return [plotter]
def movieCreatePlot(mic, saveFig):
import xmipp
meanX = []
meanY = []
figureSize = (8, 6)
#alignedMovie = mic.alignMetaData
md = xmipp.MetaData(mic.alignMetaData)
plotter = Plotter(*figureSize)
figure = plotter.getFigure()
preX = 0.0
preY = 0.0
meanX.append(0.0)
meanY.append(0.0)
ax = figure.add_subplot(111)
ax.grid()
ax.set_title('Cartesian representation')
ax.set_xlabel('Drift x (pixels)')
ax.set_ylabel('Drift y (pixels)')
ax.plot(0, 0, 'yo-')
for objId in md:
preX += md.getValue(xmipp.MDL_OPTICALFLOW_MEANX, objId)
preY += md.getValue(xmipp.MDL_OPTICALFLOW_MEANY, objId)
meanX.append(preX)
meanY.append(preY)
ax.plot(preX, preY, 'yo-')
ax.text(preX - 0.02, preY + 0.01, str(objId + 1))
ax.plot(np.asarray(meanX), np.asarray(meanY))
if saveFig:
plotter.savefig(mic.plotCart)
return plotter
def createPlot2D(self, volPrefix, md):
import xmipp
figurePath = self._getExtraPath(volPrefix +
'softAlignmentValidation2D.png')
figureSize = (8, 6)
#alignedMovie = mic.alignMetaData
plotter = Plotter(*figureSize)
figure = plotter.getFigure()
ax = figure.add_subplot(111)
ax.grid()
ax.set_title('Soft alignment validation map')
ax.set_xlabel('Angular Precision')
ax.set_ylabel('Angular Accuracy')
for objId in md:
x = md.getValue(xmipp.MDL_SCORE_BY_ALIGNABILITY_PRECISION, objId)
y = md.getValue(xmipp.MDL_SCORE_BY_ALIGNABILITY_ACCURACY, objId)
ax.plot(x, y, 'r.', markersize=1)
ax.grid(True, which='both')
ax.autoscale_view(True, True, True)
plotter.savefig(figurePath)
plotter.show()
return plotter
def createGlobalAlignmentPlot(meanX, meanY, first):
""" Create a plotter with the cumulative shift per frame. """
sumMeanX = []
sumMeanY = []
preX = 0.0
preY = 0.0
figureSize = (6, 4)
plotter = Plotter(*figureSize)
figure = plotter.getFigure()
ax = figure.add_subplot(111)
ax.grid()
ax.set_title('Global frame shift (cumulative)')
ax.set_xlabel('Shift x (pixels)')
ax.set_ylabel('Shift y (pixels)')
if meanX[0] != 0 or meanY[0] != 0:
raise Exception("First frame shift must be (0,0)!")
i = first
for x, y in izip(meanX, meanY):
preX += x
preY += y
sumMeanX.append(preX)
sumMeanY.append(preY)
ax.text(preX - 0.02, preY + 0.02, str(i))
i += 1
ax.plot(sumMeanX, sumMeanY, color='b')
ax.plot(sumMeanX, sumMeanY, 'yo')
plotter.tightLayout()
return plotter
def createAlignmentPlot(meanX, meanY):
""" Create a plotter with the cumulative shift per frame. """
sumMeanX = []
sumMeanY = []
figureSize = (8, 6)
plotter = Plotter(*figureSize)
figure = plotter.getFigure()
preX = 0.0
preY = 0.0
sumMeanX.append(0.0)
sumMeanY.append(0.0)
ax = figure.add_subplot(111)
ax.grid()
ax.set_title('Cartesian representation')
ax.set_xlabel('Drift x (pixels)')
ax.set_ylabel('Drift y (pixels)')
ax.plot(0, 0, 'yo-')
i = 1
for x, y in izip(meanX, meanY):
preX += x
preY += y
sumMeanX.append(preX)
sumMeanY.append(preY)
#ax.plot(preX, preY, 'yo-')
ax.text(preX-0.02, preY+0.02, str(i))
