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 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 plotFile(dbName, dbPreffix, plotType, columnsStr, colorsStr, linesStr,
markersStr, xcolumn, ylabel, xlabel, title, bins, orderColumn,
orderDirection):
columns = columnsStr.split()
colors = colorsStr.split()
lines = linesStr.split()
markers = markersStr.split()
data = PlotData(dbName, dbPreffix, orderColumn, orderDirection)
#setObj = getSetObject(dbName, dbPreffix)
plotter = Plotter(windowTitle=title)
ax = plotter.createSubPlot(title, xlabel, ylabel)
xvalues = data.getColumnValues(xcolumn) if xcolumn else range(0, data.getSize())
#xvalues = range(0, setObj.getSize()) if not isxvalues else []
for i, col in enumerate(columns):
yvalues = data.getColumnValues(col)
color = colors[i]
line = lines[i]
if bins:
ax.hist(yvalues, bins=int(bins), color=color, linestyle=line, label=col)
else:
if plotType == 'Plot':
marker = (markers[i] if not markers[i] == 'none' else None)
ax.plot(xvalues, yvalues, color, marker=marker, linestyle=line, label=col)
else:
ax.scatter(xvalues, yvalues, c=color, label=col, alpha=0.5)
ax.legend(columns)
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 createFromFile(cls, dbName, dbPreffix, plotType, columnsStr, colorsStr, linesStr,
markersStr, xcolumn, ylabel, xlabel, title, bins, orderColumn,
orderDirection):
columns = columnsStr.split()
colors = colorsStr.split()
lines = linesStr.split()
markers = markersStr.split()
data = PlotData(dbName, dbPreffix, orderColumn, orderDirection)
plotter = Plotter(windowTitle=title)
ax = plotter.createSubPlot(title, xlabel, ylabel)
xvalues = data.getColumnValues(xcolumn) if xcolumn else range(0, data.getSize())
for i, col in enumerate(columns):
yvalues = data.getColumnValues(col)
color = colors[i]
line = lines[i]
colLabel = col if not col.startswith("_") else col[1:]
if bins:
yvalues = data._removeInfinites(yvalues)
ax.hist(yvalues, bins=int(bins), color=color, linestyle=line, label=colLabel)
else:
if plotType == 'Plot':
marker = (markers[i] if not markers[i] == 'none' else None)
ax.plot(xvalues, yvalues, color, marker=marker, linestyle=line, label=colLabel)
else:
ax.scatter(xvalues, yvalues, c=color, label=col, alpha=0.5)
ax.legend()
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 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 plotFile(dbName, dbPreffix, plotType,
columnsStr, colorsStr, linesStr, markersStr,
xcolumn, ylabel, xlabel, title, bins, orderColumn, orderDirection):
columns = columnsStr.split()
colors = colorsStr.split()
lines = linesStr.split()
markers = markersStr.split()
data = PlotData(dbName, dbPreffix, orderColumn, orderDirection)
#setObj = getSetObject(dbName, dbPreffix)
plotter = Plotter(windowTitle=title)
ax = plotter.createSubPlot(title, xlabel, ylabel)
xvalues = data.getColumnValues(xcolumn) if xcolumn else range(0, data.getSize())
#xvalues = range(0, setObj.getSize()) if not isxvalues else []
for i, col in enumerate(columns):
yvalues = data.getColumnValues(col)
color = colors[i]
line = lines[i]
if bins:
ax.hist(yvalues, bins=int(bins), color=color, linestyle=line, label=col)
else:
if plotType == 'Plot':
marker = (markers[i] if not markers[i] == 'none' else None)
ax.plot(xvalues, yvalues, color, marker=marker, linestyle=line, label=col)
else:
ax.scatter(xvalues, yvalues, c=color, label=col, alpha=0.5)
ax.legend(columns)
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 savePlots(self, results=None):
""" Store png images of the plots to be used as images, """
# Add resmap libraries to the path
sys.path.append(os.environ['RESMAP_HOME'])
# This is needed right now because we are having
# some memory problem with matplotlib plots right now in web
Plotter.setBackend('Agg')
self._plotVolumeSlices().savefig(self._getExtraPath('volume1.map.png'))
plot = self._plotResMapSlices(results['resTOTALma'])
plot.savefig(self._getExtraPath('volume1_resmap.map.png'))
self._plotHistogram().savefig(self._getExtraPath('histogram.png'))
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 _plotGrid(self, grid, x, y):
plotter = Plotter(windowTitle="Acquisitions for grid %s" % grid)
plt = plotter.createSubPlot("Locations", "X", "Y")
plt.axis('scaled')
plt.autoscale(tight=True)
self.loadAtlasImg(plt, grid)
colors = ["cyan"] * len(x)
area = np.pi * 3
plotter.scatterP(x, y, s=area, c=colors, edgecolors='none', alpha=1)
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 _plotHistogram(self, param=None):
md = MetaData()
md.read(self.protocol._getFileName(FN_METADATA_HISTOGRAM))
x_axis = []
y_axis = []
i = 0
for idx in md:
x_axis_ = md.getValue(MDL_X, idx)
if i == 0:
x0 = x_axis_
elif i == 1:
x1 = x_axis_
y_axis_ = md.getValue(MDL_COUNT, idx)
i += 1
x_axis.append(x_axis_)
y_axis.append(y_axis_)
delta = x1 - x0
fig = plt.figure()
plt.bar(x_axis, y_axis, width=delta)
plt.title("Resolutions Histogram")
plt.xlabel("Resolution (A)")
plt.ylabel("Counts")
return [Plotter(figure2=fig)]
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 _plotResMapSlices(self, data=None, **kwargs):
from ResMap_visualization import plotResMapVolume
plotDict = loads(self.plotData.get())
if data is None:
data = self._getVolumeMatrix('volume1_resmap.map')
data = np.ma.masked_where(data > plotDict['currentRes'], data, copy=True)
kwargs.update(plotDict)
fig = plotResMapVolume(data, **kwargs)
return Plotter(figure=fig)
def _createSpectraPlot(self, label, array, index, objId=None):
if objId is None:
objId = index
# Number of harmonics calculated
plotter = Plotter()
a = plotter.createSubPlot('Spectrum for %s %d' % (label, objId),
xlabel='Harmonics', ylabel='Energy')
n = self.spectraHighHarmonic.get() - self.spectraLowHarmonic.get() + 1
i1 = (index-1) * n
i2 = i1 + n
xdata = range(self.spectraLowHarmonic.get(), self.spectraHighHarmonic.get()+1)
ydata = array[i1:i2]
a.plot(xdata, ydata)
plotFile = join(self.plotsDir, 'spectra_%s%06d.png' % (label, objId))
plotter.savefig(plotFile)
return plotFile
def _createSpectraPlot(self, label, array, index, objId=None):
if objId is None:
objId = index
# Number of harmonics calculated
plotter = Plotter()
a = plotter.createSubPlot('Spectrum for %s %d' % (label, objId),
xlabel='Harmonics', ylabel='Energy')
n = self.spectraHighHarmonic.get() - self.spectraLowHarmonic.get() + 1
i1 = (index-1) * n
i2 = i1 + n
xdata = range(self.spectraLowHarmonic.get(), self.spectraHighHarmonic.get()+1)
ydata = array[i1:i2]
a.plot(xdata, ydata)
plotFile = join(self.plotsDir, 'spectra_%s%06d.png' % (label, objId))
plotter.savefig(plotFile)
return plotFile
def main():
parser = argparse.ArgumentParser(prog='Scipion Plot')
parser.add_argument('--file', help='File to visualize', required=True)
parser.add_argument('--block', help='Block to visualize')
parser.add_argument('--type', help='Plot type')
parser.add_argument('--columns', help='Columns to plot')
parser.add_argument('--xcolumn', help='X Column to plot')
parser.add_argument('--orderColumn', help='Column to order')
parser.add_argument('--orderDir', help='Order direction(ASC, DESC)')
parser.add_argument('--bins',
help='If plot type is histogram, number of bins')
parser.add_argument('--colors', help='Colors to plot columns')