i += 1
ax.plot(sumMeanX, sumMeanY, color='b')
ax.plot(sumMeanX, sumMeanY, 'yo')
plotter.tightLayout()
return plotter
def createPlot2D(self,volPrefix,md):
import xmipp
figurePath = self._getExtraPath(volPrefix + 'softAlignmentValidation2D.png')
figureSize = (8, 6)
#alignedMovie = mic.alignMetaData
plotter = Plotter(*figureSize)
figure = plotter.getFigure()
ax = figure.add_subplot(111)
ax.grid()
ax.set_title('Soft alignment validation map')
ax.set_xlabel('Angular Precision')
ax.set_ylabel('Angular Accuracy')
for objId in md:
x = md.getValue(xmipp.MDL_SCORE_BY_ALIGNABILITY_PRECISION, objId)
y = md.getValue(xmipp.MDL_SCORE_BY_ALIGNABILITY_ACCURACY, objId)
ax.plot(x, y, 'r.',markersize=1)
ax.grid(True, which='both')
ax.autoscale_view(True,True,True)
plotter.savefig(figurePath)
plotter.show()
return plotter
def movieCreatePlot(mic, saveFig):
import xmipp
meanX = []
meanY = []
figureSize = (8, 6)
#alignedMovie = mic.alignMetaData
md = xmipp.MetaData(mic.alignMetaData)
plotter = Plotter(*figureSize)
figure = plotter.getFigure()
preX = 0.0
preY = 0.0
meanX.append(0.0)
meanY.append(0.0)
ax = figure.add_subplot(111)
ax.grid()
ax.set_title('Cartesian representation')
ax.set_xlabel('Drift x (pixels)')
ax.set_ylabel('Drift y (pixels)')
ax.plot(0, 0, 'yo-')
for objId in md:
preX += md.getValue(xmipp.MDL_OPTICALFLOW_MEANX, objId)
preY += md.getValue(xmipp.MDL_OPTICALFLOW_MEANY, objId)
meanX.append(preX)
meanY.append(preY)
ax.plot(preX, preY, 'yo-')
ax.text(preX-0.02, preY+0.01, str(objId+1))
ax.plot(np.asarray(meanX), np.asarray(meanY))
if saveFig:
plotter.savefig(mic.plotCart)
return plotter
def createGlobalAlignmentPlot(meanX, meanY, first):
""" Create a plotter with the shift per frame. """
figureSize = (6, 4)
plotter = Plotter(*figureSize)
figure = plotter.getFigure()
ax = figure.add_subplot(111)
ax.grid()
ax.set_title('Global shift')
ax.set_xlabel('Shift x (pixels)')
ax.set_ylabel('Shift y (pixels)')
i = first
skipLabels = ceil(len(meanX) / 10.0)
labelTick = 1
for x, y in izip(meanX, meanY):
if labelTick == 1:
ax.text(x - 0.02, y + 0.02, str(i))
labelTick = skipLabels
else:
labelTick -= 1
i += 1
ax.plot(meanX, meanY, color='b')
ax.plot(meanX, meanY, 'yo')
plotter.tightLayout()
return plotter
def createGlobalAlignmentPlot(meanX, meanY, first, pixSize):
""" Create a plotter with the shift per frame. """
sumMeanX = []
sumMeanY = []
def px_to_ang(px):
y1, y2 = px.get_ylim()
x1, x2 = px.get_xlim()
ax_ang2.set_ylim(y1 * pixSize, y2 * pixSize)
ax_ang.set_xlim(x1 * pixSize, x2 * pixSize)
ax_ang.figure.canvas.draw()
ax_ang2.figure.canvas.draw()
figureSize = (6, 4)
plotter = Plotter(*figureSize)
figure = plotter.getFigure()
ax_px = figure.add_subplot(111)
ax_px.grid()
ax_px.set_xlabel('Shift x (px)')
ax_px.set_ylabel('Shift y (px)')
ax_ang = ax_px.twiny()
ax_ang.set_xlabel('Shift x (A)')
ax_ang2 = ax_px.twinx()
ax_ang2.set_ylabel('Shift y (A)')