parser.add_argument('--styles', help='Styles to plot columns')
parser.add_argument('--markers', help='Markers to plot columns')
parser.add_argument('--title', help='Plot title', default='')
parser.add_argument('--ytitle', help='Y axis title', default='')
parser.add_argument('--xtitle', help='X axis title', default='')
args = parser.parse_args()
plotfile = args.file
block = args.block if args.block else ''
type = args.type
columns = args.columns
xcolumn = args.xcolumn
orderColumn = args.orderColumn
orderDir = args.orderDir
bins = args.bins
colors = args.colors
styles = args.styles
markers = args.markers
title = args.title
xtitle = args.xtitle
ytitle = args.ytitle
Plotter.setBackend('TkAgg')
plotter = EmPlotter.createFromFile(plotfile, block, type, columns, colors,
styles, markers, xcolumn, ytitle,
xtitle, title, bins, orderColumn,
orderDir)
plotter.show(block=True)
def main():
parser = argparse.ArgumentParser(prog='Scipion Plot')
parser.add_argument('--file', help='File to visualize', required=True)
parser.add_argument('--block', help='Block to visualize')
parser.add_argument('--type', help='Plot type')
parser.add_argument('--columns', help='Columns to plot')
parser.add_argument('--xcolumn', help='X Column to plot')
parser.add_argument('--orderColumn', help='Column to order')
parser.add_argument('--orderDir', help='Order direction(ASC, DESC)')
parser.add_argument('--bins', help='If plot type is histogram, number of bins')
parser.add_argument('--colors', help='Colors to plot columns')
parser.add_argument('--styles', help='Styles to plot columns')
parser.add_argument('--markers', help='Markers to plot columns')
parser.add_argument('--title', help='Plot title', default='')
parser.add_argument('--ytitle', help='Y axis title', default='')
parser.add_argument('--xtitle', help='X axis title', default='')
args = parser.parse_args()
#print args
plotfile = args.file
block = args.block if args.block else ''
type = args.type
columns = args.columns
xcolumn = args.xcolumn
orderColumn = args.orderColumn
orderDir = args.orderDir
bins = args.bins
colors = args.colors
styles = args.styles
markers = args.markers
title = args.title
xtitle = args.xtitle
ytitle = args.ytitle
Plotter.setBackend('TkAgg')
plotFile(plotfile, block, type,
columns, colors, styles, markers,
xcolumn, ytitle, xtitle, title, bins, orderColumn, orderDir).show(block=True)
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 visualize(self, obj, **args):
cls = type(obj)
if issubclass(cls, AtsasProtConvertPdbToSAXS):
if obj.experimentalSAXS.empty():
fnInt=obj._getPath("pseudoatoms00.int")
else:
fnInt=obj._getPath("pseudoatoms00.fit")
import numpy
x=numpy.loadtxt(fnInt,skiprows=1)
xplotter = Plotter(windowTitle="SAXS Curves")
a = xplotter.createSubPlot('SAXS curves', 'Angstrongs^-1', 'log(SAXS)', yformat=False)
a.plot(x[:,0], numpy.log(x[:,1]))
a.plot(x[:,0], numpy.log(x[:,2]))
if obj.experimentalSAXS.empty():
xplotter.showLegend(['SAXS in solution','SAXS in vacuo'])
else:
xplotter.showLegend(['Experimental SAXS','SAXS from volume'])
xplotter.show()
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 getTestPlot(request):
""" Just a test of a custom render function. """
from pyworkflow.gui.plotter import Plotter
xplotter = Plotter()
xplotter.createSubPlot("Particle sorting", "Particle number", "Zscore")
x = range(100)
xplotter.plot(x)
canvas = xplotter.getCanvas()
response = HttpResponse(content_type='image/png')
canvas.print_png(response)
return response
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 _visualizeLLPlot(self, e=None):
""" Plot -LL vs cycle :N:1,5:
"""