i = first
# The output and log files list the shifts relative to the first frame.
# ROB unit seems to be pixels since sampling rate is only asked
# by the program if dose filtering is required
skipLabels = ceil(len(meanX) / 10.0)
labelTick = 1
for x, y in zip(meanX, meanY):
sumMeanX.append(x)
sumMeanY.append(y)
if labelTick == 1:
ax_px.text(x - 0.02, y + 0.02, str(i))
labelTick = skipLabels
else:
labelTick -= 1
i += 1
# automatically update lim of ax_ang when lim of ax_px changes.
ax_px.callbacks.connect("ylim_changed", px_to_ang)
ax_px.callbacks.connect("xlim_changed", px_to_ang)
ax_px.plot(sumMeanX, sumMeanY, color='b')
ax_px.plot(sumMeanX, sumMeanY, 'yo')
ax_px.plot(sumMeanX[0], sumMeanY[0], 'ro', markersize=10, linewidth=0.5)
ax_px.set_title('Global frame alignment')
plotter.tightLayout()
return plotter
def createGlobalAlignmentPlot(meanX, meanY, first, pixSize):
""" Create a plotter with the shift per frame. """
sumMeanX = []
sumMeanY = []
def px_to_ang(ax_px):
y1, y2 = ax_px.get_ylim()
x1, x2 = ax_px.get_xlim()
ax_ang2.set_ylim(y1 * pixSize, y2 * pixSize)
ax_ang.set_xlim(x1 * pixSize, x2 * pixSize)
ax_ang.figure.canvas.draw()
ax_ang2.figure.canvas.draw()
figureSize = (6, 4)
plotter = Plotter(*figureSize)
figure = plotter.getFigure()
ax_px = figure.add_subplot(111)
ax_px.grid()
ax_px.set_xlabel('Shift x (px)')
ax_px.set_ylabel('Shift y (px)')
ax_ang = ax_px.twiny()
ax_ang.set_xlabel('Shift x (A)')
ax_ang2 = ax_px.twinx()
ax_ang2.set_ylabel('Shift y (A)')
i = first
# The output _rlnMicrographShiftX/Y shifts relative to the first frame.
# Unit is pixels of the original (unbinned) movies (Takanori, 2018)
skipLabels = ceil(len(meanX) / 10.0)
labelTick = 1
for x, y in zip(meanX, meanY):
sumMeanX.append(x)
sumMeanY.append(y)
if labelTick == 1:
ax_px.text(x - 0.02, y + 0.02, str(i))
labelTick = skipLabels
else:
labelTick -= 1
i += 1
# automatically update lim of ax_ang when lim of ax_px changes.
ax_px.callbacks.connect("ylim_changed", px_to_ang)
ax_px.callbacks.connect("xlim_changed", px_to_ang)
ax_px.plot(sumMeanX, sumMeanY, color='b')
ax_px.plot(sumMeanX, sumMeanY, 'yo')
ax_px.plot(sumMeanX[0], sumMeanY[0], 'ro', markersize=10, linewidth=0.5)
ax_px.set_title('Global frame alignment')
plotter.tightLayout()
return plotter
def _runPreWhiteningWeb(protocol, results):
newAng = protocol.prewhitenAng.get()
newRamp = protocol.prewhitenRamp.get()
figsize = (18, 9)
gridsize = [0, 0]
plotter = Plotter(*gridsize, figsize=figsize, windowTitle="ResMap")
myCreatePrewhiteningFigure(results, plotter.getFigure(), newAng, newRamp)
return plotter
def createGlobalAlignmentPlot(meanX, meanY, first):
""" Create a plotter with the shift per frame. """
sumMeanX = []
sumMeanY = []
preX = 0.0
preY = 0.0
figureSize = (6, 4)
plotter = Plotter(*figureSize)
figure = plotter.getFigure()
ax = figure.add_subplot(111)
ax.grid()
ax.set_title('Alignment based upon full frames')
ax.set_xlabel('Shift x (pixels)')
ax.set_ylabel('Shift y (pixels)')
# morioncor2 (1.0.2) values refer to the middle frame, so first frame is no longer 0,0
#if meanX[0] != 0 or meanY[0] != 0:
# raise Exception("First frame shift must be (0,0)!")
i = first
# ROB no accumulation is needed
# see Motioncor2 user manual: "The output and log files list the shifts relative to the first frame."
# or middle frame for motioncor2 1.0.2
# ROB unit seems to be pixels since samplingrate is only asked by the program if
# dose filtering is required
skipLabels = ceil(len(meanX) / 10.0)
labelTick = 1
for x, y in izip(meanX, meanY):
#preX += x
#preY += y
preX = x
preY = y
sumMeanX.append(preX)
sumMeanY.append(preY)
if labelTick == 1:
ax.text(preX - 0.02, preY + 0.02, str(i))
labelTick = skipLabels
else:
labelTick -= 1
i += 1
ax.plot(sumMeanX, sumMeanY, color='b')
ax.plot(sumMeanX, sumMeanY, 'yo')
plotter.tightLayout()
return plotter
def _runPreWhiteningWeb(protocol, results):
newAng = protocol.prewhitenAng.get()
newRamp = protocol.prewhitenRamp.get()
figsize = (18, 9)
gridsize = [0, 0]
plotter = Plotter(*gridsize, figsize=figsize, windowTitle="ResMap")
myCreatePrewhiteningFigure(results, plotter.getFigure(),
newAng, newRamp
)
return plotter
def createGlobalAlignmentPlot(meanX, meanY, first):
""" Create a plotter with the shift per frame. """
sumMeanX = []
sumMeanY = []
preX = 0.0
preY = 0.0
figureSize = (6, 4)
plotter = Plotter(*figureSize)
figure = plotter.getFigure()
ax = figure.add_subplot(111)
ax.grid()
ax.set_title('Alignment based upon full frames')
ax.set_xlabel('Shift x (pixels)')
ax.set_ylabel('Shift y (pixels)')
# motioncor2 (1.0.2) values refer to the middle frame, so first frame is no longer 0,0
#if meanX[0] != 0 or meanY[0] != 0:
# raise Exception("First frame shift must be (0,0)!")
i = first
# ROB no accumulation is needed
# see Motioncor2 user manual: "The output and log files list the shifts relative to the first frame."
# or middle frame for motioncor2 1.0.2
# ROB unit seems to be pixels since samplingrate is only asked by the program if
# dose filtering is required
skipLabels = ceil(len(meanX)/10.0)
labelTick = 1
for x, y in izip(meanX, meanY):
#preX += x
#preY += y
preX = x
preY = y
sumMeanX.append(preX)
sumMeanY.append(preY)
if labelTick == 1:
ax.text(preX - 0.02, preY + 0.02, str(i))
labelTick = skipLabels
else:
labelTick -= 1
i += 1
ax.plot(sumMeanX, sumMeanY, color='b')
ax.plot(sumMeanX, sumMeanY, 'yo')
plotter.tightLayout()
return plotter
def createGlobalAlignmentPlot(meanX, meanY, first):
""" Create a plotter with the shift per frame. """
sumMeanX = []
sumMeanY = []
preX = 0.0
preY = 0.0
figureSize = (6, 4)
plotter = Plotter(*figureSize)
figure = plotter.getFigure()
ax = figure.add_subplot(111)
ax.grid()
ax.set_title('Alignment based upon full frames')
ax.set_xlabel('Shift x (pixels)')
ax.set_ylabel('Shift y (pixels)')
i = first
skipLabels = ceil(len(meanX)/10.0)
labelTick = 1
for x, y in izip(meanX, meanY):
preX = x
preY = y
sumMeanX.append(preX)
sumMeanY.append(preY)
if labelTick == 1:
ax.text(preX - 0.02, preY + 0.02, str(i))
labelTick = skipLabels
else:
labelTick -= 1
i += 1
ax.plot(sumMeanX, sumMeanY, color='b')
ax.plot(sumMeanX, sumMeanY, 'yo')
plotter.tightLayout()
return plotter
def createGlobalAlignmentPlot(meanX, meanY, first):
""" Create a plotter with the shift per frame. """
sumMeanX = []
sumMeanY = []
preX = 0.0
preY = 0.0
figureSize = (6, 4)
plotter = Plotter(*figureSize)
figure = plotter.getFigure()
ax = figure.add_subplot(111)
ax.grid()
ax.set_title('Alignment based upon full frames')
ax.set_xlabel('Shift x (pixels)')
ax.set_ylabel('Shift y (pixels)')
i = first
skipLabels = ceil(len(meanX)/10.0)
labelTick = 1
for x, y in izip(meanX, meanY):
preX = x
preY = y
sumMeanX.append(preX)
sumMeanY.append(preY)
if labelTick == 1:
ax.text(preX - 0.02, preY + 0.02, str(i))
labelTick = skipLabels
else:
labelTick -= 1
i += 1
ax.plot(sumMeanX, sumMeanY, color='b')
ax.plot(sumMeanX, sumMeanY, 'yo')
plotter.tightLayout()
return plotter
def movieCreatePlot(plotType, movie, saveFig):
import xmipp
meanX = []
meanY = []
stdX = []
stdY = []
colors = []
gr = 255.0
# if movie is None:
# return [self.errorMessage("Invalid movie id *%d*" % movieId,
# title="Invalid input")]
alignedMovie = movie.alignMetaData
md = xmipp.MetaData(alignedMovie)
colorDist = 255 / md.size()
cartPosition = None
polarPosition = None
colorBarPosition = 122
figureSize = (8, 6)
if plotType == PLOT_CART:
cartPosition = 121
elif plotType == PLOT_POLAR:
polarPosition = 121
elif plotType == PLOT_POLARCART:
cartPosition = 132
polarPosition = 131
colorBarPosition = 133
plotter = Plotter(*figureSize)
figure = plotter.getFigure()
# Plot the color bar
ax = figure.add_subplot(colorBarPosition, aspect="equal", xlim=[0, 6])
ax.set_xticklabels([])
ax.set_yticklabels([])
colorBarX = np.array([1, 1])
colorBarY = np.array([2, 4])
# Read the shifts information from the Metadata
for objId in md:
meanX.append(md.getValue(xmipp.MDL_OPTICALFLOW_MEANX, objId))
meanY.append(md.getValue(xmipp.MDL_OPTICALFLOW_MEANY, objId))
stdX.append(md.getValue(xmipp.MDL_OPTICALFLOW_STDY, objId))
stdY.append(md.getValue(xmipp.MDL_OPTICALFLOW_STDY, objId))
colors.append((1, gr / 255.0, 0))
ax.plot(colorBarX, colorBarY, c=(1, gr / 255.0, 0), linewidth=10)
ax.text(2, np.mean(colorBarY), str(objId) + "-" + str(objId + 1))
colorBarY += 2
gr -= colorDist
area = (np.sqrt(np.power(np.asarray(stdX), 2) + np.power(np.asarray(stdY), 2))) * 700
# Plot in polar if needed
if polarPosition:
r = np.sqrt(np.power(np.asarray(meanX), 2) + np.power(np.asarray(meanY), 2))
theta = np.arctan2(meanY, meanX) * 180 / np.pi
ax = figure.add_subplot(polarPosition, projection="polar")
ax.set_title("Polar representation")
c = ax.scatter(theta, r, c=colors, s=area, cmap=plt.cm.hsv)
c.set_alpha(0.75)
ax.plot(theta, r, "-^")
if saveFig:
plotter.savefig(movie.plotPolar)
# Plot in cartesian if needed
if cartPosition:
ax = figure.add_subplot(cartPosition)
ax.grid()
ax.grid()
ax.set_title("Cartesian representation")
c = ax.scatter(np.asarray(meanX), np.asarray(meanY), c=colors, s=area, cmap=plt.cm.hsv)
c.set_alpha(0.75)
ax.plot(np.asarray(meanX), np.asarray(meanY), "-^")
if saveFig:
plotter.savefig(movie.plotCart)
return plotter