headerList, dataList, msg, title = self.parseFile.retrievemLLPlot()
if not dataList:
errorWindow(self.getTkRoot(), msg)
return
xplotter = Plotter(windowTitle=title)
a = xplotter.createSubPlot(title, headerList[0], '-LL', yformat=False)
# see
# https://matplotlib.org/api/_as_gen/matplotlib.axes.Axes.plot.html
a.plot(dataList[0], dataList[1], 'bx-')
xplotter.showLegend(headerList[1:])
xplotter.show()
def getTestPlot(request):
""" Just a test of a custom render function. """
from pyworkflow.gui.plotter import Plotter
xplotter = Plotter()
xplotter.createSubPlot("Particle sorting", "Particle number", "Zscore")
x = range(100)
xplotter.plot(x)
canvas = xplotter.getCanvas()
response = HttpResponse(content_type='image/png')
canvas.print_png(response)
return response
def _visualizeRFactorPlot(self, e=None):
""" Plot Rfactor and Rfree vs cycle :N:[1,3]:
"""
headerList, dataList, msg, title = self.parseFile.retrieveRFactorPlot()
if not dataList:
errorWindow(self.getTkRoot(), msg)
return
xplotter = Plotter(windowTitle=title)
a = xplotter.createSubPlot(title,
headerList[0],
'Rfactor',
yformat=False)
# see
# https://matplotlib.org/api/_as_gen/matplotlib.axes.Axes.plot.html
# for plot options
a.plot(dataList[0], dataList[1], 'bx-', dataList[0], dataList[2],
'gx-') # plot start over line in blue
xplotter.showLegend(headerList[1:])
xplotter.show()
def _visualizeGeometryPlot(self, e=None):
""" Plot rmsBOND,zBOND, rmsANGL, zANGL and rmsCHIRALvs cycle :
N:1,7,8,9,10,11:
"""
headerList, dataList, msg, title = \
self.parseFile.retrieveGeometryPlot()
if not dataList:
errorWindow(self.getTkRoot(), msg)
return
xplotter = Plotter(windowTitle=title)
a = xplotter.createSubPlot(title,
headerList[0],
'geometry',
yformat=False)
# see
# https://matplotlib.org/api/_as_gen/matplotlib.axes.Axes.plot.html
# for plot options
a.plot(
dataList[0],
dataList[1],
'bx-',
dataList[0],
dataList[2],
'gx-',
dataList[0],
dataList[3],
'rx-',
dataList[0],
dataList[4],
'cx-',
dataList[0],
dataList[5],
'mx-',
) # plot start over line in blue
xplotter.showLegend(headerList[1:])
xplotter.show()
def _plotHistogram(self):
from ResMap_visualization import plotResolutionHistogram
histogramData = loads(self.histogramData.get())
fig = plotResolutionHistogram(histogramData)
return Plotter(figure=fig)
def __init__(self, path, master=None):
# Load global configuration
self.projName = os.path.basename(path)
try:
projTitle = '%s (%s on %s)' % (self.projName,
pwutils.getLocalUserName(),
pwutils.getLocalHostName())
except Exception:
projTitle = self.projName
self.projPath = path
self.loadProject()
# TODO: put the menu part more nicely. From here:
menu = MenuConfig()
projMenu = menu.addSubMenu('Project')
projMenu.addSubMenu('Browse files', 'browse',
icon='fa-folder-open.png')
projMenu.addSubMenu('Remove temporary files', 'delete',
icon='fa-trash-o.png')
projMenu.addSubMenu('Manage project labels', 'labels',
icon=Icon.TAGS)
projMenu.addSubMenu('Toogle color mode', 'color_mode',
shortCut="Ctrl+t", icon=Icon.ACTION_VISUALIZE)
projMenu.addSubMenu('Select all protocols', 'select all',
shortCut="Ctrl+a")
projMenu.addSubMenu('Find protocol to add', 'find protocol',
shortCut="Ctrl+f")
projMenu.addSubMenu('', '') # add separator
projMenu.addSubMenu('Import workflow', 'load_workflow',
icon='fa-download.png')
projMenu.addSubMenu('Search workflow', 'search_workflow',
icon = 'fa-search.png')
projMenu.addSubMenu('Export tree graph', 'export_tree')
projMenu.addSubMenu('', '') # add separator
projMenu.addSubMenu('Notes', 'notes', icon='fa-pencil.png')
projMenu.addSubMenu('', '') # add separator
projMenu.addSubMenu('Exit', 'exit', icon='fa-sign-out.png')
helpMenu = menu.addSubMenu('Help')
helpMenu.addSubMenu('Online help', 'online_help',
icon='fa-external-link.png')
helpMenu.addSubMenu('About', 'about',
icon='fa-question-circle.png')
helpMenu.addSubMenu('Contact support', 'contact_us',
icon='fa-question-circle.png')
self.menuCfg = menu
# TODO: up to here
if self.project.openedAsReadOnly():
self.projName += "<READ ONLY>"
# Notify about the workflow in this project
self.icon = self.generalCfg.icon.get()
self.selectedProtocol = None
self.showGraph = False
Plotter.setBackend('TkAgg')
ProjectBaseWindow.__init__(self, projTitle, master,
icon=self.icon, minsize=(90,50))
self.root.attributes("-zoomed", True)
self.switchView(VIEW_PROTOCOLS)
self.initProjectTCPServer() # Socket thread to communicate with clients
ProjectWorkflowNotifier(self.project).notifyWorkflow()
def _plotVolumeSlices(self, **kwargs):
from ResMap_visualization import plotOriginalVolume
fig = plotOriginalVolume(self._getVolumeMatrix('volume1.map'), **kwargs)
return Plotter(figure=fig)
def __init__(self, x=1, y=1, mainTitle="", **kwargs):
Plotter.__init__(self, x, y, mainTitle, **kwargs)
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
def __init__(self, path, master=None):
# Load global configuration
self.projName = os.path.basename(path)
try:
projTitle = '%s (%s on %s)' % (self.projName,
pwutils.getLocalUserName(),
pwutils.getLocalHostName())
except Exception:
projTitle = self.projName
self.projPath = path
self.project = self.loadProject()
# TODO: put the menu part more nicely. From here:
menu = MenuConfig()
projMenu = menu.addSubMenu('Project')
projMenu.addSubMenu('Browse files',
'browse',
icon='fa-folder-open.gif')
projMenu.addSubMenu('Remove temporary files',
'delete',
icon='fa-trash-o.gif')
projMenu.addSubMenu('Manage project labels', 'labels', icon=Icon.TAGS)
projMenu.addSubMenu('Toggle color mode',
'color_mode',
shortCut="Ctrl+t",
icon=Icon.ACTION_VISUALIZE)
projMenu.addSubMenu('Select all protocols',
'select all',
shortCut="Ctrl+a")
projMenu.addSubMenu('Find protocol to add',
'find protocol',
shortCut="Ctrl+f")
projMenu.addSubMenu('', '') # add separator
projMenu.addSubMenu('Import workflow',
'load_workflow',
icon='fa-download.gif')
projMenu.addSubMenu('Search workflow',
'search_workflow',
icon='fa-search.gif')
if pw.Config.debugOn():
projMenu.addSubMenu('Export tree graph', 'export_tree')
projMenu.addSubMenu('', '') # add separator
projMenu.addSubMenu('Debug Mode',
'debug mode',
shortCut="Ctrl+d",
icon='debug.gif')
projMenu.addSubMenu('', '') # add separator
projMenu.addSubMenu('Notes', 'notes', icon='fa-pencil.gif')
projMenu.addSubMenu('', '') # add separator
projMenu.addSubMenu('Exit', 'exit', icon='fa-sign-out.gif')
helpMenu = menu.addSubMenu('Help')
helpMenu.addSubMenu('Online help',
'online_help',
icon='fa-external-link.gif')
helpMenu.addSubMenu('About', 'about', icon='fa-question-circle.gif')
helpMenu.addSubMenu('Contact support',
'contact_us',
icon='fa-question-circle.gif')
self.menuCfg = menu
if self.project.openedAsReadOnly():
self.projName += "<READ ONLY>"
# Notify about the workflow in this project
self.selectedProtocol = None
self.showGraph = False
Plotter.setBackend('TkAgg')
ProjectBaseWindow.__init__(self,
projTitle,
master,
minsize=(90, 50),
icon=Icon.SCIPION_ICON_PROJ)
OS.handler().maximizeWindow(self.root)
self.switchView(VIEW_PROTOCOLS)
self.initProjectTCPServer(
) # Socket thread to communicate with clients
ProjectWorkflowNotifier(self.project).notifyWorkflow()
def __init__(self, x=1, y=1, mainTitle="", **kwargs):
Plotter.__init__(self, x, y, mainTitle, **kwargs)